The question is asking me to prove that $F_{1001}$ is congruence to $1 \bmod 4$. I knew that if $n$ is odd then all prime odd divisor $p$ of $F_n$ satisfy $p \equiv 1 \pmod{4}$. However, my question is how to find the odd prime divisor? How do we factor out such a big fibonacci number?
Factoring $F_{1001}$
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It is actually possible to factor $F_{1001}$.
\begin{align*} F_{1001}=&13^2\cdot89\cdot233\cdot8009\cdot8581\cdot741469\cdot988681\cdot4832521\cdot159607993\\ &\cdot1929584153756850496621\cdot5811794973846976755532222929865278366042132879433\\ &\cdot46051361876019993056032153159112764928518076136032760569320871268374299454861127226737142167112433 \end{align*}
We have the factorizations \begin{align*} F_7&=13,\\ F_{11}&=89,\\ F_{13}&=233,\\ F_{77}&=13\cdot89\cdot988681\cdot4832521,\\ F_{91}&=13^2\cdot233\cdot741469\cdot159607993,\\ F_{143}&=89\cdot233\cdot8581\cdot1929584153756850496621. \end{align*} To factor $F_{1001}$, we first divide out by the primes that we have already found: $$F_{1001}=13^2\cdot89\cdot233\cdot8581\cdot741469\cdot988681\cdot4832521\cdot159607993\cdot1929584153756850496621\cdot C$$ where $C$ denotes a $151$-digit composite number. Suppose that $p$ is a prime number dividing $C$. Then the Fibonacci entry point $a_p$ must equal $1001$. One useful fact about Fibonacci entry points is that if $p\equiv1,4\pmod{5}$ then $a_p\bigm|p-1$ and if $p\equiv2,3\pmod{5}$ then $a_p\bigm|p+1$.
By the Chinese remainder theorem, $p$ has a remainder of $1$ or $3002$ or $3004$ or $4003$ modulo $5005$. We can do a little better by noting that $p$ must be congruent to 1 modulo 4 (by URL's comment on his answer). Then $p$ has a remainder of $1$ or $8009$ or $14013$ or $18017$ modulo $20020$. This immediately finds the prime factor $8009$ of $C$. Factoring the rest of $C$ is more challenging and is best done with the ECM.
Factoring big numbers that don't have an immediate product representation is pretty much impossible, without the correspondingly big computers to churn out the numbers. However, we can prove that $F_{1001}\equiv1\pmod{4}$ much easily.
First note that $F_0\equiv0\equiv8\equiv F_6\pmod{4}$, and that $F_1\equiv1\equiv13\equiv F_7\pmod{4}$. One can then easily prove by induction that $$F_n\equiv F_{n+6}\pmod{4}.$$ Therefore, $$F_{1001}\equiv F_{6\cdot166+5}\equiv F_5\equiv5\equiv1\pmod{4},$$as we wanted.