Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017894.1 Corchorus olitorius cultivar O-4 contig17927, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4371
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Found at i:2272 original size:15 final size:16
Alignment explanation
Indices: 2247--2276 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2237 AATAATTATT
2247 TTTAGATTATAATATA
1 TTTAGATTATAATATA
2263 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
2277 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:2938 original size:331 final size:328
Alignment explanation
Indices: 2302--4368 Score: 1744
Period size: 331 Copynumber: 6.3 Consensus size: 328
2292 TAACAAGATG
* * * * * * * * *
2302 AAAAACGCGTTCTGGAGACCTGGCTCAATTTTGCATAATTTTTTGCTCCAAGACTACTTGAAATA
1 AAAAACGCGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* * * *
2367 TCTATATTCATCTAATCAAATTTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCACCTGA
65 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGA
* ** * * * * * *
2432 ATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAATGATATTGGACA-CATC
130 ATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATT-AAAAGCGTG
* * * *
2496 AAAAGCCCTTCAATATTTTTGGCGTTGAATTATATAT-TTTTATAAGTATTTTAGCCTAAAATTG
194 AAAAG-CCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTA-TTTA-TCAAAAATTG
* * * * * *
2560 AGGACATATTTTTCTAATCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGT
256 AGGAAAAATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGT
2625 TTTTGGCT
321 TTTTGGCT
** * ** * *
2633 AAAAAAACATTATAGGGCCCCGGCTCAGTTTTGCATGATTTTTAGCACGAAGACTCCTTGAGATA
1 AAAAACGCGTT-CCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* *
2698 TCCATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGA
65 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGA
* * * *
2763 ATCTTGTTTCCATTTCATTAGAAATTAATTCAG-AAAAATATGAAAAATGATATTAAAAGCGTGA
130 ATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGA
** ** * *
2827 AAAGTTTTCCAATCCTTTTT-TTGTTAAATTATATATATTTTATGAGTACTTTATCAAGAAATAG
195 AAAGCCTT-CAAT-CTTTTTGGCGTTGAATTATATATATTTTATGAGTA-TTTATCAA-AAATTG
* * * * * *
2891 GGGAAAAATTTTTCGGGTC-ATTTTCTGCAAAGTTTTAGCCAAAATCGTTTACTAACCATCACGG
256 AGGAAAAATTTTTCGAGTCAATTTT-TGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG
*
2955 TTTTTGTCT
320 TTTTTGGCT
* * *
2964 AAAAACGCGTTTCTGGGCCCCGGCTCAGTTTTACATGATTTTTGGCACCG-ACACTCCTTGAAAT
1 AAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA-CGAAGACTCCTTGAAAT
* * * * * *
3028 ATCTATATTCATCTTATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTA
64 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG
* * * * *
3093 AATCTTGTATCGATTTAATTAAAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTG
129 AATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTG
* *
3158 AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA-TTATGACTAAAAATT
194 -AAAAGCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTAT--C-AAAAATT
* ** * * * * *
3222 GAGGAAATACCTTTCGCGTCAATTTTTGCAAAATGTTAGCCGGAATCGTGTAATAATCATCACTG
255 GAGGAAAAATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG
3287 TTTTTGGCT
320 TTTTTGGCT
** * * * **
3296 AAAAACGCGTTCCGGGATCCGGTTCAATTTTGAATGATTTTTGGTGC-CG-AGACTTTTTGAAAT
1 AAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTT-G-GCACGAAGACTCCTTGAAAT
** * * *
3359 ATCTATATGAATCTAACCAAA--T---CC-CA----A-CT----A-TTGTTTTTACAAACATCTG
64 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG
* * *
3408 AATCATGTTTCGTTTTAATTAGAAATTAATTCGGAAAATAATATGAAAAACGATATTAGAAGCGT
129 AATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATATGAAAAACGATATTAAAAGCGT
* * * *
3473 GAAAAGCCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTAGCTAAAGATT
193 GAAAAG-CCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATT-TATC-AAAAATT
* * ** * * *
3538 GA-GAGAATATTTTCCTTGTC-ATTTTATGTAAAATTTTAGCCGAAATTGTGTACTAACCATCAC
255 GAGGA-AAAATTTTTCGAGTCAATTTT-TGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAC
***
3601 GGTTTTTTTTTTATT
318 GG----TTTTTGGCT
* ** *
3616 AAAAACACGTTTTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCG-AGACTCCTCGAAAT
1 AAAAACGCG-TTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCA-CGAAGACTCCTTGAAAT
* * * * *
3680 AT-T-TA-T-A--T--T-AAATCTCAGGCACATTGCATTTAAGGAGTTATTTTTACGAGCATCTG
64 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTG
* *
3736 AATCATCTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGAG
129 AATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTG
* * * *
3800 AAAAGTCC-TCAAATCTTTTTAGAGTTGAATTATATATATTTTATGAGTATTTTAGACAGAAATT
194 AAAAG-CCTTC-AATCTTTTTGGCGTTGAATTATATATATTTTATGAGTA-TTTA-TCAAAAATT
* * * * * * * *
3864 GAGGAAAAATATTTCTG-GTAAATTTTTGCAACATATTAGCCAAAATCGTGTACGTTAGTCGAAA
255 GAGGAAAAATTTTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA--ATA-AC--CA
* *
3928 TCATGGTTTTTTGCT
314 TCACGGTTTTTGGCT
* * * * * * * *
3943 AAAAATGCGTTCCGAGTCCCGGTTC-GATGTTGCATGATTTTTTGCGCCAAGACTCCTTG-AATA
1 AAAAACGCGTTCCGGGCCCCGGCTCAG-TTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* ** * * *** *
4006 TCTACATTTTTCTAACCAAATCTCAGCCGCATTGGATTTAAGGATTT-TTAAAACAAGCATCTAA
65 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGA
* * * * *
4070 ATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAATGATATTAGAAGCATG
130 ATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATATGAAAAACGATATTAAAAGCGTG
* * *
4135 AAAACCCTTCAATATTTTTGGTGTTGAATTATATA-ATTTTTATGAGTATTGTGAAT-AAAAATT
194 AAAAGCCTTCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATT-T--ATCAAAAATT
* * * *
4198 GAGGAAATAA-CTTTCGAGTCAATTTTTGCAAAATTCTAACCGAAATCGTGTAATAATCATCATC
255 GAGGAAA-AATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCA-C
* *
4262 -TTTTTTCGCT
318 GGTTTTTGGCT
* * * * * * * *
4272 AAAAACGCGTTCCGGGGCCCGACTAAGTTTTGCATGATGTTTGGCGCCAAGACTCTTTGAGATAT
1 AAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATAT
* * * * *
4337 CCATATTCATTTAATCTAATGTCAGCTACATT
66 CTATATTCATCTAATCAAATCTCAGCCACATT
4369 AGA
Statistics
Matches: 1391, Mismatches: 264, Indels: 163
0.77 0.15 0.09
Matches are distributed among these distances:
312 3 0.00
314 1 0.00
315 60 0.04
316 120 0.09
317 3 0.00
318 4 0.00
319 4 0.00
320 17 0.01
321 42 0.03
322 1 0.00
323 1 0.00
325 11 0.01
326 144 0.10
327 29 0.02
328 50 0.04
329 65 0.05
330 82 0.06
331 417 0.30
332 133 0.10
333 62 0.04
334 111 0.08
335 30 0.02
336 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (328 bp):
AAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATAT
CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAA
TCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAA
AAGCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTATCAAAAATTGAGGAA
AAATTTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTG
GCT
Done.