Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013704.1 Corchorus capsularis cultivar CVL-1 contig13725, 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: 4719
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:2780 original size:42 final size:41
Alignment explanation
Indices: 2708--2786 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
2698 AAAAAACTTT
* *
2708 TTTATTAATTATGGAAAGATATTGTAAATCTAATATATAAA
1 TTTATTAATTATGAAAAGATATTATAAATCTAATATATAAA
* *
2749 TTTATTAAATTATTAAAAGATATTA-ATAATCTACTATA
1 TTTATT-AATTATGAAAAGATATTATA-AATCTAATATA
2787 AATGTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 7 0.22
42 25 0.78
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (41 bp):
TTTATTAATTATGAAAAGATATTATAAATCTAATATATAAA
Found at i:4108 original size:324 final size:319
Alignment explanation
Indices: 3168--4692 Score: 1522
Period size: 324 Copynumber: 4.7 Consensus size: 319
3158 AGTTTTAGCA
* * * * *
3168 TCGGGTCAGTTTTGCATGATTTTTGGCGTAAATACTCCTTGAAATATCTATATTCATCGAACAAA
1 TCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* * * * *
3233 ATCTCAGCCACGTTCGATTTAAGTATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATT
66 ATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * * * *
3298 AAAAATTAATTTA-AAAAA-TGGAAAAACAATATTAAAAACATGAAAAGACCGTCAATCTTTTTG
131 AGAAATTAATTCAGAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTG
* *
3361 GCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAGAAAAAACTTTTCGGGTCA
196 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAAGAAAAAACTTTTCGGGTCA
* ** * *
3425 GTTTTTAGCCGAAATCGTGTAC-CATCACGTTTTTTTTTTACTAAAAATGCGTTCCGAAGCC
261 GTTTTTAGCCGAAATCGTGTACTCATCACG---GTTTTTGGCTAAAAACGCGTTCCGGAGCC
* * * * ** * *
3486 CCGACTCAATTTTACATGATTTTTAGCGCAAAGACTCCTAAAAAAATCTACATTCATCGAACCAA
1 TCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* * *
3551 ATGTCAGCTACATTGGATATAA-AGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAT
66 ATCTCAGCCACATTGGATATAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * **
3615 TAGAAATTAATTCAAAAAAAAATTGGAAAAATGATATTAGAAGCTTGAAAAACCATTCAATCTTT
130 TAGAAATTAATTC--AGAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTT
* * * * * * *
3680 TCGGCATTGAATTATATATTTTTTCT-AGGTATTGTGGCAAAGAATTGAGGAAAAAAATTTTTGG
193 TTGGCGTTGAATTATATATTTTTTCTGA-GTATTGTGGCAAAAAATTCAAGAAAAAACTTTTCGG
* * ** * * *
3744 ATCAGTTTTTA--CAAAATTTTATTTGAAATCGTTTATCACGGTTTATGGCTAAAAACGCGTTCC
257 GTCAGTTTTTAGCCGAAA---T-CGTG-TA-C--TCATCACGGTTTTTGGCTAAAAACGCGTTCC
*
3807 -GAGATC
314 GGAG-CC
* * * * * * *
3813 TCGGGTCAATTTTGCAAGATTTTTGACGTAAAGGCTTCTTGAAATATTTATATTCATCGAACCAA
1 TCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* * * * * *
3878 ATCTTA-CCATATTGGATATAAGAATTTATTTTTTCGAGCATCTCAATCCTGTTTCGATTTAATT
66 ATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
*
3942 AGAAATTAATTCAGAAAAATTGGAAAAACGATATTATAAGCGTGAAAAGCCCGTCAATCTTTTTG
131 AGAAATTAATTCAGAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTG
* *
4007 GCGTTGAATTATATATATATATATATATTTTAGTATTGTGGCAAAAAATT-AAGAAAAAACTTTT
196 GCGTTGAA-T-TATATAT-T-T-T-T-TCTGAGTATTGTGGCAAAAAATTCAAGAAAAAACTTTT
* * *
4071 CAGGTCAGTTTTTAGCCGAAATCGTGTACTCATCACGGTTTTTAGTTAAAAACGCGTTCCGGAGC
254 CGGGTCAGTTTTTAGCCGAAATCGTGTACTCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGC
4136 C
319 C
* * * *
4137 CCGACTCCATTTTGCATGATTTTTGGCGCAAAGACTCCTTCAAATATCTATATTCATCGAACCAA
1 TCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* * *
4202 ATGTCA-ACACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
66 ATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * ** *
4266 AGAAATTAATTCGGAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATACCATCAATCTTTTT
131 AGAAATTAATTCAG-AAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTT
* ***
4331 GGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAA-AAAAAA-AAATCGGGTC
195 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAAGAAAAAACTTTTCGGGTC
* * * * * * * *
4394 AGATTTTAACCGAAATCGTGTAATAACCATCATGATTTTTGGGCTAAAAACGGGTTTCGG-GGC
260 AGTTTTTAGCCGAAATCGTGTACT---CATCACGGTTTTT-GGCTAAAAACGCGTTCCGGAGCC
* * * *
4457 TCCGGCTCAGTTTTGCATGATTTTTGGCAG-AAAAACTCCTTGAAATATCTATATTAATCTAACC
1 T-CGGCTCAATTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCGAACC
* * * * * * *
4521 AAATCTCAGTCACATTAGATTTAAGGATTCGTTTTTACGAGCATCTGGATATTGTTTCGATTTAA
64 AAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* * * * * ** *
4586 TTAGAACTAAATT-GGAAAAAATGGAAAAACGATATTTA-AAGCGAGCAAAA-CCTTTCAATTTT
129 TTAGAAATTAATTCAGAAAAATTGGAAAAACGATA-TTAGAAGCGTG-AAAAGCCCGTCAATCTT
* * * * *
4648 TTTGGCGTTGAGTTGTGTATTTTTTCTGACTATTGTGGTAAAAAA
192 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
4693 AATTGAGGAA
Statistics
Matches: 994, Mismatches: 173, Indels: 78
0.80 0.14 0.06
Matches are distributed among these distances:
317 27 0.03
318 145 0.15
319 3 0.00
320 85 0.09
321 95 0.10
322 138 0.14
323 30 0.03
324 204 0.21
325 59 0.06
326 72 0.07
327 77 0.08
328 3 0.00
329 2 0.00
330 30 0.03
331 19 0.02
332 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (319 bp):
TCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
ATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
AGAAATTAATTCAGAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTG
GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAAGAAAAAACTTTTCGGGTCA
GTTTTTAGCCGAAATCGTGTACTCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCC
Done.