Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010935.1 Corchorus capsularis cultivar CVL-1 contig10956, 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: 38357
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3958 original size:197 final size:197
Alignment explanation
Indices: 3146--4653 Score: 1809
Period size: 199 Copynumber: 7.6 Consensus size: 197
3136 TTTCTCCTTT
** * * * * *
3146 TCAGTGTAAATTTTACACTTCATAAGCGGGTTAAGAAGTTGACAAATAACATATTTCATATAATC
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCTATTTC--ATAATT
* ** *
3211 AACTAAATATTTAATATTAATACATATTCTTTAAGGGGACACATGTCAACTCTTAAACCCAGCAC
64 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCC-GCAC
* * * * *
3276 GTGCAGTCTTCTAAATTCGACTGACAGTGTATAGTATAATTTTTCTTATAAGATTATTATACAAT
128 GTGCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAA-TTTTCTTATAGGATTATTATACAAT
*
3341 CCACTG
192 ACACTG
* * * * * * *
3347 TCAGTGTAAATTTTGGACTCAATACGTGGGTTAAGAAGTTGACATATACCCCATTTCATAATAAA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCTATTTCATAATTAA
* * * *
3412 TTAAATATTTGATATCAATACATATTCCCTAAGGCGACACATGTCAACCCTTAAACCCCGCACAT
66 TTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCGCACGT
* * * *
3477 GCAGTCTGCTAAAATCCACTAATGATGTATTA-TATAATTTTTCTTATAGGATTATTATACAACA
130 GCAGTCTGCTAAAATCCACTGACGGTGTA-TAGTATAA-TTTTCTTATAGGATTATTATACAATA
*
3541 CCCTG
193 CACTG
* * ** * * *
3546 TCAGTATAAATTTTAGACTTTATAAGCGGGTTAAGAAGTTGACACATA-CATCATTTCATCATCA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCT-ATTTCATAATTA
* * * *
3610 ATAAAATATATAATATTAATACATATTCCCTAAGGGGACATATGTCAACTCTTAAACCCTGCACG
65 ATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCC-GCACG
* * *
3675 TGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTGTT-TTATAGGATTATCATACAATA
129 TGCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATT-TTCTTATAGGATTATTATACAATA
3739 -AGCTG
193 CA-CTG
* **
3744 TCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGATGCATATCCTATTTCATAATTAA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCTATTTCATAATTAA
*
3809 TTAAATATTTAATATTAATACATATTCCTTAA-GGGACACATGTCAACCCTTAAATCCCGCACGT
66 TTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCGCACGT
*
3873 GCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATATAATACA
130 GCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATACAATACA
*
3938 ATG
195 CTG
* *
3941 TCAGTGTAAGA-TTTGGACTCCATAAGCGGGTTAGGAAGTTGACATATATTCC-ATTTCATAATT
1 TCAGTGTAA-ATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATA-TCCTATTTCATAATT
* *
4004 AATTAAATATTTAATATTAATACATATTCCTTAA-GGGACACATGTCAACCCTTAAATCCCACAC
64 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCGCAC
* *
4068 GTCCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATATAATA
128 GTGCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATACAATA
*
4133 CAATG
193 CACTG
* * *
4138 TCAGTATAAGA-TTTGGACTCCATAAGCGGGTTAGGAAGTTGACATATATTCC-ATTTCATAATT
1 TCAGTGTAA-ATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATA-TCCTATTTCATAATT
*
4201 AATT-AA-A-TTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
64 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCGCAC
* * * *
4263 ATGCAGTTTGCTAAAATCCACTGACGGTG--TA--AT--TTTTCTTATAGGATTATTATATAACA
128 GTGCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATACAATA
*
4322 CGCTG
193 CACTG
* ** * *
4327 TCAGTATAAATTTTGGACTTTATAAACGGGTTAAGAAGTTGACACATA-CCTCATTTCATCATTA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCT-ATTTCATAATTA
* * ** * *
4391 ATTTAATATATAATATTAATACATATTCCCTAAGGGTCCACATGTCAA-CCTCTAAACCATGGAC
65 ATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT-TAAACC-CGCAC
* * * * *
4455 ATGCAGTCTGCTAAACTCCACCGACGGTGCATTGTATAATTGTTCTTATAGGATTATTATACAAT
128 GTGCAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATT-TTCTTATAGGATTATTATACAAT
*
4520 ACACTA
192 ACACTG
* * * * *
4526 TCAATGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGGCACATA-CTTCATATCATAATTA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCT-ATTTCATAATTA
* *
4590 ATTAAATATTTAATATTAATACATATTCCCTAAGGGGACATATGTCAACCTTTAAACCCCGCAC
65 ATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCGCAC
4654 AGTAAATTTT
Statistics
Matches: 1143, Mismatches: 133, Indels: 64
0.85 0.10 0.05
Matches are distributed among these distances:
187 2 0.00
188 1 0.00
189 83 0.07
190 2 0.00
191 8 0.01
192 68 0.06
193 2 0.00
194 23 0.02
195 55 0.05
196 6 0.01
197 334 0.29
198 120 0.10
199 383 0.34
200 9 0.01
201 47 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (197 bp):
TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATATCCTATTTCATAATTAA
TTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCGCACGTG
CAGTCTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATACAATACAC
TG
Found at i:4836 original size:585 final size:582
Alignment explanation
Indices: 3152--4659 Score: 1467
Period size: 594 Copynumber: 2.6 Consensus size: 582
3142 CTTTTCAGTG
** * * * * * * *
3152 TAAATTTTACACTTCATAAGCGGGTTAAGAAGTTGACAAATAACATATTTCATATAATCAACTAA
1 TAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACACATATCCTATTTC--ATAATTAATTAA
* ** * *
3217 ATATTTAATATTAATACATATTCTTTAAGGGGACACATGTCAACTCTTAAA-CCCAGCACGTGCA
64 ATATATAATATTAATACATATTCCCTAA-GGGACACATGTCAACCCTTAAATCCC-GCACATGCA
* * * * * * * * *
3281 GTCTTCTAAATTCGACTGACAGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATCCACT
127 GTCTGCTAAAATCCACCGACGGTGCATAGTATAA-TTTTCTTATAGGATTATTATACAATACAAT
* * * * * * * ** * *
3346 GTCAGTGTAA-ATTTTGGACTCAATACGTGGGTTAAGAAGTTGACATATACCCCATTTCATAATA
191 ATCAATGTAAGA-TTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATATTCCATATCATAATT
* * *
3410 AATTAAATATTTGATATCAATACATATTCCCTAAGGCGACACATGTCAACCCTTAAACCCCGCAC
255 AATTAAATATTTAATATTAATACATATTCCCTAAGG-GACACATGTCAACCCTTAAACCCCACAC
* ** * * * * *
3475 ATGCAGTCTGCTAAAATCCACTAATGATGTATTA-TATAATTTTTCTTATAGGATTATTATACAA
319 GTAAAGTCTGCTAAAATCCACTAAAGGTGTA-TAGTACAA-TTTTCTTATAGCATTATTATATAA
* ** * * * ** * *
3539 CACCCTGTCAGTATAA-ATTTTAGACTTTATAAGCGGGTTAAGAAGTTGACACATA-CATCATTT
382 TACAATCTCAG-ATAAGA-CTTGGACTCCATAA-CAGGTTAAGAAGTTGACATATATC--CATTT
* * * * * * *** * * * *
3602 CATCATCAATAAAATATATAATATTAATACATATTCCCTAAGGGGACATATGTCAACTCTTAAAC
442 CATAATTAAT-TAA-AT-TAATATTAAAAAATATACCCTAAAAAGAAACATGCCAACCCTTAAAC
* * *
3667 CCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTGTTTTATAGGATTATCA
504 CCCGCACATGCAGTCTGCTAAAATCCACTGACGGTGTA---TAT-ATTGTTTTATAGGATTATCA
* *
3732 TACAATAAGCTGTCAATG
565 TACAACAAGCTGTCAATA
* **
3750 TAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGATGCATATCCTATTTCATAATTAATTAAAT
1 TAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACACATATCCTATTTCATAATTAATTAAAT
* * *
3815 ATTTAATATTAATACATATTCCTTAAGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCT
66 ATATAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAATCCCGCACATGCAGTCT
* * * * *
3880 GCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATATAATACAATGTCAG
131 GCTAAAATCCACCGACGGTGCATAGTATAATTTTCTTATAGGATTATTATACAATACAATATCAA
* * * *
3945 TGTAAGATTTGGACTCCATAAGCGGGTTAGGAAGTTGACATATATTCCATTTCATAATTAATTAA
196 TGTAAGATTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATATTCCATATCATAATTAATTAA
* * **
4010 ATATTTAATATTAATACATATTCCTTAAGGGACACATGTCAACCCTTAAATCCCACACGTCCAGT
261 ATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAACCCCACACGTAAAGT
* * * * *
4075 CTGCTAAAATCCACTGACGGTGTATAGTATAATTTTCTTATAGGATTATTATATAATACAATGTC
326 CTGCTAAAATCCACTAAAGGTGTATAGTACAATTTTCTTATAGCATTATTATATAATACAATCTC
* * *
4140 AGTATAAGATTTGGACTCCATAAGCGGGTTAGGAAGTTGACATATATTCCATTTCATAATTAATT
391 AG-ATAAGACTTGGACTCCATAA-CAGGTTAAGAAGTTGACATATA-TCCATTTCATAATTAATT
* * * * *** * *
4205 AAATTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACATGCAGT
453 AAATTAATATTAAAAAATATACCCTAAAAAGAAACATGCCAACCCTTAAACCCCGCACATGCAGT
* * * * *
4270 TTGCTAAAATCCACTGACGGTGTA-AT-TT-TTCTTATAGGATTATTATATAACACGCTGTCAGT
518 CTGCTAAAATCCACTGACGGTGTATATATTGTT-TTATAGGATTATCATACAACAAGCTGTCAAT
4332 A
582 A
** * *
4333 TAAATTTTGGACTTTATAAACGGGTTAAGAAGTTGACACATA-CCTCATTTCATCATTAATTTAA
1 TAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACACATATCCT-ATTTCATAATTAATTAAA
* * *
4397 TATATAATATTAATACATATTCCCTAAGGGTCCACATGTCAA-CCTCTAAA-CCATGGACATGCA
65 TATATAATATTAATACATATTCCCTAAGGG-ACACATGTCAACCCT-TAAATCC-CGCACATGCA
* * *
4460 GTCTGCTAAACTCCACCGACGGTGCATTGTATAATTGTTCTTATAGGATTATTATACAATACACT
127 GTCTGCTAAAATCCACCGACGGTGCATAGTATAATT-TTCTTATAGGATTATTATACAATACAAT
*
4525 ATCAATGTAA-ATTTTGAACTCCATAAGCGGGTTAAGAAGTTGGCACATACTT-CATATCATAAT
191 ATCAATGTAAGA-TTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATA-TTCCATATCATAAT
* * *
4588 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACATATGTCAACCTTTAAACCCCGCA
254 TAATTAAATATTTAATATTAATACATATTCCCTAA-GGGACACATGTCAACCCTTAAACCCCACA
4653 CAGTAAA
318 C-GTAAA
4660 TTTTTTTTTT
Statistics
Matches: 799, Mismatches: 95, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
582 5 0.01
583 114 0.14
584 54 0.07
585 113 0.14
586 28 0.04
587 3 0.00
589 78 0.10
590 2 0.00
591 2 0.00
592 83 0.10
593 58 0.07
594 115 0.14
595 61 0.08
596 40 0.05
598 43 0.05
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (582 bp):
TAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACACATATCCTATTTCATAATTAATTAAAT
ATATAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAATCCCGCACATGCAGTCT
GCTAAAATCCACCGACGGTGCATAGTATAATTTTCTTATAGGATTATTATACAATACAATATCAA
TGTAAGATTTGAACTCCATAAGCGGGTTAAGAAGTTGACACATATTCCATATCATAATTAATTAA
ATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAACCCCACACGTAAAGT
CTGCTAAAATCCACTAAAGGTGTATAGTACAATTTTCTTATAGCATTATTATATAATACAATCTC
AGATAAGACTTGGACTCCATAACAGGTTAAGAAGTTGACATATATCCATTTCATAATTAATTAAA
TTAATATTAAAAAATATACCCTAAAAAGAAACATGCCAACCCTTAAACCCCGCACATGCAGTCTG
CTAAAATCCACTGACGGTGTATATATTGTTTTATAGGATTATCATACAACAAGCTGTCAATA
Found at i:5628 original size:26 final size:26
Alignment explanation
Indices: 5599--5649 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5589 TAACCTCGTA
* * *
5599 TTCTTAGAATTTTTAATAACTTTTCC
1 TTCTTACAAATTTTAATAACCTTTCC
*
5625 TTCTTACAAATTTTAGTAACCTTTC
1 TTCTTACAAATTTTAATAACCTTTC
5650 ATCAAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (26 bp):
TTCTTACAAATTTTAATAACCTTTCC
Found at i:9598 original size:18 final size:18
Alignment explanation
Indices: 9572--9606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9562 GTCAAGATTT
9572 GAAGAAAAAGCAAAAAAA
1 GAAGAAAAAGCAAAAAAA
* *
9590 GAAGGAAAAGGAAAAAA
1 GAAGAAAAAGCAAAAAA
9607 TGAAAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAGCAAAAAAA
Found at i:21768 original size:2 final size:2
Alignment explanation
Indices: 21761--21849 Score: 71
Period size: 2 Copynumber: 46.0 Consensus size: 2
21751 ATAAGATAAG
* * * *
21761 AT AT AT AT AT AT AT AT AT AT AT AT AT CT -T AT CT -T AC CT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
21800 AT CT -T ACT AT CT -T ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
21842 AT AT AT AT
1 AT AT AT AT
21850 CTTATCTTAC
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
1 5 0.07
2 64 0.88
3 4 0.05
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:21856 original size:63 final size:62
Alignment explanation
Indices: 21761--21886 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 62
21751 ATAAGATAAG
21761 ATATATATATATATATATATATATATCTTATCTTACCTTATCTTACTATCTTACTATATATAT
1 ATATATATATATATATATATATATATCTTATCTTACCTTATCTTACTATCTTACTAT-TATAT
21824 ATATATATATATATATATATATATATCTTATCTTACCTTATCTTACTATCTTACTATTATAT
1 ATATATATATATATATATATATATATCTTATCTTACCTTATCTTACTATCTTACTATTATAT
21886 A
1 A
21887 AAACCTCGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 6 0.10
63 57 0.90
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.51
Consensus pattern (62 bp):
ATATATATATATATATATATATATATCTTATCTTACCTTATCTTACTATCTTACTATTATAT
Found at i:32111 original size:16 final size:16
Alignment explanation
Indices: 32082--32124 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
32072 TTAATAATTT
* *
32082 ATAAAATATATAATGAA
1 ATAATATATGTAAT-AA
32099 ATAATA-ATGTAATAA
1 ATAATATATGTAATAA
32114 ATAATATATGT
1 ATAATATATGT
32125 TTAATAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (16 bp):
ATAATATATGTAATAA
Found at i:33226 original size:18 final size:18
Alignment explanation
Indices: 33189--33229 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33179 CTTTTTTTAT
**
33189 TAAAAAAATAAATTTCAA
1 TAAAAAAATAAATTAAAA
*
33207 TAAAAAAATATATTAAAA
1 TAAAAAAATAAATTAAAA
33225 TAAAA
1 TAAAA
33230 TATTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAAAATAAATTAAAA
Done.