Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010108.1 Corchorus capsularis cultivar CVL-1 contig10129, 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: 24174
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--53 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC T
1 TC TC TC TC TC T
54 TAGGGTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1169 original size:444 final size:435
Alignment explanation
Indices: 287--1082 Score: 1003
Period size: 444 Copynumber: 1.8 Consensus size: 435
277 ATTTTAATTG
* **
287 TTTTATTTTTTTCTATTTTTCCGATTAAGGTGATTTAAGTGTCCATTAAAAGGTAATTTCATGAT
1 TTTTATTTTTTTCTATTTTTCCGATTAAGGTGATTCAAACGTCCATTAAAAGGTAATTTCATGAT
* *
352 CTACTACTTTCATGAAGGACTCAAAAGCTAATTTTTATGTTTCAGCTCTAAAAAATGCTTCCGAA
66 CTACTACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAAATGCTTCCGAA
** * * *
417 ATTTGATGGTTTCGATTGTCGGTCTATTTAATTTCATATAATTTTCGATCCACATATCTTATTGA
131 ATTTGATGGTTTCGATTACCGGTCTATTTAATATCATATAACTTTCGATCCACATATCTGATTGA
* * * *
482 AGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCTGAAAGT
196 AGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGC
* * *
547 TGAATTTGATTGACGAGTTTCATGAAGGGCTCAGGAGGAAATTTTATATTTCATCTCCATCAACA
261 TGAATTTGATCGACGAGTTTCATGAAAGGCTCAAGAGGAAATTTTATATTTCATCTCCATCAACA
** * * * * *
612 AACGTTTTTTATTTGGATTATTTATCAATTGACCCTCATACTTTTCTATTTCATTCTACTTAATC
326 AAAATTTTTTATTTGGATTATTTATCAATGGACACTCATACGTCTCCATTTCATTCTACTTAATC
* ** ** * * * *
677 CTTTATTAATTCTATCTTAATTGATTAAACTCTTCAGCTTTATTT
391 ATGCAACAATTCTAGCGTAATTGATTAAACTCTTCAGATTCATTT
* *
722 TTTTATTTTTTGT-TATATTTGTCCGTTTAAGGTGATTCAAACGTCCATTAAAAGGTATTTTCAT
1 TTTTATTTTTT-TCTAT-TTT-TCCGATTAAGGTGATTCAAACGTCCATTAAAAGGTAATTTCAT
* *
786 GATCTACAAGACTACAACTTTCATTAAGGACTC-AAATCCAATTTTTATGTTTCAACTCTAAAAA
63 GATCT-----ACT---ACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAA
* * * *
850 ATGTTTCTGAAATTTGGTGGTTTCGATTACCGGTCTATTTAATATCATATAACTTTCGATCCACC
120 ATGCTTCCGAAATTTGATGGTTTCGATTACCGGTCTATTTAATATCATATAACTTTCGATCCACA
915 TAT-TCGATTGAAGTTATTCAAGT-TCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAA
185 TATCT-GATTGAAGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAA
* * * *
978 GGACCCG-ATGCTGAATTTGATCGATGAGTTTCATGAAAGGCTTAAGAGGAAATTTTTATGTTTC
249 GGACCCGAAAGCTGAATTTGATCGACGAGTTTCATGAAAGGCTCAAGAGGAAA-TTTTATATTTC
1042 GA-CT-CATCAACAAATAATTTTTTATTTGGATTATTTATCAA
313 -ATCTCCATCAACAAA-AATTTTTTATTTGGATTATTTATCAA
1083 ATGGTTACTT
Statistics
Matches: 315, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
435 14 0.04
436 4 0.01
437 43 0.14
442 51 0.16
443 82 0.26
444 105 0.33
445 16 0.05
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (435 bp):
TTTTATTTTTTTCTATTTTTCCGATTAAGGTGATTCAAACGTCCATTAAAAGGTAATTTCATGAT
CTACTACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAAATGCTTCCGAA
ATTTGATGGTTTCGATTACCGGTCTATTTAATATCATATAACTTTCGATCCACATATCTGATTGA
AGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCCGAAAGC
TGAATTTGATCGACGAGTTTCATGAAAGGCTCAAGAGGAAATTTTATATTTCATCTCCATCAACA
AAAATTTTTTATTTGGATTATTTATCAATGGACACTCATACGTCTCCATTTCATTCTACTTAATC
ATGCAACAATTCTAGCGTAATTGATTAAACTCTTCAGATTCATTT
Found at i:1344 original size:36 final size:35
Alignment explanation
Indices: 1304--1408 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 35
1294 ATCTCTACTT
1304 ATTGTTGATTTAAATTATAGTCTATTTGATTTAGGA
1 ATTGTTGATTTAAATTATAGTC-ATTTGATTTAGGA
* ** * * *
1340 ATTGTGGCCTT-AATT-TGGAC-TTT-ATTTTTGG-
1 ATTGTTGATTTAAATTATAGTCATTTGA-TTTAGGA
*
1371 GTTGTTGATTTAAATTATAGTCCATTTGATTTAGGA
1 ATTGTTGATTTAAATTATAGT-CATTTGATTTAGGA
1407 AT
1 AT
1409 AATCACACTA
Statistics
Matches: 48, Mismatches: 14, Indels: 14
0.63 0.18 0.18
Matches are distributed among these distances:
31 8 0.17
32 12 0.25
33 2 0.04
34 4 0.08
35 12 0.25
36 10 0.21
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.50
Consensus pattern (35 bp):
ATTGTTGATTTAAATTATAGTCATTTGATTTAGGA
Found at i:2112 original size:27 final size:28
Alignment explanation
Indices: 2071--2124 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
2061 TAAATATATA
2071 AATATATACTATGTAATATATAACATTAC
1 AATATATACTATGTAATATATAA-ATTAC
*
2100 AATATATA-T-TGTATTATATAAATTA
1 AATATATACTATGTAATATATAAATTA
2125 TATTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.46
28 1 0.04
29 8 0.33
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (28 bp):
AATATATACTATGTAATATATAAATTAC
Found at i:3036 original size:22 final size:22
Alignment explanation
Indices: 3010--3077 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
3000 GTGCCAAGCT
*
3010 ATAACCACACTGTGAAATTGTG
1 ATAACCACACTATGAAATTGTG
* *
3032 ATAACCACCCTATAAAATTGTG
1 ATAACCACACTATGAAATTGTG
* *
3054 ATAATCACACTATGAAATTTTG
1 ATAACCACACTATGAAATTGTG
3076 AT
1 AT
3078 GATCTCCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (22 bp):
ATAACCACACTATGAAATTGTG
Found at i:3088 original size:22 final size:22
Alignment explanation
Indices: 3022--3400 Score: 158
Period size: 22 Copynumber: 17.4 Consensus size: 22
3012 AACCACACTG
* * *
3022 TGAAATTGTGATAACCACCCTA
1 TGAAATTTTGATAATCTCCCTA
* * * *
3044 TAAAATTGTGATAATCACACTA
1 TGAAATTTTGATAATCTCCCTA
*
3066 TGAAATTTTGATGATCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
* * * **
3088 TGAAATTTCGAGAACCTTTCTA
1 TGAAATTTTGATAATCTCCCTA
* **
3110 TGAAATTTTGA-AAGCATTACTA
1 TGAAATTTTGATAATC-TCCCTA
*
3132 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AATCTCCCTA
* * * *
3155 TAAAATTTTAATAAACCTCACTA
1 TGAAATTTTGAT-AATCTCCCTA
* *
3178 TAAAATTTTGATAATCTCCTTA
1 TGAAATTTTGATAATCTCCCTA
*
3200 TGAAATTTTGTTAA----CC-A
1 TGAAATTTTGATAATCTCCCTA
* *
3217 -CAAATTTTGATAA-CATCCTTA
1 TGAAATTTTGATAATC-TCCCTA
*** * *
3238 TGGTTTTTTTGATAACCTCACTA
1 T-GAAATTTTGATAATCTCCCTA
* *
3261 TCAAATTTTGTTAA-CATCCCTA
1 TGAAATTTTGATAATC-TCCCTA
* * *
3283 TGAAATTTTGAT-CTACGCACTA
1 TGAAATTTTGATAAT-CTCCCTA
* *
3305 TGAAATTTTGA-ACCA-CACACTA
1 TGAAATTTTGATA--ATCTCCCTA
3327 TGAAATTTTGATAATC-CCCTA
1 TGAAATTTTGATAATCTCCCTA
**
3348 TGAAATTTTGGA-AA-CTAAACTA
1 TGAAATTTT-GATAATCT-CCCTA
** *
3370 TGAAATTTCAATAACCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
*
3392 TAAAATTTT
1 TGAAATTTT
3401 AAATTTTGAT
Statistics
Matches: 271, Mismatches: 62, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 1 0.00
20 2 0.01
21 22 0.08
22 178 0.66
23 52 0.19
24 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCCCTA
Found at i:3778 original size:60 final size:62
Alignment explanation
Indices: 3685--3804 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 62
3675 ATTGCTAAAG
* *
3685 AAATCTAGGATGCTATGATAGAAATTGAAATTTTCTAAAT-AAA-ATATTTTAATAATGGCA
1 AAATCTAGGATGCTACGATAGAAATTGAAATTTTATAAATAAAATATATTTTAATAATGGCA
* * *
3745 AAATCTAGGATGGTACGGTAGAAATTGAAATTTTATTAATAAAATTATATTTTAATAATG
1 AAATCTAGGATGCTACGATAGAAATTGAAATTTTATAAATAAAA-TATATTTTAATAATG
3805 ACAATTTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 35 0.67
61 3 0.06
63 14 0.27
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (62 bp):
AAATCTAGGATGCTACGATAGAAATTGAAATTTTATAAATAAAATATATTTTAATAATGGCA
Found at i:3872 original size:26 final size:25
Alignment explanation
Indices: 3784--3903 Score: 73
Period size: 27 Copynumber: 4.5 Consensus size: 25
3774 ATTTTATTAA
* *
3784 TAAAATTATATTTTAATAATGACAATT
1 TAAAA-TATA-TTTAATAATGGCAAAT
* *
3811 TAGAAATATATTTAAAAAAAGGTACAAA-
1 TA-AAATATATTT-AATAATGG--CAAAT
*
3839 -AAATTATATTTAATAATGGCATAAT
1 TAAAATATATTTAATAATGGCA-AAT
* *
3864 TAAAATATATTTTGATAATGGCAATT
1 TAAAATATA-TTTAATAATGGCAAAT
*
3890 TAGAACTATATTTA
1 TA-AAATATATTTA
3904 TTTTGTAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
23 2 0.03
24 2 0.03
25 6 0.08
26 26 0.36
27 30 0.42
28 3 0.04
29 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.38
Consensus pattern (25 bp):
TAAAATATATTTAATAATGGCAAAT
Found at i:3902 original size:27 final size:27
Alignment explanation
Indices: 3784--3886 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 27
3774 ATTTTATTAA
* *
3784 TAAAATTATATTTTAATAATGACA-ATT
1 TAAAA-TATATTTTAATAATGGCATAAT
* * * * *
3811 TAGAAATATATTTAAAAAAAGGTACAA-
1 TA-AAATATATTTTAATAATGGCATAAT
3838 -AAAAT-TATATTTAATAATGGCATAAT
1 TAAAATATAT-TTTAATAATGGCATAAT
*
3864 TAAAATATATTTTGATAATGGCA
1 TAAAATATATTTTAATAATGGCA
3887 ATTTAGAACT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
24 3 0.05
25 15 0.26
26 1 0.02
27 32 0.55
28 7 0.12
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (27 bp):
TAAAATATATTTTAATAATGGCATAAT
Found at i:3925 original size:126 final size:127
Alignment explanation
Indices: 3784--4030 Score: 390
Period size: 128 Copynumber: 2.0 Consensus size: 127
3774 ATTTTATTAA
* *
3784 TAAAATTATATTTTAATAATGACAATTTAGAAATATA-TTTAAAAAAAGGTACAAAAAATTATA-
1 TAAAATTATATTTTAATAATGACAATTTAGAAATATACTTGAAAAAAAGATACAAAAAATTATAT
* * * *
3847 TTTAATAATGGCATAATTAAAATATATTTTGATAATGGCAATTTAGAACTATATTTATTTTG
66 TTTAATAATGACATAATCAAAATATATTTTGATAATGGCAATTTAAAAATATATTTATTTTG
* *
3909 TAAAATTTATATTTTAATAATGACAATTTAGAGATATACTTGAAAAAAAGATACACAAAATTATA
1 TAAAA-TTATATTTTAATAATGACAATTTAGAAATATACTTGAAAAAAAGATACAAAAAATTATA
*
3974 TTTTAATAATGACATAATCAAAATATATTTTGATAATGGTAATTTAAAAATATATTT
65 TTTTAATAATGACATAATCAAAATATATTTTGATAATGGCAATTTAAAAATATATTT
4031 TGAAAAAAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
125 5 0.05
126 31 0.28
127 23 0.21
128 51 0.46
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.39
Consensus pattern (127 bp):
TAAAATTATATTTTAATAATGACAATTTAGAAATATACTTGAAAAAAAGATACAAAAAATTATAT
TTTAATAATGACATAATCAAAATATATTTTGATAATGGCAATTTAAAAATATATTTATTTTG
Found at i:4016 original size:25 final size:27
Alignment explanation
Indices: 3964--4033 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
3954 AAAAGATACA
*
3964 CAAAATTATATTTTAATAATGACATAA-T
1 CAAAA-TATATTTTGATAATGA-ATAATT
*
3992 CAAAATATATTTTGATAATG-GTAATTT
1 CAAAATATATTTTGATAATGAATAA-TT
*
4019 AAAAATATATTTTGA
1 CAAAATATATTTTGA
4034 AAAAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.08
27 29 0.78
28 5 0.14
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
CAAAATATATTTTGATAATGAATAATT
Found at i:5719 original size:49 final size:49
Alignment explanation
Indices: 5666--5764 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
5656 AATATAGTTT
* * *
5666 TTGCTCGATGAACTATCCATCATGCTTCGCTTTGAAAGGAAATTTCTTA
1 TTGCTCGATGAACCATCCATCATGCTTCGCTCTGAAAGCAAATTTCTTA
* * **
5715 TTGCTTGATGAACCATTCATCATGCTTTTCTCTGAAAGCAAATTTCTTA
1 TTGCTCGATGAACCATCCATCATGCTTCGCTCTGAAAGCAAATTTCTTA
5764 T
1 T
5765 ACACTGGAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (49 bp):
TTGCTCGATGAACCATCCATCATGCTTCGCTCTGAAAGCAAATTTCTTA
Found at i:10531 original size:27 final size:27
Alignment explanation
Indices: 10493--10575 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 27
10483 ACGATTTGCA
10493 TAAAATTTAATTCTAAAGAATAATGCG
1 TAAAATTTAATTCTAAAGAATAATGCG
* *
10520 TAAAATATAATTCGGTATCAA-AA-AGTTGCG
1 TAAAATTTAATTC--TA--AAGAATA-ATGCG
*
10550 TAAAATTTAATTCTTAAGAATAATGC
1 TAAAATTTAATTCTAAAGAATAATGC
10576 AGTTGTTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
26 2 0.05
27 17 0.39
28 2 0.05
29 3 0.07
30 18 0.41
31 2 0.05
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (27 bp):
TAAAATTTAATTCTAAAGAATAATGCG
Found at i:13554 original size:35 final size:36
Alignment explanation
Indices: 13513--13586 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
13503 TTATGTTGTT
**
13513 AGATTCAACTAAATCTTTTCAC-CAAA-AAAAAAAAA
1 AGATTCAACTAAATCAGTTC-CTCAAAGAAAAAAAAA
13548 AGATTCAACTAAATCAGTTCCTCAAAGAAAAAAAAA
1 AGATTCAACTAAATCAGTTCCTCAAAGAAAAAAAAA
13584 AGA
1 AGA
13587 AAAGTTCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 22 0.63
36 12 0.34
ACGTcount: A:0.57, C:0.16, G:0.07, T:0.20
Consensus pattern (36 bp):
AGATTCAACTAAATCAGTTCCTCAAAGAAAAAAAAA
Done.