Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007776.1 Corchorus capsularis cultivar CVL-1 contig07797, 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: 58999
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:11963 original size:8 final size:8
Alignment explanation
Indices: 11953--12030 Score: 84
Period size: 8 Copynumber: 9.8 Consensus size: 8
11943 TTTCTGAATA
*
11953 TATATATA
1 TATATATG
11961 TATATATG
1 TATATATG
*
11969 TATATATA
1 TATATATG
11977 TATATATG
1 TATATATG
*
11985 TATGTATG
1 TATATATG
*
11993 TATGTATG
1 TATATATG
*
12001 TATGTATG
1 TATATATG
*
12009 TATGTATG
1 TATATATG
* *
12017 TATGTATA
1 TATATATG
12025 TATATA
1 TATATA
12031 CTTCCCATCC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 64 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:11964 original size:4 final size:4
Alignment explanation
Indices: 11965--12023 Score: 91
Period size: 4 Copynumber: 14.8 Consensus size: 4
11955 TATATATATA
* * *
11965 TATG TATA TATA TATA TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12013 TATG TATG TAT
1 TATG TATG TAT
12024 ATATATACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:11967 original size:12 final size:12
Alignment explanation
Indices: 11950--12027 Score: 93
Period size: 12 Copynumber: 6.5 Consensus size: 12
11940 TGTTTTCTGA
* *
11950 ATATATATATAT
1 ATATATGTATGT
*
11962 ATATATGTATAT
1 ATATATGTATGT
*
11974 ATATATATATGT
1 ATATATGTATGT
*
11986 ATGTATGTATGT
1 ATATATGTATGT
*
11998 ATGTATGTATGT
1 ATATATGTATGT
*
12010 ATGTATGTATGT
1 ATATATGTATGT
12022 ATATAT
1 ATATAT
12028 ATACTTCCCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:11974 original size:16 final size:16
Alignment explanation
Indices: 11957--12030 Score: 103
Period size: 16 Copynumber: 4.6 Consensus size: 16
11947 TGAATATATA
*
11957 TATATATATATGTATA
1 TATATATATATGTATG
11973 TATATATATATGTATG
1 TATATATATATGTATG
* *
11989 TATGTATGTATGTATG
1 TATATATATATGTATG
* *
12005 TATGTATGTATGTATG
1 TATATATATATGTATG
12021 TATATATATA
1 TATATATATA
12031 CTTCCCATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (16 bp):
TATATATATATGTATG
Found at i:12747 original size:173 final size:174
Alignment explanation
Indices: 12458--12806 Score: 637
Period size: 173 Copynumber: 2.0 Consensus size: 174
12448 ATATTCTCCC
*
12458 TTCACTCATAGAGATGTTTCTGTTTGTTCAATTATACATTGTACTTTAAATGATGCATTCTGCTC
1 TTCACTCATAGAGATGTTTCTGTTTGTTCAATTATACATTGTACTTTAAATGATGCATTCGGCTC
*
12523 TAGCAGATGTTATGGCCTGAAAGGAAGGGCTAGCAACGCAAATTTTGCATGACTTTTAGTTTAT-
66 TAGCAGATGTTATGGCCTGAAAGGAAGGGCTAGCAACGCAAATTTTGCATGACTTTTAGCTTATA
12587 GAAACCACAAGGCTGACAGTTTTATGAACAGCCTCTTGGAAACT
131 GAAACCACAAGGCTGACAGTTTTATGAACAGCCTCTTGGAAACT
12631 TTCACTCATAGAGATGTTTCTGTTTGTTCAATTATACATTGTACTTTAAATGATGCATTCGGCTC
1 TTCACTCATAGAGATGTTTCTGTTTGTTCAATTATACATTGTACTTTAAATGATGCATTCGGCTC
* * *
12696 TATCAGATTTTATGGCCTGAAAGGAAGGGCTAGCAATGCAAATTTTGCATGACTTTTAGCTTATG
66 TAGCAGATGTTATGGCCTGAAAGGAAGGGCTAGCAACGCAAATTTTGCATGACTTTTAGCTTAT-
12761 AGAAACCACAAGGCTGACAGTTTTATGAACAGCCTCTTGGAAACT
130 AGAAACCACAAGGCTGACAGTTTTATGAACAGCCTCTTGGAAACT
12806 T
1 T
12807 ATGTTACTAT
Statistics
Matches: 169, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
173 124 0.73
175 45 0.27
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (174 bp):
TTCACTCATAGAGATGTTTCTGTTTGTTCAATTATACATTGTACTTTAAATGATGCATTCGGCTC
TAGCAGATGTTATGGCCTGAAAGGAAGGGCTAGCAACGCAAATTTTGCATGACTTTTAGCTTATA
GAAACCACAAGGCTGACAGTTTTATGAACAGCCTCTTGGAAACT
Found at i:19032 original size:15 final size:14
Alignment explanation
Indices: 18990--19033 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18980 AGTTTTATAA
*
18990 CTTTAATTTTATTC
1 CTTTAATTTTATTT
*
19004 CTTTAATTTGATTT
1 CTTTAATTTTATTT
*
19018 CTTATTATTTTATTT
1 CTT-TAATTTTATTT
19033 C
1 C
19034 ATAATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.66
Consensus pattern (14 bp):
CTTTAATTTTATTT
Found at i:23392 original size:2 final size:2
Alignment explanation
Indices: 23385--23448 Score: 71
Period size: 2 Copynumber: 32.0 Consensus size: 2
23375 TCAATTCTAC
*
23385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A TC TA GTA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA
23427 TA TA TA TA TA -A TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA
23449 ATAATGTAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
1 3 0.06
2 46 0.85
3 5 0.09
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:28611 original size:14 final size:14
Alignment explanation
Indices: 28592--28631 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
28582 GTCGGGTTGG
*
28592 ATTTGGGTTTGGTT
1 ATTTGGGTTAGGTT
28606 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
28620 AGTTTCGGGTTA
1 A-TTT-GGGTTA
28632 AGGAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.03, G:0.35, T:0.50
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:29214 original size:2 final size:2
Alignment explanation
Indices: 29167--29199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29157 GATAACTAGG
29167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29200 GCAAGTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36286 original size:21 final size:21
Alignment explanation
Indices: 36260--36304 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36250 CAATACTGGA
36260 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
36281 TTGCTATTCACCGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
36302 TTG
1 TTG
36305 ACTTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:36569 original size:32 final size:32
Alignment explanation
Indices: 36530--36603 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
36520 GCCGCCCCAG
36530 TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAA
1 TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAA
*
36562 TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAG
1 TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAA
*
36594 TGGGGAGGCT
1 TGGGGCGGCT
36604 CCGCGTGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.14, C:0.26, G:0.45, T:0.16
Consensus pattern (32 bp):
TGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAA
Found at i:36780 original size:2 final size:2
Alignment explanation
Indices: 36773--36801 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36763 ATCAATATCA
36773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36802 ATTGTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38231 original size:24 final size:26
Alignment explanation
Indices: 38186--38242 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
38176 TGAGCACCAC
*
38186 CAGCAGCATGGCCAGCACCACCA-CATG
1 CAGCAGCACGGCCA-CACCACCATCA-G
38213 CAGCAGCACGGCCA-A-CACCATCAG
1 CAGCAGCACGGCCACACCACCATCAG
38237 CAGCAG
1 CAGCAG
38243 AGCAGTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 12 0.43
25 3 0.11
27 13 0.46
ACGTcount: A:0.32, C:0.40, G:0.23, T:0.05
Consensus pattern (26 bp):
CAGCAGCACGGCCACACCACCATCAG
Found at i:43193 original size:5 final size:5
Alignment explanation
Indices: 43183--43215 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
43173 TAATTGCCTT
*
43183 TTTTC TTTTC TTTTC TTTTC ATTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
43216 TTATTTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:43207 original size:15 final size:15
Alignment explanation
Indices: 43183--43221 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43173 TAATTGCCTT
*
43183 TTTTCTTTTCTTTTC
1 TTTTCATTTCTTTTC
*
43198 TTTTCATTTCTTTTT
1 TTTTCATTTCTTTTC
*
43213 TTTTTATTT
1 TTTTCATTT
43222 ATCGTGTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCATTTCTTTTC
Found at i:58244 original size:50 final size:51
Alignment explanation
Indices: 58123--58255 Score: 153
Period size: 50 Copynumber: 2.6 Consensus size: 51
58113 CTCTAATGTT
* * ** * *
58123 TAAAAAAGTTTAGTAATTAGGAGACTGATGAAAGTTGTCTCTCCAAACATC
1 TAAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTCTCTCTCCAAACATC
* * *
58174 T-AGAAAATTGTAGTAATTAGGAGGCCGATGGGAGCTCTCTC-CCAGACATC
1 TAAAAAAATT-TAGTAATTAGGAGACCGATGGGAGCTCTCTCTCCAAACATC
*
58224 TAAAAAAATTTAGTAATTAGGAAACCGATGGG
1 TAAAAAAATTTAGTAATTAGGAGACCGATGGG
58256 CCCAAACAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 35 0.51
51 33 0.49
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (51 bp):
TAAAAAAATTTAGTAATTAGGAGACCGATGGGAGCTCTCTCTCCAAACATC
Found at i:58390 original size:50 final size:51
Alignment explanation
Indices: 58278--58394 Score: 146
Period size: 50 Copynumber: 2.3 Consensus size: 51
58268 GAAAGCGAGT
* * * * * *
58278 GATGAAAGTTGTCTCTCCAAACATCTACAAAATTGTAGTAATTAGGAGGCC
1 GATGAGAGCTGTCTCCCCAAACATCTAAAAAATTGTAGTAATTAGGAGACA
* * *
58329 GATGGGAGCTGTCTCCCCAGACATCTAAAAAATT-TAGTAATTCGGAGACA
1 GATGAGAGCTGTCTCCCCAAACATCTAAAAAATTGTAGTAATTAGGAGACA
58379 GATGAGAGCTGTCTCC
1 GATGAGAGCTGTCTCC
58395 TCCCCCCTCC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 28 0.50
51 28 0.50
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (51 bp):
GATGAGAGCTGTCTCCCCAAACATCTAAAAAATTGTAGTAATTAGGAGACA
Found at i:58574 original size:41 final size:41
Alignment explanation
Indices: 58485--58695 Score: 205
Period size: 41 Copynumber: 5.2 Consensus size: 41
58475 GAAAAAAAGT
* * * **
58485 GATGAGAGC--TCTCTCCAAATATTTTACTAAAAAGTGATA
1 GATGAGAGCTATCTCTCCAAACATTTAATTAAAAAGTGACC
* * * *
58524 AATGTGAGCTGTCTCTCCAAACATTAAATTAAAAAGTGACC
1 GATGAGAGCTATCTCTCCAAACATTTAATTAAAAAGTGACC
* * * *
58565 GATGAGAGCTATTTCTCCTAACATTTAATTAAAAAAATAACC
1 GATGAGAGCTATCTCTCCAAACATTTAATT-AAAAAGTGACC
* * *
58607 GATGAGAGCTGTCTCTCCAAACATTT-ATAAAAAAAGTGATC
1 GATGAGAGCTATCTCTCCAAACATTTAAT-TAAAAAGTGACC
* *
58648 GATGAGAGTTATCTTTCCAAACATTTAATT-AAAAGTGACC
1 GATGAGAGCTATCTCTCCAAACATTTAATTAAAAAGTGACC
*
58688 GATAAGAG
1 GATGAGAG
58696 ATTAAAAAGG
Statistics
Matches: 138, Mismatches: 29, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
39 7 0.05
40 16 0.12
41 81 0.59
42 34 0.25
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (41 bp):
GATGAGAGCTATCTCTCCAAACATTTAATTAAAAAGTGACC
Found at i:58617 original size:83 final size:83
Alignment explanation
Indices: 58529--58681 Score: 231
Period size: 83 Copynumber: 1.8 Consensus size: 83
58519 TGATAAATGT
*
58529 GAGCTGTCTCTCCAAACA-TTA-AATTAAAAAGTGACCGATGAGAGCTAT-TTCTCCTAACATTT
1 GAGCTGTCTCTCCAAACATTTATAA--AAAAAGTGACCGATGAGAGCTATCTT-TCCAAACATTT
58591 AATTAAAAAAATAACCGATGA
63 AATTAAAAAAATAACCGATGA
* *
58612 GAGCTGTCTCTCCAAACATTTATAAAAAAAGTGATCGATGAGAGTTATCTTTCCAAACATTTAAT
1 GAGCTGTCTCTCCAAACATTTATAAAAAAAGTGACCGATGAGAGCTATCTTTCCAAACATTTAAT
58677 TAAAA
66 TAAAA
58682 GTGACCGATA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
83 57 0.89
84 5 0.08
85 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (83 bp):
GAGCTGTCTCTCCAAACATTTATAAAAAAAGTGACCGATGAGAGCTATCTTTCCAAACATTTAAT
TAAAAAAATAACCGATGA
Found at i:58797 original size:29 final size:29
Alignment explanation
Indices: 58750--58817 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
58740 ATTTAGACGG
58750 TTTTGCCCCCGAACTTCAATCTT-GGACA
1 TTTTGCCCCCGAACTTCAATCTTGGGACA
* * *
58778 TTTTGCCCCATGAACTTCAATTTTGGGACG
1 TTTTGCCCC-CGAACTTCAATCTTGGGACA
58808 TTTTGCCCCC
1 TTTTGCCCCC
58818 TCAAATTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.26
29 12 0.35
30 13 0.38
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (29 bp):
TTTTGCCCCCGAACTTCAATCTTGGGACA
Done.