Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009632.1 Corchorus capsularis cultivar CVL-1 contig09653, 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: 53971
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:11766 original size:20 final size:21
Alignment explanation
Indices: 11741--11780 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
11731 TTGGGTTCTA
11741 CTCTCACGGAA-TGTGAGTTG
1 CTCTCACGGAATTGTGAGTTG
11761 CTCTCACGGAATTGTGAGTT
1 CTCTCACGGAATTGTGAGTT
11781 TTCTTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
CTCTCACGGAATTGTGAGTTG
Found at i:17332 original size:16 final size:16
Alignment explanation
Indices: 17311--17346 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
17301 TCTACTCTTA
17311 CTGAAATTTAGTCCTT
1 CTGAAATTTAGTCCTT
*
17327 CTGAAATTTAGTTCTT
1 CTGAAATTTAGTCCTT
17343 CTGA
1 CTGA
17347 GAGCAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (16 bp):
CTGAAATTTAGTCCTT
Found at i:27183 original size:5 final size:5
Alignment explanation
Indices: 27173--27200 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27163 TATTATAGTT
27173 TTATC TTATC TTATC TTATC TTATC TTA
1 TTATC TTATC TTATC TTATC TTATC TTA
27201 CCACTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATC
Found at i:27450 original size:30 final size:30
Alignment explanation
Indices: 27415--27472 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
27405 ATTTTTAATC
27415 ATTAAACTTTGATTTATTAATTATAAAATA
1 ATTAAACTTTGATTTATTAATTATAAAATA
*
27445 ATTAAACTTTTATTTATTAATTATAAAA
1 ATTAAACTTTGATTTATTAATTATAAAA
27473 AGATACTCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTAAACTTTGATTTATTAATTATAAAATA
Found at i:33943 original size:130 final size:130
Alignment explanation
Indices: 33709--34222 Score: 710
Period size: 130 Copynumber: 3.9 Consensus size: 130
33699 AATTAAAAGT
* * * * * *
33709 CGTTGCCTAAGTGATTTTGATGGTATTTTACCCAACGACTTCTTTAATTGTTGTTAATGTTTATA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAAC-ACTTTTTTAGTTGTTGCTAATGCTTACA
* * *
33774 GTTTTCGTAAC-ACTAAAAACAAAGTCGTTGCGAAATCATAACCTATTCGTAACAATTTTATAAA
65 ATTTTCGTAACAAC-AAAAACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAA
**
33838 GT
129 AA
* *
33840 CGTTGCCTAAGTTATTTTGATGGTATTTTACACAACACTTTTTTAGTCGTTGCTAATGCTTACAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCTAATGCTTACAA
* *
33905 CTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAAACTATTCGTAACGACTTTATAAAAA
66 TTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAA
33970 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTG-TCAATGCTTACA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCT-AATGCTTACA
* *
34034 ATTTTCGTAACAACAAAAACAAAATCGTTGCGAAATGATAAACTATTCGTAACAACTTTATAAAA
65 ATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAA
34099 A
130 A
* * * *
34100 CTTTGCCTAAGTGATTTTGATGGTA-TTTATACAACACTTTTTTAGTTGTTGCCAATGTTTACAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCTAATGCTTACAA
* *** * * * *
34164 TATTCGTAACAACAACTTCTGAAGTTGCTGCGAAATCATAAGCTATTCGTAACAACTTT
66 TTTTCGTAACAACAAAAAC-AAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTT
34223 GTAAGTAATT
Statistics
Matches: 344, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
129 51 0.15
130 257 0.75
131 36 0.10
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (130 bp):
CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCTAATGCTTACAA
TTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAA
Found at i:36661 original size:45 final size:46
Alignment explanation
Indices: 36577--36664 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
36567 AATTATTTCT
* *
36577 CCAGCTCATCATTAATCCTAGGGTAGGGATTTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTAGGGTAGAGATCTTTTAGTAATTCCAC
* *
36623 CCAGCTCTTCATTAATTCT-GGGTAGAGATCTTTTAGTAATTC
1 CCAGCTCATCATTAATCCTAGGGTAGAGATCTTTTAGTAATTC
36665 AAGTACTCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (46 bp):
CCAGCTCATCATTAATCCTAGGGTAGAGATCTTTTAGTAATTCCAC
Found at i:36868 original size:2 final size:2
Alignment explanation
Indices: 36861--36895 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
36851 ATATGTAGTG
36861 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36896 ATTTTACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36881 original size:17 final size:17
Alignment explanation
Indices: 36861--36893 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
36851 ATATGTAGTG
36861 TATATATATATATATAA
1 TATATATATATATATAA
36878 TATATATATATATATA
1 TATATATATATATATA
36894 TAATTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:36883 original size:19 final size:19
Alignment explanation
Indices: 36861--36897 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
36851 ATATGTAGTG
36861 TATATATATATATATAATA
1 TATATATATATATATAATA
36880 TATATATATATATATAAT
1 TATATATATATATATAAT
36898 TTTACCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATATATATAATA
Found at i:37217 original size:12 final size:12
Alignment explanation
Indices: 37202--37235 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
37192 TGAGATAAAA
37202 TAATAATAATAT
1 TAATAATAATAT
*
37214 TAATATTAATAT
1 TAATAATAATAT
37226 TAATAATAAT
1 TAATAATAAT
37236 TTTGAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:40160 original size:134 final size:131
Alignment explanation
Indices: 39989--40227 Score: 372
Period size: 134 Copynumber: 1.8 Consensus size: 131
39979 CCAATAATTA
*
39989 AAATATTGTTACATAAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAA
1 AAATATTGTTACAGAAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTG---ACAA
*
40054 CATTTT-TTCGTTTTAAAAAATTATTTGAAACCAACTAAATATCATTATAAAAAACTTTACACAA
63 CATTTTGTT-GTTTTAAAAAATTATTCGAAACCAACTAAATATCATTATAAAAAACTTTACACAA
40118 CCAAT
127 CCAAT
* *
40123 AAATATTGTTACCGAAAATTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAT
1 AAATATTGTTACAGAAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAT
** *
40188 TTTGTTGTTTTAAAATGTTATTCGCAACCAACTAAATATC
66 TTTGTTGTTTTAAAAAATTATTCGAAACCAACTAAATATC
40228 GTTGTAAATA
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
131 40 0.41
132 2 0.02
134 55 0.57
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (131 bp):
AAATATTGTTACAGAAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAT
TTTGTTGTTTTAAAAAATTATTCGAAACCAACTAAATATCATTATAAAAAACTTTACACAACCAA
T
Found at i:40185 original size:67 final size:67
Alignment explanation
Indices: 39989--40185 Score: 159
Period size: 67 Copynumber: 2.9 Consensus size: 67
39979 CCAATAATTA
* *
39989 AAATATTGTTACATAAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAA-CA
1 AAATATTGTTACAAAAAATTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACCA
40053 AC
66 AC
** * ** * * ** * * * **
40055 ATTTTTTCGTTTTAAAAAATTATTTGA-AACC-AACTAAATATCATTAT-AAAAAACTTTACACA
1 AAATATT-GTTACAAAAAATTATTT-ACAACCAAAAT-AATTTTGTTGTGTAAACA-TTTTGACA
*
40117 ACCAAT
62 ACCAAC
**
40123 AAATATTGTTACCGAAAATTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAAC
1 AAATATTGTTACAAAAAATTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAAC
40186 ATTTTGTTGT
Statistics
Matches: 90, Mismatches: 33, Indels: 15
0.65 0.24 0.11
Matches are distributed among these distances:
66 12 0.13
67 63 0.70
68 15 0.17
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (67 bp):
AAATATTGTTACAAAAAATTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACCA
AC
Found at i:40364 original size:35 final size:35
Alignment explanation
Indices: 40325--40449 Score: 83
Period size: 35 Copynumber: 3.4 Consensus size: 35
40315 AACGAATATA
40325 TGTTGTTAAAATATTTTTATGCAACAATATTTAGT
1 TGTTGTTAAAATATTTTTATGCAACAATATTTAGT
* * ** *
40360 TGTTGCGTAAAATATAATTCCTT-TAACAACAATAAAATA-A
1 TGTTG-TTAAAATAT--TT--TTAT-GCAACAAT-ATTTAGT
* * * *
40400 CGTTGTTAAAATATTTTTACGCAACGATATTGAGT
1 TGTTGTTAAAATATTTTTATGCAACAATATTTAGT
40435 TGTTGTGTAAAATAT
1 TGTTGT-TAAAATAT
40450 AATTCTTTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 19
0.66 0.15 0.19
Matches are distributed among these distances:
34 2 0.03
35 18 0.28
36 16 0.25
37 2 0.03
38 2 0.03
39 9 0.14
40 13 0.20
41 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (35 bp):
TGTTGTTAAAATATTTTTATGCAACAATATTTAGT
Found at i:40436 original size:75 final size:75
Alignment explanation
Indices: 40326--40472 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
40316 ACGAATATAT
* *
40326 GTTGTTAAAATATTTTTATGCAACAATATTTAGTTGTTGCGTAAAATATAATTCCTTTAACAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATATAATTCCTTTAACAACA
40391 ATAAAATAAC
66 ATAAAATAAC
* * *
40401 GTTGTTAAAATATTTTTACGCAACGATATTGAGTTGTTGTGTAAAATATAATTCTTTTAACAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATATAATTCCTTTAACAACA
40466 ATAAAAT
66 ATAAAAT
40473 GGTGTAACGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (75 bp):
GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATATAATTCCTTTAACAACA
ATAAAATAAC
Found at i:48239 original size:2 final size:2
Alignment explanation
Indices: 48232--48273 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
48222 ATTAACATCG
48232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48274 TCTAATAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.