Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001284.1 Corchorus capsularis cultivar CVL-1 contig01284, 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: 8252
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:2991 original size:22 final size:22
Alignment explanation
Indices: 2961--3060 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
2951 TCCAACGTAG
*
2961 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* ** *
2984 AAATTTGATAATCGTATTATG-
1 AAATTTGATAACCACACTATGA
* *
3005 AAATTTCGATAATCTA-TCTATGA
1 AAATTT-GATAA-CCACACTATGA
*
3028 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACACTATGA
*
3050 AATTTTGATAA
1 AAATTTGATAA
3061 GCATAATCTT
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
21 8 0.14
22 41 0.69
23 10 0.17
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:3157 original size:22 final size:22
Alignment explanation
Indices: 3129--3207 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
3119 TAATCCCTAT
3129 AATTTTGATAACCACTCTATGA
1 AATTTTGATAACCACTCTATGA
* *
3151 AGTTTTGATAACC-TTCATATGA
1 AATTTTGATAACCACTC-TATGA
* **
3173 AATTTTGGTAACCACAGTATGA
1 AATTTTGATAACCACTCTATGA
* *
3195 ATTTTTTATAACC
1 AATTTTGATAACC
3208 TTTGTTAAGG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCACTCTATGA
Found at i:4583 original size:22 final size:22
Alignment explanation
Indices: 4555--4613 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 22
4545 ACAACCTTCC
*
4555 TATGAAATTTTGATAATCTACT
1 TATGAAATTTTGATAACCTACT
4577 TATGAAATTTTTGATAACCTACT
1 TATGAAA-TTTTGATAACCTACT
4600 TATGAAATTTTGAT
1 TATGAAATTTTGAT
4614 TACCAGACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACT
Found at i:4737 original size:22 final size:22
Alignment explanation
Indices: 4687--4730 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4677 TAATTTTCCT
* *
4687 CATGAAAGCTTGATAATCTTAC
1 CATGAAAGATTGATAATCCTAC
4709 CATGAAAGATTGATAATCCTAC
1 CATGAAAGATTGATAATCCTAC
4731 TGTGAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
CATGAAAGATTGATAATCCTAC
Found at i:6022 original size:19 final size:20
Alignment explanation
Indices: 5998--6052 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5988 ATATAAAGAT
5998 ATAGTGTGATTATCAA-TTA
1 ATAGTGTGATTATCAATTTA
* * *
6017 ATAGTGCGGTTATCAATTTT
1 ATAGTGTGATTATCAATTTA
*
6037 ATAATGTGATTATCAA
1 ATAGTGTGATTATCAA
6053 AATTTCACAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (20 bp):
ATAGTGTGATTATCAATTTA
Found at i:6103 original size:23 final size:22
Alignment explanation
Indices: 6041--6217 Score: 74
Period size: 22 Copynumber: 7.9 Consensus size: 22
6031 AATTTTATAA
*
6041 TGTGATTATCAAAATTTCACAC
1 TGTGGTTATCAAAATTTCACAC
* * * *
6063 TGAGGTAATCAAATTTTCACAG
1 TGTGGTTATCAAAATTTCACAC
*
6085 TGTGGTTATTCAAAATTTCATA-
1 TGTGGTTA-TCAAAATTTCACAC
* * *
6107 TGGATTAGGTTATTAAAATTTTATA-
1 T-G--T-GGTTATCAAAATTTCACAC
* ** * *
6132 GGAAAGTTATCAAAATTTCATAG
1 TG-TGGTTATCAAAATTTCACAC
* * *
6155 TATGGTTCTCAAAATTTCATA-
1 TGTGGTTATCAAAATTTCACAC
* *
6176 GGTAGGTTATCAAAATTTCATAAC
1 TGT-GGTTATCAAAATTTCA-CAC
*
6200 -GAGGTTATCAAAATTTCA
1 TGTGGTTATCAAAATTTCA
6218 TAACGAGATT
Statistics
Matches: 119, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.01
22 86 0.72
23 14 0.12
24 1 0.01
25 12 0.10
26 5 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCACAC
Found at i:6146 original size:22 final size:22
Alignment explanation
Indices: 6088--6236 Score: 140
Period size: 22 Copynumber: 6.6 Consensus size: 22
6078 TTCACAGTGT
6088 GGTTATTCAAAATTTCATATGGATTA
1 GGTTA-TCAAAATTTCATA-GGA--A
* *
6114 GGTTATTAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGGAA
* * *
6136 AGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGGAA
* *
6158 GGTTCTCAAAATTTCATAGGTA
1 GGTTATCAAAATTTCATAGGAA
*
6180 GGTTATCAAAATTTCATAACG-A
1 GGTTATCAAAATTTCAT-AGGAA
*
6202 GGTTATCAAAATTTCATAACG-A
1 GGTTATCAAAATTTCAT-AGGAA
*
6224 GATTATCAAAATT
1 GGTTATCAAAATT
6237 CCATGACAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
22 86 0.80
23 2 0.02
24 3 0.03
25 11 0.10
26 5 0.05
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:6185 original size:44 final size:44
Alignment explanation
Indices: 6046--6236 Score: 158
Period size: 44 Copynumber: 4.2 Consensus size: 44
6036 TATAATGTGA
* * * *
6046 TTATCAAAATTTCACACTGA-GGTAATCAAATTTTCACAGTGT-GG
1 TTATCAAAATTTCATAC-GATGGTTATCAAAATTTCATAG-GTAGG
* * * * *
6090 TTATTCAAAATTTCATATGGATTAGGTTATTAAAATTTTATAGGAAAG
1 TTA-TCAAAATTTCATA-CGA-T-GGTTATCAAAATTTCATAGGTAGG
*
6138 TTATCAAAATTTCATA-GTATGGTTCTCAAAATTTCATAGGTAGG
1 TTATCAAAATTTCATACG-ATGGTTATCAAAATTTCATAGGTAGG
* *
6182 TTATCAAAATTTCATAACGA-GGTTATCAAAATTTCATAACG-AGA
1 TTATCAAAATTTCAT-ACGATGGTTATCAAAATTTCAT-AGGTAGG
6226 TTATCAAAATT
1 TTATCAAAATT
6237 CCATGACAAC
Statistics
Matches: 120, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
44 66 0.55
45 20 0.17
46 2 0.02
47 14 0.12
48 18 0.15
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATACGATGGTTATCAAAATTTCATAGGTAGG
Found at i:6233 original size:66 final size:68
Alignment explanation
Indices: 6046--6236 Score: 169
Period size: 66 Copynumber: 2.8 Consensus size: 68
6036 TATAATGTGA
* * * * * * *
6046 TTATCAAAATTTCACACTG-AGGTAATCAAATTTTCACAGTGTGGTTATTCAAAATTTCATATGG
1 TTATCAAAATTTCATAC-GAAAGTTATCAAAATTTCATAGTATGATTA-TCAAAATTTCATATGG
6110 ATTAGG
64 A-TAGG
* * * * *
6116 TTATTAAAATTTTATAGGAAAGTTATCAAAATTTCATAGTATGGTTCTCAAAATTTCATA-GG-T
1 TTATCAAAATTTCATACGAAAGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATATGGAT
6179 AGG
66 AGG
*
6182 TTATCAAAATTTCATAACG-AGGTTATCAAAATTTCATAACG-A-GATTATCAAAATT
1 TTATCAAAATTTCAT-ACGAAAGTTATCAAAATTTCAT-A-GTATGATTATCAAAATT
6237 CCATGACAAC
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
66 45 0.45
67 4 0.04
68 3 0.03
69 14 0.14
70 35 0.35
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (68 bp):
TTATCAAAATTTCATACGAAAGTTATCAAAATTTCATAGTATGATTATCAAAATTTCATATGGAT
AGG
Found at i:6266 original size:13 final size:13
Alignment explanation
Indices: 6248--6272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6238 CATGACAACT
6248 GAAAGATTAAAAC
1 GAAAGATTAAAAC
6261 GAAAGATTAAAA
1 GAAAGATTAAAA
6273 GGAATTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAAGATTAAAAC
Found at i:6561 original size:31 final size:30
Alignment explanation
Indices: 6457--6567 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 30
6447 AATTGAAAAA
* *
6457 GTATCAAATTAAGCAGATTTTG-AAAGGTTTG
1 GTATCAAATTGAGC--ATTTAGTAAAGGTTTG
* *
6488 GTATCAATTTGAACAATTT--TAAAGGTTTG
1 GTATCAAATTGAGC-ATTTAGTAAAGGTTTG
* *
6517 GTATCGAACTGAGCATTTAGTCAAAGGTTTG
1 GTATCAAATTGAGCATTTAGT-AAAGGTTTG
* *
6548 GTACCAAATTGAGCTTTTAG
1 GTATCAAATTGAGCATTTAG
6568 CCATATTCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.06
29 19 0.30
30 5 0.08
31 36 0.56
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (30 bp):
GTATCAAATTGAGCATTTAGTAAAGGTTTG
Done.