Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013291.1 Corchorus capsularis cultivar CVL-1 contig13312, 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: 24005
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3559 original size:21 final size:20
Alignment explanation
Indices: 3530--3577 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3520 TAGATTTAGA
* *
3530 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
3551 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
3571 TTTAATT
1 TTTAATT
3578 AATAATTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:9303 original size:87 final size:89
Alignment explanation
Indices: 9199--9367 Score: 227
Period size: 93 Copynumber: 1.9 Consensus size: 89
9189 TCTTCGATGA
* *
9199 ATTTGATTCAAGGGTC-TTGA-TAGACTTGATCTTGAATAAACAGGAA-TAATCTTCTCTGAATG
1 ATTTGATTCAAGGGTCTTTGATTAGACTTGATCTTGAACAAACA-GAATTAATCTTCTCCGAATG
9261 TGTTGGTGAAGATCGAGAGAAATTT
65 TGTTGGTGAAGATCGAGAGAAATTT
* *
9286 ATTTGCTTCAAGGGTCTTTGATTTGGTAGACTTGATCTTGAACAAACATAATTAATCTTCTCCGA
1 ATTTGATTCAAGGGTCTTTGA--T--TAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGA
*
9351 ATTTGTTGGTGAAGATC
62 ATGTGTTGGTGAAGATC
9368 AAAACAATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
87 15 0.21
88 4 0.06
92 2 0.03
93 49 0.70
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (89 bp):
ATTTGATTCAAGGGTCTTTGATTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATGT
GTTGGTGAAGATCGAGAGAAATTT
Found at i:11126 original size:112 final size:112
Alignment explanation
Indices: 11005--11301 Score: 413
Period size: 112 Copynumber: 2.7 Consensus size: 112
10995 TTATTATTTA
** *
11005 CTCGTCCTGGTGTTGGT-TTCTAACTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTA
1 CTCGTCCTGGTGTTCATCTTC-GACTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTA
11069 GTGCTCATCTGCTTTCGACC-AGG-GCAAGCGATCAAACTTTATTATTCG
65 GTGCTCATCTGCTTTCGACCAAGGCGCAAGCGATC-AACTTTATT-TTCG
* *
11117 CTCAG-CCTGGTGTTCATCTTCGCCTAGGGTTCAAGCGATCAAAATTTATTATTCGCTCGCCCTA
1 CTC-GTCCTGGTGTTCATCTTCGACTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTA
* *
11181 GTGCTCATCTGCTTTTGACCAAGGCTCAAGCGATCAACTTTATTTTCG
65 GTGCTCATCTGCTTTCGACCAAGGCGCAAGCGATCAACTTTATTTTCG
* * * * *
11229 CTCGTCCTGATGTTCATCTTCGACTAGGCCTCAAGCGATCAAAATTTATCATTCGCTCGTCTTAG
1 CTCGTCCTGGTGTTCATCTTCGACTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAG
*
11294 TACTCATC
66 TGCTCATC
11302 ATGTTTGCTT
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
111 1 0.01
112 139 0.84
113 16 0.10
114 9 0.05
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.34
Consensus pattern (112 bp):
CTCGTCCTGGTGTTCATCTTCGACTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAG
TGCTCATCTGCTTTCGACCAAGGCGCAAGCGATCAACTTTATTTTCG
Found at i:11168 original size:55 final size:59
Alignment explanation
Indices: 11028--11287 Score: 273
Period size: 57 Copynumber: 4.6 Consensus size: 59
11018 TGGTTTCTAA
11028 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTCGAC
1 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCA-CTGCTTTCGAC
* * *
11088 C-AGGG--CAAGCGATCAAACTTTATTATTCGCTCAG-CCTGGTGTTCA-T-C-TTCG-C
1 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTC-GCCCTAGTGCTCACTGCTTTCGAC
* *
11140 CTAGGGTTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTTGAC
1 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCA-CTGCTTTCGAC
* * * *
11200 C-AAGGCTCAAGCGATC-AACTTTATT-TTCGCTCGTCCT-GATGTTCA-T-C-TTCGA-
1 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAG-TGCTCACTGCTTTCGAC
* *
11252 CTAGGCCTCAAGCGATCAAAATTTATCATTCGCTCG
1 CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCG
11288 TCTTAGTACT
Statistics
Matches: 169, Mismatches: 17, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
52 3 0.02
53 25 0.15
54 10 0.06
55 45 0.27
56 1 0.01
57 52 0.31
58 10 0.06
59 20 0.12
60 3 0.02
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.32
Consensus pattern (59 bp):
CTAGGGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCACTGCTTTCGAC
Found at i:11246 original size:57 final size:59
Alignment explanation
Indices: 11032--11301 Score: 257
Period size: 55 Copynumber: 4.8 Consensus size: 59
11022 TTCTAACTAG
11032 GGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTCGACC-A
1 GGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTCGACCAA
* * * * *
11090 GG-GCAAGCGATCAAACTTTATTATTCGCTCAG-CCTGGTGTTCA--T-C-TTCG-CCTAG
1 GGCTCAAGCGATCAAAATTTATTATTCGCTC-GCCCTAGTGCTCATCTGCTTTCGACC-AA
* *
11144 GGTTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTTGACCAA
1 GGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTCGACCAA
* * * *
11203 GGCTCAAGCGATC-AACTTTATT-TTCGCTCGTCCT-GATGTTCA--T-C-TTCGA-CTA
1 GGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAG-TGCTCATCTGCTTTCGACCAA
* * * *
11255 GGCCTCAAGCGATCAAAATTTATCATTCGCTCGTCTTAGTACTCATC
1 GG-CTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATC
11302 ATGTTTGCTT
Statistics
Matches: 173, Mismatches: 22, Indels: 35
0.75 0.10 0.15
Matches are distributed among these distances:
52 6 0.03
53 19 0.11
54 12 0.07
55 52 0.30
56 2 0.01
57 52 0.30
58 12 0.07
59 16 0.09
60 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (59 bp):
GGCTCAAGCGATCAAAATTTATTATTCGCTCGCCCTAGTGCTCATCTGCTTTCGACCAA
Found at i:12213 original size:58 final size:58
Alignment explanation
Indices: 12123--12299 Score: 318
Period size: 58 Copynumber: 3.1 Consensus size: 58
12113 GTTTTTTTTT
*
12123 TTTTTGGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
*
12181 TTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACATAGCGAGC
1 TTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
* *
12239 TTTTTGTGCTCTAAATTTTGCCTAAGCCGTCCTTTGTAGGATTTTCAACTTAGCGAGC
1 TTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
12297 TTT
1 TTT
12300 GCAAGTAGTT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 114 1.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (58 bp):
TTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
Found at i:15178 original size:87 final size:89
Alignment explanation
Indices: 15075--15243 Score: 245
Period size: 93 Copynumber: 1.9 Consensus size: 89
15065 TCTTCGATGA
* *
15075 ATTTGATTCAAGGGTC-TTGA-TAGACTTGATCTTGAATAAACAGGAA-TAATCTTCTCTGAATT
1 ATTTGATTCAAGGGTCTTTGATTAGACTTGATCTTGAACAAACA-GAACTAATCTTCTCCGAATT
15137 TGTTGGTGAAGATCGAGAGAAATTT
65 TGTTGGTGAAGATCGAGAGAAATTT
*
15162 ATTTGCTTCAAGGGTCTTTGATTTGGTAGACTTGATCTTGAACAAACAGAACTAATCTTCTCCGA
1 ATTTGATTCAAGGGTCTTTGA--T--TAGACTTGATCTTGAACAAACAGAACTAATCTTCTCCGA
15227 ATTTGTTGGTGAAGATC
62 ATTTGTTGGTGAAGATC
15244 AAAACAATGA
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
87 15 0.21
88 4 0.06
92 3 0.04
93 50 0.69
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (89 bp):
ATTTGATTCAAGGGTCTTTGATTAGACTTGATCTTGAACAAACAGAACTAATCTTCTCCGAATTT
GTTGGTGAAGATCGAGAGAAATTT
Found at i:16316 original size:13 final size:16
Alignment explanation
Indices: 16284--16321 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
16274 CAATTTGGAG
16284 TGAAGATTTGATGATT
1 TGAAGATTTGATGATT
16300 TGAAG-TTTG-TG-TT
1 TGAAGATTTGATGATT
16313 TGAAGATTT
1 TGAAGATTT
16322 ATTGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 5 0.24
15 4 0.19
16 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
TGAAGATTTGATGATT
Found at i:20845 original size:10 final size:11
Alignment explanation
Indices: 20818--20844 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20808 AAAAATTCAG
20818 AATTTTCGAAA
1 AATTTTCGAAA
20829 AATTTTCGAAA
1 AATTTTCGAAA
20840 AATTT
1 AATTT
20845 CATGGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (11 bp):
AATTTTCGAAA
Found at i:21159 original size:16 final size:16
Alignment explanation
Indices: 21134--21164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21124 AGCAATAGGC
21134 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
21150 AATCATTCAAAGCAA
1 AATCAATCAAAGCAA
21165 AACAATGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:21864 original size:22 final size:21
Alignment explanation
Indices: 21839--21932 Score: 50
Period size: 22 Copynumber: 4.2 Consensus size: 21
21829 TCCGGGCACA
21839 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTA-T
* *
21861 AATTCTGATAAGTCCTCCGGG--C
1 AATTCAGA-AA--CCTCCGGGTAT
* *
21883 AATT-GGTAAGACCTCCGGGCAT
1 AATTCAG-AA-ACCTCCGGGTAT
*
21905 AATTTCAGAAACCTCCTGGTATT
1 AA-TTCAGAAACCTCCGGGTA-T
21928 AATTC
1 AATTC
21933 TGATAAGTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
20 8 0.15
21 2 0.04
22 27 0.49
23 9 0.16
24 1 0.02
25 8 0.15
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (21 bp):
AATTCAGAAACCTCCGGGTAT
Found at i:21928 original size:67 final size:67
Alignment explanation
Indices: 21820--21967 Score: 233
Period size: 67 Copynumber: 2.2 Consensus size: 67
21810 AGTTTGCATC
*
21820 GGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAA
1 GGTAAGACCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAA
**
21885 TT
66 CG
* * *
21887 GGTAAGACCTCCGGGCATAATTTCAGAAACCTCCTGGTATTAATTCTGATAAGTCCTCCGGGCAA
1 GGTAAGACCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAA
21952 CG
66 CG
*
21954 GGTAAAACCTCCGG
1 GGTAAGACCTCCGG
21968 ATACCATTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (67 bp):
GGTAAGACCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAA
CG
Found at i:22477 original size:27 final size:27
Alignment explanation
Indices: 22368--22469 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
22358 TAGAGTCATC
*
22368 CAGGGGCATTTTGGTCATTTGTGCACT
1 CAGGGGCATTTTGGTCATTTGTACACT
* * *
22395 CAGTGGCATTTTTGTCATTTGTACATT
1 CAGGGGCATTTTGGTCATTTGTACACT
*
22422 CAAGGGCATTTTGGTCATTTG-AGCACT
1 CAGGGGCATTTTGGTCATTTGTA-CACT
*
22449 CAGGGGCATTTTAGTCATTTG
1 CAGGGGCATTTTGGTCATTTG
22470 GTCCCTCACT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.02
27 63 0.98
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTGTACACT
Found at i:22748 original size:26 final size:26
Alignment explanation
Indices: 22710--22759 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
22700 GGCATATTTG
**
22710 ATTATTCTGCATTAAATTGCATTTCA
1 ATTATTCAACATTAAATTGCATTTCA
*
22736 ATTATTCAACATTAGATTGCATTT
1 ATTATTCAACATTAAATTGCATTT
22760 ACATGGAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (26 bp):
ATTATTCAACATTAAATTGCATTTCA
Done.