Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006686.1 Corchorus capsularis cultivar CVL-1 contig06707, 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: 19688
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:109 original size:26 final size:26
Alignment explanation
Indices: 80--147 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
70 TACTTAATTT
*
80 ATTAGTTAATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
106 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
132 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
148 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:124 original size:15 final size:15
Alignment explanation
Indices: 104--147 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
94 AATTAGTATC
104 TAATTAGTTTATTAT
1 TAATTAGTTTATTAT
119 TAATTAG--TA-T-T
1 TAATTAGTTTATTAT
*
130 TAATTAGTTTATGAT
1 TAATTAGTTTATTAT
145 TAA
1 TAA
148 AATGAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 4 0.17
15 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (15 bp):
TAATTAGTTTATTAT
Found at i:208 original size:25 final size:24
Alignment explanation
Indices: 156--214 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
146 AAAATGAAGG
* *
156 AAAATGAA-TTTGAAGATTTGTTA
1 AAAATGAAGTTCGAAGAGTTGTTA
179 AAAATGAAGTTCGAAGAAGTTGTTA
1 AAAATGAAGTTCGAAG-AGTTGTTA
* *
204 GAAATTAAGTT
1 AAAATGAAGTT
215 TAGGGTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.27
24 6 0.20
25 16 0.53
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (24 bp):
AAAATGAAGTTCGAAGAGTTGTTA
Found at i:1532 original size:2 final size:2
Alignment explanation
Indices: 1490--1519 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1480 CTTATCTTAC
1490 TA TA TA TA TA TA 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
1520 ATAAAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1600 original size:32 final size:32
Alignment explanation
Indices: 1549--1615 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1539 CGAACTCAAA
*
1549 AATCTTAATCAGTCAATTACCAAAATACCCTT
1 AATCATAATCAGTCAATTACCAAAATACCCTT
* * *
1581 AATCATAATTAGTCAATTACTAGAATACCCTT
1 AATCATAATCAGTCAATTACCAAAATACCCTT
1613 AAT
1 AAT
1616 ATTATAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (32 bp):
AATCATAATCAGTCAATTACCAAAATACCCTT
Found at i:2288 original size:18 final size:19
Alignment explanation
Indices: 2241--2286 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2231 ATTGTAATTA
2241 ATAATTTATTT-TTTATTT
1 ATAATTTATTTATTTATTT
*
2259 ATAATGTATTTATTTA-TT
1 ATAATTTATTTATTTATTT
2277 -TAATTTATTT
1 ATAATTTATTT
2287 TAGATTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 12 0.48
19 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATAATTTATTTATTTATTT
Found at i:4375 original size:30 final size:29
Alignment explanation
Indices: 4341--4405 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4331 CCAATTTTTG
* *
4341 AAAAAATGCTTAATTCAAGGTATATTGTT
1 AAAAAAAGCTCAATTCAAGGTATATTGTT
* * * *
4370 CAAAAAAGCTCAATTTAGGGTCTATTGTT
1 AAAAAAAGCTCAATTCAAGGTATATTGTT
4399 AAAAAAA
1 AAAAAAA
4406 CTTAAATCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAAAAAGCTCAATTCAAGGTATATTGTT
Found at i:4417 original size:28 final size:29
Alignment explanation
Indices: 4349--4417 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
4339 TGAAAAAATG
* *
4349 CTTAATTCAAGGTATATTGTTCAAAAAAG
1 CTTAATTCAGGGTATATTGTTCAAAAAAA
* * *
4378 CTCAATTTAGGGTCTATTGTT-AAAAAAA
1 CTTAATTCAGGGTATATTGTTCAAAAAAA
*
4406 CTTAAATCAGGG
1 CTTAATTCAGGG
4418 CCCAATGTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (29 bp):
CTTAATTCAGGGTATATTGTTCAAAAAAA
Found at i:4603 original size:2 final size:2
Alignment explanation
Indices: 4596--4626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4586 GCTTTTTGCG
4596 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 T
4627 TCATCTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7393 original size:28 final size:28
Alignment explanation
Indices: 7361--7419 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
7351 CTCACCCAAC
7361 GAACCACAAA-GAGAAGCAATTAATGGAG
1 GAACCACAAAGGAGAAGCAA-TAATGGAG
* *
7389 GAACCACAAAGGAGAAGGAATCATGGAG
1 GAACCACAAAGGAGAAGCAATAATGGAG
7417 GAA
1 GAA
7420 TTGCTAGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.49, C:0.14, G:0.29, T:0.08
Consensus pattern (28 bp):
GAACCACAAAGGAGAAGCAATAATGGAG
Found at i:8376 original size:106 final size:105
Alignment explanation
Indices: 8144--8401 Score: 378
Period size: 106 Copynumber: 2.5 Consensus size: 105
8134 AATTTTTCTA
* ** * *
8144 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAAGTAGTTATATATTTTA
8207 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
* *
8247 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAAGTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAAGTAGTTATATATTTTA
* *
8312 TTTCTAAAACCCTATAATAATAAATTATTAATT-TTGAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGGAATTT
* *
8353 ATCCTTAAAATAAAAATAAAATTTTAATTTGGGTCTAAACTTAGTGAAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
8402 TTAAGGCTAA
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 35 0.25
106 54 0.39
107 10 0.07
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAAGTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
Found at i:9181 original size:90 final size:90
Alignment explanation
Indices: 9026--9207 Score: 328
Period size: 90 Copynumber: 2.0 Consensus size: 90
9016 GGAAGGGGTT
* * *
9026 TGTTGGCTCATAGATTAGCGTTTCGGTAATGTGCTAATCATGTAGCGGTGTACGGGTATTTCTGT
1 TGTTGACTCATAGATTAGCGTTTCGGTAATGTGCTAATCATGTAGCGATGTACGGGTATTCCTGT
9091 GCGTTTGTAATCCCAATTTCTTGAA
66 GCGTTTGTAATCCCAATTTCTTGAA
*
9116 TGTTGACTCATATATTAGCGTTTCGGTAATGTGCTAATCATGTAGCGATGTACGGGTATTCCTGT
1 TGTTGACTCATAGATTAGCGTTTCGGTAATGTGCTAATCATGTAGCGATGTACGGGTATTCCTGT
9181 GCGTTTGTAATCCCAATTTCTTGAA
66 GCGTTTGTAATCCCAATTTCTTGAA
9206 TG
1 TG
9208 AAAATGATTC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (90 bp):
TGTTGACTCATAGATTAGCGTTTCGGTAATGTGCTAATCATGTAGCGATGTACGGGTATTCCTGT
GCGTTTGTAATCCCAATTTCTTGAA
Found at i:14516 original size:2 final size:2
Alignment explanation
Indices: 14509--14534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14499 TTATTATTAT
14509 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
14535 GATAGATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15908 original size:109 final size:109
Alignment explanation
Indices: 15746--16005 Score: 441
Period size: 109 Copynumber: 2.4 Consensus size: 109
15736 TCTTCAATTA
*
15746 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTGGATATACTAAAATTTT
1 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTAGATATACTAAAATTTT
15811 TTCTAATATACAATTTTATTTTACTAAAAACTCTATTTTCATTT
66 TTCTAATATACAATTTTATTTTACTAAAAACTCTATTTTCATTT
*
15855 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTAGATATATTAAAATTTT
1 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTAGATATACTAAAATTTT
15920 TTCTAATATACAATTTTATTTTACTAAAAACTCTATTTTCATTT
66 TTCTAATATACAATTTTATTTTACTAAAAACTCTATTTTCATTT
* **
15964 AATTAAAT-TCAATATTTTATATATATTTTTTTATTTTTACCA
1 AATTAAATCT-AATATCTT-TATA-ATTACTTTATTTTTACCA
16006 TTTTAATTTA
Statistics
Matches: 143, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
108 1 0.01
109 122 0.85
110 4 0.03
111 16 0.11
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (109 bp):
AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAATTTAGATATACTAAAATTTT
TTCTAATATACAATTTTATTTTACTAAAAACTCTATTTTCATTT
Found at i:16749 original size:60 final size:60
Alignment explanation
Indices: 16676--16798 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
16666 TCATCTCTAA
16676 TAATATAATTTTTTAGAACAAAATTAGTAGTATGCTTAAGATTTTAATCTTCATATAATT
1 TAATATAATTTTTTAGAACAAAATTAGTAGTATGCTTAAGATTTTAATCTTCATATAATT
16736 TAATATAATTTTTTAGAACAAAATTAGTAGTATGCTTAAGATTTTAATCTTCATATAATT
1 TAATATAATTTTTTAGAACAAAATTAGTAGTATGCTTAAGATTTTAATCTTCATATAATT
16796 TAA
1 TAA
16799 AGTATCACGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (60 bp):
TAATATAATTTTTTAGAACAAAATTAGTAGTATGCTTAAGATTTTAATCTTCATATAATT
Found at i:16994 original size:9 final size:9
Alignment explanation
Indices: 16980--17031 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
16970 TCTTTTAGTT
16980 TTTTCTTTG
1 TTTTCTTTG
16989 TTTTCTTTG
1 TTTTCTTTG
* *
16998 TTTGCAAAATTTA
1 TTTTC----TTTG
17011 TTTTCTTTG
1 TTTTCTTTG
17020 TTTTCTTTG
1 TTTTCTTTG
17029 TTT
1 TTT
17032 GCAAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 28 0.80
13 7 0.20
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (9 bp):
TTTTCTTTG
Found at i:17016 original size:31 final size:31
Alignment explanation
Indices: 16980--17040 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
16970 TCTTTTAGTT
16980 TTTTCTTTGTTTTCTTTGTTTGCAAAATTTA
1 TTTTCTTTGTTTTCTTTGTTTGCAAAATTTA
17011 TTTTCTTTGTTTTCTTTGTTTGCAAAATTT
1 TTTTCTTTGTTTTCTTTGTTTGCAAAATTT
17041 TATACTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (31 bp):
TTTTCTTTGTTTTCTTTGTTTGCAAAATTTA
Found at i:17111 original size:22 final size:23
Alignment explanation
Indices: 17051--17112 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
17041 TATACTGTGA
*
17051 TTATCAAAATTTCATA-TAGATG
1 TTATCAAAATTTCATAGGAGATG
* *
17073 ATATCAAAACTTCATAGGA-ATG
1 TTATCAAAATTTCATAGGAGATG
17095 TTATCAAAATTTCATAGG
1 TTATCAAAATTTCATAGG
17113 GGGTGGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAGATG
Found at i:17143 original size:22 final size:21
Alignment explanation
Indices: 17115--17155 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
17105 TTCATAGGGG
17115 GTGGTTAACAAAATATTAATGT
1 GTGGTTAACAAAAT-TTAATGT
*
17137 GTGGTTATCAAAATTTAAT
1 GTGGTTAACAAAATTTAAT
17156 AAGTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (21 bp):
GTGGTTAACAAAATTTAATGT
Found at i:19240 original size:131 final size:130
Alignment explanation
Indices: 19063--19313 Score: 459
Period size: 131 Copynumber: 1.9 Consensus size: 130
19053 GTGATGATTA
19063 TATAATTATTGGTTTGATTTTTTTTATCTTAATATCAAATATCAATGATACTAAATGACAATAAT
1 TATAATTATTGGTTTGATTTTTTTTATCTTAATATCAAATATCAATGATACTAAATGACAATAAT
19128 TATTGTAATTTCCGTTATACTTTATATATGAATATATATATATGGATTCACCTCTATAATTAATT
66 TATTGTAATTTCCGTTATACTTTATATATG-A-ATATATATATGGATTCACCTCTATAATTAATT
19193 CC
129 CC
*
19195 TATAATTATTGGTTTG-TTTTTTTTATCTTAATATCAAATATCAATGATACTAAATGACAATAGT
1 TATAATTATTGGTTTGATTTTTTTTATCTTAATATCAAATATCAATGATACTAAATGACAATAAT
*
19259 TATTGTAATTTCCGTTATACTTTATATATGACTATATATATGGATTCACCTCTAT
66 TATTGTAATTTCCGTTATACTTTATATATGAATATATATATGGATTCACCTCTAT
19314 GGCTCACTCC
Statistics
Matches: 117, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
129 23 0.20
130 1 0.01
131 77 0.66
132 16 0.14
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (130 bp):
TATAATTATTGGTTTGATTTTTTTTATCTTAATATCAAATATCAATGATACTAAATGACAATAAT
TATTGTAATTTCCGTTATACTTTATATATGAATATATATATGGATTCACCTCTATAATTAATTCC
Done.