Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014857.1 Corchorus capsularis cultivar CVL-1 contig14878, 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: 27403
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:26 original size:16 final size:15
Alignment explanation
Indices: 5--36 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1 AACC
5 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTT-TTTT
21 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
36 T
1 T
37 CAAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:30 original size:9 final size:10
Alignment explanation
Indices: 6--35 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1 AACCT
6 TTTTCTTTTTC
1 TTTT-TTTTTC
17 TTTTTTTTTC
1 TTTTTTTTTC
27 TTTTTTTTT
1 TTTTTTTTT
36 TCAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:142 original size:26 final size:26
Alignment explanation
Indices: 113--180 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
103 TACTTAGTTT
113 ATTAGTTTATGTTTAATTAATATCTA
1 ATTAGTTTATGTTTAATTAATATCTA
* *
139 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAATATCTA
*
165 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
181 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:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAATATCTA
Found at i:157 original size:15 final size:15
Alignment explanation
Indices: 137--180 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
127 AATTAATATC
137 TAATTAGTTTATTAT
1 TAATTAGTTTATTAT
152 TAATTAG--TA-T-T
1 TAATTAGTTTATTAT
*
163 TAATTAGTTTATGAT
1 TAATTAGTTTATTAT
178 TAA
1 TAA
181 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:228 original size:24 final size:25
Alignment explanation
Indices: 189--248 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
179 AAAATGAAGG
*
189 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
212 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
237 GAAATGAAGTTT
1 AAAATGAAGTTT
249 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:3118 original size:28 final size:28
Alignment explanation
Indices: 3029--3127 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 28
3019 TACCCTGTTT
* *
3029 ATGGTCCTCTGTTGAGACTT-CAATGCGA
1 ATGGTCCTCTGTTGA-AATTCCAATGCCA
* * * * * *
3057 AAGGTCATCTGTTGAGATACCAACGCTA
1 ATGGTCCTCTGTTGAAATTCCAATGCCA
* *
3085 AGGGTCCTCTGTTGAAATTCCATTGCCA
1 ATGGTCCTCTGTTGAAATTCCAATGCCA
*
3113 ATGGTCCTCTATTGA
1 ATGGTCCTCTGTTGA
3128 GACTTGGACC
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
27 1 0.02
28 53 0.98
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
ATGGTCCTCTGTTGAAATTCCAATGCCA
Found at i:3749 original size:20 final size:21
Alignment explanation
Indices: 3714--3772 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3704 GGGAAGTAAC
*
3714 TCTCTTTATATCTGTTTTACTT
1 TCTCTTAATAT-TGTTTTACTT
* *
3736 TC-CTTATTATTGTTTTTCTT
1 TCTCTTAATATTGTTTTACTT
*
3756 TCTCTTAATATTATTTT
1 TCTCTTAATATTGTTTT
3773 CATGCTAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.35
21 18 0.58
22 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.66
Consensus pattern (21 bp):
TCTCTTAATATTGTTTTACTT
Found at i:6014 original size:11 final size:11
Alignment explanation
Indices: 5947--6027 Score: 56
Period size: 11 Copynumber: 7.0 Consensus size: 11
5937 CTAAAACTTA
5947 ATATATATATAT
1 ATATATATAT-T
*
5959 ATATAATATACGT
1 ATAT-ATATA-TT
*
5972 ATATGATAAATT
1 ATAT-ATATATT
5984 ATATA-ATGATT
1 ATATATAT-ATT
* *
5995 ATTTTTATATT
1 ATATATATATT
*
6006 ATATATATAAT
1 ATATATATATT
*
6017 ATATATTTATT
1 ATATATATATT
6028 TTTTATATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
10 1 0.02
11 27 0.51
12 11 0.21
13 14 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (11 bp):
ATATATATATT
Found at i:6018 original size:9 final size:9
Alignment explanation
Indices: 5945--6022 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
5935 ATCTAAAACT
5945 TAATATATA
1 TAATATATA
5954 T-ATATATA
1 TAATATATA
**
5962 TAATATACG
1 TAATATATA
5971 T-ATATGATA
1 TAATAT-ATA
5980 -AAT-TATA
1 TAATATATA
5987 TAATGAT-TA
1 TAAT-ATATA
* *
5996 T-TTTTATA
1 TAATATATA
*
6004 TTATATATA
1 TAATATATA
6013 TAATATATA
1 TAATATATA
6022 T
1 T
6023 TTATTTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
7 4 0.08
8 20 0.38
9 27 0.52
10 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (9 bp):
TAATATATA
Found at i:6023 original size:26 final size:24
Alignment explanation
Indices: 5983--6045 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
5973 TATGATAAAT
* * *
5983 TATATAATGATTATTTTTATATTATA
1 TATATAAT-A-TATATTTATTTTTTA
6009 TATATAATATATATTTATTTTTTA
1 TATATAATATATATTTATTTTTTA
*
6033 TATAAAATATATA
1 TATATAATATATA
6046 ATCGGGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 24 0.73
25 1 0.03
26 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATAATATATATTTATTTTTTA
Found at i:6027 original size:22 final size:22
Alignment explanation
Indices: 6002--6044 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5992 ATTATTTTTA
*
6002 TATTATATATATAATATATATT
1 TATTATATATATAAAATATATT
* *
6024 TATTTTTTATATAAAATATAT
1 TATTATATATATAAAATATAT
6045 AATCGGGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATATATATAAAATATATT
Found at i:7274 original size:12 final size:14
Alignment explanation
Indices: 7246--7277 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
7236 ACATAAGTTC
7246 AATGTTATAACATA
1 AATGTTATAACATA
7260 AATGTTAT-A-ATA
1 AATGTTATAACATA
7272 AATGTT
1 AATGTT
7278 TTAGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Found at i:13349 original size:21 final size:21
Alignment explanation
Indices: 13307--13350 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13297 TAAAGATCAG
** *
13307 AGTCATCTCCTTGCTTGAGGA
1 AGTCATCTCCTTGAATCAGGA
*
13328 AGTCATCTCCTTGAATCTGGA
1 AGTCATCTCCTTGAATCAGGA
13349 AG
1 AG
13351 ACTTGGTGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
AGTCATCTCCTTGAATCAGGA
Found at i:14589 original size:148 final size:147
Alignment explanation
Indices: 14452--14891 Score: 679
Period size: 148 Copynumber: 3.0 Consensus size: 147
14442 GGTCAATCAC
14452 AATAACATTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAACATTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
14517 AAAATAGAGTTTTTAGTATAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAAT
*
14582 AAAAAATAGTAAAGTGGTAAA
131 GAAAAATAGT-AA---GTAAA
*
14603 AATAA-ACTTTTAAATTAAAATGGT-AAAATAAAATAATTATAAAAATATTAAATTTAATTAAAT
1 AATAACA-TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAAT
* *
14666 GAAAATAGAGTTTTTAGTAGAATTAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAA
65 GAAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAA
14731 TGAAAAATAGTAATGGTAAA
130 TGAAAAATAGTAA--GTAAA
* ** * * * *
14751 AATAAC-CTTTAAATTAAAATTATAAAAATAAAATAATCATTAAAGTATTGAATTTAATAAAATG
1 AATAACATTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
14815 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTAAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAAT
14880 GAAAAATAGTAA
131 GAAAAATAGTAA
14892 AATGGTAAAA
Statistics
Matches: 270, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
147 14 0.05
148 121 0.45
149 2 0.01
150 111 0.41
151 22 0.08
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (147 bp):
AATAACATTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAAT
GAAAAATAGTAAGTAAA
Found at i:14657 original size:150 final size:150
Alignment explanation
Indices: 14459--14905 Score: 738
Period size: 150 Copynumber: 3.0 Consensus size: 150
14449 CACAATAACA
14459 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
* *
14524 AGTTTTTAGTATAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATAAAAAAT
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATGAAAAAT
14589 AGTAAAGTGGTAAAAATAAAC
131 AGTAAA-TGGTAAAAATAAAC
*
14610 TTTTAAATTAAAATGGT-AAAATAAAATAATTATAAAAATATTAAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
* *
14674 AGTTTTTAGTAGAATTAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAT
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATGAAAAAT
14739 AGT-AATGGTAAAAAT-AAC
131 AGTAAATGGTAAAAATAAAC
* ** * * * *
14757 CTTTAAATTAAAATTATAAAAATAAAATAATCATTAAAGTATTGAATTTAATAAAATGAAAATAG
1 TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
*
14822 AGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTAAATGAAAAAT
66 AGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATGAAAAAT
14887 AGTAAAATGGTAAAAATAA
131 AGT-AAATGGTAAAAATAA
14906 TCATAAAAAT
Statistics
Matches: 276, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
147 17 0.06
148 117 0.42
149 2 0.01
150 122 0.44
151 18 0.07
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.35
Consensus pattern (150 bp):
TTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
AGTTTTTAGTAGAATCAAACTATATATTAAAAAAATTTAATATATCCAAGTTTTTAATGAAAAAT
AGTAAATGGTAAAAATAAAC
Found at i:14909 original size:119 final size:118
Alignment explanation
Indices: 14780--15085 Score: 425
Period size: 119 Copynumber: 2.5 Consensus size: 118
14770 TTATAAAAAT
*
14780 AAAATAATCATTAAAGTATTGAATTTAATAAAATGAAAATAGAGTTTTTAGTAGAATCAAACTAT
1 AAAATAATCATTAAAGTATTGAATTTAAT-AAATGAAAATACAGTTTTTAGTAGAATCAAACTAT
14845 ATATTAAAAAAATTTAATATATCCAAGTTTTAAATGAAAAATAGTAAAATGGTA
65 ATATTAAAAAAATTTAATATATCCAAGTTTTAAATGAAAAATAGTAAAATGGTA
* *
14899 AAAATAATCATAAAAATATTGAATTTAATCAAATGAAAATACAGTTTTTAGTAGAATCAAACTAT
1 AAAATAATCATTAAAGTATTGAATTTAAT-AAATGAAAATACAGTTTTTAGTAGAATCAAACTAT
** *
14964 ATATTAAAAAGTTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGTA
65 ATATTAAAAAAATTTAATATATCCAAGTTTTAAATGAAAAATAGTAAAATGGTA
* * * * *
15018 AAAATAAAGTAATTATAAAGATATT-AGATTTAACTAAATAAAAATATAGTTTTAAGTAGAATAA
1 AAAAT-AA-TCA-T-TAAAG-TATTGA-ATTTAA-TAAATGAAAATACAGTTTTTAGTAGAATCA
15082 AACT
59 AACT
15086 CTAATAGTTT
Statistics
Matches: 166, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
119 117 0.70
120 2 0.01
121 2 0.01
122 1 0.01
123 4 0.02
124 39 0.23
125 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (118 bp):
AAAATAATCATTAAAGTATTGAATTTAATAAATGAAAATACAGTTTTTAGTAGAATCAAACTATA
TATTAAAAAAATTTAATATATCCAAGTTTTAAATGAAAAATAGTAAAATGGTA
Found at i:15058 original size:23 final size:23
Alignment explanation
Indices: 15032--15083 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
15022 TAAAGTAATT
*
15032 ATAAAGATATTAGATTTAACTA-A
1 ATAAAAATA-TAGATTTAACTAGA
* *
15055 ATAAAAATATAGTTTTAAGTAGA
1 ATAAAAATATAGATTTAACTAGA
15078 ATAAAA
1 ATAAAA
15084 CTCTAATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.33
Consensus pattern (23 bp):
ATAAAAATATAGATTTAACTAGA
Found at i:15256 original size:16 final size:16
Alignment explanation
Indices: 15235--15267 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15225 TATTAAGAAC
*
15235 AAAAGATCAAGTATAA
1 AAAAGACCAAGTATAA
15251 AAAAGACCAAGTATAA
1 AAAAGACCAAGTATAA
15267 A
1 A
15268 TTTATAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAAGACCAAGTATAA
Found at i:16607 original size:19 final size:19
Alignment explanation
Indices: 16583--16621 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16573 TTATAAGGGT
*
16583 TTGCATTTTATAGGATGTA
1 TTGCATTTTAGAGGATGTA
16602 TTGCATTTTAGAGGATGTA
1 TTGCATTTTAGAGGATGTA
16621 T
1 T
16622 AATTAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (19 bp):
TTGCATTTTAGAGGATGTA
Found at i:18138 original size:13 final size:13
Alignment explanation
Indices: 18120--18147 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18110 ATTACCTGTC
18120 ATCCACATATACA
1 ATCCACATATACA
18133 ATCCACATATACA
1 ATCCACATATACA
18146 AT
1 AT
18148 AAGAGCAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (13 bp):
ATCCACATATACA
Done.