Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011324.1 Corchorus capsularis cultivar CVL-1 contig11345, 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: 15313
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:254 original size:33 final size:33
Alignment explanation
Indices: 160--266 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
150 AGCACAAGTG
*
160 ACCGGCCACGCGACATGGAGATGACCGACCATC
1 ACCGGCCACGCGACATGGAGATGACCGGCCATC
* * *
193 ACCAGCTACGCGAC-TCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACAT-GGAGATGACCGGCCATC
* * * *
226 ATCGGCCACGCTACATGGACATGTCCGGCCA-C
1 ACCGGCCACGCGACATGGAGATGACCGGCCATC
258 AACCGGCCA
1 -ACCGGCCA
267 TCGCTTGGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 2 0.03
33 57 0.95
34 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGACCGGCCATC
Found at i:4624 original size:60 final size:60
Alignment explanation
Indices: 4530--4710 Score: 326
Period size: 60 Copynumber: 3.0 Consensus size: 60
4520 TTCCATGGTT
*
4530 TGGTGTCAATCCCAAAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAGATTTGACTCTTGCATCCACAAGCTCTCTCGTGGA
4590 TGGTGTCAATCCCAAAAGGGATTCAGATTTGACTCTTGCATCCACAAGCTCTCTCGTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAGATTTGACTCTTGCATCCACAAGCTCTCTCGTGGA
* * *
4650 TGGTGTCAATCCCAAAAGGGATTCAGAATTAACTCTTGCATCCACAAGCTCTCTCTTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAGATTTGACTCTTGCATCCACAAGCTCTCTCGTGGA
4710 T
1 T
4711 CACCCTAAAC
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 117 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGTGTCAATCCCAAAAGGGATTCAGATTTGACTCTTGCATCCACAAGCTCTCTCGTGGA
Found at i:8247 original size:31 final size:31
Alignment explanation
Indices: 8176--8247 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
8166 GTCTATCAGC
*
8176 TTTTAATTTGTTTAATTTAAAGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAAGCTTTAATTT
* *
8207 TAATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAAGCTTTAATTT
8237 GTTTTAATTTG
1 -TTTTAATTTG
8248 CAACAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAAGCTTTAATTT
Found at i:13236 original size:25 final size:25
Alignment explanation
Indices: 13208--13257 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
13198 CTCTCGACTA
*
13208 GAAAC-CTCAAGCAGGATTTTAGAAT
1 GAAACTCTCAAACAGGATTTT-GAAT
*
13233 GAAACTCTCAAATAGGATTTTGAAT
1 GAAACTCTCAAACAGGATTTTGAAT
13258 CAAAACTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (25 bp):
GAAACTCTCAAACAGGATTTTGAAT
Found at i:13576 original size:70 final size:69
Alignment explanation
Indices: 13452--13590 Score: 170
Period size: 70 Copynumber: 2.0 Consensus size: 69
13442 TAGACCACCC
* * * *
13452 TGGATCAACTGGAAACAACTGATGAAAAACCGCCCTAGGTCAACTGAATCGATCATTCTAACATA
1 TGGATAAACTGGAAACAACTGAAGAAAAACCACCCTAGGTCAACCGAATCGATCATTCTAACATA
13517 AACT
66 AACT
* * * * * *
13521 TGGATAAACGTGGAAACTACTGAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACAT
1 TGGATAAAC-TGGAAACAACTGAAGAAAAACCACCCTAGGTCAACCGAATCGATCATTCTAACAT
*
13586 GAACT
65 AAACT
13591 GAAGAAGAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
69 8 0.14
70 50 0.86
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (69 bp):
TGGATAAACTGGAAACAACTGAAGAAAAACCACCCTAGGTCAACCGAATCGATCATTCTAACATA
AACT
Found at i:13611 original size:49 final size:49
Alignment explanation
Indices: 13539--13639 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 49
13529 CGTGGAAACT
* * * *
13539 ACTGAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATGA
1 ACTGAAGAAAGACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
*
13588 ACTGAAG-AAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAA
1 ACTGAAGAAAG-ACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
13637 ACT
1 ACT
13640 TGGATAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 3 0.07
49 43 0.93
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (49 bp):
ACTGAAGAAAGACCACCCTGGGTCAACCGAATCGATCATTCTAACATAA
Found at i:13679 original size:119 final size:119
Alignment explanation
Indices: 13468--13828 Score: 614
Period size: 119 Copynumber: 3.0 Consensus size: 119
13458 AACTGGAAAC
* * * * *
13468 AACTGATGAAAAACCGCCCTAGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACGTG
1 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
*
13533 GAAACTACTGAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
66 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
13587 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
1 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
13652 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
66 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
13706 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
1 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
* * * * * *
13771 GAAGCTACTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATA
66 GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
13825 AACT
1 AACT
13829 TCGAATAAAC
Statistics
Matches: 230, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 230 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (119 bp):
AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
GAAACTACTAAAGAAAGACCACCCTGGGTCGACCGAGTCGATCATTCTGACATG
Found at i:13824 original size:70 final size:70
Alignment explanation
Indices: 13722--13969 Score: 372
Period size: 70 Copynumber: 3.5 Consensus size: 70
13712 AGAAGAACCA
13722 CCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTGGAAGCTACTAAAGAAA
1 CCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTGGAAGCTACTAAAGAAA
13787 GACCG
66 GACCG
* * * * * *
13792 CCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAACTGAAGAA
1 CCCTGGGTCAACTGAATCGATCATTCTAACATAAACTT-GGATAAACTTGGAAGCTACTAAAGAA
13857 AGACCG
65 AGACCG
* * * *
13863 CCCTGGGTCGACCGAATCGATCATTCTAACATAAACTTGGATAAACGTGGAAGCTATTAAAGAAA
1 CCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTGGAAGCTACTAAAGAAA
13928 GACCG
66 GACCG
*
13933 CCCTGGGTCGACTGAATCGATCATTCTGAA-ATAAACT
1 CCCTGGGTCAACTGAATCGATCATTCT-AACATAAACT
13970 GGAGAAAGAC
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
70 95 0.60
71 64 0.40
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (70 bp):
CCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTGGAAGCTACTAAAGAAA
GACCG
Found at i:13960 original size:141 final size:141
Alignment explanation
Indices: 13706--13969 Score: 449
Period size: 141 Copynumber: 1.9 Consensus size: 141
13696 TTCTGACATG
* *
13706 AACTGAAGAAGAACCACCCTGGGTCAACTGAATCGATCATTCTAACATAAACTTGGATAAACTTG
1 AACTGAAGAAGAACCACCCTGGGTCAACCGAATCGATCATTCTAACATAAACTTGGATAAACGTG
*
13771 GAAGCTACTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
66 GAAGCTACTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGAAATAAACTTCGAATA
13836 AACTTGAAAAC
131 AACTTGAAAAC
* *
13847 AACTGAAGAA-AGACCGCCCTGGGTCGACCGAATCGATCATTCTAACATAAACTTGGATAAACGT
1 AACTGAAGAAGA-ACCACCCTGGGTCAACCGAATCGATCATTCTAACATAAACTTGGATAAACGT
* *
13911 GGAAGCTATTAAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGAAATAAACT
65 GGAAGCTACTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGAAATAAACT
13970 GGAGAAAGAC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
140 1 0.01
141 114 0.99
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (141 bp):
AACTGAAGAAGAACCACCCTGGGTCAACCGAATCGATCATTCTAACATAAACTTGGATAAACGTG
GAAGCTACTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGAAATAAACTTCGAATA
AACTTGAAAAC
Found at i:14011 original size:35 final size:35
Alignment explanation
Indices: 13958--14092 Score: 171
Period size: 35 Copynumber: 3.9 Consensus size: 35
13948 ATCGATCATT
* *
13958 CTGAAATAAACTGGAGAAAGACCACCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
*
13993 CTGAAATAAGCTGAAGAAAGACCGCCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * *
14028 CTGAAATAAACTCAAGAAATATCGCCCTAGATCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * *
14063 TTGAAATTAACTGAAGAAAGATCGCCCTGG
1 CTGAAATAAACTGAAGAAAGACCGCCCTGG
14093 ATTAATTAAC
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 86 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
Found at i:14109 original size:29 final size:29
Alignment explanation
Indices: 14067--14123 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
14057 GATCAATTGA
* *
14067 AATTAACTGAAGAAAGATCGCCCTGGATT
1 AATTAACTCAAGAAAGATCACCCTGGATT
*
14096 AATTAACTCAAGAAAGATCACCTTGGAT
1 AATTAACTCAAGAAAGATCACCCTGGAT
14124 CAATAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (29 bp):
AATTAACTCAAGAAAGATCACCCTGGATT
Found at i:15151 original size:23 final size:23
Alignment explanation
Indices: 15125--15192 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 23
15115 TCATCATTCA
15125 TTTTTC-TTTTTTCTTCTTTCCTTT
1 TTTTTCATTTTTTCTTCTTT--TTT
*
15149 TTTTTCATCATTTTTCTTCCTTTTT
1 TTTTTCAT--TTTTTCTTCTTTTTT
* *
15174 GTTTTCTTTTTTTCTTCTT
1 TTTTTCATTTTTTCTTCTT
15193 CTTCTTCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.27
24 6 0.16
25 10 0.27
27 11 0.30
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.76
Consensus pattern (23 bp):
TTTTTCATTTTTTCTTCTTTTTT
Found at i:15172 original size:38 final size:38
Alignment explanation
Indices: 15109--15182 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 38
15099 CTAGAGCTCC
15109 TTTTCTTCATCATTCATTTTTCTTTTT-TCTTCTTTCCT
1 TTTTCTTCATCATT-ATTTTTCTTTTTGTCTTCTTTCCT
* *
15147 TTTTTTTCATCATT-TTTCTTCCTTTTTGTTTTCTTT
1 TTTTCTTCATCATTATTT-TT-CTTTTTGTCTTCTTT
15183 TTTTCTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 3 0.10
37 2 0.06
38 19 0.61
39 7 0.23
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (38 bp):
TTTTCTTCATCATTATTTTTCTTTTTGTCTTCTTTCCT
Found at i:15183 original size:34 final size:33
Alignment explanation
Indices: 15122--15211 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
15112 TCTTCATCAT
* *
15122 TCATTTTTCTT-TTTTCTTCTTTCCTTTTTTTTCA
1 TCATTTTTCTTCCTTT-TTCTTTTC-TTTTTTTCA
* *
15156 TCATTTTTCTTCCTTTTTGTTTTCTTTTTTTCT
1 TCATTTTTCTTCCTTTTTCTTTTCTTTTTTTCA
* *
15189 TC-TTCTTCTTCTCTTTTTTTTTT
1 TCATTTTTCTTC-CTTTTTCTTTT
15212 TTACATGCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
32 8 0.17
33 20 0.42
34 17 0.35
35 3 0.06
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (33 bp):
TCATTTTTCTTCCTTTTTCTTTTCTTTTTTTCA
Found at i:15203 original size:22 final size:23
Alignment explanation
Indices: 15159--15208 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
15149 TTTTTCATCA
* * *
15159 TTTTTCTTCCTTTTTGTTTTCTT
1 TTTTTCTTCCTTCTTCTTCTCTT
15182 TTTTTCTT-CTTCTTCTTCTCTT
1 TTTTTCTTCCTTCTTCTTCTCTT
15204 TTTTT
1 TTTTT
15209 TTTTTACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTCTTCCTTCTTCTTCTCTT
Found at i:15205 original size:33 final size:33
Alignment explanation
Indices: 15147--15211 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
15137 CTTCTTTCCT
*
15147 TTTTTTTCATCATTTTTCTTCCTTTTTGTTTTC
1 TTTTTTTCATCATTCTTCTTCCTTTTTGTTTTC
* *
15180 TTTTTTTCTTC-TTCTTCTTCTCTTTTTTTTTT
1 TTTTTTTCATCATTCTTCTTC-CTTTTTGTTTT
15212 TTACATGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (33 bp):
TTTTTTTCATCATTCTTCTTCCTTTTTGTTTTC
Done.