Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012552.1 Corchorus capsularis cultivar CVL-1 contig12573, 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: 110102
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15497 original size:40 final size:40
Alignment explanation
Indices: 15442--15517 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
15432 AGTTTAGAGT
15442 TATGGTAAATTCTAACCTCTAATCATGTCACTCATCTTAG
1 TATGGTAAATTCTAACCTCTAATCATGTCACTCATCTTAG
*
15482 TATGGTAAATTCTAACCTCTGATCATGTCACTCATC
1 TATGGTAAATTCTAACCTCTAATCATGTCACTCATC
15518 ATAGGATTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (40 bp):
TATGGTAAATTCTAACCTCTAATCATGTCACTCATCTTAG
Found at i:15622 original size:28 final size:28
Alignment explanation
Indices: 15590--15648 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
15580 GAGAGTTTTG
15590 GTGAATTCTAACCTCTAATCATGTCGGA
1 GTGAATTCTAACCTCTAATCATGTCGGA
*
15618 GTGAATTCTAACCTCTAATCATGTTGGA
1 GTGAATTCTAACCTCTAATCATGTCGGA
15646 GTG
1 GTG
15649 CCCTCTCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (28 bp):
GTGAATTCTAACCTCTAATCATGTCGGA
Found at i:22791 original size:74 final size:73
Alignment explanation
Indices: 22713--22863 Score: 241
Period size: 74 Copynumber: 2.1 Consensus size: 73
22703 TGGTCTTTTC
*
22713 ACACTTTTCGGATGACTAAAAAGCCCCTCTATAAGCTTCCCCCATTCCTTTTCCTTCTATC-CTT
1 ACACTTTTCGGATGACTAAAAAACCCCTCTATAAGCTTCCCCCATTCC-TTTCCTTCTA-CACTT
22777 TTTCGTAATT
64 TTTCGTAATT
** *
22787 ACACTTTTCGGATGACTAAAAAACCCCTCTATGGGTTTCCCCCATTCCTTTCCTTCTACACTTTT
1 ACACTTTTCGGATGACTAAAAAACCCCTCTATAAGCTTCCCCCATTCCTTTCCTTCTACACTTTT
22852 TCGTAATT
66 TCGTAATT
22860 ACAC
1 ACAC
22864 ATTCCCCTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 1 0.01
73 27 0.38
74 44 0.61
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.38
Consensus pattern (73 bp):
ACACTTTTCGGATGACTAAAAAACCCCTCTATAAGCTTCCCCCATTCCTTTCCTTCTACACTTTT
TCGTAATT
Found at i:32378 original size:98 final size:98
Alignment explanation
Indices: 32208--32401 Score: 291
Period size: 98 Copynumber: 2.0 Consensus size: 98
32198 TTTTATGTTC
* * * *
32208 AGTTGTCCAAATACCAAAGAGAGCTTCAGTTGACGATATTTAAGGGAACATCCATGCTGGAGAAA
1 AGTTGTCCAAACACCAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCGGGAGAAA
* *
32273 AAGGTGCAGCTGATATCAGAATAGCTCTGTTTA
66 AAGGTGCAGCCGATATCAGAATAGCTATGTTTA
* *
32306 AGTTGTTCAAACACCAAAGGGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCGGGAGATA
1 AGTTGTCCAAACACCAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCGGGAGA-A
*
32371 AAA-GTGCAGCCGATATTAGAATAGCTATGTT
65 AAAGGTGCAGCCGATATCAGAATAGCTATGTT
32402 CATCTTTCCG
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 82 0.95
99 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (98 bp):
AGTTGTCCAAACACCAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCGGGAGAAA
AAGGTGCAGCCGATATCAGAATAGCTATGTTTA
Found at i:41667 original size:1 final size:1
Alignment explanation
Indices: 41656--41687 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
41646 CTGTCTACCC
*
41656 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41688 CATGAAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:43523 original size:25 final size:22
Alignment explanation
Indices: 43489--43549 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
43479 AAGGGAAACC
*
43489 AGAGACTAAGATTTCTTACATCTTA
1 AGAGACTAAGATTACTTA-A--TTA
* *
43514 AGAGACTAAGAATAGTTAATTA
1 AGAGACTAAGATTACTTAATTA
43536 AGAGACTAAGATTA
1 AGAGACTAAGATTA
43550 ACAGAGGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 16 0.50
24 1 0.03
25 15 0.47
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (22 bp):
AGAGACTAAGATTACTTAATTA
Found at i:68262 original size:2 final size:2
Alignment explanation
Indices: 68255--68285 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68245 ATCAGCATAG
68255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68286 AATCCTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69129 original size:29 final size:29
Alignment explanation
Indices: 69096--69155 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
69086 CAGGTTGGAC
**
69096 TTGGATTGGGTCATTTTGGGGTCTGGTAA
1 TTGGATTGGGTCATTTTGGACTCTGGTAA
69125 TTGGATTGGGTCATTTTGGACTCTGGTAA
1 TTGGATTGGGTCATTTTGGACTCTGGTAA
69154 TT
1 TT
69156 TGGCTTCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.08, G:0.33, T:0.43
Consensus pattern (29 bp):
TTGGATTGGGTCATTTTGGACTCTGGTAA
Found at i:103515 original size:40 final size:41
Alignment explanation
Indices: 103448--103529 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
103438 TCAATAAAAA
*
103448 TTTAGATTCAGAAAAAAAACTATATACAAATGTCTGTTTGG
1 TTTAGATTCAGAAAAAAAACCATATACAAATGTCTGTTTGG
*
103489 TTTAGATTCAG-AAAAAAACCATATACAAATGTTTGTTTGG
1 TTTAGATTCAGAAAAAAAACCATATACAAATGTCTGTTTGG
103529 T
1 T
103530 AGGTAAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 28 0.72
41 11 0.28
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (41 bp):
TTTAGATTCAGAAAAAAAACCATATACAAATGTCTGTTTGG
Found at i:106638 original size:5 final size:5
Alignment explanation
Indices: 106630--106669 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
106620 AGTTTATTAC
*
106630 TACTA TACTA TACTG TACTA TACTA TACTA TACTA TACTA
1 TACTA TACTA TACTA TACTA TACTA TACTA TACTA TACTA
106670 CTAGTATGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (5 bp):
TACTA
Found at i:109607 original size:332 final size:333
Alignment explanation
Indices: 108854--109739 Score: 1013
Period size: 332 Copynumber: 2.7 Consensus size: 333
108844 CTCAAAAAAA
* * ** *
108854 AAAAATCGTGATGATTAATACATGATTTTA-GTTAAAATTTTGTGAAAACTAATCCC-AAATATT
1 AAAAATCGTGATGATTAATACACGA-TTTAGGCTAAAATTTTGCAAAAACTGA-CCCGAAATATT
* * * * * * *
108917 CTTCCTC-AATTCTTGGCTAAAATATTCATTAAAAATATATAATTTAACGCCAAAAAAAGATTGG
64 TTTCCTCAAATT-TTGGCCACAATACTCA-TAAAAATATATAATTCAAC-AC-AAAAAAGATTGA
* * * *
108981 AGGACTTTTCACGCTTCTAATATCGTTTTCCCTATTTTTTTT-TAAATTAATTTCTTATTAAATC
125 AGGACATTTCACGCTTTTAATATCGTTTTCCCTATTTTTTTTCCAAATTAATTTCTGATTAAATC
** * *
109045 G-AAACCGATTTCAAATGCTTGTAAAAACATATCCTTAAATCCAATTTGGCTAAGATTTGATTAG
190 GAAAAAAGA-TTCAAATGCTTGTAAAAACATATCCTTAAATCCAATGTGACTAAGATTTGATTAG
* * * * * * * **
109109 ATAAATATAGATCTTTCAAGGACTCTCGGCACGAAAGATCATATAAAATTGAACCGGGGCCTGGA
254 ATAAATATAGATATTTCAAGGACTCTCGGCACAAAAAATCATACAAAACTGAACCGAGACCCAGA
* * *
109174 ACACGTTTTTTTGCC
319 ACACGATTTTTAGAC
* * * *
109189 AAAAATCGTGATGGTTAATACACGATTTAGGCTAAAATTTTGTAAAAATTGACCCGAAAAATTTT
1 AAAAATCGTGATGATTAATACACGATTTAGGCTAAAATTTTGCAAAAACTGACCCGAAATATTTT
* * * *
109254 TCCTTAAATTTTGGTCACAATACACATAAAAATATATAATTCAACACAAAAAATATTGAAGGACA
66 TCCTCAAATTTTGGCCACAATACTCATAAAAATATATAATTCAACACAAAAAAGATTGAAGGACA
109319 TTTCACGCTTTTAATATCGTTTTCCCTATTTTTTTTCCAAATTAATTTCTGATTAAATCGAAAAA
131 TTTCACGCTTTTAATATCGTTTTCCCTATTTTTTTTCCAAATTAATTTCTGATTAAATCGAAAAA
** * * *
109384 AGATTCAAATGCTTGTAAAGTCATATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATA
196 AGATTCAAATGCTTGTAAAAACATATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATA
* * * * * * *
109449 TAGATATTTCATGGAGTTTTGGCGCAAAAAATCATGCAAAACT-AAGCCGAGACCCAGAACGC-A
261 TAGATATTTCAAGGACTCTCGGCACAAAAAATCATACAAAACTGAA-CCGAGACCCAGAACACGA
109512 TTTTTAGAC
325 TTTTTAGAC
** * *
109521 AAAAA-CTGTGATGATTCGTACACGATTTCGGCTAAAATTTTGCAAAACCTGACCCGAAATATTT
1 AAAAATC-GTGATGATTAATACACGATTTAGGCTAAAATTTTGCAAAAACTGACCCGAAATATTT
* * * * *
109585 TTCCTCAAATTTTGGCCACAATACTCATAAATATATATAATTCAACGCCAGAAAGATTGAAGTA-
65 TTCCTCAAATTTTGGCCACAATACTCATAAAAATATATAATTCAACACAAAAAAGATTGAAGGAC
109649 ATTTTCACG-TTTCTAATATCGTATTT-CCTA-TTTTTTTCCAAATTAATTTCTGATTAAATCGA
130 A-TTTCACGCTTT-TAATATCGT-TTTCCCTATTTTTTTTCCAAATTAATTTCTGATTAAATCGA
* *
109711 AACAAGATTAAAATGCTTGTAAAAACATA
192 AAAAAGATTCAAATGCTTGTAAAAACATA
109740 CTGGATTGCT
Statistics
Matches: 470, Mismatches: 71, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
331 62 0.13
332 188 0.40
333 123 0.26
334 30 0.06
335 63 0.13
336 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (333 bp):
AAAAATCGTGATGATTAATACACGATTTAGGCTAAAATTTTGCAAAAACTGACCCGAAATATTTT
TCCTCAAATTTTGGCCACAATACTCATAAAAATATATAATTCAACACAAAAAAGATTGAAGGACA
TTTCACGCTTTTAATATCGTTTTCCCTATTTTTTTTCCAAATTAATTTCTGATTAAATCGAAAAA
AGATTCAAATGCTTGTAAAAACATATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATA
TAGATATTTCAAGGACTCTCGGCACAAAAAATCATACAAAACTGAACCGAGACCCAGAACACGAT
TTTTAGAC
Found at i:109769 original size:21 final size:21
Alignment explanation
Indices: 109745--109788 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
109735 ACATACTGGA
109745 TTGCTAAAT-ACCACCCCATTT
1 TTGCT-AATCACCACCCCATTT
* *
109766 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCACCCCATTT
109787 TT
1 TT
109789 TACACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.20, C:0.34, G:0.07, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCACCCCATTT
Found at i:110031 original size:32 final size:32
Alignment explanation
Indices: 109986--110056 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
109976 GTCCCAAGAG
* *
109986 GGCGGCTTCGCCACGGTAGGCCGCCTCGGTGA
1 GGCGGCTTCGCCACGGCAGGCCGCCCCGGTGA
* *
110018 GGCGGCTTTGCCACGGCAGGCCGCCCCGGTGG
1 GGCGGCTTCGCCACGGCAGGCCGCCCCGGTGA
110050 GGCGGCT
1 GGCGGCT
110057 CGGCTCGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.07, C:0.35, G:0.44, T:0.14
Consensus pattern (32 bp):
GGCGGCTTCGCCACGGCAGGCCGCCCCGGTGA
Done.