Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013898.1 Corchorus olitorius cultivar O-4 contig13931, 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: 32002
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:680 original size:20 final size:20
Alignment explanation
Indices: 651--690 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
641 TTTCAAAGAA
651 GAGAAAAAGCAGATCTGAAG
1 GAGAAAAAGCAGATCTGAAG
*
671 GAGAAGAAGCAGATCTGAAG
1 GAGAAAAAGCAGATCTGAAG
691 AAGAGTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.33, T:0.10
Consensus pattern (20 bp):
GAGAAAAAGCAGATCTGAAG
Found at i:1130 original size:47 final size:47
Alignment explanation
Indices: 1061--1155 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1051 CTTATTTTGT
1061 TTGATGAAATTTAGCAATTTTAATGACTTTCTTAATATGTATGAAAA
1 TTGATGAAATTTAGCAATTTTAATGACTTTCTTAATATGTATGAAAA
1108 TTGATGAAATTTAGCAATTTTAATGACTTTCTTAATATGTATGAAAA
1 TTGATGAAATTTAGCAATTTTAATGACTTTCTTAATATGTATGAAAA
1155 T
1 T
1156 GGCTAAAGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (47 bp):
TTGATGAAATTTAGCAATTTTAATGACTTTCTTAATATGTATGAAAA
Found at i:6180 original size:59 final size:58
Alignment explanation
Indices: 6055--6216 Score: 216
Period size: 59 Copynumber: 2.7 Consensus size: 58
6045 TTCGACGCCA
* * * *
6055 GACCCTTATTTGAGCATTTTCAATAACTTTATGTCCTTATTTGGCCAAATTAAAAGATT
1 GACCCTTATTTGAGCATTTTCGATAACGTTA-GTCCCTATTTGGCCAAATTAAAAGATG
* *
6114 GAGCCCTTATTTAAGCATTTTCGATAACGTTAGGCCCTATTTGGCCAAATTAAAAGATCG
1 GA-CCCTTATTTGAGCATTTTCGATAACGTTAGTCCCTATTTGGCCAAATTAAAAGAT-G
* *
6174 GACCCTTATTTGAGCATTTTGGAAAACGTTAGTCCCTTATTTG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGTCCC-TATTTG
6217 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
59 56 0.62
60 34 0.38
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (58 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGTCCCTATTTGGCCAAATTAAAAGATG
Found at i:8961 original size:7 final size:7
Alignment explanation
Indices: 8949--9014 Score: 107
Period size: 7 Copynumber: 9.4 Consensus size: 7
8939 GAGGACAGGA
8949 TTTTGTT
1 TTTTGTT
8956 TTTTGTT
1 TTTTGTT
8963 TTTTGTT
1 TTTTGTT
8970 TTTTGTT
1 TTTTGTT
8977 TTTTGTT
1 TTTTGTT
*
8984 TTTTTTT
1 TTTTGTT
8991 TTTTGTTT
1 TTTTG-TT
8999 TTTTGTT
1 TTTTGTT
9006 TTTT-TT
1 TTTTGTT
9012 TTT
1 TTT
9015 GAGGAATGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
6 5 0.09
7 44 0.79
8 7 0.12
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTGTT
Found at i:8965 original size:1 final size:1
Alignment explanation
Indices: 8949--9014 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
8939 GAGGACAGGA
* * * * * * *
8949 TTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9014 T
1 T
9015 GAGGAATGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:10403 original size:1 final size:1
Alignment explanation
Indices: 10397--10430 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
10387 AATTTAGGAA
**
10397 TTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10431 CACGATGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:11648 original size:24 final size:24
Alignment explanation
Indices: 11615--11672 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
11605 GCATCTCAGG
* *
11615 CCCAACCTCAGTTCCAAACACAAC
1 CCCAATCTCACTTCCAAACACAAC
** *
11639 CCCAATCTCACTTCCAGCCACAAT
1 CCCAATCTCACTTCCAAACACAAC
*
11663 CACAATCTCA
1 CCCAATCTCA
11673 ACCTCAACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.45, G:0.03, T:0.17
Consensus pattern (24 bp):
CCCAATCTCACTTCCAAACACAAC
Found at i:11678 original size:6 final size:6
Alignment explanation
Indices: 11669--11696 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11659 CAATCACAAT
11669 CTCAAC CTCAAC CTCAAC CTCAAC CTCA
1 CTCAAC CTCAAC CTCAAC CTCAAC CTCA
11697 GCGACAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CTCAAC
Found at i:23471 original size:76 final size:76
Alignment explanation
Indices: 23345--23496 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
23335 CAAACAAAAT
23345 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
1 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
23410 ACAAAAACAAC
66 ACAAAAACAAC
*
23421 TCATGCCTGACCAACTAATTGAGGTATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
1 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
23486 ACAAAAACAAC
66 ACAAAAACAAC
23497 ATAAGATTAC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (76 bp):
TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
ACAAAAACAAC
Found at i:24895 original size:19 final size:20
Alignment explanation
Indices: 24868--24909 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
24858 ATATTTTTCA
24868 TTTCTTTCTTCCT-TTTGTTT
1 TTTCTTTCTT-CTGTTTGTTT
*
24888 TTTC-TTCTTTTGTTTGTTT
1 TTTCTTTCTTCTGTTTGTTT
24907 TTT
1 TTT
24910 TTTTTGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.75
20 4 0.20
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTCTTTCTTCTGTTTGTTT
Found at i:24899 original size:15 final size:15
Alignment explanation
Indices: 24872--24922 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
24862 TTTTCATTTC
24872 TTTCTTCCTTTTGTTT
1 TTTCTT-CTTTTGTTT
24888 TTTCTTCTTTTGTTT
1 TTTCTTCTTTTGTTT
* *
24903 GTTTTTTTTTTTGTCTT
1 -TTTCTTCTTTTGT-TT
24920 TTT
1 TTT
24923 TTTTCTCGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 9 0.29
16 20 0.65
17 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (15 bp):
TTTCTTCTTTTGTTT
Found at i:27273 original size:89 final size:89
Alignment explanation
Indices: 27152--27441 Score: 517
Period size: 89 Copynumber: 3.3 Consensus size: 89
27142 CCTGTTGGCT
* * *
27152 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGGAAGCCATAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
*
27217 TATCTCCAATCATACTATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
*
27241 GTTTATGGCTATACCAACGCCACCCGTTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
27306 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
* *
27330 GTTTGTGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
1 GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
27395 TATCTCCAATCATACCATTTTTTG
66 TATCTCCAATCATACCATTTTTTG
27419 GTTTATGGCTATACCAACGCCAC
1 GTTTATGGCTATACCAACGCCAC
27442 ACGCCGTTTG
Statistics
Matches: 191, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 191 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (89 bp):
GTTTATGGCTATACCAACGCCACCCGCTGTTGGTATACATTCTATAGCAACGTAAGCCGTAGGTA
TATCTCCAATCATACCATTTTTTG
Found at i:27628 original size:40 final size:40
Alignment explanation
Indices: 27584--27660 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
27574 GTCATTCACA
*
27584 TTAAAAAT-ATAATCCAAAACAATTTGTTCTAATCCACACG
1 TTAAAAATGA-AATCAAAAACAATTTGTTCTAATCCACACG
*
27624 TTAAAAATGAAATTAAAAACAATTTGTTCTAATCCAC
1 TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCAC
27661 TCATGTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (40 bp):
TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCACACG
Found at i:28569 original size:16 final size:16
Alignment explanation
Indices: 28548--28598 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
28538 CGGCAAAGCA
28548 GAGAAGAGGAGTGGCG
1 GAGAAGAGGAGTGGCG
*
28564 GAGAAGAGGAGGGGCG
1 GAGAAGAGGAGTGGCG
28580 TG-GAAGAGGAGTGGCG
1 -GAGAAGAGGAGTGGCG
28596 GAG
1 GAG
28599 TGAATGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.59, T:0.06
Consensus pattern (16 bp):
GAGAAGAGGAGTGGCG
Found at i:29147 original size:125 final size:125
Alignment explanation
Indices: 28898--29140 Score: 423
Period size: 125 Copynumber: 1.9 Consensus size: 125
28888 ATTTACATTT
* * *
28898 AGGTCTATAGCTACGGGAAACATTATGTGCGTTGGTATATTACACTACTATACCTACAGCAATTA
1 AGGTCTATAGCTACGAGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAGCAATTA
* *
28963 TAACACTGTTAGAATAGCCTTAATCTATACCAATAGATGCCAAGGGCGTTGGTTAATGTC
66 CAACACTGTTAAAATAGCCTTAATCTATACCAATAGATGCCAAGGGCGTTGGTTAATGTC
29023 AGGTCTATAGCTACGAGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAGCAATTA
1 AGGTCTATAGCTACGAGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAGCAATTA
* *
29088 CAACACTGTTAAAATAGCCTTAATTTATACCAATAGATGCCACGGGCGTTGGT
66 CAACACTGTTAAAATAGCCTTAATCTATACCAATAGATGCCAAGGGCGTTGGT
29141 ATATGTCTTA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 111 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (125 bp):
AGGTCTATAGCTACGAGAAACATTATGTACGTTGGTATATTACACCACTATACCTACAGCAATTA
CAACACTGTTAAAATAGCCTTAATCTATACCAATAGATGCCAAGGGCGTTGGTTAATGTC
Found at i:29439 original size:22 final size:22
Alignment explanation
Indices: 29407--29466 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
29397 CTCGTAAGCT
* *
29407 ACTCGAGTTCGATTCGAAGAAA
1 ACTCGAATTCGACTCGAAGAAA
29429 ACTCGAATTCGACTCGAAGAAA
1 ACTCGAATTCGACTCGAAGAAA
29451 ACTCGAATTCGACTCG
1 ACTCGAATTCGACTCG
29467 GGTATTGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (22 bp):
ACTCGAATTCGACTCGAAGAAA
Done.