Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014163.1 Corchorus capsularis cultivar CVL-1 contig14184, 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: 27322
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:2342 original size:7 final size:7
Alignment explanation
Indices: 2330--2358 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2320 CAACTAGTTC
2330 TTTTTCT
1 TTTTTCT
2337 TTTTTCT
1 TTTTTCT
2344 TTTTTCT
1 TTTTTCT
2351 TTTTTCT
1 TTTTTCT
2358 T
1 T
2359 CCATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:11785 original size:27 final size:27
Alignment explanation
Indices: 11720--11788 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
11710 AGCACTTGTG
11720 GTGAGCTTGG-TGAAGCTCGATGGTTT
1 GTGAGCTTGGTTGAAGCTCGATGGTTT
* * *
11746 GTGAGATTAGTTGAAGCTCGGTGGTTT
1 GTGAGCTTGGTTGAAGCTCGATGGTTT
* *
11773 TTTAGCTTGGTTGAAG
1 GTGAGCTTGGTTGAAG
11789 TTTGGTTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 8 0.23
27 27 0.77
ACGTcount: A:0.17, C:0.09, G:0.36, T:0.38
Consensus pattern (27 bp):
GTGAGCTTGGTTGAAGCTCGATGGTTT
Found at i:18090 original size:135 final size:135
Alignment explanation
Indices: 17844--18125 Score: 381
Period size: 135 Copynumber: 2.1 Consensus size: 135
17834 AAGACTTGGA
* * * *
17844 GGGG-AAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTTCTCAACAAGTCAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGATCCTCTCCCCTCTCAACAAGTCAACCATC
* * * * *
17908 AGGTGAACAACCCACAACTCATGGCTGAGATTGGTTTCATCGATGAAAGACTTGGGTGGCAAGGA
66 AGGTGAACAACCAACAACTCATGGCTCAGATTGGCTTCATCAATGAAAGACTTGGGGGGCAAGGA
17973 CTCGG
131 CTCGG
* *
17978 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCTCGATCCTCTTCCCCT-TCAACAAGTTAACCAT
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGATCCTC-TCCCCTCTCAACAAGTCAACCAT
* ** * *
18042 CAGGTGAACAATCAACAGGTTATGGCTCAGGTTGGCCTT-ATCAATGAAAGACTTGGGGGGCAAG
65 CAGGTGAACAACCAACAACTCATGGCTCAGATTGG-CTTCATCAATGAAAGACTTGGGGGGCAAG
18106 GACTCGG
129 GACTCGG
18113 GGGGCAAAACCAA
1 GGGGCAAAACCAA
18126 AGGCCACTTG
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
134 4 0.03
135 119 0.92
136 6 0.05
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (135 bp):
GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGATCCTCTCCCCTCTCAACAAGTCAACCATC
AGGTGAACAACCAACAACTCATGGCTCAGATTGGCTTCATCAATGAAAGACTTGGGGGGCAAGGA
CTCGG
Found at i:22585 original size:183 final size:183
Alignment explanation
Indices: 22247--22593 Score: 400
Period size: 183 Copynumber: 1.9 Consensus size: 183
22237 ACTAAACCCC
** * * *
22247 CTGATTTTTGGCTTAATTAACTAATTTTTCCTAAATCACAAAAACCCTAATTCGCCAAGTGAGCT
1 CTGATTTTTGGCTTAATTAACTAATTTGGCCAAAATCACAAAAACCCTAATTCACCAAGTGAGCC
* *
22312 AATTTGCCGCCTATGTTGCAATTTTTGCAAAGAAGGACTCGGCTCATTAGGGGTAGCTTGGTTCA
66 AATTTGCCGCCTAAGTTGCAATTTTTGCAAAGAAGGACTCGGCTCATTAGGAGTAGCTTGGTTCA
* * *
22377 TTAAATTGGGCTTATATTTATGTGATATAACCTAGTTATAAGGGTTTAACCTA
131 TCAAATTAGGCTTATATTCATGTGATATAACCTAGTTATAAGGGTTTAACCTA
* * * *
22430 CTGATTTTTGGCTTAATTAA-TCAATTTGGCCAAAATCACGAAAGCCCTAATTTATCAAGCT-AG
1 CTGATTTTTGGCTTAATTAACT-AATTTGGCCAAAATCACAAAAACCCTAATTCACCAAG-TGAG
* * * *
22493 CCAATTTGCCGCC-AAGTTGCAATTTTTGCAAA-ATGG-GTCATGGC-CTATTAGGATTTGCTTG
64 CCAATTTGCCGCCTAAGTTGCAATTTTTGCAAAGAAGGACTC--GGCTC-ATTAGGAGTAGCTTG
* * * *
22554 ATTTCATCAAATTAGGTTTATGTTCATGTGATATGACCTA
126 -GTTCATCAAATTAGGCTTATATTCATGTGATATAACCTA
22594 ATTTTATGAC
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
180 2 0.01
181 4 0.03
182 34 0.25
183 95 0.70
184 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (183 bp):
CTGATTTTTGGCTTAATTAACTAATTTGGCCAAAATCACAAAAACCCTAATTCACCAAGTGAGCC
AATTTGCCGCCTAAGTTGCAATTTTTGCAAAGAAGGACTCGGCTCATTAGGAGTAGCTTGGTTCA
TCAAATTAGGCTTATATTCATGTGATATAACCTAGTTATAAGGGTTTAACCTA
Found at i:25766 original size:15 final size:15
Alignment explanation
Indices: 25746--25801 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
25736 CTTTCCATAG
25746 GAGAGTGATTCCCAT
1 GAGAGTGATTCCCAT
25761 GAGAGTGATT--CAT
1 GAGAGTGATTCCCAT
*
25774 GGGAGAGTGATTCCCAA
1 --GAGAGTGATTCCCAT
25791 GAGAGTGATTC
1 GAGAGTGATTC
25802 TATGGAAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 3 0.08
15 31 0.86
17 2 0.06
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (15 bp):
GAGAGTGATTCCCAT
Found at i:25781 original size:30 final size:31
Alignment explanation
Indices: 25745--25806 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
25735 ACTTTCCATA
*
25745 GGAGAGTGATTCCCATGAGAGTGATTC-ATG
1 GGAGAGTGATTCCCAAGAGAGTGATTCTATG
25775 GGAGAGTGATTCCCAAGAGAGTGATTCTATG
1 GGAGAGTGATTCCCAAGAGAGTGATTCTATG
25806 G
1 G
25807 AAAGTAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.26
Consensus pattern (31 bp):
GGAGAGTGATTCCCAAGAGAGTGATTCTATG
Done.