Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016834.1 Corchorus olitorius cultivar O-4 contig16867, 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: 30437
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4740 original size:22 final size:22
Alignment explanation
Indices: 4710--4752 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4700 AAAATTCAGA
* *
4710 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
4732 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
4753 TTGCGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:15469 original size:121 final size:121
Alignment explanation
Indices: 15255--15503 Score: 480
Period size: 121 Copynumber: 2.1 Consensus size: 121
15245 GCAGCCTGCA
*
15255 GTCTTCTTGTTTGTGGAAATGTATCAACTTGTATAATGACTTGTTTATATATGCCTGTTATTTTT
1 GTCTTCTTGTTTGTGGAAATGTATCAACTTGTATAATGACTAGTTTATATATGCCTGTTATTTTT
15320 GGTATGAAATCTGAGACAACATCCAAGTCCATGCAGGGTGGTTTAGGCTTTTTGAG
66 GGTATGAAATCTGAGACAACATCCAAGTCCATGCAGGGTGGTTTAGGCTTTTTGAG
15376 GTCTTCTTGTTTGTGGAAATGTATCAACTTGTATAATGACTAGTTTATATATGCCTGTTATTTTT
1 GTCTTCTTGTTTGTGGAAATGTATCAACTTGTATAATGACTAGTTTATATATGCCTGTTATTTTT
15441 GGTATGAAATCTGAGACAACATCCAAGTCCATGCAGGGTGGTTTAGGCTTTTTGAG
66 GGTATGAAATCTGAGACAACATCCAAGTCCATGCAGGGTGGTTTAGGCTTTTTGAG
*
15497 GTTTTCT
1 GTCTTCT
15504 AGATGCATGC
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 126 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (121 bp):
GTCTTCTTGTTTGTGGAAATGTATCAACTTGTATAATGACTAGTTTATATATGCCTGTTATTTTT
GGTATGAAATCTGAGACAACATCCAAGTCCATGCAGGGTGGTTTAGGCTTTTTGAG
Found at i:17285 original size:45 final size:45
Alignment explanation
Indices: 17235--17334 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
17225 TTTTAAAAAC
17235 AGTCAACACCCTTTGAACAAACCTTTGGACAACAAATAATTTAGG
1 AGTCAACACCCTTTGAACAAACCTTTGGACAACAAATAATTTAGG
17280 AGTCAACACCCTTTGAACAAACCTTTGGACAACAAATAATTTAGG
1 AGTCAACACCCTTTGAACAAACCTTTGGACAACAAATAATTTAGG
* *
17325 ACTAAACACC
1 AGTCAACACC
17335 GAAGGAAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (45 bp):
AGTCAACACCCTTTGAACAAACCTTTGGACAACAAATAATTTAGG
Found at i:19140 original size:60 final size:60
Alignment explanation
Indices: 18979--19140 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 60
18969 GCTAATTGCT
* * *
18979 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTCGC
* * *
19039 CAAATAATGGCCTAACGTTATCGAAAATGTTCAAATAAGGGTCCGATCTTTTAATTTCGC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTCGC
*
19099 CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAGGGT
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGT
19141 TTGGCGTCAG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTCGC
Found at i:19219 original size:31 final size:31
Alignment explanation
Indices: 19181--19348 Score: 149
Period size: 31 Copynumber: 5.5 Consensus size: 31
19171 TTTCGACACC
*
19181 AGGCCCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
** *
19212 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAAAG-TT
*
19241 AGGCCCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
* *
19272 AGGCCCTTATTTG-GTC-TAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CAT-TTTGGCAAAAG-TT
19301 AGGCCCTTATTTGAGCATTTTGGCAAACA-TT
1 AGGCCCTTATTTGAGCATTTTGGCAAA-AGTT
19332 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
19349 ATTAGGCTAA
Statistics
Matches: 109, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
28 8 0.07
29 35 0.32
30 6 0.06
31 52 0.48
32 7 0.06
33 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAAAGTT
Found at i:19252 original size:60 final size:60
Alignment explanation
Indices: 19180--19344 Score: 294
Period size: 60 Copynumber: 2.8 Consensus size: 60
19170 TTTTCGACAC
19180 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
19240 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGTCTAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
**
19300 CAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTG
19345 AGCAATTAGG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:19253 original size:29 final size:28
Alignment explanation
Indices: 19212--19313 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
19202 GGCAAATGTT
19212 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
** * *
19241 AGGCCCTTATTTGAGCATTTTGGCAAATG-TT
1 AGGCCCTTATTTG-GCAAATT---AAAAGATC
*
19272 AGGCCCTTATTTGGTCTAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
19301 AGGCCCTTATTTG
1 AGGCCCTTATTTG
19314 AGCATTTTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 31 0.53
30 2 0.03
31 17 0.29
32 4 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:19541 original size:2 final size:2
Alignment explanation
Indices: 19534--19567 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
19524 AAAATAATAA
19534 AT AT AT AT AT AT AGT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
19568 TTATTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19553 original size:11 final size:10
Alignment explanation
Indices: 19534--19567 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
19524 AAAATAATAA
19534 ATATATATAT
1 ATATATATAT
19544 ATAGTATATAT
1 ATA-TATATAT
19555 ATATACTATAT
1 ATATA-TATAT
19566 AT
1 AT
19568 TTATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATATAT
Found at i:19553 original size:13 final size:13
Alignment explanation
Indices: 19535--19567 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19525 AAATAATAAA
*
19535 TATATATATATAG
1 TATATATATATAC
19548 TATATATATATAC
1 TATATATATATAC
19561 TATATAT
1 TATATAT
19568 TTATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (13 bp):
TATATATATATAC
Found at i:22579 original size:20 final size:20
Alignment explanation
Indices: 22556--22598 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
22546 TATGACGTAT
22556 CCTCTGATAATTCCACGTGG
1 CCTCTGATAATTCCACGTGG
22576 CCTCTGATAATTCCACGTGG
1 CCTCTGATAATTCCACGTGG
22596 CCT
1 CCT
22599 ATATTCACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.30
Consensus pattern (20 bp):
CCTCTGATAATTCCACGTGG
Found at i:26255 original size:65 final size:65
Alignment explanation
Indices: 26147--26270 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
26137 GCATAGTTAC
* * *
26147 GCACCTAAATTAACAGAGCACTTATTTCCTAGAAAGATGTTGGTTTTCCATGTTATCTCTCATAT
1 GCACCTAAATTAACAGAGCACTTATTGCCTAGAAAGATGTTGGTCTGCCATGTTATCTCTCATAT
* *
26212 GCACCTAAATTAACAGAGCACTTATTGCCTGGAAAGATTTTGGTCTGCCATGTTATCTC
1 GCACCTAAATTAACAGAGCACTTATTGCCTAGAAAGATGTTGGTCTGCCATGTTATCTC
26271 AAATGTGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (65 bp):
GCACCTAAATTAACAGAGCACTTATTGCCTAGAAAGATGTTGGTCTGCCATGTTATCTCTCATAT
Done.