Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020379.1 Corchorus olitorius cultivar O-4 contig20412, 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: 23798
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Found at i:3464 original size:199 final size:199
Alignment explanation
Indices: 3124--3522 Score: 703
Period size: 199 Copynumber: 2.0 Consensus size: 199
3114 CTGGTGCGAG
* * *
3124 AGGGACAAATAAAATCAGGCATTAGTGTTAGTCCTCAGTCAAAAAGGTTAGCCTTTCTTTGTTCA
1 AGGGACAAATAAAATCAGCCATTAGAGTTAGTCCTCAGTCAAAAAGGTAAGCCTTTCTTTGTTCA
*
3189 TAACTTTTGGGTATTTGCTGGTGTTTTTATTTGCTATAGAATTAGGCATGATTAATAGTGTTTGA
66 TAACTTTTGGGTACTTGCTGGTGTTTTTATTTGCTATAGAATTAGGCATGATTAATAGTGTTTGA
*
3254 TTAGTCTTATGTTGTTGAAAAA-CGTCAAATCCCCTTTAGCATTTAACTCTTCTTCGTTGGACTT
131 TTAGTCTTATGTTGTTGAAAAATC-TCAAATCCCCTTTAGCATTTAACTCTTCTTCATTGGACTT
3318 ATGTT
195 ATGTT
*
3323 AGGGACAAATAGAATCAGCCATTAGAGTTAGTCCTCAGTCAAAAA-GTCAAGCCTTTCTTTGTTC
1 AGGGACAAATAAAATCAGCCATTAGAGTTAGTCCTCAGTCAAAAAGGT-AAGCCTTTCTTTGTTC
3387 ATAACTTTTGGGTACTTGCTGGTGTTTTTATTTGCTATAGAATTAGGCATGATTAATAGTGTTTG
65 ATAACTTTTGGGTACTTGCTGGTGTTTTTATTTGCTATAGAATTAGGCATGATTAATAGTGTTTG
*
3452 ATTGGTCTTATGTTGTTGAAAAATCTCAAATCCCCTTTAGCATTTAACTCTTCTTCATTGGACTT
130 ATTAGTCTTATGTTGTTGAAAAATCTCAAATCCCCTTTAGCATTTAACTCTTCTTCATTGGACTT
3517 ATGTT
195 ATGTT
3522 A
1 A
3523 ATATCTTCCA
Statistics
Matches: 191, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
198 2 0.01
199 188 0.98
200 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (199 bp):
AGGGACAAATAAAATCAGCCATTAGAGTTAGTCCTCAGTCAAAAAGGTAAGCCTTTCTTTGTTCA
TAACTTTTGGGTACTTGCTGGTGTTTTTATTTGCTATAGAATTAGGCATGATTAATAGTGTTTGA
TTAGTCTTATGTTGTTGAAAAATCTCAAATCCCCTTTAGCATTTAACTCTTCTTCATTGGACTTA
TGTT
Found at i:6624 original size:57 final size:57
Alignment explanation
Indices: 6531--6648 Score: 227
Period size: 57 Copynumber: 2.1 Consensus size: 57
6521 TAACTACATT
*
6531 CATAGTCATTGTGAAATAACCCTCCTTCAAAGAAATACACATCCCTTGACCATGAAC
1 CATAATCATTGTGAAATAACCCTCCTTCAAAGAAATACACATCCCTTGACCATGAAC
6588 CATAATCATTGTGAAATAACCCTCCTTCAAAGAAATACACATCCCTTGACCATGAAC
1 CATAATCATTGTGAAATAACCCTCCTTCAAAGAAATACACATCCCTTGACCATGAAC
6645 CATA
1 CATA
6649 TTTATTCTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (57 bp):
CATAATCATTGTGAAATAACCCTCCTTCAAAGAAATACACATCCCTTGACCATGAAC
Found at i:7055 original size:32 final size:32
Alignment explanation
Indices: 6996--7074 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 32
6986 AGCGTCGGGA
*
6996 AGCTCTTCAGCTCCTTTACAGTGAGTAGTGAGT
1 AGCTCTTTAGCT-CTTTACAGTGAGTAGTGAGT
7029 AGCTCTTTAGCTCTTCT-CAGTGAGTAGTGAGT
1 AGCTCTTTAGCTCTT-TACAGTGAGTAGTGAGT
7061 AGCTCTTTAGCTCT
1 AGCTCTTTAGCTCT
7075 CTTCTTCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 32 0.73
33 12 0.27
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (32 bp):
AGCTCTTTAGCTCTTTACAGTGAGTAGTGAGT
Found at i:7105 original size:9 final size:9
Alignment explanation
Indices: 7075--7115 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
7065 CTTTAGCTCT
7075 CTTCTTCTC
1 CTTCTTCTC
*
7084 CTTCCGTCT-
1 CTT-CTTCTC
7093 CTTCTTCTC
1 CTTCTTCTC
7102 CTTCTTCTC
1 CTTCTTCTC
7111 CTTCT
1 CTTCT
7116 GTCAGTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 4 0.14
9 20 0.71
10 4 0.14
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:7202 original size:19 final size:19
Alignment explanation
Indices: 7145--7209 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
7135 CAACTTCTCC
* *
7145 AAGTAGAAAGTGGGTATCT
1 AAGTAGAAAGTGAGTATCA
** *
7164 AAGTAGAATTCTTCAGTATCA
1 AAGTAGAA--AGTGAGTATCA
*
7185 AAGTAGAAAGTGAGTATCC
1 AAGTAGAAAGTGAGTATCA
7204 AAGTAG
1 AAGTAG
7210 GGTAGAAAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 21 0.60
21 14 0.40
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (19 bp):
AAGTAGAAAGTGAGTATCA
Found at i:7492 original size:3 final size:3
Alignment explanation
Indices: 7474--7567 Score: 50
Period size: 3 Copynumber: 34.3 Consensus size: 3
7464 CCATAAGACA
*
7474 AAG AAG AGAG AA- AAG AAG -AG TGAG AAG AAG -AG AA- AAG AAG AAG
1 AAG AAG A-AG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG
* *
7517 -AG AA- AAG AAG -AG GAG AA- AA- AAG AAG -AG TGAG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
7556 AA- AAG AAG AAG A
1 AAG AAG AAG AAG A
7568 GAAAAGGGGA
Statistics
Matches: 74, Mismatches: 3, Indels: 28
0.70 0.03 0.27
Matches are distributed among these distances:
2 24 0.32
3 43 0.58
4 7 0.09
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:7514 original size:13 final size:13
Alignment explanation
Indices: 7474--7573 Score: 118
Period size: 13 Copynumber: 8.0 Consensus size: 13
7464 CCATAAGACA
*
7474 AAGAAGAGAGAA-
1 AAGAAGAGAAAAG
**
7486 AAGAAGAG-TGAG
1 AAGAAGAGAAAAG
7498 AAGAAGAGAAAAG
1 AAGAAGAGAAAAG
7511 AAGAAGAGAAAAG
1 AAGAAGAGAAAAG
*
7524 AAGAGGAGAAAA-
1 AAGAAGAGAAAAG
**
7536 AAGAAGAG-TGAG
1 AAGAAGAGAAAAG
7548 AAGAAGAGAAAAG
1 AAGAAGAGAAAAG
7561 AAGAAGAGAAAAG
1 AAGAAGAGAAAAG
7574 GGGAGAAGAG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
11 2 0.03
12 31 0.42
13 41 0.55
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (13 bp):
AAGAAGAGAAAAG
Found at i:7518 original size:37 final size:36
Alignment explanation
Indices: 7474--7572 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
7464 CCATAAGACA
*
7474 AAGAAGAGAGAAAAGAAGAGTGAGAAGAAGAGAAAAG-
1 AAGAAGAGAGAAAAGAAGAG-GAGAA-AAAAGAAAAGT
*
7511 AAG-A-AGAGAAAAGAAGAGGAGAAAAAAGAAGAGT
1 AAGAAGAGAGAAAAGAAGAGGAGAAAAAAGAAAAGT
* *
7545 GAGAAGAAGAGAAAAGAAGAAGAGAAAA
1 AAGAAG-AGAGAAAAGAAGAGGAGAAAA
7573 GGGGAGAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
33 8 0.15
34 7 0.13
35 15 0.28
36 1 0.02
37 23 0.43
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (36 bp):
AAGAAGAGAGAAAAGAAGAGGAGAAAAAAGAAAAGT
Found at i:7545 original size:50 final size:50
Alignment explanation
Indices: 7474--7573 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
7464 CCATAAGACA
*
7474 AAGAAGAGAGAAAAGAAGAGTGAGAAGAAGAGAAAAGAAGAAGAGAAAAG
1 AAGAAGAGAAAAAAGAAGAGTGAGAAGAAGAGAAAAGAAGAAGAGAAAAG
*
7524 AAGAGGAGAAAAAAGAAGAGTGAGAAGAAGAGAAAAGAAGAAGAGAAAAG
1 AAGAAGAGAAAAAAGAAGAGTGAGAAGAAGAGAAAAGAAGAAGAGAAAAG
7574 GGGAGAAGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (50 bp):
AAGAAGAGAAAAAAGAAGAGTGAGAAGAAGAGAAAAGAAGAAGAGAAAAG
Found at i:8923 original size:101 final size:101
Alignment explanation
Indices: 8748--9043 Score: 450
Period size: 101 Copynumber: 2.9 Consensus size: 101
8738 GCAAAAAAAT
* *
8748 GTTCGTAATTGACCTTAGATTTCAATCCGGACTCGTCATGAGAACATCGAAACTAAGTTGTGGTC
1 GTTCGTAATTGACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTC
8813 GAACGTAAGCCCTGAACTCTTTGTGAGAACAACAAA
66 GAACGTAAGCCCTGAACTCTTTGTGAGAACAACAAA
* * *
8849 GTTCGTAATTGATCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTATGGCC
1 GTTCGTAATTGACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTC
* * *
8914 GAATGTAAGCCCTGTACTCTTTGTGAGAACAATAAA
66 GAACGTAAGCCCTGAACTCTTTGTGAGAACAACAAA
* * * *
8950 ATTCGTAATTGACCTTAGATTTCGATCCGGACTTATCATGACAACATCAAAACTAAGTTGTGGTC
1 GTTCGTAATTGACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTC
* *
9015 GAACGTAAG-CATCGAACTCTTTATGAGAA
66 GAACGTAAGCCCT-GAACTCTTTGTGAGAA
9044 GGACATGTTC
Statistics
Matches: 175, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 2 0.01
101 173 0.99
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (101 bp):
GTTCGTAATTGACCTTAGATTTCGATCCGGACTCATCATGAGAACATCGAAACTAAGTTGTGGTC
GAACGTAAGCCCTGAACTCTTTGTGAGAACAACAAA
Found at i:16635 original size:147 final size:148
Alignment explanation
Indices: 16367--16656 Score: 573
Period size: 147 Copynumber: 2.0 Consensus size: 148
16357 GATTCTAATA
16367 ATTTCTGGTTTTATTTCAGGGTCGTCGGCCCGTTGTCACCCTTGATCTGTCAGCTATCCCAGATG
1 ATTTCTGGTTTTATTTCAGGGTCGTCGGCCCGTTGTCACCCTTGATCTGTCAGCTATCCCAGATG
16432 ATATTCTAGCGGTGGGCTATCTCGTTCATGGGCACGCGGTTGTTGCATTTCGTGGTCTGAGGAGG
66 ATATTCTAGCGGTGGGCTATCTCGTTCATGGGCACGCGGTTGTTGCATTTCGTGGTCTGAGGAGG
16497 CTCGGGGGATGGTTTTGC
131 CTCGGGGGATGGTTTTGC
16515 ATTTCTGGTTTTATTTCAGGGTCGTCGGCCCGTTGTCACCCTTGATCT-TCAGCTATCCCAGATG
1 ATTTCTGGTTTTATTTCAGGGTCGTCGGCCCGTTGTCACCCTTGATCTGTCAGCTATCCCAGATG
16579 ATATTCTAGCGGTGGGCTATCTCGTTCATGGGCACGCGGTTGTTGCATTTCGTGGTCTGAGGAGG
66 ATATTCTAGCGGTGGGCTATCTCGTTCATGGGCACGCGGTTGTTGCATTTCGTGGTCTGAGGAGG
16644 CTCGGGGGATGGT
131 CTCGGGGGATGGT
16657 ATTGGGGTAC
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 94 0.66
148 48 0.34
ACGTcount: A:0.13, C:0.22, G:0.31, T:0.34
Consensus pattern (148 bp):
ATTTCTGGTTTTATTTCAGGGTCGTCGGCCCGTTGTCACCCTTGATCTGTCAGCTATCCCAGATG
ATATTCTAGCGGTGGGCTATCTCGTTCATGGGCACGCGGTTGTTGCATTTCGTGGTCTGAGGAGG
CTCGGGGGATGGTTTTGC
Found at i:19364 original size:30 final size:30
Alignment explanation
Indices: 19328--19387 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
19318 GGTCTACTAT
19328 GGAGTGATGGAGTATTACTATGGACTATTA
1 GGAGTGATGGAGTATTACTATGGACTATTA
19358 GGAGTGATGGAGTATTACTATGGACTATTA
1 GGAGTGATGGAGTATTACTATGGACTATTA
19388 CTTTTGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (30 bp):
GGAGTGATGGAGTATTACTATGGACTATTA
Found at i:20494 original size:22 final size:22
Alignment explanation
Indices: 20466--20509 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20456 CTGCTTACTT
*
20466 TCCATCAACTGTATCATTTGAA
1 TCCATCAACTGCATCATTTGAA
20488 TCCATCAACTGCATCATTTGAA
1 TCCATCAACTGCATCATTTGAA
20510 GCATCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (22 bp):
TCCATCAACTGCATCATTTGAA
Done.