Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015284.1 Corchorus olitorius cultivar O-4 contig15317, 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: 69775
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:16705 original size:20 final size:20
Alignment explanation
Indices: 16669--16706 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16659 GACTCGAAAA
*
16669 AAATTCGAGTTCGGCTCGGG
1 AAATTCGAGTCCGGCTCGGG
16689 AAATTCGAG-CCGAGCTCG
1 AAATTCGAGTCCG-GCTCG
16707 AGCTCGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (20 bp):
AAATTCGAGTCCGGCTCGGG
Found at i:16999 original size:16 final size:16
Alignment explanation
Indices: 16974--17010 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
16964 CTTCATCTTC
* *
16974 TTCCCTCCCTCTCCCT
1 TTCCCCCCCTCCCCCT
16990 TTCCCCCCCTCCCCCT
1 TTCCCCCCCTCCCCCT
17006 TTCCC
1 TTCCC
17011 TTTCCCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (16 bp):
TTCCCCCCCTCCCCCT
Found at i:29195 original size:18 final size:18
Alignment explanation
Indices: 29172--29206 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29162 TGATGACGTG
*
29172 GAAAAATCCACGTCAGCA
1 GAAAAAGCCACGTCAGCA
29190 GAAAAAGCCACGTCAGC
1 GAAAAAGCCACGTCAGC
29207 GACTAACAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.29, G:0.20, T:0.09
Consensus pattern (18 bp):
GAAAAAGCCACGTCAGCA
Found at i:30633 original size:19 final size:18
Alignment explanation
Indices: 30609--30644 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30599 TGAAGATTTA
30609 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
30628 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
30645 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:37544 original size:36 final size:37
Alignment explanation
Indices: 37490--37568 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 37
37480 GAAGCTAAAA
*
37490 AAAAAAAAAAACTGGGCCTAAAATAGAAAGAGGTC-G
1 AAAAAAAAAAACTGGGCCTAAAATAGAAAAAGGTCAG
* * *
37526 AAAAAGAAGAACTTGGCCTAAAATAGAAAAAGGTCAG
1 AAAAAAAAAAACTGGGCCTAAAATAGAAAAAGGTCAG
37563 AAAAAA
1 AAAAAA
37569 GAAATAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.58, C:0.10, G:0.20, T:0.11
Consensus pattern (37 bp):
AAAAAAAAAAACTGGGCCTAAAATAGAAAAAGGTCAG
Found at i:38475 original size:59 final size:59
Alignment explanation
Indices: 38414--39316 Score: 1268
Period size: 59 Copynumber: 15.3 Consensus size: 59
38404 CCCCTTTCTA
* * * *
38414 TTTTTAAAATCCTGTTCGAGGTCTCTGGTTGAGAGTTTTCAATTCAAAATCTTATCTTA
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
*
38473 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTCGTCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * *
38532 TTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTAAAAATCTTATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * *
38591 TTTTTAAAATCCTGCTCGAGGTCTCTGGTAGAGAGTTTTTAATTCAAAATCTTATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * **
38650 TTTGTAAAATCCTGATCGAGGTCCCTGGTAGAGAGTTTTCAATTCAAAATCTCATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * * **
38709 TTTCT-AAATCTTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAAACTCATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* *
38767 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAAACTCGTCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * *
38826 TTTTTAAAATCCTGATCGAGGTCTCTGGCAGAGAGTTTTCAATTCAAAAACTCGTCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * * * *
38885 TTTTTAAAATCATGTTCGACGTCTCTAGTAGAGAGTTTTCAATTCAAAATCTTATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * * * *
38944 TTTTTAAAATCTTGTTTGAGGTCTCTGGTATAGAGTTTTCAATTCAAAATCTCGTCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * * *
39003 TTTTTAAAATCCTGTTCGAGGTCTCTGGTAGATAGTTTTCAATTAAAAATCTCGTCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* ** * * * *
39062 TTTATAAAATTTTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTAAAAATCTTATCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * * *
39121 TTTATAAAATCTTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * *
39180 TTTTAAAAATCCTGATCGAGGTCACTGGTAGAGAGTTTTCAATTCAAAATCTTGCCTTG
1 TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
* * *
39239 TTGGTAAAAATCCTGATCGAGGTCTCTGGTAGACAGTTTTCAATTCAAAATCTTGTCTTG
1 TT-TTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
39299 TCTTTTAAAAATCCTGAT
1 T-TTTT-AAAATCCTGAT
39317 TAAGGTTTTT
Statistics
Matches: 772, Mismatches: 68, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
58 54 0.07
59 651 0.84
60 55 0.07
61 12 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (59 bp):
TTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATCTTGTCTTG
Found at i:46085 original size:22 final size:22
Alignment explanation
Indices: 46060--46108 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
46050 GAGGAAATCG
46060 CGGAGATTTCAGAGAAAAAGCA
1 CGGAGATTTCAGAGAAAAAGCA
* * * *
46082 CGGAGCTTTGAGAGGATAAGCA
1 CGGAGATTTCAGAGAAAAAGCA
46104 CGGAG
1 CGGAG
46109 CTTGGTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.35, T:0.14
Consensus pattern (22 bp):
CGGAGATTTCAGAGAAAAAGCA
Found at i:51099 original size:20 final size:20
Alignment explanation
Indices: 51055--51100 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
51045 TCAAGGAAAC
51055 AACCCGTTGAAACCCGGTGT
1 AACCCGTTGAAACCCGGTGT
*
51075 GACCCGTTGAAACCCGGAT-T
1 AACCCGTTGAAACCCGG-TGT
51095 AACCCG
1 AACCCG
51101 GTGACCCGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (20 bp):
AACCCGTTGAAACCCGGTGT
Found at i:52230 original size:25 final size:25
Alignment explanation
Indices: 52196--52243 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
52186 GTTAGTTTGC
*
52196 AGAGACCGAGCGAGAGTGCTCAATT
1 AGAGACCGAGCAAGAGTGCTCAATT
*
52221 AGAGACCGAGTAAGAGTGCTCAA
1 AGAGACCGAGCAAGAGTGCTCAA
52244 GATTGTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (25 bp):
AGAGACCGAGCAAGAGTGCTCAATT
Found at i:63503 original size:2 final size:2
Alignment explanation
Indices: 63496--63527 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
63486 CATAGTTCTG
63496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63528 TACAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69463 original size:36 final size:36
Alignment explanation
Indices: 69416--69521 Score: 178
Period size: 36 Copynumber: 2.9 Consensus size: 36
69406 TTCAATAACC
*
69416 TTACATCTTTTG-AGATTTTGGTTATCATATTTCTTA
1 TTACATTTTTTGTA-ATTTTGGTTATCATATTTCTTA
69452 TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
*
69488 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATTTTTTGTAATTTTGGTTATCATATTTCT
69522 CCAAAATCTC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 66 0.99
37 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.59
Consensus pattern (36 bp):
TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
Done.