Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013164.1 Corchorus olitorius cultivar O-4 contig13197, 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: 41381
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1563 original size:20 final size:20
Alignment explanation
Indices: 1538--1584 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1528 ACAATGCCAT
*
1538 AATGAATTTAATTACTAGCA
1 AATGAAATTAATTACTAGCA
1558 AATGAAATTAATTACTAGCA
1 AATGAAATTAATTACTAGCA
1578 AATGAAA
1 AATGAAA
1585 AATGCAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (20 bp):
AATGAAATTAATTACTAGCA
Found at i:1669 original size:29 final size:29
Alignment explanation
Indices: 1627--1685 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1617 ATGTGAAGCA
1627 GTCCAAATAAATCAACATGAACCAAATTG
1 GTCCAAATAAATCAACATGAACCAAATTG
1656 GTCCAAATAAATCAACATGAACCAAATTG
1 GTCCAAATAAATCAACATGAACCAAATTG
1685 G
1 G
1686 AAGTGACCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (29 bp):
GTCCAAATAAATCAACATGAACCAAATTG
Found at i:2961 original size:14 final size:15
Alignment explanation
Indices: 2944--2972 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2934 CCACTCACCA
2944 CTCACCGG-TCATCG
1 CTCACCGGTTCATCG
2958 CTCACCGGTTCATCG
1 CTCACCGGTTCATCG
2973 ATGGCGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.41, G:0.21, T:0.24
Consensus pattern (15 bp):
CTCACCGGTTCATCG
Found at i:3104 original size:23 final size:23
Alignment explanation
Indices: 3074--3117 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3064 CAAACCTGGG
3074 AAATTTCCTTTCACTCTCTCTTT
1 AAATTTCCTTTCACTCTCTCTTT
3097 AAATTTCCTTTCACTCTCTCT
1 AAATTTCCTTTCACTCTCTCT
3118 GAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTCCTTTCACTCTCTCTTT
Found at i:3132 original size:24 final size:23
Alignment explanation
Indices: 3074--3125 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
3064 CAAACCTGGG
**
3074 AAATTTCCTTTCACTCTCTCTTT
1 AAATTTCCTTTCACTCTCTCTAA
3097 AAATTTCCTTTCACTCTCTCTGAA
1 AAATTTCCTTTCACTCTCTCT-AA
3121 AAATT
1 AAATT
3126 ATCTTTCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTCCTTTCACTCTCTCTAA
Found at i:7258 original size:22 final size:22
Alignment explanation
Indices: 7231--7272 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7221 CTGTTTTTTT
*
7231 TTGTTTATATTATCTTATATTC
1 TTGTTTAGATTATCTTATATTC
7253 TTGTTTAGATTATCTTATAT
1 TTGTTTAGATTATCTTATAT
7273 GCAGACTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (22 bp):
TTGTTTAGATTATCTTATATTC
Found at i:8863 original size:12 final size:12
Alignment explanation
Indices: 8846--8872 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8836 TATCTTTGAC
8846 AAATTCCGTTGG
1 AAATTCCGTTGG
8858 AAATTCCGTTGG
1 AAATTCCGTTGG
8870 AAA
1 AAA
8873 GTTGCCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (12 bp):
AAATTCCGTTGG
Found at i:27063 original size:268 final size:268
Alignment explanation
Indices: 26581--27098 Score: 1000
Period size: 268 Copynumber: 1.9 Consensus size: 268
26571 AATTGGATGT
* *
26581 CGAATTAGCTTAGGAAAATTATCAAATATTTGTAAGATTAAGTGGTTGATCCCAGCCAATTAATT
1 CGAATTAGCCTAGGAAAATTATCAAATATTTGCAAGATTAAGTGGTTGATCCCAGCCAATTAATT
*
26646 TTAAAAAATTGGAACAATAATTGGATAAAAAACTACCTTGTATGATGGATGTTTTCTCTTGTACC
66 TTAAAAAATTGGAACAATAATTGGATAAAAAACTACCTTGTATGATGGATGGTTTCTCTTGTACC
26711 ACCATAGACTTCAATTTTGGTTGATTGGAGGAAGGTACAATGGCTTGATTTCGAGCAGAGGAACC
131 ACCATAGACTTCAATTTTGGTTGATTGGAGGAAGGTACAATGGCTTGATTTCGAGCAGAGGAACC
26776 CAAAACAGCATGCTTCACTTTGGAGGAGGACTTAGCAGCATCATCACGAGAGTTCAACAATTTTG
196 CAAAACAGCATGCTTCACTTTGGAGGAGGACTTAGCAGCATCATCACGAGAGTTCAACAATTTTG
26841 GCACCTGC
261 GCACCTGC
26849 CGAATTAGCCTAGGAAAATTATCAAATATTTGCAAGATTAAGTGGTTGATCCCAGCCAATTAATT
1 CGAATTAGCCTAGGAAAATTATCAAATATTTGCAAGATTAAGTGGTTGATCCCAGCCAATTAATT
26914 TTAAAAAATTGGAACAATAATTGGATAAAAAACTACCTTGTATGATGGATGGTTTCTCTTGTACC
66 TTAAAAAATTGGAACAATAATTGGATAAAAAACTACCTTGTATGATGGATGGTTTCTCTTGTACC
26979 ACCATAGACTTCAATTTTGGTTGATTGGAGGAAGGTACAATGGCTTGATTTCGAGCAGAGGAACC
131 ACCATAGACTTCAATTTTGGTTGATTGGAGGAAGGTACAATGGCTTGATTTCGAGCAGAGGAACC
*
27044 CAAAACAGCATGTTTCACTTTGGAGGAGGACTTAGCAGCATCATCACGAGAGTTC
196 CAAAACAGCATGCTTCACTTTGGAGGAGGACTTAGCAGCATCATCACGAGAGTTC
27099 TCCTTGGCCG
Statistics
Matches: 246, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
268 246 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (268 bp):
CGAATTAGCCTAGGAAAATTATCAAATATTTGCAAGATTAAGTGGTTGATCCCAGCCAATTAATT
TTAAAAAATTGGAACAATAATTGGATAAAAAACTACCTTGTATGATGGATGGTTTCTCTTGTACC
ACCATAGACTTCAATTTTGGTTGATTGGAGGAAGGTACAATGGCTTGATTTCGAGCAGAGGAACC
CAAAACAGCATGCTTCACTTTGGAGGAGGACTTAGCAGCATCATCACGAGAGTTCAACAATTTTG
GCACCTGC
Found at i:28877 original size:49 final size:48
Alignment explanation
Indices: 28822--28946 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 48
28812 AGTTCCTACA
* * *
28822 CTTTTTCTCAATTTTTACAACAAAATTGAATCTTTATTTTTCCTTGCAC
1 CTTTTTCTCAATTTTTACAACAAAATTGAATATTTACTTTTCATTGC-C
* *
28871 CTTTTTCTCAATTTTTA-AGATAAAATTGAATATTTACTTTTCATTGCT
1 CTTTTTCTCAATTTTTACA-ACAAAATTGAATATTTACTTTTCATTGCC
*
28919 CTTTTTATCAA-TTTT-CGAACAAAATTGA
1 CTTTTTCTCAATTTTTAC-AACAAAATTGA
28947 TTGGCACGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
47 13 0.20
48 12 0.18
49 41 0.62
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.49
Consensus pattern (48 bp):
CTTTTTCTCAATTTTTACAACAAAATTGAATATTTACTTTTCATTGCC
Found at i:32865 original size:20 final size:20
Alignment explanation
Indices: 32840--32879 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
32830 TAATTAGCTC
32840 TAATTTTTATTTCTAAATAT
1 TAATTTTTATTTCTAAATAT
32860 TAATTTTTATTTCTAAATAT
1 TAATTTTTATTTCTAAATAT
32880 CAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTTATTTCTAAATAT
Found at i:34167 original size:23 final size:23
Alignment explanation
Indices: 34141--34186 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
34131 ATTGAATTTG
*
34141 TATTTAATAATTTATTTATTAAA
1 TATTTAATAATTAATTTATTAAA
** *
34164 TATTTCTTAATTAATTTTTTAAA
1 TATTTAATAATTAATTTATTAAA
34187 AAAAACGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTAATAATTAATTTATTAAA
Found at i:37025 original size:18 final size:18
Alignment explanation
Indices: 37002--37039 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
36992 TGTATTTTTT
37002 ATTTCCACTTT-AATATTG
1 ATTTCCA-TTTCAATATTG
*
37020 ATTTCCATTTCATTATTG
1 ATTTCCATTTCAATATTG
37038 AT
1 AT
37040 AGGAGACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTCCATTTCAATATTG
Done.