Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021345.1 Corchorus olitorius cultivar O-4 contig21378, 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: 41734
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1614 original size:30 final size:30
Alignment explanation
Indices: 1579--1636 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
1569 GAGTTAGAGT
1579 AATTTCTGA-TTTAATTTTCTAAGTATTGTA
1 AATTTCTGATTTTAA-TTTCTAAGTATTGTA
1609 AATTTCTGATTTTAATTTCTAAGTATTG
1 AATTTCTGATTTTAATTTCTAAGTATTG
1637 AAAACCGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
AATTTCTGATTTTAATTTCTAAGTATTGTA
Found at i:2291 original size:19 final size:18
Alignment explanation
Indices: 2254--2293 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2244 TTCTTGAAAT
*
2254 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
2272 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
2291 AAT
1 AAT
2294 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:2907 original size:20 final size:19
Alignment explanation
Indices: 2870--2912 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
2860 ACATATATAC
2870 CCACATTGTATTAAAAAGT
1 CCACATTGTATTAAAAAGT
2889 CCACATTGT-TTCAAAAAAGT
1 CCACATTGTATT--AAAAAGT
2909 CCAC
1 CCAC
2913 GCGCATCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 9 0.41
20 11 0.50
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (19 bp):
CCACATTGTATTAAAAAGT
Found at i:4148 original size:151 final size:150
Alignment explanation
Indices: 3862--4152 Score: 430
Period size: 151 Copynumber: 2.0 Consensus size: 150
3852 GTCATGTCTC
* * *
3862 ATTAACATAATTTATTTTCCTCTACAAATCTTTAATTCAACATCAAAAATAAAATGACAAAACGT
1 ATTAACATAATTGATTGTCCTCTACAAATCTTTAATCCAACATCAAAAATAAAATGACAAAACGT
* *
3927 CATGTCTCATTAAGTTATTATTACATTAAACTTTTATTCCTCCCTTTTGCCATATATGCAATAAT
66 CATGTCTCATTAAGTGATTATTACATTAAACTTCTATTCCTCCCTTTTGCCA-ATATGCAATAAT
3992 AAATTTAATTTGTCAAATCTT
130 AAATTTAATTTGTCAAATCTT
* * * * *
4013 ATTAACATAATTGATTGTCCTTTGCAAATCTTTAATCCAACTTCAAAATTAAAATGCCAAAACGT
1 ATTAACATAATTGATTGTCCTCTACAAATCTTTAATCCAACATCAAAAATAAAATGACAAAACGT
*
4078 CATGTCTCATTAAGTGA-T-TT-CATCT-AACTTCTATTCCTTCCTTTTGCC-ATATGCAATAAT
66 CATGTCTCATTAAGTGATTATTACAT-TAAACTTCTATTCCTCCCTTTTGCCAATATGCAATAAT
4138 AAATTTAATTTGTCA
130 AAATTTAATTTGTCA
4153 TTTCTCATTA
Statistics
Matches: 128, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
146 27 0.21
148 24 0.19
149 3 0.02
150 1 0.01
151 73 0.57
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (150 bp):
ATTAACATAATTGATTGTCCTCTACAAATCTTTAATCCAACATCAAAAATAAAATGACAAAACGT
CATGTCTCATTAAGTGATTATTACATTAAACTTCTATTCCTCCCTTTTGCCAATATGCAATAATA
AATTTAATTTGTCAAATCTT
Found at i:5871 original size:218 final size:219
Alignment explanation
Indices: 5492--5889 Score: 665
Period size: 218 Copynumber: 1.8 Consensus size: 219
5482 TAAAAGCCTT
*
5492 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGCATAGTAGGAAAAG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGCATAGCAGGAAAAG
* * *
5557 GCAGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAGGCC
66 GAAGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGACCAAAAAAAGCC
*
5622 AAAAGTTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGCTGGT
131 AAAAGTTGCCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGCTGGT
5687 GAGAGGAAAAAAGAAATGGGGGAG
196 GAGAGGAAAAAAGAAATGGGGGAG
* * * *
5711 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAG-GTAGCAGGAAAGG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGCATAGCAGGAAAAG
* *
5775 GAAGGGGGAAAGTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGACTAAAAAAAGCC
66 GAAGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGACCAAAAAAAGCC
*
5840 AAAA-TGTGCCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTTCCCT
131 AAAAGT-TGCCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCT
5890 GATAACTAAA
Statistics
Matches: 166, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
217 1 0.01
218 116 0.70
219 49 0.30
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (219 bp):
AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGCATAGCAGGAAAAG
GAAGGGGGAAACTCATAGAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGACCAAAAAAAGCC
AAAAGTTGCCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTAGGTACTGAGCTGGT
GAGAGGAAAAAAGAAATGGGGGAG
Found at i:8006 original size:5 final size:5
Alignment explanation
Indices: 7996--8032 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
7986 CATAAGGGTC
7996 ATTTT ATTTT ATTTT ATTTT A-TTT A-TTT A-TTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
8033 TAGGTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.39
5 19 0.61
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:18819 original size:19 final size:19
Alignment explanation
Indices: 18797--18891 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 19
18787 ATTTGTGTTT
*
18797 ATTATTACATTATCATTTG
1 ATTAATACATTATCATTTG
*
18816 ATTAACACATTATCATTTG
1 ATTAATACATTATCATTTG
* *
18835 ATTAGT--GTTAT--TTGTG
1 ATTAATACATTATCATT-TG
**
18851 -TTGGTACATTATCATTTG
1 ATTAATACATTATCATTTG
*
18869 ATTAACACATTATCATTTG
1 ATTAATACATTATCATTTG
18888 ATTA
1 ATTA
18892 GTGTTGATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
15 6 0.10
16 2 0.03
17 8 0.13
18 2 0.03
19 42 0.70
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (19 bp):
ATTAATACATTATCATTTG
Found at i:18882 original size:53 final size:54
Alignment explanation
Indices: 18767--18896 Score: 208
Period size: 53 Copynumber: 2.4 Consensus size: 54
18757 TTATTGGTGT
*
18767 ATTATCATTTGATTAGTGTTATTTGTGTTTATTATTACATTATCATTTGATTAACAC
1 ATTATCATTTGATTAGTGTTATTTGTG--T-TTAGTACATTATCATTTGATTAACAC
*
18824 ATTATCATTTGATTAGTGTTATTTGTG-TTGGTACATTATCATTTGATTAACAC
1 ATTATCATTTGATTAGTGTTATTTGTGTTTAGTACATTATCATTTGATTAACAC
18877 ATTATCATTTGATTAGTGTT
1 ATTATCATTTGATTAGTGTT
18897 GATGATTAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
53 44 0.62
57 27 0.38
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (54 bp):
ATTATCATTTGATTAGTGTTATTTGTGTTTAGTACATTATCATTTGATTAACAC
Found at i:20094 original size:31 final size:31
Alignment explanation
Indices: 20059--20119 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
20049 TGGATCCAAC
* *
20059 CTTTTTGAAATGGCTTAATTTAGGGTCTAAT
1 CTTTTTAAAATGGCTTAACTTAGGGTCTAAT
20090 CTTTTTAAAATGGCTTAACTTAGGGTCTAA
1 CTTTTTAAAATGGCTTAACTTAGGGTCTAA
20120 CCTTCTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (31 bp):
CTTTTTAAAATGGCTTAACTTAGGGTCTAAT
Found at i:29917 original size:32 final size:32
Alignment explanation
Indices: 29844--29960 Score: 159
Period size: 32 Copynumber: 3.7 Consensus size: 32
29834 AATTTTATTA
* *
29844 ATTTCCCAAAATCTTCTTTTGG--G-TATCTT
1 ATTTTCCAAAATCTTCTTTTGGAAGTTACCTT
*
29873 AATTTTCCAAAATCTTCCTTTGGAAGTTACCTT
1 -ATTTTCCAAAATCTTCTTTTGGAAGTTACCTT
* *
29906 ATTTTCTAAAATCTTCTTTTGGGAGTTACCTT
1 ATTTTCCAAAATCTTCTTTTGGAAGTTACCTT
29938 ATTTTCCAAAATCTTCTTTTGGA
1 ATTTTCCAAAATCTTCTTTTGGA
29961 TTAGCTTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
30 20 0.26
32 51 0.67
33 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (32 bp):
ATTTTCCAAAATCTTCTTTTGGAAGTTACCTT
Found at i:34144 original size:27 final size:27
Alignment explanation
Indices: 34139--34234 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
34129 TCCTGGATGT
34139 GCAAATGACTAAAATGCCCCTGGACAC
1 GCAAATGACTAAAATGCCCCTGGACAC
34166 GCAAATGACTAAAATGCCCCTGGACAC
1 GCAAATGACTAAAATGCCCCTGGACAC
*
34193 GCAAATGACTAAAATGCCCCTGGAAAC
1 GCAAATGACTAAAATGCCCCTGGACAC
*
34220 GTC-AATGACCAAAAT
1 G-CAAATGACTAAAAT
34235 AGGAAGTAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 65 0.98
28 1 0.02
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (27 bp):
GCAAATGACTAAAATGCCCCTGGACAC
Found at i:37235 original size:15 final size:16
Alignment explanation
Indices: 37202--37241 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37192 TTGCTTTGTT
37202 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
37218 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
37233 TTGCTTTCT
1 TTGTTTTCT
37242 TTCTGTAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:37311 original size:27 final size:28
Alignment explanation
Indices: 37281--37353 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
37271 TAAAATTTTA
*
37281 TCAGGGGCATTTTGGTCA-TTTTTCACG
1 TCAGGGGCATTTTGGTCATTTTTTCACC
*
37308 TCAGGGGCATTTTGGTCATTTTTTTCGCC
1 TCAGGGGCATTTTGGTCA-TTTTTTCACC
*
37337 TCAGGGGCATTTAGGTC
1 TCAGGGGCATTTTGGTC
37354 CAAATTACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.44
29 23 0.56
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (28 bp):
TCAGGGGCATTTTGGTCATTTTTTCACC
Found at i:41522 original size:93 final size:93
Alignment explanation
Indices: 41412--41734 Score: 551
Period size: 93 Copynumber: 3.5 Consensus size: 93
41402 AATTCTAAGG
*
41412 AAGAA-AAGAAATTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTT
1 AAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTT
41476 AATTCTAGGTAATTAAACTAAGTAGTAA
66 AATTCTAGGTAATTAAACTAAGTAGTAA
* * * *
41504 AAGAAGAAGAATTTGGTTTAATTCTAGGTAATTACACTAAGTAGTAAAAGAAGGAGAATTAGTTT
1 AAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTT
41569 AATTCTAGGTAATTAAACTAAGTAGTAA
66 AATTCTAGGTAATTAAACTAAGTAGTAA
* *
41597 AAGAAGGAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTT
1 AAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAA-TTAGTT
41662 TAATTCTAGGTAATTAAACTAAGTAGTAA
65 TAATTCTAGGTAATTAAACTAAGTAGTAA
*
41691 AAGAAGGAG-AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
Statistics
Matches: 220, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 5 0.02
93 172 0.78
94 43 0.20
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (93 bp):
AAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTT
AATTCTAGGTAATTAAACTAAGTAGTAA
Found at i:41543 original size:47 final size:46
Alignment explanation
Indices: 41412--41734 Score: 540
Period size: 47 Copynumber: 7.0 Consensus size: 46
41402 AATTCTAAGG
*
41412 AAGAA-AAGAAATTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
1 AAGAAGAAG-AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
41458 AAGAAGAAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
1 AAGAAGAAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
* *
41504 AAGAAGAAGAATTTGGTTTAATTCTAGGTAATTACACTAAGTAGTAA
1 AAGAAGAAGAA-TTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
*
41551 AAGAAGGAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
1 AAGAAGAAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
*
41597 AAGAAGGAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
1 AAGAAGAAG-AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
*
41644 AAGAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
1 AAGAAGAAGAA-TTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
*
41691 AAGAAGGAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AAGAAGAAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
Statistics
Matches: 263, Mismatches: 10, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
46 128 0.49
47 135 0.51
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (46 bp):
AAGAAGAAGAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
Found at i:41652 original size:140 final size:139
Alignment explanation
Indices: 41421--41734 Score: 592
Period size: 140 Copynumber: 2.3 Consensus size: 139
41411 GAAGAAAAGA
*
41421 AATTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTTAATTCTAGGT
1 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTTAATTCTAGGT
*
41486 AATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTTTAATTCTAGGTAATTACACTAAGTAGTAA
66 AATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
41551 AAGAAGGAG
131 AAGAAGGAG
*
41560 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGGAGAAATTAGTTTAATTCTAGG
1 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAG-AATTAGTTTAATTCTAGG
41625 TAATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTA
65 TAATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTA
41690 AAAGAAGGAG
130 AAAGAAGGAG
41700 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
Statistics
Matches: 171, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
139 44 0.26
140 127 0.74
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.32
Consensus pattern (139 bp):
AATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAATTAGTTTAATTCTAGGT
AATTAAACTAAGTAGTAAAAGAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAA
AAGAAGGAG
Done.