Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017553.1 Corchorus olitorius cultivar O-4 contig17586, 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: 62943
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3756 original size:21 final size:21
Alignment explanation
Indices: 3732--3786 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3722 GGCAGTCGCA
* *
3732 GCAGCAGCTGCATCAGCTGCT
1 GCAGCAGCTGCAGCAGCTGCG
* * *
3753 GCAGCCGCTGCGGCCGCTGCG
1 GCAGCAGCTGCAGCAGCTGCG
*
3774 GCAGCAGCCGCAG
1 GCAGCAGCTGCAG
3787 TTGCAGCTGG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.38, G:0.36, T:0.11
Consensus pattern (21 bp):
GCAGCAGCTGCAGCAGCTGCG
Found at i:16789 original size:12 final size:11
Alignment explanation
Indices: 16761--16788 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16751 ATCATTAAAC
16761 TTTTTTAGGTT
1 TTTTTTAGGTT
16772 TTTTTTAGGTT
1 TTTTTTAGGTT
16783 TTTTTT
1 TTTTTT
16789 TCTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (11 bp):
TTTTTTAGGTT
Found at i:36836 original size:13 final size:13
Alignment explanation
Indices: 36818--36850 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
36808 GGAGGGGGAG
36818 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
36831 AGAAAAA-AAAAA
1 AGAAAAAGAAAAA
*
36843 AAAAAAAG
1 AGAAAAAG
36851 CTAACTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:42327 original size:20 final size:20
Alignment explanation
Indices: 42302--42342 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42292 GATGGAATGG
42302 AGATAAACATCAAGAACCTT
1 AGATAAACATCAAGAACCTT
* *
42322 AGATAAGCATCAAGAATCTT
1 AGATAAACATCAAGAACCTT
42342 A
1 A
42343 TTTACGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (20 bp):
AGATAAACATCAAGAACCTT
Found at i:49530 original size:9 final size:8
Alignment explanation
Indices: 49506--49538 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
49496 AATATAAAAC
49506 AAAGAGAG
1 AAAGAGAG
49514 AAAG-GAG
1 AAAGAGAG
49521 AAAGAAGAG
1 AAAG-AGAG
49530 AAAGAGAG
1 AAAGAGAG
49538 A
1 A
49539 GGGCTATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 9 0.39
9 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (8 bp):
AAAGAGAG
Found at i:55751 original size:24 final size:24
Alignment explanation
Indices: 55719--55765 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
55709 TTGGTACTAT
55719 GAAGTAATTGATTCTTGTCATGTA
1 GAAGTAATTGATTCTTGTCATGTA
*
55743 GAAGTAATTGATTTTTGTCATGT
1 GAAGTAATTGATTCTTGTCATGT
55766 TTGGTATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (24 bp):
GAAGTAATTGATTCTTGTCATGTA
Found at i:60430 original size:332 final size:330
Alignment explanation
Indices: 59966--60980 Score: 1417
Period size: 332 Copynumber: 3.1 Consensus size: 330
59956 GAAAAACTTT
*
59966 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAA-TTTTTGCAAAATTTTAGCAGAAATCGTGTAC
* * * ** *
60031 TATCCATCACAATTTTTAGCTAAAAACGCGTTCCAGGCCCCCAACTCAATTTTGCTTGATTTTTG
65 TATCCATCACAGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCATGATTTTTG
* *
60096 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCACAACCACATTGAATTTAAAAT
130 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAA-
* *
60161 TTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGATAAAAATTGG
194 TTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGA-AAAAATTGG
* *
60226 AAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATATTTTTGGCGTTGATTTTTATATTTTTCCT
258 AAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTCCT
60290 GAGTATTG
323 GAGTATTG
60298 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAATTTTTTGCAAAATTTTAGCAGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAA-TTTTTGCAAAATTTTAGCAGAAATCGTGTAC
* *
60363 TATCCATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAATTTTACATGATTTTTG
65 TATCCATCACAGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCATGATTTTTG
*
60428 GCGCCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAT
130 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAAT
* * *
60493 TTGATTTTACGAGCATTTGAATCTTATTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGGA
195 TTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAATTGGAA
* * * * * * * *
60558 AAACGATATTATATGGGTGAAAAGCTCATCAATATTTTTGGCATTGAATTATATTTTTTTCTCCG
260 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTC-CTG
60623 AGTATTG
324 AGTATTG
* * *
60630 TGGCCAAAAATTGAGGAAAAATTTTTTGGATCAATTTTTGCAAAATTTTAG-TGAAATTGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGAT-AATTTTTGCAAAATTTTAGCAGAAATCGTGTAC
* * ** * * * * * *
60694 TAACCATCACAGTTTTTGGCTAAAAATGCGTTTTAAGGCCCCGGCTCAAATCTGTAGGAATTTTG
65 TATCCATCACAGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCATGATTTTTG
* * * ** * **
60759 GCGCCTAGAGCCCTTGAAATTACTATATTCATCTAATGAAATCTTAGCCACATCAAATTTAAAAA
130 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTT-AAAA
* * * **
60824 TTTGATTTTAAGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATTAACT-AAAAAAAATTGGA
194 TTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAATTGGA
* *
60888 AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTG
259 AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTCCTG
*
60953 ATTATTG
324 AGTATTG
*
60960 TGG-CAAAGAATTGAGAAAAAA
1 TGGCCAAA-AATTGAGGAAAAA
60981 ATTTCGGGTC
Statistics
Matches: 606, Mismatches: 72, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
329 4 0.01
330 52 0.09
331 260 0.43
332 288 0.48
333 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
TGGCCAAAAATTGAGGAAAAATTTTTCGGATAATTTTTGCAAAATTTTAGCAGAAATCGTGTACT
ATCCATCACAGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCATGATTTTTGG
CGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAAATT
TGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCCGAAAAAATTGGAAA
AACGATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTCCTGAG
TATTG
Found at i:61959 original size:337 final size:332
Alignment explanation
Indices: 61125--62164 Score: 1549
Period size: 332 Copynumber: 3.1 Consensus size: 332
61115 GAAAAAAGTT
* *
61125 TGGCCAAAAATTGAGGAAATATTATTT-GGATCAGTTTTTGCAAAAATTTTAGCTGAAATCGTGT
1 TGGCCAAAAATTGAGGAAAAATT-TTTCGGATCATTTTTTGC-AAAATTTTAGCTGAAATCGTGT
* * *
61189 ACTATCCATCACGGTTTTTGGCTAAAAACGCGTTCCAGG-CCACGGCTCAATTTTGCTTGATTTT
64 ACTATCCATCACGTTTTTTGGCTAAAAACGCGTTCCAGGTCCCCGGCTCAATTTTGCATGATTTT
* * *
61253 TGGCGCCTAGAACCCTTGAAATTTTAATATTCAACTAACCAATTCTCAACCACATTGAATTTAAA
129 TGGCGCC-AGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAA
*
61318 AATTTGATTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
193 AATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
* *
61383 GGAAAAACGATATTAGAAGCGTGAAAACACTTCAATATTTTTGGCATTGATTTTTAGA-TTTTTC
258 GGAAAAACGATATTAGAAGCGTGAAAACACTTCAATATTTTTGGCGTTGATTTTTATATTTTTTC
61447 CTGAGTATTG
323 CTGAGTATTG
*
61457 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGCTGAAATCGTGTAC
*
61522 TATCCATCACGTTTTTTGGCTAAAAACGCGTTGCAGGGT-CCCGGCTCAATTTTGCATGATTTTT
66 TATCCATCACGTTTTTTGGCTAAAAACGCGTTCCA-GGTCCCCGGCTCAATTTTGCATGATTTTT
*
61586 GGCGCCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTTAACCACATTGAATTTAAAA
130 GGCG-CCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAA
*
61651 ATTTGATTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATATT
194 ATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-ATT
* *
61716 GGAAAAACGATATTAGAAACGTGAAAACCCTTCAATATTTTTGGCGTTGATTTTTATATTTTTTC
258 GGAAAAACGATATTAGAAGCGTGAAAACACTTCAATATTTTTGGCGTTGATTTTTATATTTTTTC
61781 CTGAGTATTG
323 CTGAGTATTG
* ** *
61791 TGGCCAAAAATTGATGAAAAATTTTTCTAATCATTTTTTGCAAAATTTTAGCTGAAATCATGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGCTGAAATCGTGTAC
* *
61856 TATCCATCACGATTTTTTTTGGCTAAAAACGCGTTTCAGGTCCCCGGCTCAATTTTACATGATTT
66 TATCCATCACG---TTTTTTGGCTAAAAACGCGTTCCAGGTCCCCGGCTCAATTTTGCATGATTT
*
61921 TTGGCGTCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAGCCACATTGAATTTAA
128 TTGGCG-CCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAA
* * * *
61986 AAATTTGATTCTATGAGCATCTGAATCTTATTTCGATTTAATTAGGAATTAATTTC-GAAAAAAA
192 AAATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAAA
* * ** * ** * *
62050 -TGGGAAAACGATATTAGAAGCGTGAAAATCTCTTCAATATAATTGGTGTAAAATTATATATTTT
256 TTGGAAAAACGATATTAGAAGCGTGAAAA-CACTTCAATATTTTTGGCGTTGATTTTTATATTTT
62114 TTCC-GAGTATTG
320 TTCCTGAGTATTG
* *
62126 TGGCCAAAAATTGACG-AAAATTTTTCAGG-TCAGTTTTTG
1 TGGCCAAAAATTGAGGAAAAATTTTTC-GGATCATTTTTTG
62165 GCCGAAATCG
Statistics
Matches: 649, Mismatches: 46, Indels: 24
0.90 0.06 0.03
Matches are distributed among these distances:
331 59 0.09
332 177 0.27
333 59 0.09
334 106 0.16
335 49 0.08
336 35 0.05
337 161 0.25
338 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (332 bp):
TGGCCAAAAATTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGCTGAAATCGTGTAC
TATCCATCACGTTTTTTGGCTAAAAACGCGTTCCAGGTCCCCGGCTCAATTTTGCATGATTTTTG
GCGCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAAT
TTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGA
AAAACGATATTAGAAGCGTGAAAACACTTCAATATTTTTGGCGTTGATTTTTATATTTTTTCCTG
AGTATTG
Done.