Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021422.1 Corchorus olitorius cultivar O-4 contig21455, 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: 46097
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2011 original size:69 final size:70
Alignment explanation
Indices: 1920--2080 Score: 225
Period size: 69 Copynumber: 2.3 Consensus size: 70
1910 ATTTCCCGCA
* * *
1920 ACAACTCCTGGACAAGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATT-TGCGCTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCA
*
1984 ACAGC
66 ACAAC
* * * * *
1989 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCTGGTCTTGTTCTGTATTTCTGCATTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCA
2054 ACAAC
66 ACAAC
*
2059 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
2081 CCAAGATCTG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 47 0.59
70 33 0.41
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (70 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTCTGCACTCCTCA
ACAAC
Found at i:14826 original size:18 final size:17
Alignment explanation
Indices: 14799--14834 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
14789 TTTCTCTTCA
14799 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
14816 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
14834 T
1 T
14835 TTAGGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:16002 original size:31 final size:31
Alignment explanation
Indices: 15967--16046 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
15957 TAAATTATTG
*
15967 CAAATTAAAACAAATTA-AGCATTAAATTAAA
1 CAAATTAAAA-AAATGATAGCATTAAATTAAA
* *
15998 CAAA-TAATTAAAATGATAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGATAGCATTAAATTAAA
16029 CAAATT-AAAAAATGATAG
1 CAAATTAAAAAAATGATAG
16047 ACCCTTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 18 0.43
31 23 0.55
32 1 0.02
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGATAGCATTAAATTAAA
Found at i:17056 original size:2 final size:2
Alignment explanation
Indices: 17049--17079 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17039 TAAAGTGGGG
17049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17080 AACAAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17472 original size:28 final size:28
Alignment explanation
Indices: 17440--17504 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
17430 GAGTAATGGC
*
17440 TCCAAATTACGAGTTCAGGGGG-AAAACA
1 TCCAAATTA-AAGTTCAGGGGGCAAAACA
* *
17468 TCCAAAATTAAAGTTTAGGGGGCAAAACG
1 TCC-AAATTAAAGTTCAGGGGGCAAAACA
17497 TCCAAATT
1 TCCAAATT
17505 GTACAAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (28 bp):
TCCAAATTAAAGTTCAGGGGGCAAAACA
Found at i:17475 original size:29 final size:30
Alignment explanation
Indices: 17443--17516 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
17433 TAATGGCTCC
*
17443 AAATTACGAGTTCAGGGGG-AAAACATCCA
1 AAATTACAAGTTCAGGGGGCAAAACATCCA
* *
17472 AAATTA-AAGTTTAGGGGGCAAAACGTCCA
1 AAATTACAAGTTCAGGGGGCAAAACATCCA
*
17501 AATTGTACAAGTTCAG
1 AAAT-TACAAGTTCAG
17517 AGAAAAAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 10 0.27
29 18 0.49
30 2 0.05
31 7 0.19
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.22
Consensus pattern (30 bp):
AAATTACAAGTTCAGGGGGCAAAACATCCA
Found at i:23040 original size:470 final size:465
Alignment explanation
Indices: 22160--23095 Score: 1694
Period size: 470 Copynumber: 2.0 Consensus size: 465
22150 TGAAGTTATG
*
22160 GAAGCCTATTAAGGTTTCGCAATCCGGGCCTGCGGTCTCGCATCTCTTTTTTGCGGATGATCTTA
1 GAAGCCTATTAAGGTTTCGCAATCCGGGCCTGCGGTCTCGCATCTCTTTTTTGCGAATGATCTTA
*
22225 TGTTGTTCAATGTTGCGGAGGGGCAAGTTGGGGTGGTTAGAGATGTTAACGGATTTTTCAAAAGC
66 TGTTGTTCAATGTTGAGGAGGGGCAAGTTGGGGTGGTTAGAGATGTTAACGGATTTTTCAAAAGC
*
22290 ATCTGGTCTTCAGGTGAATTTGGATAAATTGGAGTTATGGGTTTCCCCAAATGTCCCAAGGGATA
131 ATCTGGTCTTCAGGTGAATTTGGATAAATTGAAGTTATGGGTTTCCCCAAATGTCCCAAGGGATA
*
22355 AAGCAAGGTGTTTAAGTAGGTTATGTGAAATTCCTTTAGCTTCCGAGTTGGGGACATATTTAGGA
196 AAGCAAGGTGTTTAAGTAGGTTAGGTGAAATTCCTTTAGCTTCCGAGTTGGGGACATATTTAGGA
22420 GTGTCTATTATCCATAGCAGAGTTACCAAGAATACCTATAAGCATGTGATTGATAGAGTTCTTGG
261 GTGTCTATTATCCATAGCAGAGTTACCAAGAATACCTATAAGCATGTGATTGATAGAGTTCTTGG
*
22485 AAATTTGGCTAGTTGGAAAAGGAAGGTCTTGAGCTATGCCTGTAAAAAGACGTTGATTCAATCAA
326 AAAATTGGCTAGTTGGAAAAGGAAGGTCTTGAGCTATGCCTGTAAAAAGACGTTGATTCAATCAA
*
22550 CTTTGAGTTCACTCTCTACCTATACTATGCAATCTGCTATGTTACCAGTGGCGGTGTGTAATAGA
391 CTTTGAGTTCACTCTCTACCTATACTATCCAATCTGCTATGTTACCAGTGGCGGTGTGTAATAGA
22615 TTGGATCAGT
456 TTGGATCAGT
* *
22625 GAAGCCTATTAAGGTTTCGCAATCCGGGCCTGCGGTCTTGCATCTTTTTTTTGCGAATGATCTTA
1 GAAGCCTATTAAGGTTTCGCAATCCGGGCCTGCGGTCTCGCATCTCTTTTTTGCGAATGATCTTA
*
22690 TGTTGTTCAATGTTTCAGAGGAGGGGCAATTTGGGGTGGTTAGAGATGTATTAACGGATTTTTCA
66 TGTTGTTCAATG-TT--GAGGAGGGGCAAGTTGGGGTGGTTAGAGATG--TTAACGGATTTTTCA
22755 AAAGCATCTGGTCTTCAGGTGAATTTGGATAAATTGAAGTTATGGGTTTCCCCAAATGTCCCAAG
126 AAAGCATCTGGTCTTCAGGTGAATTTGGATAAATTGAAGTTATGGGTTTCCCCAAATGTCCCAAG
22820 GGATAAAGCAAGGTGTTTAAGTAGGTTAGGTGAAATTCCTTTAGCTTCCGAGTTGGGGACATATT
191 GGATAAAGCAAGGTGTTTAAGTAGGTTAGGTGAAATTCCTTTAGCTTCCGAGTTGGGGACATATT
* *
22885 TAGGAGTGTCTATTATCCATGGCCGAGTTACCAAGAATACCTATAAGCATGTGATTGATAGAGTT
256 TAGGAGTGTCTATTATCCATAGCAGAGTTACCAAGAATACCTATAAGCATGTGATTGATAGAGTT
*
22950 CTTGGAAAATTGGCTAGTTGGAAAGGGAAGGTCTTGAGCTATG-CTGGTAAAAAGACGTTGATTC
321 CTTGGAAAATTGGCTAGTTGGAAAAGGAAGGTCTTGAGCTATGCCT-GTAAAAAGACGTTGATTC
*
23014 AATCAACTTTGAGTTCACTTTCTACCTATACTATCCAATCTGCTATGTTACCAGTGGCGGTGTGT
385 AATCAACTTTGAGTTCACTCTCTACCTATACTATCCAATCTGCTATGTTACCAGTGGCGGTGTGT
23079 AATAGATTGGATCAGT
450 AATAGATTGGATCAGT
23095 G
1 G
23096 TAATCGGAAT
Statistics
Matches: 452, Mismatches: 13, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
465 74 0.16
466 2 0.00
468 29 0.06
469 2 0.00
470 345 0.76
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (465 bp):
GAAGCCTATTAAGGTTTCGCAATCCGGGCCTGCGGTCTCGCATCTCTTTTTTGCGAATGATCTTA
TGTTGTTCAATGTTGAGGAGGGGCAAGTTGGGGTGGTTAGAGATGTTAACGGATTTTTCAAAAGC
ATCTGGTCTTCAGGTGAATTTGGATAAATTGAAGTTATGGGTTTCCCCAAATGTCCCAAGGGATA
AAGCAAGGTGTTTAAGTAGGTTAGGTGAAATTCCTTTAGCTTCCGAGTTGGGGACATATTTAGGA
GTGTCTATTATCCATAGCAGAGTTACCAAGAATACCTATAAGCATGTGATTGATAGAGTTCTTGG
AAAATTGGCTAGTTGGAAAAGGAAGGTCTTGAGCTATGCCTGTAAAAAGACGTTGATTCAATCAA
CTTTGAGTTCACTCTCTACCTATACTATCCAATCTGCTATGTTACCAGTGGCGGTGTGTAATAGA
TTGGATCAGT
Found at i:24804 original size:31 final size:29
Alignment explanation
Indices: 24764--24823 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 29
24754 TTTTAGTTCA
24764 TTTGTAACAAAAAAAAAATAAGGCTTTCTAGT
1 TTTGTAAC--AAAAAAAA-AAGGCTTTCTAGT
24796 TTTG-AACAAAAAAAAAAGGCTTTCTAGT
1 TTTGTAACAAAAAAAAAAGGCTTTCTAGT
24824 AGTAGACAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 13 0.46
29 8 0.29
31 3 0.11
32 4 0.14
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (29 bp):
TTTGTAACAAAAAAAAAAGGCTTTCTAGT
Found at i:32249 original size:61 final size:61
Alignment explanation
Indices: 32154--32274 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
32144 CTTAATAAAG
* *
32154 GTCCCTTGGCTTTCCAATTTCGTTCAATTCAATCCTTTTTTCATTGTTTTGCATGGATATA
1 GTCCCTTGACTTTCCAATTTCATTCAATTCAATCCTTTTTTCATTGTTTTGCATGGATATA
32215 GTCCCTTGACTTTCCAATTTCATTCAATTCAATCCTTTTTTCATTGTTTTGCATGGATAT
1 GTCCCTTGACTTTCCAATTTCATTCAATTCAATCCTTTTTTCATTGTTTTGCATGGATAT
32275 TTATCTAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (61 bp):
GTCCCTTGACTTTCCAATTTCATTCAATTCAATCCTTTTTTCATTGTTTTGCATGGATATA
Found at i:32360 original size:25 final size:25
Alignment explanation
Indices: 32284--32366 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
32274 TTTATCTAAA
* *
32284 TTTAATTTTGTTCAAAATGATCATG
1 TTTAATTTTGTTCTAATTGATCATG
* *
32309 TGTAATTCTGTT-TCAATTGATCATG
1 TTTAATTTTGTTCT-AATTGATCATG
32334 TTTAATTTTGTTCTAATTGATCATG
1 TTTAATTTTGTTCTAATTGATCATG
32359 TTCTAATT
1 TT-TAATT
32367 GATTATTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
25 43 0.88
26 6 0.12
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTAATTTTGTTCTAATTGATCATG
Found at i:32362 original size:15 final size:15
Alignment explanation
Indices: 32323--32369 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
32313 ATTCTGTTTC
32323 AATTGATCATGTT-T
1 AATTGATCATGTTCT
32337 AATT--T--TGTTCT
1 AATTGATCATGTTCT
32348 AATTGATCATGTTCT
1 AATTGATCATGTTCT
32363 AATTGAT
1 AATTGAT
32370 TATTATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 1 0.04
13 1 0.04
14 4 0.14
15 13 0.46
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (15 bp):
AATTGATCATGTTCT
Found at i:32594 original size:69 final size:68
Alignment explanation
Indices: 32506--32643 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 68
32496 GACTAAAACT
* * *** **
32506 AATCAAGGAAAAAAACAATAATTCATAATTAATCTGAGCAAGAATAAAGATTATTAATGATTAGA
1 AATCAAGGAAAAAAACAATAATTCACAATCAATAAAAGCAAGAATAAAGAGGATTAATGATTAGA
32571 TTA
66 TTA
*
32574 AATCAAGGAAAAAAACCAATAATTCACAATCAATAAAAGCAAGAATAAATAGGATTAATGATTAG
1 AATCAAGGAAAAAAA-CAATAATTCACAATCAATAAAAGCAAGAATAAAGAGGATTAATGATTAG
32639 ATTA
65 ATTA
32643 A
1 A
32644 TTCATAATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
68 15 0.25
69 46 0.75
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.25
Consensus pattern (68 bp):
AATCAAGGAAAAAAACAATAATTCACAATCAATAAAAGCAAGAATAAAGAGGATTAATGATTAGA
TTA
Found at i:33827 original size:75 final size:75
Alignment explanation
Indices: 33733--33877 Score: 281
Period size: 75 Copynumber: 1.9 Consensus size: 75
33723 GGAAAATGGG
33733 TGATCGGTCGTCAACAAATCATAAAAATAAAATCCCAACAATTACTAACTAAAGATAGCTAGGGC
1 TGATCGGTCGTCAACAAATCATAAAAATAAAATCCCAACAATTACTAACTAAAGATAGCTAGGGC
33798 AAGTAGTTTA
66 AAGTAGTTTA
*
33808 TGATCGGTCGTCAGCAAATCATAAAAATAAAATCCCAACAATTACTAACTAAAGATAGCTAGGGC
1 TGATCGGTCGTCAACAAATCATAAAAATAAAATCCCAACAATTACTAACTAAAGATAGCTAGGGC
33873 AAGTA
66 AAGTA
33878 AGGGTCGATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (75 bp):
TGATCGGTCGTCAACAAATCATAAAAATAAAATCCCAACAATTACTAACTAAAGATAGCTAGGGC
AAGTAGTTTA
Found at i:40278 original size:22 final size:22
Alignment explanation
Indices: 40253--40300 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40243 GATCATCAAT
* *
40253 TGAAATAACTAAAAAGCAAATA
1 TGAAATAACCAAAAAACAAATA
* *
40275 TGAAATACCCAAAAAACCAATA
1 TGAAATAACCAAAAAACAAATA
40297 TGAA
1 TGAA
40301 TAGTGCATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (22 bp):
TGAAATAACCAAAAAACAAATA
Done.