Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015996.1 Corchorus olitorius cultivar O-4 contig16029, 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: 44040
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:147 original size:15 final size:15
Alignment explanation
Indices: 127--193 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
117 TGAAGTTGGT
127 GATGATGCAAATGTA
1 GATGATGCAAATGTA
142 GATGATGCAAATGTA
1 GATGATGCAAATGTA
* **
157 GGTGAT---TTTGTA
1 GATGATGCAAATGTA
169 GATGATGCAAATGTA
1 GATGATGCAAATGTA
*
184 GGTGATGCAA
1 GATGATGCAA
194 GGGACGAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 9 0.21
15 33 0.79
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (15 bp):
GATGATGCAAATGTA
Found at i:176 original size:27 final size:27
Alignment explanation
Indices: 138--189 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
128 ATGATGCAAA
138 TGTAGATGATGCAAATGTAGGTGATTT
1 TGTAGATGATGCAAATGTAGGTGATTT
165 TGTAGATGATGCAAATGTAGGTGAT
1 TGTAGATGATGCAAATGTAGGTGAT
190 GCAAGGGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (27 bp):
TGTAGATGATGCAAATGTAGGTGATTT
Found at i:2553 original size:33 final size:33
Alignment explanation
Indices: 2516--2648 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 33
2506 TAGAAAGGCA
* **
2516 ACAAGAGCTTGCAAGAATTGAAGAAGAAAGAAG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* * *
2549 ACAAGAGCTGGCTCGCATTGAAGAAGATAGACG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* * *
2582 ACAGGAGCTGGCTCGAGTTGAAGAAGAGAGAAG
1 ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
* ** *
2615 A-AATGAGCTAGCTCGCCTTGAAGAAGACAGAAG
1 ACAA-GAGCTGGCTCGAATTGAAGAAGAAAGAAG
2648 A
1 A
2649 AATGAGATTG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.41, C:0.14, G:0.31, T:0.14
Consensus pattern (33 bp):
ACAAGAGCTGGCTCGAATTGAAGAAGAAAGAAG
Found at i:2649 original size:33 final size:33
Alignment explanation
Indices: 2532--2654 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
2522 GCTTGCAAGA
2532 ATTGAAGAAGAAAGAAGACAA-GAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGA-AATGAGCTGGCTCGC
* * * *
2565 ATTGAAGAAGATAGACGACAGGAGCTGGCTCG-
1 ATTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
* *
2597 AGTTGAAGAAGAGAGAAGAAATGAGCTAGCTCGC
1 A-TTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
* *
2631 CTTGAAGAAGACAGAAGAAATGAG
1 ATTGAAGAAGAAAGAAGAAATGAG
2655 ATTGATCGTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 75 0.97
ACGTcount: A:0.41, C:0.13, G:0.32, T:0.14
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGAAATGAGCTGGCTCGC
Found at i:3381 original size:32 final size:32
Alignment explanation
Indices: 3339--3592 Score: 364
Period size: 32 Copynumber: 7.9 Consensus size: 32
3329 ATGGTGTTTA
* * ** *
3339 TTGAATAAAACGCCACAAATCAGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
*
3371 TTGAAGAAAACGCCACTAATTTGTGGCGTTCT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
* *
3403 TGGAAGAAAATGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
3435 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
3467 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
* *
3499 TTGAAGAAAAAAGCCACTAATTTGTGGCGTTCT
1 TTGAAG-AAAACGCCACTAATTTGTGGCGTACT
* * *
3532 TGGAAGAAAATGCCACTAATTTGTGGTGTACT
1 TTGAAGAAAACGCCACTAATTTGTGGCGTACT
* *
3564 TTGAAGAAAACGCCACCAATCTGTGGCGT
1 TTGAAGAAAACGCCACTAATTTGTGGCGT
3593 TTGTCTTTAA
Statistics
Matches: 201, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
32 172 0.86
33 29 0.14
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (32 bp):
TTGAAGAAAACGCCACTAATTTGTGGCGTACT
Found at i:3539 original size:129 final size:128
Alignment explanation
Indices: 3339--3592 Score: 418
Period size: 129 Copynumber: 2.0 Consensus size: 128
3329 ATGGTGTTTA
* * *
3339 TTGAATAAAACGCCACAAATCAGTGGCGTTCTTTGAAGAAAACGCCACTAATTTGTGGCGTTCTT
1 TTGAAGAAAACGCCACAAATCAGTGGCGTACTTTGAAGAAAAAGCCACTAATTTGTGGCGTTCTT
* *
3404 GGAAGAAAATGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACTAATTTGTGGCGTACT
66 GGAAGAAAATGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGTACT
* **
3467 TTGAAGAAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAAAAGCCACTAATTTGTGGCGTTCT
1 TTGAAGAAAACGCCACAAATCAGTGGCGTACTTTGAAG-AAAAAGCCACTAATTTGTGGCGTTCT
*
3532 TGGAAGAAAATGCCACTAATTTGTGGTGTACTTTGAAGAAAACGCCACCAATCTGTGGCGT
65 TGGAAGAAAATGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGT
3593 TTGTCTTTAA
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
128 33 0.28
129 83 0.72
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (128 bp):
TTGAAGAAAACGCCACAAATCAGTGGCGTACTTTGAAGAAAAAGCCACTAATTTGTGGCGTTCTT
GGAAGAAAATGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGTACT
Found at i:3626 original size:97 final size:96
Alignment explanation
Indices: 3345--3592 Score: 336
Period size: 97 Copynumber: 2.6 Consensus size: 96
3335 TTTATTGAAT
* ** * * * * *
3345 AAAACGCCACAAATCAGTGGCGTTCTTTGAAGAAAACGCCACTAATTTGTGGCGTTCTTGGAAG-
1 AAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGTACTT-TAAGA
* * *
3409 AAAATGCCACTAATTTGTGGCGTACTTTGAAG
65 AAAAAGCCACTAATTTGTGGCGTTCTTGGAAG
* *
3441 AAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACTAATTTGTGGCGTACTTTGAAGA
1 AAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGTACTTT-AAGA
3506 AAAAAGCCACTAATTTGTGGCGTTCTTGGAAG
65 AAAAAGCCACTAATTTGTGGCGTTCTTGGAAG
* *
3538 AAAATGCCACTAATTTGTGGTGTACTTTGAAGAAAACGCCACCAATCTGTGGCGT
1 AAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGT
3593 TTGTCTTTAA
Statistics
Matches: 137, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
96 57 0.42
97 80 0.58
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (96 bp):
AAAACGCCACTAATTTGTGGCGTACTTTGAAGAAAACGCCACCAATCTGTGGCGTACTTTAAGAA
AAAAGCCACTAATTTGTGGCGTTCTTGGAAG
Found at i:12695 original size:2 final size:2
Alignment explanation
Indices: 12688--12732 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
12678 ATATCTCTAC
* * * *
12688 AT AT AT AT AT AC AT AC AT AT AT AC AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12730 AT A
1 AT A
12733 AATAAAGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:12700 original size:12 final size:12
Alignment explanation
Indices: 12685--12732 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
12675 AAGATATCTC
12685 TACATATATATA
1 TACATATATATA
*
12697 TACATACATATA
1 TACATATATATA
*
12709 TACATATACATA
1 TACATATATATA
*
12721 TATATATATATA
1 TACATATATATA
12733 AATAAAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TACATATATATA
Found at i:31473 original size:24 final size:24
Alignment explanation
Indices: 31444--31614 Score: 76
Period size: 24 Copynumber: 7.2 Consensus size: 24
31434 TCAGCAGCAG
31444 CAACAGCCGCAGCCATTCCCACAA
1 CAACAGCCGCAGCCATTCCCACAA
*** *
31468 CAACAGTTTCAGCC---CCAGCAGCAG
1 CAACAGCCGCAGCCATTCC--CA-CAA
31492 CAACAGCCGCAGCCATTCCCACAA
1 CAACAGCCGCAGCCATTCCCACAA
*** *
31516 CAACAGTTTCAGCC---CCAGCAGCAG
1 CAACAGCCGCAGCCATTCC--CA-CAA
*
31540 CAACAGCGGCAGCCATTCCCACAA
1 CAACAGCCGCAGCCATTCCCACAA
* ***
31564 CAGCAGTTTCAGCCA----CAGCAA
1 CAACAGCCGCAGCCATTCCCA-CAA
31585 CAACAGCCGCAAG-CATTCCCACAA
1 CAACAGCCGC-AGCCATTCCCACAA
31609 CAACAG
1 CAACAG
31615 TTTCAGCCGC
Statistics
Matches: 105, Mismatches: 24, Indels: 36
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.02
21 15 0.14
22 2 0.02
23 4 0.04
24 72 0.69
25 6 0.06
27 4 0.04
ACGTcount: A:0.33, C:0.40, G:0.16, T:0.10
Consensus pattern (24 bp):
CAACAGCCGCAGCCATTCCCACAA
Found at i:31506 original size:48 final size:48
Alignment explanation
Indices: 31435--31632 Score: 314
Period size: 48 Copynumber: 4.2 Consensus size: 48
31425 TCAGAATAAT
31435 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
1 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
31483 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
1 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
* *
31531 CAGCAGCAGCAACAGCGGCAGCCATTCCCACAACAGCAGTTTCAG--C
1 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
* *
31577 CA-CAGCAACAACAGCCGCAAG-CATTCCCACAACAACAGTTTCAGCCG
1 CAGCAGCAGCAACAGCCGC-AGCCATTCCCACAACAACAGTTTCAGCCC
31624 CAGCCAGCA
1 CAG-CAGCA
31633 CAATACCCTC
Statistics
Matches: 139, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
45 36 0.26
46 5 0.04
47 2 0.01
48 91 0.65
49 5 0.04
ACGTcount: A:0.32, C:0.40, G:0.18, T:0.10
Consensus pattern (48 bp):
CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCC
Found at i:31612 original size:96 final size:95
Alignment explanation
Indices: 31435--31632 Score: 312
Period size: 93 Copynumber: 2.1 Consensus size: 95
31425 TCAGAATAAT
*
31435 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCCCAGCAGCAGCAACAGCC
1 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAG-CCCAGCAGCAACAACAGCC
31500 GCAGCCATTCCCACAACAACAGTTTCAGCCC
65 GCAGCCATTCCCACAACAACAGTTTCAGCCC
* *
31531 CAGCAGCAGCAACAGCGGCAGCCATTCCCACAACAGCAGTTTCAG-CCA-CAGCAACAACAGCCG
1 CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCCAGCAGCAACAACAGCCG
*
31594 CAAG-CATTCCCACAACAACAGTTTCAGCCG
66 C-AGCCATTCCCACAACAACAGTTTCAGCCC
31624 CAGCCAGCA
1 CAG-CAGCA
31633 CAATACCCTC
Statistics
Matches: 96, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
93 43 0.45
94 10 0.10
96 43 0.45
ACGTcount: A:0.32, C:0.40, G:0.18, T:0.10
Consensus pattern (95 bp):
CAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTTTCAGCCCAGCAGCAACAACAGCCG
CAGCCATTCCCACAACAACAGTTTCAGCCC
Found at i:31717 original size:24 final size:24
Alignment explanation
Indices: 31663--31747 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
31653 TAACCAAGCC
* * *
31663 TATCCACCGCAGCAGGCC-GCACCA
1 TATCCACCACAACA-GCCTGCAGCA
* * *
31687 TACCCACCGCAACAGCCTGCAGCG
1 TATCCACCACAACAGCCTGCAGCA
*
31711 TATCCACCACAACAGCCTGCTGCA
1 TATCCACCACAACAGCCTGCAGCA
31735 TATCCACCACAAC
1 TATCCACCACAAC
31748 CAGTGCAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 3 0.06
24 49 0.94
ACGTcount: A:0.28, C:0.45, G:0.15, T:0.12
Consensus pattern (24 bp):
TATCCACCACAACAGCCTGCAGCA
Found at i:37331 original size:29 final size:30
Alignment explanation
Indices: 37271--37331 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
37261 GCAACAGATG
* * *
37271 AAATTGATAGTTCAGGAGGTAATTTGTACA
1 AAATTGATAATTCAGGAGGTAACTCGTACA
*
37301 AAATTGA-AATTCAGGAGGTAACTCGTCCA
1 AAATTGATAATTCAGGAGGTAACTCGTACA
37330 AA
1 AA
37332 TGGTATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (30 bp):
AAATTGATAATTCAGGAGGTAACTCGTACA
Found at i:43749 original size:81 final size:82
Alignment explanation
Indices: 43653--43815 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 82
43643 TTTTACTCAC
* *
43653 GTATTTTAAAATATTATATTCTATATTAACCCTTATAAGATAAAATTAAAATTTTAAAATTAAAA
1 GTATTTTAAAATATTATATTCCATATTAACCCTTATAAGATAAAACTAAAATTTTAAAATTAAAA
43718 AGGGTATTTTAGATATT
66 AGGGTATTTTAGATATT
43735 GTATTTT-AAATATTATATTCCATATTAACCCTTATAAGATAAAACTAAAATTTTAAAATTAAAA
1 GTATTTTAAAATATTATATTCCATATTAACCCTTATAAGATAAAACTAAAATTTTAAAATTAAAA
43799 AGGGTATTTTAGATATT
66 AGGGTATTTTAGATATT
43816 TCAGGTCAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
81 72 0.91
82 7 0.09
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (82 bp):
GTATTTTAAAATATTATATTCCATATTAACCCTTATAAGATAAAACTAAAATTTTAAAATTAAAA
AGGGTATTTTAGATATT
Done.