Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013714.1 Corchorus olitorius cultivar O-4 contig13747, 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: 31370
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:1042 original size:27 final size:25
Alignment explanation
Indices: 992--1044 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
982 ATTTCCATTA
992 TTTTAATAATGGAATAATTAAAATAT
1 TTTTAATAATGGAAT-ATTAAAATAT
1018 TTTTCAATAATGGCAAT-TTAGAAATAT
1 TTTT-AATAATGG-AATATTA-AAATAT
1045 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (25 bp):
TTTTAATAATGGAATATTAAAATAT
Found at i:3145 original size:27 final size:25
Alignment explanation
Indices: 3124--3172 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
3114 AAAAGATAAG
3124 GAAAAAGAAAAAGGGAAAAAAGGAAGA
1 GAAAAAG--AAAGGGAAAAAAGGAAGA
3151 GAAAAAGAAAGGG-AAAAAGGAA
1 GAAAAAGAAAGGGAAAAAAGGAA
3173 AATAAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 6 0.27
27 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (25 bp):
GAAAAAGAAAGGGAAAAAAGGAAGA
Found at i:6301 original size:163 final size:161
Alignment explanation
Indices: 6045--6439 Score: 519
Period size: 163 Copynumber: 2.4 Consensus size: 161
6035 CGATAGAAAG
*
6045 ACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTTTTCTCTTTTTTTGGAGGGAAAAATTCC
1 ACGCCG-C-TATTAATATATGGA-GGAGAGATTTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCC
* *
6110 CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGACATTTTGACATC
63 CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGACATTTTCACACC
6175 -GGACGCCGCTAAGTAGTGGCGTCTA-GAAAAGGAA
128 AGG-CGCCGCTAAGTAGTGGCGTCTATG-AAAGGAA
6209 ACGCCGCTATT-ATATATGGATGGAGAGATTTTTTTTTTCCTTTTTTTTTGGAGGGAAAAATTCC
1 ACGCCGCTATTAATATATGGA-GGAGAGA-TTTTTTTTT-CTTTTTTTTTGGAGGGAAAAATTCC
* * * * *
6273 CTCCCCCCTAAAACAAAGAAATTTTCCAACTCTACGCCTATAATATATAGTGGCGTTTTCTCACC
63 CTCCCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGACATTTTCACACC
* * *
6338 AGGCGCCGCTAATTAGTGGCTTCTATGAAAGGGA
128 AGGCGCCGCTAAGTAGTGGCGTCTATGAAAGGAA
* * * *
6372 ACGCCACAATTGTAATATATGGAGTGAGAGAATTTTTTTTTC-TTTGTTTTGGATGGAAAAATTC
1 ACGCCGCTA-T-TAATATATGGAG-GAGAG-ATTTTTTTTTCTTTTTTTTTGGAGGGAAAAATTC
6436 CCTC
62 CCTC
6440 GCCTATAATA
Statistics
Matches: 206, Mismatches: 16, Indels: 18
0.86 0.07 0.08
Matches are distributed among these distances:
161 16 0.08
162 13 0.06
163 116 0.56
164 34 0.17
165 3 0.01
166 23 0.11
167 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (161 bp):
ACGCCGCTATTAATATATGGAGGAGAGATTTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCTC
CCCCCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGACATTTTCACACCAGG
CGCCGCTAAGTAGTGGCGTCTATGAAAGGAA
Found at i:11411 original size:13 final size:13
Alignment explanation
Indices: 11393--11419 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11383 GAAAACGCCG
11393 CTAAATATAATTT
1 CTAAATATAATTT
11406 CTAAATATAATTT
1 CTAAATATAATTT
11419 C
1 C
11420 ATTACATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (13 bp):
CTAAATATAATTT
Found at i:13559 original size:27 final size:27
Alignment explanation
Indices: 13521--13649 Score: 177
Period size: 27 Copynumber: 4.8 Consensus size: 27
13511 GACTGTTGCC
* *
13521 GCAGTGGATCCTCTCACTTCGACCCTA
1 GCAGTGGATCCTCCCACTTCGACCCCA
* *
13548 GCAGTCGATCCTCCTACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
13575 GCAGTGGATCCTCCCATTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
13602 GAAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
* * *
13629 ACAGTGGGTCCTCCCATTTCG
1 GCAGTGGATCCTCCCACTTCG
13650 CCTCGGGTCG
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.23
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:14453 original size:17 final size:17
Alignment explanation
Indices: 14431--14465 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
14421 GAAAAAGTGC
14431 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
14448 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
14465 A
1 A
14466 ACGTTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:15603 original size:6 final size:6
Alignment explanation
Indices: 15593--15645 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
15583 CTAATACTAG
* * *
15593 TGGCGG TGGCGA TGGAGA TGGCGA TGGCGA TGGCGA TGGTGA TGGCGA
1 TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA TGGCGA
15641 TGGCG
1 TGGCG
15646 GTAACTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.15, C:0.13, G:0.53, T:0.19
Consensus pattern (6 bp):
TGGCGA
Found at i:16050 original size:32 final size:32
Alignment explanation
Indices: 16014--16116 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
16004 GTGTGAAAAG
*
16014 AAAACGCTCTTATTTAGCGGCGTCTATAGAAG
1 AAAACGCTCTTATTTAGCGGCGTCTATAGAAC
16046 AAAACGCTCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCTCTTATTTAGCGGCGTCTATAGAAC
* *
16078 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCTCTTATTTAGCGGCGTCTATAGAAC
16110 AAAACGC
1 AAAACGC
16117 AGCTACATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (32 bp):
AAAACGCTCTTATTTAGCGGCGTCTATAGAAC
Found at i:17699 original size:20 final size:20
Alignment explanation
Indices: 17674--17727 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
17664 TTTTGGAGGG
*
17674 TTATTAACACTTATAAAGGC
1 TTATTAAGACTTATAAAGGC
* * *
17694 TTATTAAGTCTTATGAAGGG
1 TTATTAAGACTTATAAAGGC
17714 TTATTAAGACTTAT
1 TTATTAAGACTTAT
17728 TGAAGCAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (20 bp):
TTATTAAGACTTATAAAGGC
Found at i:17916 original size:71 final size:71
Alignment explanation
Indices: 17742--17923 Score: 201
Period size: 71 Copynumber: 2.6 Consensus size: 71
17732 GCAGTTTGAA
* * * * *
17742 TATATAATTAGCTTAACTTAGCTTAGCAAAAT-TTAACTTACTATTTTACTTAATGTCAGAAATT
1 TATATAATTAGCTTAACTTAG-TTAACTATATCTTAACTTACTATTTTACTTAATGTAACAAATT
*
17806 TTTAAAC
65 TTGAAAC
* * * *
17813 TATTTAATTAGCTTAACTTAGCTAAGCT-TATCTTAACTTACTGTTTTAGTTAAT-TAACAAA-T
1 TATATAATTAGCTTAACTTAGTTAA-CTATATCTTAACTTACTATTTTACTTAATGTAACAAATT
*
17875 TTGAAAG
65 TTGAAAC
17882 TATATAATTAGCTTAACTTAGTTAACTTAGTATCTTAACTTA
1 TATATAATTAGCTTAACTTAGTTAAC-TA-TATCTTAACTTA
17924 AGTAGCTAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
68 1 0.01
69 30 0.32
70 9 0.10
71 53 0.57
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (71 bp):
TATATAATTAGCTTAACTTAGTTAACTATATCTTAACTTACTATTTTACTTAATGTAACAAATTT
TGAAAC
Found at i:21651 original size:24 final size:24
Alignment explanation
Indices: 21619--21716 Score: 124
Period size: 24 Copynumber: 4.1 Consensus size: 24
21609 TGTCGATGAC
*
21619 TCTGGTTTTGACGACCGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
*
21643 TCTGGTTTTGACGATTGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
* * * * *
21667 TTTGCTTTTGACTATTGTGCTTTT
1 TCTGGTTTTGACGACTGTGATTTT
*
21691 TCTGGTTCTGACGACTGTGATTTT
1 TCTGGTTTTGACGACTGTGATTTT
21715 TC
1 TC
21717 GGATTTTTCG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.11, C:0.14, G:0.22, T:0.52
Consensus pattern (24 bp):
TCTGGTTTTGACGACTGTGATTTT
Found at i:22543 original size:15 final size:15
Alignment explanation
Indices: 22523--22558 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
22513 AATAATTTAC
22523 AGCCAAGAGAACAGA
1 AGCCAAGAGAACAGA
*
22538 AGCCAAGAGAACATA
1 AGCCAAGAGAACAGA
22553 AGCCAA
1 AGCCAA
22559 ACACTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.22, G:0.22, T:0.03
Consensus pattern (15 bp):
AGCCAAGAGAACAGA
Found at i:24287 original size:14 final size:13
Alignment explanation
Indices: 24251--24289 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
24241 TATATATTAG
24251 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
24264 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
24278 AATTTTTTAAAT
1 AATTTTTTAAAT
24290 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:24474 original size:84 final size:85
Alignment explanation
Indices: 24305--24474 Score: 306
Period size: 84 Copynumber: 2.0 Consensus size: 85
24295 AATTTTTTTA
*
24305 GAAATAAACTTTTACAGTTATTCTACTAAAAAAATCTATTTTTATTTAATTAAATTCAATATTAT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAAA-CTATTTTTATTTAATTAAATTCAATATTAT
24370 TATAAATATTTTATTTTTACC
65 TATAAATATTTTATTTTTACC
24391 GAAATAAACTTTTACAATTATTCTACTAAAAAAA-TATTTTTATTTAATTAAATTCAATATTATT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAAACTATTTTTATTTAATTAAATTCAATATTATT
*
24455 ATAACTATTTTATTTTTACC
66 ATAAATATTTTATTTTTACC
24475 ATTTTAATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 49 0.60
86 33 0.40
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (85 bp):
GAAATAAACTTTTACAATTATTCTACTAAAAAAACTATTTTTATTTAATTAAATTCAATATTATT
ATAAATATTTTATTTTTACC
Found at i:27518 original size:17 final size:17
Alignment explanation
Indices: 27496--27529 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27486 AGTCCAGTCG
27496 GGGTTATCTTATAGGCC
1 GGGTTATCTTATAGGCC
27513 GGGTTATCTTATAGGCC
1 GGGTTATCTTATAGGCC
27530 AAAGTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
GGGTTATCTTATAGGCC
Found at i:27608 original size:32 final size:32
Alignment explanation
Indices: 27572--27671 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 32
27562 GTCGGTCAAG
27572 GTCCAATCCAGTAAGGGTGATAAGGCCAGGTA
1 GTCCAATCCAGTAAGGGTGATAAGGCCAGGTA
*
27604 GTCCAACTTCC---AA-GGT--TCAA-GTC-GGTCAA
1 GTCCAA--TCCAGTAAGGGTGAT-AAGGCCAGGT--A
27633 GGTCCAATCCAGTAAGGGTGATAAGGCCAGGTA
1 -GTCCAATCCAGTAAGGGTGATAAGGCCAGGTA
27666 GTCCAA
1 GTCCAA
27672 CTTCCAAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 28
0.63 0.02 0.34
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 3 0.06
30 9 0.17
31 4 0.08
32 15 0.29
33 3 0.06
34 6 0.12
35 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (32 bp):
GTCCAATCCAGTAAGGGTGATAAGGCCAGGTA
Found at i:27632 original size:62 final size:62
Alignment explanation
Indices: 27554--27679 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
27544 TCTAGTCTTG
27554 AGGTTCAAGTCGGTCAAGGTCCAATCCAGTAAGGGTGATAAGGCCAGGTAGTCCAACTTCCA
1 AGGTTCAAGTCGGTCAAGGTCCAATCCAGTAAGGGTGATAAGGCCAGGTAGTCCAACTTCCA
27616 AGGTTCAAGTCGGTCAAGGTCCAATCCAGTAAGGGTGATAAGGCCAGGTAGTCCAACTTCCA
1 AGGTTCAAGTCGGTCAAGGTCCAATCCAGTAAGGGTGATAAGGCCAGGTAGTCCAACTTCCA
27678 AG
1 AG
27680 AGTGAGGTGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (62 bp):
AGGTTCAAGTCGGTCAAGGTCCAATCCAGTAAGGGTGATAAGGCCAGGTAGTCCAACTTCCA
Found at i:27696 original size:25 final size:25
Alignment explanation
Indices: 27668--27717 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27658 GCCAGGTAGT
27668 CCAACTTCCAAGAGTGAGGTGAAGG
1 CCAACTTCCAAGAGTGAGGTGAAGG
27693 CCAACTTCCAAGAGTGAGGTGAAGG
1 CCAACTTCCAAGAGTGAGGTGAAGG
27718 TAGCCACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (25 bp):
CCAACTTCCAAGAGTGAGGTGAAGG
Done.