Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016449.1 Corchorus olitorius cultivar O-4 contig16482, 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: 73822
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16684 original size:215 final size:211
Alignment explanation
Indices: 16307--16726 Score: 655
Period size: 215 Copynumber: 2.0 Consensus size: 211
16297 AAGATATAGA
*
16307 TAATAATATGGGTAATTATTTGATATACCGGCGGTGTAAATTTTGAACTCCACAAACGGGTTGTG
1 TAATAATATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAACGGGTTGTG
*
16372 GAGACACATGTCCGTTTTTTTAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACA
66 GAGACACATGTCCATTTTTTTAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACA
*
16437 TATGTCACCCATCAGAACCCGCTTGTGTAGTCTGCTAAACTCCACCACCGGTGTATTGTATAATT
131 CATGTCACCCATCAGAACCCGCTTGTGTAGTCTGCTAAACTCCACCACCGGTGTATTGTATAATT
16502 TACC-TAATAATATTC
196 TACCATAATAATATTC
* *
16517 TAATAATATTGGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTG
1 TAATAATA-T-GGGTAATTATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAACGGGTTG
* *
16582 TGGAGTTGATACATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGA
64 TGGA---GACACATGTCCATTTTTTTAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGA
* * * ** *
16647 GGACACATGTTACCCTTCA-AGACCCGCTTGTGTAGTCTGCTTAACTCCACTGCTGGTGTATTGT
126 GGACACATGTCACCCATCAGA-ACCCGCTTGTGTAGTCTGCTAAACTCCACCACCGGTGTATTGT
16711 ATAATTTACCATAATA
190 ATAATTTACCATAATA
16727 TTGATATGTG
Statistics
Matches: 190, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
210 8 0.04
211 1 0.01
212 55 0.29
214 1 0.01
215 120 0.63
216 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (211 bp):
TAATAATATGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGAACTCCACAAACGGGTTGTG
GAGACACATGTCCATTTTTTTAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGAGGACA
CATGTCACCCATCAGAACCCGCTTGTGTAGTCTGCTAAACTCCACCACCGGTGTATTGTATAATT
TACCATAATAATATTC
Found at i:27729 original size:16 final size:15
Alignment explanation
Indices: 27708--27752 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
27698 CTCACCCAAT
27708 TTTTTAAAAATATATA
1 TTTTTAAAAATAT-TA
*
27724 TTTTTAAAAATATTT
1 TTTTTAAAAATATTA
27739 TTTTATAAAAATAT
1 TTTT-TAAAAATAT
27753 GACGTGGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTAAAAATATTA
Found at i:34472 original size:28 final size:28
Alignment explanation
Indices: 34432--34488 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
34422 AAACAGGTTG
34432 TGGAGTTGATACATGTCTATTTTTTTAA
1 TGGAGTTGATACATGTCTATTTTTTTAA
34460 TGGAGTTGATACATGTCTATTTTTTTAA
1 TGGAGTTGATACATGTCTATTTTTTTAA
34488 T
1 T
34489 TAATTAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.51
Consensus pattern (28 bp):
TGGAGTTGATACATGTCTATTTTTTTAA
Found at i:38287 original size:38 final size:37
Alignment explanation
Indices: 38245--38316 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
38235 CTGTTGATTC
*
38245 ACTAGAAAGAGTTTGATATTTTGGATTGAACTTTTTTT
1 ACTAGAAAGAGTTGGATATTTTGGATTGAA-TTTTTTT
*
38283 ACTAGGAAGAGTTGGATATTTTGGATTGAATTTT
1 ACTAGAAAGAGTTGGATATTTTGGATTGAATTTT
38317 CTTATCAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (37 bp):
ACTAGAAAGAGTTGGATATTTTGGATTGAATTTTTTT
Found at i:44574 original size:31 final size:31
Alignment explanation
Indices: 44484--44594 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
44474 TCCTTTTGTG
* *
44484 CACGTGACATGCCACATGTCACTATTTTTTGGTA
1 CACGTGGCGTGCCACATGTCAC---TTTTTGGTA
* ** * *
44518 CACATGGCGTGATACGTGTCACTTTTTGATA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* *
44549 CACGTGGCGTGCCACATGTCGCTTTTTGGCA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
*
44580 CACGTGGCATGCCAC
1 CACGTGGCGTGCCAC
44595 GTCGGACACC
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
31 46 0.74
34 16 0.26
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (31 bp):
CACGTGGCGTGCCACATGTCACTTTTTGGTA
Found at i:48241 original size:7 final size:7
Alignment explanation
Indices: 48228--48259 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
48218 CATATGAGAA
48228 ATAAATT
1 ATAAATT
*
48235 GTAAATT
1 ATAAATT
48242 ATAAATT
1 ATAAATT
48249 ATAAATT
1 ATAAATT
48256 ATAA
1 ATAA
48260 TATAATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (7 bp):
ATAAATT
Found at i:50922 original size:494 final size:495
Alignment explanation
Indices: 49994--50982 Score: 1827
Period size: 494 Copynumber: 2.0 Consensus size: 495
49984 AAATAGTATT
49994 TGAAAGACCCAGGGAATTTACCAAAGGCCACTTTTGAGGATCGATGAGGAGGCTCCATTTGAACT
1 TGAAAGACCCAGGGAATTTACCAAAGGCCACTTTTGAGGATCGATGAGGAGGCTCCATTTGAACT
* * *
50059 TTTTTTTATCTTTTTCTGTTTTTTCTCAATTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTCT
66 TTTTTTTATCCTTTTCTGTCTTTTCTCAATTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTAT
50124 AGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATA
131 AGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATA
* *
50189 AATCCTATCCCCCTTAATTATCTAGAATTGTAACCTATCTTCAGGCTTTTCATGTCCATATGAAG
196 AATCCTATCCCCCTTAATTATCTAGAATTGTAACATATCTTCAGGCCTTTCATGTCCATATGAAG
50254 AAGAGAGTAAACTTAGTTTTTGTTTAAGTGTTACACACTTTAAAGGAGGAAACAAAATTGAAGCT
261 AAGAGAGTAAACTTAGTTTTTGTTTAAGTGTTACACACTTTAAAGGAGGAAACAAAATTGAAGCT
* *
50319 ATTGCATCTGTCCATGTACAAACTAATATTTATTATTTATTGTTAACTTTAGGGCATATGTTCAA
326 ATTGCATCTGTCCATGTACAAACTAATATTTACTATTTATTGTTAACTTTAGGGCATATGCTCAA
50384 TGTTAATATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAATACTTTCGAAATCTCC
391 TGTTAATATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAATACTTTCGAAATCTCC
50449 TACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAA
456 TACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAA
50489 TGAAAGACCCAGGGAATTTACCAAAGGCCACTTTTGAGGATCGATGAGGAGGCTCCATTTGAAC-
1 TGAAAGACCCAGGGAATTTACCAAAGGCCACTTTTGAGGATCGATGAGGAGGCTCCATTTGAACT
* *
50553 TTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTAT
66 TTTTTTTATCCTTTTCTGTCTTTTCTCAATTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTAT
50618 AGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATA
131 AGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATA
**
50683 AATGTTATCCCCCTTAATTATCTAGAATTGTAACATATCTTCAGGCCTTTCATGTCCATATGAAG
196 AATCCTATCCCCCTTAATTATCTAGAATTGTAACATATCTTCAGGCCTTTCATGTCCATATGAAG
*
50748 AAGAGAGTAAACTTAGTTTTTGTTTAAGTGTTACACACTTTAGAGGAGGAAACAAAATTGAAGCT
261 AAGAGAGTAAACTTAGTTTTTGTTTAAGTGTTACACACTTTAAAGGAGGAAACAAAATTGAAGCT
50813 ATTGCATCTGTCCATGTACAAACTAATATTTACTATTTATTGTTAACTTTAGGGCATATGCTCAA
326 ATTGCATCTGTCCATGTACAAACTAATATTTACTATTTATTGTTAACTTTAGGGCATATGCTCAA
* * *
50878 TGTTAATATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAGTAGTTTCGAAATTTCC
391 TGTTAATATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAATACTTTCGAAATCTCC
*
50943 TACGTATCAAACAATTTAATTTGAATAGAAAATTTTTCAA
456 TACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAA
50983 AAAACTAGAT
Statistics
Matches: 478, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
494 414 0.87
495 64 0.13
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (495 bp):
TGAAAGACCCAGGGAATTTACCAAAGGCCACTTTTGAGGATCGATGAGGAGGCTCCATTTGAACT
TTTTTTTATCCTTTTCTGTCTTTTCTCAATTGCCAAATTACTAAGAAGACCCTAGGTTAGTTTAT
AGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATA
AATCCTATCCCCCTTAATTATCTAGAATTGTAACATATCTTCAGGCCTTTCATGTCCATATGAAG
AAGAGAGTAAACTTAGTTTTTGTTTAAGTGTTACACACTTTAAAGGAGGAAACAAAATTGAAGCT
ATTGCATCTGTCCATGTACAAACTAATATTTACTATTTATTGTTAACTTTAGGGCATATGCTCAA
TGTTAATATAGTATAGCCTTTTAAAGATGCAACACATTTAAAATCATAATACTTTCGAAATCTCC
TACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAA
Found at i:51697 original size:18 final size:18
Alignment explanation
Indices: 51674--51717 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
51664 GGAGGAAATC
*
51674 GAAGAGGAAGTAGAAGTA
1 GAAGAGGAAGTAGAAGAA
*
51692 GAAGAGGAAGTTGAAGAA
1 GAAGAGGAAGTAGAAGAA
51710 GAAGAGGA
1 GAAGAGGA
51718 GGAGGAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (18 bp):
GAAGAGGAAGTAGAAGAA
Found at i:51765 original size:21 final size:20
Alignment explanation
Indices: 51704--51772 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
51694 AGAGGAAGTT
*
51704 GAAGAAGAAGAGGAGGAGGAA
1 GAAGAAGAAGAGGA-GACGAA
* *
51725 GAGGACGAAGAGGAGAACGAA
1 GAAGAAGAAGAGGAG-ACGAA
* *
51746 GAAGAAGAAGACGACGACGAC
1 GAAGAAGAAGAGGA-GACGAA
51767 GAAGAA
1 GAAGAA
51773 ACTGATAACC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.41, T:0.00
Consensus pattern (20 bp):
GAAGAAGAAGAGGAGACGAA
Found at i:63447 original size:120 final size:120
Alignment explanation
Indices: 63234--63458 Score: 441
Period size: 120 Copynumber: 1.9 Consensus size: 120
63224 TGAATAGAGA
*
63234 CAAACACCACAAATCCAAAATCTTGGATGGTGACTAAATGATCTTTATGGAGGACCTTTTCTTGT
1 CAAACACCACAAATCCAAAATCTTGGATGCTGACTAAATGATCTTTATGGAGGACCTTTTCTTGT
63299 CTCACATTTTGACATTCTCTTCAATTGAAGGACACCGAAAGTTCAAGGATTGCCT
66 CTCACATTTTGACATTCTCTTCAATTGAAGGACACCGAAAGTTCAAGGATTGCCT
63354 CAAACACCACAAATCCAAAATCTTGGATGCTGACTAAATGATCTTTATGGAGGACCTTTTCTTGT
1 CAAACACCACAAATCCAAAATCTTGGATGCTGACTAAATGATCTTTATGGAGGACCTTTTCTTGT
63419 CTCACATTTTGACATTCTCTTCAATTGAAGGACACCGAAA
66 CTCACATTTTGACATTCTCTTCAATTGAAGGACACCGAAA
63459 AGAGAAGACT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 104 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (120 bp):
CAAACACCACAAATCCAAAATCTTGGATGCTGACTAAATGATCTTTATGGAGGACCTTTTCTTGT
CTCACATTTTGACATTCTCTTCAATTGAAGGACACCGAAAGTTCAAGGATTGCCT
Found at i:73454 original size:322 final size:323
Alignment explanation
Indices: 72857--73462 Score: 1151
Period size: 322 Copynumber: 1.9 Consensus size: 323
72847 GGAAATTTAC
72857 CAAAGACCCCTTTTGAGGATCGATGAGGAGACTCCGTTTGAACTTTTTTTGTCCTTTTCAGTCTT
1 CAAAGACCCCTTTTGAGGATCGATGAGGAGACTCCGTTTGAACTTTTTTTGTCCTTTTCAGTCTT
*
72922 TTCTCACTTACCAAATTACTAAGAAGACCCTAGGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGTC
66 TTCTCACTTACCAAATTACTAAGAAGACCCTAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGTC
*
72987 TTTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
131 TCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
73052 CTAGAATTGTAACTTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAATTTAGTTTTT
196 CTAGAATTGTAACTTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAATTTAGTTTTT
*
73117 GTTTAAGTGCTACACACTTTAGAGTGTGTAGCACTCTAAAGTGTGTACTTTTCAGTCTTTTCT
261 GTTTAAGTACTACACACTTTAGAGTGTGTAGCACTCTAAAGTGTGTACTTTTCAGTCTTTTCT
* *
73180 CAAAGGCCCCTTTTGAGGATTGATGAGGAGACTCCGTTTGAACTTTTTTTGTCCTTTTCAGTCTT
1 CAAAGACCCCTTTTGAGGATCGATGAGGAGACTCCGTTTGAACTTTTTTTGTCCTTTTCAGTCTT
*
73245 TTCTCACTTACCAAATTACTAAGAAGACTCTAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGTC
66 TTCTCACTTACCAAATTACTAAGAAGACCCTAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGTC
73310 -CTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
131 TCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
73374 CTAGAATTGTAACTTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAATTTAGTTTTT
196 CTAGAATTGTAACTTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAATTTAGTTTTT
73439 GTTTAAGTACTACACACTTTAGAG
261 GTTTAAGTACTACACACTTTAGAG
73463 GAGGAAACAA
Statistics
Matches: 277, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
322 151 0.55
323 126 0.45
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (323 bp):
CAAAGACCCCTTTTGAGGATCGATGAGGAGACTCCGTTTGAACTTTTTTTGTCCTTTTCAGTCTT
TTCTCACTTACCAAATTACTAAGAAGACCCTAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGTC
TCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTATAATAAATCCTATCCCCCTTAATTAT
CTAGAATTGTAACTTCTCTTCAGGCCTTTCATGTCCATATGAAGAAGAGAGTAAATTTAGTTTTT
GTTTAAGTACTACACACTTTAGAGTGTGTAGCACTCTAAAGTGTGTACTTTTCAGTCTTTTCT
Done.