Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014983.1 Corchorus olitorius cultivar O-4 contig15016, 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: 86029
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:182 original size:18 final size:18
Alignment explanation
Indices: 155--189 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
145 AATTATTACA
155 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
173 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
190 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:1553 original size:30 final size:30
Alignment explanation
Indices: 1517--1578 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1507 ATTTTTATCT
1517 TGACTTTCCTCTTATACCCTCAAATTCTAA
1 TGACTTTCCTCTTATACCCTCAAATTCTAA
* *
1547 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTCTAA
1577 TG
1 TG
1579 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTCTAA
Found at i:14227 original size:141 final size:139
Alignment explanation
Indices: 13970--14249 Score: 470
Period size: 141 Copynumber: 2.0 Consensus size: 139
13960 TTCTCTGATG
* * *
13970 ATTTTGGGTGGTAATTTCAAATCACCTTGTTTGATTTGTAGATCACTCATGGTGATTTTGGATGG
1 ATTTTGGGTGGTAATCTCAAATCACCTTGTTTGATTTGCAGATCACCCATGGTGATTTTGGATGG
*
14035 TAATATTAGAGCACTCCGTTTAGTTTGTAGATCAGTAGATGTTGCACTTTTTTTGGTGTGGTAAT
66 TAATATTAGAGCAATCCGTTTAGTTTGTAGATCAGTAGATGTTGCA-TTTTTTT-GTGTGGTAAT
14100 CTGAATTACCC
129 CTGAATTACCC
* * *
14111 ATTTTGGGTGGTAATCTCAAATCACCTTGTTTGGTTTGCAGATTACCCATGGTGATTTTGGGTGG
1 ATTTTGGGTGGTAATCTCAAATCACCTTGTTTGATTTGCAGATCACCCATGGTGATTTTGGATGG
14176 TAATATTAGAGCAATCCGTTTAGTTTGTAGATCAGTAGATGTTGCATTTTTTTGTGTGGTAATCT
66 TAATATTAGAGCAATCCGTTTAGTTTGTAGATCAGTAGATGTTGCATTTTTTTGTGTGGTAATCT
*
14241 GGATTACCC
131 GAATTACCC
14250 CTGATCACCC
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
139 20 0.15
140 7 0.05
141 104 0.79
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (139 bp):
ATTTTGGGTGGTAATCTCAAATCACCTTGTTTGATTTGCAGATCACCCATGGTGATTTTGGATGG
TAATATTAGAGCAATCCGTTTAGTTTGTAGATCAGTAGATGTTGCATTTTTTTGTGTGGTAATCT
GAATTACCC
Found at i:14368 original size:17 final size:17
Alignment explanation
Indices: 14315--14369 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
14305 GATCACCCCC
*
14315 AGATCACTAGTGAT-ATA
1 AGATCACCAGTGATCA-A
*
14332 AGACCACCAGTGATGC-A
1 AGATCACCAGTGAT-CAA
14349 AGATCACCAGTGATCAA
1 AGATCACCAGTGATCAA
14366 AGAT
1 AGAT
14370 TACATGTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.03
17 31 0.97
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:22299 original size:20 final size:20
Alignment explanation
Indices: 22274--22312 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22264 AAATCGCTGA
22274 CCCGATTTGGAATTTACGGC
1 CCCGATTTGGAATTTACGGC
22294 CCCGATTTGGAATTTACGG
1 CCCGATTTGGAATTTACGG
22313 ATCCATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (20 bp):
CCCGATTTGGAATTTACGGC
Found at i:26526 original size:2 final size:2
Alignment explanation
Indices: 26521--26547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26511 CTCTCTCTCC
26521 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 A
26548 CATACATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28390 original size:17 final size:17
Alignment explanation
Indices: 28363--28417 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
28353 AACCCATGTA
* *
28363 ATCTTTGATCACCAGTG
1 ATCTTAGATCACTAGTG
*
28380 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
28397 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTAGTG
28414 ATCT
1 ATCT
28418 GGGAGTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:30326 original size:25 final size:25
Alignment explanation
Indices: 30293--30343 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
30283 TATCTTAGAT
*
30293 ATAATATATATTAT-TA-AATAAATA
1 ATAA-ATATATTATAAATAATAAATA
30317 ATAAATATATTATAAATAATAAATA
1 ATAAATATATTATAAATAATAAATA
30342 AT
1 AT
30344 GAGTTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
25 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAATATATTATAAATAATAAATA
Found at i:30337 original size:21 final size:24
Alignment explanation
Indices: 30293--30343 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
30283 TATCTTAGAT
30293 ATAATATATATTATTAAATAAATA
1 ATAATATATATTATTAAATAAATA
30317 ATAA-ATATATTA-TAAAT-AATAA
1 ATAATATATATTATTAAATAAAT-A
30339 ATAAT
1 ATAAT
30344 GAGTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 8 0.32
24 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATATATATTATTAAATAAATA
Found at i:33672 original size:13 final size:13
Alignment explanation
Indices: 33654--33678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33644 ATTTTATCAC
33654 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
33667 CTTTTTCTTTTT
1 CTTTTTCTTTTT
33679 CTCTCCTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:44513 original size:55 final size:55
Alignment explanation
Indices: 44447--44554 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
44437 ATGTGTCAGA
*
44447 TAGCTCTCGTTATGCCAAAGAACTTTGAATAA-ATTCATTACTGTGGACATTGCAT
1 TAGCTCTCGTTATGCCAAAGAAATTTGAATAATA-TCATTACTGTGGACATTGCAT
*
44502 TAGCTCTCGTTATGCCAAAGAAATTTGAATCATATCATTACTGTGGACATTGC
1 TAGCTCTCGTTATGCCAAAGAAATTTGAATAATATCATTACTGTGGACATTGC
44555 GCCAAGTAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 49 0.98
56 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (55 bp):
TAGCTCTCGTTATGCCAAAGAAATTTGAATAATATCATTACTGTGGACATTGCAT
Found at i:56766 original size:3 final size:3
Alignment explanation
Indices: 56758--56801 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
56748 TTATAGAGTA
56758 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
56802 AGAGTAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:69807 original size:59 final size:59
Alignment explanation
Indices: 69735--69853 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
69725 GGTTCCATAT
69735 ATTCTATACCCATTTATGAGCAAAGTCCCTCTTGTCCGTATTGCCAAGTCTTTACAATA
1 ATTCTATACCCATTTATGAGCAAAGTCCCTCTTGTCCGTATTGCCAAGTCTTTACAATA
* *
69794 ATTCTATACCCATTTATGAGCAAAGTCCCTTTTGTCCGTATTGCTAAGTCTTTACAATA
1 ATTCTATACCCATTTATGAGCAAAGTCCCTCTTGTCCGTATTGCCAAGTCTTTACAATA
69853 A
1 A
69854 GAAGAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.37
Consensus pattern (59 bp):
ATTCTATACCCATTTATGAGCAAAGTCCCTCTTGTCCGTATTGCCAAGTCTTTACAATA
Found at i:74087 original size:17 final size:16
Alignment explanation
Indices: 74037--74083 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
74027 TTAGGATCAC
74037 CACTAGTGATCTAAGAT
1 CACTAGTGATC-AAGAT
*
74054 CACCAGTGATGCAAGAT
1 CACTAGTGAT-CAAGAT
*
74071 CACTGGTGATCAA
1 CACTAGTGATCAA
74084 AGATTACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 22 0.85
18 1 0.04
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (16 bp):
CACTAGTGATCAAGAT
Found at i:76301 original size:3 final size:3
Alignment explanation
Indices: 76283--76330 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
76273 ATACTGATAT
76283 ATA AT- ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
76329 AT
1 AT
76331 TAATTGAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:84581 original size:130 final size:123
Alignment explanation
Indices: 84345--84598 Score: 384
Period size: 122 Copynumber: 2.0 Consensus size: 123
84335 TATTGTTTAA
* *
84345 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTGATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
84410 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
84467 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C---T-T-
* *
84532 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATA
60 TA--TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
84597 T
123 T
84598 A
1 A
84599 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
122 53 0.45
123 1 0.01
126 1 0.01
127 1 0.01
128 2 0.02
130 48 0.41
131 12 0.10
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:84620 original size:14 final size:13
Alignment explanation
Indices: 84584--84622 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
84574 TATATATTAG
84584 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
84597 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
84611 AATTTTTTAAAT
1 AATTTTTTAAAT
84623 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:85545 original size:73 final size:73
Alignment explanation
Indices: 85425--85564 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 73
85415 GAAGACTAGT
* * *
85425 TATATTAAAAAGTACGTTCACCTGTAAAATTTTTGAATCGCCCATTATATCCTTATTTTTCAAAT
1 TATATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTTTCAAAT
85490 ATCTATAC
66 ATCTATAC
* * * *
85498 TATATTAAATAGTACGTTCAGCTGTAAAACTTTTGAATCACCTATTATACCCTTATTTTTTAAAT
1 TATATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTTTCAAAT
85563 AT
66 AT
85565 ATTTCTTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.42
Consensus pattern (73 bp):
TATATTAAAAAGTACGTTCACCTGTAAAACTTTTGAATCACCCATTATACCCTTATTTTTCAAAT
ATCTATAC
Done.