Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007448.1 Corchorus capsularis cultivar CVL-1 contig07469, 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: 104101
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1321 original size:15 final size:16
Alignment explanation
Indices: 1298--1343 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 16
1288 TTCGAAATTA
1298 AATTCCTTTCCTTGTT
1 AATTCCTTTCCTTGTT
1314 AA-TCCTTT-C-TGTT
1 AATTCCTTTCCTTGTT
*
1327 AATTCCCTTCTCTTGTT
1 AATTCCTTTC-CTTGTT
1344 TCATCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 6 0.24
16 3 0.12
17 4 0.16
ACGTcount: A:0.13, C:0.26, G:0.07, T:0.54
Consensus pattern (16 bp):
AATTCCTTTCCTTGTT
Found at i:11261 original size:36 final size:37
Alignment explanation
Indices: 11212--11296 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
11202 AAACTACAGC
** * * *
11212 GTCACAAAAATTGACTTCACTAGTGAGCAAC-TCGTT
1 GTCACAACTATTGAATTCAATAGTGACCAACTTCGTT
* *
11248 GTCACAACTATTGAATTCAATAGTGACCACCTTTGTT
1 GTCACAACTATTGAATTCAATAGTGACCAACTTCGTT
11285 GTCACAACTATT
1 GTCACAACTATT
11297 TGATTGAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 25 0.61
37 16 0.39
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (37 bp):
GTCACAACTATTGAATTCAATAGTGACCAACTTCGTT
Found at i:15240 original size:35 final size:35
Alignment explanation
Indices: 15200--15267 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
15190 AAATAAGGGT
15200 CTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
1 CTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
15235 CTGATCTTTTAATTTGGCCAAATAAGGGCCTAA
1 CTGATCTTTTAATTTGGCCAAATAAGGGCCTAA
15268 GGTGTGATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (35 bp):
CTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
Found at i:20462 original size:37 final size:37
Alignment explanation
Indices: 20412--20482 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
20402 ATTCTACTCA
20412 AGAATCAGAAAGTGCAATCTAATTTAGTAGTACTTCC
1 AGAATCAGAAAGTGCAATCTAATTTAGTAGTACTTCC
20449 AGAATCAGAAAGTGCAATCTAATTTAGTAGTACT
1 AGAATCAGAAAGTGCAATCTAATTTAGTAGTACT
20483 AATACAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (37 bp):
AGAATCAGAAAGTGCAATCTAATTTAGTAGTACTTCC
Found at i:26666 original size:22 final size:22
Alignment explanation
Indices: 26626--26668 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
26616 TTTTTATTTT
*
26626 ATAAAATAAAAAAATAAAAAAA
1 ATAAAATAAAAAAAGAAAAAAA
* *
26648 ATAAAATGAAAAACGAAAAAA
1 ATAAAATAAAAAAAGAAAAAA
26669 TTAAAGTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
ATAAAATAAAAAAAGAAAAAAA
Found at i:28354 original size:2 final size:2
Alignment explanation
Indices: 28349--28389 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
28339 ACACACACAC
*
28349 AT AT AT AT AT AT AT AT AT AT AT -T AT AC AT CAT AT -T 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
28390 TTAATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31108 original size:2 final size:2
Alignment explanation
Indices: 31103--31131 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31093 GTTGGCTTAT
31103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31132 TTCCAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31691 original size:12 final size:12
Alignment explanation
Indices: 31674--31698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31664 GACACCGCTC
31674 CACTTGAACTCG
1 CACTTGAACTCG
31686 CACTTGAACTCG
1 CACTTGAACTCG
31698 C
1 C
31699 GTCGCACGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (12 bp):
CACTTGAACTCG
Found at i:39949 original size:1 final size:1
Alignment explanation
Indices: 39943--40028 Score: 82
Period size: 1 Copynumber: 86.0 Consensus size: 1
39933 GCAAACATTT
** * * * * * *
39943 AAAAAAAAAAAAAAAAAAAAAACCAAAAAAAAACAAAACAAAACAAAACAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
40008 AACAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
40029 CACTTCTACA
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:58429 original size:46 final size:46
Alignment explanation
Indices: 58362--58456 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
58352 CCGAAATGGC
58362 TTAACACTACACCACATGGTCTAGACCTAATTGGGTTGATATATAT
1 TTAACACTACACCACATGGTCTAGACCTAATTGGGTTGATATATAT
58408 TTAACACTACACCACATGGTCTAGACCTAATTGGGTTGATATATAT
1 TTAACACTACACCACATGGTCTAGACCTAATTGGGTTGATATATAT
58454 TTA
1 TTA
58457 TGTAAATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (46 bp):
TTAACACTACACCACATGGTCTAGACCTAATTGGGTTGATATATAT
Found at i:59188 original size:109 final size:109
Alignment explanation
Indices: 58992--59266 Score: 444
Period size: 109 Copynumber: 2.5 Consensus size: 109
58982 ACTATTATAG
* * *
58992 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCCAATATCTTTATAATTACTT
59057 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
59106 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCCAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCCAATATCTTTATAATTACTTTATTT
*
59171 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
59215 CTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCCAATATCTTTATA
59267 TATATATATA
Statistics
Matches: 155, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
108 6 0.04
109 123 0.79
110 3 0.02
111 2 0.01
114 21 0.14
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCCAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:61688 original size:11 final size:11
Alignment explanation
Indices: 61672--61701 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
61662 TTTCCTTCAT
61672 CTTTTTTCGCG
1 CTTTTTTCGCG
61683 CTTTTTTCGCG
1 CTTTTTTCGCG
61694 CTTTTTTC
1 CTTTTTTC
61702 CTTCTCAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.13, T:0.60
Consensus pattern (11 bp):
CTTTTTTCGCG
Found at i:67075 original size:47 final size:47
Alignment explanation
Indices: 67021--67110 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
67011 AGTGGTCATT
67021 TATACAATTTTTGTGTACTCTTGCATCATATATTGCTCTTGAAGATA
1 TATACAATTTTTGTGTACTCTTGCATCATATATTGCTCTTGAAGATA
* * *
67068 TATACAATTTTTGTTTATTCTTGCTTCATATATTGCTCTTGAA
1 TATACAATTTTTGTGTACTCTTGCATCATATATTGCTCTTGAA
67111 CCTCGTGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (47 bp):
TATACAATTTTTGTGTACTCTTGCATCATATATTGCTCTTGAAGATA
Found at i:75351 original size:31 final size:31
Alignment explanation
Indices: 75301--75438 Score: 159
Period size: 31 Copynumber: 4.5 Consensus size: 31
75291 ACGGCGTCCG
* *
75301 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* * *
75332 ATGTGGCATGCTACATGTACAAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* * * *
75363 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
** * *
75394 ACGTGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
75425 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
75439 GTGCACAAAA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGAC
Found at i:75438 original size:62 final size:62
Alignment explanation
Indices: 75301--75441 Score: 203
Period size: 62 Copynumber: 2.3 Consensus size: 62
75291 ACGGCGTCCG
* *
75301 ACGTGGCACGCCACGTGTACCAAAAAGTGACATGTGGCATGCTACATGTACAAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTACAAAAAAGTGAC
* * * *
75363 ACATGTCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTTTCAAAAAA-TGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATG-TACAAAAAAGTGAC
*
75425 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
75442 CACAAAAGGA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 61 0.88
63 8 0.12
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (62 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCACATGTACAAAAAAGTGAC
Found at i:76499 original size:7 final size:7
Alignment explanation
Indices: 76484--76516 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
76474 ATCTTACAAC
76484 TTATATAT
1 TTAT-TAT
76492 TTATTAT
1 TTATTAT
76499 TTATTAT
1 TTATTAT
76506 TTATTAT
1 TTATTAT
76513 TTAT
1 TTAT
76517 AGGTGAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTAT
Found at i:80502 original size:23 final size:23
Alignment explanation
Indices: 80476--80520 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
80466 TTATTTTTGA
*
80476 TAGAAAATAAGTTTAAATTTATT
1 TAGAAAAAAAGTTTAAATTTATT
80499 TAGAAAAAAAGTTTAAATTTAT
1 TAGAAAAAAAGTTTAAATTTAT
80521 CCAGATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (23 bp):
TAGAAAAAAAGTTTAAATTTATT
Found at i:89888 original size:44 final size:44
Alignment explanation
Indices: 89837--89934 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
89827 AAAACCAAAG
89837 CATCTCTCGATTACATTCCTTGCCGAGGAATGCCTGTAATTGAA
1 CATCTCTCGATTACATTCCTTGCCGAGGAATGCCTGTAATTGAA
*
89881 TATCTCTCGATTACATTCCTTGCCGAGGAATGCCTGTAATTGAA
1 CATCTCTCGATTACATTCCTTGCCGAGGAATGCCTGTAATTGAA
*
89925 CAACTCTCGA
1 CATCTCTCGA
89935 GGCGTTCTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (44 bp):
CATCTCTCGATTACATTCCTTGCCGAGGAATGCCTGTAATTGAA
Found at i:91162 original size:35 final size:35
Alignment explanation
Indices: 91123--91231 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
91113 CTACCAAAAT
*
91123 ATTAAACATATGTACTAACAGCAAGCAAAACCACA
1 ATTAAACCTATGTACTAACAGCAAGCAAAACCACA
* * * * ** *
91158 ATTAAACCTCTGTACCACCAGGAAATTAAAGA-AACA
1 ATTAAACCTATGTACTAACA-GCAAGCAAA-ACCACA
** *
91194 AAAAAACCTATGTACTAGCAGCAAGCAAAACCACA
1 ATTAAACCTATGTACTAACAGCAAGCAAAACCACA
91229 ATT
1 ATT
91232 GCTACCAAAA
Statistics
Matches: 52, Mismatches: 19, Indels: 6
0.68 0.25 0.08
Matches are distributed among these distances:
34 1 0.02
35 26 0.50
36 24 0.46
37 1 0.02
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (35 bp):
ATTAAACCTATGTACTAACAGCAAGCAAAACCACA
Done.