Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014985.1 Corchorus capsularis cultivar CVL-1 contig15006, 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: 174730
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:26453 original size:13 final size:14
Alignment explanation
Indices: 26435--26468 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26425 GAAAAATTAT
26435 AAGCCCAAT-AATA
1 AAGCCCAATAAATA
26448 AAGCCCAATAAATA
1 AAGCCCAATAAATA
*
26462 AATCCCA
1 AAGCCCA
26469 GAACAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.53, C:0.26, G:0.06, T:0.15
Consensus pattern (14 bp):
AAGCCCAATAAATA
Found at i:34405 original size:30 final size:29
Alignment explanation
Indices: 34355--34415 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
34345 AAATAAAAAC
* * **
34355 TACCCATTTTAGATAAAAACTGTCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
34384 TACCAATTTTAGAAAAAAAACTACCCATTA
1 TACCAATTTTAG-AAAAAAACTACCCATTA
34414 TA
1 TA
34416 AGATAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (29 bp):
TACCAATTTTAGAAAAAAACTACCCATTA
Found at i:35211 original size:6 final size:6
Alignment explanation
Indices: 35200--35225 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35190 TTTGCTATTA
35200 TACTAG TACTAG TACTAG TACTAG TA
1 TACTAG TACTAG TACTAG TACTAG TA
35226 AGACATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
TACTAG
Found at i:39937 original size:12 final size:12
Alignment explanation
Indices: 39905--39943 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39895 ATGGAATTAA
39905 ATATCCGTCG--
1 ATATCCGTCGAT
39915 ATA-CC-TCGAT
1 ATATCCGTCGAT
39925 ATATCCGTCGAT
1 ATATCCGTCGAT
39937 ATATCCG
1 ATATCCG
39944 AAATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:46169 original size:18 final size:19
Alignment explanation
Indices: 46146--46182 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
46136 ATCCCACATA
46146 TAGGTAATTAGAA-TCATC
1 TAGGTAATTAGAATTCATC
46164 TAGGTAATTAGAATTCATC
1 TAGGTAATTAGAATTCATC
46183 CACACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
TAGGTAATTAGAATTCATC
Found at i:68151 original size:33 final size:32
Alignment explanation
Indices: 68055--68171 Score: 136
Period size: 33 Copynumber: 3.8 Consensus size: 32
68045 AAAATTGTTC
* *
68055 CTGGTGCTCTGTTTCTCTTGTTAA-TTTTTAT
1 CTGGTACTCTGTTTCTCTTGTTAATTTTTTTT
** *
68086 CTGGTACTCTG-TTCT-TACTT--TTTTTTTC
1 CTGGTACTCTGTTTCTCTTGTTAATTTTTTTT
68114 CTGGTACTCTGTTTCTCTTGTTAACTTTTTTTT
1 CTGGTACTCTGTTTCTCTTGTTAA-TTTTTTTT
*
68147 CTGGTACTCTGTTTTTCTTGTTAAT
1 CTGGTACTCTGTTTCTCTTGTTAAT
68172 AACAATACTA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
28 16 0.23
29 7 0.10
30 7 0.10
31 10 0.14
32 1 0.01
33 30 0.42
ACGTcount: A:0.09, C:0.18, G:0.14, T:0.59
Consensus pattern (32 bp):
CTGGTACTCTGTTTCTCTTGTTAATTTTTTTT
Found at i:68163 original size:16 final size:16
Alignment explanation
Indices: 68108--68164 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
68098 TCTTACTTTT
68108 TTTTTCCTGGTACTCTG
1 TTTTT-CTGGTACTCTG
* * *
68125 TTTCTCTTGTTAACT-TT
1 TTTTTC-TGGT-ACTCTG
68142 TTTTTCTGGTACTCTG
1 TTTTTCTGGTACTCTG
68158 TTTTTCT
1 TTTTTCT
68165 TGTTAATAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 13 0.42
18 3 0.10
ACGTcount: A:0.07, C:0.19, G:0.12, T:0.61
Consensus pattern (16 bp):
TTTTTCTGGTACTCTG
Found at i:76707 original size:2 final size:2
Alignment explanation
Indices: 76700--76744 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
76690 ACTTGCAAAC
* *
76700 AT AT AT AT AT AT AT AT AG AT AT AG AT AT AT 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
76742 AT A
1 AT A
76745 ATTATAATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:79246 original size:10 final size:10
Alignment explanation
Indices: 79234--79269 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
79224 AATTTAATAT
*
79234 GGATATTTAT
1 GGATATTTAC
79244 GGATATTTAC
1 GGATATTTAC
79254 GGATATTTAC
1 GGATATTTAC
79264 GGATAT
1 GGATAT
79270 ATCGAGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:79362 original size:12 final size:12
Alignment explanation
Indices: 79345--79369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79335 ATCGAGGGGT
79345 ACAGATATATCG
1 ACAGATATATCG
79357 ACAGATATATCG
1 ACAGATATATCG
79369 A
1 A
79370 GGTATAGACG
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
ACAGATATATCG
Found at i:80076 original size:34 final size:34
Alignment explanation
Indices: 80004--80089 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
79994 AAAATTGTTA
* * * **
80004 TTTTTCCCCCGGTACTCTGTTTCTCTTGTTGATT
1 TTTTTTCCCTGGTACTCTGTTTCTCTTGTTAACC
80038 TTTTTTCCCTGGTACTCTGTTTCTCTTGTTAACC
1 TTTTTTCCCTGGTACTCTGTTTCTCTTGTTAACC
80072 -TTTTT--CTGGTACTCTGTT
1 TTTTTTCCCTGGTACTCTGTT
80090 ACATCCGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
31 13 0.28
33 5 0.11
34 29 0.62
ACGTcount: A:0.07, C:0.24, G:0.14, T:0.55
Consensus pattern (34 bp):
TTTTTTCCCTGGTACTCTGTTTCTCTTGTTAACC
Found at i:103294 original size:15 final size:17
Alignment explanation
Indices: 103259--103299 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
103249 CCTTTATGCA
*
103259 TTCCAATCTTTGCCAAT
1 TTCCAATCTTTGCCAAC
103276 TTCCAAT-TTT-CCAAC
1 TTCCAATCTTTGCCAAC
103291 TTCCAATCT
1 TTCCAATCT
103300 ATATCTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.41
Consensus pattern (17 bp):
TTCCAATCTTTGCCAAC
Found at i:107528 original size:35 final size:35
Alignment explanation
Indices: 107489--107558 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
107479 ATAATTATGG
* *
107489 GACCATATAATTAAAGCCAAGTGTTTGATGGATGA
1 GACCATATAACTAAAGCCAAGTGTTTGATGCATGA
* *
107524 GACCATTTGACTAAAGCCAAGTGTTTGATGCATGA
1 GACCATATAACTAAAGCCAAGTGTTTGATGCATGA
107559 TGAAACAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (35 bp):
GACCATATAACTAAAGCCAAGTGTTTGATGCATGA
Found at i:108012 original size:26 final size:25
Alignment explanation
Indices: 107954--108020 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
107944 CAGCCAGCTG
* *
107954 ACACTCCACGCGTGACCTCCAGCGT
1 ACACTCCACACGTGACCTCCAGAGT
107979 ACAACTCCACACGTGACCTCCAACGAGT
1 AC-ACTCCACACGTGACCTCC-A-GAGT
108007 AC-CTCCACACGTGA
1 ACACTCCACACGTGA
108021 TACGACTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.05
26 29 0.78
27 1 0.03
28 5 0.14
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.15
Consensus pattern (25 bp):
ACACTCCACACGTGACCTCCAGAGT
Found at i:114385 original size:116 final size:117
Alignment explanation
Indices: 114239--114472 Score: 425
Period size: 116 Copynumber: 2.0 Consensus size: 117
114229 TGAAGCTTGT
*
114239 ATCATTCTTCTTCCTTCCATCCTTATTTGTTCCATACTTCTGCAATTTATAATTCCCAACAAGTT
1 ATCATTCTTCTTCCTTCCATCCTCATTTGTTCCATACTTCTGCAATTTATAATTCCCAACAAGTT
114304 TAGATGCGTCATATTTACCAATGATAAAATATCCAATTCCTTCGACTCCACA
66 TAGATGCGTCATATTTACCAATGATAAAATATCCAATTCCTTCGACTCCACA
* *
114356 ATCATTCTTC-TCCTTCCATCCTCATTTGTTCCATACTTCTGCAATTTCTAATTCCCAGCAAGTT
1 ATCATTCTTCTTCCTTCCATCCTCATTTGTTCCATACTTCTGCAATTTATAATTCCCAACAAGTT
*
114420 TAGATGCGTCATATTTACCAATGATGAAATATCCAATTCCTTCGACTCCACA
66 TAGATGCGTCATATTTACCAATGATAAAATATCCAATTCCTTCGACTCCACA
114472 A
1 A
114473 ACCCATTGAG
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 103 0.91
117 10 0.09
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (117 bp):
ATCATTCTTCTTCCTTCCATCCTCATTTGTTCCATACTTCTGCAATTTATAATTCCCAACAAGTT
TAGATGCGTCATATTTACCAATGATAAAATATCCAATTCCTTCGACTCCACA
Found at i:120722 original size:117 final size:117
Alignment explanation
Indices: 120516--120727 Score: 415
Period size: 117 Copynumber: 1.8 Consensus size: 117
120506 TACCATGTAT
120516 AATTCAATTTCCTTATCAGGTAATTTTCCTTTTTACAATATATCTTAGAAGTTTATTATTATAAT
1 AATTCAATTTCCTTATCAGGTAATTTTCCTTTTTACAATATATCTTAGAAGTTTATTATTATAAT
*
120581 AATAATAGTAGTGTGAACTAAAGTTTTTGTATATGCCTCAATATCCAAATAC
66 AACAATAGTAGTGTGAACTAAAGTTTTTGTATATGCCTCAATATCCAAATAC
120633 AATTCAATTTCCTTATCAGGTAATTTTCCTTTTTACAATATATCTTAGAAGTTTATTATTATAAT
1 AATTCAATTTCCTTATCAGGTAATTTTCCTTTTTACAATATATCTTAGAAGTTTATTATTATAAT
120698 AACAATAGTAGTGTGAACTAAAGTTTTTGT
66 AACAATAGTAGTGTGAACTAAAGTTTTTGT
120728 GTTTTTACTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 94 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (117 bp):
AATTCAATTTCCTTATCAGGTAATTTTCCTTTTTACAATATATCTTAGAAGTTTATTATTATAAT
AACAATAGTAGTGTGAACTAAAGTTTTTGTATATGCCTCAATATCCAAATAC
Found at i:137904 original size:15 final size:15
Alignment explanation
Indices: 137884--137919 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
137874 CGGGAATCAC
137884 GATTATCATACCTCT
1 GATTATCATACCTCT
137899 GATTATCATACCTCT
1 GATTATCATACCTCT
*
137914 GGTTAT
1 GATTAT
137920 TTTGTCCACC
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:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (15 bp):
GATTATCATACCTCT
Found at i:143049 original size:33 final size:33
Alignment explanation
Indices: 143009--143093 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
142999 CCTGGCCGGA
*
143009 GGGTTATAGTA-TCT-GGAAAACGGCCCTGCTAAC
1 GGGTTATAGTAGT-TAGCAAAA-GGCCCTGCTAAC
**
143042 GGGTTATAGTAGTTAGCTTAAGGCCCTGCTAAC
1 GGGTTATAGTAGTTAGCAAAAGGCCCTGCTAAC
143075 GGGTTATAGTAGTTAGCAA
1 GGGTTATAGTAGTTAGCAA
143094 TATGTCGATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 41 0.91
34 4 0.09
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (33 bp):
GGGTTATAGTAGTTAGCAAAAGGCCCTGCTAAC
Found at i:143457 original size:20 final size:20
Alignment explanation
Indices: 143432--143492 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
143422 AATCGTTTAT
143432 TGATTTATGTTAGTTTTGTG
1 TGATTTATGTTAGTTTTGTG
* *
143452 TGA-TT-TG--AATATTGT-
1 TGATTTATGTTAGTTTTGTG
143467 TGATTTATGTTAGTTTTGTG
1 TGATTTATGTTAGTTTTGTG
143487 TGATTT
1 TGATTT
143493 GAATATTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 8 0.25
17 2 0.06
18 2 0.06
19 8 0.25
20 9 0.28
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (20 bp):
TGATTTATGTTAGTTTTGTG
Found at i:143472 original size:35 final size:35
Alignment explanation
Indices: 143431--143501 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
143421 AAATCGTTTA
143431 TTGATTTATGTTAGTTTTGTGTGATTTGAATATTG
1 TTGATTTATGTTAGTTTTGTGTGATTTGAATATTG
143466 TTGATTTATGTTAGTTTTGTGTGATTTGAATATTG
1 TTGATTTATGTTAGTTTTGTGTGATTTGAATATTG
143501 T
1 T
143502 GATGGAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.58
Consensus pattern (35 bp):
TTGATTTATGTTAGTTTTGTGTGATTTGAATATTG
Found at i:143736 original size:2 final size:2
Alignment explanation
Indices: 143729--143761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
143719 AGCTATAAAG
143729 AT AT AT 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 AT AT AT A
143762 ATTATGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:169691 original size:3 final size:3
Alignment explanation
Indices: 169683--169713 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
169673 GTGATATATT
169683 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
169714 GTTGAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.