Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006319.1 Corchorus capsularis cultivar CVL-1 contig06340, 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: 51049
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1664 original size:15 final size:15
Alignment explanation
Indices: 1652--1682 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1642 TTATTAGGAT
1652 TATTATGATTAGGGA
1 TATTATGATTAGGGA
*
1667 TATTATGATTTGGGA
1 TATTATGATTAGGGA
1682 T
1 T
1683 TGCCGGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
TATTATGATTAGGGA
Found at i:2155 original size:109 final size:109
Alignment explanation
Indices: 1954--2255 Score: 435
Period size: 109 Copynumber: 2.7 Consensus size: 109
1944 GCTTAACTAT
* * *
1954 TATAGTTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAAT
1 TATAATTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAAT
*
2019 TGCTTTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATA
61 TACTTTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATA
2068 TATAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTT
1 TATAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTT
* *
2133 TATTTTTACCAAAAATTTTGGATATATTAAAATTTTTTCTAATA
66 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATA
* *
2177 TACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTA
1 TATAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTA
*
2241 TTTTTATTTTTACCA
63 -CTTTATTTTTACCA
2256 TTTTAATTTA
Statistics
Matches: 175, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
108 1 0.01
109 123 0.70
110 8 0.05
111 5 0.03
112 13 0.07
114 25 0.14
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TATAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTT
TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATA
Found at i:3587 original size:14 final size:14
Alignment explanation
Indices: 3568--3607 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3558 GTCGGGTTGG
*
3568 ATTTGGGTTTGGTT
1 ATTTGGGTTAGGTT
3582 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
3596 AGTTTCGGGTTA
1 A-TTT-GGGTTA
3608 AGGAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.03, G:0.35, T:0.50
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:3790 original size:16 final size:17
Alignment explanation
Indices: 3769--3805 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
3759 TGAGCCTCCG
3769 ATTTTCAGG-TTC-AATT
1 ATTTTC-GGATTCAAATT
3785 ATTTTCGGATTCAAATT
1 ATTTTCGGATTCAAATT
3802 ATTT
1 ATTT
3806 AAATATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 9 0.47
17 8 0.42
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (17 bp):
ATTTTCGGATTCAAATT
Found at i:8170 original size:15 final size:15
Alignment explanation
Indices: 8146--8175 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8136 TCCAAAGCCC
8146 GGCGCCCGACCACCT
1 GGCGCCCGACCACCT
*
8161 GGCGCTCGACCACCT
1 GGCGCCCGACCACCT
8176 ATGACCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.27, T:0.10
Consensus pattern (15 bp):
GGCGCCCGACCACCT
Found at i:8252 original size:14 final size:13
Alignment explanation
Indices: 8217--8312 Score: 53
Period size: 13 Copynumber: 7.3 Consensus size: 13
8207 CCAGCTGGCA
8217 CTCCACACGTGAC
1 CTCCACACGTGAC
8230 CTCCA-ACGTACGAC
1 CTCCACACGT--GAC
*
8244 C-CCACACGTGAT
1 CTCCACACGTGAC
8256 CTCCGA-A-GT-AC
1 CTCC-ACACGTGAC
8267 AACTCCACACGTGAC
1 --CTCCACACGTGAC
8282 CTCC-CACG-GATAC
1 CTCCACACGTG--AC
*
8295 CTTCAACACGTGAC
1 C-TCCACACGTGAC
8309 CTCC
1 CTCC
8313 GAAGTACAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 30
0.65 0.04 0.31
Matches are distributed among these distances:
11 2 0.03
12 14 0.22
13 25 0.39
14 16 0.25
15 6 0.09
16 1 0.02
ACGTcount: A:0.26, C:0.43, G:0.15, T:0.17
Consensus pattern (13 bp):
CTCCACACGTGAC
Found at i:8259 original size:26 final size:26
Alignment explanation
Indices: 8219--8337 Score: 116
Period size: 26 Copynumber: 4.5 Consensus size: 26
8209 AGCTGGCACT
*
8219 CCACACGTGACCTCC-AACGTACGACC
1 CCACACGTGACCTCCGAA-GTACAACC
* *
8245 CCACACGTGATCTCCGAAGTACAACT
1 CCACACGTGACCTCCGAAGTACAACC
* * * *
8271 CCACACGTGACCTCCCACGGA-TACC
1 CCACACGTGACCTCCGAAGTACAACC
*
8296 TTCAACACGTGACCTCCGAAGTACAACC
1 --CCACACGTGACCTCCGAAGTACAACC
*
8324 CCACATGTGACCTC
1 CCACACGTGACCTC
8338 GAGGTGCGAC
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
25 2 0.03
26 49 0.67
27 19 0.26
28 3 0.04
ACGTcount: A:0.28, C:0.41, G:0.15, T:0.16
Consensus pattern (26 bp):
CCACACGTGACCTCCGAAGTACAACC
Found at i:8318 original size:53 final size:52
Alignment explanation
Indices: 8216--8337 Score: 156
Period size: 53 Copynumber: 2.3 Consensus size: 52
8206 GCCAGCTGGC
* * *
8216 ACTCCACACGTGACCTCCAACGTACGACCCCACACGTGATCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGACCTCCGAAGTACA
* *
8268 ACTCCACACGTGACCTCCCACGGA-TACCTTCAACACGTGACCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACC--CAACACGTGACCTCCGAAGTACA
* *
8321 ACCCCACATGTGACCTC
1 ACTCCACACGTGACCTC
8338 GAGGTGCGAC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 3 0.05
52 22 0.36
53 36 0.59
ACGTcount: A:0.28, C:0.41, G:0.15, T:0.16
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGACCTCCGAAGTACA
Found at i:9148 original size:2 final size:2
Alignment explanation
Indices: 9141--9175 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9131 ACCGAAAAAG
9141 AT 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 AT A
9176 AATACTCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11771 original size:41 final size:41
Alignment explanation
Indices: 11708--11792 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
11698 TATGAAACCC
*
11708 AAACCCTAACAAACAATATAAACCCTA-AGTGAGAT-AAAAG
1 AAACCCTAAAAAACAATATAAACCCTAGA-TGAGATAAAAAG
11748 AAACCCTCAAAAAACACAT-TAAACCCTAGATGAGATAAAAAG
1 AAACCCT-AAAAAACA-ATATAAACCCTAGATGAGATAAAAAG
11790 AAA
1 AAA
11793 AAATATGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
40 7 0.17
41 22 0.55
42 11 0.28
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.14
Consensus pattern (41 bp):
AAACCCTAAAAAACAATATAAACCCTAGATGAGATAAAAAG
Found at i:16150 original size:31 final size:30
Alignment explanation
Indices: 16108--16166 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
16098 ACCCCATTAG
*
16108 ATGCCAATTTAGGCCTAAAACTTTAAAGAA
1 ATGCCAATTTAGGCCTAAAACCTTAAAGAA
* *
16138 ATGCTCAATTTAGGCTTAAAGCCTTAAAG
1 ATGC-CAATTTAGGCCTAAAACCTTAAAG
16167 TCTAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (30 bp):
ATGCCAATTTAGGCCTAAAACCTTAAAGAA
Found at i:23608 original size:2 final size:2
Alignment explanation
Indices: 23601--23625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23591 AATATTGGAA
23601 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 A
23626 ACGACGAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26981 original size:33 final size:33
Alignment explanation
Indices: 26914--27052 Score: 203
Period size: 33 Copynumber: 4.3 Consensus size: 33
26904 TTCTCGTCAC
* * *
26914 CCAAAACAGATTTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
26944 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
26977 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
27010 CCAAAACAGAATTATTTGCAATGCGATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
27043 CCAAAACAGA
1 CCAAAACAGA
27053 TTTGTTTTCA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.21
33 77 0.79
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:27080 original size:66 final size:66
Alignment explanation
Indices: 26941--27085 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
26931 TCAATGCCAT
* * * *
26941 CAACCAAAACAGGATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATGCTATGA
1 CAACCAAAACAGAATTATTTGCAATGCGATGATCAACCAAAACAAAATTATTTGCAATACAATGA
*
27006 T
66 G
* * * * *
27007 CAACCAAAACAGAATTATTTGCAATGCGATGATCAACCAAAACAGATTTGTTTTC-ATCACAATT
1 CAACCAAAACAGAATTATTTGCAATGCGATGATCAACCAAAACAAAATTATTTGCAAT-ACAATG
27071 AG
65 AG
*
27073 CATCCAAAACAGA
1 CAACCAAAACAGA
27086 TTTAGTATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 65 0.97
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.26
Consensus pattern (66 bp):
CAACCAAAACAGAATTATTTGCAATGCGATGATCAACCAAAACAAAATTATTTGCAATACAATGA
G
Found at i:27115 original size:33 final size:33
Alignment explanation
Indices: 27078--27182 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
27068 ATTAGCATCC
*
27078 AAAACAGATTTAGTATCATTACAAACAACACTT
1 AAAACAGATTTAGTATCATTGCAAACAACACTT
*
27111 AAAACAGATTTAGTGTCATTGCAAACAACAC-T
1 AAAACAGATTTAGTATCATTGCAAACAACACTT
* * *
27143 CAAACTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAAC-AGATTTAGTATCATTGCAAACAACACT-T
27177 AAAACA
1 AAAACA
27183 CTCTTTGCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 5 0.08
33 52 0.84
34 5 0.08
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATTGCAAACAACACTT
Found at i:42232 original size:16 final size:15
Alignment explanation
Indices: 42193--42237 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
42183 GCTGAAAGAT
**
42193 TAAGTACTGAATTTT
1 TAAGTACTGAATTCA
42208 TAA-TACTGAATCTCA
1 TAAGTACTGAAT-TCA
42223 TAAGTACTGAATTCA
1 TAAGTACTGAATTCA
42238 AACTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (15 bp):
TAAGTACTGAATTCA
Found at i:47993 original size:19 final size:19
Alignment explanation
Indices: 47969--48013 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
47959 AGAAATTTGA
*
47969 AAACTTATAATTTGGAACT
1 AAACTTAAAATTTGGAACT
* *
47988 AAACTTTAAAATTTGTAATT
1 AAAC-TTAAAATTTGGAACT
48008 AAACTT
1 AAACTT
48014 TTGTTACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (19 bp):
AAACTTAAAATTTGGAACT
Found at i:48002 original size:20 final size:20
Alignment explanation
Indices: 47977--48014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47967 GAAAACTTAT
47977 AATTTGGAACTAAACTTTAA
1 AATTTGGAACTAAACTTTAA
* *
47997 AATTTGTAATTAAACTTT
1 AATTTGGAACTAAACTTT
48015 TGTTACATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
AATTTGGAACTAAACTTTAA
Found at i:48281 original size:16 final size:16
Alignment explanation
Indices: 48256--48289 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48246 AATAAATTAG
48256 TTTTAATATTATATTT
1 TTTTAATATTATATTT
* *
48272 TTTTAGTATTATCTTT
1 TTTTAATATTATATTT
48288 TT
1 TT
48290 ATTTTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAATATTATATTT
Done.