Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020346.1 Corchorus olitorius cultivar O-4 contig20379, 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: 30257
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--34 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 C
2 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
35 GATAGAGGTG
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:368 original size:2 final size:2
Alignment explanation
Indices: 357--393 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
347 ATGATTACCC
357 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394 ATAACATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5000 original size:65 final size:65
Alignment explanation
Indices: 4913--5112 Score: 215
Period size: 65 Copynumber: 3.0 Consensus size: 65
4903 ATAAAATGGA
* *
4913 CAACGATTTTTTTACTTTAGGCAACATCTTTTGATAATTTTAAGCAACACTATTTTCTACTATAT
1 CAACGA-TTTTTTACTTAAGGCAACATCTTTTGATAATTGTAAGCAACACTATTTTCTACTATAT
4978 G
65 G
* ** * * * * *
4979 CAACAATTGTTTTAC-TAAGGCAACCCCCTTTAATAATTGTATGCAACACTATTTTCCAATATAT
1 CAACGATT-TTTTACTTAAGGCAACATCTTTTGATAATTGTAAGCAACACTATTTTCTACTATAT
5043 G
65 G
** * * *
5044 CAACGATTTTCTTACTTCTGGCAACAAT-TTTTGATAATTGCAAGCAACACTATTATCTACAATA
1 CAACGATTTT-TTACTTAAGGCAAC-ATCTTTTGATAATTGTAAGCAACACTATTTTCTACTATA
5108 TG
64 TG
5110 CAA
1 CAA
5113 TGCTTTTGCA
Statistics
Matches: 107, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
64 2 0.02
65 54 0.50
66 51 0.48
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (65 bp):
CAACGATTTTTTACTTAAGGCAACATCTTTTGATAATTGTAAGCAACACTATTTTCTACTATATG
Found at i:8059 original size:24 final size:24
Alignment explanation
Indices: 8032--8089 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
8022 CATGTTCTTG
8032 AATTTCAGCAGCCCCATCTTCATC
1 AATTTCAGCAGCCCCATCTTCATC
8056 AATTTCAGCAGCCCCATCTTCATC
1 AATTTCAGCAGCCCCATCTTCATC
8080 AATTTCAGCA
1 AATTTCAGCA
8090 TCATTCTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.29
Consensus pattern (24 bp):
AATTTCAGCAGCCCCATCTTCATC
Found at i:10378 original size:12 final size:12
Alignment explanation
Indices: 10361--10387 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10351 AAAATAAATA
10361 TATACTTTACAT
1 TATACTTTACAT
10373 TATACTTTACAT
1 TATACTTTACAT
10385 TAT
1 TAT
10388 TATATACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TATACTTTACAT
Found at i:20835 original size:13 final size:13
Alignment explanation
Indices: 20817--20841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20807 TAATCATATA
20817 CTTGGGTATTTCG
1 CTTGGGTATTTCG
20830 CTTGGGTATTTC
1 CTTGGGTATTTC
20842 AGATATCCGT
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:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (13 bp):
CTTGGGTATTTCG
Found at i:21655 original size:17 final size:16
Alignment explanation
Indices: 21608--21658 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
21598 CATGTAATCT
*
21608 TTGATTACCGGTGATC
1 TTGATTACTGGTGATC
*
21624 TTGCATCACTGGTGATC
1 TTG-ATTACTGGTGATC
*
21641 TTAGATTACTAGTGATC
1 TT-GATTACTGGTGATC
21658 T
1 T
21659 GGGGGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (16 bp):
TTGATTACTGGTGATC
Found at i:22105 original size:7 final size:7
Alignment explanation
Indices: 22095--22144 Score: 73
Period size: 7 Copynumber: 7.0 Consensus size: 7
22085 ATAATTTGTA
22095 ATCTACT
1 ATCTACT
22102 ATCTACT
1 ATCTACT
*
22109 ATCTATAT
1 ATCTA-CT
*
22117 ATCTACA
1 ATCTACT
22124 ATCTACT
1 ATCTACT
22131 ATCTACT
1 ATCTACT
22138 ATCTACT
1 ATCTACT
22145 CCTATCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 32 0.84
8 6 0.16
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (7 bp):
ATCTACT
Found at i:22127 original size:22 final size:21
Alignment explanation
Indices: 22095--22143 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
22085 ATAATTTGTA
*
22095 ATCTACTATCTACTATCTATAT
1 ATCTACAATCTACTATCTA-AT
*
22117 ATCTACAATCTACTATCTACT
1 ATCTACAATCTACTATCTAAT
22138 ATCTAC
1 ATCTAC
22144 TCCTATCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.41
Consensus pattern (21 bp):
ATCTACAATCTACTATCTAAT
Found at i:22180 original size:21 final size:22
Alignment explanation
Indices: 22131--22181 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
22121 ACAATCTACT
*
22131 ATCTACTATCTACTCCTATCTA
1 ATCTACTATCTACTCCTATATA
*
22153 TTC-ACTATCTA-T-CTATATAA
1 ATCTACTATCTACTCCTATAT-A
22173 ATCTACTAT
1 ATCTACTAT
22182 AAGTCAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 13 0.54
22 2 0.08
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.43
Consensus pattern (22 bp):
ATCTACTATCTACTCCTATATA
Found at i:22977 original size:144 final size:145
Alignment explanation
Indices: 22706--23001 Score: 531
Period size: 144 Copynumber: 2.0 Consensus size: 145
22696 CAAAGTTAAA
22706 TGTCGTTGGACTCAAATATGACAAATAAATAGGAATCGAAGGGAGTAACTTATTGGGCCGACCTC
1 TGTCGTTGGACTCAAATATGACAAATAAATAGGAATCGAAGGGAGTAACTTATTGGGCCG----C
22771 TAAACAAAATTAATGTGCCTAATAAAGCTCTAGTTCATTTTCTTGTCGCTTTCGTGCTTTTGTAA
62 --AACAAAATTAATGTGCCTAATAAAGCTCTAGTTCATTTTCTTGTCGCTTTCGTGCTTTTGTAA
22836 ATAAGTATAATTTATCATTAT
125 ATAAGTATAATTTATCATTAT
22857 TGTCGTTGGACTCAAATATGACAAATAAATAGGAATCGAAGGGAGTAACTTATTGGGCCG-AACA
1 TGTCGTTGGACTCAAATATGACAAATAAATAGGAATCGAAGGGAGTAACTTATTGGGCCGCAACA
22921 AAATTAATGTGCCTAATAAAGCTCTAGTTCATTTTCTTGTCGCTTTCGTGCTTTTGTAAATAAGT
66 AAATTAATGTGCCTAATAAAGCTCTAGTTCATTTTCTTGTCGCTTTCGTGCTTTTGTAAATAAGT
22986 ATAATTTATCATTAT
131 ATAATTTATCATTAT
23001 T
1 T
23002 TAATTTCAAG
Statistics
Matches: 145, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
144 85 0.59
151 60 0.41
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (145 bp):
TGTCGTTGGACTCAAATATGACAAATAAATAGGAATCGAAGGGAGTAACTTATTGGGCCGCAACA
AAATTAATGTGCCTAATAAAGCTCTAGTTCATTTTCTTGTCGCTTTCGTGCTTTTGTAAATAAGT
ATAATTTATCATTAT
Found at i:26427 original size:31 final size:31
Alignment explanation
Indices: 26360--26446 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
26350 TGTTAAGGGT
* * * *
26360 AAAATATCTTGAATTTAGGAAGTTCAAGGGAC
1 AAAATGTCCTGAATTT-GGAAGTTTAGGGGAC
**
26392 AAAATGTCCTGAATTTGGAAGTTTAGGGGGG
1 AAAATGTCCTGAATTTGGAAGTTTAGGGGAC
*
26423 AAAATGTCCTG-ATTT-GAGGTTTAG
1 AAAATGTCCTGAATTTGGAAGTTTAG
26447 CAGGCAAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 8 0.17
30 4 0.08
31 22 0.46
32 14 0.29
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (31 bp):
AAAATGTCCTGAATTTGGAAGTTTAGGGGAC
Found at i:26455 original size:29 final size:31
Alignment explanation
Indices: 26391--26455 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
26381 GTTCAAGGGA
**
26391 CAAAATGTCCTGAATTTGGAAGTTTAGGGGG
1 CAAAATGTCCTGAATTTGGAAGTTTAGCAGG
* *
26422 GAAAATGTCCTG-ATTT-GAGGTTTAGCAGG
1 CAAAATGTCCTGAATTTGGAAGTTTAGCAGG
26451 CAAAA
1 CAAAA
26456 CGTTCTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 14 0.48
30 4 0.14
31 11 0.38
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (31 bp):
CAAAATGTCCTGAATTTGGAAGTTTAGCAGG
Found at i:28699 original size:14 final size:13
Alignment explanation
Indices: 28668--28713 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
28658 ATCGGGTTTT
28668 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
28681 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
28695 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
28710 AGTC
1 AGTC
28714 TGAGTCTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:30018 original size:26 final size:26
Alignment explanation
Indices: 29962--30013 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
29952 TATATATATC
**
29962 ATTAGTCATTACGTTTTTTTTTGAGGA
1 ATTAGTCATTACGTTTTTTTTCCA-GA
29989 ATTAGTCATTACGTTTTTCTTTCCA
1 ATTAGTCATTACGTTTTT-TTTCCA
30014 TATTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (26 bp):
ATTAGTCATTACGTTTTTTTTCCAGA
Found at i:30071 original size:143 final size:141
Alignment explanation
Indices: 29862--30122 Score: 443
Period size: 143 Copynumber: 1.8 Consensus size: 141
29852 TCCAATCAGA
29862 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT
1 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT
29927 TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTGAGGAATT
66 TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTGAGGAATT
29992 AGTCATTACGT
131 AGTCATTACGT
* * * * *
30003 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATT-TTTTTACTTTAAACAACTTAT
1 TTTTATTTCCATATTAAAAAAGTC-TAAA--ATAATAACAATTATTTTTACATTAAACAACTTAT
30067 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT
63 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT
30123 CTTTCCATAT
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
141 22 0.20
142 4 0.04
143 76 0.68
144 10 0.09
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (141 bp):
TTTTATTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACATTAAACAACTTATTAT
TATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTGAGGAATT
AGTCATTACGT
Found at i:30121 original size:116 final size:114
Alignment explanation
Indices: 29989--30212 Score: 360
Period size: 115 Copynumber: 1.9 Consensus size: 114
29979 TTTTTGAGGA
* *
29989 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAGTCTT-AAATGATACTAATAATTTTTTTAC
1 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAAT-TTAAAATAATACTAAT-ATTTTTTTAC
*
30053 TTTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATC
64 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTA-TTATATATATC
30105 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATTTAAAATAATACTAATATTTTTTTACGT
1 ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATTTAAAATAATACTAATATTTTTTTACGT
* * *
30170 TAAACATCTTCTTATTATAATTATTAAACTTATTATTATTATA
66 TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATA
30213 ACAATTATTA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
114 5 0.05
115 48 0.48
116 48 0.48
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (114 bp):
ATTAGTCATTACGTTTTTCTTTCCATATTACAAAAATTTAAAATAATACTAATATTTTTTTACGT
TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATATATATC
Found at i:30207 original size:15 final size:16
Alignment explanation
Indices: 30184--30231 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
30174 CATCTTCTTA
*
30184 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
30199 TTATTATTATTATAAC
1 TTATTATTATTATAAC
30215 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
30232 TGATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:30220 original size:18 final size:17
Alignment explanation
Indices: 30181--30231 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
30171 AAACATCTTC
* *
30181 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
30199 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
30217 TTATTATTAGTTATA
1 TTATTATTA-TTATA
30232 TGATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Done.