Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008523.1 Corchorus capsularis cultivar CVL-1 contig08544, 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: 17474
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Found at i:88 original size:33 final size:32
Alignment explanation
Indices: 1--91 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
* *
1 ATGGCTAGCCGCCCGAGTTGGGCGACCTTGCC
1 ATGGCTAGCCGCCCAAGTTGGGCGGCCTTGCC
* *
33 ATGGCTAGCTGCCCAAGCTGGGCGGCCTTGACC
1 ATGGCTAGCCGCCCAAGTTGGGCGGCCTTG-CC
66 ATGGCTAGCCGCCC-AGTTTGGGCGGC
1 ATGGCTAGCCGCCCAAG-TTGGGCGGC
92 TCGGCCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.13, C:0.33, G:0.35, T:0.19
Consensus pattern (32 bp):
ATGGCTAGCCGCCCAAGTTGGGCGGCCTTGCC
Found at i:210 original size:15 final size:15
Alignment explanation
Indices: 151--210 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
141 ATGATTAGTT
*
151 TTAATTAGTTTATGT
1 TTAATTAGTTTATGA
*
166 TTAATTAGTTTATTA
1 TTAATTAGTTTATGA
181 TTAATTAG--TAT--
1 TTAATTAGTTTATGA
192 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
207 TTAA
1 TTAA
211 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 8 0.21
13 6 0.15
15 25 0.64
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
TTAATTAGTTTATGA
Found at i:258 original size:24 final size:25
Alignment explanation
Indices: 219--278 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
209 AAAATGAAGG
*
219 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
242 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
267 GAAATGAAGTTT
1 AAAATGAAGTTT
279 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:9152 original size:2 final size:2
Alignment explanation
Indices: 9145--9170 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9135 GATATTTAAA
9145 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9171 GATCATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9223 original size:6 final size:6
Alignment explanation
Indices: 9212--9242 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
9202 TGATTGAGAG
9212 GAAAAA GAAAAA -AAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA
9243 GGGTACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:9229 original size:11 final size:12
Alignment explanation
Indices: 9212--9242 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
9202 TGATTGAGAG
9212 GAAAAAGAAAAA
1 GAAAAAGAAAAA
9224 -AAAAAGAAAAA
1 GAAAAAGAAAAA
9235 GAAAAAGA
1 GAAAAAGA
9243 GGGTACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:9817 original size:2 final size:2
Alignment explanation
Indices: 9810--9837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9800 CAATATTATA
9810 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9838 AATTTACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11815 original size:20 final size:20
Alignment explanation
Indices: 11786--11836 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
11776 ATCGGATATC
*
11786 TCGACGGATATATCGAGGTA
1 TCGACGGATATATCAAGGTA
*
11806 TCGACCGATATATCAAGGTA
1 TCGACGGATATATCAAGGTA
11826 TCGACGGATAT
1 TCGACGGATAT
11837 TTAATTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (20 bp):
TCGACGGATATATCAAGGTA
Found at i:12238 original size:33 final size:33
Alignment explanation
Indices: 12201--12285 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
12191 AGCACTAGTG
*
12201 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* * *
12234 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* *
12267 AACGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
12286 CATGTCCGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.24, C:0.38, G:0.31, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Found at i:12306 original size:33 final size:34
Alignment explanation
Indices: 12201--12307 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 34
12191 AGCACTAGTG
* * * * * *
12201 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC-
1 ACCGGCCACGCGACTCGGACATGCCCGACCATCA
* *
12234 ACCGGCCACGCGACTCGGAGATGCCCGGCCATCA
1 ACCGGCCACGCGACTCGGACATGCCCGACCATCA
*
12268 A-CGGCCACGCGACAT-GGACATGTCCGACCA-CA
1 ACCGGCCACGCGAC-TCGGACATGCCCGACCATCA
12300 ACCGGCCA
1 ACCGGCCA
12308 TCGCTTGGCG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 59 0.92
34 2 0.03
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.08
Consensus pattern (34 bp):
ACCGGCCACGCGACTCGGACATGCCCGACCATCA
Found at i:13402 original size:9 final size:9
Alignment explanation
Indices: 13375--13410 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
13365 AGTTATATCG
*
13375 AAAAATATA
1 AAAAAAATA
13384 AAAGAAAATA
1 AAA-AAAATA
13394 AAAAAAATA
1 AAAAAAATA
13403 AAAAAAAT
1 AAAAAAAT
13411 TTCGACCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Found at i:13403 original size:19 final size:18
Alignment explanation
Indices: 13375--13410 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13365 AGTTATATCG
*
13375 AAAAATATAAAAGAAAATA
1 AAAAAAATAAAA-AAAATA
13394 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
13411 TTCGACCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAATAAAAAAAATA
Found at i:14826 original size:33 final size:33
Alignment explanation
Indices: 14789--14859 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
14779 TTGAAAAGAG
14789 TGTTTC-AGATGTTGTTT-TCAATGATACTAAACC
1 TGTTTCAAG-TGTTGTTTGT-AATGATACTAAACC
* * *
14822 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTCAAGTGTTGTTTGTAATGATACTAAACC
14855 TGTTT
1 TGTTT
14860 TGGATGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (33 bp):
TGTTTCAAGTGTTGTTTGTAATGATACTAAACC
Found at i:14916 original size:33 final size:32
Alignment explanation
Indices: 14879--14960 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 32
14869 ATTGTGATGA
14879 AAATAATTCTGTTTTGGTTGATCATAGCATTAC
1 AAATAA-TCTGTTTTGGTTGATCATAGCATTAC
*
14912 AAATAA----TTTT-GTTGATCATAGCATTGC
1 AAATAATCTGTTTTGGTTGATCATAGCATTAC
14939 AAATAATCCTGTTTTGGTTGAT
1 AAATAAT-CTGTTTTGGTTGAT
14961 GGCATTGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
27 22 0.52
28 4 0.10
32 4 0.10
33 12 0.29
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (32 bp):
AAATAATCTGTTTTGGTTGATCATAGCATTAC
Found at i:16776 original size:33 final size:33
Alignment explanation
Indices: 16738--16822 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
16728 AGCACTAGTG
*
16738 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
* * *
16771 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
*
16804 ACCGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
16823 CATGTCCGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.22, C:0.39, G:0.31, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC
Found at i:16841 original size:33 final size:33
Alignment explanation
Indices: 16738--16844 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
16728 AGCACTAGTG
* * * * * *
16738 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGACATGCCCGACCATC
* *
16771 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTCGGACATGCCCGACCATC
*
16804 ACCGGCCACGCGACAT-GGACATGTCCGACCA-C
1 ACCGGCCACGCGAC-TCGGACATGCCCGACCATC
16836 AACCGGCCA
1 -ACCGGCCA
16845 TCGCTTGGCG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.02
33 63 0.97
34 1 0.02
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGACATGCCCGACCATC
Done.