Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015232.1 Corchorus olitorius cultivar O-4 contig15265, 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: 23661
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:5515 original size:12 final size:12
Alignment explanation
Indices: 5500--5534 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5490 TGTTAAGTAA
5500 CCATCTAAGGAG
1 CCATCTAAGGAG
* *
5512 CCATCCAAGCAG
1 CCATCTAAGGAG
5524 CCATCTAAGGA
1 CCATCTAAGGA
5535 AGGAGAACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.14
Consensus pattern (12 bp):
CCATCTAAGGAG
Found at i:10168 original size:12 final size:12
Alignment explanation
Indices: 10151--10193 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
10141 GGGGGAGTGT
10151 TAAGGAACCATC
1 TAAGGAACCATC
*
10163 TAAGGAGCCATC
1 TAAGGAACCATC
* * *
10175 CAAGCAGCCATC
1 TAAGGAACCATC
10187 TAAGGAA
1 TAAGGAA
10194 GGAGAACCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (12 bp):
TAAGGAACCATC
Found at i:12665 original size:21 final size:20
Alignment explanation
Indices: 12623--12666 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
12613 TCTTGTAATC
*
12623 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
12643 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
12664 TAA
1 TAA
12667 TACTTTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:14492 original size:344 final size:346
Alignment explanation
Indices: 13838--14503 Score: 903
Period size: 344 Copynumber: 1.9 Consensus size: 346
13828 AATATTGGTC
* * * * * * *
13838 ATTGATTTTTTTATCTAAGATTTCTTAAAAGGTTATAAAGTTTATTGAAAACATTATAGTACTAT
1 ATTGAATTTCTTATCCAAGATTACTTAAAAGATTATAAAGGTTATGGAAAACATTATAGTACTAT
* * * * *
13903 TTAGATTCAAGTAATCTTAGATCCTTAATAATTTTAGTAACCTTTTATCAATAATGAAAGTTACC
66 CTAGATTCAAATAACCTTACATCCTTAATAATTTTAGTAACCTTTTATCAATAATAAAAGTTACC
* **
13968 AATTTTATTATTTAAGTAATCTACTAAAAAAACTATGGAAGTTATTAAAATTGTATTTAACAATC
131 AATTTTATTACTTAAGT-ATCTACTAAAAAAACTATAAAAGTTATTAAAATTGTATTTAACAATC
* ** * * *
14033 GTTACATTCTAAATAACATTAGTAAACTTTCATTAATGGTTAAGATTTACCATTTTTTTTACTAA
195 CTTACATTCTAAATAACATTAGTAAACTTGAATCAATGGTGAAGATTTACAATTTTTTTTACTAA
14098 AAAATTACCGAAAAACCTATACTAATCATAAAAAAGATATGATATACTATCAACTAATTCAATGA
260 AAAATTACCGAAAAACCTATACTAATCATAAAAAAGATATGATATACTATCAACTAATTCAATGA
14163 CCTTACATTATAAAGCTATAGT
325 CCTTACATTATAAAGCTATAGT
*
14185 ATTGAATTTCTTATCCAAGATTACTTAAAAGATTATAAGGGTTATGGAAAACATTATAGTACTAT
1 ATTGAATTTCTTATCCAAGATTACTTAAAAGATTATAAAGGTTATGGAAAACATTATAGTACTAT
* ** * *
14250 CTAGATTGAAATAACCTTACATCCTTGTTAATTTTAGTAACTTTTTATCATTAATAAAAGTTACC
66 CTAGATTCAAATAACCTTACATCCTTAATAATTTTAGTAACCTTTTATCAATAATAAAAGTTACC
* * *
14315 AATTTTATTACTTAAGT-T-TACTATAAAAGCTATAAAAGTTATTAAAATTGTATTTACCAATCC
131 AATTTTATTACTTAAGTATCTACTAAAAAAACTATAAAAGTTATTAAAATTGTATTTAACAATCC
* * * *
14378 TTACATTCTTAATAACATTAGTAAACTTGAATCAATGGTGAATATTTTCAATTTTTTTCT-CTCA
196 TTACATTCTAAATAACATTAGTAAACTTGAATCAATGGTGAAGATTTACAATTTTTTT-TACTAA
* * * *
14442 AAAGTTACTGAAAAACCTATA-TAATGATCATAAAAGAGGTAT-AT-TACTATCAACTAATTCAA
260 AAAATTACCGAAAAACCTATACT-A--ATCATAAAAAAGATATGATATACTATCAACTAATTCAA
14504 ATACCTTGCA
Statistics
Matches: 277, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
343 1 0.00
344 130 0.47
345 4 0.01
346 14 0.05
347 128 0.46
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (346 bp):
ATTGAATTTCTTATCCAAGATTACTTAAAAGATTATAAAGGTTATGGAAAACATTATAGTACTAT
CTAGATTCAAATAACCTTACATCCTTAATAATTTTAGTAACCTTTTATCAATAATAAAAGTTACC
AATTTTATTACTTAAGTATCTACTAAAAAAACTATAAAAGTTATTAAAATTGTATTTAACAATCC
TTACATTCTAAATAACATTAGTAAACTTGAATCAATGGTGAAGATTTACAATTTTTTTTACTAAA
AAATTACCGAAAAACCTATACTAATCATAAAAAAGATATGATATACTATCAACTAATTCAATGAC
CTTACATTATAAAGCTATAGT
Found at i:17029 original size:90 final size:89
Alignment explanation
Indices: 16901--17078 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 89
16891 ACACATGAAT
**
16901 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTTCAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
16966 AATATTTAAAAGTTAAAAAGGACAC
66 AATATTTAAAA-TTAAAAAGGACAC
*
16991 ATGATAAATAATCCTTAATTTAATTGTTAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
1 ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
17056 AATATTTAAAATTAAAAAGGACA
66 AATATTTAAAATTAAAAAGGACA
17079 TTTTGGATAT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 12 0.14
90 73 0.86
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (89 bp):
ATGATAAATAATCCTTAATTTAATTGATAAATAAAATTACATATTAAACCTTAAAAGTTATTGAT
AATATTTAAAATTAAAAAGGACAC
Found at i:18274 original size:39 final size:38
Alignment explanation
Indices: 18226--18300 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
18216 TCCTATATAA
*
18226 AATATATAATAACTAAAATATTTACATTAATTAAATGT
1 AATATATAATAACTAAAATACTTACATTAATTAAATGT
*
18264 AATACTATAATAACTGAAATACTTACATTAATTAAAT
1 AATA-TATAATAACTAAAATACTTACATTAATTAAAT
18301 TCTTAGGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (38 bp):
AATATATAATAACTAAAATACTTACATTAATTAAATGT
Found at i:22757 original size:25 final size:24
Alignment explanation
Indices: 22722--22768 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
22712 ACGTTTGCAC
22722 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
*
22747 AAATACGTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
22769 TGTAAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:22813 original size:39 final size:40
Alignment explanation
Indices: 22759--22839 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
22749 ATACGTAAGA
*
22759 ATTTAATTAATGTAAGT-TTTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTT-AGTTATTATATATATTAC
22798 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
22838 AT
1 AT
22840 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 27 0.69
40 12 0.31
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
Done.