Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015708.1 Corchorus olitorius cultivar O-4 contig15741, 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: 90442
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:306 original size:27 final size:27
Alignment explanation
Indices: 231--313 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
221 ATACCACTAA
*
231 TAATAATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
258 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
288 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
314 CTAAATTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:5609 original size:12 final size:14
Alignment explanation
Indices: 5592--5624 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
5582 ATGGATTGTT
5592 TGTGCTGTTGT-TG
1 TGTGCTGTTGTCTG
5605 T-TGCTGTTGTCTG
1 TGTGCTGTTGTCTG
5618 TGTGCTG
1 TGTGCTG
5625 ACACATACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 4 0.22
14 5 0.28
ACGTcount: A:0.00, C:0.12, G:0.36, T:0.52
Consensus pattern (14 bp):
TGTGCTGTTGTCTG
Found at i:6317 original size:31 final size:31
Alignment explanation
Indices: 6282--6416 Score: 162
Period size: 31 Copynumber: 4.4 Consensus size: 31
6272 TTTGTGCACG
* **
6282 TGGCATGCCATGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
*
6313 TGGCATGCCACGTTTCACTTTTTGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* ** * *
6344 TGGCGTGATATGTGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * *
6375 TGGCATGCCACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
6406 TGGCATGCCAC
1 TGGCATGCCAC
6417 CGTCGGACAC
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:9688 original size:23 final size:22
Alignment explanation
Indices: 9662--9706 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
9652 TCTTTTTTTA
9662 TTTCTCGAGAAAACCGGAATAAT
1 TTTCTCGAGAAAACC-GAATAAT
*
9685 TTTCTCGAGAAAATCGAATAAT
1 TTTCTCGAGAAAACCGAATAAT
9707 ATGAAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (22 bp):
TTTCTCGAGAAAACCGAATAAT
Found at i:18725 original size:3 final size:3
Alignment explanation
Indices: 18719--18743 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18709 AAAGGTGAGA
18719 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
18744 GAGGGCTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43456 original size:19 final size:18
Alignment explanation
Indices: 43428--43469 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
43418 AATTAATTGT
43428 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
43446 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
43465 CTTAA
1 TTTAA
43470 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:44649 original size:18 final size:18
Alignment explanation
Indices: 44626--44660 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
44616 AATATCCAAT
44626 ATATATGCTTATGGATTG
1 ATATATGCTTATGGATTG
44644 ATATATGCTTATGGATT
1 ATATATGCTTATGGATT
44661 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (18 bp):
ATATATGCTTATGGATTG
Found at i:44920 original size:44 final size:44
Alignment explanation
Indices: 44865--44951 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
44855 TATAGATAAA
* *
44865 CTACCTGCCTACCAAATACACAAACAAATTACAAACAAACTCAG
1 CTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCAG
44909 CTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
1 CTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
44952 CACTCCGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.51, C:0.31, G:0.02, T:0.16
Consensus pattern (44 bp):
CTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCAG
Found at i:48511 original size:91 final size:91
Alignment explanation
Indices: 48356--48539 Score: 323
Period size: 91 Copynumber: 2.0 Consensus size: 91
48346 TTAATAATCA
48356 TATCCAATTAATGATTATTTTATAGTATACTAATAATATGTTAGGTTGAGTGAGAAGAACTCGAT
1 TATCCAATTAATGATTATTTTATAGTATACTAATAATATGTTAGGTTGAGTGAGAAGAACTCGAT
* **
48421 GTCCCTTGTTTTAAATTTGAGTTTTG
66 GTCACTTACTTTAAATTTGAGTTTTG
* *
48447 TATCCAATTAATGATTATTTTATAGTATACTAATAATTTGTTAGGTTGAGTGAGAAGAGCTCGAT
1 TATCCAATTAATGATTATTTTATAGTATACTAATAATATGTTAGGTTGAGTGAGAAGAACTCGAT
48512 GTCACTTACTTTAAATTTGAGTTTTG
66 GTCACTTACTTTAAATTTGAGTTTTG
48538 TA
1 TA
48540 AATGAAAAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (91 bp):
TATCCAATTAATGATTATTTTATAGTATACTAATAATATGTTAGGTTGAGTGAGAAGAACTCGAT
GTCACTTACTTTAAATTTGAGTTTTG
Found at i:70767 original size:12 final size:12
Alignment explanation
Indices: 70750--70793 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
70740 AAGCGAAAGA
*
70750 AAGAAGAAGAAG
1 AAGAAGAGGAAG
*
70762 AAGAAGAGGGAG
1 AAGAAGAGGAAG
*
70774 AGGAAGAGGAAG
1 AAGAAGAGGAAG
70786 AAGAAGAG
1 AAGAAGAG
70794 AATGAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AAGAAGAGGAAG
Found at i:70808 original size:3 final size:3
Alignment explanation
Indices: 70750--70792 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
70740 AAGCGAAAGA
* * * *
70750 AAG AAG AAG AAG AAG AAG AGG GAG AGG AAG AGG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
70793 GAATGAAATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:72853 original size:13 final size:13
Alignment explanation
Indices: 72835--72861 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
72825 AAACAACTGA
72835 AAAGCACTTCTGG
1 AAAGCACTTCTGG
72848 AAAGCACTTCTGG
1 AAAGCACTTCTGG
72861 A
1 A
72862 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:73384 original size:2 final size:2
Alignment explanation
Indices: 73377--73402 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73367 GATTTCATGA
73377 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
73403 TATTAAGTTA
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:81163 original size:18 final size:18
Alignment explanation
Indices: 81140--81175 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
81130 CACCCTTTTA
*
81140 GATGGGAATGTCATTCCC
1 GATGGGAATGACATTCCC
81158 GATGGGAATGACATTCCC
1 GATGGGAATGACATTCCC
81176 ACCTAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (18 bp):
GATGGGAATGACATTCCC
Found at i:88450 original size:2 final size:2
Alignment explanation
Indices: 88443--88481 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
88433 TTTCAAATAC
88443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
88482 AGTCTAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:88756 original size:42 final size:40
Alignment explanation
Indices: 88697--88780 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 40
88687 TTTAATTCCT
88697 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
88737 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
88779 AT
1 AT
88781 TCTTAGGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.07
42 31 0.76
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:88811 original size:25 final size:24
Alignment explanation
Indices: 88771--88817 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
88761 AATACTTACA
88771 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
*
88795 TTAATTCAAATTTTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
88818 GTGCAAACGT
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:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:89133 original size:204 final size:203
Alignment explanation
Indices: 88891--89298 Score: 728
Period size: 204 Copynumber: 2.0 Consensus size: 203
88881 TTCCTTAATA
88891 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
88956 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATAT-ATAATAG
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTT-GTATAGTTCTATATATAATAATAA
89020 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
*
89085 TTACCATTG
195 TCACCATTG
89094 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * * *
89159 AATTTATTAAATCAACCACTAATGTTTAACTACTTTTTTTTGTATAGTTTTATATATAATAATAA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGTATAGTTCTATATATAATAATAA
*
89224 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAATAT
130 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
89289 TCACCATTG
195 TCACCATTG
89298 A
1 A
89299 AAAAGTTATT
Statistics
Matches: 196, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
203 31 0.16
204 165 0.84
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGTATAGTTCTATATATAATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCATTG
Done.