Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012595.1 Corchorus olitorius cultivar O-4 contig12628, 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: 48790
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Found at i:413 original size:36 final size:36
Alignment explanation
Indices: 366--435 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
356 TTCAATAACC
* *
366 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
402 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
436 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:864 original size:42 final size:43
Alignment explanation
Indices: 813--906 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
803 AGTGCATTAC
*
813 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
854 CTAATATTCTAGTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
899 CTAATATT
1 CTAATATT
907 AATTATTGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:3254 original size:204 final size:201
Alignment explanation
Indices: 2882--3283 Score: 732
Period size: 204 Copynumber: 2.0 Consensus size: 201
2872 TATCAATGAT
2882 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
1 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
*
2947 CAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTT
66 CAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTT
*
3012 ATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCTAT
131 ATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGAT
3077 TTATATA
195 TTATATA
3084 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
1 TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
*
3149 CAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGAT
66 CAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGAT
**
3214 TTATTTTATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGA
129 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGA
3279 TTTAT
194 TTTAT
3284 TTATTCTTAG
Statistics
Matches: 193, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
202 86 0.45
203 14 0.07
204 93 0.48
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (201 bp):
TCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATA
CAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTT
ATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATT
TATATA
Found at i:3395 original size:25 final size:24
Alignment explanation
Indices: 3361--3407 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
3351 ACGTTTGCAC
3361 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
3386 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
3408 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:3453 original size:39 final size:40
Alignment explanation
Indices: 3398--3478 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
3388 ATACCTAAGA
* *
3398 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
*
3437 ATTTAATTAATATAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
3477 AT
1 AT
3479 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATATATATTAC
Found at i:7326 original size:25 final size:25
Alignment explanation
Indices: 7289--7337 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
7279 CCAAACAATC
*
7289 TTGAGCACTCTCGCTCAGTCTCTAT
1 TTGAGCACCCTCGCTCAGTCTCTAT
*
7314 TTGAGCACCCTCGCTCGGTCTCTA
1 TTGAGCACCCTCGCTCAGTCTCTA
7338 CAAACTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.18, T:0.33
Consensus pattern (25 bp):
TTGAGCACCCTCGCTCAGTCTCTAT
Found at i:10591 original size:2 final size:2
Alignment explanation
Indices: 10584--10614 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10574 ACCTCACCAG
10584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10615 TCATGCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11256 original size:24 final size:25
Alignment explanation
Indices: 11227--11277 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
11217 TTATGTGAAC
*
11227 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
11251 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
11276 AA
1 AA
11278 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:23179 original size:38 final size:38
Alignment explanation
Indices: 23115--23194 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
23105 CCGCACCTAA
* * * *
23115 CACACACATATAAATATTCCATACACATATCCACATTC
1 CACACACATATAAATAATCCACACACACATCAACATTC
* * *
23153 CACACACATGTGAATAATCCACACACACATGAACATTC
1 CACACACATATAAATAATCCACACACACATCAACATTC
23191 CACA
1 CACA
23195 AATAAAATAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.33, G:0.04, T:0.21
Consensus pattern (38 bp):
CACACACATATAAATAATCCACACACACATCAACATTC
Found at i:23192 original size:19 final size:19
Alignment explanation
Indices: 23115--23194 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
23105 CCGCACCTAA
* *
23115 CACACACATATAAATATTC
1 CACACACATATGAACATTC
* **
23134 CATACACATATCCACATTC
1 CACACACATATGAACATTC
* * *
23153 CACACACATGTGAATAATC
1 CACACACATATGAACATTC
*
23172 CACACACACATGAACATTC
1 CACACACATATGAACATTC
23191 CACA
1 CACA
23195 AATAAAATAC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.42, C:0.33, G:0.04, T:0.21
Consensus pattern (19 bp):
CACACACATATGAACATTC
Found at i:29071 original size:14 final size:14
Alignment explanation
Indices: 29052--29104 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
29042 GGGGAGGCTA
*
29052 AAGATGCCGCAGGG
1 AAGATGCCGAAGGG
29066 AAGATGCCGAAGGG
1 AAGATGCCGAAGGG
29080 AAGATGCCGAAGGG
1 AAGATGCCGAAGGG
29094 AAGATGCCGAA
1 AAGATGCCGAA
29105 ATGGGAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.40, T:0.08
Consensus pattern (14 bp):
AAGATGCCGAAGGG
Found at i:44067 original size:41 final size:40
Alignment explanation
Indices: 43965--44292 Score: 320
Period size: 41 Copynumber: 7.8 Consensus size: 40
43955 CAATAACCAA
* *
43965 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-CCTATT-C
* *
44008 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTAAATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCT-ATTC
* * * *
44050 CAAGTCCCCAAACAC--ATATAACACAGGGGCGTCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-AC-CTATT-C
* *
44091 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTAT-TC
44132 AAAGTCCCCAAACACATATATAACACA-AGAGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAG-GC-AC-CTATT-C
* * **
44175 AAAGTCCTCAAACACATATATAACACAGAGACATTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTAT-TC
*
44216 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-C-CTATT-C
* *
44259 AAAAGTCCTCAAACACATATATAACACATAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
44293 TTTCTCCTTA
Statistics
Matches: 237, Mismatches: 30, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
39 14 0.06
40 5 0.02
41 94 0.40
42 9 0.04
43 53 0.22
44 62 0.26
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (40 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACCTATTC
Found at i:44184 original size:84 final size:85
Alignment explanation
Indices: 43965--44293 Score: 504
Period size: 84 Copynumber: 3.9 Consensus size: 85
43955 CAATAACCAA
* *
43965 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
* *
44030 AACACAGAGGCACCTAAATC
66 AACACAGAGGCATCTATATC
* ** *
44050 CAAGTCCCCAAACAC--ATATAACACAGGGGCGTCTTTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
44112 AACACAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
* *
44132 AAAGTCCCCAAACACATATATAACACAAGAGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
* *
44196 AACACAGAGACATTTATATC
66 AACACAGAGGCATCTATATC
*
44216 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
44281 AACACATAGGCAT
66 AACACAGAGGCAT
44294 TTCTCCTTAT
Statistics
Matches: 220, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
82 53 0.24
83 21 0.10
84 100 0.45
85 46 0.21
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC
Found at i:45181 original size:22 final size:24
Alignment explanation
Indices: 45156--45201 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
45146 CGAAAATGGC
45156 AATCAA-T-CAACTCTAAGAGAAA
1 AATCAACTACAACTCTAAGAGAAA
45178 AATCAACTAACAACTCTAAGAGAA
1 AATCAACT-ACAACTCTAAGAGAA
45202 GAGAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
25 14 0.67
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (24 bp):
AATCAACTACAACTCTAAGAGAAA
Done.