Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012081.1 Corchorus olitorius cultivar O-4 contig12114, 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: 61758
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5099 original size:23 final size:23
Alignment explanation
Indices: 5069--5145 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
5059 ATTCAAAAAG
5069 GCAAAATCTAGCAAAGTAAGATT
1 GCAAAATCTAGCAAAGTAAGATT
* * * **
5092 GCAAAATCT--CCAATTCAAAAAG
1 GCAAAATCTAGCAAAGT-AAGATT
*
5114 GCAAAATCTAGCACAGTAAGATT
1 GCAAAATCTAGCAAAGTAAGATT
5137 GCAAAATCT
1 GCAAAATCT
5146 CCAATTTTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 4 0.10
22 12 0.30
23 21 0.52
24 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (23 bp):
GCAAAATCTAGCAAAGTAAGATT
Found at i:5108 original size:45 final size:45
Alignment explanation
Indices: 5058--5151 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
5048 TACCATTGAG
5058 AATTCAAAAAGGCAAAATCTAGCAAAGTAAGATTGCAAAATCTCC
1 AATTCAAAAAGGCAAAATCTAGCAAAGTAAGATTGCAAAATCTCC
*
5103 AATTCAAAAAGGCAAAATCTAGCACAGTAAGATTGCAAAATCTCC
1 AATTCAAAAAGGCAAAATCTAGCAAAGTAAGATTGCAAAATCTCC
5148 AATT
1 AATT
5152 TTAACTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (45 bp):
AATTCAAAAAGGCAAAATCTAGCAAAGTAAGATTGCAAAATCTCC
Found at i:6274 original size:21 final size:21
Alignment explanation
Indices: 6233--6278 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6223 ACAAGTTCTG
* *
6233 TAAAATAACAATTTTTTATTT
1 TAAAATAACAATATTTGATTT
6254 TAAAACTAA-AATATTTGATTT
1 TAAAA-TAACAATATTTGATTT
6275 TAAA
1 TAAA
6279 TATTCATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAAATAACAATATTTGATTT
Found at i:9009 original size:88 final size:87
Alignment explanation
Indices: 8903--9067 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 87
8893 CTTGATAATT
* * *
8903 ATACATTTATTAGTTTATATTATAATTGAAATGGGTCCAGACCTACCAAAAAGTCTTTAATTTTT
1 ATACATTTATTAGTTTATATTATAAATGAAATGGGTCCAAACCTACCAAAAAGTCTCTAATTTTT
8968 TTAAATATTAAAAAAATAAACAA
66 TTAAA-ATTAAAAAAATAAACAA
* *
8991 ATACTTTTATTAGTTTATATTATAAATGAAATGGGTCTAAACCTACCAAAAAGTCTCTAATTTTT
1 ATACATTTATTAGTTTATATTATAAATGAAATGGGTCCAAACCTACCAAAAAGTCTCTAATTTTT
9056 TTAAAATTAAAA
66 TTAAAATTAAAA
9068 TGGTAAAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
87 7 0.10
88 65 0.90
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (87 bp):
ATACATTTATTAGTTTATATTATAAATGAAATGGGTCCAAACCTACCAAAAAGTCTCTAATTTTT
TTAAAATTAAAAAAATAAACAA
Found at i:9583 original size:6 final size:6
Alignment explanation
Indices: 9548--9581 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
9538 TTCTTTAAAG
9548 TTTTCT TTTTCT TTTTCTT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTT
9582 TTACATAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:9583 original size:13 final size:13
Alignment explanation
Indices: 9548--9583 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
9538 TTCTTTAAAG
*
9548 TTTTCTTTTTCTT
1 TTTTTTTTTTCTT
*
9561 TTTCTTTTTTCTT
1 TTTTTTTTTTCTT
9574 TTTTTTTTTT
1 TTTTTTTTTT
9584 ACATAGGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:10493 original size:16 final size:17
Alignment explanation
Indices: 10461--10494 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10451 TTTTTATTTT
*
10461 TATTTATTGATATATAA
1 TATTTATTGAAATATAA
10478 TATTTATT-AAATATAA
1 TATTTATTGAAATATAA
10494 T
1 T
10495 TTATACATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTATTGAAATATAA
Found at i:10939 original size:39 final size:40
Alignment explanation
Indices: 10896--10976 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
10886 TCAAACATAT
*
10896 TGTACCGAGTCTTAAT-AAAACCAACATCGAAGGTGATTA
1 TGTACCGAGTCTTAATAAAAACCAACATCAAAGGTGATTA
10935 TGTACCGAGTCTTAATAAAAACCAACATCAAAGGTGATTA
1 TGTACCGAGTCTTAATAAAAACCAACATCAAAGGTGATTA
10975 TG
1 TG
10977 ATTTCCTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 16 0.40
40 24 0.60
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (40 bp):
TGTACCGAGTCTTAATAAAAACCAACATCAAAGGTGATTA
Found at i:23299 original size:29 final size:30
Alignment explanation
Indices: 23260--23319 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
23250 TATAAATAAT
* *
23260 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
23289 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
23319 A
1 A
23320 CTGAGGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:26682 original size:29 final size:29
Alignment explanation
Indices: 26640--26695 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
26630 CCTTGCACGG
* *
26640 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGATGTTGAT
26669 TGTTGAAAACTTGTAATTGTGATGTTG
1 TGTTGAAAACTTGTAATTGTGATGTTG
26696 TAAACTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGATGTTGAT
Found at i:33971 original size:14 final size:14
Alignment explanation
Indices: 33952--33979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33942 CAAATTGCAC
33952 GTATGAACTTCTAA
1 GTATGAACTTCTAA
33966 GTATGAACTTCTAA
1 GTATGAACTTCTAA
33980 AAAAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GTATGAACTTCTAA
Found at i:34908 original size:27 final size:27
Alignment explanation
Indices: 34851--34908 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
34841 AGTTTGGTGT
** * ** *
34851 AGTTTGGTGTTGTTAAGGAGTAGGAAC
1 AGTTTGGTAATGTAAAGGAGTAAAAAA
34878 AGTTTGGTAATGTAAAGGAGTAAAAAA
1 AGTTTGGTAATGTAAAGGAGTAAAAAA
34905 AGTT
1 AGTT
34909 GAGTAGCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGGAGTAAAAAA
Found at i:37721 original size:430 final size:432
Alignment explanation
Indices: 36993--38289 Score: 1530
Period size: 430 Copynumber: 3.0 Consensus size: 432
36983 ATTTTCTTTA
* * * *
36993 TTTTT-TTTCTATTTGTCTAATTAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTA
1 TTTTTGTTT-TATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTA
* * *
37057 CAACCTTCGTG-AAGGACTT-AAAAGTCAA-TTTTATTGTTTCAATT-TGAAAAAAAAAAGCGCT
65 CAACTTTCATGAAAGGA-TTCAAAAGTCAATTTTTA-TGTTTCAATTCT----AAAAAAA-TGCT
* * * * **
37118 TCTGAAATTTTGTGGTTTTGATTGTC-GGTCTATTTAATATCATATAATTTTTGATCCGTATGTC
123 TCTAAAATTGT-TGGTTTCGATTG-CAGGTCTATTTAATACCATATAATTTTTGATCCACATGTC
* * * *
37182 CGATTAAAGTTATTCAAGTTTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACA
186 CAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTATT--ATGATCTACGACTTTCATTAAGGACT
* *
37247 CGAAAGCTAAATTTGATATACGAGTTTCATGAAGGGATCAAAAGGGAATTTTTATGTTTCAAGAT
249 CGAAAGCTAAATTTGATCTACGAG-TTCATGAAGGGCTCAAAAGGGAATTTTTATGTTTCAAGAT
* * * *
37312 TTCCATCAACAAACATTTTCTTATTTGGCTTATTTATCGAATGATCATCATATTTTTCTACTTTA
313 CTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTA
*
37377 TAATACTTAGTCCTTTACTAATTCTATCTTAATCGATTTAACATTTCAG-CTGTAC
378 TAATACTTAGTCCTTTACTAATTCTATCTTAATCGATTTAACACTTCAGTCT-TAC
* *
37432 TTTTTGTTTTATTTGTCTGATTAAGGTAATTCAGGTGTCTATTAAAAGATAATTTCATGATTTAC
1 TTTTTGTTTTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTAC
* * * *
37497 AACTTTCTTGAAAGGATTCAAAAGTCAATTTTTATGTTTCAATTCT-AAAAAATGTTTTTAAAGT
66 AACTTTCATGAAAGGATTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCTTCTAAAAT
* *
37561 TGTTGGTTTCGATTGCAGGTCTATTTAATACCAAATAATTTTCT-ATCCACATGTCCAATTAAAA
131 TGTTGGTTTCGATTGCAGGTCTATTTAATACCATATAATTTT-TGATCCACATGTCCAATTAAAG
* * * *
37625 TTATTCCAGTGTCGGTTAACAGGTTA-T-TGATCTAC-AGTTTTCATTAAGGGCTCGAAAGCTAA
195 TTATTCAAGTGTCGGTTAAAAGGTTATTATGATCTACGA-CTTTCATTAAGGACTCGAAAGCTAA
* *
37687 ATTTGATCTACGAGTTCGATGAAGGGCTCAAAAGGAAATTTTTATGTTTCAAGATCTCCACCAAC
259 ATTTGATCTACGAGTTC-ATGAAGGGCTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAAC
* * * * *
37752 AAACATTTTCCTATTTGAATTATTTATCAAATGA-CCCCGTATTTTTCTACTTTATAATATTTAG
323 AAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAATACTTAG
* * * **
37816 TCTTTTACTAATTCTATTTTAATCGATTTAACGCTTCAAGTTCTTTT
388 TCCTTTACTAATTCTATCTTAATCGATTTAACACTTC-AG-TCTTAC
** * *
37863 TTTTTGTTCCATTTGTCTGATTAAGGTAATGCAAGTGTTTATTAAAAGGTAATTTCATGATTTAC
1 TTTTTGTTTTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTAC
* * * *
37928 AACTTCCATGAAA-GACTCAAAAGCCAATTTTTATGTTTCAATTCTAAAAAAATGCTTCCAAAAT
66 AACTTTCATGAAAGGATTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCTTCTAAAA-
* * * * *
37992 TTGGTCGTTTCGATT-AATGGTCTGTTTAATACTATATAATTTTTGATCCACATGTCCAATTAAA
130 TTGTTGGTTTCGATTGCA-GGTCTATTTAATACCATATAATTTTTGATCCACATGTCCAATTAAA
* * * * * *
38056 GTTATTTAAGTGTTGGTTAAAAGGTTATTGCATGATCTATGACTTTCA-TGAGGAATCTAAAAGC
194 GTTATTCAAGTGTCGGTTAAAAGGTTATT--ATGATCTACGACTTTCATTAAGGACTC-GAAAGC
* * * * * * *
38120 TAAATTTGATCTACGAGTTTTACGAAGGACTCATAAGAGAATTTTTATGTTTTAAGATCTCCATT
256 TAAATTTGATCTACGAG-TTCATGAAGGGCTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATC
* * *
38185 AACAAATATTTT-TTCTTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATACTACT
320 AACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAATACT
* * *
38249 TAATTCTTTAATAATTCTATCTTAATCGATTTAACACTTCA
385 TAGTCCTTTACTAATTCTATCTTAATCGATTTAACACTTCA
38290 ATTTTATTTT
Statistics
Matches: 734, Mismatches: 100, Indels: 52
0.83 0.11 0.06
Matches are distributed among these distances:
429 63 0.09
430 147 0.20
431 86 0.12
432 78 0.11
433 3 0.00
434 73 0.10
435 38 0.05
436 144 0.20
437 3 0.00
439 66 0.09
440 27 0.04
441 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (432 bp):
TTTTTGTTTTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTAC
AACTTTCATGAAAGGATTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCTTCTAAAAT
TGTTGGTTTCGATTGCAGGTCTATTTAATACCATATAATTTTTGATCCACATGTCCAATTAAAGT
TATTCAAGTGTCGGTTAAAAGGTTATTATGATCTACGACTTTCATTAAGGACTCGAAAGCTAAAT
TTGATCTACGAGTTCATGAAGGGCTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATCAACAAA
CATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAATACTTAGTCC
TTTACTAATTCTATCTTAATCGATTTAACACTTCAGTCTTAC
Found at i:38238 original size:436 final size:432
Alignment explanation
Indices: 36986--38290 Score: 1520
Period size: 436 Copynumber: 3.0 Consensus size: 432
36976 TAGCTTTATT
* * *
36986 TTCTTTATTTTTT-TTCTATTTGTCTAATTAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCA
1 TTCTTT-TTTTTTGTTCTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCA
* * * *
37050 TGATCTACAACCTTCGTGAAGGACTTAAAAGTCAA-TTTTATTGTTTCAATT-TGAAAAAAAAAA
65 TGATTTACAA-CTTCATGAAAGACTCAAAAGTCAATTTTTA-TGTTTCAATTCT----AAAAAAA
* * * * * **
37113 GCGCTTCTGAAATTTTGTGGTTTTGATTGTCGGTCTATTTAATA-TCATATAATTTTTGATCCGT
124 -TGCTTCTAAAATTTGGTGGTTTCGATTAT-GGTCTATTTAATACT-ATATAATTTTTGATCCAC
*
37177 ATGTCCGATTAAAGTTATTCAAGT-TTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGA
186 ATGTCCAATTAAAGTTATTCAAGTGTT-GGTTAAAAGGTTATTGCATGATCTA-GACTTTCATG-
*
37241 AGGACA-CGAAAGCTAAATTTGATATACGAGTTTCATGAAGGGA-TCAAAAGGGAATTTTTATGT
248 AGGA-ATCGAAAGCTAAATTTGATCTACGAGTTTCATGAA-GGACTCAAAA-GGAATTTTTATGT
* * * *
37304 TTCAAGATTTCCATCAACAAACATTTTCTTATTTGGCTTATTTATCGAATGATCATCATATTTTT
310 TTCAAGATCTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTT
* *
37369 CTACTTTATAATACTTAGTCCTTTACTAATTCTATCTTAATCGATTTAACATTTC-AG
375 CTACTTTATAATACTTAGTCTTTTACTAATTCTATCTTAATCGATTTAACACTTCAAG
** * * *
37426 --CTGTACTTTTTGTTTTATTTGTCTGATTAAGGTAATTCAGGTGTCTATTAAAAGATAATTTCA
1 TTCT-TTTTTTTTGTTCTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCA
* *
37489 TGATTTACAACTTTCTTGAAAGGATTCAAAAGTCAATTTTTATGTTTCAATTCT-AAAAAATG-T
65 TGATTTACAAC-TTCATGAAA-GACTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCT
* * * * * *
37552 TTTTAAAGTTGTTGGTTTCGATTGCA-GGTCTATTTAATACCAAATAATTTTCT-ATCCACATGT
128 TCTAAAATTTGGTGGTTTCGATT--ATGGTCTATTTAATACTATATAATTTT-TGATCCACATGT
* * * * * * * **
37615 CCAATTAAAATTATTCCAGTGTCGGTTAACAGGTTA-T---TGATCTACAGTTTTCATTAAGGGC
190 CCAATTAAAGTTATTCAAGTGTTGGTTAAAAGGTTATTGCATGATCTAGA-CTTTCA-TGAGGAA
*
37676 TCGAAAGCTAAATTTGATCTACGAG-TTCGATGAAGGGCTCAAAAGGAAATTTTTATGTTTCAAG
253 TCGAAAGCTAAATTTGATCTACGAGTTTC-ATGAAGGACTCAAAAGG-AATTTTTATGTTTCAAG
* * * * *
37740 ATCTCCACCAACAAACATTTTCCTATTTGAATTATTTATCAAATGA-CCCCGTATTTTTCTACTT
316 ATCTCCATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTT
* * *
37804 TATAATATTTAGTCTTTTACTAATTCTATTTTAATCGATTTAACGCTTCAAG
381 TATAATACTTAGTCTTTTACTAATTCTATCTTAATCGATTTAACACTTCAAG
* * *
37856 TTCTTTTTTTTTGTTCCATTTGTCTGATTAAGGTAATGCAAGTGTTTATTAAAAGGTAATTTCAT
1 TTCTTTTTTTTTGTTCTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCAT
*
37921 GATTTACAACTTCCATGAAAGACTCAAAAGCCAATTTTTATGTTTCAATTCTAAAAAAATGCTTC
66 GATTTACAACTT-CATGAAAGACTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCTTC
* * *
37986 CAAAATTTGGTCGTTTCGATTAATGGTCTGTTTAATACTATATAATTTTTGATCCACATGTCCAA
130 TAAAATTTGGTGGTTTCGATT-ATGGTCTATTTAATACTATATAATTTTTGATCCACATGTCCAA
* *
38051 TTAAAGTTATTTAAGTGTTGGTTAAAAGGTTATTGCATGATCTATGACTTTCATGAGGAATCTAA
194 TTAAAGTTATTCAAGTGTTGGTTAAAAGGTTATTGCATGATCTA-GACTTTCATGAGGAATC-GA
* * * *
38116 AAGCTAAATTTGATCTACGAGTTTTACGAAGGACTCATAAGAGAATTTTTATGTTTTAAGATCTC
257 AAGCTAAATTTGATCTACGAGTTTCATGAAGGACTCAAAAG-GAATTTTTATGTTTCAAGATCTC
* * * *
38181 CATTAACAAATATTTT-TTCTTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAC
321 CATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAA
* *
38245 TACTTAAT-TCTTTAATAATTCTATCTTAATCGATTTAACACTTCAA
386 TACTTAGTCT-TTTACTAATTCTATCTTAATCGATTTAACACTTCAA
38291 TTTTATTTTT
Statistics
Matches: 729, Mismatches: 101, Indels: 74
0.81 0.11 0.08
Matches are distributed among these distances:
429 67 0.09
430 140 0.19
431 80 0.11
432 83 0.11
433 2 0.00
434 77 0.11
435 31 0.04
436 146 0.20
437 4 0.01
438 8 0.01
439 63 0.09
440 22 0.03
441 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (432 bp):
TTCTTTTTTTTTGTTCTATTTGTCTGATTAAGGTAATTCAAGTGTCTATTAAAAGGTAATTTCAT
GATTTACAACTTCATGAAAGACTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAAATGCTTCT
AAAATTTGGTGGTTTCGATTATGGTCTATTTAATACTATATAATTTTTGATCCACATGTCCAATT
AAAGTTATTCAAGTGTTGGTTAAAAGGTTATTGCATGATCTAGACTTTCATGAGGAATCGAAAGC
TAAATTTGATCTACGAGTTTCATGAAGGACTCAAAAGGAATTTTTATGTTTCAAGATCTCCATCA
ACAAACATTTTCTTATTTGGATTATTTATCAAATGATCCTCATATTTTTCTACTTTATAATACTT
AGTCTTTTACTAATTCTATCTTAATCGATTTAACACTTCAAG
Found at i:39001 original size:12 final size:13
Alignment explanation
Indices: 38984--39012 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38974 CGTTTCATCT
38984 AAAAATCTA-GAC
1 AAAAATCTATGAC
38996 AAAAATCTATGAC
1 AAAAATCTATGAC
39009 AAAA
1 AAAA
39013 TGGGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAAATCTATGAC
Found at i:40471 original size:60 final size:60
Alignment explanation
Indices: 40398--40578 Score: 362
Period size: 60 Copynumber: 3.0 Consensus size: 60
40388 AAGCAAGATC
40398 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
1 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
40458 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
1 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
40518 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
1 TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
40578 T
1 T
40579 AATGTCACTG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 121 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (60 bp):
TCATTAAGGCCCAGAATCAAGCTCAACATTATACAGTAGATTGCATTAAGTTAAATAACA
Found at i:47771 original size:17 final size:17
Alignment explanation
Indices: 47751--47787 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
47741 GTGGCTTTGG
47751 AATGCAATTTTAGCTGC
1 AATGCAATTTTAGCTGC
47768 AATGCAATTTTAGCTGC
1 AATGCAATTTTAGCTGC
47785 AAT
1 AAT
47788 TTGCTTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (17 bp):
AATGCAATTTTAGCTGC
Found at i:61577 original size:13 final size:13
Alignment explanation
Indices: 61559--61584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61549 CTTGGCATGA
61559 GTGATGATTTTTG
1 GTGATGATTTTTG
61572 GTGATGATTTTTG
1 GTGATGATTTTTG
61585 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Done.