Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014426.1 Corchorus capsularis cultivar CVL-1 contig14447, 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: 61296
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:419 original size:49 final size:49
Alignment explanation
Indices: 347--444 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
337 TAAGTTTAGT
347 TTGTAATTTGGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATA
1 TTGTAATTTGGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATA
396 TTGTAATTTGGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATA
1 TTGTAATTTGGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATA
445 GTAGTTTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (49 bp):
TTGTAATTTGGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATA
Found at i:5371 original size:9 final size:9
Alignment explanation
Indices: 5355--5387 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5345 CCCCCCCCCC
5355 AAAA-AAAA
1 AAAAGAAAA
5363 AAAAGAAAA
1 AAAAGAAAA
5372 AAAAGAAAA
1 AAAAGAAAA
*
5381 AGAAGAA
1 AAAAGAA
5388 GAAGGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:5375 original size:15 final size:15
Alignment explanation
Indices: 5355--5384 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5345 CCCCCCCCCC
5355 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
5370 AAAAAAGAAAAAGAA
1 AAAAAAAAAAAAGAA
5385 GAAGAAGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:13398 original size:30 final size:31
Alignment explanation
Indices: 13338--13404 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
13328 AAATTGGGTG
13338 AGGGAC-CTAATTGCTCAATTAACTCAACTTC
1 AGGGACTC-AATTGCTCAATTAACTCAACTTC
* *
13369 GGGGACTCAATTGCTC-ATTAAGTTC-ACTTC
1 AGGGACTCAATTGCTCAATTAA-CTCAACTTC
13399 AGGGAC
1 AGGGAC
13405 CCATTTGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 15 0.48
31 15 0.48
32 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (31 bp):
AGGGACTCAATTGCTCAATTAACTCAACTTC
Found at i:20060 original size:14 final size:15
Alignment explanation
Indices: 20043--20089 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
20033 GCATTAGCAG
*
20043 AAAAATAAGAAG-GA
1 AAAAAAAAGAAGAGA
20057 AAAAAAAAGAAGAGA
1 AAAAAAAAGAAGAGA
20072 AAAAACAACAG-AGAGA
1 AAAAA-AA-AGAAGAGA
20088 AA
1 AA
20090 GAGGCGGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.38
15 7 0.24
16 9 0.31
17 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAGAGA
Found at i:27983 original size:31 final size:33
Alignment explanation
Indices: 27927--27989 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
27917 AAATTTATGT
*
27927 TTTCCGATTGTACCCTTATTTTTAAAA-ATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATATA
27959 TTTCCAATTGTACCCTT-TTTTTAAAACATAT
1 TTTCCAATTGTACCCTTATTTTTAAAACATAT
27990 TTCTAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (33 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATATA
Found at i:27999 original size:31 final size:32
Alignment explanation
Indices: 27933--28000 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
27923 ATGTTTTCCG
* *
27933 ATTGTACCCTTATTTTTAAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAAACATATTTCAA
27965 ATTGTACCCTT-TTTTT-AAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAAACATATTTC-AA
27996 ATTGT
1 ATTGT
28001 CATTGCCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 11 0.33
31 11 0.33
32 11 0.33
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (32 bp):
ATTGTACCCTTATTTTTAAAAACATATTTCAA
Found at i:28550 original size:168 final size:166
Alignment explanation
Indices: 28159--28609 Score: 557
Period size: 168 Copynumber: 2.7 Consensus size: 166
28149 TGAGTCATTT
*
28159 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
* * * * * ** *
28224 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTTTCTAGCT-CATCATCAATCCTT
65 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCAAAATCAAGCCTT
* * *
28288 GATGGAGATCTTTTATTAATTCCACTATTCTATTCAA
130 GATGGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * * *
28325 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCGAGAATTAAAAGTTATGATAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
*
28390 TTAAGTAATCTGTCAAGTAGGAAAAGACGGAAAAAAATAAGTTCTCTAACTCCAAAAGT-AAGCC
65 TTAAGTAATCTGTCAAGTAGGAAAAGAC-GAAAAAAATTAGTTCTCTAACTCCAAAA-TCAAGCC
*
28454 TTGGTAGG-GATCTTTTAGTAATTCCACTACTCTATTAAA
128 TTGAT-GGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * ** * * *
28493 GTTAATTGAAAAATGACCAAAAAGTCTAGTTATTTAATGACCTTAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACAT
* * *
28558 TTAAGTAATCGGTCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCTCACTCC
65 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCC
28610 TCATTAATCC
Statistics
Matches: 243, Mismatches: 37, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
166 83 0.34
167 41 0.17
168 116 0.48
169 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATAAAAAGTTAGGACATT
TAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCAAAATCAAGCCTTG
ATGGAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:29557 original size:19 final size:20
Alignment explanation
Indices: 29529--29566 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29519 TACTATTATT
29529 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
29549 TTTTG-ATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
29567 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:29785 original size:22 final size:21
Alignment explanation
Indices: 29730--29834 Score: 102
Period size: 22 Copynumber: 4.8 Consensus size: 21
29720 TCTCTATGTG
* *
29730 GTTATCAAAATTTCATAAGACG
1 GTTATCAAAATTTCATAGGA-A
* *
29752 GTTATTATAATTTCATGAGGAA
1 GTTATCAAAATTTCAT-AGGAA
* **
29774 GTTATCAAAATTCCATAGTGTG
1 GTTATCAAAATTTCATAG-GAA
*
29796 GTTAGCAAAATTTCATATGGAA
1 GTTATCAAAATTTCATA-GGAA
29818 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
29835 TGGTGTGGTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.03
22 60 0.91
23 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAA
Found at i:29799 original size:44 final size:45
Alignment explanation
Indices: 29760--29858 Score: 148
Period size: 44 Copynumber: 2.2 Consensus size: 45
29750 CGGTTATTAT
29760 AATTTCATGA-GGAAGTTATCAAAATTCCATA-GTGTGGTTAGCAA
1 AATTTCAT-ATGGAAGTTATCAAAATTCCATAGGTGTGGTTAGCAA
* *
29804 AATTTCATATGGAAGTTATCAAAATTTCATATGGTGTGGTTACCAA
1 AATTTCATATGGAAGTTATCAAAATTCCATA-GGTGTGGTTAGCAA
29850 AATTTCATA
1 AATTTCATA
29859 AGATCAGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.02
44 28 0.56
46 21 0.42
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (45 bp):
AATTTCATATGGAAGTTATCAAAATTCCATAGGTGTGGTTAGCAA
Found at i:29890 original size:46 final size:46
Alignment explanation
Indices: 29771--29891 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
29761 ATTTCATGAG
* * *
29771 GAAGTTATCAAAATTCCATA--GTGTGGTTAGCAAAATTTCATATG
1 GAAGTTATCAAAATTTCATATGGTGTGGTTACCAAAATTTCATATA
29815 GAAGTTATCAAAATTTCATATGGTGTGGTTACCAAAATTTCATA-A
1 GAAGTTATCAAAATTTCATATGGTGTGGTTACCAAAATTTCATATA
* *
29860 GATCAGGTTATTAAAATTTCTTA-GGT-TGGTTA
1 GA--A-GTTATCAAAATTTCATATGGTGTGGTTA
29892 TTGAAATTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 19 0.28
45 2 0.03
46 27 0.40
47 4 0.06
48 15 0.22
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (46 bp):
GAAGTTATCAAAATTTCATATGGTGTGGTTACCAAAATTTCATATA
Found at i:29893 original size:22 final size:22
Alignment explanation
Indices: 29728--29906 Score: 94
Period size: 22 Copynumber: 8.0 Consensus size: 22
29718 TGTCTCTATG
* * *
29728 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGT
* *
29750 CGGTTATTATAATTTCATGAGG-
1 TGGTTATTAAAATTTCAT-AGGT
** * *
29772 AAGTTATCAAAATTCCATA-GT
1 TGGTTATTAAAATTTCATAGGT
**
29793 GTGGTTAGCAAAATTTCATATGG-
1 -TGGTTATTAAAATTTCATA-GGT
** *
29816 AAGTTATCAAAATTTCATATGGT
1 TGGTTATTAAAATTTCATA-GGT
** *
29839 GTGGTTACCAAAATTTCATAAGAT
1 -TGGTTATTAAAATTTCAT-AGGT
* *
29863 CAGGTTATTAAAATTTCTTAGGT
1 -TGGTTATTAAAATTTCATAGGT
*
29886 TGGTTATTGAAATTTCATAGG
1 TGGTTATTAAAATTTCATAGG
29907 GTGCTTAATT
Statistics
Matches: 120, Mismatches: 29, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 80 0.67
23 5 0.04
24 32 0.27
25 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:29993 original size:22 final size:21
Alignment explanation
Indices: 29953--30085 Score: 92
Period size: 22 Copynumber: 6.1 Consensus size: 21
29943 AAGAGATATC
* *
29953 AAAATGTCATAGCGAGGTTAT
1 AAAATTTCATAGTGAGGTTAT
* *
29974 AAGAATTTCATAGTGTGGTTAAC
1 AA-AATTTCATAGTGAGGTT-AT
29997 AAAATTTCATTAG-GAGGTTACT
1 AAAATTTCA-TAGTGAGGTTA-T
* * *
30019 AATATTTCATGGGGAGGTTAT
1 AAAATTTCATAGTGAGGTTAT
*
30040 CAAAATTTTATAGTGTA-GTTAT
1 -AAAATTTCATAGTG-AGGTTAT
*
30062 CAAAATTTGATA-TGAAGGTTAT
1 -AAAATTTCATAGTG-AGGTTAT
30084 AA
1 AA
30086 GAGTCTCAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
21 11 0.12
22 72 0.80
23 7 0.08
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (21 bp):
AAAATTTCATAGTGAGGTTAT
Found at i:30014 original size:44 final size:44
Alignment explanation
Indices: 29952--30052 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
29942 AAAGAGATAT
* * *
29952 CAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGCGAGGTTACTAA-AATTTCATAGGGAGGTTAA
* * *
29996 CAAAATTTCATTAG-GAGGTTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCA-TAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
*
30040 CAAAATTTTATAG
1 CAAAATTTCATAG
30053 TGTAGTTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 3 0.06
44 39 0.81
45 6 0.12
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
Found at i:30163 original size:22 final size:23
Alignment explanation
Indices: 30137--30226 Score: 98
Period size: 22 Copynumber: 4.0 Consensus size: 23
30127 TTATCAAACC
*
30137 TCATAGAG-TGATTATCGAAATT
1 TCATAGAGATGATTATCAAAATT
30159 TCATAGAGATCAGATTATCAAAATT
1 TCATAGAGAT--GATTATCAAAATT
*
30184 T-ATAG-GAAGATTATCAAAATT
1 TCATAGAGATGATTATCAAAATT
* *
30205 TCATAGTGTTG-TTATCAAAATT
1 TCATAGAGATGATTATCAAAATT
30227 CCAAAGCGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
21 14 0.24
22 23 0.39
23 5 0.08
24 4 0.07
25 13 0.22
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (23 bp):
TCATAGAGATGATTATCAAAATT
Found at i:30194 original size:21 final size:24
Alignment explanation
Indices: 30146--30210 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
30136 CTCATAGAGT
*
30146 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
30171 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
30192 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
30211 TGTTGTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
23 2 0.05
24 4 0.11
25 13 0.34
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:30491 original size:22 final size:22
Alignment explanation
Indices: 30466--30690 Score: 83
Period size: 22 Copynumber: 10.4 Consensus size: 22
30456 AGTTTAGTTT
30466 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
30488 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
* * * *
30510 TCAAAATTTTATAGGAAGATTA
1 TCAAAATTTCATAAGAGGGTTA
* * * *
30532 ACAAAATTTCATAATAAGATTA
1 TCAAAATTTCATAAGAGGGTTA
**
30554 TCAAAAAATCATAAG-GAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
30576 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* * **
30592 TCAAGATTTCATGAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * **
30614 TCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATA-AGAGGGTTA
* * **
30637 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
*
30660 TCAAAATTTCAT-AGCGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
30682 TCACAATTT
1 TCAAAATTT
30691 TATATTGTGA
Statistics
Matches: 154, Mismatches: 34, Indels: 30
0.71 0.16 0.14
Matches are distributed among these distances:
16 12 0.08
17 1 0.01
20 1 0.01
21 6 0.04
22 95 0.62
23 39 0.25
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:30496 original size:44 final size:44
Alignment explanation
Indices: 30442--30673 Score: 135
Period size: 44 Copynumber: 5.4 Consensus size: 44
30432 TCAGGGAGGA
*
30442 TATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
* * * *
30486 TATCAAAATTTCATAGTATGTAG--ATCAAAATTTTATAGGAAGAT
1 TATCAAAATTTCATAGT-T-TAGTTATCAAAATTTCATAAGAGGGT
* * * **
30530 TAACAAAATTTCATA-ATAAGATTATCAAAAAATCATAAG-GAGGT
1 TATCAAAATTTCATAGTTTAG-TTATCAAAATTTCATAAGAG-GGT
* * **
30574 TATCAAAA-TT--T-G--TAGTTATCAAGATTTCATGAGAAAGT
1 TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
* ** * * **
30612 TATCAAAATTTTATAG-GGAGATTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGTTTAG--TTATCAAAATTTCATAAG-AGGGT
30658 TATCAAAATTTCATAG
1 TATCAAAATTTCATAG
30674 CGAGGTTATC
Statistics
Matches: 142, Mismatches: 30, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
38 24 0.17
39 4 0.03
41 4 0.03
42 2 0.01
43 4 0.03
44 68 0.48
45 15 0.11
46 21 0.15
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGTTTAGTTATCAAAATTTCATAAGAGGGT
Found at i:30639 original size:23 final size:23
Alignment explanation
Indices: 30611--30694 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
30601 CATGAGAAAG
30611 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGGAGAT
*
30634 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGAT
* * *
30657 TTATCAAAATTTCATAGCGAG-G
1 TTATCAAAATTTTATAGGGAGAT
*
30679 TTATCACAATTTTATA
1 TTATCAAAATTTTATA
30695 TTGTGATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 14 0.26
23 40 0.74
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGAT
Found at i:30899 original size:22 final size:22
Alignment explanation
Indices: 30874--30922 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
30864 TTCCTTAGGG
*
30874 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAACAAAATTT-ATAAAA
*
30896 AGGTTAAAGAAAATTTATAAAA
1 AGGTTAAACAAAATTTATAAAA
30918 AGGTT
1 AGGTT
30923 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (22 bp):
AGGTTAAACAAAATTTATAAAA
Found at i:31018 original size:22 final size:22
Alignment explanation
Indices: 31002--31052 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
30992 AAATAGTGTA
31002 ATTATCATAATTTAATAGAGAT
1 ATTATCATAATTTAATAGAGAT
* *
31024 GTTATCATAATTTCATATGA-AT
1 ATTATCATAATTTAATA-GAGAT
31046 ATT-TCAT
1 ATTATCAT
31053 TTAAACACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (22 bp):
ATTATCATAATTTAATAGAGAT
Found at i:31223 original size:5 final size:5
Alignment explanation
Indices: 31213--31242 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
31203 CACGGCTTAA
*
31213 TCGTG TCGTG TCGTG TCGTG TCGTA TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
31243 CCCCGTGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.20, G:0.37, T:0.40
Consensus pattern (5 bp):
TCGTG
Found at i:43687 original size:37 final size:36
Alignment explanation
Indices: 43637--43708 Score: 135
Period size: 37 Copynumber: 2.0 Consensus size: 36
43627 TGCTGCCTAC
43637 TTCAGGGCCTCATAAGAATTCAATCTCACCAAAATAG
1 TTCAGGGCCTCATAAGAATTCAATCTCA-CAAAATAG
43674 TTCAGGGCCTCATAAGAATTCAATCTCACAAAATA
1 TTCAGGGCCTCATAAGAATTCAATCTCACAAAATA
43709 TGACTATGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (36 bp):
TTCAGGGCCTCATAAGAATTCAATCTCACAAAATAG
Found at i:43725 original size:37 final size:37
Alignment explanation
Indices: 43638--43725 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
43628 GCTGCCTACT
** *
43638 TCAGGGCCTCATAAGAATTCAATCTCACCAAAATAGT
1 TCAGGGCAACATAAGAATTCAATCTCACCAAAATAGC
**
43675 TCAGGGCCTCATAAGAATTCAATCTCA-CAAAATATGAC
1 TCAGGGCAACATAAGAATTCAATCTCACCAAAATA-G-C
*
43713 T-ATGGCAACATAA
1 TCAGGGCAACATAA
43726 CATAATCTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 7 0.16
37 37 0.82
38 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.24
Consensus pattern (37 bp):
TCAGGGCAACATAAGAATTCAATCTCACCAAAATAGC
Found at i:51470 original size:36 final size:37
Alignment explanation
Indices: 51424--51496 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
51414 AGGTCATTGC
* *
51424 TACGTTTAAAGCTA-CTT-TTTTTTTTTTTTGTGAAA
1 TACGTTTAAAGCTAGCTTCTTCTTTTTTTTCGTGAAA
51459 TACGTTTTAAAGCTAGCTTCTTCTTTTTTTTCGTGAAA
1 TACG-TTTAAAGCTAGCTTCTTCTTTTTTTTCGTGAAA
51497 ATAAAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.12
36 10 0.30
37 3 0.09
38 16 0.48
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (37 bp):
TACGTTTAAAGCTAGCTTCTTCTTTTTTTTCGTGAAA
Found at i:52664 original size:7 final size:7
Alignment explanation
Indices: 52652--52677 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52642 ATTGACGTAC
52652 CAATTAG
1 CAATTAG
52659 CAATTAG
1 CAATTAG
52666 CAATTAG
1 CAATTAG
52673 CAATT
1 CAATT
52678 TAATTGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (7 bp):
CAATTAG
Found at i:52879 original size:2 final size:2
Alignment explanation
Indices: 52872--52905 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52862 CGAAAAGTCA
52872 AT AT AT AT 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 AT AT AT AT
52906 GAAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58058 original size:63 final size:65
Alignment explanation
Indices: 57965--58094 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 65
57955 CGATGAGAAG
*
57965 ATTAGAAAGCTTGCTATCAAATTAAATCTTAATTTCCAAAACAATGACAGCCACGATGGGAAAAT
1 ATTAGAAAGCTTGCTATCAAATT--ATCTTAATTTCCAAAACAATGACAACCACGATGGGAAAAT
58030 TA
64 TA
* *
58032 ATTAGAAAGCTTGCTATCAAA-T-TCTTAATTTCCAAAACAATGACAACTACGGTGGGAAAATTA
1 ATTAGAAAGCTTGCTATCAAATTATCTTAATTTCCAAAACAATGACAACCACGATGGGAAAATTA
58095 GAAAGCTATG
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
63 38 0.63
66 1 0.02
67 21 0.35
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (65 bp):
ATTAGAAAGCTTGCTATCAAATTATCTTAATTTCCAAAACAATGACAACCACGATGGGAAAATTA
Done.