Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006729.1 Corchorus capsularis cultivar CVL-1 contig06750, 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: 80699
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:340 original size:37 final size:38
Alignment explanation
Indices: 274--366 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
264 TTGGCTTTTC
*
274 GTTTCCAACGTCCTATTTAATTTTGTC-TTTTGTCTTT
1 GTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTATTT
**
311 GTTTCCAATCGTTGTATTTAATTTT-TCTTTTTGTATTT
1 GTTTCCAA-CGTCCTATTTAATTTTGTCTTTTTGTATTT
*
349 GTCTCCAACGTCCTATTT
1 GTTTCCAACGTCCTATTT
367 GGGCTTAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 18 0.38
38 30 0.62
ACGTcount: A:0.15, C:0.18, G:0.11, T:0.56
Consensus pattern (38 bp):
GTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTATTT
Found at i:1557 original size:20 final size:19
Alignment explanation
Indices: 1532--1569 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1522 TACTATTATT
1532 TTTTAAATTT-AATATTTTAC
1 TTTT-AATTTCAAT-TTTTAC
1552 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
1570 AATGCCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:1763 original size:22 final size:22
Alignment explanation
Indices: 1735--1859 Score: 87
Period size: 22 Copynumber: 5.7 Consensus size: 22
1725 TGTCTCTATG
*
1735 TGGTTATCAAAATTTCATAAGA
1 TGGTTACCAAAATTTCATAAGA
** * *
1757 TGGTTATTATAATTTCATGAGGA
1 TGGTTACCAAAATTTCAT-AAGA
* * *
1780 -GGTTATCAAAATTCCAT-AGCG
1 TGGTTACCAAAATTTCATAAG-A
*
1801 TGGTTACCAAAATTTCATATGGA
1 TGGTTACCAAAATTTCATA-AGA
* *
1824 -AGTTACCAAAATTTCAT-AGTG
1 TGGTTACCAAAATTTCATAAG-A
1845 TGGTTACCAAAATTT
1 TGGTTACCAAAATTT
1860 TTATAGGATC
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
20 2 0.03
22 74 0.93
23 3 0.04
24 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTACCAAAATTTCATAAGA
Found at i:1805 original size:44 final size:43
Alignment explanation
Indices: 1736--1859 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 43
1726 GTCTCTATGT
* ** *
1736 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGGTGGTTACCAAAATTTCAT-ATGGA
*
1780 GGTTATCAAAATTCCATAGCGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTTCATATGGA
* *
1824 AGTTACCAAAATTTCATAGTGTGGTTACCAAAATTT
1 GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTT
1860 TTATAGGATC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.04
44 66 0.96
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGTGGTTACCAAAATTTCATATGGA
Found at i:1984 original size:22 final size:22
Alignment explanation
Indices: 1959--2102 Score: 127
Period size: 22 Copynumber: 6.6 Consensus size: 22
1949 GGTTATCAAA
* *
1959 GAGGTTATCAAAATGTCATAGC
1 GAGGTTATCAAAATTTCATAGT
1981 GAGGTTAT-AAGAATTTCATAGT
1 GAGGTTATCAA-AATTTCATAGT
* *
2003 GTGGTTAACAAAATTTCATTAG-
1 GAGGTTATCAAAATTTCA-TAGT
* * *
2025 GAGGTTA-CTAATATTTCATGGG
1 GAGGTTATC-AAAATTTCATAGT
* *
2047 GAGGTTATCAAAATTTTATATT
1 GAGGTTATCAAAATTTCATAGT
*
2069 GTGGTTATCAAAATTTCATA-T
1 GAGGTTATCAAAATTTCATAGT
2090 GAAGGTTAT-AAAA
1 G-AGGTTATCAAAA
2103 GTCTCAATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
21 11 0.11
22 83 0.83
23 6 0.06
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:2180 original size:22 final size:22
Alignment explanation
Indices: 2152--2357 Score: 118
Period size: 22 Copynumber: 9.3 Consensus size: 22
2142 TTGTCCAATC
*
2152 TCATAGAGTGATTATCGAAATT
1 TCATAGAGTGATTATCAAAATT
2174 TCATAGAGATCGGATTATCAAAATT
1 TCATAGAG-T--GATTATCAAAATT
**
2199 T-ATAGAAAGATTATCAAAATT
1 TCATAGAGTGATTATCAAAATT
*
2220 TCATAGAGTTG-TTATCAAAAAT
1 TCATAGAG-TGATTATCAAAATT
* * *
2242 TCAAAGCGAGATTATCAAAATT
1 TCATAGAGTGATTATCAAAATT
* *
2264 ACATA-ATATGATTAT-AAGAATT
1 TCATAGA-GTGATTATCAA-AATT
* * * * *
2286 TCATAAAGGGGTCAACAAAATT
1 TCATAGAGTGATTATCAAAATT
* * * * *
2308 TTATAAAGAGGTTATCAAATTT
1 TCATAGAGTGATTATCAAAATT
*
2330 TCAGA-ATGTGATTA-CAAAAATT
1 TCATAGA-GTGATTATC-AAAATT
2352 TCATAG
1 TCATAG
2358 TGGTATGTCT
Statistics
Matches: 139, Mismatches: 32, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
21 19 0.14
22 97 0.70
23 5 0.04
24 5 0.04
25 13 0.09
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATAGAGTGATTATCAAAATT
Found at i:3001 original size:15 final size:15
Alignment explanation
Indices: 2981--3014 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2971 AAAACAACTT
2981 ATAAAACAAGTTA-TA
1 ATAAAACAA-TTAGTA
2996 ATAAAACAATTAGTA
1 ATAAAACAATTAGTA
3011 ATAA
1 ATAA
3015 TAAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAAAACAATTAGTA
Found at i:6833 original size:11 final size:11
Alignment explanation
Indices: 6805--6834 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6795 CCCCTCAGCG
*
6805 TCTTTTCCTTT
1 TCTTTTTCTTT
6816 TCTTTTTCTTT
1 TCTTTTTCTTT
6827 TCTTTTTC
1 TCTTTTTC
6835 ATTTAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:14799 original size:22 final size:22
Alignment explanation
Indices: 14769--14974 Score: 105
Period size: 22 Copynumber: 9.6 Consensus size: 22
14759 TCAGGGAGGA
***
14769 TATCAAAATTTCATAATTTAGT
1 TATCAAAATTTCATAAGAGAGT
*
14791 TTTCAAAATTTCATAAGAGAGT
1 TATCAAAATTTCATAAGAGAGT
* *
14813 TATCAAAATTTCAT-AGTGTGT
1 TATCAAAATTTCATAAGAGAGT
* *
14834 AGATCAAAATTTCATATG-GAGAT
1 -TATCAAAATTTCATAAGAGAG-T
14857 TAAT-AAAATTTCATAATGAG-GT
1 T-ATCAAAATTTCATAA-GAGAGT
** * *
14879 TATCAAAAAATCAT-CGGGAGGT
1 TATCAAAATTTCATAAGAGA-GT
*
14901 TATCAAAA-TT--T--G-TAGT
1 TATCAAAATTTCATAAGAGAGT
* * *
14917 TATCAAGATTTTATAAGAAAGT
1 TATCAAAATTTCATAAGAGAGT
14939 TATCAAAATTTCAT-AGCA-AGGT
1 TATCAAAATTTCATAAG-AGA-GT
*
14961 TATCACAATTTCAT
1 TATCAAAATTTCAT
14975 TGTGTGATTA
Statistics
Matches: 144, Mismatches: 23, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
16 9 0.06
17 3 0.02
18 1 0.01
19 2 0.01
20 2 0.01
21 12 0.08
22 108 0.75
23 6 0.04
24 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAGAGT
Found at i:14884 original size:44 final size:43
Alignment explanation
Indices: 14769--14953 Score: 134
Period size: 44 Copynumber: 4.3 Consensus size: 43
14759 TCAGGGAGGA
* *
14769 TATCAAAATTTCATAATTTAGTTTTCAAAATTTCATAAGAGAGT
1 TATCAAAATTTCATAA-TGAGTTATCAAAATTTCATAAGAGAGT
* * * *
14813 TATCAAAATTTCATAGTGTGTAGATCAAAATTTCATATG-GAGAT
1 TATCAAAATTTCATAATGAGT-TATCAAAATTTCATAAGAGAG-T
** * *
14857 TAAT-AAAATTTCATAATGAGGTTATCAAAAAATCAT-CGGGAGGT
1 T-ATCAAAATTTCATAATGA-GTTATCAAAATTTCATAAGAGA-GT
* * * *
14901 TATCAAAA-TT--T-GT-AGTTATCAAGATTTTATAAGAAAGT
1 TATCAAAATTTCATAATGAGTTATCAAAATTTCATAAGAGAGT
14939 TATCAAAATTTCATA
1 TATCAAAATTTCATA
14954 GCAAGGTTAT
Statistics
Matches: 109, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
38 22 0.20
39 5 0.05
40 1 0.01
41 2 0.02
43 11 0.10
44 63 0.58
45 5 0.05
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAATGAGTTATCAAAATTTCATAAGAGAGT
Found at i:14985 original size:22 final size:22
Alignment explanation
Indices: 14960--15015 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
14950 CATAGCAAGG
**
14960 TTATCACAATTTCATTGTGTGA
1 TTATCACAATTTCAGAGTGTGA
*
14982 TTATCAAAATTTCAGAGTGTGA
1 TTATCACAATTTCAGAGTGTGA
*
15004 TTACTAACAATT
1 TTA-TCACAATT
15016 CATATGGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCACAATTTCAGAGTGTGA
Found at i:15062 original size:22 final size:22
Alignment explanation
Indices: 15037--15099 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
15027 TTTTAAATTT
*
15037 TCATAACGTGGTTATCAATATA
1 TCATAACGTGGTTATCAACATA
** * *
15059 TCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAACATA
**
15081 TCATAGTGTTGGTTATCAA
1 TCATAACG-TGGTTATCAA
15100 AATTTCATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (22 bp):
TCATAACGTGGTTATCAACATA
Found at i:15098 original size:23 final size:22
Alignment explanation
Indices: 15044--15099 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
15034 TTTTCATAAC
*
15044 GTGGTTATCAATATATCATATG
1 GTGGTTATCAACATATCATATG
* *
15066 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAACATATCATA-TG
*
15089 TTGGTTATCAA
1 GTGGTTATCAA
15100 AATTTCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAACATATCATATG
Found at i:15193 original size:21 final size:22
Alignment explanation
Indices: 15159--15204 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
15149 CTTAGGGAGA
* *
15159 TTAACAAAATTTTATAAGAAGG
1 TTAACAAAAATTTATAAAAAGG
15181 TTAA-AAAAATTTATAAAAAGG
1 TTAACAAAAATTTATAAAAAGG
15202 TTA
1 TTA
15205 TCGAAATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (22 bp):
TTAACAAAAATTTATAAAAAGG
Found at i:15662 original size:2 final size:2
Alignment explanation
Indices: 15655--15679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15645 CTCAGTTTTA
15655 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15680 ACTAGTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18633 original size:13 final size:13
Alignment explanation
Indices: 18615--18640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18605 GGTGATAAAG
18615 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
18628 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
18641 GGAAAAGGCT
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:18865 original size:8 final size:7
Alignment explanation
Indices: 18819--18863 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
18809 AGAAAAGAAA
18819 GAAAAAG
1 GAAAAAG
18826 G--AAAG
1 GAAAAAG
18831 GAAAAA-
1 GAAAAAG
18837 GAAAAAG
1 GAAAAAG
18844 GAAAAAGG
1 GAAAAA-G
*
18852 GAAATAG
1 GAAAAAG
18859 GAAAA
1 GAAAA
18864 TAAGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.16
6 6 0.19
7 15 0.47
8 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (7 bp):
GAAAAAG
Found at i:21468 original size:30 final size:31
Alignment explanation
Indices: 21432--21504 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 31
21422 AAGGATCCAT
21432 TGGCCGGTTGT-GCGCG-GATGCCCCATGCGA
1 TGGCCGGTTGTGGCG-GTGATGCCCCATGCGA
*
21462 TGGCCGGTTGTGGCTGGTTGATGCCGCATGCGA
1 TGGCCGGTTGTGGC-GG-TGATGCCCCATGCGA
21495 TGGCCGGTTG
1 TGGCCGGTTG
21505 CCCCATGCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
30 11 0.29
31 3 0.08
32 1 0.03
33 23 0.61
ACGTcount: A:0.08, C:0.25, G:0.42, T:0.25
Consensus pattern (31 bp):
TGGCCGGTTGTGGCGGTGATGCCCCATGCGA
Found at i:21542 original size:12 final size:12
Alignment explanation
Indices: 21527--21558 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21517 GCGCATGCGA
21527 TGGCCGGTCAAG
1 TGGCCGGTCAAG
*
21539 TGGCCGGTCATG
1 TGGCCGGTCAAG
21551 TGGCCGGT
1 TGGCCGGT
21559 GTTGCGCGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (12 bp):
TGGCCGGTCAAG
Found at i:26485 original size:23 final size:23
Alignment explanation
Indices: 26458--26501 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
26448 TACTTTTATT
26458 TGATCTTTTAAAGCTTCTTGAGG
1 TGATCTTTTAAAGCTTCTTGAGG
26481 TGATCTTTTAAAGCTTCTTGA
1 TGATCTTTTAAAGCTTCTTGA
26502 TAGACCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (23 bp):
TGATCTTTTAAAGCTTCTTGAGG
Found at i:31900 original size:14 final size:14
Alignment explanation
Indices: 31877--31909 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
31867 GAAGGAGGCT
*
31877 TTGAAGAATTGAAA
1 TTGAAAAATTGAAA
31891 TTGAAAAATTGAAA
1 TTGAAAAATTGAAA
31905 TTGAA
1 TTGAA
31910 GCATGGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (14 bp):
TTGAAAAATTGAAA
Found at i:31921 original size:36 final size:36
Alignment explanation
Indices: 31877--32350 Score: 211
Period size: 36 Copynumber: 12.6 Consensus size: 36
31867 GAAGGAGGCT
31877 TTGAAGAATTGAAATTGAAAAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAAAATTGAAATTGAAGCA
* * *
31913 TGGAAGAATCGAAATTGAAGCATTGACATATTGAAATTGAAACA
1 TTGAAGAATTGAAATTG-A--A---A-A-ATTGAAATTGAAGCA
* * * * * *
31957 TTG-ACATTTGGAATTTGAAGAATTGGATTTGAAGCA
1 TTGAAGAATT-GAAATTGAAAAATTGAAATTGAAGCA
* * * *
31993 ATGAA-ATATTGAGATTGAAACATTGAAAAATTGAAGTA
1 TTGAAGA-ATTGAAATTGAAAAATTG--AAATTGAAGCA
* ** * *
32031 TTGAAGAATCGAAATTGAAGCATTGACATTTGGAA--T
1 TTGAAGAATTGAAATTGAAAAATTGA-AATT-GAAGCA
* ** *
32067 TTGAAGAACTGAAATTGAAGCATTGAAGGATTGAA--T
1 TTGAAGAATTGAAATTGAAAAATTGAA--ATTGAAGCA
32103 TTGAAGAATTGAAATTGAAGCACTAAAGTTGAAATTGAAGCA
1 TTGAAGAATTGAAATTG-A--A--AAA-TTGAAATTGAAGCA
*
32145 TTGAAGAATTGAAATTG--AAATTGAAACATTGAAGAA
1 TTGAAGAATTGAAATTGAAAAATTG-AA-ATTGAAGCA
* ** *
32181 TTG-A-AATTGAAACACTGAAGGATTGAAATTAAAGCA
1 TTGAAGAATTG-AA-ATTGAAAAATTGAAATTGAAGCA
* *
32217 TTGAA-AGATTGAATTTGAAGAATTGAAATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATT---GAA---AAATTGAAATTGAAGCA
* *
32259 TTGAAGAATTGAATTTGAAGAATTGAAATTGAAAG-A
1 TTGAAGAATTGAAATTGAAAAATTGAAATTG-AAGCA
* * *
32295 TTGAAGGATTGAATTTGAAGAATTGAAATTGAA-C-
1 TTGAAGAATTGAAATTGAAAAATTGAAATTGAAGCA
*
32329 TTGAAGCATTGAGGAATTGAAA
1 TTGAAGAATTGA--AATTGAAA
32351 TTGATGAATT
Statistics
Matches: 341, Mismatches: 52, Indels: 90
0.71 0.11 0.19
Matches are distributed among these distances:
34 19 0.06
35 11 0.03
36 159 0.47
37 19 0.06
38 38 0.11
39 9 0.03
40 6 0.02
41 2 0.01
42 50 0.15
43 6 0.02
44 22 0.06
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (36 bp):
TTGAAGAATTGAAATTGAAAAATTGAAATTGAAGCA
Found at i:31948 original size:22 final size:22
Alignment explanation
Indices: 31898--31981 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
31888 AAATTGAAAA
* *
31898 ATTGAAATTGAAGCATGGA-AGA
1 ATTGAAATTGAAGCATTGACA-T
*
31920 ATCGAAATTGAAGCATTGACAT
1 ATTGAAATTGAAGCATTGACAT
*
31942 ATTGAAATTGAAACATTGACAT
1 ATTGAAATTGAAGCATTGACAT
* *
31964 -TTGGAATTTGAAGAATTG
1 ATT-GAAATTGAAGCATTG
31982 GATTTGAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
21 2 0.04
22 49 0.94
23 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (22 bp):
ATTGAAATTGAAGCATTGACAT
Found at i:31959 original size:14 final size:14
Alignment explanation
Indices: 31884--31960 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
31874 GCTTTGAAGA
*
31884 ATTGAAATTGAAAA
1 ATTGAAATTGAAAC
*
31898 ATTGAAATTGAAGC
1 ATTGAAATTGAAAC
* *
31912 ATGGAAGAATCG-AA-
1 ATTG-A-AATTGAAAC
* *
31926 ATTGAAGCATTGACAT
1 ATTGAA--ATTGAAAC
31942 ATTGAAATTGAAAC
1 ATTGAAATTGAAAC
31956 ATTGA
1 ATTGA
31961 CATTTGGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 32 0.68
15 3 0.06
16 10 0.21
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.27
Consensus pattern (14 bp):
ATTGAAATTGAAAC
Found at i:32003 original size:22 final size:22
Alignment explanation
Indices: 31972--32035 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
31962 ATTTGGAATT
* *
31972 TGAAGAATTG-GATTTGAAGCAA
1 TGAAAAATTGAGA-TTGAAACAA
* *
31994 TGAAATATTGAGATTGAAACAT
1 TGAAAAATTGAGATTGAAACAA
32016 TGAAAAATTGAAGTATTGAA
1 TGAAAAATTG-AG-ATTGAA
32036 GAATCGAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 24 0.71
23 4 0.12
24 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (22 bp):
TGAAAAATTGAGATTGAAACAA
Found at i:32092 original size:22 final size:21
Alignment explanation
Indices: 32067--32307 Score: 163
Period size: 22 Copynumber: 11.2 Consensus size: 21
32057 CATTTGGAAT
*
32067 TTGAAGAACTGAAATTGAAGCA
1 TTGAA-AATTGAAATTGAAGCA
* * *
32089 TTGAAGGATTGAATTTGAAGAA
1 TTGAA-AATTGAAATTGAAGCA
* *
32111 TTG-AAATTGAAGCACTAAAG--
1 TTGAAAATTGAA--ATTGAAGCA
*
32131 TTG-AAATTGAAGCATTGAAGAA
1 TTGAAAATTGAA--ATTGAAGCA
*
32153 TTG-AAATTGAAATTGAAACA
1 TTGAAAATTGAAATTGAAGCA
*
32173 TTGAAGAATTGAAATTGAAACA
1 TTGAA-AATTGAAATTGAAGCA
* * *
32195 CTGAAGGATTGAAATTAAAGCA
1 TTGAA-AATTGAAATTGAAGCA
* *
32217 TTGAAAGATTGAATTTGAAGAA
1 TTGAAA-ATTGAAATTGAAGCA
*
32239 TTG-AAATTGAAATTGAAACA
1 TTGAAAATTGAAATTGAAGCA
* *
32259 TTGAAGAATTGAATTTGAAGAA
1 TTGAA-AATTGAAATTGAAGCA
*
32281 TTG-AAATTGAAAGATTGAAGGA
1 TTGAAAATTG-AA-ATTGAAGCA
32303 TTGAA
1 TTGAA
32308 TTTGAAGAAT
Statistics
Matches: 178, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
20 54 0.30
21 8 0.04
22 115 0.65
23 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (21 bp):
TTGAAAATTGAAATTGAAGCA
Found at i:32106 original size:14 final size:14
Alignment explanation
Indices: 32088--32375 Score: 166
Period size: 14 Copynumber: 20.9 Consensus size: 14
32078 AAATTGAAGC
*
32088 ATTGAAGGATTGAA
1 ATTGAAGAATTGAA
*
32102 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
32116 ATTGAAGCACT-AA
1 ATTGAAGAATTGAA
32129 AGTTG-A-AATTGAA
1 A-TTGAAGAATTGAA
32142 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
32158 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
32171 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
*
32186 ATTGAA-ACACTGAA
1 ATTGAAGA-ATTGAA
*
32200 GGATTG-A-AATTAAA
1 --ATTGAAGAATTGAA
32214 GCATTGAA-AGATTGAA
1 --ATTGAAGA-ATTGAA
*
32230 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
32244 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
32257 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
*
32272 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
32286 ATTG-A-AA--G--
1 ATTGAAGAATTGAA
*
32294 ATTGAAGGATTGAA
1 ATTGAAGAATTGAA
*
32308 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
32322 ATTG-A-ACTTGAA
1 ATTGAAGAATTGAA
*
32334 GCATTGAGGAATTGAA
1 --ATTGAAGAATTGAA
*
32350 ATTGATGAATT-AGA
1 ATTGAAGAATTGA-A
*
32364 ATTGAAGGATTG
1 ATTGAAGAATTG
32376 TTGGAATGCC
Statistics
Matches: 216, Mismatches: 26, Indels: 63
0.71 0.09 0.21
Matches are distributed among these distances:
8 4 0.02
9 1 0.00
10 2 0.01
12 21 0.10
13 16 0.07
14 127 0.59
15 13 0.06
16 32 0.15
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:32285 original size:78 final size:78
Alignment explanation
Indices: 31883--32375 Score: 322
Period size: 78 Copynumber: 6.2 Consensus size: 78
31873 GGCTTTGAAG
* * * * * * *
31883 AATTG-AA-ATTGAAAAATTGAAATTGAAGCATGGAAGAATCGAAATTGAAGCATTGACA-TATT
1 AATTGAAAGATTGAAAGATTGAATTTGAAGAATTG-A-AATTGAAATTGAAACATTGA-AGAATT
31945 GAAATTGAA-ACATTGA
63 GAAATTGAAGA-ATTGA
* * * * * *
31961 CATTTGGAA-TTTG-AAGAATTGGATTTGAAGCAA-TGAAATATTGAGATTGAAACATTGAAAAA
1 -AATTGAAAGATTGAAAG-ATTGAATTTGAAG-AATTG-AA-ATTGAAATTGAAACATTGAAGAA
*
32023 TTGAAGTATTGAAGAATCGA
61 TTGAA--ATTGAAGAATTGA
* * * *
32043 AATTG-AAGCATTGACA-TTTGGAATTTGAAGAACTGAAATTG-AA--G---CATTGAAGGATTG
1 AATTGAAAG-ATTGAAAGATT-GAATTTGAAGAATTGAAATTGAAATTGAAACATTGAAGAATTG
*
32100 AATTTGAAGAATTGA
64 AAATTGAAGAATTGA
* *
32115 AATTG-AAGCACT-AAAGTTGAAATTGAAGCATTGAAGAATTGAAATTGAAATTGAAACATTGAA
1 AATTGAAAG-ATTGAAA---G--ATTGAA--TTTGAAGAATTGAAATTGAAATTGAAACATTGAA
32178 GAATTGAAATTGAAACACTGAAGGATTGA
58 GAATTGAAATTG--A-A--G-A--ATTGA
32207 AATT-AAAGCATTGAAAGATTGAATTTGAAGAATTGAAATTGAAATTGAAACATTGAAGAATTGA
1 AATTGAAAG-ATTGAAAGATTGAATTTGAAGAATTGAAATTGAAATTGAAACATTGAAGAATTGA
*
32271 ATTTGAAGAATTGA
65 AATTGAAGAATTGA
* * * *
32285 AATTGAAAGATTGAAGGATTGAATTTGAAGAATTGAAATTGAACTTGAAGCATTGAGGAATTGAA
1 AATTGAAAGATTGAAAGATTGAATTTGAAGAATTGAAATTGAAATTGAAACATTGAAGAATTGAA
*
32350 ATTGATGAATT-A
66 ATTGAAGAATTGA
*
32362 GAATTGAAGGATTG
1 -AATTGAAAGATTG
32376 TTGGAATGCC
Statistics
Matches: 336, Mismatches: 39, Indels: 79
0.74 0.09 0.17
Matches are distributed among these distances:
71 2 0.01
72 22 0.07
74 13 0.04
76 3 0.01
77 4 0.01
78 98 0.29
79 15 0.04
80 48 0.14
81 13 0.04
82 24 0.07
83 3 0.01
84 18 0.05
86 45 0.13
87 1 0.00
88 6 0.02
89 1 0.00
90 2 0.01
92 15 0.04
93 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (78 bp):
AATTGAAAGATTGAAAGATTGAATTTGAAGAATTGAAATTGAAATTGAAACATTGAAGAATTGAA
ATTGAAGAATTGA
Found at i:32289 original size:28 final size:28
Alignment explanation
Indices: 32014--32354 Score: 193
Period size: 28 Copynumber: 12.2 Consensus size: 28
32004 AGATTGAAAC
* *
32014 ATTGAAAAATTGAAGTATTGAAGAATCGAA
1 ATTG-AAAATTGAA-CATTGAAGAATTGAA
*
32044 ATTGAAGCATTG-ACATTTG--GAATTTGAAGA
1 ATTGAA-AATTGAACA-TTGAAGAA-TTG-A-A
* *
32074 ACTG-AAATTGAAGCATTGAAGGATTGAA
1 ATTGAAAATTGAA-CATTGAAGAATTGAA
* * *
32102 TTTGAAGAATTGAA-ATTGAAGCACT-AA
1 ATTGAA-AATTGAACATTGAAGAATTGAA
32129 AGTTG-AAATTGAAGCATTGAAGAATTGAA
1 A-TTGAAAATTGAA-CATTGAAGAATTGAA
32158 ATTG-AAATTGAAACATTGAAGAATTGAA
1 ATTGAAAATTG-AACATTGAAGAATTGAA
* * *
32186 ATTGAAACACTGAAGGATTG-A-AATTAAA
1 ATTGAAA-ATTGAA-CATTGAAGAATTGAA
*
32214 GCATTGAAAGATTGAA-TTTGAAGAATTGAA
1 --ATTGAAA-ATTGAACATTGAAGAATTGAA
32244 ATTG-AAATTGAAACATTGAAGAATTGAA
1 ATTGAAAATTG-AACATTGAAGAATTGAA
*
32272 TTTGAAGAATTGAA-ATTG-A-AA--G--
1 ATTGAA-AATTGAACATTGAAGAATTGAA
* *
32294 ATTGAAGGATTGAA-TTTGAAGAATTGAA
1 ATTGAA-AATTGAACATTGAAGAATTGAA
* *
32322 ATTG-AACTTGAAGCATTGAGGAATTGAA
1 ATTGAAAATTGAA-CATTGAAGAATTGAA
32350 ATTGA
1 ATTGA
32355 TGAATTAGAA
Statistics
Matches: 246, Mismatches: 29, Indels: 73
0.71 0.08 0.21
Matches are distributed among these distances:
22 15 0.06
23 1 0.00
24 3 0.01
26 19 0.08
27 12 0.05
28 112 0.46
29 28 0.11
30 54 0.22
31 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (28 bp):
ATTGAAAATTGAACATTGAAGAATTGAA
Found at i:32312 original size:22 final size:22
Alignment explanation
Indices: 32103--32360 Score: 93
Period size: 22 Copynumber: 12.1 Consensus size: 22
32093 AGGATTGAAT
* *
32103 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGGATTGAAATTGAAGAA
* * *
32125 CT-AAAG-TTGAAATTGAAGCA
1 TTGAAGGATTGAAATTGAAGAA
*
32145 TTGAAGAATTGAAATTG-A-AA
1 TTGAAGGATTGAAATTGAAGAA
**
32165 TTGAAACATTGAAGAATTG-A-AA
1 TTGAAGGATTG-A-AATTGAAGAA
** *
32187 TTGAAACACTGAAGGATTG-A-AA
1 TTGAAGGATTGAA--ATTGAAGAA
* * *
32209 TTAAAGCATTGAAAGATTG-A-AT
1 TTGAAGGATTG-AA-ATTGAAGAA
*
32231 TTGAAGAATTGAAATTG-A-AA
1 TTGAAGGATTGAAATTGAAGAA
** *
32251 TTGAAACATTGAAGAATTG-A-AT
1 TTGAAGGATTG-A-AATTGAAGAA
*
32273 TTGAAGAATTGAAATTGAA-AGA
1 TTGAAGGATTGAAATTGAAGA-A
*
32295 TTGAAGGATTGAATTTGAAGAA
1 TTGAAGGATTGAAATTGAAGAA
* *
32317 TTGAA--ATTGAACTTGAAGCA
1 TTGAAGGATTGAAATTGAAGAA
*
32337 TTG-AGGAATTGAAATTGATGAA
1 TTGAAGG-ATTGAAATTGAAGAA
32359 TT
1 TT
32361 AGAATTGAAG
Statistics
Matches: 191, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.01
20 62 0.32
21 13 0.07
22 112 0.59
23 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (22 bp):
TTGAAGGATTGAAATTGAAGAA
Found at i:32446 original size:43 final size:42
Alignment explanation
Indices: 32377--32462 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
32367 GAAGGATTGT
* *
32377 TGGAATGCCCTCCCTTCGGAGCAACTGAAAACTGTAAAGTTG
1 TGGAATGCCCCCCCTTCGGAGCAACTGAAAACTGAAAAGTTG
* * *
32419 TGGAGATGCCCCCCCTTGGGAGTAACTGAAGACTGAAAAGTTG
1 TGGA-ATGCCCCCCCTTCGGAGCAACTGAAAACTGAAAAGTTG
32462 T
1 T
32463 AAATTGAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 4 0.11
43 34 0.89
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (42 bp):
TGGAATGCCCCCCCTTCGGAGCAACTGAAAACTGAAAAGTTG
Found at i:32588 original size:37 final size:38
Alignment explanation
Indices: 32532--32619 Score: 133
Period size: 37 Copynumber: 2.3 Consensus size: 38
32522 AGCAACCGAC
* *
32532 AACTGTTGAAAGATGACCTGTTTCCAGTC-AACTTGAT
1 AACTGCTGAAAGACGACCTGTTTCCAGTCGAACTTGAT
* *
32569 AAGTGCTGAAAGACGACCTGTTTCCAGTCGATCTTGAT
1 AACTGCTGAAAGACGACCTGTTTCCAGTCGAACTTGAT
32607 AACTGCTGAAAGA
1 AACTGCTGAAAGA
32620 TAACCTCTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 26 0.58
38 19 0.42
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (38 bp):
AACTGCTGAAAGACGACCTGTTTCCAGTCGAACTTGAT
Found at i:32691 original size:22 final size:22
Alignment explanation
Indices: 32663--32705 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
32653 CAGTCAAGTT
32663 TGATAATTTGGAA-GATGACCTC
1 TGATAATTT-GAAGGATGACCTC
32685 TGATAATTTGAAGGATGACCT
1 TGATAATTTGAAGGATGACCT
32706 GTTTTCAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (22 bp):
TGATAATTTGAAGGATGACCTC
Found at i:32751 original size:22 final size:22
Alignment explanation
Indices: 32721--32765 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32711 CAGTCAAGCT
* * *
32721 TGATTATTTGGAAGATGACCTG
1 TGATAATTTGAAAGATGAACTG
32743 TGATAATTTGAAAGATGAACTG
1 TGATAATTTGAAAGATGAACTG
32765 T
1 T
32766 TTTCAGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (22 bp):
TGATAATTTGAAAGATGAACTG
Found at i:32781 original size:58 final size:58
Alignment explanation
Indices: 32575--32800 Score: 263
Period size: 58 Copynumber: 3.8 Consensus size: 58
32565 TGATAAGTGC
* * * * * * * * *
32575 TGAAAGACGACCTGTTTCCAGTCGATCTTGATAACTGCTGAAAGATAACCTCTGATAATA
1 TGAAAGATGACCTGTTTTCAGTCAAGCTTGATTA-T-TTGGAAGATGACCTCTGATAATT
* * *
32635 TGAAAGATGACCTGTTTCCAGTCAAGTTTGATAATTTGGAAGATGACCTCTGATAATT
1 TGAAAGATGACCTGTTTTCAGTCAAGCTTGATTATTTGGAAGATGACCTCTGATAATT
* *
32693 TGAAGGATGACCTGTTTTCAGTCAAGCTTGATTATTTGGAAGATGACCTGTGATAATT
1 TGAAAGATGACCTGTTTTCAGTCAAGCTTGATTATTTGGAAGATGACCTCTGATAATT
* * *
32751 TGAAAGATGAACTGTTTTCAGTCAACCTTGATTATTGCTGAAAGATGACC
1 TGAAAGATGACCTGTTTTCAGTCAAGCTTGATTATT--TGGAAGATGACC
32801 CGTTTCCCGT
Statistics
Matches: 147, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
58 105 0.71
59 1 0.01
60 41 0.28
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (58 bp):
TGAAAGATGACCTGTTTTCAGTCAAGCTTGATTATTTGGAAGATGACCTCTGATAATT
Found at i:32855 original size:48 final size:48
Alignment explanation
Indices: 32778--32957 Score: 297
Period size: 48 Copynumber: 3.8 Consensus size: 48
32768 TCAGTCAACC
* * * *
32778 TTGATTATTGCTGAAAGATGACCCGTTTCCCGTCAACTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
* *
32826 TTGATGATTGCTGAAATGTGACCTATTTCCAGTCAACTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
32874 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
*
32922 TCGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAA
1 TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAA
32958 TTTCGATGAC
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 123 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (48 bp):
TTGATGATTGCTGAAAGGTGACCTGTTTCCAGTCAACTTTGATAAACT
Found at i:34190 original size:100 final size:100
Alignment explanation
Indices: 34078--34269 Score: 264
Period size: 100 Copynumber: 1.9 Consensus size: 100
34068 CTCTTTTTTC
*
34078 ATGCACTTGCTTTTGAAAAAC-TTTTGAAACCAATTTTCTCTAAGAACC-TTTTTAAGAA-AAAC
1 ATGCACTTGC-TTTGAAAAACTTTTTGAAACCAATTTTCTCTAAAAACCTTTTTTAAGAATAAAC
* *
34140 ACTTTTCTTTTGCAAAAACTATATTTTTAATTTCACT
65 ACTTCTCTTTTGCAAAAACAAT-TTTTTAATTTCACT
* * * *
34177 ATGCGCTTGGCTTTGAAAAACTTTTTGATACCAATTTTCTTTAAAAACCTTTTTTTGAGAATAAA
1 ATGCACTT-GCTTTGAAAAACTTTTTGAAACCAATTTTCTCTAAAAACC-TTTTTTAAGAATAAA
34242 CACTTCTCTTTTGCAAAAACAATTTTTT
64 CACTTCTCTTTTGCAAAAACAATTTTTT
34270 GTTTTAGGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
99 17 0.21
100 26 0.32
102 14 0.17
103 24 0.30
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (100 bp):
ATGCACTTGCTTTGAAAAACTTTTTGAAACCAATTTTCTCTAAAAACCTTTTTTAAGAATAAACA
CTTCTCTTTTGCAAAAACAATTTTTTAATTTCACT
Found at i:34549 original size:12 final size:12
Alignment explanation
Indices: 34532--34578 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
34522 TTGATTCACT
34532 TTTGATTTGAAC
1 TTTGATTTGAAC
*
34544 TTTGATTTAAAC
1 TTTGATTTGAAC
*
34556 TTTGATTCGAAC
1 TTTGATTTGAAC
*
34568 TTGGATTTGAA
1 TTTGATTTGAA
34579 TTATTTGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.47
Consensus pattern (12 bp):
TTTGATTTGAAC
Found at i:34918 original size:28 final size:29
Alignment explanation
Indices: 34866--34929 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
34856 TGGAAAAACT
*
34866 AAAAACCTTTTTTGAAAATTCATTTTC-G
1 AAAAACCTTTTTTGAAAATTAATTTTCTG
*
34894 AAAAACCTTTTCTTGAAGA-TAATTTTCTTG
1 AAAAACCTTTT-TTGAAAATTAATTTTC-TG
34924 AAAAAC
1 AAAAAC
34930 GTCTCTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 18 0.58
29 6 0.19
30 7 0.23
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (29 bp):
AAAAACCTTTTTTGAAAATTAATTTTCTG
Found at i:36186 original size:39 final size:38
Alignment explanation
Indices: 36126--36224 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 38
36116 AACTTAGGTG
* *
36126 CAAATGAATGTATAATGCATGATCAATGCATGAGTATATA
1 CAAAGGAATG-ATAATGCATGATCAATGCATGA-CATATA
* * *
36166 TAAAGGAATGATAATGCATGATGAATGTATGACATATA
1 CAAAGGAATGATAATGCATGATCAATGCATGACATATA
* *
36204 CAAATGATTGACTAATGCATG
1 CAAAGGAATGA-TAATGCATG
36225 TATGAGCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 13 0.26
39 29 0.58
40 8 0.16
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (38 bp):
CAAAGGAATGATAATGCATGATCAATGCATGACATATA
Found at i:43752 original size:30 final size:29
Alignment explanation
Indices: 43656--43752 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 29
43646 AAGGATCCAT
* *
43656 TGGCCGGTTGTGCGCGGATGCCGCATGCGA
1 TGGCCGGTTGTGC-CGGTTGCCCCATGCGA
* *
43686 TGGCCGGTTGTGGCCGGTTGATGCCCGATGCAA
1 TGGCCGGTTGT-GCCGG-T--TGCCCCATGCGA
*
43719 TGGCCGGTTGTGACCAGTTGCCCCATGCGA
1 TGGCCGGTTGTG-CCGGTTGCCCCATGCGA
43749 TGGC
1 TGGC
43753 GCATGCGATG
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
30 28 0.51
31 2 0.04
32 2 0.04
33 23 0.42
ACGTcount: A:0.11, C:0.27, G:0.39, T:0.23
Consensus pattern (29 bp):
TGGCCGGTTGTGCCGGTTGCCCCATGCGA
Found at i:48954 original size:39 final size:40
Alignment explanation
Indices: 48911--48988 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
48901 CTATTCAATG
* * * *
48911 AGGAATTCTCTCTCCATGTTTA-TTTGTCTATTTTCAAAA
1 AGGAATTATCTCTCCAAGTCTATTTTGTCTATTTACAAAA
*
48950 AGGAATTATCTCTTCAAGTCTATTTTGTCTATTTACAAA
1 AGGAATTATCTCTCCAAGTCTATTTTGTCTATTTACAAA
48989 TTAAACTCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 18 0.55
40 15 0.45
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (40 bp):
AGGAATTATCTCTCCAAGTCTATTTTGTCTATTTACAAAA
Found at i:49101 original size:44 final size:44
Alignment explanation
Indices: 49038--49121 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
49028 CTAAACGAAT
49038 GACTTATAAGTGCTTAATTACAAAAATATAATTTTTATTAGAAA
1 GACTTATAAGTGCTTAATTACAAAAATATAATTTTTATTAGAAA
49082 GACTTATAAGTGCTTAATTACAAAAATATAATTTTTATTA
1 GACTTATAAGTGCTTAATTACAAAAATATAATTTTTATTA
49122 AACTTCCACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (44 bp):
GACTTATAAGTGCTTAATTACAAAAATATAATTTTTATTAGAAA
Found at i:50106 original size:9 final size:9
Alignment explanation
Indices: 50092--50120 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
50082 AACTTTGTAT
50092 GTGCTTAAA
1 GTGCTTAAA
50101 GTGCTTAAA
1 GTGCTTAAA
50110 GTGCTTAAA
1 GTGCTTAAA
50119 GT
1 GT
50121 TGCACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (9 bp):
GTGCTTAAA
Found at i:56325 original size:13 final size:13
Alignment explanation
Indices: 56306--56341 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
56296 CCCGTGTCAC
56306 ATGTCCCTCCAACT
1 ATGTCCCTCCAA-T
56320 -TGTCCCTCCAAT
1 ATGTCCCTCCAAT
56332 ATGTCCCTCC
1 ATGTCCCTCC
56342 TGACGTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.17, C:0.44, G:0.08, T:0.31
Consensus pattern (13 bp):
ATGTCCCTCCAAT
Found at i:56501 original size:41 final size:41
Alignment explanation
Indices: 56442--56523 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
56432 TTTATAACTA
* * *
56442 GGGGCTAAATCTGGATTTAATTTCTTACCTTGATTATTAGG
1 GGGGCTAAATCTGAATTTAATTTATTACCTTAATTATTAGG
*
56483 GGGGCTAAA-CTTGAATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAATC-TGAATTTAATTTATTACCTTAATTATTAGG
56524 AGGATCAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (41 bp):
GGGGCTAAATCTGAATTTAATTTATTACCTTAATTATTAGG
Found at i:66020 original size:22 final size:22
Alignment explanation
Indices: 65995--66046 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
65985 AAAATTCTTT
*
65995 TTGCGTTTTTCTAAAAAAAAAA
1 TTGCGTTTTTCAAAAAAAAAAA
66017 TTGCGTTTTTCAAAAAAAAAAA
1 TTGCGTTTTTCAAAAAAAAAAA
*
66039 TTGGGTTT
1 TTGCGTTT
66047 GCGTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (22 bp):
TTGCGTTTTTCAAAAAAAAAAA
Found at i:70506 original size:11 final size:12
Alignment explanation
Indices: 70490--70521 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
70480 GAAGTTCGTG
70490 TTTGAAGATTA-
1 TTTGAAGATTAT
70501 TTTGAAGA-TAT
1 TTTGAAGATTAT
70512 TTTGAAGATT
1 TTTGAAGATT
70522 TGAAGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:72507 original size:11 final size:11
Alignment explanation
Indices: 72491--72523 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
72481 AGAAGGACCA
72491 ATTTGAAGATT
1 ATTTGAAGATT
72502 ATTTGAAGA-T
1 ATTTGAAGATT
72512 ATTTTGAAGATT
1 A-TTTGAAGATT
72524 TGAAGTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 17 0.85
12 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (11 bp):
ATTTGAAGATT
Found at i:74021 original size:14 final size:14
Alignment explanation
Indices: 74002--74031 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
73992 CCACCGTATA
74002 AAAACAGTTCAACC
1 AAAACAGTTCAACC
74016 AAAACAGTTCAACC
1 AAAACAGTTCAACC
74030 AA
1 AA
74032 GATGGCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAACAGTTCAACC
Found at i:75355 original size:3 final size:3
Alignment explanation
Indices: 75347--75381 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
75337 ATTAAGAATT
75347 TAA TAA TAA TAA TAA TAA TGAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T
75382 TTTAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Done.