Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1917.1
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: 334236
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:593 original size:27 final size:28
Alignment explanation
Indices: 562--617 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
552 ATGCTTAGAG
*
562 ATCTATTAAA-TAA-TAACTTTATTTTAC
1 ATCTATAAAATTAACTAACTTT-TTTTAC
589 ATCTATAAAATTAACGTAACTTTTTTTAC
1 ATCTATAAAATTAAC-TAACTTTTTTTAC
618 TTCAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 9 0.36
28 3 0.12
29 6 0.24
30 7 0.28
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (28 bp):
ATCTATAAAATTAACTAACTTTTTTTAC
Found at i:7793 original size:17 final size:17
Alignment explanation
Indices: 7771--7849 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
7761 ATTTATCTCA
7771 AAATTTAATATATGATT
1 AAATTTAATATATGATT
* *
7788 AAATTTAAAATAAGATTT
1 AAATTTAATATATGA-TT
*
7806 AAATATTTA-ATATGCCATT
1 AAAT-TTAATATATG--ATT
* *
7825 AAATTAGAATATA-AATT
1 AAATT-TAATATATGATT
7842 AAATTTAA
1 AAATTTAA
7850 AACTAATTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.04
17 21 0.44
18 11 0.23
19 10 0.21
20 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (17 bp):
AAATTTAATATATGATT
Found at i:8101 original size:16 final size:16
Alignment explanation
Indices: 8082--8130 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
8072 TTTGAGTATG
*
8082 AGAAAATTGGAGCCCA
1 AGAAAATTTGAGCCCA
* * *
8098 AGAAAGTTTGAGCTCG
1 AGAAAATTTGAGCCCA
*
8114 AGCAAATTTGAGCCCA
1 AGAAAATTTGAGCCCA
8130 A
1 A
8131 ACCCGAAATA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (16 bp):
AGAAAATTTGAGCCCA
Found at i:8443 original size:9 final size:9
Alignment explanation
Indices: 8429--8492 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
8419 TTAATAATCG
8429 ATAATTTTT
1 ATAATTTTT
8438 ATAA-TTTT
1 ATAATTTTT
8446 ATAATTTTT
1 ATAATTTTT
* * *
8455 ACAACATGTT
1 ATAA-TTTTT
* *
8465 AAAAATTTT
1 ATAATTTTT
8474 ATAATTTTT
1 ATAATTTTT
8483 ATAATATTTT
1 ATAAT-TTTT
8493 GAACTACATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
8 8 0.18
9 27 0.60
10 10 0.22
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (9 bp):
ATAATTTTT
Found at i:10756 original size:32 final size:32
Alignment explanation
Indices: 10677--10756 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
10667 TGTGACAGGC
* *
10677 CGTGTGAGCCACACGATCTAAGCCAATTGGGT
1 CGTGTGGGCCACACGATCTAAGCCAATTAGGT
* * * *
10709 TGTGTGGGTCGCACGATCTGAGCCAATTAGGT
1 CGTGTGGGCCACACGATCTAAGCCAATTAGGT
10741 CGTGTGGGCCACACGA
1 CGTGTGGGCCACACGA
10757 GCGTGTAAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.23
Consensus pattern (32 bp):
CGTGTGGGCCACACGATCTAAGCCAATTAGGT
Found at i:11270 original size:39 final size:38
Alignment explanation
Indices: 11202--11276 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
11192 CTAAAGGTAG
11202 AGCATTAACGGCGCTTTTCAGAAAACGCCGCTAAAAATT
1 AGCATTAACGGCGCTTTTCAGAAAACGCCGC-AAAAATT
* *
11241 AGCATTAGCGGCG-TTTTCTGAAAATCGCCGCAAAAA
1 AGCATTAACGGCGCTTTTCAGAAAA-CGCCGCAAAAA
11277 GCCTAAGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (38 bp):
AGCATTAACGGCGCTTTTCAGAAAACGCCGCAAAAATT
Found at i:11276 original size:38 final size:39
Alignment explanation
Indices: 11143--11276 Score: 112
Period size: 40 Copynumber: 3.4 Consensus size: 39
11133 GTTTGGACAA
* * * * *
11143 AAAACGCCACTAAAAATCGAGCATTAGCGGCACTTTT-ATA
1 AAAACGCCGCTAAAAAT-TAGCATTAACGGCGCTTTTCA-G
* ** *
11183 AAAACACCGCTAAAGGTAGAGCATTAACGGCGCTTTTCAG
1 AAAACGCCGCTAAAAAT-TAGCATTAACGGCGCTTTTCAG
* *
11223 AAAACGCCGCTAAAAATTAGCATTAGCGGCG-TTTTCTG
1 AAAACGCCGCTAAAAATTAGCATTAACGGCGCTTTTCAG
11261 AAAATCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
11277 GCCTAAGCCA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 15 0.19
39 18 0.23
40 44 0.56
41 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATTAGCATTAACGGCGCTTTTCAG
Found at i:11378 original size:41 final size:41
Alignment explanation
Indices: 11318--11430 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
11308 TTTGGGGCCC
* *
11318 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAG-CCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCT-AAGACCT
* *
11359 TTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTAAGATCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGACCT
*
11400 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
11431 ATTTTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.03
41 63 0.97
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGACCT
Found at i:11737 original size:15 final size:16
Alignment explanation
Indices: 11717--11750 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
11707 CAAATATGGT
11717 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
11732 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
11748 GTT
1 GTT
11751 AGAGGTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:11921 original size:22 final size:21
Alignment explanation
Indices: 11881--11929 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
11871 TAGGATTTAA
*
11881 GATTTAGGGGTTAGGGCTAGAG
1 GATTTAGGGGTTAGAGCTA-AG
11903 G-TTTAGGGGTTTAGAGCTAAG
1 GATTTAGGGG-TTAGAGCTAAG
11924 GATTTA
1 GATTTA
11930 TAGTTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.24, C:0.04, G:0.39, T:0.33
Consensus pattern (21 bp):
GATTTAGGGGTTAGAGCTAAG
Found at i:12211 original size:24 final size:23
Alignment explanation
Indices: 12176--12222 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
12166 TATGGTTTAA
* *
12176 GGTTTAGGGGTTAGGAGTTAGGG
1 GGTTTAGGGGTTAAGAGCTAGGG
12199 GGTTTATGGGGTTAAGAGCTAGGG
1 GGTTTA-GGGGTTAAGAGCTAGGG
12223 ATTTAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.19, C:0.02, G:0.49, T:0.30
Consensus pattern (23 bp):
GGTTTAGGGGTTAAGAGCTAGGG
Found at i:12593 original size:19 final size:18
Alignment explanation
Indices: 12569--12607 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12559 AATTATAAGA
12569 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
12588 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
12606 AA
1 AA
12608 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:12622 original size:83 final size:83
Alignment explanation
Indices: 12533--12918 Score: 763
Period size: 83 Copynumber: 4.7 Consensus size: 83
12523 GGATAGATAG
*
12533 GTAATTATTTAAATTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
1 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
12598 TAAAAAATAATTCTTTAT
66 TAAAAAATAATTCTTTAT
12616 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
1 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
12681 TAAAAAATAATTCTTTAT
66 TAAAAAATAATTCTTTAT
12699 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
1 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
12764 TAAAAAATAATTCTTTAT
66 TAAAAAATAATTCTTTAT
12782 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
1 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
12847 TAAAAAATAATTCTTTAT
66 TAAAAAATAATTCTTTAT
12865 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAA
1 GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAA
12919 AAATGAAATA
Statistics
Matches: 302, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 302 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.30
Consensus pattern (83 bp):
GTAATTATTTAATTTGGATAGGACCAAATTATAAGAAAAAATAAAATACAAAAATAAAAATGGAA
TAAAAAATAATTCTTTAT
Found at i:12676 original size:19 final size:18
Alignment explanation
Indices: 12652--12690 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12642 AATTATAAGA
12652 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
12671 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
12689 AA
1 AA
12691 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:12759 original size:19 final size:18
Alignment explanation
Indices: 12735--12773 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12725 AATTATAAGA
12735 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
12754 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
12772 AA
1 AA
12774 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:12842 original size:19 final size:18
Alignment explanation
Indices: 12818--12856 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12808 AATTATAAGA
12818 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
12837 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
12855 AA
1 AA
12857 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:13504 original size:47 final size:48
Alignment explanation
Indices: 13453--13550 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 48
13443 TAAAAAAATA
*
13453 AAAACACTAAAATTTATAATTTTATCTA-AAAT-TTATAAATATTAGTT
1 AAAACACTAAAATTTATAATTTTA-CTACAAATATTATAAATATTACTT
*
13500 AAAACACTAAAATTTATAATTTTACTACTATATATTATAAATATTACTT
1 AAAACACTAAAATTTATAATTTTACTAC-AAATATTATAAATATTACTT
13549 AA
1 AA
13551 CAAAACTATG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 3 0.07
47 24 0.52
48 3 0.07
49 16 0.35
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (48 bp):
AAAACACTAAAATTTATAATTTTACTACAAATATTATAAATATTACTT
Found at i:14267 original size:29 final size:29
Alignment explanation
Indices: 14232--14359 Score: 111
Period size: 29 Copynumber: 4.6 Consensus size: 29
14222 TTTTCTTTTT
*
14232 TGTTTTGTCGGTGAGGTTTCAATTTTTAA
1 TGTTTTGTCGGTGAGGTTTCAATTTATAA
* *** *
14261 TGTTTTG-C--TGAAGCGACAATTTATGA
1 TGTTTTGTCGGTGAGGTTTCAATTTATAA
* *** *
14287 TGTTAT-TCACAGAGGTTTCAATTTTTAA
1 TGTTTTGTCGGTGAGGTTTCAATTTATAA
*
14315 TGTTTTTTCGGTGAGGTTTCAATTTATAA
1 TGTTTTGTCGGTGAGGTTTCAATTTATAA
*
14344 TTTTTTGTCGGTGAGG
1 TGTTTTGTCGGTGAGG
14360 ATTTATTTGC
Statistics
Matches: 74, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
26 18 0.24
28 17 0.23
29 39 0.53
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.48
Consensus pattern (29 bp):
TGTTTTGTCGGTGAGGTTTCAATTTATAA
Found at i:15001 original size:25 final size:23
Alignment explanation
Indices: 14956--15002 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
14946 ATTACTTACA
* *
14956 TTAAATAATATTTTTATAATTTT
1 TTAAATAATATATTTAAAATTTT
14979 TTAATATATATATATTTAAAATTT
1 TTAA-ATA-ATATATTTAAAATTT
15003 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAATAATATATTTAAAATTTT
Found at i:15005 original size:19 final size:19
Alignment explanation
Indices: 14983--15020 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14973 AATTTTTTAA
14983 TATATATATATTTAAAATT
1 TATATATATATTTAAAATT
15002 TATATATATATTTAAAATT
1 TATATATATATTTAAAATT
15021 CGAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATATATTTAAAATT
Found at i:15725 original size:12 final size:12
Alignment explanation
Indices: 15710--15743 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15700 TAACCTACAT
15710 AACTTACATAGA
1 AACTTACATAGA
*
15722 AACTTATATAGA
1 AACTTACATAGA
*
15734 AACTTGCATA
1 AACTTACATA
15744 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:15802 original size:16 final size:16
Alignment explanation
Indices: 15783--15894 Score: 65
Period size: 16 Copynumber: 7.2 Consensus size: 16
15773 ATACATAGCG
15783 TACATAACTTACATAA
1 TACATAACTTACATAA
** *
15799 TACACCATTTACAT-A
1 TACATAACTTACATAA
*
15814 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
**
15828 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
15843 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
* * *
15857 TACATAGCCTACGTAA
1 TACATAACTTACATAA
*
15873 CTTACTTAACTTACATAA
1 --TACATAACTTACATAA
15891 TACA
1 TACA
15895 CCACTTACGT
Statistics
Matches: 66, Mismatches: 22, Indels: 16
0.63 0.21 0.15
Matches are distributed among these distances:
13 15 0.23
14 4 0.06
15 4 0.06
16 31 0.47
18 12 0.18
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:15828 original size:29 final size:29
Alignment explanation
Indices: 15786--15860 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
15776 CATAGCGTAC
* *
15786 ATAACTTACATAATACACCATTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
15815 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
15844 ATAACTTGCATAATACA
1 ATAACTTGCATAATACA
15861 TAGCCTACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:15910 original size:34 final size:29
Alignment explanation
Indices: 15786--15902 Score: 126
Period size: 29 Copynumber: 3.9 Consensus size: 29
15776 CATAGCGTAC
*
15786 ATAACTTACATAATACACCATTTACATAA
1 ATAACTTACATAATACACCACTTACATAA
*
15815 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTACATAATACACCACTTACATAA
* * * *
15844 ATAACTTGCATAATACATAGCCTACGTAACTTAC
1 ATAACTTACATAATAC--A-CC-AC-TTACATAA
*
15878 TTAACTTACATAATACACCACTTAC
1 ATAACTTACATAATACACCACTTAC
15903 GTAACTTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
29 46 0.61
30 2 0.03
31 3 0.04
32 3 0.04
33 2 0.03
34 19 0.25
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAACTTACATAATACACCACTTACATAA
Found at i:16082 original size:24 final size:24
Alignment explanation
Indices: 16029--16091 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
16019 ATCATATCAC
* *
16029 AACTTACATAACCAACATATATAAT
1 AACTTACATAA-TAACATAAATAAT
* *
16054 GACTTACATAATAACCTAAATAAT
1 AACTTACATAATAACATAAATAAT
16078 AACTTACATAATAA
1 AACTTACATAATAA
16092 TACATAACCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (24 bp):
AACTTACATAATAACATAAATAAT
Found at i:16154 original size:9 final size:9
Alignment explanation
Indices: 16140--16234 Score: 94
Period size: 9 Copynumber: 11.2 Consensus size: 9
16130 CAAAAACAAA
16140 AACTTACAT
1 AACTTACAT
16149 AACTTACAT
1 AACTTACAT
*
16158 AA--GACAT
1 AACTTACAT
*
16165 AAATTACAT
1 AACTTACAT
* *
16174 AACCTACTT
1 AACTTACAT
16183 AA--TACAT
1 AACTTACAT
16190 AACTTACAT
1 AACTTACAT
* *
16199 AATTTACTT
1 AACTTACAT
16208 AA--TACAT
1 AACTTACAT
16215 AACTTACAT
1 AACTTACAT
16224 AACTTACAT
1 AACTTACAT
16233 AA
1 AA
16235 ATATCCCTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
7 18 0.25
9 53 0.75
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:16171 original size:25 final size:25
Alignment explanation
Indices: 16140--16234 Score: 136
Period size: 25 Copynumber: 3.8 Consensus size: 25
16130 CAAAAACAAA
*
16140 AACTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
16165 AAATTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
* *
16190 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
16215 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
16235 ATATCCCTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:16201 original size:16 final size:17
Alignment explanation
Indices: 16140--16234 Score: 83
Period size: 16 Copynumber: 5.6 Consensus size: 17
16130 CAAAAACAAA
16140 AACTTACATAACTTACAT
1 AACTTACATAA-TTACAT
*
16158 AA--GACATAAATTACAT
1 AACTTACAT-AATTACAT
* *
16174 AACCTACTTAA-TACAT
1 AACTTACATAATTACAT
*
16190 AACTTACATAATTTACTT
1 AACTTACATAA-TTACAT
16208 AA--TACATAACTTACAT
1 AACTTACATAA-TTACAT
16224 AACTTACATAA
1 AACTTACATAA
16235 ATATCCCTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
16 40 0.65
17 4 0.06
18 18 0.29
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (17 bp):
AACTTACATAATTACAT
Found at i:21905 original size:66 final size:66
Alignment explanation
Indices: 21756--21886 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
21746 AGCAAATTAC
* * * * * *
21756 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGTTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
21821 T
66 T
*
21822 ACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAG
1 ACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
21886 C
65 C
21887 AGCAGCTTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (66 bp):
ACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:21917 original size:66 final size:66
Alignment explanation
Indices: 21781--21925 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
21771 GGCAACATCG
*
21781 AGAGAAGTTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTAAAAGCAGATGCAGCAGC
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTAAAAGCAGATGCAGCAGC
*
21846 G
66 A
* * * * *
21847 AGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGC-AGCAGCTTAAAGTAGATGCGGCA
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTAAAAGCAGATGCAGCA
*
21910 GTA
64 GCA
*
21913 AGAGAAGCAGAGG
1 AGAGAAGCTGAGG
21926 CGGCAGCTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 63 0.93
67 4 0.06
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.14
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTAAAAGCAGATGCAGCAGC
A
Found at i:21928 original size:21 final size:20
Alignment explanation
Indices: 21904--21968 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
21894 TAAAGTAGAT
21904 GCGGCAGTAAGAGAAGCAGAG
1 GCGGCAGT-AGAGAAGCAGAG
* *
21925 GCGGCAGCTAGAGAAGTACAG
1 GCGGCAG-TAGAGAAGCAGAG
* * *
21946 GCTGTAGTGAGGGAAGCAGAG
1 GCGGCAGT-AGAGAAGCAGAG
21967 GC
1 GC
21969 TAAAGCGAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.43, T:0.09
Consensus pattern (20 bp):
GCGGCAGTAGAGAAGCAGAG
Found at i:21969 original size:21 final size:21
Alignment explanation
Indices: 21916--22008 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
21906 GGCAGTAAGA
* * * *
21916 GAAGCAGAGGCGGCAGCTAGA
1 GAAGCAGAGGCTGAAGCGAGG
* * * *
21937 GAAGTACAGGCTGTAGTGAGG
1 GAAGCAGAGGCTGAAGCGAGG
*
21958 GAAGCAGAGGCTAAAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
*
21979 GAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
*
22000 GAAGTAGAG
1 GAAGCAGAG
22009 CAGCGTCAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.44, T:0.09
Consensus pattern (21 bp):
GAAGCAGAGGCTGAAGCGAGG
Found at i:22457 original size:86 final size:86
Alignment explanation
Indices: 22374--22733 Score: 562
Period size: 86 Copynumber: 4.2 Consensus size: 86
22364 ATTTTTGGTC
* * ** * * *
22374 AAAGCGCCGCTAAAGATAAGAG-TCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATG
1 AAAGCGCCGCTAAAGATTAG-GTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGG
* *
22438 GTCT-TTAGCGGCGTTTTTGGGG
65 GTCTATT-GCGGCGTTTTAGGAG
*
22460 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
22525 TCTATTGCGGCGTTTTAGGAG
66 TCTATTGCGGCGTTTTAGGAG
22546 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
22611 TCTATTGCGGCGTTTTAGGAG
66 TCTATTGCGGCGTTTTAGGAG
22632 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
* * *
22697 TCTATTGCGGCGTTTGAGAAA
66 TCTATTGCGGCGTTTTAGGAG
*
22718 AAAACGCCGCTAAAGA
1 AAAGCGCCGCTAAAGA
22734 CCCTGATCTA
Statistics
Matches: 257, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
85 1 0.00
86 254 0.99
87 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGG
TCTATTGCGGCGTTTTAGGAG
Found at i:22660 original size:172 final size:172
Alignment explanation
Indices: 22374--22797 Score: 568
Period size: 172 Copynumber: 2.5 Consensus size: 172
22364 ATTTTTGGTC
*
22374 AAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGGG
* * *
22439 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTTGGTCA
66 TCTTTAGCGGCGTTTTAGGAGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCA
* * *
22504 AAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTTAGGAG
131 AAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGAAA
* * ** * *
22546 AAAGCGCCGCTAAAGATTAG-GTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATAAGAG-TCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGG
22610 GTCTATT-GCGGCGTTTTAGGAGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGT
65 GTCT-TTAGCGGCGTTTTAGGAGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGT
22674 CAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGAAA
129 CAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGAAA
* *** * * * * * *
22718 AAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTCTAGCACAAA-CGCCGCTAAAGATCAG
1 AAAGCGCCGCTAAAGA-TAAGAGTCTTTAGCGGCGTTTGT-GGAAAAAGCGCCACTAAAGATCAG
*
22781 GGTCTTTAGCGACGTTT
64 GGTCTTTAGCGGCGTTT
22798 CCACTAAAGT
Statistics
Matches: 221, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
171 3 0.01
172 210 0.95
173 8 0.04
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (172 bp):
AAAGCGCCGCTAAAGATAAGAGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGGG
TCTTTAGCGGCGTTTTAGGAGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCA
AAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGAAA
Found at i:22712 original size:43 final size:43
Alignment explanation
Indices: 22354--22797 Score: 396
Period size: 43 Copynumber: 10.3 Consensus size: 43
22344 AGGTGTTGGC
* * * * *
22354 CTTTAGTGGCATTTTTGGTCAAAGCGCCGCTAAAGATAAGAGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
22397 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
22440 CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * *
22483 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
22526 CTATT-GCGGCGTTT-TAGGAGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGT-GGTCAAAGCGCCGCTAAAGATCAGGGT
* *
22569 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
22612 CTATT-GCGGCGTTT-TAGGAGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGT-GGTCAAAGCGCCGCTAAAGATCAGGGT
* *
22655 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *** * * ** *
22698 CTATT-GCGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGAT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * * *
22741 CTATAGCGGCGCTTCTAG-CACAAACGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTAAAGATCAGGGT
*
22784 CTTTAGCGACGTTT
1 CTTTAGCGGCGTTT
22798 CCACTAAAGT
Statistics
Matches: 319, Mismatches: 71, Indels: 22
0.77 0.17 0.05
Matches are distributed among these distances:
42 8 0.03
43 303 0.95
44 8 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:31800 original size:7 final size:7
Alignment explanation
Indices: 31788--31819 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
31778 TACAAATTGC
31788 TTTTCAT
1 TTTTCAT
31795 TTTTCAT
1 TTTTCAT
31802 TTTTCAT
1 TTTTCAT
31809 TTTTCAT
1 TTTTCAT
31816 TTTT
1 TTTT
31820 GACCCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCAT
Found at i:39598 original size:3 final size:3
Alignment explanation
Indices: 39590--39622 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39580 ATGTAAAATA
*
39590 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39623 GAAAGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39953 original size:10 final size:9
Alignment explanation
Indices: 39931--39981 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
39921 TTATAAAAAT
39931 ATTATATTA
1 ATTATATTA
39940 ATTATATATA
1 ATTATAT-TA
39950 ATTATATTTA
1 ATTATA-TTA
39960 TATTTATATTA
1 -A-TTATATTA
*
39971 AAT-TATTA
1 ATTATATTA
39979 ATT
1 ATT
39982 CAATAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 11 0.31
11 5 0.14
12 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATTA
Found at i:41793 original size:12 final size:12
Alignment explanation
Indices: 41776--41800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41766 GGTGGAGGAA
41776 CAACAGTTCACT
1 CAACAGTTCACT
41788 CAACAGTTCACT
1 CAACAGTTCACT
41800 C
1 C
41801 TTCAGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CAACAGTTCACT
Found at i:42580 original size:29 final size:30
Alignment explanation
Indices: 42548--42609 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
42538 TCGATTTAAT
42548 ATGCAATTTGATA-CATG-AACTTTGATT-TG
1 ATGCAA-TT-ATAGCATGAAACTTTGATTGTG
42577 ATGCAATTATAGGCATGAAACTTTGATTGTG
1 ATGCAATTATA-GCATGAAACTTTGATTGTG
42608 AT
1 AT
42610 TAAAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
28 2 0.07
29 10 0.34
30 10 0.34
31 4 0.14
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (30 bp):
ATGCAATTATAGCATGAAACTTTGATTGTG
Found at i:43555 original size:18 final size:18
Alignment explanation
Indices: 43532--43570 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
43522 ATGAATTAAT
43532 TAAGCAGTTGGGATATAA
1 TAAGCAGTTGGGATATAA
43550 TAAGCAGTTGGGATATAA
1 TAAGCAGTTGGGATATAA
43568 TAA
1 TAA
43571 AAAATTTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (18 bp):
TAAGCAGTTGGGATATAA
Found at i:44122 original size:21 final size:21
Alignment explanation
Indices: 44098--44142 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
44088 ATCTTAATTT
44098 TATTGGAAGACTTACCATGTG
1 TATTGGAAGACTTACCATGTG
44119 TATTGGAAGACTTACCATGTG
1 TATTGGAAGACTTACCATGTG
44140 TAT
1 TAT
44143 AGGCAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (21 bp):
TATTGGAAGACTTACCATGTG
Found at i:47033 original size:18 final size:19
Alignment explanation
Indices: 47001--47043 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
46991 GTCTTCTGCC
47001 AAAATAATACAAAAAAAAT
1 AAAATAATACAAAAAAAAT
* *
47020 AAAA-AATACTAAAATAAT
1 AAAATAATACAAAAAAAAT
47038 ATAAAT
1 A-AAAT
47044 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAATACAAAAAAAAT
Found at i:47866 original size:153 final size:151
Alignment explanation
Indices: 47149--47942 Score: 1113
Period size: 152 Copynumber: 5.2 Consensus size: 151
47139 ATTTTGGCAT
* *
47149 TTTGTTCGTATTTTTTTCC-GAAGTTTATTACTTCTAAAAAATATACTATTTTTTAA-TTTTTTA
1 TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTTA
* *
47212 TTTTACATTATTTTCGTACATTATATTTGAAATGTATTAATTTAGTGTCTTTTTTAAATAAA--T
66 TTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGT-GTTTTTAAATAAATTT
*
47275 TAAAAAAATCCTTATTTCGGCCC
130 TAAAAAACT-CTTATTTCGGCCC
* * * *
47298 TTTGTTCGTATTTTTTCCCTG-ATTTTATTACTTTCAATAAAAATATACTATTTTATAATTTTAT
1 TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTT-TA-AAAAATATACTATTTTTTAATTTTTT
*
47362 TATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTGTGTTTTTAAATAAATT
64 TATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATT
*
47427 TAAAAAAAACTCTTATTTCGGCCC
129 T-TAAAAAACTCTTATTTCGGCCC
* * * *
47451 TTTGTTCGTATTTTTTCCCT-AGATTTTATTACTTTAAAAAAATATACTATTTTATAATTTTATT
1 TTTGTTCGTATTTTTTTCCTGA-ATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTT
** * * *
47515 ATTTCGCATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGCTTTTAAATAAA-TT
65 ATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTT
*
47579 TATTAAAA-TCTTATTTCGGCCC
130 TA-AAAAACTCTTATTTCGGCCC
* *
47601 TTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTT-AAAAATATACTATTTTTTAATTTTTTAA
1 TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTTA
* *
47665 TTTTACATTATTTTAGTATATTATATTTGAAATGCATTAATTTAGTGTGTTTTTAAATAAATTTT
66 TTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTT
*
47730 AAAAAACTCATATTTCGGCCC
131 AAAAAACTCTTATTTCGGCCC
*
47751 TATGTTCGTATTTTTTTCCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTTT
1 TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAA--TTTTTT
*
47816 TATTTTACATTATTTTAGTATATTATATTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAAT
64 TATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTG-TTTTTAAATAAAT
* *
47881 TTTAAAAAAAAACCCTTATTTTGGCCC
128 TTT---AAAAAACTCTTATTTCGGCCC
* *
47908 TATGTTCGTA-TTTTTTCCCGAATTTTATTACTTTT
1 TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTTT
47943 TATTATTCGA
Statistics
Matches: 585, Mismatches: 40, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
149 112 0.19
150 99 0.17
151 58 0.10
152 137 0.23
153 91 0.16
154 36 0.06
156 24 0.04
157 28 0.05
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.53
Consensus pattern (151 bp):
TTTGTTCGTATTTTTTTCCTGAATTTTATTACTTTTAAAAAATATACTATTTTTTAATTTTTTTA
TTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTT
AAAAAACTCTTATTTCGGCCC
Found at i:50415 original size:16 final size:17
Alignment explanation
Indices: 50390--50427 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
50380 ACATTATCTG
50390 AAAAAATAAA-TAAAGT
1 AAAAAATAAATTAAAGT
* *
50406 AAAAATTAAATTAAATT
1 AAAAAATAAATTAAAGT
50423 AAAAA
1 AAAAA
50428 CAAAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAATAAATTAAAGT
Found at i:53305 original size:13 final size:14
Alignment explanation
Indices: 53281--53309 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53271 TTATATTTTT
53281 TAAAATAAATTATA
1 TAAAATAAATTATA
53295 TAAAA-AAATTATA
1 TAAAATAAATTATA
53308 TA
1 TA
53310 GACAGGCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAATAAATTATA
Found at i:54544 original size:21 final size:19
Alignment explanation
Indices: 54520--54561 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
54510 AATTCGTTGG
54520 TTAAGCTCAGAATATATATAA
1 TTAAGCTCA-AATATAT-TAA
*
54541 TTAAGTTCAAATATATTAA
1 TTAAGCTCAAATATATTAA
54560 TT
1 TT
54562 TATATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAAGCTCAAATATATTAA
Found at i:73941 original size:32 final size:32
Alignment explanation
Indices: 73890--73950 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
73880 TTATTTACTT
* * * *
73890 TTTATTTTACGTTACTTTTACTTTAAGTTCAG
1 TTTATTTTAAGCTACTTTTAATTAAAGTTCAG
*
73922 TTTATTTTAAGCTATTTTTAATTAAAGTT
1 TTTATTTTAAGCTACTTTTAATTAAAGTT
73951 GTTTTATTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.57
Consensus pattern (32 bp):
TTTATTTTAAGCTACTTTTAATTAAAGTTCAG
Found at i:91588 original size:13 final size:13
Alignment explanation
Indices: 91553--91591 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
91543 ATTAAGATTA
91553 TTATTTTTTAATAT
1 TTATTTTTT-ATAT
*
91567 TT-TTATTTATAT
1 TTATTTTTTATAT
91579 TTATTTTTTATAT
1 TTATTTTTTATAT
91592 AATTTCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 14 0.64
14 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTTTATAT
Found at i:95058 original size:31 final size:30
Alignment explanation
Indices: 94974--95058 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
94964 CTCTAAAAAA
* *
94974 TTTTAACTT-AGTTTTTAAATT-TTAAAATT
1 TTTTAA-TTGAGTTTTTAAATTATAAAAATG
* *
95003 TTTTAATTGAGTTTTTGAACTATAAATAATG
1 TTTTAATTGAGTTTTTAAATTATAAA-AATG
*
95034 TTTTAATTGAGTTCTTAAATTATAA
1 TTTTAATTGAGTTTTTAAATTATAA
95059 GTATTTGTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 16 0.35
30 3 0.07
31 25 0.54
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTAATTGAGTTTTTAAATTATAAAAATG
Found at i:97595 original size:22 final size:24
Alignment explanation
Indices: 97555--97598 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
97545 TGATAATATG
97555 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
97579 TTTTGA-ATAA-AAATTAAAGT
1 TTTTGATATAACAAATTAAAGT
97599 TGAACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:97651 original size:20 final size:20
Alignment explanation
Indices: 97628--97665 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
97618 GATAAAATCA
97628 AGTTAAAAC-TGTTTCAATTG
1 AGTTAAAACAT-TTTCAATTG
97648 AGTTAAAACATTTTCAAT
1 AGTTAAAACATTTTCAAT
97666 CATGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTTAAAACATTTTCAATTG
Found at i:97672 original size:20 final size:19
Alignment explanation
Indices: 97623--97681 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
97613 AAAATGATAA
97623 AATCAAGTTAAAACTGTTTC
1 AATC-AGTTAAAACTGTTTC
*
97643 AATTGAGTTAAAACAT-TTTC
1 AA-TCAGTTAAAAC-TGTTTC
*
97663 AATCATGTTAAAATTGTTT
1 AATCA-GTTAAAACTGTTT
97682 TTAAACAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.09
20 27 0.84
21 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
AATCAGTTAAAACTGTTTC
Found at i:99417 original size:3 final size:3
Alignment explanation
Indices: 99387--99459 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
99377 CACAAAGCGG
* * * * *
99387 TAA TAG TAA TAA TAG TAA CAA TAG TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
99435 -AA T-T TAA TTA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
99460 CAGTAACAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:103942 original size:14 final size:14
Alignment explanation
Indices: 103923--103950 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
103913 AGTCAAATTT
103923 AACCAGTTGACCTC
1 AACCAGTTGACCTC
103937 AACCAGTTGACCTC
1 AACCAGTTGACCTC
103951 GTTGAGTGAT
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:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
AACCAGTTGACCTC
Found at i:107666 original size:196 final size:196
Alignment explanation
Indices: 107332--107721 Score: 602
Period size: 196 Copynumber: 2.0 Consensus size: 196
107322 TTAAAAAGTG
* * *
107332 CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCAACGCAATTTGACCTATAATAATTAGT
1 CAAGCACATTCCATTTTCATCTCAAGTGGTTTCAATCCAACACAACTTGACCTATAATAATTAGT
* *
107397 AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGTTACCTCTCCATCCC
* *
107462 TTGAGCAC-AAGTAAGCTTAAAGTGAATTAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
131 TAGAGCACAAAG-AAGCTTAAAGTGAATCAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
107526 CA
195 CA
*
107528 CAAGCACATTCCATTTTCATCTCAAGTGGTTTCAATCCGACACAACTTGACCTATAATAATTAGT
1 CAAGCACATTCCATTTTCATCTCAAGTGGTTTCAATCCAACACAACTTGACCTATAATAATTAGT
* * * *
107593 AATATAAGATATCCTTCCAAGAAATTACGTCATGGTGCATTTAGTATGTGTTCCCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGTTACCTCTCCATCCC
* * * * * *
107658 TAGAGCACAAAGAAGTTTTAAGTGAATCAAACTCAACCACAAGAGTGTCTTTTTATACAGAAAG
131 TAGAGCACAAAGAAGCTTAAAGTGAATCAAACACAACCACAAGAATGTCCTTTTATACAAAAAG
107722 TCCTACAAGG
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
196 172 0.98
197 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (196 bp):
CAAGCACATTCCATTTTCATCTCAAGTGGTTTCAATCCAACACAACTTGACCTATAATAATTAGT
AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGTTACCTCTCCATCCC
TAGAGCACAAAGAAGCTTAAAGTGAATCAAACACAACCACAAGAATGTCCTTTTATACAAAAAGC
A
Found at i:121445 original size:23 final size:23
Alignment explanation
Indices: 121402--121445 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
121392 TCAACATTCT
* *
121402 TTAACTCTATTTCAGTTATCTGG
1 TTAACTCTATGTCAGTGATCTGG
121425 TTAACTCATATGTCA-TGATCT
1 TTAACTC-TATGTCAGTGATCT
121446 CTCAGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (23 bp):
TTAACTCTATGTCAGTGATCTGG
Found at i:124302 original size:11 final size:11
Alignment explanation
Indices: 124286--124336 Score: 93
Period size: 11 Copynumber: 4.6 Consensus size: 11
124276 CTTTAAGAAT
124286 GAAGGCAATGC
1 GAAGGCAATGC
124297 GAAGGCAATGC
1 GAAGGCAATGC
124308 GAAGGCAATGC
1 GAAGGCAATGC
124319 GAAGGCAATGC
1 GAAGGCAATGC
*
124330 AAAGGCA
1 GAAGGCA
124337 GCCTTGTGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.35, T:0.08
Consensus pattern (11 bp):
GAAGGCAATGC
Found at i:125126 original size:18 final size:18
Alignment explanation
Indices: 125102--125147 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
125092 TCTAAATCTA
*
125102 CCCCATCAACATTACCCT
1 CCCCATCAACATCACCCT
*
125120 TCCCATCAACATCACCCT
1 CCCCATCAACATCACCCT
125138 CCCCATCAAC
1 CCCCATCAAC
125148 TTTTACCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.52, G:0.00, T:0.20
Consensus pattern (18 bp):
CCCCATCAACATCACCCT
Found at i:134498 original size:38 final size:38
Alignment explanation
Indices: 134435--134511 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
134425 TAAAGGTTGT
* * *
134435 GATCGTAAATTAGTGAATTGCGAGATTCATAAAATCTC
1 GATCGTAAATTAGCGAACTGCGAGATTAATAAAATCTC
* *
134473 GATCGTAAATTAGCGGACTGTGAGATTAATAAAATCTC
1 GATCGTAAATTAGCGAACTGCGAGATTAATAAAATCTC
134511 G
1 G
134512 TAAGTAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (38 bp):
GATCGTAAATTAGCGAACTGCGAGATTAATAAAATCTC
Found at i:141826 original size:44 final size:44
Alignment explanation
Indices: 141674--141878 Score: 197
Period size: 44 Copynumber: 4.7 Consensus size: 44
141664 ACATACAATT
* * ** *
141674 CCATATCCCACATATGGTCTTACATGTTATCAC--ATATCGGTG
1 CCATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* *
141716 CCAATAGCCCAGCTATGGTCTTACACG-AAT--CATATATCGATG
1 CC-ATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* * *
141758 CCAATGTTCCAGATATGGTCTTACACGTAATCACATATATCGATG
1 CC-ATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* *
141803 CCATATCCTAGATATGGTCTTACAC-AAAGTCTCATATATCGATG
1 CCATATCCCAGATATGGTCTTACACGAAA-TCACATATATCGATG
* * * *
141847 TCATAGCCCAGCTATGGTCTTATACGAAATCA
1 CCATATCCCAGATATGGTCTTACACGAAATCA
141879 TGTAATGCCA
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
40 1 0.01
42 35 0.26
43 25 0.19
44 56 0.42
45 17 0.13
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
CCATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
Found at i:150732 original size:23 final size:23
Alignment explanation
Indices: 150689--150737 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
150679 TTTAAATGTT
*
150689 TATTTGTTTAATTTATTAAATAA
1 TATTTGTTTAATTTATAAAATAA
*
150712 TATTTTTTATAATTT-TAAAATAA
1 TATTTGTT-TAATTTATAAAATAA
150735 TAT
1 TAT
150738 ACTTGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTGTTTAATTTATAAAATAA
Found at i:159813 original size:21 final size:21
Alignment explanation
Indices: 159787--159827 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
159777 ATCTGCTCAA
* *
159787 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
159808 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
159828 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:169071 original size:21 final size:21
Alignment explanation
Indices: 169045--169085 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
169035 ATCTGCTCAA
* *
169045 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
169066 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
169086 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:176106 original size:37 final size:37
Alignment explanation
Indices: 176045--176190 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
176035 TACGTATGAT
* *
176045 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
176080 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
176117 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
176154 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
176191 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:176207 original size:46 final size:46
Alignment explanation
Indices: 176154--176422 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
176144 TAAGTGTAGC
* **
176154 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
176200 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
176246 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
176298 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
176344 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
176396 CACTTATCATTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
176423 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 112 0.57
48 1 0.01
49 2 0.01
50 1 0.01
52 82 0.41
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:176273 original size:52 final size:52
Alignment explanation
Indices: 176197--176416 Score: 290
Period size: 52 Copynumber: 4.3 Consensus size: 52
176187 TAGCTAAAGC
* *
176197 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
176250 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
176302 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
176348 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
176400 TATCATTTTGTCACTTG
1 TATCACTTT-TCACTTG
176417 ATCAGAAGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 85 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:176319 original size:98 final size:98
Alignment explanation
Indices: 176154--176422 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
176144 TAAGTGTAGC
* * *
176154 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
176219 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
176253 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
176318 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
176351 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
176416 GATCAGA
66 GATCAGA
176423 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:182159 original size:28 final size:28
Alignment explanation
Indices: 182127--182253 Score: 85
Period size: 28 Copynumber: 4.6 Consensus size: 28
182117 AATAAGTTCG
*
182127 CACACTTAGTGCTCAATAATCAAACTCA
1 CACACTTAGTGCTCAACAATCAAACTCA
** * * *
182155 CACACTTAGTGCTTTACCATTAAACTCG
1 CACACTTAGTGCTCAACAATCAAACTCA
*** * **
182183 CACACTTAGTGCTTTTCAATTAAACTTG
1 CACACTTAGTGCTCAACAATCAAACTCA
* ** * * *
182211 CACAATTAGTGCTTTACAATTAAATTCG
1 CACACTTAGTGCTCAACAATCAAACTCA
182239 CACACTTAGTG-TCAA
1 CACACTTAGTGCTCAA
182254 AAGTCAACAA
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
27 2 0.02
28 81 0.98
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.32
Consensus pattern (28 bp):
CACACTTAGTGCTCAACAATCAAACTCA
Found at i:182190 original size:56 final size:57
Alignment explanation
Indices: 182124--182253 Score: 167
Period size: 56 Copynumber: 2.3 Consensus size: 57
182114 TTTAATAAGT
* *
182124 TCGCACACTTAGTGCTCAAT-AATCAAACTCACACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTCAATCAATCAAACTCACACAATTAGTGCTTTACAATTAAAC
** * ** *
182180 TCGCACACTTAGTGCT-TTTCAATTAAACTTGCACAATTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTCAATCAATCAAACTCACACAATTAGTGCTTTACAATTAAAC
182236 TCGCACACTTAGTG-TCAA
1 TCGCACACTTAGTGCTCAA
182254 AAGTCAACAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
55 2 0.03
56 60 0.97
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (57 bp):
TCGCACACTTAGTGCTCAATCAATCAAACTCACACAATTAGTGCTTTACAATTAAAC
Found at i:199066 original size:44 final size:44
Alignment explanation
Indices: 198913--199117 Score: 188
Period size: 44 Copynumber: 4.7 Consensus size: 44
198903 ACATACAATT
* * ** *
198913 CCATATCCCACATATGGTCTTACATGTTATCAC--ATATCGGTG
1 CCATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* *
198955 CCAATAGCCCAGCTATGGTCTTACACG-AAT--CATATATCGATG
1 CC-ATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* * * *
198997 CCAATGTTCCAGATATAGTCTTACACGTAATCACATATATCGATG
1 CC-ATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
* *
199042 CCATATCCTAGATATGGTCTTACAC-AAAGTCTCATATATCGATG
1 CCATATCCCAGATATGGTCTTACACGAAA-TCACATATATCGATG
* * * *
199086 TCATAGCCCAGCTATGGTCTTATACGAAATCA
1 CCATATCCCAGATATGGTCTTACACGAAATCA
199118 TGTAATGCCA
Statistics
Matches: 132, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.01
42 34 0.26
43 25 0.19
44 55 0.42
45 17 0.13
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
CCATATCCCAGATATGGTCTTACACGAAATCACATATATCGATG
Found at i:207275 original size:37 final size:37
Alignment explanation
Indices: 207218--207323 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
207208 TATGATCACT
*
207218 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
207253 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
207290 TATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
207324 GAAGCTATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 54 0.84
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:207365 original size:52 final size:52
Alignment explanation
Indices: 207297--207494 Score: 309
Period size: 52 Copynumber: 3.9 Consensus size: 52
207287 ACTTATCACT
* *
207297 TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCAC
*
207349 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCAC
*
207395 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCAC
*
207447 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT
207495 GTCACTTGAT
Statistics
Matches: 133, Mismatches: 7, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
46 43 0.32
48 1 0.01
50 1 0.01
52 88 0.66
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (52 bp):
TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCAC
Found at i:207407 original size:46 final size:46
Alignment explanation
Indices: 207336--207508 Score: 251
Period size: 46 Copynumber: 3.7 Consensus size: 46
207326 AGCTATTACT
207336 TATCACTT-TCCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTAT-CACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
207381 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
207427 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
207479 TATCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTTGTCACTTGATCAGA
207509 AGTACTCAAA
Statistics
Matches: 116, Mismatches: 4, Indels: 15
0.86 0.03 0.11
Matches are distributed among these distances:
45 11 0.09
46 60 0.52
48 1 0.01
50 1 0.01
52 43 0.37
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:207452 original size:98 final size:98
Alignment explanation
Indices: 207286--207508 Score: 437
Period size: 98 Copynumber: 2.3 Consensus size: 98
207276 TAAGTGTAGC
*
207286 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
207351 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
207384 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
207449 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
207482 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
207509 AGTACTCAAA
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 124 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:209570 original size:13 final size:13
Alignment explanation
Indices: 209552--209586 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
209542 ATATTCAAAT
209552 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
* *
209565 TTTTTAAAGGTAT
1 TTTTTAAAAGTAC
209578 TTTTTAAAA
1 TTTTTAAAA
209587 ACAATTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:213614 original size:22 final size:22
Alignment explanation
Indices: 213575--213636 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
213565 GTTATTACTA
213575 TTATAT-TTATT-TATATATCT
1 TTATATCTTATTATATATATCT
213595 TTATATCTTATTATATATATCT
1 TTATATCTTATTATATATATCT
*
213617 ATATATCTTATTATATATAT
1 TTATATCTTATTATATATAT
213637 ATGTATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 6 0.15
21 5 0.13
22 28 0.72
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATCTTATTATATATATCT
Found at i:213643 original size:8 final size:8
Alignment explanation
Indices: 213586--213656 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
213576 TATATTTATT
213586 TATATATC
1 TATATATC
*
213594 TTTATATC
1 TATATATC
*
213602 T-TAT-TA
1 TATATATC
213608 TATATATC
1 TATATATC
213616 TATATATC
1 TATATATC
*
213624 T-TATTATA
1 TATA-TATC
*
213632 TATATATG
1 TATATATC
*
213640 TATATATA
1 TATATATC
*
213648 TACATATC
1 TATATATC
213656 T
1 T
213657 CTTTATAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.04
7 8 0.16
8 39 0.76
9 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (8 bp):
TATATATC
Found at i:213647 original size:12 final size:11
Alignment explanation
Indices: 213573--213649 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
213563 TTGTTATTAC
*
213573 TATTATATTTA
1 TATTATATATA
*
213584 T-TTATATATC
1 TATTATATATA
*
213594 T-TTATATCT-
1 TATTATATATA
213603 TATTATATATA
1 TATTATATATA
* *
213614 T-CTATATATCT
1 TATTATATAT-A
213625 TATTATATATA
1 TATTATATATA
213636 TATGTATATATA
1 TAT-TATATATA
213648 TA
1 TA
213650 CATATCTCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 1 0.02
10 29 0.55
11 6 0.11
12 17 0.32
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (11 bp):
TATTATATATA
Found at i:213688 original size:4 final size:4
Alignment explanation
Indices: 213679--213734 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
213669 TTTTTTAGCT
213679 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
213727 TACA TACA
1 TACA TACA
213735 CATATTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:213775 original size:43 final size:43
Alignment explanation
Indices: 213720--213802 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
213710 ATACATACAT
213720 ACATACATACATACACATAT-TTTTTATATACTTTATAATTCTA
1 ACATACATACATACACATATCTTTTTATAT-CTTTATAATTCTA
* * * * *
213763 ACATACGTACATATATATATCTTTTTTTATTTTTATAATT
1 ACATACATACATACACATATCTTTTTATATCTTTATAATT
213803 TTACTCATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 26 0.76
44 8 0.24
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.49
Consensus pattern (43 bp):
ACATACATACATACACATATCTTTTTATATCTTTATAATTCTA
Found at i:214905 original size:24 final size:23
Alignment explanation
Indices: 214854--214919 Score: 123
Period size: 23 Copynumber: 2.8 Consensus size: 23
214844 GTTTTTCATC
214854 CAAAAAATGGTGTCAACAGCTAT
1 CAAAAAATGGTGTCAACAGCTAT
214877 CAAAAAATGGTGTCAACAGCTAT
1 CAAAAAATGGTGTCAACAGCTAT
214900 CAAAAAAATGGTGTCAACAG
1 C-AAAAAATGGTGTCAACAG
214920 ATTGAACAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 24 0.57
24 18 0.43
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (23 bp):
CAAAAAATGGTGTCAACAGCTAT
Found at i:221516 original size:26 final size:26
Alignment explanation
Indices: 221480--221531 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
221470 ATGAGTTCAT
221480 TTTTAAATTTCCATATAATAGAAAGG
1 TTTTAAATTTCCATATAATAGAAAGG
* *
221506 TTTTCAATTTCCATATAATCGAAAGG
1 TTTTAAATTTCCATATAATAGAAAGG
221532 GTGTAGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTTAAATTTCCATATAATAGAAAGG
Found at i:228847 original size:12 final size:12
Alignment explanation
Indices: 228830--228856 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
228820 AAGTGCTTAG
228830 AAAAAAAAAAGA
1 AAAAAAAAAAGA
228842 AAAAAAAAAAGA
1 AAAAAAAAAAGA
228854 AAA
1 AAA
228857 GAGATTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:231951 original size:25 final size:25
Alignment explanation
Indices: 231923--231977 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
231913 AATTATATGT
*
231923 CAGAAAAAAGACAGTTCTATGGAAC
1 CAGAAAAAAGACAGTTCTAAGGAAC
231948 CAGAAAAAAGACAGTTCTAAGGAAC
1 CAGAAAAAAGACAGTTCTAAGGAAC
231973 CAGAA
1 CAGAA
231978 CTCAATGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.13
Consensus pattern (25 bp):
CAGAAAAAAGACAGTTCTAAGGAAC
Found at i:232247 original size:58 final size:58
Alignment explanation
Indices: 232183--232302 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
232173 AAGACCCCAC
232183 ACCCATAAATGAAAAAAGTAAGCACACATGAAATTAATATTTCAATGCCAACAAGAAT
1 ACCCATAAATGAAAAAAGTAAGCACACATGAAATTAATATTTCAATGCCAACAAGAAT
*
232241 ACCCATAAATGAAAAAATTAAGCACACATGAAATTAATATTTCAATGCCAACAAGAAT
1 ACCCATAAATGAAAAAAGTAAGCACACATGAAATTAATATTTCAATGCCAACAAGAAT
232299 ACCC
1 ACCC
232303 TGCAAAAAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (58 bp):
ACCCATAAATGAAAAAAGTAAGCACACATGAAATTAATATTTCAATGCCAACAAGAAT
Found at i:237968 original size:72 final size:73
Alignment explanation
Indices: 237883--238021 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
237873 CCATTTGCTG
* * * *
237883 TTTTATTTAGTTTTTATTAAAATG-AAAAGACTAAAATACTCTTAAATCGTATAACTTATTTTAA
1 TTTTATTTAGTTTTTATTAAAACGAAAAAAACTAAAATACTCTCAAATAGTATAACTTATTTTAA
237947 TTTACATA
66 TTTACATA
* * *
237955 TTTTATTTGGTTTTTATTAAAACGAAAAAAATTAAAATATTCTCAAATAGTATAACTTATTTTAA
1 TTTTATTTAGTTTTTATTAAAACGAAAAAAACTAAAATACTCTCAAATAGTATAACTTATTTTAA
238020 TT
66 TT
238022 CGGGAAAGAC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 22 0.37
73 37 0.63
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (73 bp):
TTTTATTTAGTTTTTATTAAAACGAAAAAAACTAAAATACTCTCAAATAGTATAACTTATTTTAA
TTTACATA
Found at i:243887 original size:26 final size:26
Alignment explanation
Indices: 243856--243908 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
243846 TGGTGACTTC
243856 ATGCATGCGATTTTATAATGGTGCAA
1 ATGCATGCGATTTTATAATGGTGCAA
243882 ATGCATGCGATTTTATAATGGTGCAA
1 ATGCATGCGATTTTATAATGGTGCAA
243908 A
1 A
243909 CTTATATTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (26 bp):
ATGCATGCGATTTTATAATGGTGCAA
Found at i:244099 original size:28 final size:28
Alignment explanation
Indices: 244059--244189 Score: 111
Period size: 28 Copynumber: 4.7 Consensus size: 28
244049 TTCGAAATCT
*
244059 AATCCATACAAACTCTTACTTGGAAGAA
1 AATCCATACAAACTCTTACTTGAAAGAA
*
244087 AATCCATACAAACTCGTT-CTTGAAAGAT
1 AATCCATACAAACTC-TTACTTGAAAGAA
* ** * * * *
244115 AATTCATGTAGACTCTTACCTGGATGAA
1 AATCCATACAAACTCTTACTTGAAAGAA
* * * *
244143 AATCCGTACAAACTCGTGCTTGAAAGAT
1 AATCCATACAAACTCTTACTTGAAAGAA
* *
244171 AATTCATACAAACTTTTAC
1 AATCCATACAAACTCTTAC
244190 GTGCGAATTC
Statistics
Matches: 75, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
27 2 0.03
28 71 0.95
29 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (28 bp):
AATCCATACAAACTCTTACTTGAAAGAA
Found at i:244131 original size:56 final size:56
Alignment explanation
Indices: 244070--244177 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
244060 ATCCATACAA
* *
244070 ACTCTTACTTGGAAGAAAATCCATACAAACTCGTTCTTGAAAGATAATTCATGTAG
1 ACTCTTACCTGGAAGAAAATCCATACAAACTCGTGCTTGAAAGATAATTCATGTAG
* *
244126 ACTCTTACCTGGATGAAAATCCGTACAAACTCGTGCTTGAAAGATAATTCAT
1 ACTCTTACCTGGAAGAAAATCCATACAAACTCGTGCTTGAAAGATAATTCAT
244178 ACAAACTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (56 bp):
ACTCTTACCTGGAAGAAAATCCATACAAACTCGTGCTTGAAAGATAATTCATGTAG
Found at i:249881 original size:21 final size:20
Alignment explanation
Indices: 249857--249896 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
249847 TATTTATATA
* *
249857 TATTATCTATGATAATAAATT
1 TATTAACTAT-ATAAAAAATT
249878 TATTAACTATATAAAAAAT
1 TATTAACTATATAAAAAAT
249897 AAAATTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTAACTATATAAAAAATT
Found at i:254749 original size:28 final size:28
Alignment explanation
Indices: 254717--254772 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
254707 TTAAATAAAT
*
254717 AATATTAAAAA-ATAATTAATTACAAAAA
1 AATATGAAAAACA-AATTAATTACAAAAA
* *
254745 AATATGAAAAACAGATTAATTACGAAAA
1 AATATGAAAAACAAATTAATTACAAAAA
254773 TAAACATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (28 bp):
AATATGAAAAACAAATTAATTACAAAAA
Found at i:257805 original size:11 final size:11
Alignment explanation
Indices: 257767--257806 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 11
257757 CAAATGAATA
257767 TTTTAATAA-T
1 TTTTAATAATT
257777 TTTTAATATATAT
1 TTTTAATA-AT-T
257790 TTTTAATAATT
1 TTTTAATAATT
257801 TTTTAA
1 TTTTAA
257807 GTTTTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.30
11 8 0.30
12 2 0.07
13 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:263750 original size:371 final size:373
Alignment explanation
Indices: 263052--263799 Score: 1101
Period size: 371 Copynumber: 2.0 Consensus size: 373
263042 AATTGAGCAT
* * * *
263052 TACTATCGGTTTTATATATTCATTGTTGGTATCAATTCACTGCTAACAGAAATAAATTCTCGCTT
1 TACTATAGGTTTGATATATTCATTGTCGGTATCAATTAACTGCTAACAGAAATAAATTCTCGCTT
* * *
263117 TAATGATGAAGCAGTTGAGTGACTTGTTCTTAACTCCACTTTGGATCTACGCGATAATTACAAAG
66 TAATGACGAAGCAGTTGAGTGACTTGTTCTTAACTCCACTTTGGATCCACGCGATAATTACAAAA
* * *
263182 CTTTTTTGTGTGGGAGATATTTGCAAGCCTATGAATGATTTTTATCCAAACAATTTTATGGAGCA
131 CTTTTTTGTATGGAAGATATATGCAAGCCTATGAATGATTTTTATCCAAACAATTTTATGGAGCA
*
263247 AAAAAAGCTACACATGAAGATTCGATTGGAGCATTTTCAACTTAATGCTCATCAAAGCACAGAGT
196 AAAAAAGCTACACATGAAGATTCGATTGGAGCATTTTCAACTTAATACTCATCAAAGCACAGAGT
* *
263312 TGCAGAAAGCTTCTACAGTTGCCAAGTTGTGTCAAGTGCTAGCTAAGACAAATAAGTCAAGTATT
261 TGCAGAAAGCTTCTACAGTTGCCAAGTTGTGTCAAGTGCTAACTAAGACAAATAACTCAAGTATT
* * * * *
263377 TATCCTCTTCTTGATAGAATTATTT-GTCTTGTGGACTCTTCTCGTGTC
326 TATCATCTTCTTGATAGAATT-TTTCATCTCGTGCACTCTTCTCGTATC
* * * * *
263425 TACTATAGGTTTGATATATTCATTGTCGGTATCGATTAATTGTTAATAGAAATGAATTCTCGCTT
1 TACTATAGGTTTGATATATTCATTGTCGGTATCAATTAACTGCTAACAGAAATAAATTCTCGCTT
* * * *
263490 TAATGACGAGGCAG-TGAAGTTACTTGTTCTTAGCTCTACTTTGGATCCACGCGATAATTACAAA
66 TAATGACGAAGCAGTTG-AGTGACTTGTTCTTAACTCCACTTTGGATCCACGCGATAATTACAAA
* ** *
263554 ACTTTTTT-TATGGAAGATATATGCAAGCTTATGAATGATTTTTATCTGAATAATTTTATGGAGC
130 ACTTTTTTGTATGGAAGATATATGCAAGCCTATGAATGATTTTTATCCAAACAATTTTATGGAGC
* *
263618 -AAGAAAGCTACATATGAAGATTCGATTGGAGCATTTTCAACTTAATACTCATCAAAGCACAGAG
195 AAAAAAAGCTACACATGAAGATTCGATTGGAGCATTTTCAACTTAATACTCATCAAAGCACAGAG
*** *
263682 TTGCAGAAAGCTTCTACAGTTGTTGAGTTGTGTC-AGATGCTAACTAAGACAAATAACTTAAGTA
260 TTGCAGAAAGCTTCTACAGTTGCCAAGTTGTGTCAAG-TGCTAACTAAGACAAATAACTCAAGTA
263746 TTTATCATCTTCTTGATAGAATTTTTCATCTCGTGCACTCTTCTCGTATC
324 TTTATCATCTTCTTGATAGAATTTTTCATCTCGTGCACTCTTCTCGTATC
263796 TACT
1 TACT
263800 GCAACAACCA
Statistics
Matches: 335, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
370 5 0.01
371 161 0.48
372 51 0.15
373 118 0.35
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (373 bp):
TACTATAGGTTTGATATATTCATTGTCGGTATCAATTAACTGCTAACAGAAATAAATTCTCGCTT
TAATGACGAAGCAGTTGAGTGACTTGTTCTTAACTCCACTTTGGATCCACGCGATAATTACAAAA
CTTTTTTGTATGGAAGATATATGCAAGCCTATGAATGATTTTTATCCAAACAATTTTATGGAGCA
AAAAAAGCTACACATGAAGATTCGATTGGAGCATTTTCAACTTAATACTCATCAAAGCACAGAGT
TGCAGAAAGCTTCTACAGTTGCCAAGTTGTGTCAAGTGCTAACTAAGACAAATAACTCAAGTATT
TATCATCTTCTTGATAGAATTTTTCATCTCGTGCACTCTTCTCGTATC
Found at i:265991 original size:48 final size:48
Alignment explanation
Indices: 265935--266028 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
265925 AGGGAATTCT
* * *
265935 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
265983 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
266029 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:269541 original size:11 final size:11
Alignment explanation
Indices: 269527--269567 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
269517 AAAAGACCAT
*
269527 AAAAA-TTATA
1 AAAAATTTACA
269537 AAAAATTTACA
1 AAAAATTTACA
269548 AAAAATTTACA
1 AAAAATTTACA
269559 AAAAATTTA
1 AAAAATTTA
269568 AAATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 5 0.17
11 24 0.83
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTTACA
Found at i:270246 original size:17 final size:17
Alignment explanation
Indices: 270224--270257 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
270214 AATAAGGAAA
*
270224 GTAATCTTAGAAGATTT
1 GTAATCCTAGAAGATTT
*
270241 GTAATCCTATAAGATTT
1 GTAATCCTAGAAGATTT
270258 AATTTTGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (17 bp):
GTAATCCTAGAAGATTT
Found at i:281324 original size:59 final size:59
Alignment explanation
Indices: 281228--281339 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
281218 TCTTGTTTTT
* * * * *
281228 TTGGTTTGTTTTGATTCTTTTAGGATACTTTACAAGTTCGAATAATTCTTCTTCATTTG
1 TTGGGTTGTTTAGATTCTCTTAGGACACTTTACAAGTTCGAACAATTCTTCTTCATTTG
* * * *
281287 TTGGGTTGTTTAGATTCTCTTAGTACATTTTATAAGTTTGAACAATTCTTCTT
1 TTGGGTTGTTTAGATTCTCTTAGGACACTTTACAAGTTCGAACAATTCTTCTT
281340 TTAAGGAAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (59 bp):
TTGGGTTGTTTAGATTCTCTTAGGACACTTTACAAGTTCGAACAATTCTTCTTCATTTG
Found at i:283582 original size:11 final size:13
Alignment explanation
Indices: 283554--283598 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 13
283544 AATAATAAAA
*
283554 TTTAATTGATAGTT
1 TTTAATTTATA-TT
283568 TTTAATTT-T-TT
1 TTTAATTTATATT
283579 TTTAATTTATATT
1 TTTAATTTATATT
283592 TTTAATT
1 TTTAATT
283599 GAATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 1 0.04
13 10 0.36
14 7 0.25
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTAATTTATATT
Found at i:285849 original size:162 final size:159
Alignment explanation
Indices: 285546--285853 Score: 472
Period size: 162 Copynumber: 1.9 Consensus size: 159
285536 TTTAGTAAGC
* * * *
285546 AAATTATCACAGTTATAATGGTAAAACCAAAGAAAAAGTGCTAGCATGGTACATAATGTTAAGCA
1 AAATTATCACAGTTATAATGATAAAACCAAAGAAAAAGTGATAGCACGGTACAAAATGTTAAGCA
* * * *
285611 CCCAAGCAAGAACCAATATACTAGGCAAGAAACCTAATTTGAATATCGAGCCACAGAAAACTAAA
66 CCCAAGCAAGAACCAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACTAAA
285676 GACTTAACTAATGAACAGTGAGACCAGTT
131 GACTTAACTAATGAACAGTGAGACCAGTT
*
285705 AAATTATCACAGTTATAATGATAAAACCAAAGTAAAAGTGATAGCTACGGTACAAAATGTTAAGC
1 AAATTATCACAGTTATAATGATAAAACCAAAGAAAAAGTGATAGC-ACGGTACAAAATGTTAAGC
* * *
285770 ATCCAAGCAAGAACCAATAGACTATAGGCAAGAAGCCTAATTCGAACATCAAGCCACAGAGAACT
65 ACCCAAGCAAGAACCAATAGAC--TAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACT
*
285835 AATGACTTAACTAATGAAC
128 AAAGACTTAACTAATGAAC
285854 GAAAAGACCA
Statistics
Matches: 133, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
159 42 0.32
160 37 0.28
162 54 0.41
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (159 bp):
AAATTATCACAGTTATAATGATAAAACCAAAGAAAAAGTGATAGCACGGTACAAAATGTTAAGCA
CCCAAGCAAGAACCAATAGACTAGGCAAGAAACCTAATTCGAACATCAAGCCACAGAAAACTAAA
GACTTAACTAATGAACAGTGAGACCAGTT
Found at i:295468 original size:40 final size:40
Alignment explanation
Indices: 295391--295471 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
295381 ATTTATCTTG
* *
295391 ATCCCTTAGGATGTCCATTGGTAGATAATGTACCTCATTA
1 ATCCCTTAGGATATCCATTGGTAGATAATATACCTCATTA
* * **
295431 ATCCCTTTGGATATCTATTGGTAGATAATATGGCTCATTA
1 ATCCCTTAGGATATCCATTGGTAGATAATATACCTCATTA
295471 A
1 A
295472 AACCTAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (40 bp):
ATCCCTTAGGATATCCATTGGTAGATAATATACCTCATTA
Found at i:308009 original size:25 final size:25
Alignment explanation
Indices: 307975--308026 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
307965 TCAAGCTAGT
307975 AGCTTATCATATTAAATTGTTATTG
1 AGCTTATCATATTAAATTGTTATTG
308000 AGCTTATCATATTAAATTGTTATTG
1 AGCTTATCATATTAAATTGTTATTG
308025 AG
1 AG
308027 GTAAGTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (25 bp):
AGCTTATCATATTAAATTGTTATTG
Found at i:309334 original size:12 final size:12
Alignment explanation
Indices: 309298--309336 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
309288 TAGAAAACCT
*
309298 TAACTTTAACTT
1 TAACTTTAACTC
*
309310 TAACTTTATCTC
1 TAACTTTAACTC
*
309322 TAACTCTAACTC
1 TAACTTTAACTC
309334 TAA
1 TAA
309337 TGGTCATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACTTTAACTC
Found at i:318746 original size:21 final size:19
Alignment explanation
Indices: 318722--318779 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
318712 ATTTATTTAT
318722 AATTAATTATTATTTTAATAA
1 AATTAATTATT-TTTTAA-AA
*
318743 AATTAATTTTTTATTTAAAA
1 AATTAATTATTT-TTTAAAA
318763 ATATTATATTATTTTTT
1 A-ATTA-ATTATTTTTT
318780 GTTTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 22 0.69
22 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTAATTATTTTTTAAAA
Done.