Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 148 of 279
Found at i:48126844 original size:42 final size:42
Alignment explanation
Indices: 48126785--48126866 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
48126775 ATTTTAGGTC
48126785 CACACGGCCAGACACAC-GAGCGTGTAACTTGGTCGTGTGAGA
1 CACACGGCCAGACACACGGA-CGTGTAACTTGGTCGTGTGAGA
* **
48126827 CACACGGCCTGACACACGGACGTGTGGCTTGGTCGTGTGA
1 CACACGGCCAGACACACGGACGTGTAACTTGGTCGTGTGA
48126867 CCCAAGTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (42 bp):
CACACGGCCAGACACACGGACGTGTAACTTGGTCGTGTGAGA
Found at i:48128695 original size:20 final size:20
Alignment explanation
Indices: 48128653--48128711 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
48128643 TAAACATTGA
48128653 AATAAATTTAATATTAAGAT
1 AATAAATTTAATATTAAGAT
*
48128673 AATAACTTTAATATTAA-ATT
1 AATAAATTTAATATTAAGA-T
* *
48128693 AATAAA-ATACTATTAAGAT
1 AATAAATTTAATATTAAGAT
48128712 GAGTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AATAAATTTAATATTAAGAT
Found at i:48135905 original size:41 final size:41
Alignment explanation
Indices: 48135859--48135998 Score: 153
Period size: 41 Copynumber: 3.4 Consensus size: 41
48135849 TTCCATTAGT
* * *
48135859 GGTGTTTTTCTTA-AAATCGCTGCA-AATGGTAAGGTAATAGC
1 GGTGTTTTTCTCATAAA-CGCCGCAGAA-GGTAAGGCAATAGC
*
48135900 GGTGTTTCTCTCATAAACGCCGCAGAAGGTAAGGCAATAGC
1 GGTGTTTTTCTCATAAACGCCGCAGAAGGTAAGGCAATAGC
* * *
48135941 GGCG-TTTTCTCCATAAACACCGCA-AAGGTAAGACAATAGC
1 GGTGTTTTTCT-CATAAACGCCGCAGAAGGTAAGGCAATAGC
*
48135981 GGCGTTTTTCTCATAAAC
1 GGTGTTTTTCTCATAAAC
48135999 ACCGTGAATT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
40 31 0.36
41 51 0.59
42 5 0.06
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
GGTGTTTTTCTCATAAACGCCGCAGAAGGTAAGGCAATAGC
Found at i:48135980 original size:40 final size:41
Alignment explanation
Indices: 48135880--48136002 Score: 171
Period size: 40 Copynumber: 3.0 Consensus size: 41
48135870 TAAAATCGCT
* * *
48135880 GCAAATGGTAAGGTAATAGCGGTG-TTTCTCTCATAAACGCC
1 GCAAA-GGTAAGGCAATAGCGGCGTTTTCTCTCATAAACACC
48135921 GCAGAAGGTAAGGCAATAGCGGCGTTTTCTC-CATAAACACC
1 GCA-AAGGTAAGGCAATAGCGGCGTTTTCTCTCATAAACACC
*
48135962 GCAAAGGTAAGACAATAGCGGCGTTTT-TCTCATAAACACC
1 GCAAAGGTAAGGCAATAGCGGCGTTTTCTCTCATAAACACC
48136002 G
1 G
48136003 TGAATTTTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
39 2 0.03
40 34 0.45
41 31 0.41
42 8 0.11
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
GCAAAGGTAAGGCAATAGCGGCGTTTTCTCTCATAAACACC
Found at i:48138422 original size:17 final size:19
Alignment explanation
Indices: 48138386--48138422 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
48138376 TACTATGTTA
48138386 AATTATATTTTTATAATTAT
1 AATTATATTTTTAT-ATTAT
48138406 AATTAT-TTTTTAT-TTAT
1 AATTATATTTTTATATTAT
48138423 TTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTATATTTTTATATTAT
Found at i:48138855 original size:13 final size:13
Alignment explanation
Indices: 48138818--48138857 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
48138808 AGCTTGACAA
*
48138818 AATATTTGTAACT
1 AATATTTGTAATT
48138831 AATATTTGTAATT
1 AATATTTGTAATT
48138844 AACT-TTTGTAATT
1 AA-TATTTGTAATT
48138857 A
1 A
48138858 TTTAGGTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (13 bp):
AATATTTGTAATT
Found at i:48148740 original size:6 final size:6
Alignment explanation
Indices: 48148729--48148766 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
48148719 ATAAATAAAT
48148729 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
48148767 CTTTACAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:48157549 original size:21 final size:19
Alignment explanation
Indices: 48157513--48157556 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
48157503 TTTATTTTGA
48157513 TTAAATTTTATTTTTACAGTT
1 TTAAATTTTATTTTTA-A-TT
48157534 TTAAATTTT-TTATTTAATT
1 TTAAATTTTATT-TTTAATT
48157553 TTAA
1 TTAA
48157557 TTTAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 13 0.59
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTAAATTTTATTTTTAATT
Found at i:48161895 original size:27 final size:26
Alignment explanation
Indices: 48161839--48161912 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 26
48161829 TCTCATCACT
48161839 ATTTTACCCTTAGTAAAATTTTGATG
1 ATTTTACCCTTAGTAAAATTTTGATG
*
48161865 ATTTTA-CCTTTGATAAAATTTTTGATG
1 ATTTTACCCTTAG-TAAAA-TTTTGATG
*
48161892 ATTTTACCCCTAGTAAAATTT
1 ATTTTACCCTTAGTAAAATTT
48161913 CGAGAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.12
26 14 0.33
27 19 0.45
28 4 0.10
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTGATG
Found at i:48174851 original size:59 final size:59
Alignment explanation
Indices: 48174759--48174878 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
48174749 AATTCTAGAC
48174759 AAAATGTTTGACATGTAATAATCAGACATATTAAAGTTATTGCATGAAATTGTGCATCA
1 AAAATGTTTGACATGTAATAATCAGACATATTAAAGTTATTGCATGAAATTGTGCATCA
*
48174818 AAAATGTTTGACATGTCATAATCAGACATATTAAAGTTATTGCATGAAATTGTGCATCA
1 AAAATGTTTGACATGTAATAATCAGACATATTAAAGTTATTGCATGAAATTGTGCATCA
48174877 AA
1 AA
48174879 TTAAATGGGC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (59 bp):
AAAATGTTTGACATGTAATAATCAGACATATTAAAGTTATTGCATGAAATTGTGCATCA
Found at i:48176223 original size:23 final size:24
Alignment explanation
Indices: 48176193--48176254 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
48176183 ACGCCACAAT
48176193 AGGTAAAGCACTAGCTGCCGC-AA
1 AGGTAAAGCACTAGCTGCCGCAAA
48176216 AGGTAAAGCACTAGCTGCCGCAAA
1 AGGTAAAGCACTAGCTGCCGCAAA
* *
48176240 AGGTCAAGCATTAGC
1 AGGTAAAGCACTAGC
48176255 AAAATTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (24 bp):
AGGTAAAGCACTAGCTGCCGCAAA
Found at i:48176392 original size:21 final size:21
Alignment explanation
Indices: 48176366--48176409 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48176356 CTTATTTTTT
48176366 TCCCTAAACATT-TTCCCCAAA
1 TCCCTAAA-ATTATTCCCCAAA
*
48176387 TCCCTAAATTTATTCCCCAAA
1 TCCCTAAAATTATTCCCCAAA
48176408 TC
1 TC
48176410 AAAATCCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (21 bp):
TCCCTAAAATTATTCCCCAAA
Found at i:48179997 original size:13 final size:13
Alignment explanation
Indices: 48179981--48180007 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48179971 TAATTAAAGG
48179981 GTTAAAATTTAAA
1 GTTAAAATTTAAA
48179994 GTTAAAATTTAAA
1 GTTAAAATTTAAA
48180007 G
1 G
48180008 ATGATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:48180075 original size:9 final size:9
Alignment explanation
Indices: 48180061--48180153 Score: 68
Period size: 9 Copynumber: 10.6 Consensus size: 9
48180051 AACTTTGGAT
48180061 CATAACTTA
1 CATAACTTA
48180070 CATAACTTA
1 CATAACTTA
48180079 CATAA--TA
1 CATAACTTA
*
48180086 CATAA-ATA
1 CATAACTTA
* * *
48180094 TATATCATA
1 CATAACTTA
48180103 TCATAACTTA
1 -CATAACTTA
48180113 CATAACTTA
1 CATAACTTA
*
48180122 CATAA-ATA
1 CATAACTTA
* * *
48180130 TATATCATA
1 CATAACTTA
48180139 TCATAACTTA
1 -CATAACTTA
48180149 CATAA
1 CATAA
48180154 AACTTTGGAT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
7 7 0.10
8 10 0.15
9 39 0.57
10 12 0.18
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:48180131 original size:36 final size:34
Alignment explanation
Indices: 48180070--48180153 Score: 150
Period size: 36 Copynumber: 2.4 Consensus size: 34
48180060 TCATAACTTA
48180070 CATAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACATAATACATAAATATATATCATAT
48180104 CATAACTTACATAACTTACATAAATATATATCATAT
1 CATAACTTACATAA--TACATAAATATATATCATAT
48180140 CATAACTTACATAA
1 CATAACTTACATAA
48180154 AACTTTGGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 14 0.29
36 34 0.71
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.35
Consensus pattern (34 bp):
CATAACTTACATAATACATAAATATATATCATAT
Found at i:48187177 original size:33 final size:34
Alignment explanation
Indices: 48187131--48187367 Score: 145
Period size: 33 Copynumber: 6.7 Consensus size: 34
48187121 TTAACCGTTA
* *
48187131 TCGGTGGATTCAGCACTTAGCAACCACCAGT-GAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATAGAT
48187165 TCGGGGAATCAGCACTTAGCAACCACTTTCACATTCAAAGAT
1 TCGGGGAATCAGCACTTAGCAACCAC---CA-A-T---AGAT
*
48187207 AT-GGTGGAATCAGCACTTAGCAACCACCAATGGA-
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATAGAT
48187241 TCGGGGAATCAGCACTTAGCAACC-CC------T
1 TCGGGGAATCAGCACTTAGCAACCACCAATAGAT
* * *
48187268 TGGGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGAT
1 TCGGGGAATCAGCACTTAGCAACCACC---A-A--T--AGAT
* *
48187310 ACGGTGGAATCAGCACTTAGCAACCACCAATGGA-
1 TCGG-GGAATCAGCACTTAGCAACCACCAATAGAT
48187344 TCGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
48187368 CCTTGGGGGA
Statistics
Matches: 163, Mismatches: 11, Indels: 59
0.70 0.05 0.25
Matches are distributed among these distances:
27 22 0.13
28 2 0.01
32 2 0.01
33 62 0.38
34 9 0.06
35 4 0.02
36 2 0.01
37 1 0.01
38 2 0.01
39 2 0.01
40 3 0.02
42 8 0.05
43 44 0.27
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (34 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATAGAT
Found at i:48187286 original size:103 final size:103
Alignment explanation
Indices: 48187167--48187435 Score: 477
Period size: 103 Copynumber: 2.6 Consensus size: 103
48187157 CCAGTGATTC
* * * * *
48187167 GGGGAATCAGCACTTAGCAA-CCACTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGAACTTAGCAACCCCCTTT-ATATTTAAAGATACGGTGGAATCAGCACTTAGCAAC
48187231 CACCAATGGATCGGGGAATCAGCACTTAGCAACCCCTTG
65 CACCAATGGATCGGGGAATCAGCACTTAGCAACCCCTTG
48187270 GGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
48187335 ACCAATGGATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGGATCGGGGAATCAGCACTTAGCAACCCCTTG
48187373 GGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAA
1 GGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAA
48187436 TCCCTTCATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 154 0.96
104 6 0.04
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (103 bp):
GGGGAATCAGAACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGGATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:48188531 original size:11 final size:12
Alignment explanation
Indices: 48188503--48188536 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
48188493 GCCCAAACGT
48188503 CGAAATTTTTGAA
1 CGAAATTTTT-AA
48188516 CGAAATTTTT-A
1 CGAAATTTTTAA
48188527 CGAAATTTTT
1 CGAAATTTTT
48188537 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:48188747 original size:42 final size:43
Alignment explanation
Indices: 48188696--48188879 Score: 196
Period size: 42 Copynumber: 4.3 Consensus size: 43
48188686 AAGCGCAATG
* * **
48188696 AAAGGTCATGTTCTTTAGCGGTGTTTGT-GGAAAAGCGTTGCT
1 AAAGCTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* * *
48188738 AAAGCTCATGTTCTTTAGTGGCGTTTGTGGGGAAAGCGCAGCT
1 AAAGCTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
*
48188781 AAA-CATCATGTTCTATAGCGGCGTTTGTGGG-AAAGCGCCGCT
1 AAAGC-TCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* * * *
48188823 AAATG-TCATGTTCTTTAGTGGTGTTTTTGGGAAAAGCGTCGCT
1 AAA-GCTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
**
48188866 AAATTTCATGTTCT
1 AAAGCTCATGTTCT
48188880 ATAGTAATGT
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
42 61 0.50
43 60 0.50
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.34
Consensus pattern (43 bp):
AAAGCTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
Found at i:48188790 original size:43 final size:43
Alignment explanation
Indices: 48188666--48188879 Score: 204
Period size: 43 Copynumber: 5.0 Consensus size: 43
48188656 TAACATGACT
* * *
48188666 TTTAGCGGTGTTTCTGGGGAAAGCGCA-ATGAAAGGTCATGTTC
1 TTTAGCGGTGTTTGTGGGGAAAGCGCAGCT-AAACGTCATGTTC
* **
48188709 TTTAGCGGTGTTTGT-GGAAAAGCGTTGCTAAA-GCTCATGTTC
1 TTTAGCGGTGTTTGTGGGGAAAGCGCAGCTAAACG-TCATGTTC
* * *
48188751 TTTAGTGGCGTTTGTGGGGAAAGCGCAGCTAAACATCATGTTC
1 TTTAGCGGTGTTTGTGGGGAAAGCGCAGCTAAACGTCATGTTC
* * * *
48188794 TATAGCGGCGTTTGT-GGGAAAGCGCCGCTAAATGTCATGTTC
1 TTTAGCGGTGTTTGTGGGGAAAGCGCAGCTAAACGTCATGTTC
* * * **
48188836 TTTAGTGGTGTTTTTGGGAAAAGCGTC-GCTAAATTTCATGTTC
1 TTTAGCGGTGTTTGTGGGGAAAGCG-CAGCTAAACGTCATGTTC
48188879 T
1 T
48188880 ATAGTAATGT
Statistics
Matches: 143, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 67 0.47
43 74 0.52
44 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (43 bp):
TTTAGCGGTGTTTGTGGGGAAAGCGCAGCTAAACGTCATGTTC
Found at i:48188809 original size:85 final size:85
Alignment explanation
Indices: 48188666--48188883 Score: 253
Period size: 85 Copynumber: 2.6 Consensus size: 85
48188656 TAACATGACT
* * ** * *
48188666 TTTAGCGGTGTTTCTGGGGAAAGCGCA-ATGAAAGGTCATGTTCTTTAGCGGTGTTTGTGGAAAA
1 TTTAGTGGTGTTTCTGGGGAAAGCGCAGCT-AAACATCATGTTCTATAGCGGCGTTTGTGGAAAA
**
48188730 GCGTTGCTAAA-GCTCATGTTC
65 GCGCCGCTAAATG-TCATGTTC
* * *
48188751 TTTAGTGGCGTTTGTGGGGAAAGCGCAGCTAAACATCATGTTCTATAGCGGCGTTTGTGGGAAAG
1 TTTAGTGGTGTTTCTGGGGAAAGCGCAGCTAAACATCATGTTCTATAGCGGCGTTTGTGGAAAAG
48188816 CGCCGCTAAATGTCATGTTC
66 CGCCGCTAAATGTCATGTTC
* * **
48188836 TTTAGTGGTGTTTTTGGGAAAAGCGTC-GCTAAATTTCATGTTCTATAG
1 TTTAGTGGTGTTTCTGGGGAAAGCG-CAGCTAAACATCATGTTCTATAG
48188884 TAATGTTTTT
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
85 111 0.97
86 3 0.03
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.33
Consensus pattern (85 bp):
TTTAGTGGTGTTTCTGGGGAAAGCGCAGCTAAACATCATGTTCTATAGCGGCGTTTGTGGAAAAG
CGCCGCTAAATGTCATGTTC
Found at i:48197150 original size:19 final size:19
Alignment explanation
Indices: 48197126--48197181 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
48197116 CATTAGTTCT
48197126 TCTTC-TTCTATTTTTTTCC
1 TCTTCTTTCT-TTTTTTTCC
48197145 TCTTCTTTCTTTTTTTT-C
1 TCTTCTTTCTTTTTTTTCC
*
48197163 TTTTCTTTTCTTTATTTTT
1 TCTTC-TTTCTTT-TTTTT
48197182 TGATTCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 5 0.15
19 19 0.58
20 9 0.27
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (19 bp):
TCTTCTTTCTTTTTTTTCC
Found at i:48197192 original size:26 final size:24
Alignment explanation
Indices: 48197138--48197208 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
48197128 TTCTTCTATT
* *
48197138 TTTTTCCTCTTCTTTCTTTTTTTTC
1 TTTTT-CTTTTCTTTATTTTTTTTC
48197163 -TTTTCTTTTCTTTATTTTTTGATTC
1 TTTTTCTTTTCTTTATTTTTT--TTC
48197188 TTTTTCTTTCCTCTTTATTTT
1 TTTTTCTTT--TCTTTATTTT
48197209 GATCACTACC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 14 0.36
24 4 0.10
25 3 0.08
26 8 0.21
28 10 0.26
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTCTTTTCTTTATTTTTTTTC
Found at i:48198369 original size:316 final size:316
Alignment explanation
Indices: 48197796--48198428 Score: 1140
Period size: 316 Copynumber: 2.0 Consensus size: 316
48197786 ACACGGCATG
*
48197796 TTAGTGCTGGGTTAACACGGACTAAAGACACGGGCATGTGTCTAGGCCGTGTAACACACTGTTTG
1 TTAGTGCTGGGTTAACACAGACTAAAGACACGGGCATGTGTCTAGGCCGTGTAACACACTGTTTG
* *
48197861 TGATTTAGGACTACACGGGCATATGTCAAGCCGTGTGAAACACACGGCTAGGAACACGAGCGTGT
66 TGATTTAGGACTACACGAGCATATGTCAAGCCGTGTGAAACACACGACTAGGAACACGAGCGTGT
*
48197926 GCTAGGTCATGTGGAACCACACAGGCGTCTGGGTCAGGTTTGGAATTCATCCTTGGGGCTGTAAG
131 GCTAGGTCATGTGGAACCACACAGGCGTCTGGGTCAGGTTTGGAATTCATCCTTGGGGCCGTAAG
48197991 CATTGTTAACGCGAATGTAGGGCATCCGTAGTGTATATGTATGATCTGATTAGACTGTATGACTG
196 CATTGTTAACGCGAATGTAGGGCATCCGTAGTGTATATGTATGATCTGATTAGACTGTATGACTG
*
48198056 CTATTTGACAATTTTAGACTGAAATTTTGATTATACAAATGTTTATTGAAACTGAA
261 CTATCTGACAATTTTAGACTGAAATTTTGATTATACAAATGTTTATTGAAACTGAA
48198112 TTAGTGCTGGGTTAACACAGACTAAAGACACGGGCATGTGTCTAGGCCGTGTAACACACTGTTTG
1 TTAGTGCTGGGTTAACACAGACTAAAGACACGGGCATGTGTCTAGGCCGTGTAACACACTGTTTG
* * *
48198177 TGATTTAGGACTATACGAGCATATGTCAAGCCGTGTGAAACACACGACTGGGCACACGAGCGTGT
66 TGATTTAGGACTACACGAGCATATGTCAAGCCGTGTGAAACACACGACTAGGAACACGAGCGTGT
*
48198242 GCTCGGTCATGTGGAACCACACAGGCGTCTGGGTCAGGTTTGGAATTCATCCTTGGGGCCGTAAG
131 GCTAGGTCATGTGGAACCACACAGGCGTCTGGGTCAGGTTTGGAATTCATCCTTGGGGCCGTAAG
* * *
48198307 CATTGTTAACGCGACTGTAGGGCATTCGTAGTGTATATGTATGATCTGTTTAGACTGTATGACTG
196 CATTGTTAACGCGAATGTAGGGCATCCGTAGTGTATATGTATGATCTGATTAGACTGTATGACTG
* *
48198372 CTATCTGACAATTTTAGACTGAAATTTTGATTATACAATTGTTTATTGAAATTGAA
261 CTATCTGACAATTTTAGACTGAAATTTTGATTATACAAATGTTTATTGAAACTGAA
48198428 T
1 T
48198429 GACTATGCAT
Statistics
Matches: 303, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
316 303 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (316 bp):
TTAGTGCTGGGTTAACACAGACTAAAGACACGGGCATGTGTCTAGGCCGTGTAACACACTGTTTG
TGATTTAGGACTACACGAGCATATGTCAAGCCGTGTGAAACACACGACTAGGAACACGAGCGTGT
GCTAGGTCATGTGGAACCACACAGGCGTCTGGGTCAGGTTTGGAATTCATCCTTGGGGCCGTAAG
CATTGTTAACGCGAATGTAGGGCATCCGTAGTGTATATGTATGATCTGATTAGACTGTATGACTG
CTATCTGACAATTTTAGACTGAAATTTTGATTATACAAATGTTTATTGAAACTGAA
Found at i:48205407 original size:308 final size:308
Alignment explanation
Indices: 48204849--48205464 Score: 1232
Period size: 308 Copynumber: 2.0 Consensus size: 308
48204839 GGGCCAACAG
48204849 GATAAAGATTATAAAATGTTTGCACTTTCTAACGAGGAGTGGAGAAATGTTGTTATTCTTTGCAA
1 GATAAAGATTATAAAATGTTTGCACTTTCTAACGAGGAGTGGAGAAATGTTGTTATTCTTTGCAA
48204914 ATTTTTGAAAGTCTTGTATGATGCGACTTGTGTTTTTTCTAGTTCTAATTATCCAACGAATAATC
66 ATTTTTGAAAGTCTTGTATGATGCGACTTGTGTTTTTTCTAGTTCTAATTATCCAACGAATAATC
48204979 TTTATTATAAAGGGGTTTGGAAGGTTCACAAGGTCTTGCTTGATACAGTTAAAGGTCCTTATTCG
131 TTTATTATAAAGGGGTTTGGAAGGTTCACAAGGTCTTGCTTGATACAGTTAAAGGTCCTTATTCG
48205044 TTTTTAACTCCAATGGTTAAGCAAATTCAAGAGAAATTTAATAAATATTGGGCTAAGTATTCATT
196 TTTTTAACTCCAATGGTTAAGCAAATTCAAGAGAAATTTAATAAATATTGGGCTAAGTATTCATT
48205109 GATATTGTCATGTGCTGCAATTTTAGATCCTCGTTACAAGTTGAATTA
261 GATATTGTCATGTGCTGCAATTTTAGATCCTCGTTACAAGTTGAATTA
48205157 GATAAAGATTATAAAATGTTTGCACTTTCTAACGAGGAGTGGAGAAATGTTGTTATTCTTTGCAA
1 GATAAAGATTATAAAATGTTTGCACTTTCTAACGAGGAGTGGAGAAATGTTGTTATTCTTTGCAA
48205222 ATTTTTGAAAGTCTTGTATGATGCGACTTGTGTTTTTTCTAGTTCTAATTATCCAACGAATAATC
66 ATTTTTGAAAGTCTTGTATGATGCGACTTGTGTTTTTTCTAGTTCTAATTATCCAACGAATAATC
48205287 TTTATTATAAAGGGGTTTGGAAGGTTCACAAGGTCTTGCTTGATACAGTTAAAGGTCCTTATTCG
131 TTTATTATAAAGGGGTTTGGAAGGTTCACAAGGTCTTGCTTGATACAGTTAAAGGTCCTTATTCG
48205352 TTTTTAACTCCAATGGTTAAGCAAATTCAAGAGAAATTTAATAAATATTGGGCTAAGTATTCATT
196 TTTTTAACTCCAATGGTTAAGCAAATTCAAGAGAAATTTAATAAATATTGGGCTAAGTATTCATT
48205417 GATATTGTCATGTGCTGCAATTTTAGATCCTCGTTACAAGTTGAATTA
261 GATATTGTCATGTGCTGCAATTTTAGATCCTCGTTACAAGTTGAATTA
48205465 TGTGCAATAT
Statistics
Matches: 308, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 308 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (308 bp):
GATAAAGATTATAAAATGTTTGCACTTTCTAACGAGGAGTGGAGAAATGTTGTTATTCTTTGCAA
ATTTTTGAAAGTCTTGTATGATGCGACTTGTGTTTTTTCTAGTTCTAATTATCCAACGAATAATC
TTTATTATAAAGGGGTTTGGAAGGTTCACAAGGTCTTGCTTGATACAGTTAAAGGTCCTTATTCG
TTTTTAACTCCAATGGTTAAGCAAATTCAAGAGAAATTTAATAAATATTGGGCTAAGTATTCATT
GATATTGTCATGTGCTGCAATTTTAGATCCTCGTTACAAGTTGAATTA
Found at i:48209775 original size:31 final size:32
Alignment explanation
Indices: 48209739--48209801 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
48209729 AGATAATTTT
48209739 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
48209770 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
48209802 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:48210278 original size:63 final size:63
Alignment explanation
Indices: 48210199--48210329 Score: 190
Period size: 63 Copynumber: 2.1 Consensus size: 63
48210189 TTCCGCATCA
* **
48210199 TGCCCAGGCCTTGTAACTCACAATTTATGATTTAGAACCACATGGGCAGACGACATGGGCGTG
1 TGCCCAGGCCGTGTAACTCACAATTTATGATTTAGAACCACACAGGCAGACGACATGGGCGTG
** * * *
48210262 TGCCCAGGCCGTGTAACTCACTGTTTATGGTTTAGAACCACACAGGTAGACGACATGGGTGTG
1 TGCCCAGGCCGTGTAACTCACAATTTATGATTTAGAACCACACAGGCAGACGACATGGGCGTG
48210325 TGCCC
1 TGCCC
48210330 TGGCTATGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (63 bp):
TGCCCAGGCCGTGTAACTCACAATTTATGATTTAGAACCACACAGGCAGACGACATGGGCGTG
Found at i:48211177 original size:20 final size:20
Alignment explanation
Indices: 48211154--48211196 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
48211144 CTATGTTCTG
* * *
48211154 CTCCGTTCTGTTCTGTTCAA
1 CTCCGCTCTGCTCTGCTCAA
48211174 CTCCGCTCTGCTCTGCTCAA
1 CTCCGCTCTGCTCTGCTCAA
48211194 CTC
1 CTC
48211197 TGTACCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.40, G:0.14, T:0.37
Consensus pattern (20 bp):
CTCCGCTCTGCTCTGCTCAA
Found at i:48215502 original size:59 final size:58
Alignment explanation
Indices: 48215390--48215533 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 58
48215380 ATACTGAGTC
* *
48215390 TGGTGCCGGCCATTGACAAGCCAGTACC--AAAG----TTTTTTTAAAACACGTACTT
1 TGGTGCCGACCATTGACAAGCCAGCACCAAAAAGAATTTTTTTTTAAAACACGTACTT
* * *
48215442 TGGTGCCGACCATTGACAGGCCAGCACCAAAAAGAATTTTTTTTCTAAAACTCGTGCTT
1 TGGTGCCGACCATTGACAAGCCAGCACCAAAAAGAATTTTTTTT-TAAAACACGTACTT
**
48215501 TGGTGCCGGTCATTGACAAGCCAGCACCAAAAA
1 TGGTGCCGACCATTGACAAGCCAGCACCAAAAA
48215534 AATGTGATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
52 25 0.32
54 4 0.05
58 6 0.08
59 42 0.55
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (58 bp):
TGGTGCCGACCATTGACAAGCCAGCACCAAAAAGAATTTTTTTTTAAAACACGTACTT
Found at i:48215587 original size:54 final size:53
Alignment explanation
Indices: 48215511--48215683 Score: 229
Period size: 54 Copynumber: 3.2 Consensus size: 53
48215501 TGGTGCCGGT
* * *
48215511 CATTGACAAGCCAGCACCAAAAAAATGTGATTTTTTTTTGTACTTGGTGGTGGT
1 CATTGACAGGCCAGCA-CAAAAAAATATGATTTTTTTTTGTACTTGGTGGTGGC
* * *
48215565 CATTGACAGGCCAACACAAAAAAAAAATTATTTTTTTTTGTACTTGGTGGTGGC
1 CATTGACAGGCCAGCAC-AAAAAAATATGATTTTTTTTTGTACTTGGTGGTGGC
* * * *
48215619 CATTGACAGGCTAGGACAAAAAAATTTGATTTTTTTTTTGTATTTGGTGGTGGC
1 CATTGACAGGCCAGCACAAAAAAATATGA-TTTTTTTTTGTACTTGGTGGTGGC
48215673 CATTGACAGGC
1 CATTGACAGGC
48215684 TAGGAGCAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 10 0.10
54 94 0.90
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (53 bp):
CATTGACAGGCCAGCACAAAAAAATATGATTTTTTTTTGTACTTGGTGGTGGC
Found at i:48220868 original size:28 final size:27
Alignment explanation
Indices: 48220803--48220868 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
48220793 TTTAATAGTA
*
48220803 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGTACAGTGTGGGCCTAAGCCCAAT
** *
48220830 ACAAAAACAGTGTGGGCCTAAGCCCGAT
1 AC-AGTACAGTGTGGGCCTAAGCCCAAT
48220858 ACAGTATCAGT
1 ACAGTA-CAGT
48220869 ATGGTGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (27 bp):
ACAGTACAGTGTGGGCCTAAGCCCAAT
Found at i:48221066 original size:22 final size:22
Alignment explanation
Indices: 48221041--48221087 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48221031 CTAAGAGCCG
* *
48221041 TAAACAGGATAACTATAAGCTA
1 TAAACAGAATAACTACAAGCTA
**
48221063 TAAACAGAATGGCTACAAGCTA
1 TAAACAGAATAACTACAAGCTA
48221085 TAA
1 TAA
48221088 GTATAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (22 bp):
TAAACAGAATAACTACAAGCTA
Found at i:48221181 original size:32 final size:32
Alignment explanation
Indices: 48221145--48221281 Score: 105
Period size: 32 Copynumber: 4.3 Consensus size: 32
48221135 CTATAGACAA
* * *
48221145 CCATCAGTAACGGTAACATGATCGGTACAAAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
* * * * *
48221177 CCATCAGTAGCAGTGATATGATAGGTACACAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
* * * * *
48221209 CCATCAATAATAGTGAA-ATGACCGACACACAG
1 CCATCAGTAACAGT-AATATGATCGGCACAAAG
* * *
48221241 CCATCGGTAACGGTAATATGATTGGCACAAAG
1 CCATCAGTAACAGTAATATGATCGGCACAAAG
*
48221273 CTATCAGTA
1 CCATCAGTA
48221282 GCATCGTAGC
Statistics
Matches: 79, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
31 2 0.03
32 76 0.96
33 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (32 bp):
CCATCAGTAACAGTAATATGATCGGCACAAAG
Found at i:48227904 original size:22 final size:19
Alignment explanation
Indices: 48227873--48227928 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
48227863 TACTTATGGT
* *
48227873 TTTTGAATTTAGAATTGATGA
1 TTTTAAATTTA-AATTAAT-A
48227894 TTTTAACATTTTAAATTAATA
1 TTTTAA-A-TTTAAATTAATA
48227915 TTTTAAATTTAAAT
1 TTTTAAATTTAAAT
48227929 AATTATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 7 0.23
20 1 0.03
21 12 0.39
22 7 0.23
23 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTTAAATTTAAATTAATA
Found at i:48242998 original size:26 final size:26
Alignment explanation
Indices: 48242962--48243037 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
48242952 ACATATTTTC
*
48242962 TCAAAATTTTACTAGAGGCAAAATCG
1 TCAAAATTTTACTAGAGGAAAAATCG
* * *
48242988 TCAAAATTTTACCA-AGGGTAAAATTG
1 TCAAAATTTTACTAGA-GGAAAAATCG
* *
48243014 TTAAAATTTTACTGGAGGAAAAAT
1 TCAAAATTTTACTAGAGGAAAAAT
48243038 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACTAGAGGAAAAATCG
Found at i:48244120 original size:210 final size:210
Alignment explanation
Indices: 48243752--48244176 Score: 787
Period size: 210 Copynumber: 2.0 Consensus size: 210
48243742 TAACAATTGG
*
48243752 TATCAGAGTCATGTTGTGCTATGATTATGTTGTAAACTAAGACTAAATCTCTCTCTTCATCTATT
1 TATCAGAGCCATGTTGTGCTATGATTATGTTGTAAACTAAGACTAAATCTCTCTCTTCATCTATT
48243817 TGATTAATATTTGATAAGATGTGACATACTTGTAATTATTCACATGTTTAGGGAAATGGATGTGA
66 TGATTAATATTTGATAAGATGTGACATACTTGTAATTATTCACATGTTTAGGGAAATGGATGTGA
*
48243882 AAAAAATGCAATAATATATATTTGTTATATAATTATTATTTTTTGCCAAGGTTGTGGTTCTTAGG
131 AAAAAATGCAATAATATATATGTGTTATATAATTATTATTTTTTGCCAAGGTTGTGGTTCTTAGG
48243947 AAATAGACCGTGGAC
196 AAATAGACCGTGGAC
* * *
48243962 TATCAGAGCCATGTTGTGCTATGATTATGTTGTAAACTGAGACTAAATCTCTCTTTTTATCTATT
1 TATCAGAGCCATGTTGTGCTATGATTATGTTGTAAACTAAGACTAAATCTCTCTCTTCATCTATT
48244027 TGATTAATATTTGATAAGATGTGACATACTTGTAATTATTCACATGTTTAGGGAAATGGATGTGA
66 TGATTAATATTTGATAAGATGTGACATACTTGTAATTATTCACATGTTTAGGGAAATGGATGTGA
* *
48244092 AAAAAGTGCAATGATATATATGTGTTATATAATTATTATTTTTTGCCAAGGTTGTGGTTCTTAGG
131 AAAAAATGCAATAATATATATGTGTTATATAATTATTATTTTTTGCCAAGGTTGTGGTTCTTAGG
48244157 AAATAGACCGTGGAC
196 AAATAGACCGTGGAC
48244172 TATCA
1 TATCA
48244177 TCTTCACATA
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (210 bp):
TATCAGAGCCATGTTGTGCTATGATTATGTTGTAAACTAAGACTAAATCTCTCTCTTCATCTATT
TGATTAATATTTGATAAGATGTGACATACTTGTAATTATTCACATGTTTAGGGAAATGGATGTGA
AAAAAATGCAATAATATATATGTGTTATATAATTATTATTTTTTGCCAAGGTTGTGGTTCTTAGG
AAATAGACCGTGGAC
Found at i:48249577 original size:49 final size:49
Alignment explanation
Indices: 48249468--48249580 Score: 154
Period size: 49 Copynumber: 2.3 Consensus size: 49
48249458 GATATTGCAG
* * *
48249468 ACAAGCTGCCAAATACAGATATATATGAACAAGCCACCAAAAATTGCAA
1 ACAAACTGCCAGATACAGATATATATGAACAAGCCACCAAAAATTCCAA
* * * *
48249517 ACAAACTGCCAGATACAGATATATGTGGACAAGCCACTAGAAATTCCAA
1 ACAAACTGCCAGATACAGATATATATGAACAAGCCACCAAAAATTCCAA
*
48249566 ATAAACTGCCAGATA
1 ACAAACTGCCAGATA
48249581 AATGTGGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.18
Consensus pattern (49 bp):
ACAAACTGCCAGATACAGATATATATGAACAAGCCACCAAAAATTCCAA
Found at i:48252107 original size:65 final size:65
Alignment explanation
Indices: 48252002--48252129 Score: 211
Period size: 65 Copynumber: 2.0 Consensus size: 65
48251992 TCCATAAATT
48252002 ACTATCCATTATGGCGACTCTCGATTACAAGATCTAGAAAATAGATGTCAAGACAATCTTTTTTA
1 ACTATCCATTATGGCGACTCTCGATTACAAGATCTAGAAAATAGATGTCAAGACAATCTTTTTTA
* * * * *
48252067 ACTATCTATTATGGCGACTCTTGATTACGAGATCTGGAAAATAGATGTCAAGACAATGTTTTT
1 ACTATCCATTATGGCGACTCTCGATTACAAGATCTAGAAAATAGATGTCAAGACAATCTTTTT
48252130 GAACAATTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (65 bp):
ACTATCCATTATGGCGACTCTCGATTACAAGATCTAGAAAATAGATGTCAAGACAATCTTTTTTA
Found at i:48254611 original size:17 final size:18
Alignment explanation
Indices: 48254580--48254613 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48254570 TAAGTTTCTA
*
48254580 AAAATGGAAATGGAAATG
1 AAAATGGAAAAGGAAATG
48254598 AAAA-GGAAAAGGAAAT
1 AAAATGGAAAAGGAAAT
48254614 AATCCATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (18 bp):
AAAATGGAAAAGGAAATG
Found at i:48259102 original size:140 final size:138
Alignment explanation
Indices: 48258779--48259134 Score: 348
Period size: 140 Copynumber: 2.6 Consensus size: 138
48258769 GAAAGTTATT
* *
48258779 TTTAAGAAAAAAATACAATATAGGTTTTGAATTG-GG-GTG-AAGGAATCGAAATCGAGATTTAA
1 TTTAAGAAAAAAATAC-ATA-A-GTTTTGAATTGAGGTGAGAAAGGAATCGAAATCGAGGTTTAA
* * * * * * *
48258841 AAATGGAAAAGAAGTTCGTTTGGAATTTGGGTTTTGTCACCAAAAATAAGGTTTGTATGAGTTTT
63 AAATGGAAAAGAAGCTAGTTCGGAATTAGAGTTTTGTCACCAAAAATAAGGTTTGGATCAGTTTT
**
48258906 GATGGGTTATT
128 GATGGGTTAGC
* * * ** * * *
48258917 TTTAAGAAAAACAGTACAT-AGAATTTGTATCAATGTGAGAAAGGAATTGAAATCAAGGTTTAAA
1 TTTAAGAAAAA-AATACATAAG-TTTTGAATTGAGGTGAGAAAGGAATCGAAATCGAGGTTTAAA
*** * *
48258981 AATGGAAAAGAAGCTAG-TCGGAATTAGAGTTTTGTTGTCGAAAATAGGGTTTGGATCAGTTTTT
64 AATGGAAAAGAAGCTAGTTCGGAATTAGAGTTTTGTCACCAAAAATAAGGTTTGGATCAG--TTT
48259045 TGATGGGTT-GC
127 TGATGGGTTAGC
* *
48259056 TTTAACGAAAAATAATACATAAGTTTTGAATTGAGGTGAGAAAGGAATCAAAATCGATGTTTAAA
1 TTTAA-GAAAAA-AATACATAAGTTTTGAATTGAGGTGAGAAAGGAATCGAAATCGAGGTTTAAA
48259121 AATGG-AAAGAAGCT
64 AATGGAAAAGAAGCT
48259135 CATTAAATTT
Statistics
Matches: 174, Mismatches: 35, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
135 1 0.01
136 7 0.04
137 1 0.01
138 47 0.27
139 54 0.31
140 62 0.36
141 2 0.01
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (138 bp):
TTTAAGAAAAAAATACATAAGTTTTGAATTGAGGTGAGAAAGGAATCGAAATCGAGGTTTAAAAA
TGGAAAAGAAGCTAGTTCGGAATTAGAGTTTTGTCACCAAAAATAAGGTTTGGATCAGTTTTGAT
GGGTTAGC
Found at i:48261504 original size:44 final size:44
Alignment explanation
Indices: 48261432--48261523 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
48261422 GTTTATATTT
* * * *
48261432 TCAAGTTCAAATATCAGAATGGACCTAGTTTTCAATTTCAAGTG
1 TCAAGTTCAAATATCAAAATGAAACTAGTTGTCAATTTCAAGTG
48261476 TCAAGTTCAAATATCAAAATGAAACTAGTTGTCAATTTCAAGTG
1 TCAAGTTCAAATATCAAAATGAAACTAGTTGTCAATTTCAAGTG
48261520 TCAA
1 TCAA
48261524 AGCGTAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (44 bp):
TCAAGTTCAAATATCAAAATGAAACTAGTTGTCAATTTCAAGTG
Found at i:48263318 original size:20 final size:19
Alignment explanation
Indices: 48263275--48263325 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
48263265 GATATATGTT
*
48263275 GATTAATTAAGTAAAATAA
1 GATTAATTAAGTAAAAGAA
48263294 GATTAATTAAGATAAAAGATA
1 GATTAATTAAG-TAAAAGA-A
48263315 -ATTAATTAAGT
1 GATTAATTAAGT
48263326 TAATTAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 16 0.55
21 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (19 bp):
GATTAATTAAGTAAAAGAA
Found at i:48265656 original size:14 final size:14
Alignment explanation
Indices: 48265637--48265808 Score: 105
Period size: 14 Copynumber: 12.3 Consensus size: 14
48265627 TCTGCAGGAC
48265637 AATCTGCATCTATG
1 AATCTGCATCTATG
* *
48265651 AATCTGTATTTATG
1 AATCTGCATCTATG
*
48265665 AATCTGCATCTATA
1 AATCTGCATCTATG
* * *
48265679 AATCTACATGTATT
1 AATCTGCATCTATG
48265693 AAT-TCGCATCTATG
1 AATCT-GCATCTATG
* **
48265707 GATCCACATCTATG
1 AATCTGCATCTATG
* * **
48265721 AATCCGCATGTACA
1 AATCTGCATCTATG
*
48265735 AATCTGCATCTATA
1 AATCTGCATCTATG
**
48265749 AATCAACA-CATATG
1 AATCTGCATC-TATG
* *
48265763 GATCCGCATCTATG
1 AATCTGCATCTATG
* *
48265777 AATCTGCATGTATA
1 AATCTGCATCTATG
** *
48265791 AATCCACATTTATG
1 AATCTGCATCTATG
48265805 AATC
1 AATC
48265809 CACATGTGAG
Statistics
Matches: 118, Mismatches: 36, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
13 2 0.02
14 115 0.97
15 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (14 bp):
AATCTGCATCTATG
Found at i:48265731 original size:42 final size:42
Alignment explanation
Indices: 48265671--48265815 Score: 125
Period size: 42 Copynumber: 3.5 Consensus size: 42
48265661 TATGAATCTG
* * * **
48265671 CATCTATAAATCTACATGTATTAAT-TCGCATCTATGGATCCA
1 CATCTATGAATCCACATGTATCAATCT-GCATCTATAAATCCA
* *
48265713 CATCTATGAATCCGCATGTA-CAAATCTGCATCTATAAATCAA
1 CATCTATGAATCCACATGTATC-AATCTGCATCTATAAATCCA
* * * * *
48265755 CA-CATATGGATCCGCATCTATGAATCTGCATGTATAAATCCA
1 CATC-TATGAATCCACATGTATCAATCTGCATCTATAAATCCA
*
48265797 CATTTATGAATCCACATGT
1 CATCTATGAATCCACATGT
48265816 GAGAGTCTGC
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.01
42 80 0.98
43 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (42 bp):
CATCTATGAATCCACATGTATCAATCTGCATCTATAAATCCA
Found at i:48265826 original size:42 final size:42
Alignment explanation
Indices: 48265698--48265815 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
48265688 GTATTAATTC
** * *
48265698 GCATCTATGGATCCACATCTATGAATCCGCATGTACAAATCT
1 GCATCTATAAATCCACATATATGAATCCGCATGTACGAATCT
* * * * *
48265740 GCATCTATAAATCAACACATATGGATCCGCATCTATGAATCT
1 GCATCTATAAATCCACATATATGAATCCGCATGTACGAATCT
* * *
48265782 GCATGTATAAATCCACATTTATGAATCCACATGT
1 GCATCTATAAATCCACATATATGAATCCGCATGT
48265816 GAGAGTCTGC
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
GCATCTATAAATCCACATATATGAATCCGCATGTACGAATCT
Found at i:48267069 original size:42 final size:42
Alignment explanation
Indices: 48267018--48267337 Score: 390
Period size: 42 Copynumber: 7.3 Consensus size: 42
48267008 ATTTTTAGAA
48267018 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCC
*
48267060 ACAAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCC
*
48267102 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTGTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCC
*
48267144 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTT-CC
* * *
48267187 ACAAACGCCGCTAAAGAACATGACCTTTAGCNNNNNNNNNAGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGC---------GGCGCTTTT-CC
* *
48267239 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCGTC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC--C
* * * *
48267283 AAAAACGCCGCTATAGATCAA-ACCTTTAGCGGCGCTTCTCAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTC-C
*
48267325 AAAAACGCCGCTA
1 ACAAACGCCGCTA
48267338 GAAACATAAC
Statistics
Matches: 252, Mismatches: 14, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
42 134 0.53
43 58 0.23
44 18 0.07
52 42 0.17
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.19
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCC
Found at i:48270639 original size:200 final size:200
Alignment explanation
Indices: 48270296--48270695 Score: 782
Period size: 200 Copynumber: 2.0 Consensus size: 200
48270286 GTCCAGCAGT
48270296 ACCCATTTTCGAAAATATCAGTCTAATCTAGTAAACTCAAAAAGAACAAAGGCAATACCTTTTTC
1 ACCCATTTTCGAAAATATCAGTCTAATCTAGTAAACTCAAAAAGAACAAAGGCAATACCTTTTTC
48270361 ACTCGTATGCACATCTATTTCGCCTCGAAAAGGATACAAGAAGTCAAACAACTATAAAGGATACA
66 ACTCGTATGCACATCTATTTCGCCTCGAAAAGGATACAAGAAGTCAAACAACTATAAAGGATACA
48270426 AGGGTTAGGAAATTTCAAGTTCAAAACTCCAAATTTCAATAATTTCTTGATCCAAAGCTACCAAA
131 AGGGTTAGGAAATTTCAAGTTCAAAACTCCAAATTTCAATAATTTCTTGATCCAAAGCTACCAAA
48270491 AATCA
196 AATCA
48270496 ACCCATTTTCGAAAATATCAGTCTAATCTAGTAAACTCAAAAAGAACAAAGGCAATACCTTTTTC
1 ACCCATTTTCGAAAATATCAGTCTAATCTAGTAAACTCAAAAAGAACAAAGGCAATACCTTTTTC
48270561 ACTCGTATGCACATCTATTTCGCCTCGAAAAGGATACAAGAAGTCAAACAACTATAAAGGATACA
66 ACTCGTATGCACATCTATTTCGCCTCGAAAAGGATACAAGAAGTCAAACAACTATAAAGGATACA
* *
48270626 AGGGTTAGGAAATTTCAAGTTCAAAACTCCAAATTTTAATAATTTCTTTATCCAAAGCTACCAAA
131 AGGGTTAGGAAATTTCAAGTTCAAAACTCCAAATTTCAATAATTTCTTGATCCAAAGCTACCAAA
48270691 AATCA
196 AATCA
48270696 GAAATAATAG
Statistics
Matches: 198, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (200 bp):
ACCCATTTTCGAAAATATCAGTCTAATCTAGTAAACTCAAAAAGAACAAAGGCAATACCTTTTTC
ACTCGTATGCACATCTATTTCGCCTCGAAAAGGATACAAGAAGTCAAACAACTATAAAGGATACA
AGGGTTAGGAAATTTCAAGTTCAAAACTCCAAATTTCAATAATTTCTTGATCCAAAGCTACCAAA
AATCA
Found at i:48271542 original size:23 final size:23
Alignment explanation
Indices: 48271500--48271543 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
48271490 AGCTCTCTAT
*
48271500 ATATAAACAAGAAGGAAAGAAAG
1 ATATAAACAAGAAGAAAAGAAAG
48271523 ATATAAA-AAGAAGAAGAAGAA
1 ATATAAACAAGAAGAA-AAGAA
48271544 GAAGGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.09
Consensus pattern (23 bp):
ATATAAACAAGAAGAAAAGAAAG
Found at i:48272482 original size:134 final size:135
Alignment explanation
Indices: 48272249--48272502 Score: 456
Period size: 134 Copynumber: 1.9 Consensus size: 135
48272239 CTAAAATAGA
*
48272249 TAGTTGCCTATTCATATCAATATGTTACTTTTTTTTATTTATTTATCAATGTTTTTTTTAAATCT
1 TAGTTGCCTATTCATATCAATATGTTACTTTTTTTTATTCATTTATCAA--TTTTTTTTAAATCT
* *
48272314 AGTATTTAAATATATCAAATGGTTTAGATTAAATATTTTTAAATATAAAAGCATTAATTTGAAGA
64 AATATTTAAATATATCAAATAGTTTAGATTAAATATTTTTAAATATAAAAGCATTAATTTGAAGA
48272379 ACTACTT
129 ACTACTT
48272386 TAGTTGCCTATTCATATCAATATGTTACTTTTTTTTATTCATTTATCAA-TTTTTTTAAATCTAA
1 TAGTTGCCTATTCATATCAATATGTTACTTTTTTTTATTCATTTATCAATTTTTTTTAAATCTAA
48272450 TATTTAAATATATCAAATAGTTTAGATTAAATATTTTTAAATATAAAAGCATT
66 TATTTAAATATATCAAATAGTTTAGATTAAATATTTTTAAATATAAAAGCATT
48272503 TTTAAATATA
Statistics
Matches: 114, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
134 66 0.58
137 48 0.42
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (135 bp):
TAGTTGCCTATTCATATCAATATGTTACTTTTTTTTATTCATTTATCAATTTTTTTTAAATCTAA
TATTTAAATATATCAAATAGTTTAGATTAAATATTTTTAAATATAAAAGCATTAATTTGAAGAAC
TACTT
Found at i:48273523 original size:41 final size:41
Alignment explanation
Indices: 48273410--48273678 Score: 348
Period size: 41 Copynumber: 6.6 Consensus size: 41
48273400 AGATTTTATT
*
48273410 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGG-TC-AGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCACGAGC
* * * *
48273449 ATTAACGGCGCTTTTTTTAGAAATGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGC-TTTTTCAAAAACGCCGCTAAAGGCACGAGC
* * *
48273491 ATTAGCGGCTCTTTATCAAAAACGTCGCTAAAGGTCA-GAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGG-CACGAGC
* *
48273532 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCAAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCACGAGC
* *
48273573 ATTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGGCACAAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCACGAGC
*
48273614 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGTCA-GAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGG-CACGAGC
* *
48273655 CTTAGTGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACG
48273679 TCACTAAATG
Statistics
Matches: 198, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
39 10 0.05
40 22 0.11
41 150 0.76
42 16 0.08
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCACGAGC
Found at i:48273686 original size:123 final size:122
Alignment explanation
Indices: 48273410--48273678 Score: 389
Period size: 123 Copynumber: 2.2 Consensus size: 122
48273400 AGATTTTATT
* * *
48273410 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCAGCATTAACGGCGCTTTTTTTAGAAATGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCAGCATTAACGGCGCTTTTTTCAAAAAAGC
* * **
48273475 CGCTAAAGGCACGAGCATTAGCGGCTCTTTATCAAAAACGTCGCTAAAGGTCAGAGC
66 CGCTAAAGGCACAAGCATTAGCGGCGCTTTATCAAAAACACCGCTAAAGGTCAGAGC
* *
48273532 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGG-CAAGAGCATTAGCGGCGC-TTTTTCAAAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTC---AGCATTAACGGCGCTTTTTTCAAAAA
*
48273595 AGCCGCTAAAGGCACAAGCATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGTCAGAGC
63 AGCCGCTAAAGGCACAAGCATTAGCGGCGCTTTATCAAAAACACCGCTAAAGGTCAGAGC
* *
48273655 CTTAGTGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTCAAAAACG
48273679 TCACTAAATG
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
121 1 0.01
122 33 0.25
123 84 0.64
124 13 0.10
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (122 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGTCAGCATTAACGGCGCTTTTTTCAAAAAAGC
CGCTAAAGGCACAAGCATTAGCGGCGCTTTATCAAAAACACCGCTAAAGGTCAGAGC
Found at i:48273769 original size:39 final size:39
Alignment explanation
Indices: 48273726--48273861 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 39
48273716 TGGGCTTAGG
* *
48273726 TTTTTTGCGGCGCTTTTTGGAAAA-CGCCGCTAATGCTTA
1 TTTTTAGCGGCG-TTTTTGCAAAATCGCCGCTAATGCTTA
* * * *
48273765 TTTTTGGCGGCG-TTTTCCAAAATTCACCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTGCAAAA-TCGCCGCTAATGCT-TA
* * *
48273805 TCTTTAGCGGCGTTTTTGTAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTGCAAAATCGCCGCTAATGCTT-A
*
48273845 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
48273862 AATTCAAACG
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 8 0.10
39 23 0.29
40 39 0.50
41 8 0.10
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTGCAAAATCGCCGCTAATGCTTA
Found at i:48275607 original size:29 final size:30
Alignment explanation
Indices: 48275562--48275618 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
48275552 GTCAAGTTTT
*
48275562 ATTATGATATTTTTTTTAGTT-TAAATTAA
1 ATTATGATATTTGTTTTAGTTATAAATTAA
* *
48275591 ATTATGTTATTTGTTTTATTTATAAATT
1 ATTATGATATTTGTTTTAGTTATAAATT
48275619 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (30 bp):
ATTATGATATTTGTTTTAGTTATAAATTAA
Found at i:48276376 original size:17 final size:17
Alignment explanation
Indices: 48276351--48276383 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48276341 ATAGTTTACT
*
48276351 AAAACTTAAATATGAAG
1 AAAAATTAAATATGAAG
48276368 AAAAATTAAATATGAA
1 AAAAATTAAATATGAA
48276384 ATATAAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAATTAAATATGAAG
Found at i:48276651 original size:29 final size:29
Alignment explanation
Indices: 48276596--48276651 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
48276586 TAAATTACTT
* **
48276596 TTAAAAAATCAAATCAATTAATTTTTTTA
1 TTAAAAAATCAAATCAAATAAAATTTTTA
* *
48276625 TTAAAAATTTAAATCAAATAAAATTTT
1 TTAAAAAATCAAATCAAATAAAATTTT
48276652 GTTATCATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAAAAAATCAAATCAAATAAAATTTTTA
Found at i:48276994 original size:18 final size:19
Alignment explanation
Indices: 48276971--48277024 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
48276961 TTAAAATCTA
48276971 ATTAAAT-AAAAT-ATTAAT
1 ATTAAATAAAAATAATT-AT
48276989 ATTAAATAAAAATAATTAT
1 ATTAAATAAAAATAATTAT
48277008 ATTAATATTAAAAATAA
1 ATTAA-A-TAAAAATAA
48277025 AAATGATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 4 0.12
21 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAAATAAAAATAATTAT
Found at i:48278675 original size:41 final size:41
Alignment explanation
Indices: 48278630--48278714 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
48278620 AAAATAATGA
48278630 CATAACCATTATTTAACCTATGTTTCATATACCAAACTTTT
1 CATAACCATTATTTAACCTATGTTTCATATACCAAACTTTT
48278671 CATAACCATTATTTAACCTATGTTTCATATACCAAACTTTT
1 CATAACCATTATTTAACCTATGTTTCATATACCAAACTTTT
48278712 CAT
1 CAT
48278715 TGTTCATTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.41
Consensus pattern (41 bp):
CATAACCATTATTTAACCTATGTTTCATATACCAAACTTTT
Found at i:48279436 original size:31 final size:31
Alignment explanation
Indices: 48279343--48279438 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
48279333 GGCAAATTAC
*
48279343 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
48279374 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
48279406 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
48279437 AA
1 AA
48279439 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:48280605 original size:13 final size:13
Alignment explanation
Indices: 48280587--48280613 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48280577 CACAGACGAT
48280587 AAAATTTTCACAC
1 AAAATTTTCACAC
48280600 AAAATTTTCACAC
1 AAAATTTTCACAC
48280613 A
1 A
48280614 TATAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:48283032 original size:49 final size:49
Alignment explanation
Indices: 48282952--48283075 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
48282942 GTCCGTGACA
* * *
48282952 CTTACACGTAATCACATATCACATACCGATGCCATAGCCCAGCTATGGT
1 CTTACACGGAATCACATATCACATACCGATGCCATAGCCCAACTATGGC
* *
48283001 CTTACACGGAATCACATATCACTTACTGATGCCATAGCCCAACTATGGC
1 CTTACACGGAATCACATATCACATACCGATGCCATAGCCCAACTATGGC
48283050 CTTACACGGAAATCACATAATCACAT
1 CTTACACGG-AATCACAT-ATCACAT
48283076 TTTCACATGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 53 0.79
50 8 0.12
51 6 0.09
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (49 bp):
CTTACACGGAATCACATATCACATACCGATGCCATAGCCCAACTATGGC
Found at i:48284725 original size:67 final size:67
Alignment explanation
Indices: 48284617--48284747 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
48284607 TTTTCAATTC
* *
48284617 AGAGACCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGACCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
48284682 CA
66 CA
* *
48284684 AGAGAGCACACTCCCGCAAACTTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGACCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
48284748 ATAATATAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (67 bp):
AGAGACCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:48284974 original size:57 final size:59
Alignment explanation
Indices: 48284870--48285017 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 59
48284860 ACCCTAATTC
* * * *
48284870 GGATTACCCATCCGGGCTAAATCTATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCT-TTTTCCACATATTCTTCCGGAGGGCTATATCGATA
*
48284928 -GATCACCCGTTCGGGCTAGATCTTTTTCACACATATTCTTCCGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCTTTTTC-CACATATTCTTCCGGAGGGCTATATC--GATA
48284989 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGAT-CTTTTT
48285018 ACCGTCAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
56 5 0.06
57 44 0.57
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (59 bp):
GGATCACCCGTCCGGGCTAGATCTTTTTCCACATATTCTTCCGGAGGGCTATATCGATA
Found at i:48291703 original size:23 final size:24
Alignment explanation
Indices: 48291666--48291714 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
48291656 CTCATTTCAT
* *
48291666 TTCTTTGTACTTAAATAGA-CCTA
1 TTCTTTGTACCTAAATAAATCCTA
*
48291689 TTCTTTTTACCTAAATAAATCCTA
1 TTCTTTGTACCTAAATAAATCCTA
48291713 TT
1 TT
48291715 AAAAGCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (24 bp):
TTCTTTGTACCTAAATAAATCCTA
Found at i:48294744 original size:13 final size:13
Alignment explanation
Indices: 48294728--48294769 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
48294718 AACCTAATCT
*
48294728 AAAAATAAGAAGA
1 AAAAAAAAGAAGA
48294741 AAAAAAAAGAA-A
1 AAAAAAAAGAAGA
*
48294753 AAAGAAGAAGAAGA
1 AAA-AAAAAGAAGA
48294767 AAA
1 AAA
48294770 GAACCCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:48297511 original size:26 final size:26
Alignment explanation
Indices: 48297457--48297531 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
48297447 TCCCATCCAT
* * **
48297457 ATTTTACCTCA-GCAAAATTTTGATG
1 ATTTTACCCCAGGAAAAATTTTGACA
* *
48297482 ATTTTACCCCAGGTAATATTTTGACA
1 ATTTTACCCCAGGAAAAATTTTGACA
* *
48297508 ATTTTGCCCTAGGAAAAATTTTGA
1 ATTTTACCCCAGGAAAAATTTTGA
48297532 GAAAATATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCAGGAAAAATTTTGACA
Found at i:48298533 original size:26 final size:26
Alignment explanation
Indices: 48298479--48298553 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
48298469 TCCCATCCAT
* * **
48298479 ATTTTACCTCA-GCAAAATTTTGATG
1 ATTTTACCCCAGGAAAAATTTTGACA
* *
48298504 ATTTTACCCCAGGTAATATTTTGACA
1 ATTTTACCCCAGGAAAAATTTTGACA
* *
48298530 ATTTTGCCCTAGGAAAAATTTTGA
1 ATTTTACCCCAGGAAAAATTTTGA
48298554 GAAAATATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCAGGAAAAATTTTGACA
Found at i:48302043 original size:12 final size:12
Alignment explanation
Indices: 48302026--48302051 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48302016 AGGATATGCA
48302026 ATCTTAGATATG
1 ATCTTAGATATG
48302038 ATCTTAGATATG
1 ATCTTAGATATG
48302050 AT
1 AT
48302052 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:48302088 original size:23 final size:24
Alignment explanation
Indices: 48302043--48302089 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
48302033 ATATGATCTT
48302043 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
48302067 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
48302090 GATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:48302593 original size:17 final size:17
Alignment explanation
Indices: 48302571--48302605 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
48302561 TATATACGTA
*
48302571 TATATACATTTACATTT
1 TATATACATATACATTT
48302588 TATATACATATACATTT
1 TATATACATATACATTT
48302605 T
1 T
48302606 TTATTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:48302754 original size:27 final size:26
Alignment explanation
Indices: 48302697--48302780 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
48302687 TTATTATTTG
* *
48302697 TTTATATATATATATATGTAATTATCTTT
1 TTTATATATATATACATGT-A-TAT-ATT
*
48302726 TTTATAATCTATATA-ATGTATATAATT
1 TTTAT-ATATATATACATGTATAT-ATT
*
48302753 TTTATATATATGTACATGTATATATT
1 TTTATATATATATACATGTATATATT
48302779 TT
1 TT
48302781 GTACACTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
26 12 0.25
27 18 0.38
28 1 0.02
29 9 0.19
30 8 0.17
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTATATATATATACATGTATATATT
Found at i:48302755 original size:29 final size:29
Alignment explanation
Indices: 48302692--48302760 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
48302682 AATTATTATT
* *
48302692 ATTTGTTTAT-ATATATATATATGTAATT
1 ATTTTTTTATAATATATATATATGTAATA
*
48302720 ATCTTTTTTATAATCTATATA-ATGTATATA
1 AT-TTTTTTATAATATATATATATGTA-ATA
*
48302750 ATTTTTATATA
1 ATTTTTTTATA
48302761 TATGTACATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.06
29 20 0.59
30 12 0.35
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (29 bp):
ATTTTTTTATAATATATATATATGTAATA
Found at i:48316745 original size:20 final size:19
Alignment explanation
Indices: 48316717--48316776 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
48316707 GTTACAAAGT
* *
48316717 AATTCAAAATAATTTTTAAA
1 AATTAAAAAT-ATTTATAAA
48316737 AATTAAAAATATTTATAAA
1 AATTAAAAATATTTATAAA
* *
48316756 AAATATAAAT-TTTA-AAA
1 AATTAAAAATATTTATAAA
48316773 AATT
1 AATT
48316777 TTCTAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 6 0.17
18 4 0.11
19 16 0.46
20 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATATTTATAAA
Found at i:48320201 original size:20 final size:20
Alignment explanation
Indices: 48320178--48320234 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
48320168 ATAAGTATCG
48320178 ATACTTTGCTCAAAGTACCT
1 ATACTTTGCTCAAAGTACCT
48320198 ATACTTTGCTCAAAGTACCT
1 ATACTTTGCTCAAAGTACCT
*
48320218 CTACTTT-CTTCAAAGTA
1 ATACTTTGC-TCAAAGTA
48320235 TCAATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (20 bp):
ATACTTTGCTCAAAGTACCT
Found at i:48324057 original size:11 final size:11
Alignment explanation
Indices: 48324041--48324066 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48324031 ATTTTTTAAA
48324041 AAAAGTATTTT
1 AAAAGTATTTT
48324052 AAAAGTATTTT
1 AAAAGTATTTT
48324063 AAAA
1 AAAA
48324067 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:48324395 original size:2 final size:2
Alignment explanation
Indices: 48324390--48324430 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
48324380 ACATTTTTTA
48324390 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
48324431 TTTCTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:48324790 original size:49 final size:48
Alignment explanation
Indices: 48324696--48324792 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
48324686 TTTCTTTGCT
* * *
48324696 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAATGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
*
48324744 TAAAAACACCTAAGTTAGCCTAATCTCGCAACGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCGCAACGATAAAGGATTCAACAG
48324793 AATTCCTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 21 0.48
49 23 0.52
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
Found at i:48341828 original size:99 final size:99
Alignment explanation
Indices: 48341652--48341841 Score: 283
Period size: 99 Copynumber: 1.9 Consensus size: 99
48341642 TTGTTCTTTC
* * * *
48341652 TGCTACTGCTTGCTTCTGAAAGCATACATCGGCAGGCATTGTTTTTTGAACTTTAAAGGAAACTT
1 TGCTACTGCTTGCTTCTGAAAGCATACATAGGCAGGCATCGGTTTTTGAACCTTAAAGGAAACTT
*
48341717 GCTTTATCTGCTGTTTAGCTTGTATTAGTTACAT
66 GCTTTATCTGCTGCTTAGCTTGTATTAGTTACAT
* * * *
48341751 TGCTCCTGCTTGCTTTTGAAAGCATACATAGGTAGGCATCGGTTTTTGGACCTTAAAGGAAACTT
1 TGCTACTGCTTGCTTCTGAAAGCATACATAGGCAGGCATCGGTTTTTGAACCTTAAAGGAAACTT
48341816 GCTTT-TACTGCTGCTTAGCTTGTATT
66 GCTTTAT-CTGCTGCTTAGCTTGTATT
48341842 GTTGCTGCTT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 80 0.99
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (99 bp):
TGCTACTGCTTGCTTCTGAAAGCATACATAGGCAGGCATCGGTTTTTGAACCTTAAAGGAAACTT
GCTTTATCTGCTGCTTAGCTTGTATTAGTTACAT
Found at i:48349962 original size:27 final size:25
Alignment explanation
Indices: 48349910--48349967 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
48349900 GGCATTGGGG
48349910 TTAAGGTTTAAATTAGGGTTAGGGT
1 TTAAGGTTTAAATTAGGGTTAGGGT
* *
48349935 TTAAGGTTTTAAAGTTTGTGTTAGGGT
1 TTAAGG-TTTAAA-TTAGGGTTAGGGT
48349962 TTAAGG
1 TTAAGG
48349968 GTTGTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (25 bp):
TTAAGGTTTAAATTAGGGTTAGGGT
Found at i:48349972 original size:19 final size:20
Alignment explanation
Indices: 48349950--48349987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48349940 GTTTTAAAGT
48349950 TTGT-GTTAGGGTTTAAGGG
1 TTGTAGTTAGGGTTTAAGGG
*
48349969 TTGTATTTAGGGTTTAAGG
1 TTGTAGTTAGGGTTTAAGG
48349988 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (20 bp):
TTGTAGTTAGGGTTTAAGGG
Found at i:48350067 original size:15 final size:15
Alignment explanation
Indices: 48350044--48350098 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
48350034 GATTTAGTGT
*
48350044 TTTAGGGTTTTAAAG
1 TTTATGGTTTTAAAG
48350059 TTTATGGTTTTAAAG
1 TTTATGGTTTTAAAG
48350074 TTTA-GGATTTTAAAG
1 TTTATGG-TTTTAAAG
48350089 TTTAT-GTTTT
1 TTTATGGTTTT
48350099 GGGTTTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (15 bp):
TTTATGGTTTTAAAG
Found at i:48350197 original size:21 final size:21
Alignment explanation
Indices: 48350157--48350197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48350147 TAAATTATGG
*
48350157 GTTAAAGTTTTAAGGTTTATA
1 GTTAAAGTTTTAAGGCTTATA
* *
48350178 GTTAAGGTTTTATGGCTTAT
1 GTTAAAGTTTTAAGGCTTAT
48350198 GATTTTAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (21 bp):
GTTAAAGTTTTAAGGCTTATA
Found at i:48350220 original size:44 final size:44
Alignment explanation
Indices: 48350163--48350248 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
48350153 ATGGGTTAAA
*
48350163 GTTTTAAGGTTTATAG-TTAAGGTTTTATGGCTTATGATTTTAGG
1 GTTTTAAGATTTAT-GTTTAAGGTTTTATGGCTTATGATTTTAGG
* * * *
48350207 GTTTTAATATTTATGTTTAGGGTTTTATTGTTTATGATTTTA
1 GTTTTAAGATTTATGTTTAAGGTTTTATGGCTTATGATTTTA
48350249 AAGTTTATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.22, C:0.01, G:0.21, T:0.56
Consensus pattern (44 bp):
GTTTTAAGATTTATGTTTAAGGTTTTATGGCTTATGATTTTAGG
Found at i:48350227 original size:21 final size:21
Alignment explanation
Indices: 48350201--48350242 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48350191 GGCTTATGAT
48350201 TTTAGGGTTTTAATATTTATG
1 TTTAGGGTTTTAATATTTATG
* *
48350222 TTTAGGGTTTTATTGTTTATG
1 TTTAGGGTTTTAATATTTATG
48350243 ATTTTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (21 bp):
TTTAGGGTTTTAATATTTATG
Found at i:48350256 original size:36 final size:36
Alignment explanation
Indices: 48350208--48350299 Score: 95
Period size: 36 Copynumber: 2.6 Consensus size: 36
48350198 GATTTTAGGG
* **
48350208 TTTTAATATTTAT-GTTTAGGGTTTTATTGTTTATGA
1 TTTTAATATTTATAGTTTAAGG-TTTAAAGTTTATGA
48350244 TTTTAA-AGTTTATAGTTTAAGGTTTAAAGTTTATGA
1 TTTTAATA-TTTATAGTTTAAGGTTTAAAGTTTATGA
48350280 -TTT-ATATTTA-AGGTTTAAGG
1 TTTTAATATTTATA-GTTTAAGG
48350300 ATTGTGTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 1 0.02
34 13 0.27
35 5 0.10
36 23 0.47
37 7 0.14
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.54
Consensus pattern (36 bp):
TTTTAATATTTATAGTTTAAGGTTTAAAGTTTATGA
Found at i:48350268 original size:14 final size:14
Alignment explanation
Indices: 48350245--48350296 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
48350235 TGTTTATGAT
*
48350245 TTTAAAGTTTATAG
1 TTTAAGGTTTATAG
*
48350259 TTTAAGGTTTAAAG
1 TTTAAGGTTTATAG
* *
48350273 TTTATGATTTATA-
1 TTTAAGGTTTATAG
48350286 TTTAAGGTTTA
1 TTTAAGGTTTA
48350297 AGGATTGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TTTAAGGTTTATAG
Found at i:48350309 original size:20 final size:19
Alignment explanation
Indices: 48350286--48350334 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
48350276 ATGATTTATA
*
48350286 TTTAAGGTTTAAGGATT-GTG
1 TTTAAGGTTTAA--ATTAGGG
*
48350306 TTTAGGGTTTAAATTAGGG
1 TTTAAGGTTTAAATTAGGG
48350325 TTTAAGGTTT
1 TTTAAGGTTT
48350335 TAGTATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (19 bp):
TTTAAGGTTTAAATTAGGG
Found at i:48350363 original size:35 final size:35
Alignment explanation
Indices: 48350319--48350438 Score: 115
Period size: 35 Copynumber: 3.5 Consensus size: 35
48350309 AGGGTTTAAA
48350319 TTAGGGTTTAAGGTTTTAGTATTTATAGTTTGTTT
1 TTAGGGTTTAAGGTTTTAGTATTTATAGTTTGTTT
* *
48350354 TTAGGGTTTAAGG-TTTACTATTTATGGTTTAAG-TT
1 TTAGGGTTTAAGGTTTTAGTATTTATAGTTT--GTTT
* * *
48350389 TTAGGGTTT-ATGATTTAGTATTTGTA-TTCATGTTT
1 TTAGGGTTTAAGGTTTTAGTATTTATAGTT--TGTTT
*
48350424 TGA-GGTTTAAGGTTT
1 TTAGGGTTTAAGGTTT
48350439 AGTGTTTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
34 25 0.36
35 42 0.61
36 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.54
Consensus pattern (35 bp):
TTAGGGTTTAAGGTTTTAGTATTTATAGTTTGTTT
Found at i:48350510 original size:35 final size:36
Alignment explanation
Indices: 48350459--48350541 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
48350449 GGTTTAACAT
* * *
48350459 TTTAGGGTTTATTATTTAGAGTTTAAAGTTTAAGGG
1 TTTAAGGTTTAGTATTTAGAATTTAAAGTTTAAGGG
* * *
48350495 -TTAAGGTTTAGTATTTATAATTTATAGTTTTAGGG
1 TTTAAGGTTTAGTATTTAGAATTTAAAGTTTAAGGG
48350530 TTTTAAGGTTTA
1 -TTTAAGGTTTA
48350542 ATGTTTATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 29 0.74
37 10 0.26
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.51
Consensus pattern (36 bp):
TTTAAGGTTTAGTATTTAGAATTTAAAGTTTAAGGG
Found at i:48350549 original size:37 final size:36
Alignment explanation
Indices: 48350495--48350605 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 36
48350485 AGTTTAAGGG
* *
48350495 TTAAGGTTTAGTATTTATAATTTATAGTTTTAGGGTT
1 TTAAGGTTTAATGTTTATAATTTATAG-TTTAGGGTT
** * *
48350532 TTAAGGTTTAATGTTTATGCTTTATAATTTAGAG-T
1 TTAAGGTTTAATGTTTATAATTTATAGTTTAGGGTT
* *
48350567 TTAAGGTTTTAAAGTTTA-AATATGTAAAGTTTAGGGTT
1 TTAAGG-TTTAATGTTTATAAT-T-TATAGTTTAGGGTT
48350605 T
1 T
48350606 AAAATTTAGG
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
35 8 0.14
36 17 0.29
37 31 0.53
38 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.50
Consensus pattern (36 bp):
TTAAGGTTTAATGTTTATAATTTATAGTTTAGGGTT
Found at i:48350582 original size:15 final size:15
Alignment explanation
Indices: 48350559--48350695 Score: 56
Period size: 14 Copynumber: 9.3 Consensus size: 15
48350549 TGCTTTATAA
*
48350559 TTTAGAGTTTAAGGT
1 TTTAAAGTTTAAGGT
*
48350574 TTTAAAGTTTAA-AT
1 TTTAAAGTTTAAGGT
* *
48350588 ATGTAAAGTTT-AGGG
1 -TTTAAAGTTTAAGGT
* *
48350603 TTTAAAATTT-AGGG
1 TTTAAAGTTTAAGGT
* *
48350617 TTTAGAGTTTATA--A
1 TTTAAAGTTTA-AGGT
48350631 TTTAAAGTTTAAGGT
1 TTTAAAGTTTAAGGT
** *
48350646 TGTTAGTGTTT-AGGG
1 T-TTAAAGTTTAAGGT
* *
48350661 TTTAGGATTTTAAGG-
1 TTTA-AAGTTTAAGGT
48350676 TTTATAA-TTTAAGGT
1 TTTA-AAGTTTAAGGT
48350691 TTTAA
1 TTTAA
48350696 GATTTTAGGA
Statistics
Matches: 93, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
13 1 0.01
14 43 0.46
15 38 0.41
16 11 0.12
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (15 bp):
TTTAAAGTTTAAGGT
Found at i:48350679 original size:7 final size:7
Alignment explanation
Indices: 48350631--48351274 Score: 184
Period size: 7 Copynumber: 88.4 Consensus size: 7
48350621 GAGTTTATAA
*
48350631 TTTAAAG
1 TTTAAGG
48350638 TTTAAGG
1 TTTAAGG
*
48350645 TTGTTAGTG
1 TT-TAAG-G
*
48350654 TTTAGGG
1 TTTAAGG
48350661 TTT-AGG
1 TTTAAGG
48350667 ATTTTAAGG
1 --TTTAAGG
*
48350676 TTTATA-A
1 TTTA-AGG
48350683 TTTAAGG
1 TTTAAGG
*
48350690 TTTTAAGA
1 -TTTAAGG
*
48350698 TTTTAGG
1 TTTAAGG
48350705 ATTT-AGG
1 -TTTAAGG
48350712 CATTTGAA-G
1 --TTT-AAGG
*
48350721 TTTAGGG
1 TTTAAGG
*
48350728 TTTAGGG
1 TTTAAGG
* *
48350735 TTTATGA
1 TTTAAGG
48350742 TTTAAGG
1 TTTAAGG
*
48350749 TTTAGGG
1 TTTAAGG
*
48350756 TTTAAGTA
1 TTTAAG-G
48350764 TTTAAGG
1 TTTAAGG
*
48350771 TTTAGGG
1 TTTAAGG
*
48350778 TTTATA-A
1 TTTA-AGG
48350785 TTTAAGG
1 TTTAAGG
* *
48350792 TTTATGCA
1 TTTAAG-G
*
48350800 TTTAAAG
1 TTTAAGG
48350807 TTTAAGG
1 TTTAAGG
48350814 TTTAAGG
1 TTTAAGG
**
48350821 TTTATATA
1 TTTA-AGG
48350829 TTTGAA-G
1 TTT-AAGG
48350836 TTTAAGG
1 TTTAAGG
48350843 TTT-AGG
1 TTTAAGG
*
48350849 ATTTAGGG
1 -TTTAAGG
48350857 TTTAAGG
1 TTTAAGG
*
48350864 TTTAAAG
1 TTTAAGG
*
48350871 TTTAGAGT
1 TTTA-AGG
48350879 TTTAAGG
1 TTTAAGG
* * *
48350886 CTTATGTA
1 TTTAAG-G
* *
48350894 TTTGAGA
1 TTTAAGG
*
48350901 TTTAGGG
1 TTTAAGG
**
48350908 TTTAAAA
1 TTTAAGG
* *
48350915 TTTATGA
1 TTTAAGG
48350922 TTT-AGTG
1 TTTAAG-G
*
48350929 TTTAGGG
1 TTTAAGG
*
48350936 TTTTAGAG
1 TTTAAG-G
*
48350944 TTTAAGA
1 TTTAAGG
*
48350951 TTTAGAGT
1 TTTA-AGG
48350959 TTTAAGG
1 TTTAAGG
* *
48350966 TTCAGGG
1 TTTAAGG
*
48350973 TTTAAAGT
1 TTT-AAGG
**
48350981 TTTATTG
1 TTTAAGG
*
48350988 TTTAGGTG
1 TTTAAG-G
* *
48350996 TTTGAGA
1 TTTAAGG
48351003 TTTAAGG
1 TTTAAGG
*
48351010 TTTGAGAG
1 TTTAAG-G
48351018 TTTAAGG
1 TTTAAGG
48351025 TTTAAGG
1 TTTAAGG
*
48351032 TTT-AGAA
1 TTTAAG-G
**
48351039 TTTAATA
1 TTTAAGG
48351046 TTTAAGG
1 TTTAAGG
*
48351053 TCATTTGAGG
1 ---TTTAAGG
*
48351063 TTTAGGG
1 TTTAAGG
*
48351070 TTTAATG
1 TTTAAGG
**
48351077 TTTAGATA
1 TTTA-AGG
*
48351085 TTTAGGG
1 TTTAAGG
*
48351092 ATT-AGTG
1 TTTAAG-G
* *
48351099 TTTATGTT
1 TTTAAG-G
48351107 TTTAAGG
1 TTTAAGG
*
48351114 TTTAGAGT
1 TTTA-AGG
48351122 TTTAAGG
1 TTTAAGG
*
48351129 TTTTAGGG
1 -TTTAAGG
* *
48351137 TTTATGCA
1 TTTAAG-G
48351145 TTTAAGG
1 TTTAAGG
*
48351152 TTTAAGA
1 TTTAAGG
*
48351159 TTTAGGG
1 TTTAAGG
48351166 TTTAA--
1 TTTAAGG
**
48351171 TATTAATA
1 T-TTAAGG
*
48351179 TTTAGGAG
1 TTTAAG-G
48351187 TTTGAA-G
1 TTT-AAGG
48351194 TTTAAGG
1 TTTAAGG
*
48351201 TTTAGGG
1 TTTAAGG
*
48351208 TTTAAGT
1 TTTAAGG
48351215 TTTAA-G
1 TTTAAGG
48351221 TTTAAGGG
1 TTTAA-GG
48351229 TTT-AGTG
1 TTTAAG-G
48351236 TTTAAGG
1 TTTAAGG
*
48351243 TTTAGGG
1 TTTAAGG
48351250 TTTTAAGG
1 -TTTAAGG
*
48351258 TTTAAGA
1 TTTAAGG
*
48351265 TTTAGGG
1 TTTAAGG
48351272 TTT
1 TTT
48351275 TAATATTGAT
Statistics
Matches: 462, Mismatches: 122, Indels: 106
0.67 0.18 0.15
Matches are distributed among these distances:
5 1 0.00
6 26 0.06
7 296 0.64
8 123 0.27
9 9 0.02
10 7 0.02
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:48350692 original size:29 final size:28
Alignment explanation
Indices: 48350654--48350846 Score: 106
Period size: 29 Copynumber: 6.6 Consensus size: 28
48350644 GTTGTTAGTG
* *
48350654 TTTAGGGTTTAGGATTTTAAGGTTTATAA
1 TTTAAGGTTTAGG-GTTTAAGGTTTATAA
* * * **
48350683 TTTAAGGTTTTAAGATTTTAGGATTTAGGCA
1 TTTAAGG-TTTAGGGTTTAAGG-TTTA-TAA
* *
48350714 TTTGAA-GTTTAGGGTTTAGGGTTTATGA
1 TTT-AAGGTTTAGGGTTTAAGGTTTATAA
48350742 TTTAAGGTTTAGGGTTTAA-GTATT-TAA
1 TTTAAGGTTTAGGGTTTAAGGT-TTATAA
* *** *
48350769 GGTTTAGGGTTTATAATTTAAGGTTTATGCA
1 --TTTAAGGTTTAGGGTTTAAGGTTTAT-AA
* *
48350800 TTTAAAGTTTAAGGTTTAAGGTTTATATA
1 TTTAAGGTTTAGGGTTTAAGGTTTATA-A
*
48350829 TTTGAA-GTTTAAGGTTTA
1 TTT-AAGGTTTAGGGTTTA
48350847 GGATTTAGGG
Statistics
Matches: 126, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
27 6 0.05
28 18 0.14
29 70 0.56
30 24 0.19
31 6 0.05
32 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (28 bp):
TTTAAGGTTTAGGGTTTAAGGTTTATAA
Found at i:48350703 original size:45 final size:44
Alignment explanation
Indices: 48350610--48350724 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 44
48350600 GGGTTTAAAA
48350610 TTTAGGGTTTA-GAGTTTATAA-TTTAAAGTTTAAGGTTGTTAGTG
1 TTTAGGGTTTAGGA-TTT-TAAGTTTAAAGTTTAAGGTTGTTAGTG
48350654 TTTAGGGTTTAGGATTTTAAGGTTTATAA-TTTAAGGTT-TTAAGAT-
1 TTTAGGGTTTAGGATTTTAA-GTTTA-AAGTTTAAGGTTGTT-AG-TG
* *
48350699 TTTAGGATTTAGGCATTTGAAGTTTA
1 TTTAGGGTTTAGG-ATTTTAAGTTTA
48350725 GGGTTTAGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
43 3 0.05
44 16 0.26
45 34 0.55
46 9 0.15
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.48
Consensus pattern (44 bp):
TTTAGGGTTTAGGATTTTAAGTTTAAAGTTTAAGGTTGTTAGTG
Found at i:48350769 original size:22 final size:22
Alignment explanation
Indices: 48350566--48351274 Score: 203
Period size: 22 Copynumber: 32.8 Consensus size: 22
48350556 TAATTTAGAG
** *
48350566 TTTAAGGTTTTAAAGTTTAAATA
1 TTTAAGG-TTTAGGGTTTAAGTA
* * *
48350589 TGTAAAGTTTAGGGTTTAA-AA
1 TTTAAGGTTTAGGGTTTAAGTA
* *
48350610 TTTAGGGTTTAGAGTTT-A-TAA
1 TTTAAGGTTTAGGGTTTAAGT-A
* * * *
48350631 TTTAAAGTTTAAGGTTGTTAGTG
1 TTTAAGGTTTAGGGTT-TAAGTA
* *
48350654 TTTAGGGTTTAGGATTTTAAGGT-
1 TTTAAGGTTTAGG-GTTTAA-GTA
*
48350677 TTATAA--TTTAAGGTTTTAAG-A
1 TT-TAAGGTTT-AGGGTTTAAGTA
* *
48350698 TTTTAGGATTTAGGCATTTGAAG--
1 TTTAAGG-TTTAGG-GTTT-AAGTA
* *
48350721 TTTAGGGTTTAGGGTTTATG-A
1 TTTAAGGTTTAGGGTTTAAGTA
48350742 TTTAAGGTTTAGGGTTTAAGTA
1 TTTAAGGTTTAGGGTTTAAGTA
48350764 TTTAAGGTTTAGGGTTT-A-TAA
1 TTTAAGGTTTAGGGTTTAAGT-A
**
48350785 TTTAAGGTTTATGCATTTAA--A
1 TTTAAGGTTTA-GGGTTTAAGTA
*
48350806 GTTTAAGGTTTAAGGTTTATA-TA
1 -TTTAAGGTTTAGGGTTTA-AGTA
* *
48350829 TTTGAA-GTTTAAGGTTT-AGGA
1 TTT-AAGGTTTAGGGTTTAAGTA
* *
48350850 TTTAGGGTTTAAGGTTTAA--A
1 TTTAAGGTTTAGGGTTTAAGTA
* * * *
48350870 GTTTAGAGTTTTAAGGCTTATGTA
1 -TTTA-AGGTTTAGGGTTTAAGTA
* * *
48350894 TTTGAGATTTAGGGTTTAA-AA
1 TTTAAGGTTTAGGGTTTAAGTA
* * * *
48350915 TTTATGATTTAGTGTTTAGGGT-
1 TTTAAGGTTTAGGGTTTA-AGTA
* *
48350937 TTT-AGAGTTTAAGATTTAGAGT-
1 TTTAAG-GTTTAGGGTTTA-AGTA
*
48350959 TTTAAGGTTCAGGGTTTAAAGT-
1 TTTAAGGTTTAGGGTTT-AAGTA
** *
48350981 TTTATTGTTTAGGTGTTTGAG-A
1 TTTAAGGTTTAGG-GTTTAAGTA
* *
48351003 TTTAAGGTTTGAGAGTTTAAG-G
1 TTTAAGGTTT-AGGGTTTAAGTA
**
48351025 TTTAAGGTTTAGAATTTAA-TA
1 TTTAAGGTTTAGGGTTTAAGTA
* **
48351046 TTTAAGGTCATTTGAGGTTT-AGGG
1 TTTAAGGT--TTAG-GGTTTAAGTA
*
48351070 TTTAATGTTTA--G----A-TA
1 TTTAAGGTTTAGGGTTTAAGTA
* * * * *
48351085 TTTAGGGATTAGTGTTTATGTT
1 TTTAAGGTTTAGGGTTTAAGTA
*
48351107 TTTAAGGTTTAGAGTTTTAAGGT-
1 TTTAAGGTTTAG-GGTTTAA-GTA
* ** *
48351130 TTTAGGGTTTATGCATTTAAG-G
1 TTTAAGGTTTA-GGGTTTAAGTA
*
48351152 TTTAAGATTTAGGGTTTAA-TA
1 TTTAAGGTTTAGGGTTTAAGTA
**
48351173 -TTAATATTTAGGAGTTTGAAG--
1 TTTAAGGTTTAGG-GTTT-AAGTA
48351194 TTTAAGGTTTAGGGTTTAAGT-
1 TTTAAGGTTTAGGGTTTAAGTA
*
48351215 TTTAA-GTTTAAGGGTTT-AGTG
1 TTTAAGGTTT-AGGGTTTAAGTA
*
48351236 TTTAAGGTTTAGGGTTTTAAG-G
1 TTTAAGGTTTAGGG-TTTAAGTA
*
48351258 TTTAAGATTTAGGGTTT
1 TTTAAGGTTTAGGGTTT
48351275 TAATATTGAT
Statistics
Matches: 519, Mismatches: 102, Indels: 132
0.69 0.14 0.18
Matches are distributed among these distances:
15 8 0.02
16 1 0.00
17 1 0.00
19 1 0.00
20 30 0.06
21 159 0.31
22 220 0.42
23 75 0.14
24 24 0.05
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.47
Consensus pattern (22 bp):
TTTAAGGTTTAGGGTTTAAGTA
Found at i:48350940 original size:29 final size:28
Alignment explanation
Indices: 48350893--48350960 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
48350883 AGGCTTATGT
*
48350893 ATTT-GAGATTTAGGGTTTAAAATTTATG
1 ATTTAGAG-TTTAGGGTTTAAAATTTAAG
* * *
48350921 ATTTAGTGTTTAGGGTTTTAGAGTTTAAG
1 ATTTAGAGTTTAGGG-TTTAAAATTTAAG
48350950 ATTTAGAGTTT
1 ATTTAGAGTTT
48350961 TAAGGTTCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.49
Consensus pattern (28 bp):
ATTTAGAGTTTAGGGTTTAAAATTTAAG
Found at i:48351034 original size:14 final size:14
Alignment explanation
Indices: 48350631--48351274 Score: 184
Period size: 15 Copynumber: 44.2 Consensus size: 14
48350621 GAGTTTATAA
*
48350631 TTTAAAGTTTAAGG
1 TTTAAGGTTTAAGG
* *
48350645 TTGTTAGTGTTTAGGG
1 TT-TAAG-GTTTAAGG
48350661 TTT-AGGATTTTAAGG
1 TTTAAGG--TTTAAGG
*
48350676 TTTATA-ATTTAAGG
1 TTTA-AGGTTTAAGG
* *
48350690 TTTTAAGATTTTAGG
1 -TTTAAGGTTTAAGG
48350705 ATTT-AGGCATTTGAA-G
1 -TTTAAGG--TTT-AAGG
* *
48350721 TTTAGGGTTTAGGG
1 TTTAAGGTTTAAGG
* *
48350735 TTTATGATTTAAGG
1 TTTAAGGTTTAAGG
* *
48350749 TTTAGGGTTTAAGTA
1 TTTAAGGTTTAAG-G
*
48350764 TTTAAGGTTTAGGG
1 TTTAAGGTTTAAGG
*
48350778 TTTATA-ATTTAAGG
1 TTTA-AGGTTTAAGG
* * *
48350792 TTTATGCATTTAAAG
1 TTTAAG-GTTTAAGG
48350807 TTTAAGGTTTAAGG
1 TTTAAGGTTTAAGG
**
48350821 TTTATATATTTGAA-G
1 TTTA-AGGTTT-AAGG
48350836 TTTAAGGTTT-AGG
1 TTTAAGGTTTAAGG
*
48350849 ATTTAGGGTTTAAGG
1 -TTTAAGGTTTAAGG
* *
48350864 TTTAAAGTTTAGAGT
1 TTTAAGGTTTA-AGG
* * *
48350879 TTTAAGGCTTATGTA
1 TTTAAGGTTTAAG-G
* * *
48350894 TTTGAGATTTAGGG
1 TTTAAGGTTTAAGG
** * *
48350908 TTTAAAATTTATGA
1 TTTAAGGTTTAAGG
*
48350922 TTT-AGTGTTTAGGG
1 TTTAAG-GTTTAAGG
* *
48350936 TTTTAGAGTTTAAGA
1 TTTAAG-GTTTAAGG
*
48350951 TTTAGAGTTTTAAGG
1 TTTA-AGGTTTAAGG
* * *
48350966 TTCAGGGTTTAAAGT
1 TTTAAGGTTT-AAGG
** *
48350981 TTTATTGTTTAGGTG
1 TTTAAGGTTTAAG-G
* *
48350996 TTTGAGATTTAAGG
1 TTTAAGGTTTAAGG
*
48351010 TTTGAGAGTTTAAGG
1 TTTAAG-GTTTAAGG
*
48351025 TTTAAGGTTT-AGAA
1 TTTAAGGTTTAAG-G
**
48351039 TTTAATATTTAAGG
1 TTTAAGGTTTAAGG
* *
48351053 TCATTTGAGGTTTAGGG
1 ---TTTAAGGTTTAAGG
* **
48351070 TTTAATGTTTAGATA
1 TTTAAGGTTTA-AGG
* *
48351085 TTTAGGGATT-AGTG
1 TTTAAGGTTTAAG-G
* *
48351099 TTTATGTTTTTAAGG
1 TTTAAG-GTTTAAGG
*
48351114 TTTAGAGTTTTAAGG
1 TTTA-AGGTTTAAGG
* * *
48351129 TTTTAGGGTTTATGCA
1 -TTTAAGGTTTAAG-G
*
48351145 TTTAAGGTTTAAGA
1 TTTAAGGTTTAAGG
*
48351159 TTTAGGGTTTAA--
1 TTTAAGGTTTAAGG
** *
48351171 TATTAATATTTAGGAG
1 T-TTAAGGTTTAAG-G
48351187 TTTGAA-GTTTAAGG
1 TTT-AAGGTTTAAGG
* *
48351201 TTTAGGGTTTAAGT
1 TTTAAGGTTTAAGG
48351215 TTTAA-GTTTAAGGG
1 TTTAAGGTTTAA-GG
48351229 TTT-AGTGTTTAAGG
1 TTTAAG-GTTTAAGG
*
48351243 TTTAGGGTTTTAAGG
1 TTTAAGG-TTTAAGG
* *
48351258 TTTAAGATTTAGGG
1 TTTAAGGTTTAAGG
48351272 TTT
1 TTT
48351275 TAATATTGAT
Statistics
Matches: 460, Mismatches: 117, Indels: 106
0.67 0.17 0.16
Matches are distributed among these distances:
12 2 0.00
13 22 0.05
14 193 0.42
15 202 0.44
16 29 0.06
17 12 0.03
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTAAGG
Found at i:48351149 original size:38 final size:37
Alignment explanation
Indices: 48351093--48351276 Score: 98
Period size: 36 Copynumber: 5.1 Consensus size: 37
48351083 TATTTAGGGA
* ** *
48351093 TTAGTGTTTATGTTTTTAAGGTTTAGAGTTTTAAGGTT
1 TTAGGGTTTATGCATTTAAGGTTTA-AGATTTAAGGTT
*
48351131 TTAGGGTTTATGCATTTAAGGTTTAAGATTT-AGGGT
1 TTAGGGTTTATGCATTTAAGGTTTAAGATTTAAGGTT
*** * *
48351167 TTAATATTAAT--ATTTAGGAGTTTGAAG-TTTAAGG-T
1 TTAGGGTTTATGCATTTAAG-GTTT-AAGATTTAAGGTT
* * *
48351202 TTAGGGTTTAAG-TTTTAA-GTTTAAGGGTTT-A-GTGT
1 TTAGGGTTTATGCATTTAAGGTTTAA-GATTTAAGGT-T
* * ** *
48351237 TTAAGGTTTAGGGTTTTAAGGTTTAAGATTTAGGGTT
1 TTAGGGTTTATGCATTTAAGGTTTAAGATTTAAGGTT
48351274 TTA
1 TTA
48351277 ATATTGATGA
Statistics
Matches: 113, Mismatches: 21, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
33 3 0.03
34 12 0.11
35 28 0.25
36 31 0.27
37 15 0.13
38 24 0.21
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.48
Consensus pattern (37 bp):
TTAGGGTTTATGCATTTAAGGTTTAAGATTTAAGGTT
Found at i:48351288 original size:22 final size:22
Alignment explanation
Indices: 48351145--48351291 Score: 74
Period size: 22 Copynumber: 6.9 Consensus size: 22
48351135 GGTTTATGCA
* *
48351145 TTTAAGGTTTAAGATTTAGGG-
1 TTTAAGATTGAAGATTTAGGGT
* *
48351166 TTTAATATT-AATATTTAGGAGT
1 TTTAAGATTGAAGATTTAGG-GT
* * *
48351188 TTGAAG-TTTAAGGTTTAGGG-
1 TTTAAGATTGAAGATTTAGGGT
* *
48351208 TTTAAGTTTTAAG-TTTAAGGG-
1 TTTAAGATTGAAGATTT-AGGGT
* * *
48351229 TTT-AGTGTTTAAGGTTTAGGGT
1 TTTAAG-ATTGAAGATTTAGGGT
* *
48351251 TTTAAGGTTTAAGATTTAGGGT
1 TTTAAGATTGAAGATTTAGGGT
* *
48351273 TTTAATATTGATGATTTAG
1 TTTAAGATTGAAGATTTAG
48351292 TATTTGTATT
Statistics
Matches: 103, Mismatches: 14, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
20 19 0.18
21 34 0.33
22 48 0.47
23 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (22 bp):
TTTAAGATTGAAGATTTAGGGT
Found at i:48351402 original size:14 final size:13
Alignment explanation
Indices: 48351385--48351436 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
48351375 GTGTTTAAAA
48351385 TTTAGGATTTAGTG
1 TTTAGGATTTA-TG
* *
48351399 TTTAGGGTTTAAG
1 TTTAGGATTTATG
*
48351412 TTTATGATTTATG
1 TTTAGGATTTATG
*
48351425 TTAAGG-TTTATG
1 TTTAGGATTTATG
48351437 GCTTATGATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 6 0.19
13 15 0.48
14 10 0.32
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (13 bp):
TTTAGGATTTATG
Found at i:48351435 original size:19 final size:20
Alignment explanation
Indices: 48351407--48351455 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
48351397 TGTTTAGGGT
*
48351407 TTAA-GTTTATGATTTATG-
1 TTAAGGTTTATGACTTATGA
*
48351425 TTAAGGTTTATGGCTTATGA
1 TTAAGGTTTATGACTTATGA
48351445 TTAAGGGTTTA
1 TTAA-GGTTTA
48351456 GGGTAACGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 4 0.15
21 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (20 bp):
TTAAGGTTTATGACTTATGA
Found at i:48352111 original size:15 final size:15
Alignment explanation
Indices: 48352091--48352119 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48352081 GACTTACAGA
48352091 GCACCTATTAAACAC
1 GCACCTATTAAACAC
48352106 GCACCTATTAAACA
1 GCACCTATTAAACA
48352120 ACGAAGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (15 bp):
GCACCTATTAAACAC
Found at i:48357094 original size:171 final size:171
Alignment explanation
Indices: 48356809--48357318 Score: 1011
Period size: 171 Copynumber: 3.0 Consensus size: 171
48356799 TTTTCATGAT
*
48356809 TGGCTTTTGCAAACACTACAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
1 TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
48356874 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
66 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
48356939 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAAATA
131 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAAATA
48356980 TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
1 TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
48357045 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
66 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
48357110 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAAATA
131 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAAATA
48357151 TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
1 TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
48357216 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
66 CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
48357281 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAA
131 ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAA
48357319 CTTTCTTCAA
Statistics
Matches: 338, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 338 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (171 bp):
TGGCTTTTGCAAACACTGCAGCTTGTACACTTTTACTTGTGTCTAAATATGGATGTCAAATCTAT
CCCTTTTTCTATTTGTGGATTCAATATTTTGGGTGAGATATGCTAGGGAAACTCTTTTCATGGTC
ATAATAAATTCTTTACTGATTGCTTTACAGAGAGGCAAATA
Found at i:48364230 original size:25 final size:24
Alignment explanation
Indices: 48364201--48364279 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 24
48364191 AAAAAATATT
48364201 ATATAAAAAATTTTAATAAATAAAA
1 ATATAAAAAATTTTAA-AAATAAAA
* *
48364226 ATATATAAAATATT-AAAATAATATA
1 ATATAAAAAATTTTAAAAATAA-A-A
* *
48364251 ATATAAATACTTTTAAAAAATTAAAA
1 ATATAAAAAATTTT-AAAAA-TAAAA
48364277 ATA
1 ATA
48364280 ATATAGGTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
23 6 0.14
24 2 0.05
25 23 0.53
26 4 0.09
27 5 0.12
28 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (24 bp):
ATATAAAAAATTTTAAAAATAAAA
Found at i:48364584 original size:31 final size:31
Alignment explanation
Indices: 48364519--48364582 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
48364509 CTATTCTCTT
* * *
48364519 AAATAAATTTTTTTATTTAAATAATAATAAA
1 AAATAAACTTTTTGATTAAAATAATAATAAA
48364550 AAATAAACTTTTTGATTAAAATAAT-ATAAA
1 AAATAAACTTTTTGATTAAAATAATAATAAA
48364580 AAA
1 AAA
48364583 ATTATTTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
AAATAAACTTTTTGATTAAAATAATAATAAA
Found at i:48367943 original size:5 final size:5
Alignment explanation
Indices: 48367933--48367963 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
48367923 CTCGAAAATT
48367933 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
48367964 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:48368110 original size:21 final size:22
Alignment explanation
Indices: 48368080--48368120 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48368070 AACATAATAA
*
48368080 TAAATAAAT-ATTGAAAATTCT
1 TAAATAAATAATTAAAAATTCT
*
48368101 TAAATCAATAATTAAAAATT
1 TAAATAAATAATTAAAAATT
48368121 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAATAAATAATTAAAAATTCT
Found at i:48368957 original size:19 final size:19
Alignment explanation
Indices: 48368935--48368984 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
48368925 ATAAAATATC
* *
48368935 ATAAACAAAATTGGGAAAA
1 ATAAACAAAATTAGAAAAA
48368954 ATAAACAAAATTAGAAAAA
1 ATAAACAAAATTAGAAAAA
48368973 ATAAACTAAAAT
1 ATAAAC-AAAAT
48368985 CAACCATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (19 bp):
ATAAACAAAATTAGAAAAA
Found at i:48369010 original size:14 final size:15
Alignment explanation
Indices: 48368993--48369022 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
48368983 ATCAACCATT
48368993 AAAAATCTAG-AAAA
1 AAAAATCTAGTAAAA
48369007 AAAAATCTAGTAAAA
1 AAAAATCTAGTAAAA
48369022 A
1 A
48369023 CTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAATCTAGTAAAA
Found at i:48374837 original size:53 final size:53
Alignment explanation
Indices: 48374714--48374841 Score: 139
Period size: 53 Copynumber: 2.4 Consensus size: 53
48374704 ATCCAACCTA
* * * * *
48374714 GCTTACAAGGAGCATGCAGAATGAGACATATCACAAATCTCACAAAAACCCAT
1 GCTTTCAAGGAGCACGCAGAGTGAAACATATCACAAAACTCACAAAAACCCAT
* ** * * **
48374767 GCTTTTAAATAGTACGCAGAGTGAAACTTATCACAAAACTCACAAAAGTCCAT
1 GCTTTCAAGGAGCACGCAGAGTGAAACATATCACAAAACTCACAAAAACCCAT
*
48374820 GCTTTCGAGGAGCACGCAGAGT
1 GCTTTCAAGGAGCACGCAGAGT
48374842 AAGGCTCACA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (53 bp):
GCTTTCAAGGAGCACGCAGAGTGAAACATATCACAAAACTCACAAAAACCCAT
Found at i:48375494 original size:10 final size:10
Alignment explanation
Indices: 48375479--48375512 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
48375469 TTGAATTGAA
48375479 TACTTGAAGT
1 TACTTGAAGT
48375489 TACTTGAAGT
1 TACTTGAAGT
*
48375499 TATTTGAAG-
1 TACTTGAAGT
48375508 TACTT
1 TACTT
48375513 AATTGAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (10 bp):
TACTTGAAGT
Found at i:48379617 original size:66 final size:66
Alignment explanation
Indices: 48379329--48379609 Score: 379
Period size: 66 Copynumber: 4.3 Consensus size: 66
48379319 CTTAGTCATT
* * *
48379329 TTACCATT-CTAATTCAAATTTTCAAATCTGCCTATCTTTAAATTTTATAGTCGTTTTCCACCTA
1 TTACCATTCCT-ATTCAAATTTTCAAACCCGCCTATCTTCAAATTTTATAGTCGTTTTCCACCTA
48379393 TC
65 TC
* * * * *
48379395 TTATCATTCCTATTTAAATTTTCAAACCCG-CTATCTTCAAATTTTACAGTCTTTTTCCATCTAT
1 TTACCATTCCTATTCAAATTTTCAAACCCGCCTATCTTCAAATTTTATAGTCGTTTTCCACCTAT
48379459 C
66 C
* * * * *
48379460 TTACCA-TCCTTAATCAAATTTTCAAATCCACCTATCTTCAGATTTTATAGTCGTTTTCCACTTA
1 TTACCATTCC-TATTCAAATTTTCAAACCCGCCTATCTTCAAATTTTATAGTCGTTTTCCACCTA
48379524 TC
65 TC
* *
48379526 TTACCATTCCTATTCAAAATTTCAAACCCGCCTATCTTCAAATTTTATAATCGTTTTCCACCTAT
1 TTACCATTCCTATTCAAATTTTCAAACCCGCCTATCTTCAAATTTTATAGTCGTTTTCCACCTAT
48379591 C
66 C
*
48379592 TTACCTTTCCTATTCAAA
1 TTACCATTCCTATTCAAA
48379610 AATTCAAAAT
Statistics
Matches: 185, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
64 3 0.02
65 52 0.28
66 125 0.68
67 5 0.03
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.43
Consensus pattern (66 bp):
TTACCATTCCTATTCAAATTTTCAAACCCGCCTATCTTCAAATTTTATAGTCGTTTTCCACCTAT
C
Found at i:48379836 original size:31 final size:31
Alignment explanation
Indices: 48379768--48379849 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
48379758 AAAGTTTGTG
* ** *
48379768 TATTATTTTAGTAAATA-ATTCTTTTTTATA
1 TATTATTTTAGTAAAAATATTAATTTTCATA
48379798 TATTATTTTAGTCAAAAATATTAATTTTCAT-
1 TATTATTTTAGT-AAAAATATTAATTTTCATA
* *
48379829 TATTATTTAAATAAAAATATT
1 TATTATTTTAGTAAAAATATT
48379850 TTATTCAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 21 0.48
31 14 0.32
32 9 0.20
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (31 bp):
TATTATTTTAGTAAAAATATTAATTTTCATA
Found at i:48380314 original size:124 final size:124
Alignment explanation
Indices: 48380169--48380448 Score: 368
Period size: 124 Copynumber: 2.3 Consensus size: 124
48380159 TTTTTTCGAG
* ** ** * *
48380169 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* * *
48380233 GAAATAGTGGCCTCGTGGACGCGATTTCGCTACA-ATGGTCATGT-GAGAAATATTTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGATGGTCATGTAG-GAAATAATTTTTT
* * *
48380292 TTGACGTTTTCTGAGGAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* *
48380357 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGATGGTCATGTAGGAAATAATTTTTT
*
48380417 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
48380449 GCCCTCGTGG
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
123 6 0.04
124 101 0.74
125 28 0.21
126 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACGCGATTTCGCTACAGATGGTCATGTAGGAAATAATTTTTT
Found at i:48380499 original size:84 final size:84
Alignment explanation
Indices: 48380358--48380560 Score: 397
Period size: 84 Copynumber: 2.4 Consensus size: 84
48380348 AGAAATTGTG
48380358 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
48380423 TTTCTGAGCAAATAGTGTC
66 TTTCTGAGCAAATAGTGTC
*
48380442 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTACG
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
48380507 TTTCTGAGCAAATAGTGTC
66 TTTCTGAGCAAATAGTGTC
48380526 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
48380561 AGCAAGTTTG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 118 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (84 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACG
TTTCTGAGCAAATAGTGTC
Found at i:48384164 original size:51 final size:50
Alignment explanation
Indices: 48383847--48384185 Score: 340
Period size: 51 Copynumber: 6.7 Consensus size: 50
48383837 NAGGGTTTTA
*
48383847 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGTTT--TT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTAATT
*
48383898 AATTAAATTAGGTTAGGGTTTTTAATTAATTAGGTTAGGTTAGGGTTTTTAATTT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAA--A--TTAGGTTAGGGTTTTTAA-TT
* * *
48383953 AATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
* * *
48384003 -A--AA-TTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGATTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
* * * *
48384049 AAATTAGGTTAGGGTAGGGTTTTTAATTTAATTAAATAAGGTTAGGATTTTTAA-T
1 -AATTAAGTTAGGTTAGGG---TT--TTTAATTAAATTAGGTTAGGGTTTTTAATT
48384104 --TTAAG-TAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
*
48384151 AAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAG
1 -AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAG
48384186 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 13, Indels: 46
0.81 0.04 0.15
Matches are distributed among these distances:
46 68 0.27
47 3 0.01
48 3 0.01
49 1 0.00
50 7 0.03
51 91 0.36
52 7 0.03
53 2 0.01
54 2 0.01
55 39 0.15
56 29 0.12
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (50 bp):
AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
Found at i:48384185 original size:28 final size:27
Alignment explanation
Indices: 48383847--48384180 Score: 356
Period size: 23 Copynumber: 13.1 Consensus size: 27
48383837 NAGGGTTTTA
*
48383847 AATTAAATTAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
*
48383874 AAATTAGGTTAGGTTAGGGTTTTTAATT
1 -AATTAAGTTAGGTTAGGGTTTTTAATT
48383902 -A--AA-TTAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
*
48383925 AATTAGGTTAGGTTAGGGTTTTTAATTT
1 AATTAAGTTAGGTTAGGGTTTTTAA-TT
*
48383953 AATTAAATTAGGTTAGGGTTTTTAA-T
1 AATTAAGTTAGGTTAGGGTTTTTAATT
48383979 --TTAAG-TAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
48384003 -A--AA-TTAGGTTAGGGTTTTTAA-T
1 AATTAAGTTAGGTTAGGGTTTTTAATT
*
48384025 --TTAAG-TAGGTTAGGATTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
* *
48384049 AAATTAGGTTAGGGTAGGGTTTTTAATTT
1 -AATTAAGTTAGGTTAGGGTTTTTAA-TT
* * *
48384078 AATTAAATAAGGTTAGGATTTTTAA-T
1 AATTAAGTTAGGTTAGGGTTTTTAATT
48384104 --TTAAG-TAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
48384128 -A--AA-TTAGGTTAGGGTTTTTAATT
1 AATTAAGTTAGGTTAGGGTTTTTAATT
*
48384151 AAATTAGGTTAGGTTAGGGTTTTTAATT
1 -AATTAAGTTAGGTTAGGGTTTTTAATT
48384179 AA
1 AA
48384181 ATTAGNNNNN
Statistics
Matches: 261, Mismatches: 20, Indels: 51
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.00
23 110 0.42
24 13 0.05
25 1 0.00
26 4 0.02
27 25 0.10
28 105 0.40
29 2 0.01
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (27 bp):
AATTAAGTTAGGTTAGGGTTTTTAATT
Found at i:48387599 original size:69 final size:69
Alignment explanation
Indices: 48387488--48387625 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
48387478 TGCCCTCGTA
* *
48387488 GTTTTGTCCCCTTGGATTTTGAGGCCCGCGCCTTTCCCTTCCGACACGTATTTGCCGCTGCCTCT
1 GTTTTGTCCCCTTAGATTTTGAGGCCCGCGCCTTTCCCTTCCGACACGTATTTGCCGCCGCCTCT
48387553 CCTC
66 CCTC
*
48387557 GTTTTGTCCCCTTAGATTTTGAGGCCCGTGCCTTTCCCTTCCGACACGTATTTGCCGCCGCCTCT
1 GTTTTGTCCCCTTAGATTTTGAGGCCCGCGCCTTTCCCTTCCGACACGTATTTGCCGCCGCCTCT
48387622 CCTC
66 CCTC
48387626 CGGCGTAAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.08, C:0.38, G:0.20, T:0.35
Consensus pattern (69 bp):
GTTTTGTCCCCTTAGATTTTGAGGCCCGCGCCTTTCCCTTCCGACACGTATTTGCCGCCGCCTCT
CCTC
Found at i:48388776 original size:22 final size:22
Alignment explanation
Indices: 48388746--48388787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48388736 ATTTGGAGAT
*
48388746 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
48388768 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
48388788 TTTAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:48388834 original size:22 final size:22
Alignment explanation
Indices: 48388792--48388880 Score: 119
Period size: 22 Copynumber: 4.0 Consensus size: 22
48388782 TGAGAGTTTA
48388792 AGAG-AATTTTGGAAAGAAATTG
1 AGAGAAATTTT-GAAAGAAATTG
*
48388814 ATG-GAAATTTTGAAAGGAATTG
1 A-GAGAAATTTTGAAAGAAATTG
*
48388836 AGAGAAATTTTGAAAGGAATTG
1 AGAGAAATTTTGAAAGAAATTG
*
48388858 AGAGAATTTTTGAAAGAAATTG
1 AGAGAAATTTTGAAAGAAATTG
48388880 A
1 A
48388881 TATTGAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.02
22 53 0.87
23 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (22 bp):
AGAGAAATTTTGAAAGAAATTG
Found at i:48390703 original size:16 final size:15
Alignment explanation
Indices: 48390679--48390733 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
48390669 AAGCATACCA
48390679 AAATATTCAAAGTTAC
1 AAATATTCAAAGTT-C
*
48390695 AAATCTTCAAA--TC
1 AAATATTCAAAGTTC
48390708 AAATATTCAAAGTTTC
1 AAATATTCAAAG-TTC
*
48390724 AAATCTTCAA
1 AAATATTCAA
48390734 TTCAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.33
14 1 0.03
16 21 0.64
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (15 bp):
AAATATTCAAAGTTC
Done.