Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 133 of 175
Found at i:41399206 original size:15 final size:16
Alignment explanation
Indices: 41399167--41399210 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
41399157 GGTCCGCATG
*
41399167 CAAGAGGGTTCACTTG
1 CAAGAGGGTTCACTTA
* *
41399183 CAAGGGGGTTCGC-TA
1 CAAGAGGGTTCACTTA
41399198 CAAGAGGGTTCAC
1 CAAGAGGGTTCAC
41399211 ATATGGGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.20
Consensus pattern (16 bp):
CAAGAGGGTTCACTTA
Found at i:41401688 original size:10 final size:10
Alignment explanation
Indices: 41401642--41401733 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 10
41401632 GAGTAATTTC
41401642 TTAAATAATTA
1 TTAAA-AATTA
41401653 TTAAATAATTA
1 TTAAA-AATTA
41401664 -TATAAAATTA
1 TTA-AAAATTA
41401674 TTTAAAAATTA
1 -TTAAAAATTA
* *
41401685 TTAAGAGTTA
1 TTAAAAATTA
41401695 -TAAGAAATTA
1 TTAA-AAATTA
* *
41401705 -CAAATAATGA
1 TTAAA-AATTA
*
41401715 TTAAAAGTT-
1 TTAAAAATTA
41401724 TTAAAAATTA
1 TTAAAAATTA
41401734 CAAAAAATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
9 12 0.19
10 27 0.42
11 23 0.36
12 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:41405708 original size:78 final size:77
Alignment explanation
Indices: 41405576--41405730 Score: 256
Period size: 78 Copynumber: 2.0 Consensus size: 77
41405566 ATAGAAATTA
* *
41405576 ATATTATTTTGGAAAGAATATATTTCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
1 ATATTATTTTGGAAAAAATATAATTCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
41405641 GGGAATAATCCT
66 GGGAATAATCCT
* * *
41405653 ATATTCTTTTGGAAAAAATATAATTCTTTTTTTTTCTAACTTTTCATTTGCCTTCTCTATTAATA
1 ATATTATTTTGGAAAAAATATAATTC-ATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATA
41405718 AGGGAATAATCCT
65 AGGGAATAATCCT
41405731 GATTTTCCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
77 23 0.32
78 49 0.68
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (77 bp):
ATATTATTTTGGAAAAAATATAATTCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
GGGAATAATCCT
Found at i:41409914 original size:42 final size:42
Alignment explanation
Indices: 41409868--41409959 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
41409858 CCGTGTCCCA
*
41409868 GCCCGTGTCCTCA-CCCATGTAACTCACTGAGTTGCCCCACAT
1 GCCCGTGT-CTCAGCCCATGTAACTCACTGAGTTGCCACACAT
* * * *
41409910 GCCCGTGTGTCAGGCCGTGTAACTCTCTGAGTTGCCACACAT
1 GCCCGTGTCTCAGCCCATGTAACTCACTGAGTTGCCACACAT
41409952 GCCCGTGT
1 GCCCGTGT
41409960 GCTATGTCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 3 0.07
42 41 0.93
ACGTcount: A:0.16, C:0.36, G:0.23, T:0.25
Consensus pattern (42 bp):
GCCCGTGTCTCAGCCCATGTAACTCACTGAGTTGCCACACAT
Found at i:41425652 original size:43 final size:41
Alignment explanation
Indices: 41425586--41425699 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 41
41425576 AACTCGTACA
* * ** * *
41425586 ATGCCAACGTCCAAGACGTGGTCTTACATGTAATCATATATCG
1 ATGCCAATGTCCCAGACACGGTCTTACACG-AATCAAATA-CG
*
41425629 ATGCCACTGTCCCAGACACGGTCTTACACGAATCAAATACG
1 ATGCCAATGTCCCAGACACGGTCTTACACGAATCAAATACG
* *
41425670 ATGCCAATGTCCCAGACATGGTCTTTCACG
1 ATGCCAATGTCCCAGACACGGTCTTACACG
41425700 TTCACATAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 29 0.48
42 8 0.13
43 24 0.39
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACACGGTCTTACACGAATCAAATACG
Found at i:41425681 original size:41 final size:43
Alignment explanation
Indices: 41425586--41425742 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
41425576 AACTCGTACA
* * * * *
41425586 ATGCCAACGTCCAAGACGTGGTCTTACATGTAATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCG
* *
41425629 ATGCCACTGTCCCAGACACGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCG
* * *
41425670 ATGCCAATGTCCCAGACATGGTCTTTCACGT--TCACATAAGTTG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAAT-A-TCG
* * *
41425713 ATGCCAACGTCTCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
41425743 AAAACACAGA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
40 5 0.05
41 30 0.32
42 8 0.09
43 51 0.54
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCG
Found at i:41426914 original size:14 final size:15
Alignment explanation
Indices: 41426895--41426923 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41426885 TCATGAAACT
41426895 TTCACACAT-ATAAA
1 TTCACACATAATAAA
41426909 TTCACACATAATAAA
1 TTCACACATAATAAA
41426924 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:41433180 original size:27 final size:26
Alignment explanation
Indices: 41433133--41433211 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
41433123 TTTCTCATCC
*
41433133 CAATTTTA-CCCCAGTAAAATTTTTGA
1 CAATTTTACCCCCAATAAAA-TTTTGA
* *
41433159 CGATTTTACCCCCAATATAATTTTGA
1 CAATTTTACCCCCAATAAAATTTTGA
* * *
41433185 TAATTTTACCCCTCGATAAAGTTTTGA
1 CAATTTTACCCC-CAATAAAATTTTGA
41433212 GAAAATTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 23 0.53
27 20 0.47
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (26 bp):
CAATTTTACCCCCAATAAAATTTTGA
Found at i:41433373 original size:12 final size:12
Alignment explanation
Indices: 41433352--41433386 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
41433342 GGATTGCAAG
41433352 TTTCCATTTTTA
1 TTTCCATTTTTA
*
41433364 TTTTCATTTTTA
1 TTTCCATTTTTA
41433376 TTTCCATTTTT
1 TTTCCATTTTT
41433387 GAAAACCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCCATTTTTA
Found at i:41444470 original size:31 final size:32
Alignment explanation
Indices: 41444407--41444470 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
41444397 ATGTATGGGT
*
41444407 TGCTATGAACATATATGATATTCAGAATAGGC
1 TGCTATAAACATATATGATATTCAGAATAGGC
41444439 TGCTATAAACATATATGATATTCA-AATAGGC
1 TGCTATAAACATATATGATATTCAGAATAGGC
41444470 T
1 T
41444471 TGGGTAGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (32 bp):
TGCTATAAACATATATGATATTCAGAATAGGC
Found at i:41447700 original size:38 final size:38
Alignment explanation
Indices: 41447658--41447759 Score: 136
Period size: 37 Copynumber: 2.7 Consensus size: 38
41447648 ACAATCTACT
* **
41447658 TTAAGATTTCTACCTAAAATTTTAAGATCGCAACTCCC
1 TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
* *
41447696 TTAAGGTTTCTACC-CAAACCTTAAGATTGCAACTCCC
1 TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
*
41447733 TTATGGTTTCTACCT-AAACCTTAAGAT
1 TTAAGGTTTCTACCTAAAACCTTAAGAT
41447760 ACAACCCTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 44 0.77
38 13 0.23
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (38 bp):
TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
Found at i:41448399 original size:20 final size:18
Alignment explanation
Indices: 41448348--41448400 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 18
41448338 ACTTGTTTTA
41448348 AAACAATTTTAACTTCATTG
1 AAAC-ATTTTAAC-TCATTG
41448368 AAA-ATGTTTAACTCATCTG
1 AAACAT-TTTAACTCAT-TG
41448387 AAACTATTTTAACT
1 AAAC-ATTTTAACT
41448401 TGATTTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 10 0.34
21 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (18 bp):
AAACATTTTAACTCATTG
Found at i:41448458 original size:22 final size:24
Alignment explanation
Indices: 41448430--41448473 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41448420 ATTTTGTTTA
41448430 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
41448452 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
41448474 TATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:41448817 original size:33 final size:32
Alignment explanation
Indices: 41448769--41448835 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
41448759 TAGAATTTTC
41448769 AAAAATTATAAAAAAATATATAAAAAAACAACA
1 AAAAATTATAAAAAAAT-TATAAAAAAACAACA
** * * *
41448802 AAAAATTATTTAAAAATTATGAAAATATAACA
1 AAAAATTATAAAAAAATTATAAAAAAACAACA
41448834 AA
1 AA
41448836 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (32 bp):
AAAAATTATAAAAAAATTATAAAAAAACAACA
Found at i:41449086 original size:18 final size:17
Alignment explanation
Indices: 41449065--41449113 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
41449055 AATTTTCTAT
41449065 TTTTAATATTATTTGCAA
1 TTTT-ATATTATTTGCAA
* *
41449083 TTTTTATATTTTTTTCAA
1 -TTTTATATTATTTGCAA
41449101 TTTTATATTATTT
1 TTTTATATTATTT
41449114 TAAATAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATATTATTTGCAA
Found at i:41449114 original size:18 final size:19
Alignment explanation
Indices: 41449045--41449114 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 19
41449035 AATTTTATAA
*
41449045 AATTTTTA-ATAATTTT-C
1 AATTTTTATATTATTTTGC
*
41449062 TATTTTTAATATTA-TTTGC
1 AATTTTT-ATATTATTTTGC
*
41449081 AATTTTTATATT-TTTTTC
1 AATTTTTATATTATTTTGC
41449099 AA-TTTTATATTATTTT
1 AATTTTTATATTATTTT
41449115 AAATAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.34
18 19 0.43
19 10 0.23
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (19 bp):
AATTTTTATATTATTTTGC
Found at i:41449153 original size:16 final size:17
Alignment explanation
Indices: 41449132--41449163 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41449122 TTTTAATATA
41449132 TTTTTAT-ATTTTTTTC
1 TTTTTATAATTTTTTTC
41449148 TTTTTATAATTTTTTT
1 TTTTTATAATTTTTTT
41449164 GAAAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTATAATTTTTTTC
Found at i:41449175 original size:18 final size:18
Alignment explanation
Indices: 41449154--41449217 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
41449144 TTTCTTTTTA
41449154 TAATTTTTTTGAAAATTC
1 TAATTTTTTTGAAAATTC
* * *
41449172 TAATTCTTTT-ACAATTTT
1 TAATTTTTTTGA-AAATTC
*
41449190 TATAATTTTTTGAAAATTC
1 TA-ATTTTTTTGAAAATTC
41449209 TAATTTTTT
1 TAATTTTTT
41449218 AAATAATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 1 0.03
18 21 0.60
19 12 0.34
20 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATTTTTTTGAAAATTC
Found at i:41449190 original size:38 final size:36
Alignment explanation
Indices: 41449148--41449293 Score: 136
Period size: 37 Copynumber: 3.9 Consensus size: 36
41449138 TATTTTTTTC
41449148 TTTTTATAATTTTTTTGAAAATTCTAATTCTTTTACAA
1 TTTTTATAA-TTTTTTGAAAATTCTAATT-TTTTACAA
*
41449186 TTTTTATAATTTTTTGAAAATTCTAATTTTTTAAATAA
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT--ACAA
* * *
41449224 TTTTCTATTATTTTTAGATAAATTTCCATATATTTTTA-AA
1 TTTT-TATAATTTTTTGA-AAA-TTCTA-AT-TTTTTACAA
* *
41449264 TTTTTATAA--TTTTAAAAATTCTATTTTTTT
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT
41449294 GAAATTCTAA
Statistics
Matches: 92, Mismatches: 9, Indels: 19
0.77 0.08 0.16
Matches are distributed among these distances:
33 5 0.05
34 1 0.01
35 4 0.04
36 7 0.08
37 23 0.25
38 16 0.17
39 15 0.16
40 9 0.10
41 5 0.05
42 2 0.02
43 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (36 bp):
TTTTTATAATTTTTTGAAAATTCTAATTTTTTACAA
Found at i:41449212 original size:17 final size:17
Alignment explanation
Indices: 41449158--41449217 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
41449148 TTTTTATAAT
41449158 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
* *
41449175 TTCTTTT-ACAATTTTTATAA
1 TT-TTTTGA-AA--ATTCTAA
41449195 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
41449212 TTTTTT
1 TTTTTT
41449218 AAATAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 14 0.41
18 6 0.18
19 6 0.18
20 8 0.24
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTTGAAAATTCTAA
Found at i:41449239 original size:21 final size:22
Alignment explanation
Indices: 41449213--41449264 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
41449203 AAATTCTAAT
* *
41449213 TTTTTAAATAATTTTCTAT-TA
1 TTTTTAAATAAATTTCCATATA
*
41449234 TTTTTAGATAAATTTCCATATA
1 TTTTTAAATAAATTTCCATATA
41449256 TTTTTAAAT
1 TTTTTAAAT
41449265 TTTTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTTAAATAAATTTCCATATA
Found at i:41449247 original size:22 final size:21
Alignment explanation
Indices: 41449213--41449264 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
41449203 AAATTCTAAT
*
41449213 TTTTTAAATAATTTTC-TATTA
1 TTTTTAAATAATTTCCATA-TA
*
41449234 TTTTTAGATAAATTTCCATATA
1 TTTTTAAAT-AATTTCCATATA
41449256 TTTTTAAAT
1 TTTTTAAAT
41449265 TTTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTAAATAATTTCCATATA
Found at i:41449322 original size:76 final size:76
Alignment explanation
Indices: 41449178--41449346 Score: 168
Period size: 76 Copynumber: 2.2 Consensus size: 76
41449168 ATTCTAATTC
*
41449178 TTTTACAATTTTTATAATTTTTTGAAAATTCTAATTTTTTAAATAATTTTCTATTATTTTTAGAT
1 TTTTA-AATTTTTATAA-TTTTTAAAAATTCTAATTTTTTAAATAA-TTTCTATTATTTTTAGAT
41449243 AAATTTCCATA-TAT
63 AAATTT-CATATTAT
** *
41449257 TTTTAAATTTTTATAA-TTTTAAAAATTCT-ATTTTTTTGA-AA-TTCTAATTATTTTATAAGTT
1 TTTTAAATTTTTATAATTTTTAAAAATTCTAATTTTTTAAATAATTTCT-ATTATTTT-T-AG-A
**
41449318 TAAATTTTTTATTAT
62 TAAATTTCATATTAT
41449333 TTTTAAATATTTTA
1 TTTTAAAT-TTTTA
41449347 AATGAAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
72 4 0.05
73 8 0.10
74 3 0.04
75 12 0.15
76 30 0.38
77 5 0.06
78 11 0.14
79 5 0.06
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.59
Consensus pattern (76 bp):
TTTTAAATTTTTATAATTTTTAAAAATTCTAATTTTTTAAATAATTTCTATTATTTTTAGATAAA
TTTCATATTAT
Found at i:41451918 original size:6 final size:7
Alignment explanation
Indices: 41451901--41451927 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
41451891 TCATGTGACA
41451901 AAAAATT
1 AAAAATT
41451908 AAAAATT
1 AAAAATT
41451915 AAAAATT
1 AAAAATT
41451922 AAAAAT
1 AAAAAT
41451928 CCCTAAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:41456841 original size:30 final size:30
Alignment explanation
Indices: 41456790--41456869 Score: 153
Period size: 30 Copynumber: 2.7 Consensus size: 30
41456780 TCTTTAACCG
41456790 TTAACCGAACCGAAA-TTTTTTTAAAAAAA
1 TTAACCGAACCGAAATTTTTTTTAAAAAAA
41456819 TTAACCGAACCGAAATTTTTTTTAAAAAAA
1 TTAACCGAACCGAAATTTTTTTTAAAAAAA
41456849 TTAACCGAACCGAAATTTTTT
1 TTAACCGAACCGAAATTTTTT
41456870 CGGTTAATTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.30
30 35 0.70
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (30 bp):
TTAACCGAACCGAAATTTTTTTTAAAAAAA
Found at i:41456953 original size:9 final size:9
Alignment explanation
Indices: 41456935--41457020 Score: 118
Period size: 9 Copynumber: 9.6 Consensus size: 9
41456925 TTTGGTTAAA
*
41456935 AATTAACCG
1 AATTACCCG
41456944 AATTACCCG
1 AATTACCCG
*
41456953 AATTAACCG
1 AATTACCCG
41456962 AATTACCCG
1 AATTACCCG
* *
41456971 AATTAACCA
1 AATTACCCG
41456980 AATTACCCG
1 AATTACCCG
41456989 AATTACCCG
1 AATTACCCG
**
41456998 AATTAATCG
1 AATTACCCG
41457007 AATTACCCG
1 AATTACCCG
41457016 AATTA
1 AATTA
41457021 ACCAAATTGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:41457365 original size:18 final size:18
Alignment explanation
Indices: 41457322--41457357 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41457312 ATCGATCCCC
* *
41457322 GATCGATTAACCGAATTT
1 GATCGGTTAACCAAATTT
41457340 GATCGGTTAACCAAATTT
1 GATCGGTTAACCAAATTT
41457358 TTTCGGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
GATCGGTTAACCAAATTT
Found at i:41458237 original size:29 final size:29
Alignment explanation
Indices: 41458167--41458758 Score: 644
Period size: 29 Copynumber: 19.9 Consensus size: 29
41458157 TTTTGTTAAT
41458167 GGTTAGGGTTTTTAATTAAATTA----AG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
41458192 GGTTTAGGATTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
41458222 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
41458251 GGTTTAGGATTTAGGATTTTAATTAAATTAGGTTAG
1 GG-TTA-G-----GGTTTTTAATTAAATTAGGTTAG
41458287 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * * *
41458316 GGTTTAGAGTTTTAAAATAAATTAGGGTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458346 GGTTTGGGTTTTTGATTAAA-T---TTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
41458371 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
41458400 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458429 GGTTTTA-GGTTTTAAAATAAATTAGGTTAG
1 GG--TTAGGGTTTTTAATTAAATTAGGTTAG
* * * ** *
41458459 GGTTAGGATTAGGATTAGGATTTTTAATTAAATTAA
1 GGTTAGGGTT---TTTA--A--TTAAATTAGGTTAG
* *
41458495 GTTAGGTTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGT-----TAGGGTTTTTAATTAAATTAGGTTAG
*
41458529 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
41458558 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458587 GGTTAGGGTTTTTAATTAAATTAAGTTAA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
41458616 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458645 GGTTTAGGGTTTTAAAATAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
41458675 GGTTAGAGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
41458704 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458733 GGTTTAGGGTTTTAAAATAAATTAGG
1 GG-TTAGGGTTTTTAATTAAATTAGG
41458759 ATTTTTTTAC
Statistics
Matches: 479, Mismatches: 54, Indels: 63
0.80 0.09 0.11
Matches are distributed among these distances:
25 23 0.05
26 21 0.04
28 4 0.01
29 261 0.54
30 103 0.22
31 4 0.01
32 2 0.00
34 13 0.03
35 3 0.01
36 36 0.08
38 3 0.01
41 6 0.01
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:41458258 original size:36 final size:36
Alignment explanation
Indices: 41458218--41458322 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 36
41458208 TTAAATTAGG
41458218 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
41458254 TTAGGATTTA-GGATTTTAATT-AA--A--TTA-GG-
1 TTAGG-GTTAGGGTTTTTAATTAAATTAGGTTAGGGT
41458283 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
41458319 TTAG
1 TTAG
41458323 AGTTTTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
28 3 0.05
29 15 0.27
30 4 0.07
31 3 0.05
32 1 0.02
33 1 0.02
34 3 0.05
35 4 0.07
36 19 0.34
37 3 0.05
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (36 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:41458338 original size:59 final size:59
Alignment explanation
Indices: 41458167--41458758 Score: 708
Period size: 59 Copynumber: 9.9 Consensus size: 59
41458157 TTTTGTTAAT
*
41458167 GGTTAGGGTTTTTAATTAAATTA----AGGGTTTAGGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
*
41458222 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGATTTAGGATTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTA-G-----GGTTTTTAATTAAATTAGGTTAG
* * * *
41458287 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGAGTTTTAAAATAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
41458346 GGTTTGGGTTTTTGATTAAA-T---TTAGGG-TTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458400 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTA-GGTTTTAAAATAAATTAGGTTAGGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTAGGGTTTTTAATTAAATTAGGTTA--G
*
41458461 TTAGGATTAGGATTAGGATTTTTAATTAAATTAAGTTA-GGTTTAGGGTTTTTAATTAAATTAGG
1 ---GG-TTA-G----GG-TTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGG
*
41458525 GTAG
56 TTAG
* *
41458529 GGTTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458587 GGTTAGGGTTTTTAATTAAATTAAGTTAAGG-TTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
41458645 GGTTTAGGGTTTTAAAATAAATTAGGTTAGGG-TTAGAGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41458704 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTAAAATAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGG
41458759 ATTTTTTTAC
Statistics
Matches: 472, Mismatches: 33, Indels: 60
0.84 0.06 0.11
Matches are distributed among these distances:
54 42 0.09
55 30 0.06
58 139 0.29
59 140 0.30
60 4 0.01
61 1 0.00
63 1 0.00
64 6 0.01
65 61 0.13
66 1 0.00
68 1 0.00
69 4 0.01
70 23 0.05
71 19 0.04
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (59 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:41460959 original size:24 final size:24
Alignment explanation
Indices: 41460920--41460980 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
41460910 CTTTTATAAC
* *
41460920 AAATAATAAATTAATAAT-TATC-T
1 AAATAATATA-TAAAAATATATCTT
41460943 AAA-AATATATAAAAATATATCTT
1 AAATAATATATAAAAATATATCTT
*
41460966 AAATAATATTTAAAA
1 AAATAATATATAAAA
41460981 TTTAAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.19
22 9 0.28
23 7 0.22
24 10 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATATATAAAAATATATCTT
Found at i:41461159 original size:22 final size:22
Alignment explanation
Indices: 41461134--41461205 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
41461124 TAATATGGAT
41461134 TTGAGA-GATTTTTAGAAGGAAA
1 TTGAGAGGA-TTTTAGAAGGAAA
*
41461156 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTAGAAGGAAA
41461178 TTGAGAGGATTTTAGAAGGAAA
1 TTGAGAGGATTTTAGAAGGAAA
41461200 TTGAGA
1 TTGAGA
41461206 TAGGATTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 45 0.96
23 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGGATTTTAGAAGGAAA
Found at i:41469683 original size:5 final size:6
Alignment explanation
Indices: 41469650--41469693 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
41469640 TAACAATCAT
* *
41469650 TTTTTA TTATT- TTTTTA CATTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TT
41469694 CCAAATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 4 0.12
6 23 0.72
7 5 0.16
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:41480673 original size:114 final size:114
Alignment explanation
Indices: 41480461--41480690 Score: 415
Period size: 114 Copynumber: 2.0 Consensus size: 114
41480451 CTATAATTAG
*
41480461 TCATTTCTACAATTTAGTCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
1 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
*
41480526 TATTATTTTTTCTCTAATTATTTGATTTATATATATGTGAAATTACTTC
66 TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
*
41480575 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTTACTTGTGAT
1 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
41480640 TATTATTTTTGTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
66 TATTA-TTTT-TTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
41480691 GGTTATTTAT
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
114 68 0.61
115 4 0.04
116 39 0.35
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (114 bp):
TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
Found at i:41480891 original size:40 final size:40
Alignment explanation
Indices: 41480833--41480948 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
41480823 AAATGAAGAA
* * *
41480833 GTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATTT
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
*
41480873 GTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATAT
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
** * * * *
41480913 GTGCCCCTAATTACATTTCGATGCCCCTGATTGCAC
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCAC
41480949 TTCGGTGCCC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (40 bp):
GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
Found at i:41480952 original size:20 final size:19
Alignment explanation
Indices: 41480833--41480960 Score: 96
Period size: 20 Copynumber: 6.4 Consensus size: 19
41480823 AAATGAAGAA
* *
41480833 GTGCCCCTGTTTGTACTTC
1 GTGCCCCTGATTGCACTTC
* * *
41480852 GGTACCCCTGAATGCACATTT
1 -GTGCCCCTGATTGCAC-TTC
*
41480873 GTGCCCCTGTTTGCACTTC
1 GTGCCCCTGATTGCACTTC
*
41480892 GATGCCCCTGAATGCACATAT-
1 G-TGCCCCTGATTGCAC-T-TC
* * *
41480913 GTGCCCCTAATTACATTTC
1 GTGCCCCTGATTGCACTTC
41480932 GATGCCCCTGATTGCACTTC
1 G-TGCCCCTGATTGCACTTC
41480952 GGTGCCCCT
1 -GTGCCCCT
41480961 ATTATACATC
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 5 0.06
20 71 0.86
21 5 0.06
22 1 0.01
ACGTcount: A:0.16, C:0.33, G:0.20, T:0.32
Consensus pattern (19 bp):
GTGCCCCTGATTGCACTTC
Found at i:41480957 original size:40 final size:42
Alignment explanation
Indices: 41480856--41480983 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 42
41480846 TACTTCGGTA
** * * *
41480856 CCCCTGAATGCACATTTGTGCCCCT-GTTTGCA-CTTCGATG
1 CCCCTGAATGCACATAGGTGCCCCTAATATACATCTTCGATG
*
41480896 CCCCTGAATGCACATATGTGCCCCTAAT-TACAT-TTCGATG
1 CCCCTGAATGCACATAGGTGCCCCTAATATACATCTTCGATG
* * * *
41480936 CCCCTGATTGCACTTCGGTGCCCCTATTATACATCTAT-GATG
1 CCCCTGAATGCACATAGGTGCCCCTAATATACATCT-TCGATG
41480978 CCCCTG
1 CCCCTG
41480984 GTGTGGTGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
40 57 0.76
41 6 0.08
42 11 0.15
43 1 0.01
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (42 bp):
CCCCTGAATGCACATAGGTGCCCCTAATATACATCTTCGATG
Found at i:41485825 original size:134 final size:134
Alignment explanation
Indices: 41485582--41485901 Score: 365
Period size: 134 Copynumber: 2.4 Consensus size: 134
41485572 ATAAGGTGTA
* * * * ** *
41485582 ATGGGGTATACTGTGTAAGACCATAGCTCAGCTATGGCAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
* * * * *
41485647 ACATGGGGTATAATGTGTAAGACCATAGCTATGCTACGATAACATAGCGAATCCACTAGAACATT
66 ACATGGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
41485712 AAAC
131 AAAC
* * *
41485716 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
* * * * ** *
41485781 ATATGGGGTATAAAGTGTAAGACCATAGCT-CGACTATGACAACATAGATAGTCTTCCAGGACAT
66 ACATGGGGTATAAAGTGTAAGACCATAGCTACG-CTACGACAACATAGAGAATCCACCAGAACAT
41485845 TAAAC
130 TAAAC
* * * * *
41485850 ATGGGGTATGATGTGTAAAACCATAACTTAG-TGATGGCAACATATAAAGTCC
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGCT-ATGGCAACATAGAAAGTCC
41485902 ATTGGGACAA
Statistics
Matches: 155, Mismatches: 29, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
133 2 0.01
134 153 0.99
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (134 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCAGCTATGGCAACATAGAAAGTCCGCTAGAACATTAA
ACATGGGGTATAAAGTGTAAGACCATAGCTACGCTACGACAACATAGAGAATCCACCAGAACATT
AAAC
Found at i:41485891 original size:67 final size:66
Alignment explanation
Indices: 41485582--41485901 Score: 284
Period size: 67 Copynumber: 4.8 Consensus size: 66
41485572 ATAAGGTGTA
* * * * ** ** *
41485582 ATGGGGTATACTGTGTAAGACCATAGCTCAGCTATGGCAGCAGAGAGAGTTTGTTAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAG-TATGGCAACATAGAAAGTCCGCCAGGACATTAA
41485647 AC
65 AC
* ** * * * *
41485649 ATGGGGTATAATGTGTAAGACCATAGCT-ATGCTACGATAACATAGCGAA-TCCACTAGAACATT
1 ATGGGGTATAATGTGTAAGACCATAGCTCA-G-TATGGCAACATAG-AAAGTCCGCCAGGACATT
41485712 AAAC
63 AAAC
* * *
41485716 ATGGGGTATAATGCGTAAGACCATAGCTCGGCTATGGCAACATAGAAAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCAG-TATGGCAACATAGAAAGTCCGCCAGGACATTAA
*
41485781 AT
65 AC
* * * * **
41485783 ATGGGGTATAAAGTGTAAGACCATAGCTCGACTATGACAACATAGATAGTCTTCCAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTC-AGTATGGCAACATAGAAAGTCCGCCAGGACATTAA
41485848 AC
65 AC
* * * * *
41485850 ATGGGGTATGATGTGTAAAACCATAACTTAGTGATGGCAACATATAAAGTCC
1 ATGGGGTATAATGTGTAAGACCATAGCTCAGT-ATGGCAACATAGAAAGTCC
41485902 ATTGGGACAA
Statistics
Matches: 206, Mismatches: 41, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
66 5 0.02
67 200 0.97
68 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (66 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCAGTATGGCAACATAGAAAGTCCGCCAGGACATTAAA
C
Found at i:41492538 original size:11 final size:11
Alignment explanation
Indices: 41492522--41492548 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41492512 ATGATAAATA
41492522 AGCCTATTTAT
1 AGCCTATTTAT
41492533 AGCCTATTTAT
1 AGCCTATTTAT
41492544 AGCCT
1 AGCCT
41492549 TCAAGTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (11 bp):
AGCCTATTTAT
Found at i:41502812 original size:159 final size:158
Alignment explanation
Indices: 41502513--41502829 Score: 598
Period size: 159 Copynumber: 2.0 Consensus size: 158
41502503 TGGTTGCATG
41502513 AGTATAACATAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTCA
1 AGTATAACATAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTCA
*
41502578 AGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAGTCT
66 AGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATCT
41502643 CTGTTCCTGTTGTTTACATCTGCCTAAC
131 CTGTTCCTGTTGTTTACATCTGCCTAAC
*
41502671 AGTATAACATAAAAATGATAACAAGTCCAACTCCTGAAGAATTCTGAGGGAAAACAAAATATTTC
1 AGTATAACAT-AAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTC
*
41502736 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAATTAGATAACATGGTTAAAACAGTAATC
65 AAGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATC
41502801 TCTGTTCCTGTTGTTTACATCTGCCTAAC
130 TCTGTTCCTGTTGTTTACATCTGCCTAAC
41502830 TTACCCAACC
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
158 10 0.06
159 145 0.94
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (158 bp):
AGTATAACATAAAATGATAACAAGTCCAACTCCTGAAGAATTCCGAGGGAAAACAAAATATTTCA
AGTCCTTGGACCGAGTAAAATTTGTTCTACAGACAAACTAGATAACATGGTTAAAACAGTAATCT
CTGTTCCTGTTGTTTACATCTGCCTAAC
Found at i:41503089 original size:21 final size:21
Alignment explanation
Indices: 41503056--41503099 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41503046 CACTCATTTC
* * *
41503056 TTTTTTCAGAATTAATTTTAT
1 TTTTTTAAAAATTAATTTCAT
*
41503077 TTTTTTAAAAATTGATTTCAT
1 TTTTTTAAAAATTAATTTCAT
41503098 TT
1 TT
41503100 ACGAAAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTTTAAAAATTAATTTCAT
Found at i:41503337 original size:22 final size:22
Alignment explanation
Indices: 41503303--41503344 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41503293 AATTGTTCTA
41503303 TAAAAATCTAAATAATTCCATG
1 TAAAAATCTAAATAATTCCATG
*
41503325 TAAAACATC-AAATTATTCCA
1 TAAAA-ATCTAAATAATTCCA
41503345 CAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAATCTAAATAATTCCATG
Found at i:41508572 original size:3 final size:3
Alignment explanation
Indices: 41508564--41508595 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41508554 AATCACATGT
41508564 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41508596 TGGATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41508673 original size:72 final size:72
Alignment explanation
Indices: 41508596--41508851 Score: 494
Period size: 72 Copynumber: 3.6 Consensus size: 72
41508586 TATTATTATT
41508596 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41508661 TTTTAAG
66 TTTTAAG
41508668 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41508733 TTTTAAG
66 TTTTAAG
41508740 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41508805 TTTTAAG
66 TTTTAAG
* *
41508812 TGGGTGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
41508852 GTCAAGTTGT
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 182 1.00
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:41513078 original size:3 final size:3
Alignment explanation
Indices: 41513070--41513110 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
41513060 ATCACATGTT
41513070 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41513111 TGGATGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41513192 original size:72 final size:72
Alignment explanation
Indices: 41513111--41513366 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
41513101 TATTATTATT
41513111 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41513176 TTTTAAG
66 TTTTAAG
41513183 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41513248 TTTTAAG
66 TTTTAAG
41513255 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41513320 TTTTAAG
66 TTTTAAG
*
41513327 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
41513367 GTCAAGTTGT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:41523858 original size:18 final size:19
Alignment explanation
Indices: 41523832--41523868 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41523822 ATTGAAATAG
*
41523832 TTATTATTATTTT-GATTC
1 TTATAATTATTTTAGATTC
41523850 TTATAATTATTTTAGATTC
1 TTATAATTATTTTAGATTC
41523869 ACATGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATAATTATTTTAGATTC
Found at i:41525411 original size:43 final size:43
Alignment explanation
Indices: 41525313--41525537 Score: 179
Period size: 43 Copynumber: 5.3 Consensus size: 43
41525303 CTTTAGAAAT
* * * *
41525313 AAACGCCGCTAAAGGTCATGACCTTTAGGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGGTCATCACTTTTA-GCGGCGCTTTTCCCAC
*
41525357 AAATGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
* * * ** *
41525400 AAACACTGCTATAGATCATCACTTTTAGTAGCG-TTTTTCCAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
*** * * **
41525442 AAACGCCGCTATAAAACA-GA-TCTTTAGCGACGCTTTTTCGTAC
1 AAACGCCGCTATAGGTCATCACT-TTTAGCGGCGC-TTTTCCCAC
* * * * * *
41525485 AAACGCCGCTATAGGACA-AACCTTTAGCTGCACTTTTCACAC
1 AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
41525527 AAACGCCGCTA
1 AAACGCCGCTA
41525538 AAGGCATATC
Statistics
Matches: 145, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 1 0.01
41 8 0.06
42 40 0.28
43 73 0.50
44 23 0.16
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGGTCATCACTTTTAGCGGCGCTTTTCCCAC
Found at i:41525807 original size:43 final size:43
Alignment explanation
Indices: 41525730--41525813 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
41525720 ACATATGCAC
* * ** *
41525730 GGTAATAAAACATACAATGCATTTTCTTGGTCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
41525773 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATC
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATC
41525814 GTGTAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:41528932 original size:21 final size:22
Alignment explanation
Indices: 41528906--41528956 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
41528896 TTTCAAGGCA
*
41528906 GAAAATTAGGGATTTTA-GGAG
1 GAAAATTAGGGATATTAGGGAG
*
41528927 GAAAATTGGGGATATTAGGGAG
1 GAAAATTAGGGATATTAGGGAG
41528949 GAAAATTA
1 GAAAATTA
41528957 TAAAATGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.25
Consensus pattern (22 bp):
GAAAATTAGGGATATTAGGGAG
Found at i:41529121 original size:24 final size:23
Alignment explanation
Indices: 41529094--41529138 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41529084 AATGATGTTG
41529094 TTTTGCTCTGCTAAAAATTATTTA
1 TTTTG-TCTGCTAAAAATTATTTA
* *
41529118 TTTTGTTTGTTAAAAATTATT
1 TTTTGTCTGCTAAAAATTATT
41529139 AGTTAAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTGTCTGCTAAAAATTATTTA
Found at i:41529949 original size:21 final size:21
Alignment explanation
Indices: 41529925--41530005 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
41529915 TCTAACCTCT
41529925 AACCCCTAAACCTTAAATCTC
1 AACCCCTAAACCTTAAATCTC
* *
41529946 AACCCTTAAACCAT-AATCTC
1 AACCCCTAAACCTTAAATCTC
* * * *
41529966 TAATCCATAATCCCTAAATC-C
1 -AACCCCTAAACCTTAAATCTC
41529987 ATACTCCCTAAACCTTAAA
1 A-AC-CCCTAAACCTTAAA
41530006 ATATGAACTC
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.15
21 24 0.52
22 15 0.33
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCCTAAACCTTAAATCTC
Found at i:41529987 original size:15 final size:15
Alignment explanation
Indices: 41529952--41529998 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
41529942 TCTCAACCCT
*
41529952 TAAA-CCATAATCTC
1 TAAATCCATAATCCC
41529966 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
41529980 TAAATCCATACTCCC
1 TAAATCCATAATCCC
41529995 TAAA
1 TAAA
41529999 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.38
15 16 0.55
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:41530110 original size:295 final size:301
Alignment explanation
Indices: 41529777--41530374 Score: 860
Period size: 295 Copynumber: 2.0 Consensus size: 301
41529767 CAATATATTT
*
41529777 AATTTATTATTATCTCTTTTATAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
* * *
41529842 TAATCTAAACCCAAAACCCTAACCCGACCCTTGAATCCCTAAAC-CTTAAATCCCT-A-GCTCTT
66 TAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCT-AACTCTT-AACCCCTAATG-TC-T
* * *
41529904 AACCCCT-AACATCT-AACCTCT-AACCCCTAAACCTTAAATCTCAACCCTTAAACCATAAT-C-
127 AACCCCTAAACACCTAAACC-CTAAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCA
41529964 T-C-TAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATA-TGAACTCCTAAACCGGC
191 TCCATAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGT-AACTCCTAAACCGGC
* *
41530026 CTTAAATCTTAAAT-AATCATATAACCTAAACTAAAAACCCTAAACA
255 CTTAAATCTTAAATAAATCATACAACCTAAACCAAAAACCCTAAACA
*
41530072 AATTTATTATTATCTCTTTTACGATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
* ** *
41530137 TAATCTAAACCCAAAACCTTAACTTGACCCCTAAATCTCTAACTCTTAACCCCTAATGTCTAACC
66 TAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAACTCTTAACCCCTAATGTCTAACC
* *
41530202 CCTAAACCCCTAAACCCTAAACCCTTAAACCTTAAAACCCAACCCTTAAACCATAATCCATAATC
131 CCTAAACACCTAAACCCTAAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCC---ATC
* *
41530267 CATAATCCATAATTCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACTGGCCTT
193 CATAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGGCCTT
*
41530332 AAATCTTAAATAAATCATACACCCTAAACCAAAAACCCTAAAC
258 AAATCTTAAATAAATCATACAACCTAAACCAAAAACCCTAAAC
41530375 TATAATGATA
Statistics
Matches: 269, Mismatches: 19, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
294 17 0.06
295 110 0.41
296 40 0.15
297 1 0.00
301 1 0.00
302 1 0.00
303 70 0.26
304 29 0.11
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.28
Consensus pattern (301 bp):
AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
TAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAACTCTTAACCCCTAATGTCTAACC
CCTAAACACCTAAACCCTAAACCCCTAAACCTTAAAACCCAACCCTTAAACCATAATCCATCCAT
AATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAA
TCTTAAATAAATCATACAACCTAAACCAAAAACCCTAAACA
Found at i:41530189 original size:22 final size:23
Alignment explanation
Indices: 41530163--41530232 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
41530153 CCTTAACTTG
* *
41530163 ACCCCTAAATCTCTAA-CTCTTA
1 ACCCCTAAATCTCTAACCCCTAA
*
41530185 ACCCCT-AATGTCTAACCCCTAA
1 ACCCCTAAATCTCTAACCCCTAA
* *
41530207 ACCCCTAAA-CCCTAAACCCTTAA
1 ACCCCTAAATCTCT-AACCCCTAA
41530230 ACC
1 ACC
41530233 TTAAAACCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 8 0.21
22 18 0.46
23 13 0.33
ACGTcount: A:0.34, C:0.41, G:0.01, T:0.23
Consensus pattern (23 bp):
ACCCCTAAATCTCTAACCCCTAA
Found at i:41530211 original size:8 final size:8
Alignment explanation
Indices: 41530198--41530232 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
41530188 CCTAATGTCT
41530198 AACCCCTA
1 AACCCCTA
41530206 AACCCCTA
1 AACCCCTA
41530214 AA-CCCTA
1 AACCCCTA
*
41530221 AACCCTTA
1 AACCCCTA
41530229 AACC
1 AACC
41530233 TTAAAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.14
Consensus pattern (8 bp):
AACCCCTA
Found at i:41530219 original size:15 final size:15
Alignment explanation
Indices: 41530196--41530237 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
41530186 CCCCTAATGT
*
41530196 CTAACCCCTAAACCC
1 CTAAACCCTAAACCC
41530211 CTAAACCCTAAACCC
1 CTAAACCCTAAACCC
* *
41530226 TTAAACCTTAAA
1 CTAAACCCTAAA
41530238 ACCCAACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (15 bp):
CTAAACCCTAAACCC
Found at i:41530253 original size:8 final size:8
Alignment explanation
Indices: 41530198--41530253 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
41530188 CCTAATGTCT
*
41530198 AACCCCTA
1 AACCCTTA
*
41530206 AACCCCTA
1 AACCCTTA
41530214 AACCC-TA
1 AACCCTTA
41530221 AACCCTTA
1 AACCCTTA
41530229 AA-CCTTAA
1 AACCCTT-A
41530237 AACCC---
1 AACCCTTA
41530242 AACCCTTA
1 AACCCTTA
41530250 AACC
1 AACC
41530254 ATAATCCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.12
7 11 0.26
8 24 0.57
9 2 0.05
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (8 bp):
AACCCTTA
Found at i:41530264 original size:7 final size:7
Alignment explanation
Indices: 41530252--41530292 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
41530242 AACCCTTAAA
41530252 CCATAAT
1 CCATAAT
41530259 CCATAAT
1 CCATAAT
41530266 CCATAAT
1 CCATAAT
41530273 CCATAATT
1 CCATAA-T
41530281 CC-TAAAT
1 CCAT-AAT
41530288 CCATA
1 CCATA
41530293 CTCCCTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
CCATAAT
Found at i:41530299 original size:15 final size:15
Alignment explanation
Indices: 41530256--41530301 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
41530246 CTTAAACCAT
*
41530256 AATCCATAATCCAT-
1 AATCCATAATCCCTA
*
41530270 AATCCATAATTCCTA
1 AATCCATAATCCCTA
*
41530285 AATCCATACTCCCTA
1 AATCCATAATCCCTA
41530300 AA
1 AA
41530302 CCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.28
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:41530702 original size:41 final size:41
Alignment explanation
Indices: 41530648--41531011 Score: 419
Period size: 41 Copynumber: 8.9 Consensus size: 41
41530638 TAAAATGTTT
* * *
41530648 TTAGTGGCTCTTTTTCAAAAACGCTGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* ** * *
41530689 TTAGCGGCACTTTTTAAAAAATACCGCTAAAATCCCGAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* * *
41530730 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* *
41530771 TTAGCGACACTTTTTCAAAAACGCCGCTAAAGCCCCCAA-CA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA-ACCCCAAGCA
* *
41530812 TTAGCGGCACCTTTTCAAAAACGCCGCTAAAGCCCCCAA-CA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAA-ACCCCAAGCA
*
41530853 TTAGCGGCACCTTTTCAAAAACGCCGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* ** * ** *
41530894 CTAGCGGCGTTTTTTAAAAAATACCGCTAAAACACCGAA-CA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAAC-CCCAAGCA
* * *
41530935 TTAGCGGCGCTTTTTTAAAAACGCTGCTAAAACCCCAAGCA
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
* * *
41530976 TTAGCGGCGCATTTTCAAAAACGCCGCTAAAGCCCC
1 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCC
41531012 GAAAGGTAAG
Statistics
Matches: 278, Mismatches: 41, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.04
41 259 0.93
42 9 0.03
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (41 bp):
TTAGCGGCACTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
Found at i:41531108 original size:39 final size:40
Alignment explanation
Indices: 41531043--41531170 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
41531033 GTTGGGCTTT
* * * *
41531043 GATTTTTTGCGGCGTTTTTCTCAAAAACGCCGCGAATGCTC
1 GATTTTTAGCGGCGTTTTTC-AAAAAACACCGCTAATGCTC
* *
41531084 -ATTTTTAGCGGTGTTTTTCAAAAAATACCGCTAATGCTC
1 GATTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTC
* * * * * *
41531123 GATCTTTAGTGGCGATTTCCATAAAGCACCGCTAATGCTC
1 GATTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTC
41531163 GATTTTTA
1 GATTTTTA
41531171 CCGGTATTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 16 0.23
40 55 0.77
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (40 bp):
GATTTTTAGCGGCGTTTTTCAAAAAACACCGCTAATGCTC
Found at i:41534515 original size:36 final size:36
Alignment explanation
Indices: 41534436--41534552 Score: 137
Period size: 36 Copynumber: 3.3 Consensus size: 36
41534426 ACTCTCTATT
* * * *
41534436 TGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCAT-
1 TGGTGTGTTTCGGATGGATTAGCTCATGTGAGCATC
* * * *
41534471 TAGTGTGTTTTGGATGGATTGGCTCGTGTGAGCATC
1 TGGTGTGTTTCGGATGGATTAGCTCATGTGAGCATC
* *
41534507 TGGTGTGTTTCGGAGGGATTAGCTCATGTGATCATC
1 TGGTGTGTTTCGGATGGATTAGCTCATGTGAGCATC
41534543 TGGTGTGTTT
1 TGGTGTGTTT
41534553 TGGTTGATCT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 28 0.41
36 40 0.59
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.40
Consensus pattern (36 bp):
TGGTGTGTTTCGGATGGATTAGCTCATGTGAGCATC
Found at i:41535165 original size:19 final size:19
Alignment explanation
Indices: 41535141--41535215 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
41535131 AATCTTCAAG
41535141 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
41535160 GATATGCAATCTTAGATAC
1 GATATGCAATCTTAGATAT
41535179 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
41535200 TATATGCAATCTTAGA
1 GATATGCAATCTTAGA
41535216 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 34 0.67
21 17 0.33
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41535486 original size:23 final size:23
Alignment explanation
Indices: 41535442--41535486 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41535432 TCTTTTTTTG
* *
41535442 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
41535465 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
41535487 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:41535841 original size:37 final size:37
Alignment explanation
Indices: 41535765--41535841 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
41535755 CATACATACG
*
41535765 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
41535803 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
41535840 TT
1 TT
41535842 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:41544218 original size:19 final size:18
Alignment explanation
Indices: 41544172--41544219 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
41544162 GATAGAATTT
*
41544172 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
41544191 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
41544209 TTGTATTAAAA
1 TTGTA-TAAAA
41544220 ATTTGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:41544866 original size:19 final size:18
Alignment explanation
Indices: 41544838--41544880 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
41544828 CTCATTCACA
*
41544838 TCTCTTCTCTTACAACTTT
1 TCTCTCCTCTTAC-ACTTT
*
41544857 TCTCTCCTCTTTCACTTT
1 TCTCTCCTCTTACACTTT
*
41544875 TTTCTC
1 TCTCTC
41544881 TCATTTTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.09, C:0.35, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTCTCCTCTTACACTTT
Found at i:41548307 original size:35 final size:35
Alignment explanation
Indices: 41548268--41548424 Score: 118
Period size: 36 Copynumber: 4.4 Consensus size: 35
41548258 TACTTTATGT
** *
41548268 TTGGTGTGTTTTGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
* * *
41548303 TTGGTGTGTTTTGGAGGGATTGGCTCATGTGAGCA
1 TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
** * * * *
41548338 TCTGGTGTGTTTCAGAGGGATTGGCTCGTGTGAGCA
1 T-TGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
* * * * *
41548374 TCTGGTGTGTTTCT-GAGGGATTGGCTCGTGTGATCA
1 T-TGGTGTGTTT-TGGAGGGACTAGCTCATATGAGCA
41548410 TCTGGTGTGTTTTGG
1 T-TGGTGTGTTTTGG
41548425 TTGATTTGAC
Statistics
Matches: 108, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
35 31 0.29
36 77 0.71
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTTGGAGGGACTAGCTCATATGAGCA
Found at i:41548356 original size:36 final size:36
Alignment explanation
Indices: 41548297--41548421 Score: 198
Period size: 36 Copynumber: 3.5 Consensus size: 36
41548287 CTAGCTCTTA
** *
41548297 TGAGCAT-TGGTGTGTTTTGGAGGGATTGGCTCATG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
41548332 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
*
41548368 TGAGCATCTGGTGTGTTTCTGAGGGATTGGCTCGTG
1 TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
*
41548404 TGATCATCTGGTGTGTTT
1 TGAGCATCTGGTGTGTTT
41548422 TGGTTGATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.08
36 77 0.92
ACGTcount: A:0.13, C:0.12, G:0.38, T:0.38
Consensus pattern (36 bp):
TGAGCATCTGGTGTGTTTCAGAGGGATTGGCTCGTG
Found at i:41563347 original size:30 final size:31
Alignment explanation
Indices: 41563311--41563378 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
41563301 TTTGAGGGGA
*
41563311 TGAAAATCAAATTATATATCTTT-ATTATAG
1 TGAAAATCAAATTATATATATTTCATTATAG
*
41563341 TGAAAATTAAATTATATATATTTCATTATAG
1 TGAAAATCAAATTATATATATTTCATTATAG
*
41563372 TAAAAAT
1 TGAAAAT
41563379 ATAGTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (31 bp):
TGAAAATCAAATTATATATATTTCATTATAG
Found at i:41573098 original size:5 final size:5
Alignment explanation
Indices: 41573088--41573159 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
41573078 TGTTAAAAAA
* *
41573088 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
41573134 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
41573160 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:41573141 original size:19 final size:19
Alignment explanation
Indices: 41573117--41573159 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
41573107 ATTATGTTTT
41573117 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
41573136 TATATTATATTATATTATA
1 TATATTATATTATATTATA
41573155 TATAT
1 TATAT
41573160 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:41573192 original size:18 final size:19
Alignment explanation
Indices: 41573164--41573203 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
41573154 ATATATACAT
*
41573164 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
41573183 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
41573201 AAA
1 AAA
41573204 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:41574168 original size:44 final size:45
Alignment explanation
Indices: 41574073--41574206 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
41574063 ACAGGACAGA
* *
41574073 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
41574119 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
41574163 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
41574207 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:41579749 original size:18 final size:17
Alignment explanation
Indices: 41579722--41579755 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41579712 TTTACCTAAA
*
41579722 AAGGGAGAGGACAACTC
1 AAGGGAGAGGAAAACTC
41579739 AAGGCGAGAGGAAAACT
1 AAGG-GAGAGGAAAACT
41579756 TGCCCAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.15, G:0.35, T:0.06
Consensus pattern (17 bp):
AAGGGAGAGGAAAACTC
Found at i:41580821 original size:137 final size:137
Alignment explanation
Indices: 41580599--41581042 Score: 492
Period size: 137 Copynumber: 3.3 Consensus size: 137
41580589 AATAGATCAG
* * * *
41580599 TGAAACTACAAATTCTATACCCTTGAAGTTGTAGTGGGTCGGATTGAAGTC-ACCATAACGAATT
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAA-TCTACCAT-ACGAATT
* *
41580663 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATAAATCTTATC-CCCTAAAGTTGCAGT
64 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGT
*
41580727 GGAGTAGAT
129 GGAGCAGAT
* *
41580736 TGAAGCTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGACTGAATCTACCATAGCGAATTT
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATA-CGAATTT
* *
41580801 TATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACGAATCTTATCTCCCTAAAGTTGTAGTG
65 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
41580866 GAGCAGAT
130 GAGCAGAT
* *** ** * ** * *
41580874 TGAAACTACAAATCTTATGTCCCTGAAGTTACAGTGGAATAGATTGAAGCTA-C--A--AATCTT
1 TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATACGAATTTT
* * * * *
41580934 ATCTCCTTGAAGTTGCAGTGAAGCATAAT-GAATCTACAAATCGTATCTCCCTAAAGTTGTAGTG
66 ATCTCCCTGAAGTTGCAGTGGAGCA-GATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTG
41580998 GAGCAGAT
130 GAGCAGAT
* * * * *
41581006 TGAAGCAACAAATCTTATC-TCCTTGAAGTTGTAGTGG
1 TGAAACTACAAATCCTA-CACCCCTGAAGTTGTAGTGG
41581043 AGTAAGATGA
Statistics
Matches: 265, Mismatches: 37, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
132 97 0.37
133 2 0.01
135 1 0.00
136 3 0.01
137 100 0.38
138 62 0.23
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (137 bp):
TGAAACTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGATTGAATCTACCATACGAATTTT
ATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGG
AGCAGAT
Found at i:41580857 original size:44 final size:44
Alignment explanation
Indices: 41580663--41581094 Score: 404
Period size: 44 Copynumber: 9.7 Consensus size: 44
41580653 ATAACGAATT
* * *
41580663 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
*
41580707 TTATC-CCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* * * * * * * *
41580750 CTA-CACCCCTGAAGTTGTAGTGG-GACGGACTGAATCTACCATAGCGAATT
1 TTATC-TCCCTAAAGTTGCAGTGGAG-CAGATTGAAGCTA-C--A---AATC
* *
41580800 TTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACGAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* *
41580844 TTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAACTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* * * **
41580888 TTATGTCCCTGAAGTTACAGTGGAATAGATTGAAGCTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* * * * * *
41580932 TTATCTCCTTGAAGTTGCAGTGAAGCATAATGAATCTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* * *
41580976 GTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCAACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
* * * * *
41581020 TTATCTCCTTGAAGTTGTAGTGGAGTAAGA-TGAAGCTACAACTC
1 TTATCTCCCTAAAGTTGCAGTGGAG-CAGATTGAAGCTACAAATC
* * * *
41581064 CTATATCCCTAAAGTTGTAGTGGATCAGATT
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGATT
41581095 AAACCTATAA
Statistics
Matches: 312, Mismatches: 63, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.00
43 40 0.13
44 234 0.75
45 4 0.01
47 1 0.00
49 1 0.00
50 29 0.09
51 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAATC
Found at i:41580998 original size:132 final size:131
Alignment explanation
Indices: 41580663--41581093 Score: 470
Period size: 132 Copynumber: 3.2 Consensus size: 131
41580653 ATAACGAATT
* *
41580663 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTATAAATCTTATC-CCCTAAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGT
* * * * * ** *
41580727 GGAGTAGATTGAAGCTACAAATCCTACACCCCTGAAGTTGTAGTGGGACGGACTGAATCTACCAT
66 GGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGA-TGAAGCTA-C--
*
41580792 AGCGAATT
127 A---AATC
* *
41580800 TTATCTCCCTAAAGTTGCAGTGGAGCAGATCGAAGCTACGAATCTTATCTCCCTAAAGTTGTAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGT
* * **
41580865 GGAGCAGATTGAAACTACAAATCTTATGTCCCTGAAGTTACAGTGGAATAGATTGAAGCTACAAA
66 GGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGA-TGAAGCTACAAA
41580930 TC
130 TC
* * * * *
41580932 TTATCTCCTTGAAGTTGCAGTGAAGCATAAT-GAATCTACAAATCGTATCTCCCTAAAGTTGTAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCA-GATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAG
* * * *
41580996 TGGAGCAGATTGAAGCAACAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAGATGAAGCTACAA
65 TGGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAAT-AGATGAAGCTACAA
*
41581061 CTC
129 ATC
* * * * *
41581064 CTATATCCCTAAAGTTGTAGTGGATCAGAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGAT
41581094 TAAACCTATA
Statistics
Matches: 250, Mismatches: 41, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
131 2 0.01
132 133 0.53
133 5 0.02
135 1 0.00
137 47 0.19
138 62 0.25
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (131 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGCTACAAATCTTATCTCCCTAAAGTTGTAGT
GGAGCAGATTGAAGCTACAAATCTTATATCCCTGAAGTTGTAGTGGAATAGATGAAGCTACAAAT
C
Found at i:41581141 original size:88 final size:89
Alignment explanation
Indices: 41580925--41581149 Score: 215
Period size: 88 Copynumber: 2.6 Consensus size: 89
41580915 GATTGAAGCT
* * * * * * * * * *
41580925 ACAAATCTTATCTCCTTGAAGTTGCAGTGAAG-CATAATGAATCTACAAATCGTATCTCCCTAAA
1 ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
* *
41580989 GTTGTAGTGGAGCAGATTGAAGCA
66 GTTGTAGTGGAGCAGATTAAACCA
* ** *
41581013 ACAAATCTTATCTCCTTGAAGTTGTAGTGGAGTAAG-ATGAAGCTACAACTCCTATATCCCTAAA
1 ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
* *
41581077 GTTGTAGTGGATCAGATTAAACCT
66 GTTGTAGTGGAGCAGATTAAACCA
* * * *
41581101 ATAATTCCTATAC-CCTTGAGGTTACAATGG-GTTAGAATGAAGCTACAAC
1 ACAAATCCTAT-CTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAAC
41581150 AACAAATTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
87 4 0.04
88 108 0.95
89 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (89 bp):
ACAAATCCTATCTCCTTGAAGTTACAATGGAGTAAGAATGAAGCTACAACTCCTATATCCCTAAA
GTTGTAGTGGAGCAGATTAAACCA
Found at i:41586182 original size:21 final size:20
Alignment explanation
Indices: 41586144--41586182 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41586134 TTGAAATGGA
*
41586144 AAATTGGACTCTATAATAAT
1 AAATTGGACTCTAAAATAAT
*
41586164 AAATTGGATTTCTAAAATA
1 AAATTGGA-CTCTAAAATA
41586183 TTTCCAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AAATTGGACTCTAAAATAAT
Found at i:41588086 original size:20 final size:22
Alignment explanation
Indices: 41588050--41588089 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
41588040 AAATTATGAA
41588050 TAAATCATGTAGGTATCGATAC
1 TAAATCATGTAGGTATCGATAC
41588072 TAAATCAT-T-GGTATCGAT
1 TAAATCATGTAGGTATCGAT
41588090 GATTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAATCATGTAGGTATCGATAC
Found at i:41594541 original size:19 final size:19
Alignment explanation
Indices: 41594513--41594576 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
41594503 AATTTTCGAG
*
41594513 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41594532 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41594551 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
41594572 GATAT
1 GATAT
41594577 ATACAATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41594594 original size:19 final size:21
Alignment explanation
Indices: 41594514--41594589 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
41594504 ATTTTCGAGG
41594514 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
41594533 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
41594554 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
41594575 ATATACAATATTAGA
1 ATATACAATCTTAGA
41594590 AGATACGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 18 0.35
21 34 0.65
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:41594808 original size:19 final size:21
Alignment explanation
Indices: 41594784--41594822 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
41594774 TTGTTTTCTT
*
41594784 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
41594803 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
41594823 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:41595048 original size:3 final size:3
Alignment explanation
Indices: 41595040--41595079 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
41595030 TTTATTAAAT
41595040 TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
41595080 ACCTACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41595060 original size:24 final size:24
Alignment explanation
Indices: 41595027--41595079 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
41595017 GTTTTTAGTC
41595027 TATT-TTATTAAATT-TATTATTAT
1 TATTATTATTAAATTATA-TATTAT
*
41595050 TATTATTATTATATTATATATTAT
1 TATTATTATTAAATTATATATTAT
41595074 TATTAT
1 TATTAT
41595080 ACCTACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 21 0.78
25 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATTATTAAATTATATATTAT
Found at i:41595446 original size:51 final size:53
Alignment explanation
Indices: 41595342--41595458 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 53
41595332 ATTTTCCACG
**
41595342 TTTT-TATAT-TATACTTATATATTTCATTTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATACTTATATATTTCATTTTTTTCATAAATGCATGAATATA
* * * *
41595393 TTTTATATGTATATATTTATAT-TTTC-TTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATACTTATATATTTCATTT-TTTTCATAAATGCATGAATATA
41595444 TTTTATATATATATA
1 TTTTATATATATATA
41595459 AGTTTTATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 25 0.45
52 21 0.38
53 10 0.18
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (53 bp):
TTTTATATATATATACTTATATATTTCATTTTTTTCATAAATGCATGAATATA
Found at i:41596209 original size:18 final size:18
Alignment explanation
Indices: 41596186--41596220 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41596176 ATTTTCGACA
41596186 TTAAAATTAATTAGAATT
1 TTAAAATTAATTAGAATT
41596204 TTAAAATTAATTAGAAT
1 TTAAAATTAATTAGAAT
41596221 GTTTGCTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TTAAAATTAATTAGAATT
Found at i:41600223 original size:19 final size:20
Alignment explanation
Indices: 41600178--41600224 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
41600168 CAAATTTTTC
41600178 AAAA-AAAAAAGAGAAAGAG
1 AAAACAAAAAAGAGAAAGAG
*
41600197 AGAACAAAAAA-AGAAAGA-
1 AAAACAAAAAAGAGAAAGAG
41600215 AAAAGCAAAA
1 AAAA-CAAAA
41600225 GAAAAGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAACAAAAAAGAGAAAGAG
Found at i:41601939 original size:44 final size:44
Alignment explanation
Indices: 41601763--41601943 Score: 107
Period size: 44 Copynumber: 4.1 Consensus size: 44
41601753 TTGTAGATCC
* *
41601763 TATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
* ** * ** **
41601807 TATCTTTCC-AAG-A-TAATGGGAAGCAGATTTAAGCCACCAAGCCT
1 TATC-TCCCTAAGCAGTAAT-GG-AGCAGATCAAAGACGGCAAATCT
* * * ** * * * ** * *
41601851 TGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
*
41601895 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCT
1 TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
41601939 TATCT
1 TATCT
41601944 TTCCAAGATA
Statistics
Matches: 94, Mismatches: 37, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 77 0.82
45 6 0.06
46 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAATGGAGCAGATCAAAGACGGCAAATCT
Found at i:41601946 original size:132 final size:132
Alignment explanation
Indices: 41601455--41602060 Score: 881
Period size: 132 Copynumber: 4.7 Consensus size: 132
41601445 ACCGGTGAAA
* * *
41601455 CACCAAGCTTTGTCTCTCTGAGAAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
41601520 GCAGTAGTGGAGAAAATCGAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
41601585 GC
131 GC
*
41601587 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGA-T-T-GATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
41601649 GCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
41601714 GC
131 GC
* ** * *
41601716 CACAAAGCCTTGTCTCCCTGAGCAGCA-ATG-G-A-G-T--AGGTTGTAGATCCTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
41601774 GCAGTAATGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
41601839 GC
131 GC
*
41601841 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
41601906 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
41601971 GC
131 GC
* * * * *
41601973 CACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAATCTTATCTCCCTGA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT-A
** * *
41602038 AGTTGCAGTGGAGCAGATTAAAG
65 AGCAGTAGTGGAGCAGATCAAAG
41602061 CCGATAATCC
Statistics
Matches: 425, Mismatches: 38, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
122 2 0.00
123 1 0.00
124 2 0.00
125 104 0.24
126 2 0.00
127 2 0.00
128 2 0.00
129 105 0.25
130 2 0.00
131 1 0.00
132 182 0.43
133 20 0.05
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:41602009 original size:257 final size:254
Alignment explanation
Indices: 41601499--41602017 Score: 912
Period size: 254 Copynumber: 2.0 Consensus size: 254
41601489 AGGTTGAAGA
* *
41601499 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGAAAATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGAAAATCGAAGACGGTAAATCTTATCTTTCCAA
* * *
41601564 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
66 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
41601629 GATTGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
131 GATTGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
*
41601694 ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAATGGAGTAGG
196 ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAACGGAGTAGG
* *
41601753 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGAAAATCGAAGACGGTAAATCTTATCTTTCCAA
41601818 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
66 GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
*
41601883 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCC
131 GA-T-T-GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCC
*
41601948 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
193 AAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAACGGAGTAGG
*
41602010 TTGAAGAT
1 TTGTAGAT
41602018 GGCAAATCTT
Statistics
Matches: 251, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
254 125 0.50
255 1 0.00
256 1 0.00
257 124 0.49
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (254 bp):
TTGTAGATCCTATCTCCCTAAGCAGTAATGGAGAAAATCGAAGACGGTAAATCTTATCTTTCCAA
GATAATGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAA
GATTGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAACGGAGTAGG
Found at i:41602075 original size:44 final size:43
Alignment explanation
Indices: 41602022--41602397 Score: 256
Period size: 44 Copynumber: 8.8 Consensus size: 43
41602012 GAAGATGGCA
41602022 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * * *
41602066 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * *** *
41602109 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCC--
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* *
41602150 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAG-CA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * * * *
41602194 AGTCTTATC-CTCTTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAT
* *
41602239 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CAT
* * * * *
41602283 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAACCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* *** *
41602326 AGATCTTATCTCTCTGAAGTTGCA---GAGCAGA-TCGCGTC-T
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
*
41602365 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
41602398 CTAAGTAAAC
Statistics
Matches: 261, Mismatches: 52, Indels: 41
0.74 0.15 0.12
Matches are distributed among these distances:
38 20 0.08
39 2 0.01
40 22 0.08
41 20 0.08
42 4 0.02
43 20 0.08
44 143 0.55
45 27 0.10
46 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:41602260 original size:45 final size:44
Alignment explanation
Indices: 41602019--41602480 Score: 229
Period size: 44 Copynumber: 10.7 Consensus size: 44
41602009 GTTGAAGATG
* *
41602019 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-C
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAA
* * * * *
41602063 G-ATAATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAA--AA
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* ** * * *
41602105 CCTTGGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-A
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * * *
41602147 TCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * * *
41602191 GCAAGTCTTATC-CTCTTGAAGTTGCAGT-GAGGTAGACTGAAG-ATG
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGCA-A
* *
41602236 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC-T
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCAA
* *
41602280 G-ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGA-TCAA--AA
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGCAA
* * * *
41602322 CCTTAGATCTTATCTCTCTGAAGTTGCA---GAGCAGA-T-CGC--
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* * *
41602361 GTCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 G-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
* ** **
41602406 ACAAGGCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAATAA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAGCAA
* * * *
41602450 ACAAATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
41602481 TGGGTTAGAG
Statistics
Matches: 321, Mismatches: 58, Indels: 79
0.70 0.13 0.17
Matches are distributed among these distances:
38 20 0.06
40 22 0.07
41 21 0.07
42 5 0.02
43 31 0.10
44 184 0.57
45 35 0.11
46 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAA
Found at i:41602268 original size:217 final size:215
Alignment explanation
Indices: 41602011--41602443 Score: 722
Period size: 217 Copynumber: 2.0 Consensus size: 215
41602001 CGGAGTAGGT
41602011 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
* * *
41602076 CCTTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTGAAGTTACAGTGGAGCGGATCAAAACCTTAGATCTTATCTCTCTGAAGTTGC--AGAGCAG
* * *
41602141 ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCAAGTCTTATCCTC
129 ATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTC
* *
41602206 TTGAAGTTGCAGTGAGGTAGAC
194 CTGAAGTTGCAGTGAGGCAGAC
* *
41602228 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCTGATAATCCTATCT
1 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
*
41602293 CCCTGAAGTTGCAGTGGAGCGGATCAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGCAGAT
66 CCCTGAAGTTACAGTGGAGCGGATCAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGCAGAT
* * *
41602358 CGCGTCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGGCTTATCCTCCT
131 CGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTCCT
41602423 GAAGTTGCAGTGAGGCAGAC
196 GAAGTTGCAGTGAGGCAGAC
41602443 T
1 T
41602444 AAATAAACAA
Statistics
Matches: 202, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
215 87 0.43
217 115 0.57
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (215 bp):
TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
CCCTGAAGTTACAGTGGAGCGGATCAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGCAGAT
CGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAACAAGGCTTATCCTCCT
GAAGTTGCAGTGAGGCAGAC
Found at i:41602872 original size:19 final size:21
Alignment explanation
Indices: 41602791--41602866 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
41602781 ATTTTTGAGG
41602791 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
41602812 AT-GA-AATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
41602831 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
41602852 ATATACAATCTTAGA
1 ATATACAATCTTAGA
41602867 AAATATGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.35
20 1 0.02
21 31 0.63
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:41603087 original size:19 final size:21
Alignment explanation
Indices: 41603063--41603101 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
41603053 GTTTTCTTTT
*
41603063 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
41603082 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
41603102 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:41603329 original size:3 final size:3
Alignment explanation
Indices: 41603304--41603360 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
41603294 GGTTTTTAGT
* *
41603304 TTA TT- TTA TTAA TT- TTG TTA TTA TTA TTT TTA TTA TTA -TA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41603347 TATA TTA TTA TTA T
1 T-TA TTA TTA TTA T
41603361 ACCTACATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 6 0.13
3 34 0.74
4 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41608170 original size:14 final size:14
Alignment explanation
Indices: 41608151--41608185 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41608141 AATCCAAGTC
41608151 AAATAAAAAAATTA
1 AAATAAAAAAATTA
**
41608165 AAATAAATTAATTA
1 AAATAAAAAAATTA
41608179 AAATAAA
1 AAATAAA
41608186 TAACAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAAAAATTA
Found at i:41608186 original size:14 final size:14
Alignment explanation
Indices: 41608160--41608186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41608150 CAAATAAAAA
41608160 AATTAAAATAAATT
1 AATTAAAATAAATT
41608174 AATTAAAATAAAT
1 AATTAAAATAAAT
41608187 AACAAAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAAATAAATT
Found at i:41608561 original size:39 final size:40
Alignment explanation
Indices: 41608518--41608603 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
41608508 CACTTAATAA
*
41608518 TTATAAAAAATTTGGAAT-AAAAAATAAAATAAAAAGAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
*
41608557 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAATAGC
1 TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
41608597 TTATAAA
1 TTATAAA
41608604 TAAAATATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 17 0.39
40 27 0.61
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (40 bp):
TTATAAAAAATTTGCAATAAAAAAATAAAATAAAAAGAGC
Found at i:41610483 original size:15 final size:15
Alignment explanation
Indices: 41610465--41610494 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41610455 ATAAATGTCG
41610465 CAATAACAAATACAA
1 CAATAACAAATACAA
*
41610480 CAATAATAAATACAA
1 CAATAACAAATACAA
41610495 AAATGGCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:41610524 original size:13 final size:14
Alignment explanation
Indices: 41610505--41610542 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
41610495 AAATGGCATA
41610505 GAAATAATATAAAC
1 GAAATAATATAAAC
41610519 -AAATAA-ATAAAC
1 GAAATAATATAAAC
41610531 GAAACTAATATA
1 GAAA-TAATATA
41610543 CATAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:41614559 original size:195 final size:197
Alignment explanation
Indices: 41614219--41614617 Score: 658
Period size: 195 Copynumber: 2.0 Consensus size: 197
41614209 TAATAATGTA
*
41614219 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCGTCAATTCAATTCATTGTTCAAATCA
1 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-----AT-A
41614284 TCAAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAA
60 TCAAATCATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAA
* *
41614349 TTTCACTATTTTCAATTCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACTAA
125 TTTCACTATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAA
41614414 TTCAATTC
190 TTCAATTC
41614422 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTG-T-TCAAAT
1 ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAAT
*
41614485 CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTTAATTCCATAATTTCATCGAATTTCAC
66 CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCAC
* * * *
41614550 TATTTTCAATCCTATTTAATTTAGTTCTCCATCTCAAAAATTAAACTTTTATATACCAATTCAAT
131 TATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAAT
41614615 TC
196 TC
41614617 A
1 A
41614618 ACTAATCAAT
Statistics
Matches: 188, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
195 132 0.70
197 1 0.01
203 55 0.29
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.40
Consensus pattern (197 bp):
ACAATTTATCCAATCATCATTTTGTTTAATTCACATCTCATCAATTCAATTCATTGATATCAAAT
CATCACATAGCAAATTTTATTTCAACCCAATTCAAAGTCAATTCCATAATTTCATCGAATTTCAC
TATTTTCAATCCTATTTAATTTACTCCTCCATCTCAAAAATTAAACATTTAGATACCAATTCAAT
TC
Found at i:41618869 original size:76 final size:78
Alignment explanation
Indices: 41618737--41618879 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 78
41618727 TTGGACTTGG
* *
41618737 TTAAAGGTATGAATGTTATATATATGTATAAGTGAGTTGGAACATATATGTATATACATGAATAA
1 TTAAAGGTATGAATGTTATATATATGTATAAGTAAGTTCGAACATATATGTATATACATGAATAA
41618802 GTCTTGAATATAT
66 GTCTTGAATATAT
* * * * * *
41618815 TTAAAGGTATGAATG-T-TATGTATGTATATGTAATTTCGAATATGTATGTATATACATGTATAA
1 TTAAAGGTATGAATGTTATATATATGTATAAGTAAGTTCGAACATATATGTATATACATGAATAA
41618878 GT
66 GT
41618880 TTTTTTTTGT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 41 0.72
77 1 0.02
78 15 0.26
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (78 bp):
TTAAAGGTATGAATGTTATATATATGTATAAGTAAGTTCGAACATATATGTATATACATGAATAA
GTCTTGAATATAT
Found at i:41623337 original size:28 final size:30
Alignment explanation
Indices: 41623306--41623366 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
41623296 TGATATTGAT
41623306 TTAGTTA-TTGATTAATATG-TTTTGTT-TG
1 TTAGTTAGTTG-TTAATATGATTTTGTTATG
*
41623334 TTAGTTAGTTGTTTATATGATTTTGTTATG
1 TTAGTTAGTTGTTAATATGATTTTGTTATG
41623364 TTA
1 TTA
41623367 CATTTGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 14 0.48
29 10 0.34
30 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (30 bp):
TTAGTTAGTTGTTAATATGATTTTGTTATG
Found at i:41624439 original size:24 final size:24
Alignment explanation
Indices: 41624370--41624439 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
41624360 GGTAAGACCC
*
41624370 TAGTTGAAAGATACTACGGCACCA
1 TAGTTGAAAGATACTATGGCACCA
* * *
41624394 TA-TCGAAA-A-ACAATCAAG-ACCA
1 TAGTTGAAAGATACTAT--GGCACCA
41624416 TAGTTGAAAGATACTATGGCACCA
1 TAGTTGAAAGATACTATGGCACCA
41624440 CTTTGGGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 12 0.36
24 7 0.21
25 4 0.12
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
TAGTTGAAAGATACTATGGCACCA
Found at i:41627970 original size:87 final size:87
Alignment explanation
Indices: 41627855--41628029 Score: 262
Period size: 87 Copynumber: 2.0 Consensus size: 87
41627845 CATTCCTTTT
* * * *
41627855 TTTTTTTGCACTCAGTTGAGTACTTGAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTTCTT-
1 TTTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATT-TTC
*
41627919 CAAAAAAGCAATTAATCCCCTGC
65 CAAAAAAGCAATTAAGCCCCTGC
* *
41627942 TTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTTAAAATTTTCC
1 TTTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTTTCC
*
41628007 AAAAAAGCAATTAAGCCCTTGC
66 AAAAAAGCAATTAAGCCCCTGC
41628029 T
1 T
41628030 CTTATTAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 2 0.03
87 77 0.97
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (87 bp):
TTTTTTTCCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTTTCC
AAAAAAGCAATTAAGCCCCTGC
Found at i:41628062 original size:23 final size:25
Alignment explanation
Indices: 41628031--41628087 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
41628021 GCCCTTGCTC
* *
41628031 TTATTAAAAATTAGAA-AA-AAAAT
1 TTATAAAAAATTAAAATAATAAAAT
41628054 TTATAAAAAATTAAAATAATAAAAT
1 TTATAAAAAATTAAAATAATAAAAT
*
41628079 TTAGAAAAA
1 TTATAAAAA
41628088 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.48
24 2 0.07
25 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (25 bp):
TTATAAAAAATTAAAATAATAAAAT
Found at i:41628388 original size:10 final size:10
Alignment explanation
Indices: 41628373--41628398 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41628363 TTCTTACGGC
41628373 TTTATAAAAT
1 TTTATAAAAT
41628383 TTTATAAAAT
1 TTTATAAAAT
41628393 TTTATA
1 TTTATA
41628399 TTTCTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:41628422 original size:10 final size:10
Alignment explanation
Indices: 41628409--41628499 Score: 57
Period size: 10 Copynumber: 9.5 Consensus size: 10
41628399 TTTCTATATA
41628409 TTTTATAATT
1 TTTTATAATT
**
41628419 TTTTACGA-T
1 TTTTATAATT
**
41628428 TTTTATAAAA
1 TTTTATAATT
*
41628438 TTTTACAATT
1 TTTTATAATT
41628448 TTTT-T-ATT
1 TTTTATAATT
*
41628456 TTTTATGA-T
1 TTTTATAATT
41628465 TTTTAT-ATT
1 TTTTATAATT
*
41628474 ATTTTCTAATT
1 -TTTTATAATT
* *
41628485 TTTAATAAAT
1 TTTTATAATT
41628495 TTTTA
1 TTTTA
41628500 ATATTTGATA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
8 8 0.13
9 16 0.26
10 34 0.56
11 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:41628422 original size:27 final size:28
Alignment explanation
Indices: 41628375--41628456 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 28
41628365 CTTACGGCTT
**
41628375 TATAAAATTTTATAAAATTTTATATTTC
1 TATAAAATTTTATAATTTTTTATATTTC
* * *
41628403 TAT-ATATTTTATAATTTTTTACGATTTT
1 TATAAAATTTTATAATTTTTTA-TATTTC
*
41628431 TATAAAATTTTACAATTTTTT-TATTT
1 TATAAAATTTTATAATTTTTTATATTT
41628457 TTTATGATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
27 19 0.43
28 10 0.23
29 15 0.34
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (28 bp):
TATAAAATTTTATAATTTTTTATATTTC
Found at i:41628433 original size:19 final size:19
Alignment explanation
Indices: 41628409--41628471 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
41628399 TTTCTATATA
41628409 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACGAT
** *
41628428 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACGAT
* *
41628447 TTTT-TTATTTTTTATGAT
1 TTTTATAATTTTTTACGAT
41628465 TTTTATA
1 TTTTATA
41628472 TTATTTTCTA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAT
Found at i:41628433 original size:56 final size:58
Alignment explanation
Indices: 41628335--41628442 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 58
41628325 ATTTACGAAA
*
41628335 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTATAAAAT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTATAAAAT
* **
41628393 TTTATATTTCTATATA-TTT-TATAATTTT-TTACGATTTTTATAAAATTTTA
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACG-GCTTTATAAAATTTTA
41628443 CAATTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
55 5 0.11
56 23 0.51
57 3 0.07
58 14 0.31
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGGCTTTATAAAATTTTATAAAAT
Found at i:41628469 original size:56 final size:55
Alignment explanation
Indices: 41628326--41628480 Score: 136
Period size: 56 Copynumber: 2.7 Consensus size: 55
41628316 ATAAAAATAA
* *
41628326 TTTACGAAA-TTTATATTTCTTTACATTTTGTATAATTTTCTTACGGCTTTATAAAAT
1 TTTACAAAATTTTATATTTC--TATATTTT-TATAATTTTCTTACGGCTTTATAAAAT
* **
41628383 TTTATAAAATTTTATATTTCTATATATTTTATAATTTT-TTACGATTTTTATAAAAT
1 TTTACAAAATTTTATATTTCTATAT-TTTTATAATTTTCTTACG-GCTTTATAAAAT
* * *
41628439 TTTAC-AATTTTTTTATTTTTTATGATTTTTATATTATTTTCT
1 TTTACAAAATTTTATA-TTTCTAT-ATTTTTATA--ATTTTCT
41628481 AATTTTTAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
55 13 0.16
56 40 0.49
57 12 0.15
58 15 0.19
59 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (55 bp):
TTTACAAAATTTTATATTTCTATATTTTTATAATTTTCTTACGGCTTTATAAAAT
Found at i:41628478 original size:19 final size:18
Alignment explanation
Indices: 41628409--41628488 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
41628399 TTTCTATATA
*
41628409 TTTTATAATTTTTTACGAT
1 TTTTAT-ATTTTTTACAAT
**
41628428 TTTTATAAAATTTTACAAT
1 TTTTAT-ATTTTTTACAAT
* **
41628447 TTTTTTATTTTTTATGAT
1 TTTTATATTTTTTACAAT
41628465 TTTTATATTATTTT-CTAAT
1 TTTTATATT-TTTTAC-AAT
41628484 TTTTA
1 TTTTA
41628489 ATAAATTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
18 16 0.33
19 32 0.67
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:41628478 original size:37 final size:37
Alignment explanation
Indices: 41628416--41628487 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
41628406 ATATTTTATA
41628416 ATTTTTTACGATTTTTATAAAATTTTAC-AATTTTTTT
1 ATTTTTTACGATTTTTATAAAATTTT-CTAATTTTTTT
* **
41628453 ATTTTTTATGATTTTTATATTATTTTCTAATTTTT
1 ATTTTTTACGATTTTTATAAAATTTTCTAATTTTT
41628488 AATAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (37 bp):
ATTTTTTACGATTTTTATAAAATTTTCTAATTTTTTT
Found at i:41628728 original size:92 final size:91
Alignment explanation
Indices: 41628573--41628773 Score: 269
Period size: 92 Copynumber: 2.2 Consensus size: 91
41628563 AATTTTAAAT
* * * * *
41628573 AAAAGCAGGGGCTTACTTCCTTTTTTTGAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAG
1 AAAAGTAGGGGCTTAATTCCTTTTTTTGAAAAAAGTTTGAGGGCCTCTTTAATGCATTTTGAAAG
* *
41628638 TTCAAGTACTCAATTGAGTGC-AAAA
66 TTCAAGTACCCAAATGAGTGCAAAAA
* * *
41628663 AAAAGTAGGGGCTTAATTGCTCTTTTTTTTAACAAGGTTTGAGGGCCTCTTTAATGCATTTTGAA
1 AAAAGTAGGGGCTTAATT-C-CTTTTTTTGAAAAAAGTTTGAGGGCCTCTTTAATGCATTTTGAA
*
41628728 AGTTTAAGTACCCAAATGAGTGCAAAAA
64 AGTTCAAGTACCCAAATGAGTGCAAAAA
*
41628756 AAAAATAGGGGCTTAATT
1 AAAAGTAGGGGCTTAATT
41628774 TATTGGTACA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 16 0.17
91 1 0.01
92 58 0.60
93 21 0.22
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (91 bp):
AAAAGTAGGGGCTTAATTCCTTTTTTTGAAAAAAGTTTGAGGGCCTCTTTAATGCATTTTGAAAG
TTCAAGTACCCAAATGAGTGCAAAAA
Done.