Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 71 of 75
Found at i:23171581 original size:12 final size:13
Alignment explanation
Indices: 23171564--23171595 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23171554 GATTTCCATC
23171564 AATTCAAT-CACT
1 AATTCAATCCACT
23171576 AATTC-ATCCACT
1 AATTCAATCCACT
23171588 AATTCAAT
1 AATTCAAT
23171596 ATAAGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (13 bp):
AATTCAATCCACT
Found at i:23171785 original size:11 final size:11
Alignment explanation
Indices: 23171769--23171794 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23171759 TCTTTCTTTC
23171769 TTTCTCCCCTG
1 TTTCTCCCCTG
23171780 TTTCTCCCCTG
1 TTTCTCCCCTG
23171791 TTTC
1 TTTC
23171795 GTTTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:23174887 original size:42 final size:42
Alignment explanation
Indices: 23174794--23174902 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
23174784 GCCCGAAGGC
*
23174794 TGAACAGAAGCTCATGAGAGCTAAACAAAAACGCTTAAGGGT
1 TGAACAGAAGCTCATGAGAGCTAAACAAAAACGCTTAAGAGT
* * * * *
23174836 TAAATAGAAGCTCA-GTAGAGCTGAATAAAAACTCATT-AGAGT
1 TGAACAGAAGCTCATG-AGAGCTAAACAAAAACGC-TTAAGAGT
* *
23174878 TGAACAGAAGCCCGTGAGAGCTAAA
1 TGAACAGAAGCTCATGAGAGCTAAA
23174903 TGGAAAGTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
41 1 0.02
42 49 0.92
43 3 0.06
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCATGAGAGCTAAACAAAAACGCTTAAGAGT
Found at i:23177195 original size:27 final size:26
Alignment explanation
Indices: 23177165--23177247 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
23177155 AGTCCCAGTT
23177165 GACTACCTTGTGTTTGATGTCTCGATG
1 GACTACCTTGTGTTT-ATGTCTCGATG
* *
23177192 GACTACCATGTGTTTA-GTATCCTGATG
1 GACTACCTTGTGTTTATGTCT-C-GATG
*
23177219 GACTA-CTATGTGTTTAGTGTCTCGGTG
1 GACTACCT-TGTGTTTA-TGTCTCGATG
23177246 GA
1 GA
23177248 ATACACAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 36 0.78
28 1 0.02
29 3 0.07
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.39
Consensus pattern (26 bp):
GACTACCTTGTGTTTATGTCTCGATG
Found at i:23181627 original size:16 final size:17
Alignment explanation
Indices: 23181596--23181659 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
23181586 ATCAAATTTT
*
23181596 TCGTGTTTTAAAAAATT-
1 TCGTG-TTTCAAAAATTC
*
23181613 TCATGTTTCAAAAATTC
1 TCGTGTTTCAAAAATTC
23181630 TCGTGTTTCAAAAATTC
1 TCGTGTTTCAAAAATTC
*
23181647 TCGTGTTTTAAAA
1 TCGTGTTTCAAAA
23181660 TAAAATGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.24
17 32 0.76
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:23181777 original size:18 final size:18
Alignment explanation
Indices: 23181756--23181803 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
23181746 AAAAAAAAAA
23181756 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
*
23181774 TCGT-ATTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
*
23181791 TTGTGTTTT-AAAA
1 TCGTGTTTTCAAAA
23181804 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:23181828 original size:144 final size:141
Alignment explanation
Indices: 23181500--23181929 Score: 634
Period size: 144 Copynumber: 3.0 Consensus size: 141
23181490 TAAAAAATTA
* * *
23181500 AAAAATT-TTAGTGCTTTAAAATAAAATGTTTATTTTTTTAAAATTATCAAATTATATTTAAACG
1 AAAAATTCTT-GTGTTTTAAAATAAAATGTTTATTTTTTTTAAATTATCAAATTATATTTAAATG
* * * *
23181564 GAGATATAATAATATGTAATTTATCAAATTTTTCGTGTTT-TAAAAAATTTCATG-TTTCAAAAA
65 GATATATAATAATATGTAATTTATCAAAATTTTCGTGTTTCAAAAAAATTTCGTGTTTTCAAAAA
23181627 TTCTCGTGTTTC
130 TTCTCGTGTTTC
*
23181639 AAAAATTCTCGTGTTTTAAAATAAAATGTTTAATTTTTTTCTAAATTATCAAATTATATTTAAAT
1 AAAAATTCTTGTGTTTTAAAATAAAATGTTT-ATTTTTTT-TAAATTATCAAATTATATTTAAAT
* **
23181704 GGATATATAATATTATGTAATTTATCAAAATTTTCGTGTTTCAAAAAAAAAATCGTGTTTTCAAA
64 GGATATATAATAATATGTAATTTATCAAAATTTTCGTGTTTC-AAAAAAATTTCGTGTTTTCAAA
*
23181769 AATTCTCGTATTTC
128 AATTCTCGTGTTTC
23181783 AAAAATTCTTGTGTTTTAAAATAAAATGTTTATTTTTTTTGTAAATTATCAAATTATATTTAAAT
1 AAAAATTCTTGTGTTTTAAAATAAAATGTTTA-TTTTTTT-TAAATTATCAAATTATATTTAAAT
* *
23181848 GGATATATAATAATATATAATTTATCAAAATTTT-GTGTTTCAAAAAATTTTCGTGTTTTTCAAA
64 GGATATATAATAATATGTAATTTATCAAAATTTTCGTGTTTCAAAAAAATTTCGTG-TTTTCAAA
*
23181912 AATTCTCGTGTTTT
128 AATTCTCGTGTTTC
23181926 AAAA
1 AAAA
23181930 TAAAATGTTT
Statistics
Matches: 262, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
139 27 0.10
140 9 0.03
141 60 0.23
142 11 0.04
143 42 0.16
144 113 0.43
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (141 bp):
AAAAATTCTTGTGTTTTAAAATAAAATGTTTATTTTTTTTAAATTATCAAATTATATTTAAATGG
ATATATAATAATATGTAATTTATCAAAATTTTCGTGTTTCAAAAAAATTTCGTGTTTTCAAAAAT
TCTCGTGTTTC
Found at i:23181914 original size:19 final size:20
Alignment explanation
Indices: 23181874--23181925 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
23181864 ATAATTTATC
23181874 AAAATTTT-GTG--TTTCAA
1 AAAATTTTCGTGTTTTTCAA
23181891 AAAATTTTCGTGTTTTTC-A
1 AAAATTTTCGTGTTTTTCAA
*
23181910 AAAATTCTCGTGTTTT
1 AAAATTTTCGTGTTTT
23181926 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 16 0.52
20 4 0.13
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
AAAATTTTCGTGTTTTTCAA
Found at i:23181982 original size:125 final size:127
Alignment explanation
Indices: 23181779--23182016 Score: 435
Period size: 125 Copynumber: 1.9 Consensus size: 127
23181769 AATTCTCGTA
*
23181779 TTTCAAAAATTCTTGTGTTTTAAAATAAAATGTTTATTTTTTTTGTAAATTATCAAATTATATTT
1 TTTCAAAAATTCTCGTGTTTTAAAATAAAATGTTTATTTTTTTTGTAAATTATCAAATTATATTT
23181844 AAATGGATATATAATAATATATAATTTATCAAAA-TTTTGTGTTTCAAAAAATTTTCGTGTT
66 AAATGGATATATAATAATATATAATTTATCAAAATTTTTGTGTTTCAAAAAATTTTCGTGTT
23181905 TTTCAAAAATTCTCGTGTTTTAAAATAAAATGTTTA-TTTTTTTGTAAATTATCAAATTATATTT
1 TTTCAAAAATTCTCGTGTTTTAAAATAAAATGTTTATTTTTTTTGTAAATTATCAAATTATATTT
* *
23181969 AAATGGATATATAATAATATGTAGTTTATCAAAATTTTTGTGTTTCAA
66 AAATGGATATATAATAATATATAATTTATCAAAATTTTTGTGTTTCAA
23182017 TCGGATCATA
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
125 60 0.56
126 48 0.44
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (127 bp):
TTTCAAAAATTCTCGTGTTTTAAAATAAAATGTTTATTTTTTTTGTAAATTATCAAATTATATTT
AAATGGATATATAATAATATATAATTTATCAAAATTTTTGTGTTTCAAAAAATTTTCGTGTT
Found at i:23185248 original size:18 final size:18
Alignment explanation
Indices: 23185227--23185269 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
23185217 ACTTAAATAA
*
23185227 TAAAAATTAAATTTATTT
1 TAAAAATGAAATTTATTT
*
23185245 TAAATATGAAATTTATTT
1 TAAAAATGAAATTTATTT
23185263 TAAAAAT
1 TAAAAAT
23185270 ATTTCATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAAATGAAATTTATTT
Found at i:23185425 original size:9 final size:10
Alignment explanation
Indices: 23185407--23185440 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
23185397 TTGTGTACGT
23185407 AAAATCAATA
1 AAAATCAATA
23185417 AAAAT-AATA
1 AAAATCAATA
*
23185426 AAATTCAATA
1 AAAATCAATA
23185436 AAAAT
1 AAAAT
23185441 TATGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATCAATA
Found at i:23186804 original size:76 final size:75
Alignment explanation
Indices: 23186678--23186912 Score: 265
Period size: 86 Copynumber: 3.0 Consensus size: 75
23186668 CTTGTTGTGG
* *
23186678 GTGCACAACATATTTTCAGATTAAACAAACTGCCACTTGGTTCATGATTGAACCATATTGTTTGC
1 GTGCACAACATATTTACAGATTAAACAAACTGCCACTTGGTTCATGATTGAACCA-A-TATTTGC
23186743 AGTTACTGCA-A
64 AGTTACTGCATA
* * *
23186754 GTGCACAACATATTTGCAGATTAAACAAACTGCGACTTGGTTCATGATTGAACCACGTATTTGCA
1 GTGCACAACATATTTACAGATTAAACAAACTGCCACTTGGTTCATGATTGAACCA-ATATTTGCA
23186819 GTTACTGCCATTTTTTTGTGA
65 GTTACTG-CA--------T-A
* * *
23186840 GTGCACAACATATTTACAGATTAAACAAACTACCACTCGGTTCGTGATTGAACCACATATTTGCA
1 GTGCACAACATATTTACAGATTAAACAAACTGCCACTTGGTTCATGATTGAACCA-ATATTTGCA
23186905 GTTACTGC
65 GTTACTGC
23186913 CACTTGGTTC
Statistics
Matches: 137, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
75 14 0.10
76 55 0.40
85 1 0.01
86 67 0.49
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (75 bp):
GTGCACAACATATTTACAGATTAAACAAACTGCCACTTGGTTCATGATTGAACCAATATTTGCAG
TTACTGCATA
Found at i:23186901 original size:86 final size:86
Alignment explanation
Indices: 23186753--23186914 Score: 270
Period size: 86 Copynumber: 1.9 Consensus size: 86
23186743 AGTTACTGCA
* * * * *
23186753 AGTGCACAACATATTTGCAGATTAAACAAACTGCGACTTGGTTCATGATTGAACCACGTATTTGC
1 AGTGCACAACATATTTACAGATTAAACAAACTACCACTCGGTTCATGATTGAACCACATATTTGC
23186818 AGTTACTGCCATTTTTTTGTG
66 AGTTACTGCCATTTTTTTGTG
*
23186839 AGTGCACAACATATTTACAGATTAAACAAACTACCACTCGGTTCGTGATTGAACCACATATTTGC
1 AGTGCACAACATATTTACAGATTAAACAAACTACCACTCGGTTCATGATTGAACCACATATTTGC
23186904 AGTTACTGCCA
66 AGTTACTGCCA
23186915 CTTGGTTCGT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 70 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (86 bp):
AGTGCACAACATATTTACAGATTAAACAAACTACCACTCGGTTCATGATTGAACCACATATTTGC
AGTTACTGCCATTTTTTTGTG
Found at i:23186927 original size:40 final size:43
Alignment explanation
Indices: 23186781--23186962 Score: 137
Period size: 40 Copynumber: 4.3 Consensus size: 43
23186771 AGATTAAACA
* * *
23186781 AACTGCGACTTGGTTCATGATTGAACCAC-GTATTTGCAG-TT
1 AACTGCCACTTGGTTCGTGATTGAACCACACTATTTGCAGATT
** * * * * *
23186822 -ACTGCCA-TTTTTTTGTGAGTGCACAACA-TATTTACAGATT
1 AACTGCCACTTGGTTCGTGATTGAACCACACTATTTGCAGATT
* *
23186862 AAACAAACTACCACTCGGTTCGTGATTGAACCACA-TATTTGCAG-TT
1 -----AACTGCCACTTGGTTCGTGATTGAACCACACTATTTGCAGATT
*
23186908 -ACTGCCACTTGGTTCGTGATTGAACCACACTGTTTGCAGATT
1 AACTGCCACTTGGTTCGTGATTGAACCACACTATTTGCAGATT
23186950 AAACTGCCACTTG
1 -AACTGCCACTTG
23186963 TCCTCCGTAC
Statistics
Matches: 107, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
39 21 0.20
40 35 0.33
41 8 0.07
42 2 0.02
44 11 0.10
46 8 0.07
47 22 0.21
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (43 bp):
AACTGCCACTTGGTTCGTGATTGAACCACACTATTTGCAGATT
Found at i:23187086 original size:34 final size:35
Alignment explanation
Indices: 23187021--23187087 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
23187011 CAAAATGGAT
* * *
23187021 CAATAAGGTAACATTTAATTATGCTTTTAACAGAA
1 CAATAAGGTAACATTCAATTATGATTATAACAGAA
* *
23187056 CAATACGGTAGCATTCAA-TATGATTATAACAG
1 CAATAAGGTAACATTCAATTATGATTATAACAG
23187088 TTCAATTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 12 0.44
35 15 0.56
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (35 bp):
CAATAAGGTAACATTCAATTATGATTATAACAGAA
Found at i:23187134 original size:34 final size:35
Alignment explanation
Indices: 23187072--23187139 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
23187062 GGTAGCATTC
* * *
23187072 AATATGATTATAACAGTTCAATTTAGTAG-AAAAT
1 AATATGATTATAACAGATCAACTCAGTAGCAAAAT
* *
23187106 AATATGCTTATAATAGATCAACTCAGTAGCAAAA
1 AATATGATTATAACAGATCAACTCAGTAGCAAAA
23187140 AGTCATGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (35 bp):
AATATGATTATAACAGATCAACTCAGTAGCAAAAT
Found at i:23188614 original size:21 final size:22
Alignment explanation
Indices: 23188576--23188636 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
23188566 TTCTTTTTAA
*
23188576 ATTAATTAA-TA-TAATAATAC
1 ATTAATTAATTATTTATAATAC
*
23188596 A-TGATTATATTATTT-TAATAC
1 ATTAATTA-ATTATTTATAATAC
23188617 ATTAATTAATTATTTATAAT
1 ATTAATTAATTATTTATAAT
23188637 CCTAATTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
21 16 0.48
22 10 0.30
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTAATTAATTATTTATAATAC
Found at i:23195212 original size:45 final size:45
Alignment explanation
Indices: 23195162--23195259 Score: 196
Period size: 45 Copynumber: 2.2 Consensus size: 45
23195152 AAAACTGATA
23195162 AGGTAAATGAGGAAGTGTCTATTCCCCCAAACACATGACACTAAT
1 AGGTAAATGAGGAAGTGTCTATTCCCCCAAACACATGACACTAAT
23195207 AGGTAAATGAGGAAGTGTCTATTCCCCCAAACACATGACACTAAT
1 AGGTAAATGAGGAAGTGTCTATTCCCCCAAACACATGACACTAAT
23195252 AGGTAAAT
1 AGGTAAAT
23195260 CAGACTGCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
AGGTAAATGAGGAAGTGTCTATTCCCCCAAACACATGACACTAAT
Found at i:23208938 original size:31 final size:31
Alignment explanation
Indices: 23208902--23208971 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
23208892 CTTAACATCC
*
23208902 CAGTGACTTAAATAAAAACTTTCGAATAGTT
1 CAGTGACTTAAATAAAAACTTTCAAATAGTT
* *
23208933 CAGTGATTTAAATGAAAACTTTCAAATAGTT
1 CAGTGACTTAAATAAAAACTTTCAAATAGTT
23208964 CAGTGACT
1 CAGTGACT
23208972 ATTTTGTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCAAATAGTT
Found at i:23210333 original size:14 final size:14
Alignment explanation
Indices: 23210314--23210346 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23210304 TTCATGATCG
23210314 TAATAAAA-AATTA
1 TAATAAAATAATTA
23210327 TTAATAAAATAATTA
1 -TAATAAAATAATTA
23210342 TAATA
1 TAATA
23210347 TTTTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAAAATAATTA
Found at i:23214326 original size:2 final size:2
Alignment explanation
Indices: 23214319--23214343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23214309 CTGGAAAAAG
23214319 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23214344 GTAGAGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23231578 original size:43 final size:43
Alignment explanation
Indices: 23231490--23231614 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
23231480 TTTATGTGGG
* * * * *
23231490 AAAATGCCGCTATAGAACATAATCTTTAGCGGTGCTTCTCATA
1 AAAATGCCGCTAAAGAACATAATTTTTAGCGGCGTTTGTCATA
23231533 AAAATGCCGCTAAAGAACATAATTTTTAGCGGCGTTTGT-AGTA
1 AAAATGCCGCTAAAGAACATAATTTTTAGCGGCGTTTGTCA-TA
** * * *
23231576 AAAGCGCTGCTAAAGATCAT-GTTCTTTAGCGGCGTTTGT
1 AAAATGCCGCTAAAGAACATAATT-TTTAGCGGCGTTTGT
23231615 GAGAAAACGC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.04
43 67 0.96
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
AAAATGCCGCTAAAGAACATAATTTTTAGCGGCGTTTGTCATA
Found at i:23232829 original size:330 final size:330
Alignment explanation
Indices: 23232228--23232881 Score: 1308
Period size: 330 Copynumber: 2.0 Consensus size: 330
23232218 AAACTTCAGT
23232228 AATAATTCGGTTATCAATGTCGTCCAGATTAACAGAACCATCACTTAAAGCGATCGCTGTATACT
1 AATAATTCGGTTATCAATGTCGTCCAGATTAACAGAACCATCACTTAAAGCGATCGCTGTATACT
23232293 CCATCTTTTTTATCCTTTAGTTTCTCCTAATAAATCAATCAAGGAGTTAGAAAGGAAATATATAA
66 CCATCTTTTTTATCCTTTAGTTTCTCCTAATAAATCAATCAAGGAGTTAGAAAGGAAATATATAA
23232358 TAAAACAAATGTAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTAAAAAT
131 TAAAACAAATGTAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTAAAAAT
23232423 AAACATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCT
196 AAACATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCT
23232488 TCAGTAGTCATAGGAGATCCATCTTTAAAATAACTCCTACTTGTAGTTCAAACTCACTTACGATT
261 TCAGTAGTCATAGGAGATCCATCTTTAAAATAACTCCTACTTGTAGTTCAAACTCACTTACGATT
23232553 AACAG
326 AACAG
23232558 AATAATTCGGTTATCAATGTCGTCCAGATTAACAGAACCATCACTTAAAGCGATCGCTGTATACT
1 AATAATTCGGTTATCAATGTCGTCCAGATTAACAGAACCATCACTTAAAGCGATCGCTGTATACT
23232623 CCATCTTTTTTATCCTTTAGTTTCTCCTAATAAATCAATCAAGGAGTTAGAAAGGAAATATATAA
66 CCATCTTTTTTATCCTTTAGTTTCTCCTAATAAATCAATCAAGGAGTTAGAAAGGAAATATATAA
23232688 TAAAACAAATGTAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTAAAAAT
131 TAAAACAAATGTAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTAAAAAT
23232753 AAACATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCT
196 AAACATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCT
23232818 TCAGTAGTCATAGGAGATCCATCTTTAAAATAACTCCTACTTGTAGTTCAAACTCACTTACGAT
261 TCAGTAGTCATAGGAGATCCATCTTTAAAATAACTCCTACTTGTAGTTCAAACTCACTTACGAT
23232882 CCTACATTAT
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 324 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (330 bp):
AATAATTCGGTTATCAATGTCGTCCAGATTAACAGAACCATCACTTAAAGCGATCGCTGTATACT
CCATCTTTTTTATCCTTTAGTTTCTCCTAATAAATCAATCAAGGAGTTAGAAAGGAAATATATAA
TAAAACAAATGTAACATAACTTGGCATTATTTGCATTACAAATGACAAATTAAACCATTAAAAAT
AAACATGATAAATATTTAAAATAATTCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCT
TCAGTAGTCATAGGAGATCCATCTTTAAAATAACTCCTACTTGTAGTTCAAACTCACTTACGATT
AACAG
Found at i:23257756 original size:294 final size:282
Alignment explanation
Indices: 23257415--23257999 Score: 683
Period size: 282 Copynumber: 2.0 Consensus size: 282
23257405 TTTTCTAAAT
* *
23257415 AGTATAAATATACAATTGATGGAAGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAAAT
1 AGTATAAATATACAATTGATGGAAGTAATAAAGTGTACATAATAAAATTAAAACGTATAAAAAAT
* * * * *
23257480 TGAAAATAAAGCTTT-AGTTTAGTAGTAAATTT-AAGATTTTACGCGTTGGCGTGGGTTCAAATC
66 TGAAAATAAAGCTTTGA-TTGAATAGTAAATTTAAAG-CTTTACGCATTGGCGTGAGTTCAAATC
* * * *
23257543 CCACCATAAGCATTTTTGTTTTTGTTTTTTTTAATAGAAAA-ATTAAAGTATCCTCGAATAATAT
129 CCACCAT-A--A-----G----TATTTTTTTTAATA-AAAAGACTAAAGCACCCTCGAATAATAT
* * * *
23257607 AACTTATTTTAAATTTGAAATGATATTTTTGTAATTTTCCT-ATCTAAGTTGTTGTCCGGTTGAC
181 AACTTATTTTAAATATGAAAAGATATTTTTGTAATTTTCCTAAT-TAAGTTGGTGTCCAGTTGAC
* * * *
23257671 TCGTGATACCAGCTCAATCAAGGGTTTAAATAATAGTA
245 TCGTAAAACCAACTCAATCAAGGGCTTAAATAATAGTA
* * * *
23257709 AGTATAGATATACAATTGGTGGAGGTAATAAAGTGTACATAATAAAATTAAAACGTATAAAAAGT
1 AGTATAAATATACAATTGATGGAAGTAATAAAGTGTACATAATAAAATTAAAACGTATAAAAAAT
* * * * *
23257774 TTAAAATAAAGCTTTGATTGAATGGTAAATTTAAAGCTTTATGCATTGGTGTGAGTTCAAATCTC
66 TGAAAATAAAGCTTTGATTGAATAGTAAATTTAAAGCTTTACGCATTGGCGTGAGTTCAAATCCC
*
23257839 ACCATAAGTATTTTTTTTAATAAAAAGACTAAGGCACCCTCGAATAATATAACTTATTTTAAATA
131 ACCATAAGTATTTTTTTTAATAAAAAGACTAAAGCACCCTCGAATAATATAACTTATTTTAAATA
* * * * *
23257904 TGAAAAGATTTTTTTGTAATTTTTCTAATTGAGTTGGTGTCTAGTTGACTTGTAAAACCAACTCA
196 TGAAAAGATATTTTTGTAATTTTCCTAATTAAGTTGGTGTCCAGTTGACTCGTAAAACCAACTCA
*
23257969 ATCAGGGGCTTAAATAATAGTA
261 ATCAAGGGCTTAAATAATAGTA
23257991 AGTATAAAT
1 AGTATAAAT
23258000 TTATAACTAG
Statistics
Matches: 251, Mismatches: 36, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
281 4 0.02
282 125 0.50
283 2 0.01
286 1 0.00
291 1 0.00
293 1 0.00
294 113 0.45
295 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (282 bp):
AGTATAAATATACAATTGATGGAAGTAATAAAGTGTACATAATAAAATTAAAACGTATAAAAAAT
TGAAAATAAAGCTTTGATTGAATAGTAAATTTAAAGCTTTACGCATTGGCGTGAGTTCAAATCCC
ACCATAAGTATTTTTTTTAATAAAAAGACTAAAGCACCCTCGAATAATATAACTTATTTTAAATA
TGAAAAGATATTTTTGTAATTTTCCTAATTAAGTTGGTGTCCAGTTGACTCGTAAAACCAACTCA
ATCAAGGGCTTAAATAATAGTA
Found at i:23258605 original size:8 final size:9
Alignment explanation
Indices: 23258586--23258628 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
23258576 AATTAATTAC
23258586 TTTTAAATT
1 TTTTAAATT
23258595 TTTTAAATT
1 TTTTAAATT
23258604 TTTTAATAATT
1 TTTT-A-AATT
* *
23258615 TTATAATTT
1 TTTTAAATT
23258624 TTTTA
1 TTTTA
23258629 TTTTTACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 20 0.69
10 2 0.07
11 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAAATT
Found at i:23258614 original size:20 final size:20
Alignment explanation
Indices: 23258591--23258628 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23258581 ATTACTTTTA
*
23258591 AATTTTTTAAATTTTTTAAT
1 AATTTTATAAATTTTTTAAT
*
23258611 AATTTTATAATTTTTTTA
1 AATTTTATAAATTTTTTA
23258629 TTTTTACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
AATTTTATAAATTTTTTAAT
Found at i:23259397 original size:16 final size:16
Alignment explanation
Indices: 23259366--23259396 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
23259356 CCTATAGGGG
23259366 TGTATAATATTAAAAA
1 TGTATAATATTAAAAA
23259382 TGTA-AATATTAAAAA
1 TGTATAATATTAAAAA
23259397 AAAGACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TGTATAATATTAAAAA
Found at i:23261572 original size:45 final size:45
Alignment explanation
Indices: 23261469--23261575 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
23261459 AGCAGCTTGC
* * * **
23261469 CTGCACCGTTTAGTGGTTAATCTACATTGTATTAGTAGCTTTTAT
1 CTGCACCGATTAGTGGTCAATCCACATTGTATTAACAGCTTTTAT
* *
23261514 CTGTATC-ATTTAGTGGTCAATCCAC-TTCGTATTAACAGCTTTTAT
1 CTGCACCGA-TTAGTGGTCAATCCACATT-GTATTAACAGCTTTTAT
23261559 CTGCACCGATTAGTGGT
1 CTGCACCGATTAGTGGT
23261576 TTTTCCACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.04
45 47 0.94
46 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (45 bp):
CTGCACCGATTAGTGGTCAATCCACATTGTATTAACAGCTTTTAT
Found at i:23271823 original size:26 final size:26
Alignment explanation
Indices: 23271794--23271845 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
23271784 TCTCTCTTTT
23271794 CTTTTC-GATATATTAACAGAAAATTC
1 CTTTTCAG-TATATTAACAGAAAATTC
*
23271820 CTTTTCAGTATATTAATAGAAAATTC
1 CTTTTCAGTATATTAACAGAAAATTC
23271846 AAATTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
CTTTTCAGTATATTAACAGAAAATTC
Found at i:23286397 original size:61 final size:60
Alignment explanation
Indices: 23286294--23286414 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 60
23286284 ACAAAAAGAA
23286294 TGATTGTTTCAATGGATGCTACTTCTTTGAATCCAACTTTTCTTTAGATCTCATCTTCAG
1 TGATTGTTTCAATGGATGCTACTTCTTTGAATCCAACTTTTCTTTAGATCTCATCTTCAG
23286354 TGATTGTTTCAATGGATGCTACCTTCTTTGAATCCAACTTTTCTTTAGATCTCATCTTCAG
1 TGATTGTTTCAATGGATGCTA-CTTCTTTGAATCCAACTTTTCTTTAGATCTCATCTTCAG
23286415 GGGGATACTT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 21 0.35
61 39 0.65
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (60 bp):
TGATTGTTTCAATGGATGCTACTTCTTTGAATCCAACTTTTCTTTAGATCTCATCTTCAG
Found at i:23289893 original size:19 final size:21
Alignment explanation
Indices: 23289853--23289893 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
23289843 TTTTTATCAG
23289853 TCCACTCACTCTCCACTTCTC
1 TCCACTCACTCTCCACTTCTC
*
23289874 TCCAC-CACT-TCCATTTCTC
1 TCCACTCACTCTCCACTTCTC
23289893 T
1 T
23289894 TTCAACTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.15, C:0.49, G:0.00, T:0.37
Consensus pattern (21 bp):
TCCACTCACTCTCCACTTCTC
Found at i:23289986 original size:29 final size:31
Alignment explanation
Indices: 23289954--23290042 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 31
23289944 CCAATTATTA
*
23289954 TTTTTTTTTTATCATTCAACTATCAA-T-TT
1 TTTTTTTTTTATCACTCAACTATCAACTCTT
** ** *
23289983 TTTTAATTTGCTCACTCAACTATTAACTCTTT
1 TTTTTTTTTTATCACTCAACTATCAACTC-TT
*
23290015 TTTTTTTTTTCGTCACTCAACTAATCAA
1 TTTTTTTTTT-ATCACTCAACT-ATCAA
23290043 TATCATTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
29 20 0.45
30 1 0.02
32 9 0.20
33 10 0.23
34 4 0.09
ACGTcount: A:0.25, C:0.19, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTTTTTTTTATCACTCAACTATCAACTCTT
Found at i:23290147 original size:4 final size:4
Alignment explanation
Indices: 23290138--23290162 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
23290128 TTCTGCGGTC
23290138 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
23290163 TAGCAGTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:23290661 original size:59 final size:60
Alignment explanation
Indices: 23290558--23290681 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
23290548 CAATCTTGAT
* * *
23290558 TAGTTGGATGAGTAAATTAGAAAAATTGATAGTTGGGTGACCAAAAAAG-AAAGGGGACAA
1 TAGTTGGATGAGTAAATTAAAAAAATTGATAATTGAGTGACCAAAAAAGAAAAGGGGA-AA
* *
23290618 TAGTTGGGTGA-TCAAATTAAAAAAATT-ATAATTGAGTGACCAAAAAAGAAAATGGGAAA
1 TAGTTGGATGAGT-AAATTAAAAAAATTGATAATTGAGTGACCAAAAAAGAAAAGGGGAAA
23290677 TAGTT
1 TAGTT
23290682 AACTGACTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
59 27 0.47
60 30 0.53
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (60 bp):
TAGTTGGATGAGTAAATTAAAAAAATTGATAATTGAGTGACCAAAAAAGAAAAGGGGAAA
Found at i:23296703 original size:19 final size:19
Alignment explanation
Indices: 23296647--23296704 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
23296637 GAAAATAAAT
23296647 AATT-TATACAAATAATTTCA
1 AATTGTATA-AAATAATTT-A
* *
23296667 AATCTGTA-AACAT-TTTTA
1 AAT-TGTATAAAATAATTTA
23296685 AATTGTATAAAATAATTTA
1 AATTGTATAAAATAATTTA
23296704 A
1 A
23296705 TTAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 8 0.27
20 6 0.20
21 2 0.07
22 2 0.07
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (19 bp):
AATTGTATAAAATAATTTA
Found at i:23298648 original size:19 final size:19
Alignment explanation
Indices: 23298626--23298685 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
23298616 TAAATTCTTT
23298626 AAAAACTATAAGAAT-TATA
1 AAAAACTATAA-AATATATA
* *
23298645 AAAAATTATAAAATATATT
1 AAAAACTATAAAATATATA
*
23298664 AAAAA-TA-AAATATATTTA
1 AAAAACTATAAA-ATATATA
23298682 AAAA
1 AAAA
23298686 TAATTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.09
18 14 0.40
19 18 0.51
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAACTATAAAATATATA
Found at i:23298673 original size:16 final size:17
Alignment explanation
Indices: 23298652--23298688 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
23298642 ATAAAAAATT
23298652 ATAAAATATA-TTAAAA
1 ATAAAATATATTTAAAA
23298668 ATAAAATATATTTAAAA
1 ATAAAATATATTTAAAA
23298685 ATAA
1 ATAA
23298689 TTAAAAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAATATATTTAAAA
Found at i:23303959 original size:27 final size:29
Alignment explanation
Indices: 23303905--23303960 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
23303895 TTAATTTTTT
*
23303905 ATTAAAAATTTATAATTAATTATAATTAA
1 ATTAAAAATTTATAATAAATTATAATTAA
23303934 ATTAAAAA-TT-TAATAAATTCAT-ATTAA
1 ATTAAAAATTTATAATAAATT-ATAATTAA
23303961 GATAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 4 0.16
29 8 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTAAAAATTTATAATAAATTATAATTAA
Found at i:23303974 original size:27 final size:27
Alignment explanation
Indices: 23303910--23303974 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
23303900 TTTTTATTAA
* *
23303910 AAATTTATAATTAATTATAATTAAATT
1 AAATATATAATAAATTATAATTAAATT
* *
23303937 AAAAATTTAATAAATTCAT-ATTAAGA-T
1 AAATATATAATAAATT-ATAATTAA-ATT
23303964 AAATATATAAT
1 AAATATATAAT
23303975 TGAATTGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATATATAATAAATTATAATTAAATT
Found at i:23306726 original size:14 final size:14
Alignment explanation
Indices: 23306709--23306769 Score: 70
Period size: 13 Copynumber: 4.2 Consensus size: 14
23306699 AATTTTTTAA
23306709 TTTTAAAATACTTT
1 TTTTAAAATACTTT
23306723 TTTT-AAATACTTT
1 TTTTAAAATACTTT
* *
23306736 TTTTAAATCTTAATTT
1 TTTTAAA--ATACTTT
23306752 TTTTAAAAATACTTT
1 TTTT-AAAATACTTT
23306767 TTT
1 TTT
23306770 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 13 0.33
14 6 0.15
15 8 0.21
16 9 0.23
17 3 0.08
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAAATACTTT
Found at i:23306799 original size:13 final size:13
Alignment explanation
Indices: 23306709--23306799 Score: 58
Period size: 13 Copynumber: 6.5 Consensus size: 13
23306699 AATTTTTTAA
23306709 TTTTAAAATACTTT
1 TTTTAAAATA-TTT
23306723 TTTT-AAATACTTT
1 TTTTAAAATA-TTT
*
23306736 TTTTAAATCTTAATTT
1 TTTTAAA--AT-ATTT
*
23306752 TTTTAAAAATACTT
1 TTTT-AAAATATTT
** *
23306766 TTTTAATTTTTTT
1 TTTTAAAATATTT
23306779 AATTTTAAAATATTT
1 --TTTTAAAATATTT
23306794 TTTTAA
1 TTTTAA
23306800 TTTTTGTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
13 24 0.40
14 13 0.22
15 11 0.18
16 8 0.13
17 4 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAAAATATTT
Found at i:23308891 original size:19 final size:18
Alignment explanation
Indices: 23308863--23308899 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
23308853 GTTTAAAAAT
*
23308863 TTAAAGAAATAATAATAAA
1 TTAAACAAATAA-AATAAA
23308882 TTAAACAAATAAAATAAA
1 TTAAACAAATAAAATAAA
23308900 AATAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
TTAAACAAATAAAATAAA
Found at i:23308905 original size:19 final size:19
Alignment explanation
Indices: 23308864--23308905 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
23308854 TTTAAAAATT
* *
23308864 TAAAGAAATAATAATAAAT
1 TAAACAAATAATAATAAAA
23308883 TAAACAAATAA-AATAAAAA
1 TAAACAAATAATAAT-AAAA
23308902 TAAA
1 TAAA
23308906 TGAAAGTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAACAAATAATAATAAAA
Found at i:23311352 original size:75 final size:75
Alignment explanation
Indices: 23311126--23311352 Score: 339
Period size: 75 Copynumber: 3.0 Consensus size: 75
23311116 TTTGGTGGAT
* * *
23311126 TCAGCACTTCGCAACCACTAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCGAAG
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTC-AAG
* *
23311191 ATACGGTGGAA
65 TTACGGTGGGA
* * *
23311202 TCA-AACTTAGCAACCACCAATGATTCGGCGAATAAGCACTTAGCAACCCCTTTCACATTCAAGT
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGT
*
23311266 TACGGTAGGA
66 TACGGTGGGA
* *
23311276 TCAGCACTTAGCAACCACCGATGATTTGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGT
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGT
23311341 TACGGTGGGA
66 TACGGTGGGA
23311351 TC
1 TC
23311353 CCTTTCACAT
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 14 0.10
75 118 0.87
76 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (75 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGT
TACGGTGGGA
Found at i:23311364 original size:28 final size:28
Alignment explanation
Indices: 23311324--23311380 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
23311314 ACTTAGCAAC
23311324 CCCTTTCACATTCAAGTTACGGTGGGAT
1 CCCTTTCACATTCAAGTTACGGTGGGAT
23311352 CCCTTTCACATTCAAGTTACGGTGGGAT
1 CCCTTTCACATTCAAGTTACGGTGGGAT
23311380 C
1 C
23311381 AGCAGTTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
CCCTTTCACATTCAAGTTACGGTGGGAT
Found at i:23311423 original size:33 final size:32
Alignment explanation
Indices: 23311378--23311529 Score: 98
Period size: 33 Copynumber: 4.5 Consensus size: 32
23311368 TTACGGTGGG
* *
23311378 ATCAGCAGTTAGCAACCACCGATGATTTGGGGA
1 ATCAGCACTTAGCAACCACC-ATGATTCGGGGA
* *
23311411 ATCAGCACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGA
1 ATCAGCACTTAGCAA--CC--AC-CA-T-GA-TT-CGG-GGA
* *
23311453 ATCAGCACTTAACAACCACCAAGGATTCGGGGA
1 ATCAGCACTTAGCAACCACC-ATGATTCGGGGA
*
23311486 ATCAGCACTTAGCAACC-CC----TTGGGGGA
1 ATCAGCACTTAGCAACCACCATGATTCGGGGA
23311513 ATCAGCACTTAGCAACC
1 ATCAGCACTTAGCAACC
23311530 CCCTTTTATA
Statistics
Matches: 98, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
27 24 0.24
32 2 0.02
33 33 0.34
34 3 0.03
35 4 0.04
36 1 0.01
37 3 0.03
38 4 0.04
39 1 0.01
40 4 0.04
41 2 0.02
42 17 0.17
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (32 bp):
ATCAGCACTTAGCAACCACCATGATTCGGGGA
Found at i:23311428 original size:103 final size:103
Alignment explanation
Indices: 23311249--23311451 Score: 388
Period size: 103 Copynumber: 2.0 Consensus size: 103
23311239 ACTTAGCAAC
23311249 CCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAGCAACCACCGATGATTTGGGGAATCAGC
1 CCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAGCAACCACCGATGATTTGGGGAATCAGC
23311314 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
66 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
* *
23311352 CCCTTTCACATTCAAGTTACGGTGGGATCAGCAGTTAGCAACCACCGATGATTTGGGGAATCAGC
1 CCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAGCAACCACCGATGATTTGGGGAATCAGC
23311417 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGG
66 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGG
23311452 AATCAGCACT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (103 bp):
CCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAGCAACCACCGATGATTTGGGGAATCAGC
ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
Found at i:23311442 original size:75 final size:75
Alignment explanation
Indices: 23311352--23311506 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
23311342 ACGGTGGGAT
* * * * * *
23311352 CCCTTTCACATTCAAGTTACGGTGGGATCAGCAGTTAGCAACCACCGATGATTTGGGGAATCAGC
1 CCCTTTCACATTCAAGTTACGGTGGAATCAGCACTTAACAACCACCAAGGATTCGGGGAATCAGC
23311417 ACTTAGCAAC
66 ACTTAGCAAC
23311427 CCCTTTCACATTCAAGTTACGGTGGAATCAGCACTTAACAACCACCAAGGATTCGGGGAATCAGC
1 CCCTTTCACATTCAAGTTACGGTGGAATCAGCACTTAACAACCACCAAGGATTCGGGGAATCAGC
23311492 ACTTAGCAAC
66 ACTTAGCAAC
23311502 CCCTT
1 CCCTT
23311507 GGGGGAATCA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (75 bp):
CCCTTTCACATTCAAGTTACGGTGGAATCAGCACTTAACAACCACCAAGGATTCGGGGAATCAGC
ACTTAGCAAC
Found at i:23311487 original size:178 final size:178
Alignment explanation
Indices: 23311174--23311506 Score: 526
Period size: 178 Copynumber: 1.9 Consensus size: 178
23311164 ACTTAGCAAC
23311174 CCCTTTCACATTCGAAGATACGGTGGAATCAAACTTAGCAACCACCAATGATTCGGCGAATAAGC
1 CCCTTTCACATTCGAAGATACGGTGGAATCAAACTTAGCAACCACCAATGATTCGGCGAATAAGC
* * * *
23311239 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAGCAACCACCGATGATTTG
66 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAACAACCACCAAGGATTCG
23311304 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
131 GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
* * * * * * * *
23311352 CCCTTTCACATTC-AAGTTACGGTGGGATCAGCAGTTAGCAACCACCGATGATTTGGGGAATCAG
1 CCCTTTCACATTCGAAGATACGGTGGAATCA-AACTTAGCAACCACCAATGATTCGGCGAATAAG
23311416 CACTTAGCAACCCCTTTCACATTCAAGTTACGGT-GGAATCAGCACTTAACAACCACCAAGGATT
65 CACTTAGCAACCCCTTTCACATTCAAGTTACGGTAGG-ATCAGCACTTAACAACCACCAAGGATT
23311480 CGGGGAATCAGCACTTAGCAACCCCTT
129 CGGGGAATCAGCACTTAGCAACCCCTT
23311507 GGGGGAATCA
Statistics
Matches: 141, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
177 17 0.12
178 124 0.88
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (178 bp):
CCCTTTCACATTCGAAGATACGGTGGAATCAAACTTAGCAACCACCAATGATTCGGCGAATAAGC
ACTTAGCAACCCCTTTCACATTCAAGTTACGGTAGGATCAGCACTTAACAACCACCAAGGATTCG
GGGAATCAGCACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
Found at i:23311535 original size:103 final size:99
Alignment explanation
Indices: 23311249--23311531 Score: 290
Period size: 103 Copynumber: 2.7 Consensus size: 99
23311239 ACTTAGCAAC
* * *
23311249 CCCTTTCACATTCAAGTTACGGTAGG-ATCAGCACTTAGCAACCACCGATGATTTGGGGAATCAG
1 CCCTTACACATCCAAGTTACGGT-GGAATCAGCACTTAGCAACCACC----ATTGGGGGAATCAG
*
23311313 CACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGGAT
61 CACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGAAT
* * * * *
23311352 CCCTTTCACATTCAAGTTACGGTGGGATCAGCAGTTAGCAACCACCGATGATTTGGGGAATCAGC
1 CCCTTACACATCCAAGTTACGGTGGAATCAGCACTTAGCAACCACC----ATTGGGGGAATCAGC
23311417 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGAAT
62 ACTTAGCAACCCCTTTCACATTCAAGTTACGGTGGAAT
23311455 CAGCACTTAACAACCA-CCAAGGATT-CGG-GGAATCAGCACTTAGCAACC-CC-TTGGGGGAAT
1 C--C-CTT-AC-A-CATCCAA-G-TTACGGTGGAATCAGCACTTAGCAACCACCATTGGGGGAAT
23311515 CAGCACTTAGCAACCCC
58 CAGCACTTAGCAACCCC
23311532 CTTTTATATT
Statistics
Matches: 164, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
102 28 0.17
103 99 0.60
105 1 0.01
106 3 0.02
107 3 0.02
108 22 0.13
109 6 0.04
110 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (99 bp):
CCCTTACACATCCAAGTTACGGTGGAATCAGCACTTAGCAACCACCATTGGGGGAATCAGCACTT
AGCAACCCCTTTCACATTCAAGTTACGGTGGAAT
Found at i:23311718 original size:9 final size:8
Alignment explanation
Indices: 23311685--23311727 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
23311675 GTGCTTTTTT
23311685 TAAAAAATA
1 TAAAAAA-A
23311694 TATATAAAAA
1 TA-A-AAAAA
23311704 TAAAAAAA
1 TAAAAAAA
23311712 TACAAAAAA
1 TA-AAAAAA
23311721 TAAAAAA
1 TAAAAAA
23311728 TTATATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 12 0.39
9 11 0.35
10 4 0.13
11 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:23311719 original size:17 final size:19
Alignment explanation
Indices: 23311685--23311728 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
23311675 GTGCTTTTTT
*
23311685 TAAAAAATATATATAAAAA
1 TAAAAAATATACATAAAAA
23311704 TAAAAAA-ATACA-AAAAA
1 TAAAAAATATACATAAAAA
23311721 TAAAAAAT
1 TAAAAAAT
23311729 TATATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 7 0.30
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
TAAAAAATATACATAAAAA
Found at i:23311834 original size:29 final size:29
Alignment explanation
Indices: 23311724--23311838 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
23311714 CAAAAAATAA
* * *
23311724 AAAATTATATTTTGACCCCCTAAACTTTTT
1 AAAATTACATTTT-AACCCATAAACTTTTT
* ** *
23311754 GAAATTGTATTTTAACCCCTAAA-TTTTCCT
1 AAAATTACATTTTAACCCATAAACTTTT--T
**
23311784 AAAATTACATTTTAACATATAAACTTTTT
1 AAAATTACATTTTAACCCATAAACTTTTT
*
23311813 AAAATTACATTTTGACCCATAAACTT
1 AAAATTACATTTTAACCCATAAACTT
23311839 CCTCAAAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.06
29 33 0.47
30 29 0.41
31 4 0.06
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTAACCCATAAACTTTTT
Found at i:23311849 original size:30 final size:29
Alignment explanation
Indices: 23311779--23311849 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
23311769 CCCCTAAATT
*
23311779 TTCCTAAAATTACATTTTAACATATAAAC
1 TTCCTAAAATTACATTTTAACACATAAAC
** * *
23311808 TTTTTAAAATTACATTTTGACCCATAAAC
1 TTCCTAAAATTACATTTTAACACATAAAC
23311837 TTCCTCAAAATTA
1 TTCCT-AAAATTA
23311850 TGTTTTAGCC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.39
Consensus pattern (29 bp):
TTCCTAAAATTACATTTTAACACATAAAC
Found at i:23312259 original size:18 final size:18
Alignment explanation
Indices: 23312225--23312271 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
23312215 AAGAAGAAGC
23312225 AGAAAGAAAA-AAGAAAAA
1 AGAAA-AAAATAAGAAAAA
*
23312243 AGAAAAAAATAATAAAAA
1 AGAAAAAAATAAGAAAAA
23312261 A-ATAAAAAATA
1 AGA-AAAAAATA
23312272 TTATAACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (18 bp):
AGAAAAAAATAAGAAAAA
Found at i:23312332 original size:21 final size:21
Alignment explanation
Indices: 23312289--23312360 Score: 108
Period size: 21 Copynumber: 3.3 Consensus size: 21
23312279 AGTCGGGTCA
23312289 ACCCGACCCGACCGAATCGATCCG
1 ACCCGACCC-ACCG-A-CGATCCG
23312313 ACCCGACCCACCGACGATCCG
1 ACCCGACCCACCGACGATCCG
*
23312334 ACCCGACCCACCAACGATCCG
1 ACCCGACCCACCGACGATCCG
23312355 ACCCGA
1 ACCCGA
23312361 ACAGCAACCC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
21 33 0.70
22 1 0.02
23 4 0.09
24 9 0.19
ACGTcount: A:0.26, C:0.50, G:0.18, T:0.06
Consensus pattern (21 bp):
ACCCGACCCACCGACGATCCG
Found at i:23312507 original size:23 final size:23
Alignment explanation
Indices: 23312479--23312532 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
23312469 AGCCCAGCAA
23312479 GCCAGCAGCCCAGCCCCTAACAG
1 GCCAGCAGCCCAGCCCCTAACAG
*
23312502 GCCAGCAGCCCAGCCCCTAGCAG
1 GCCAGCAGCCCAGCCCCTAACAG
23312525 GCCAGCAG
1 GCCAGCAG
23312533 GCCTCCAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.46, G:0.26, T:0.04
Consensus pattern (23 bp):
GCCAGCAGCCCAGCCCCTAACAG
Found at i:23312584 original size:12 final size:12
Alignment explanation
Indices: 23312567--23312612 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
23312557 AGCAGGCCAG
23312567 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
23312579 AAAAAGAAGAGGA
1 AAAAAGAA-AAGA
*
23312592 AAAAAGAGAA-A
1 AAAAAGAAAAGA
23312603 AAAAAGAAAA
1 AAAAAGAAAA
23312613 AATAAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 10 0.34
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:23312957 original size:17 final size:18
Alignment explanation
Indices: 23312923--23312963 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
23312913 ACGTCCTTTT
23312923 AAAAATTGTAAATATTCAA
1 AAAAATTGT-AATATTCAA
*
23312942 AAAAATTGT-ATTTTCAA
1 AAAAATTGTAATATTCAA
23312959 AAAAA
1 AAAAA
23312964 ATCCTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAATTGTAATATTCAA
Found at i:23313154 original size:17 final size:17
Alignment explanation
Indices: 23313130--23313288 Score: 146
Period size: 17 Copynumber: 9.0 Consensus size: 17
23313120 TTGGAAAATT
23313130 TTTCGTGTTTTC-AAAA
1 TTTCGTGTTTTCAAAAA
23313146 TTCTCGTG-TTTCAAAAA
1 TT-TCGTGTTTTCAAAAA
*
23313163 GTTTCATGTTTTCAAAAA
1 -TTTCGTGTTTTCAAAAA
**
23313181 TTCTCGTGTTTAAAAAAAAA
1 TT-TCGTGTTT--TCAAAAA
23313201 TTTCGTG-TTTCAAAAA
1 TTTCGTGTTTTCAAAAA
*
23313217 TCCTCGTGATTTTCTAAAAA
1 T-TTCGTG-TTTTC-AAAAA
23313237 TTTCCGTG-TTTCAAAAA
1 TTT-CGTGTTTTCAAAAA
* *
23313254 TTTCGGTGTTTTGAAAAT
1 TTTC-GTGTTTTCAAAAA
23313272 TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAA
23313289 AAAATCACGT
Statistics
Matches: 117, Mismatches: 12, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
16 13 0.11
17 42 0.36
18 35 0.30
19 10 0.09
20 17 0.15
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (17 bp):
TTTCGTGTTTTCAAAAA
Found at i:23313198 original size:19 final size:18
Alignment explanation
Indices: 23313176--23313216 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 18
23313166 TCATGTTTTC
23313176 AAAAATTCTCGTGTTTAAAA
1 AAAAATT-TCGTGTTT-AAA
23313196 AAAAATTTCGTGTTTCAAA
1 AAAAATTTCGTGTTT-AAA
23313215 AA
1 AA
23313217 TCCTCGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (18 bp):
AAAAATTTCGTGTTTAAA
Found at i:23313201 original size:20 final size:20
Alignment explanation
Indices: 23313176--23313216 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
23313166 TCATGTTTTC
23313176 AAAAATTCTCGTGTTT-AAAA
1 AAAAATT-TCGTGTTTCAAAA
23313196 AAAAATTTCGTGTTTCAAAA
1 AAAAATTTCGTGTTTCAAAA
23313216 A
1 A
23313217 TCCTCGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
AAAAATTTCGTGTTTCAAAA
Found at i:23313212 original size:36 final size:35
Alignment explanation
Indices: 23313130--23313288 Score: 164
Period size: 35 Copynumber: 4.5 Consensus size: 35
23313120 TTGGAAAATT
*
23313130 TTTCGTGTTTTC-AAAATTCTCGTGTTTCAAAAAG
1 TTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAAA
* *
23313164 TTTCATGTTTTCAAAAATTCTCGTGTTTAAAAAAAAA
1 TTTCGTGTTTTCAAAAATTCTCGTGTTT--CAAAAAA
* *
23313201 TTTCGTG-TTTCAAAAATCCTCGTGATTTTCTAAAAA
1 TTTCGTGTTTTCAAAAATTCTCGTG--TTTCAAAAAA
** *
23313237 TTTCCGTG-TTTCAAAAATT-TCGGTGTTTTGAAAAT
1 TTT-CGTGTTTTCAAAAATTCTC-GTGTTTCAAAAAA
23313272 TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAA
23313289 AAAATCACGT
Statistics
Matches: 106, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
34 15 0.14
35 34 0.32
36 26 0.25
37 28 0.26
38 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAAA
Found at i:23323585 original size:229 final size:229
Alignment explanation
Indices: 23323184--23323642 Score: 866
Period size: 229 Copynumber: 2.0 Consensus size: 229
23323174 ACGATGGAAA
*
23323184 GGGATTGCATTGGTTTCGCACGAAAGTGCCACAAATGTCAAATTTATGGTGATAAAATTCATGCA
1 GGGATTGCATTGGTTACGCACGAAAGTGCCACAAATGTCAAATTTATGGTGATAAAATTCATGCA
*
23323249 GCTCCGTCGCCCCTTCATGTCATGACTTCTCCGTGGCCTTTTTCTATGTGGGGCATGGATGTTAT
66 GCTCCGTCGCCCCTTCATGTCATGACTTCTCCGTGGCCTTTTTCTACGTGGGGCATGGATGTTAT
23323314 AGGGCCAATTTCCCCGAAAGCTTCCAATGGGCATCGATTCATCTTTGTGGTTATAGACTACTTCA
131 AGGGCCAATTTCCCCGAAAGCTTCCAATGGGCATCGATTCATCTTTGTGGTTATAGACTACTTCA
*
23323379 CAAAATGGGTAGAAGCCACTTCGTTTGCTAATGT
196 CAAAATAGGTAGAAGCCACTTCGTTTGCTAATGT
23323413 GGGATTGCATTGGTTACGCACGAAAGTGCCACAAATTGTCAAATTT-TGGTGATAAAATTCATGC
1 GGGATTGCATTGGTTACGCACGAAAGTGCCACAAA-TGTCAAATTTATGGTGATAAAATTCATGC
23323477 AGCTCCGTCGCCCCTTCATGTCATGACTTCTCCGTGGCCTTTTTCTACGTGGGGCATGGATGTTA
65 AGCTCCGTCGCCCCTTCATGTCATGACTTCTCCGTGGCCTTTTTCTACGTGGGGCATGGATGTTA
23323542 TAGGGCCAATTTCCCCGAAAGCTTCCAATGGGCATCGATTCATCTTTGTGGTTATAGACTACTTC
130 TAGGGCCAATTTCCCCGAAAGCTTCCAATGGGCATCGATTCATCTTTGTGGTTATAGACTACTTC
*
23323607 ACAAAATAGGTAGAAGCCATTTCGTTTGCTAATGT
195 ACAAAATAGGTAGAAGCCACTTCGTTTGCTAATGT
23323642 G
1 G
23323643 ACAAAGGCTG
Statistics
Matches: 225, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
229 215 0.96
230 10 0.04
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (229 bp):
GGGATTGCATTGGTTACGCACGAAAGTGCCACAAATGTCAAATTTATGGTGATAAAATTCATGCA
GCTCCGTCGCCCCTTCATGTCATGACTTCTCCGTGGCCTTTTTCTACGTGGGGCATGGATGTTAT
AGGGCCAATTTCCCCGAAAGCTTCCAATGGGCATCGATTCATCTTTGTGGTTATAGACTACTTCA
CAAAATAGGTAGAAGCCACTTCGTTTGCTAATGT
Found at i:23324388 original size:8 final size:8
Alignment explanation
Indices: 23324375--23324472 Score: 56
Period size: 8 Copynumber: 11.8 Consensus size: 8
23324365 TATTATGCTT
23324375 AAAAAACAA
1 AAAAAAC-A
*
23324384 AAAAAATA
1 AAAAAACA
*
23324392 GGAAAAAATA
1 --AAAAAACA
23324402 GAAAAAACAA
1 -AAAAAAC-A
23324412 AAAAAACA
1 AAAAAACA
**
23324420 GTCAAAAC-
1 -AAAAAACA
23324428 AAAAAACA
1 AAAAAACA
**
23324436 AAAAAAGG
1 AAAAAACA
23324444 AAAAAAC-
1 AAAAAACA
**
23324451 AAAAAAGG
1 AAAAAACA
23324459 AAAAAACA
1 AAAAAACA
23324467 AAAAAA
1 AAAAAA
23324473 AAGAAAAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
7 11 0.15
8 26 0.37
9 25 0.35
10 9 0.13
ACGTcount: A:0.81, C:0.08, G:0.08, T:0.03
Consensus pattern (8 bp):
AAAAAACA
Found at i:23324389 original size:9 final size:9
Alignment explanation
Indices: 23324375--23324473 Score: 51
Period size: 9 Copynumber: 10.7 Consensus size: 9
23324365 TATTATGCTT
23324375 AAAAAACAA
1 AAAAAACAA
* *
23324384 AAAAAATAGG
1 AAAAAACA-A
* *
23324394 AAAAAATAG
1 AAAAAACAA
23324403 AAAAAACAA
1 AAAAAACAA
*
23324412 AAAAAACAG
1 AAAAAACAA
**
23324421 TCAAAACAA
1 AAAAAACAA
23324430 AAAACAA-AA
1 AAAA-AACAA
23324439 AAAGGAAA-AA
1 AAA--AAACAA
*
23324449 ACAAAAA-AGG
1 A-AAAAACA-A
23324459 AAAAAACAA
1 AAAAAACAA
23324468 AAAAAA
1 AAAAAA
23324474 AGAAAAAATC
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
9 51 0.72
10 17 0.24
11 3 0.04
ACGTcount: A:0.81, C:0.08, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAACAA
Found at i:23324426 original size:28 final size:25
Alignment explanation
Indices: 23324375--23324456 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 25
23324365 TATTATGCTT
* *
23324375 AAAAAACAAAAAAAATAGGAAAAAATAG
1 AAAAAACAAAAAAAACAGG--AAAA-AC
**
23324403 AAAAAACAAAAAAAACAGTCAAAAC
1 AAAAAACAAAAAAAACAGGAAAAAC
23324428 AAAAAAC--AAAAAA-AGGAAAAAAC
1 AAAAAACAAAAAAAACAGG-AAAAAC
23324451 AAAAAA
1 AAAAAA
23324457 GGAAAAAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.04
23 17 0.36
25 8 0.17
26 3 0.06
28 17 0.36
ACGTcount: A:0.80, C:0.09, G:0.07, T:0.04
Consensus pattern (25 bp):
AAAAAACAAAAAAAACAGGAAAAAC
Found at i:23324447 original size:16 final size:16
Alignment explanation
Indices: 23324428--23324472 Score: 83
Period size: 15 Copynumber: 2.9 Consensus size: 16
23324418 CAGTCAAAAC
23324428 AAAAAACAAAAAAAGG
1 AAAAAACAAAAAAAGG
23324444 AAAAAAC-AAAAAAGG
1 AAAAAACAAAAAAAGG
23324459 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
23324473 AAGAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAAGG
Found at i:23324479 original size:8 final size:8
Alignment explanation
Indices: 23324428--23324481 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
23324418 CAGTCAAAAC
*
23324428 AAAAAACA
1 AAAAAAGA
*
23324436 AAAAAAGG
1 AAAAAAGA
*
23324444 AAAAAACA
1 AAAAAAGA
*
23324452 AAAAAGGA
1 AAAAAAGA
*
23324460 AAAAACAAA
1 AAAAA-AGA
23324469 AAAAAAGA
1 AAAAAAGA
23324477 AAAAA
1 AAAAA
23324482 TCAAGATGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
8 30 0.83
9 6 0.17
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:23324479 original size:16 final size:17
Alignment explanation
Indices: 23324375--23324481 Score: 80
Period size: 16 Copynumber: 6.4 Consensus size: 17
23324365 TATTATGCTT
23324375 AAAAAACAAAAAAAATAGG
1 AAAAAACAAAAAAAA-A-G
*
23324394 AAAAAATAGAAAAAACAA-
1 AAAAAACA-AAAAAA-AAG
*** *
23324412 AAAAAAC-AGTCAAAAC
1 AAAAAACAAAAAAAAAG
*
23324428 AAAAAAC-AAAAAAAGG
1 AAAAAACAAAAAAAAAG
*
23324444 AAAAAAC--AAAAAAGG
1 AAAAAACAAAAAAAAAG
23324459 AAAAAACAAAAAAAAAG
1 AAAAAACAAAAAAAAAG
23324476 AAAAAA
1 AAAAAA
23324482 TCAAGATGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
15 17 0.24
16 21 0.29
17 13 0.18
18 6 0.08
19 7 0.10
20 7 0.10
21 1 0.01
ACGTcount: A:0.81, C:0.07, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAG
Found at i:23325850 original size:79 final size:80
Alignment explanation
Indices: 23325719--23326530 Score: 998
Period size: 79 Copynumber: 10.2 Consensus size: 80
23325709 NNNNNNNNNN
23325719 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
23325784 TCATAATAC-AGAGG
66 TCATAATACGAGAGG
23325798 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
23325863 TCATAATAC-AGAGG
66 TCATAATACGAGAGG
23325877 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
23325942 TCATAATAC-AGAGG
66 TCATAATACGAGAGG
23325956 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
23326021 TCATAATAC-AGAGG
66 TCATAATACGAGAGG
* *
23326035 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAA-ATCT-CTGTTTTTCAAAAAAAATCA
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCT-TTTTTC-AAAAAAATCA
* * *
23326098 ACTCATATTGCGAGAAG
64 ACTCATAATACGAGAGG
* *
23326115 TGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTAAATTTCT--ATTTTTCAAAAAAAAA
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTATTT-TTTTTAATTTCTGCTTTTTTC---AAAAAA
*
23326178 ATCAACTCATATTAC-AGAGG
60 ATCAACTCATAATACGAGAGG
* * *
23326198 TGAGTTGAGCATCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTGTTTTTTTC-AAAAAATCAA
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTTAATTTCTGCTTTTTTCAAAAAAATCAA
* *
23326262 CTCATATTGCGAGAGG
65 CTCATAATACGAGAGG
*** * * * *
23326278 TGAGTTGAGCCTCGAACCATGCCGAGGTATTTCTTTTATATTTCTG-TTTTTT----TAAATCAA
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTA-ATTTCTGCTTTTTTCAAAAAAATCAA
* *
23326338 CTCATATTGCGAGAGG
65 CTCATAATACGAGAGG
* * * * * **
23326354 TGAGTTGAACCTC-GGACACATGCCGAGGTATTTCGTTTAAATTTCTG--TTTTAAAAAAAAATC
1 TGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTT-TTTTTAATTTCTGCTTTTTTCAAAAAAATC
*
23326416 AACTCATAATGCGAGAGG
63 AACTCATAATACGAGAGG
* *
23326434 TGAGTTGAGCCTCGAGTCACATGCCGAGGTATTTTCTTTTAAATTTCTG--TTTTTCAAAAAAAA
1 TGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTT-TTTT-AATTTCTGCTTTTTTC--AAAAAA
* * *
23326497 ATCAACTCATATTGCGAGAAG
60 ATCAACTCATAATACGAGAGG
23326518 TGAGTTGAGCCTC
1 TGAGTTGAGCCTC
23326531 AGGCCACACG
Statistics
Matches: 666, Mismatches: 42, Indels: 45
0.88 0.06 0.06
Matches are distributed among these distances:
75 2 0.00
76 39 0.06
77 21 0.03
78 13 0.02
79 323 0.48
80 93 0.14
81 49 0.07
82 33 0.05
83 31 0.05
84 62 0.09
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (80 bp):
TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAAATCAAC
TCATAATACGAGAGG
Found at i:23326780 original size:30 final size:29
Alignment explanation
Indices: 23326739--23326852 Score: 133
Period size: 29 Copynumber: 3.9 Consensus size: 29
23326729 AAAAAATAAA
* *
23326739 AAATTATATTTTGACCCCCTAAACTTTTTG
1 AAATTACATTTTGA-CCCATAAACTTTTTG
* * *
23326769 AAATTGCATTTTAAACCC-TAAA-TTTTCCTA
1 AAATTACATTTT-GACCCATAAACTTTT--TG
23326799 AAATTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTGACCCATAAACTTTTTG
23326828 AAATTACATTTTGACCCATAAACTT
1 AAATTACATTTTGACCCATAAACTT
23326853 CCTCAAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.06
29 34 0.47
30 29 0.40
31 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGACCCATAAACTTTTTG
Found at i:23326861 original size:59 final size:60
Alignment explanation
Indices: 23326738--23326863 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 60
23326728 CAAAAAATAA
* * * *
23326738 AAAATTATATTTTGACCCCCTAAACTTTTTGAAATTGCATTTTAAACCCTAAATTTTCCT
1 AAAATTACATTTTGACCCCATAAACTTTTTGAAATTACATTTTAAACCCTAAATCTTCCT
*
23326798 AAAATTACATTTTGA-CCCATAAACTTTTTGAAATTACATTTT-GACCCATAAA-CTTCCT
1 AAAATTACATTTTGACCCCATAAACTTTTTGAAATTACATTTTAAACCC-TAAATCTTCCT
23326856 CAAAATTA
1 -AAAATTA
23326864 TGTTTCAGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
58 9 0.15
59 36 0.61
60 14 0.24
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCATAAACTTTTTGAAATTACATTTTAAACCCTAAATCTTCCT
Found at i:23326881 original size:59 final size:58
Alignment explanation
Indices: 23326754--23326884 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 58
23326744 ATATTTTGAC
* * * *
23326754 CCCCTAAACTTTTTGAAATTGCATTTTAAACCCTAAATTTTCCTAAAATTACATTTTG
1 CCCCAAAACTTTTTGAAATTACATTTTAAACCCTAAATCTTCCTAAAATTACATTTAG
* * **
23326812 ACCCATAAACTTTTTGAAATTACATTTT-GACCCATAAA-CTTCCTCAAAATTATGTTTCAG
1 CCCCA-AAACTTTTTGAAATTACATTTTAAACCC-TAAATCTTCCT-AAAATTACATTT-AG
23326872 CCCCAAAACTTTT
1 CCCCAAAACTTTT
23326885 GCTGCATTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 12 0.20
59 43 0.72
60 5 0.08
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (58 bp):
CCCCAAAACTTTTTGAAATTACATTTTAAACCCTAAATCTTCCTAAAATTACATTTAG
Found at i:23327350 original size:21 final size:21
Alignment explanation
Indices: 23327306--23327377 Score: 108
Period size: 21 Copynumber: 3.3 Consensus size: 21
23327296 AGTCGGGTCA
23327306 ACCCGACCCGACCGAATCGATCCG
1 ACCCGACCC-ACCG-AT-GATCCG
23327330 ACCCGACCCACCGATGATCCG
1 ACCCGACCCACCGATGATCCG
*
23327351 ACCCGACCCACCGACGATCCG
1 ACCCGACCCACCGATGATCCG
23327372 ACCCGA
1 ACCCGA
23327378 ACAGCAACCC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
21 32 0.68
22 2 0.04
23 4 0.09
24 9 0.19
ACGTcount: A:0.25, C:0.49, G:0.19, T:0.07
Consensus pattern (21 bp):
ACCCGACCCACCGATGATCCG
Found at i:23327575 original size:10 final size:10
Alignment explanation
Indices: 23327560--23327609 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
23327550 CCAGCATGCC
23327560 AGAAAAAAAA
1 AGAAAAAAAA
23327570 AGAAAAAAGAA
1 AGAAAAAA-AA
* *
23327581 GAGGAAAAAAG
1 -AGAAAAAAAA
23327592 AGAAAAAAAA
1 AGAAAAAAAA
23327602 AGAAAAAA
1 AGAAAAAA
23327610 GAAAAAGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 24 0.71
11 3 0.09
12 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:23327577 original size:7 final size:7
Alignment explanation
Indices: 23327565--23327615 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
23327555 ATGCCAGAAA
23327565 AAAAAAG
1 AAAAAAG
23327572 AAAAAAG
1 AAAAAAG
* *
23327579 -AAGAGG
1 AAAAAAG
23327585 AAAAAAG
1 AAAAAAG
*
23327592 -AGAAA-
1 AAAAAAG
23327597 AAAAAAG
1 AAAAAAG
23327604 AAAAAAG
1 AAAAAAG
23327611 AAAAA
1 AAAAA
23327616 GGGGCCCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:23327590 original size:22 final size:22
Alignment explanation
Indices: 23327563--23327604 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23327553 GCATGCCAGA
*
23327563 AAAAAAAAGAAAAAAGAAGAGG
1 AAAAAAAAGAAAAAAAAAGAGG
*
23327585 AAAAAAGAGAAAAAAAAAGA
1 AAAAAAAAGAAAAAAAAAGA
23327605 AAAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAAAAGAGG
Found at i:23327952 original size:17 final size:18
Alignment explanation
Indices: 23327918--23327958 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
23327908 ACGTCCTTTT
23327918 AAAAATTGTAAATATTCAA
1 AAAAATTGT-AATATTCAA
*
23327937 AAAAATTGT-ATTTTCAA
1 AAAAATTGTAATATTCAA
23327954 AAAAA
1 AAAAA
23327959 ATCCTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAATTGTAATATTCAA
Found at i:23328184 original size:18 final size:18
Alignment explanation
Indices: 23328119--23328281 Score: 128
Period size: 17 Copynumber: 9.3 Consensus size: 18
23328109 ATAAAATTGG
*
23328119 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
23328137 -AAAATTCCCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
23328153 AAAAGTT-TCATGTTTTC
1 AAAAATTCTCGTGTTTTC
*
23328170 AAAAATTCTCGTGTTTTAA
1 AAAAATTCTCGTGTTTT-C
*
23328189 AAAAAAT-TCGTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
23328205 AAAAATCCTCATGATTTTC
1 AAAAATTCTCGTG-TTTTC
23328224 TAAAAAGTTCT-GTG-TTTC
1 -AAAAA-TTCTCGTGTTTTC
23328242 AAAAATT-TCGGTGTTTT-
1 AAAAATTCTC-GTGTTTTC
* *
23328259 GAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
23328277 AAAAA
1 AAAAA
23328282 AAATAAATTT
Statistics
Matches: 114, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
15 1 0.01
16 14 0.12
17 53 0.46
18 26 0.23
19 10 0.09
20 7 0.06
21 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:23328239 original size:37 final size:36
Alignment explanation
Indices: 23328153--23328247 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 36
23328143 CCCGTGTTTC
* *
23328153 AAAAGTTTCATGT-TTTCAAAAATTCTCGTGTTTTAAA
1 AAAAG-TTC-TGTGTTTCAAAAATCCTCATGTTTTAAA
* **
23328190 AAAAATTC-GTGTTTCAAAAATCCTCATGATTTTCTA
1 AAAAGTTCTGTGTTTCAAAAATCCTCATG-TTTTAAA
23328226 AAAAGTTCTGTGTTTCAAAAAT
1 AAAAGTTCTGTGTTTCAAAAAT
23328248 TTCGGTGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.04
35 15 0.31
36 15 0.31
37 17 0.35
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (36 bp):
AAAAGTTCTGTGTTTCAAAAATCCTCATGTTTTAAA
Found at i:23337534 original size:25 final size:25
Alignment explanation
Indices: 23337505--23337552 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
23337495 AGTATATCTA
23337505 TTTAAACTATTTTATTAA-ATTTTAT
1 TTTAAACTATTTT-TTAATATTTTAT
**
23337530 TTTAATTTATTTTTTAATATTTT
1 TTTAAACTATTTTTTAATATTTT
23337553 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTAAACTATTTTTTAATATTTTAT
Found at i:23338661 original size:32 final size:32
Alignment explanation
Indices: 23338632--23338692 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
23338622 TCTTTTTGCT
*
23338632 ATTGT-ATTGTTGATTTG-ATCATTTGTTTTGG
1 ATTGTGATT-TTGATTTGAATAATTTGTTTTGG
*
23338663 ATTTTGATTTTGATTTGAATAATTTGTTTT
1 ATTGTGATTTTGATTTGAATAATTTGTTTT
23338693 TACAGTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.20, C:0.02, G:0.18, T:0.61
Consensus pattern (32 bp):
ATTGTGATTTTGATTTGAATAATTTGTTTTGG
Found at i:23347297 original size:99 final size:98
Alignment explanation
Indices: 23347127--23347324 Score: 360
Period size: 99 Copynumber: 2.0 Consensus size: 98
23347117 TGGATGGCAG
* *
23347127 ATTGTTGGAGATGAAAAGAGAAAAGTCAAAGATACTTTATAACCATAAGAATAAAACAAATTCAC
1 ATTGTTGGAGATGAAAAGAGAAAAGTCAAAGATACTTCATAACCATAAGAATAAAACAAACTCAC
23347192 GATAATTTCCTAATATATCAATTATGAATCTTC
66 GATAATTTCCTAATATATCAATTATGAATCTTC
*
23347225 ATTGTTGGAGATGCAAAAGGGAAAAGTCAAAGATACTTCATAACCATAAGAATAAAACAAACTCA
1 ATTGTTGGAGATG-AAAAGAGAAAAGTCAAAGATACTTCATAACCATAAGAATAAAACAAACTCA
23347290 CGATAATTTCCTAATATATCAATTATGAATCTTC
65 CGATAATTTCCTAATATATCAATTATGAATCTTC
23347324 A
1 A
23347325 ATAGTGACGG
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 13 0.14
99 83 0.86
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (98 bp):
ATTGTTGGAGATGAAAAGAGAAAAGTCAAAGATACTTCATAACCATAAGAATAAAACAAACTCAC
GATAATTTCCTAATATATCAATTATGAATCTTC
Found at i:23349111 original size:21 final size:21
Alignment explanation
Indices: 23349086--23349126 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
23349076 GCGATGGCAC
23349086 CACCTCCACAGTATGCTGCTG
1 CACCTCCACAGTATGCTGCTG
*
23349107 CACCTCCACATTATGCTGCT
1 CACCTCCACAGTATGCTGCT
23349127 CCTTACCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.39, G:0.15, T:0.27
Consensus pattern (21 bp):
CACCTCCACAGTATGCTGCTG
Found at i:23349178 original size:78 final size:78
Alignment explanation
Indices: 23349049--23349192 Score: 261
Period size: 78 Copynumber: 1.8 Consensus size: 78
23349039 TTGTCCTGAC
*
23349049 CCTTACCCTCCTCAAGGTTATCCCCCAGCGATGGCACCACCTCCACAGTATGCTGCTGCACCTCC
1 CCTTACCCTCCTCAAGGTTATCCCCCAGCGATGGCACCACCTCCACAGTATGCTGCTCCACCTCC
23349114 ACATTATGCTGCT
66 ACATTATGCTGCT
* *
23349127 CCTTACCCTGCTCAAGGTTATCCCCCAGTGATGGCACCACCTCCACAGTATGCTGCTCCACCTCC
1 CCTTACCCTCCTCAAGGTTATCCCCCAGCGATGGCACCACCTCCACAGTATGCTGCTCCACCTCC
23349192 A
66 A
23349193 AGGCCTGGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.19, C:0.42, G:0.15, T:0.24
Consensus pattern (78 bp):
CCTTACCCTCCTCAAGGTTATCCCCCAGCGATGGCACCACCTCCACAGTATGCTGCTCCACCTCC
ACATTATGCTGCT
Found at i:23350733 original size:23 final size:24
Alignment explanation
Indices: 23350707--23350755 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
23350697 GTGACATGTT
* *
23350707 ATTATT-CACTGATGGTACATAAA
1 ATTATTACACCGACGGTACATAAA
*
23350730 ATTATTACACCGACGGTGCATAAA
1 ATTATTACACCGACGGTACATAAA
23350754 AT
1 AT
23350756 ATTGTTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (24 bp):
ATTATTACACCGACGGTACATAAA
Found at i:23352449 original size:12 final size:11
Alignment explanation
Indices: 23352421--23352488 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 11
23352411 GCAATTTTTT
23352421 TATTTTTAAAA
1 TATTTTTAAAA
23352432 TATTTTTAAAA
1 TATTTTTAAAA
***
23352443 TACTTTTTTATTTTGT
1 TA--TTTTTA---AAA
23352459 TATTTTTAAAA
1 TATTTTTAAAA
23352470 TATTTTTAAAA
1 TATTTTTAAAA
23352481 TACTTTTT
1 TA-TTTTT
23352489 TTATTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
11 26 0.58
12 5 0.11
13 6 0.13
14 6 0.13
16 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:23352465 original size:38 final size:39
Alignment explanation
Indices: 23352414--23352495 Score: 148
Period size: 38 Copynumber: 2.1 Consensus size: 39
23352404 GGCTTGGGCA
*
23352414 ATTTTTTTATTTTTAAAATATTTTTAAAATAC-TTTTTT
1 ATTTTGTTATTTTTAAAATATTTTTAAAATACTTTTTTT
23352452 ATTTTGTTATTTTTAAAATATTTTTAAAATACTTTTTTT
1 ATTTTGTTATTTTTAAAATATTTTTAAAATACTTTTTTT
23352491 ATTTT
1 ATTTT
23352496 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 31 0.74
39 11 0.26
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (39 bp):
ATTTTGTTATTTTTAAAATATTTTTAAAATACTTTTTTT
Found at i:23352545 original size:15 final size:16
Alignment explanation
Indices: 23352525--23352554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23352515 TTTAAAAAAT
23352525 GGGTCGGGC-CGGGCC
1 GGGTCGGGCTCGGGCC
23352540 GGGTCGGGCTCGGGC
1 GGGTCGGGCTCGGGC
23352555 TTATGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.30, G:0.60, T:0.10
Consensus pattern (16 bp):
GGGTCGGGCTCGGGCC
Found at i:23353023 original size:19 final size:17
Alignment explanation
Indices: 23352978--23353026 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
23352968 AAAATATATA
*
23352978 AAAATGTTAAATTTTTT
1 AAAATTTTAAATTTTTT
23352995 AATAACTTTTAAATTTTTTGT
1 AA-AA-TTTTAAA-TTTTT-T
23353016 AAAATTTTAAA
1 AAAATTTTAAA
23353027 AATTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 13 0.48
20 7 0.26
21 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
AAAATTTTAAATTTTTT
Found at i:23356510 original size:25 final size:25
Alignment explanation
Indices: 23356482--23356534 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
23356472 AAAATTTGCC
*
23356482 TTTAATGAAAATATAATATTTTAAT
1 TTTAATGAAAATAAAATATTTTAAT
* * *
23356507 TTTAATTAATATAAAATATTTTACT
1 TTTAATGAAAATAAAATATTTTAAT
23356532 TTT
1 TTT
23356535 TCGTTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTAATGAAAATAAAATATTTTAAT
Found at i:23364759 original size:33 final size:33
Alignment explanation
Indices: 23364715--23364834 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
23364705 GAAAGTTAGA
* *
23364715 AAGATGGGTATAAATACCTTCTACGGGAGAAAG
1 AAGAAGGGTATAAACACCTTCTACGGGAGAAAG
23364748 AAGAAGGGTATAAACA-C--CTACGGGAGAAAG
1 AAGAAGGGTATAAACACCTTCTACGGGAGAAAG
*
23364778 AAGAAGGGTTTAAACACCTTCTACGGGAGAAAG
1 AAGAAGGGTATAAACACCTTCTACGGGAGAAAG
*
23364811 AAGAAGGGTATAAAAACCTTCTAC
1 AAGAAGGGTATAAACACCTTCTAC
23364835 TGGGTGATGA
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
30 28 0.35
31 1 0.01
32 1 0.01
33 49 0.62
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.17
Consensus pattern (33 bp):
AAGAAGGGTATAAACACCTTCTACGGGAGAAAG
Found at i:23371581 original size:39 final size:39
Alignment explanation
Indices: 23371529--23371695 Score: 316
Period size: 39 Copynumber: 4.3 Consensus size: 39
23371519 AGAGCCGAAT
*
23371529 GATGTAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
1 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
23371568 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
1 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
23371607 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
1 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
23371646 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
1 GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
*
23371685 GATGGAGTAGA
1 GATGAAGTAGA
23371696 GCCGAAGTTG
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 126 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (39 bp):
GATGAAGTAGAAGATGAAAAGCCGAAGCCAGGAGCTGTC
Found at i:23374968 original size:3 final size:3
Alignment explanation
Indices: 23374960--23374994 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23374950 AATCTCACTC
23374960 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
23374995 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:23376049 original size:16 final size:16
Alignment explanation
Indices: 23376012--23376055 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
23376002 TTTCTTTCCC
*
23376012 CTGTTTCGTTTGCTTCT
1 CTGTTTC-TTTTCTTCT
23376029 CTGTTTCTTTTCTTCT
1 CTGTTTCTTTTCTTCT
*
23376045 TTGTTTCTTTT
1 CTGTTTCTTTT
23376056 TTTTACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.00, C:0.20, G:0.11, T:0.68
Consensus pattern (16 bp):
CTGTTTCTTTTCTTCT
Found at i:23376120 original size:16 final size:17
Alignment explanation
Indices: 23376090--23376122 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23376080 TTGTTTATTA
*
23376090 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
23376107 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
23376123 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:23378769 original size:50 final size:47
Alignment explanation
Indices: 23378714--23378844 Score: 189
Period size: 50 Copynumber: 2.8 Consensus size: 47
23378704 ATTATCTCTG
*
23378714 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTTACTTGTCACTT
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCAC---TTACTTGTCACTA
23378764 ATCAGATAAGTGTAGCTAAGCTACCACTTAT--C--ACTTGTCACTA
1 ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTACTTGTCACTA
23378807 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTA
1 ATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTA
23378845 TCACTGATCA
Statistics
Matches: 75, Mismatches: 1, Indels: 12
0.85 0.01 0.14
Matches are distributed among these distances:
43 27 0.36
44 14 0.19
46 1 0.01
48 2 0.03
50 31 0.41
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (47 bp):
ATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTACTTGTCACTA
Found at i:23378800 original size:43 final size:44
Alignment explanation
Indices: 23378753--23378856 Score: 174
Period size: 44 Copynumber: 2.4 Consensus size: 44
23378743 ATCACTTGTT
*
23378753 ACTTGTCACTTATCAGATAAGTGTAGCT-AAGCTACCACTTATC
1 ACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATC
23378796 ACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATC
1 ACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATC
* *
23378840 ACTTATCACTGATCAGA
1 ACTTGTCACTAATCAGA
23378857 AGTACTCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 27 0.47
44 30 0.53
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (44 bp):
ACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTATC
Found at i:23382577 original size:24 final size:24
Alignment explanation
Indices: 23382563--23382672 Score: 102
Period size: 24 Copynumber: 4.7 Consensus size: 24
23382553 AAATATGAGA
23382563 TAACTTT-AAATAATAATACATAG
1 TAACTTTAAAATAATAATACATAG
* *
23382586 TAACTTTAAAATAATAATACACAA
1 TAACTTTAAAATAATAATACATAG
* * *
23382610 TAATTTTAAAACAATAATACATAA
1 TAACTTTAAAATAATAATACATAG
* * *
23382634 TAGA-TTTAAAACAA-CATACATAA
1 TA-ACTTTAAAATAATAATACATAG
23382657 TGAAC-TTAAAATAATA
1 T-AACTTTAAAATAATA
23382673 TAACACCAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
23 25 0.34
24 48 0.65
25 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (24 bp):
TAACTTTAAAATAATAATACATAG
Found at i:23382580 original size:23 final size:22
Alignment explanation
Indices: 23382547--23382604 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
23382537 ATTAAAACAA
23382547 TAAAAT-A-AATATGAGATAACTT
1 TAAAATAATAATAT-AG-TAACTT
23382569 T-AAATAATAATACATAGTAACTT
1 TAAAATAATAAT--ATAGTAACTT
23382592 TAAAATAATAATA
1 TAAAATAATAATA
23382605 CACAATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 10 0.32
24 12 0.39
25 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAAATAATAATATAGTAACTT
Found at i:23384951 original size:17 final size:17
Alignment explanation
Indices: 23384907--23384950 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
23384897 TTTCATTTAA
*
23384907 AATAATTTCCTATTTTTT
1 AATAATTT-TTATTTTTT
23384925 AATAATTTTTATTTTTT
1 AATAATTTTTATTTTTT
23384942 AA-AATTTTT
1 AATAATTTTT
23384951 TGAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 8 0.32
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
AATAATTTTTATTTTTT
Found at i:23389200 original size:33 final size:33
Alignment explanation
Indices: 23389158--23389238 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
23389148 AAGGGTATAA
*
23389158 ATAAACACCTTCTTCGGGAGAAAGAAGAAGGGT
1 ATAAACACCTTCTACGGGAGAAAGAAGAAGGGT
*
23389191 TTAAACACCTTCTACGGGAGAAAGAAGAAGGGT
1 ATAAACACCTTCTACGGGAGAAAGAAGAAGGGT
*
23389224 ATAAAAACCTTCTAC
1 ATAAACACCTTCTAC
23389239 TGGGTGATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (33 bp):
ATAAACACCTTCTACGGGAGAAAGAAGAAGGGT
Found at i:23389670 original size:29 final size:31
Alignment explanation
Indices: 23389637--23389698 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
23389627 AAATTTAGAA
23389637 TTTATTTAT-TATACTTTT-A-ATTTCAAAAT
1 TTTATTT-TCTATACTTTTCAGATTTCAAAAT
* *
23389666 TTTATTTTCTTTATTTTTCAGATTTCAAAAT
1 TTTATTTTCTATACTTTTCAGATTTCAAAAT
23389697 TT
1 TT
23389699 AGGTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 14 0.50
30 1 0.04
31 12 0.43
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTATACTTTTCAGATTTCAAAAT
Found at i:23390791 original size:20 final size:21
Alignment explanation
Indices: 23390766--23390819 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
23390756 TTGAATAAGG
23390766 TATTTTTAAATTTAAATT-AA
1 TATTTTTAAATTTAAATTAAA
* *
23390786 TATTTTT-ATTTTAATTTAAA
1 TATTTTTAAATTTAAATTAAA
23390806 TATTTTTAATATTT
1 TATTTTTAA-ATTT
23390820 CATTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 1 0.04
22 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAATTTAAATTAAA
Found at i:23393169 original size:59 final size:61
Alignment explanation
Indices: 23393098--23393214 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 61
23393088 CTCATTTTAA
* * * *
23393098 TATTAAATTAATATAATATTTAT-A-AAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATAACAAGATAAACATTAAATTAAATTTAATATTAAATCT
23393157 TATTAAAATAATAGAATATTTATCAACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTAT-AACAAGATAAACATTAAATTAAATTTAATATTAA
23393215 GATAATTACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.41
61 1 0.02
62 29 0.57
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (61 bp):
TATTAAAATAATAGAATATTTATAACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:23393240 original size:20 final size:18
Alignment explanation
Indices: 23393193--23393241 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
23393183 CAAGATAAAC
23393193 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
23393210 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
23393230 ATTAAATTAATA
1 ATTAAATTAATA
23393242 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 4 0.15
20 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:23395496 original size:31 final size:31
Alignment explanation
Indices: 23395458--23395527 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
23395448 AACAAGGATG
*
23395458 CATTTGAGCATTTGATGCAATATATAGATTA
1 CATTTGAGCATTTGATGCAATATATAAATTA
23395489 CATTTGAGCATTTGATGCAATATATAAATTA
1 CATTTGAGCATTTGATGCAATATATAAATTA
23395520 CATTTGAG
1 CATTTGAG
23395528 GGCTTCTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (31 bp):
CATTTGAGCATTTGATGCAATATATAAATTA
Found at i:23398146 original size:12 final size:12
Alignment explanation
Indices: 23398129--23398154 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23398119 AGTTTAGCTC
23398129 GGGAACTCTAAT
1 GGGAACTCTAAT
23398141 GGGAACTCTAAT
1 GGGAACTCTAAT
23398153 GG
1 GG
23398155 TATCATCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (12 bp):
GGGAACTCTAAT
Found at i:23400110 original size:21 final size:21
Alignment explanation
Indices: 23400070--23400108 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
23400060 TTTCGATTCG
23400070 CTTTTTATCTTCTTTATTTTC
1 CTTTTTATCTTCTTTATTTTC
23400091 CTTTTTAT-TT-TTTATTTT
1 CTTTTTATCTTCTTTATTTT
23400109 TTACTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (21 bp):
CTTTTTATCTTCTTTATTTTC
Found at i:23418366 original size:44 final size:44
Alignment explanation
Indices: 23418299--23418639 Score: 180
Period size: 44 Copynumber: 7.8 Consensus size: 44
23418289 GAAGAATTTT
* *
23418299 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* **
23418343 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCCAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * * * *
23418386 CTATCTTATCTCCCTGA-AGTTACAGTGGAGCGGCTT-AAAATTTAG
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGA--CAG
* * * * * * * *
23418431 -GATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCA-TCTG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * ** * *
23418473 -G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAATTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA--G
* * * * *
23418517 AGGTCTTATCTCTCTAAGATTACAGCGGAGCAGATTGAAGATA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * * * * *
23418560 ATAATCCTATCTCCCTGAAATTACAGTGGAGCGGATT-AAAATAA
1 A-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * *
23418604 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT
23418640 CACATCAGAT
Statistics
Matches: 226, Mismatches: 57, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
41 32 0.14
42 6 0.03
43 35 0.15
44 119 0.53
45 2 0.01
46 32 0.14
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
Found at i:23418447 original size:87 final size:88
Alignment explanation
Indices: 23418305--23418814 Score: 360
Period size: 87 Copynumber: 5.7 Consensus size: 88
23418295 TTTTAGATCT
* * * ** *
23418305 TATCTCCCTGAGGTTACAGTGGAGCAGATT-GAAGCCAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTCAG-GATCTTATCTCTCTGAGATTACAGC
*
23418369 GGAGCAGATCCAAGACACT-ATCT
65 GGAGCAGATCCAAGACACTAATCC
* * * **
23418392 TATCTCCCTGAAGTTACAGTGGAGCGGCTTAAAATTTAGGATCTTATCTCTCTGAGGTTACAGTA
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTCAGGATCTTATCTCTCTGAGATTACAGCG
* ** *
23418457 GAGTAGAT-C--G-CATCTGGTCT
66 GAGCAGATCCAAGACA-CTAATCC
* ** ** *
23418477 TATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAATTCAGG-TCTTATCTCTCTAAGATTACA
1 TATCTCCCTGAAGTTACAGTGGAGCGGA--TTA-AAATTCAGGATCTTATCTCTCTGAGATTACA
** * *
23418541 GCGGAGCAGATTGAAGATAATAATCC
63 GCGGAGCAGATCCAAGACACTAATCC
* ** *
23418567 TATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTCAGGATCTTATCTCTCTGAGA-TTACAGC
* * *
23418631 AGAGTAGATCACATCAGATTGAAGCCGATAATCC
65 GGAGCAGATC-CA--AGA---CA--C--TAATCC
* * *
23418665 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTTAGGATCTTATCTCCCTGAGATTATAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTCAGGATCTTATCTCTCTGAGATTACAGCG
**
23418730 GAGCAGATGGAAGACACT-ATCC
66 GAGCAGATCCAAGACACTAATCC
* * *** **
23418752 TATC-CCCTTG-AGATTTCAGTAGAATAGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACA
1 TATCTCCC-TGAAG-TTACAGTGGAGCGGATTAAAATTCAGGATCTTATCTCTCTGAGA-TTACA
23418814 G
63 G
23418815 TAGAGTAGAT
Statistics
Matches: 330, Mismatches: 67, Indels: 52
0.73 0.15 0.12
Matches are distributed among these distances:
83 2 0.01
84 3 0.01
85 27 0.08
86 7 0.02
87 141 0.43
88 40 0.12
89 1 0.00
90 29 0.09
91 4 0.01
92 1 0.00
94 1 0.00
95 3 0.01
97 1 0.00
98 69 0.21
99 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (88 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATTCAGGATCTTATCTCTCTGAGATTACAGCG
GAGCAGATCCAAGACACTAATCC
Found at i:23418527 original size:131 final size:130
Alignment explanation
Indices: 23418296--23418547 Score: 289
Period size: 131 Copynumber: 1.9 Consensus size: 130
23418286 ACCGAAGAAT
* *
23418296 TTTAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAG
1 TTTAGATCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGAAGCCAGAGATCTTATCTCCCTGAG
* *
23418361 ATTACAGCGGAGCAGATCCAAGACACTATCTTATCTCCCTGAAG-TTACAGTGGAGCGGCTTAAA
66 ATTACAGCGGAGCAGATCCAAGAAACTATCTTATCTCCCT-AAGATTACAGCGGAGCGGCTTAAA
23418425 A
130 A
* * * * *
23418426 TTTAGGATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCA-TCTG-G-TCTTATCTCCCTGA
1 TTTA-GATCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGAAGCCAGAGATCTTATCTCCCTGA
* * * * *
23418488 GGTTACAGTGGAGTAGA-CCGAAGAAATTCAGGTCTTATCTCTCTAAGATTACAGCGGAGC
65 GATTACAGCGGAGCAGATCC-AAGAAACT-A--TCTTATCTCCCTAAGATTACAGCGGAGC
23418548 AGATTGAAGA
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
127 2 0.02
128 34 0.33
129 2 0.02
130 9 0.09
131 55 0.54
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (130 bp):
TTTAGATCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGAAGCCAGAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATCCAAGAAACTATCTTATCTCCCTAAGATTACAGCGGAGCGGCTTAAAA
Found at i:23418601 original size:175 final size:172
Alignment explanation
Indices: 23418302--23418825 Score: 514
Period size: 175 Copynumber: 3.0 Consensus size: 172
23418292 GAATTTTAGA
** ** * *
23418302 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCTAAGATTACA
* * * * **
23418367 GCGGAGCAGATCCAAGACACTATCTTATCTCCCTGAAGTTACAGTGGAGCGGCTTAAAATTTAGG
66 GCGGAGCAGATCCAAGACAATATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGG
* *
23418432 ATCTTATCTCTCTGAGGTTACAGTAGAGTAGATCGCATCTGG
131 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCTGG
* * *
23418474 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAATTCAGGTCTTATCTCTCTAAGATTA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAA--CAGATCTTATCTCCCTAAGATTA
** *
23418539 CAGCGGAGCAGATTGAAGATAATAATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAA
64 CAGCGGAGCAGATCCAAGACAAT-ATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAA
23418604 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGATTGAAGCCG
128 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATC----T---G--G
* * * ** ** *
23418658 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AATTTAGGATCTTATCTCCCTGAG
1 ----TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAA-ACA-GATCTTATCTCCCTAAG
* ** * * * * ***
23418721 ATTATAGCGGAGCAGATGGAAGACACTATCCTATC-CCCTTGAGATTTCAGTAGAATAGATTAAA
60 ATTACAGCGGAGCAGATCCAAGACAATATCCTATCTCCC-TGAAATTACAGTGGAGCGGATTAAA
23418785 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
124 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
23418826 GTGTCAGATA
Statistics
Matches: 292, Mismatches: 41, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
172 35 0.12
174 38 0.13
175 76 0.26
179 1 0.00
182 1 0.00
184 4 0.01
185 69 0.24
186 39 0.13
187 2 0.01
188 27 0.09
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (172 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAACAGATCTTATCTCCCTAAGATTACA
GCGGAGCAGATCCAAGACAATATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGG
ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCTGG
Found at i:23419746 original size:21 final size:21
Alignment explanation
Indices: 23419706--23419744 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
23419696 TTTCGATTCG
23419706 CTTTTTATCTTTTTTATTTTC
1 CTTTTTATCTTTTTTATTTTC
23419727 CTTTTTA--TTTTTTATTTT
1 CTTTTTATCTTTTTTATTTT
23419745 TTACTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
21 7 0.39
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTTATCTTTTTTATTTTC
Found at i:23421970 original size:15 final size:16
Alignment explanation
Indices: 23421942--23421981 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
23421932 ACTTAAGAAA
23421942 TATTTTA-A-TTCTTT
1 TATTTTACATTTCTTT
23421956 TATTTT-CATTTCTTT
1 TATTTTACATTTCTTT
*
23421971 TCTTTTACATT
1 TATTTTACATT
23421982 ATTTTCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 11 0.50
16 4 0.18
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTACATTTCTTT
Found at i:23430640 original size:46 final size:45
Alignment explanation
Indices: 23430573--23430712 Score: 244
Period size: 46 Copynumber: 3.1 Consensus size: 45
23430563 TTTGAGTACT
23430573 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
23430619 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
23430665 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
23430710 TCT
1 TCT
23430713 ACAAAGTGAT
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
45 16 0.18
46 74 0.81
47 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:23431643 original size:17 final size:17
Alignment explanation
Indices: 23431621--23431654 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23431611 TCACGTTAGC
23431621 AATT-AATTAATTTTAAA
1 AATTAAATT-ATTTTAAA
23431638 AATTAAATTATTTTAAA
1 AATTAAATTATTTTAAA
23431655 TTATTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTATTTTAAA
Found at i:23431716 original size:17 final size:18
Alignment explanation
Indices: 23431694--23431735 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
23431684 AACAAAATAA
*
23431694 TTTTAATAATT-ATTTAT
1 TTTTAATAATTCATATAT
23431711 TTTTAATAATTCATATAT
1 TTTTAATAATTCATATAT
23431729 TTTTAAT
1 TTTTAAT
23431736 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAATAATTCATATAT
Found at i:23432827 original size:13 final size:15
Alignment explanation
Indices: 23432809--23432841 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23432799 ACAGTTGAAC
23432809 TAAAATTT-T-AAAA
1 TAAAATTTATAAAAA
23432822 TAAAATTTATAAAAA
1 TAAAATTTATAAAAA
23432837 TAAAA
1 TAAAA
23432842 ATATGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 1 0.06
15 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATTTATAAAAA
Done.