Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 102 of 128
Found at i:33940582 original size:108 final size:107
Alignment explanation
Indices: 33940453--33940659 Score: 328
Period size: 108 Copynumber: 1.9 Consensus size: 107
33940443 AAATTTTGCT
*
33940453 TTTTAACCCCCCAGAAAACTTTCAACTGTTGTTTAGTTTTTTTTAATAAACTA-AAAAATAGTCA
1 TTTTAACCCCCCAAAAAACTTTCAACTGTTGTTTAG-TTTTTTTAATAAACTATAAAAATAGTCA
*
33940517 TATATCTTTTTT-AGTCATTAATGTTTTAATTCTTACAATTAGG
65 TATATCTTTTTTCA-TCACTAATGTTTTAATTCTTACAATTAGG
* *
33940560 TTTTAACCCCCCAAAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATACAAATTGTCA
1 TTTTAACCCCCC-AAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATAAAAATAGTCA
*
33940625 TATATCTTTTTTCATCACTAATTTTTTAATTCTTA
65 TATATCTTTTTTCATCACTAATGTTTTAATTCTTA
33940660 AAGTCAATTG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
107 28 0.30
108 63 0.68
109 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (107 bp):
TTTTAACCCCCCAAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATAAAAATAGTCAT
ATATCTTTTTTCATCACTAATGTTTTAATTCTTACAATTAGG
Found at i:33942918 original size:9 final size:9
Alignment explanation
Indices: 33942887--33942987 Score: 53
Period size: 9 Copynumber: 10.3 Consensus size: 9
33942877 TATGAAGAAA
33942887 AAAAATTAT
1 AAAAATTAT
*
33942896 AAAAAAATCAAT
1 --AAAAAT-TAT
33942908 AAAAATTAT
1 AAAAATTAT
*
33942917 AAAAATTAGAA
1 AAAAATT--AT
33942928 AAAAGATTAT
1 AAAA-ATTAT
33942938 AAAAATCCTA-
1 AAAAAT--TAT
33942948 AAAAATTAT
1 AAAAATTAT
* *
33942957 AAATA-TAGA
1 AAAAATTA-T
33942966 AAAAATATAT
1 AAAAAT-TAT
*
33942976 AAAATTTAT
1 AAAAATTAT
33942985 AAA
1 AAA
33942988 GTCGTAAGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
8 4 0.06
9 25 0.35
10 22 0.31
11 15 0.21
12 5 0.07
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:33942923 original size:30 final size:30
Alignment explanation
Indices: 33942886--33942959 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
33942876 ATATGAAGAA
33942886 AAAAAATTATAAAAAA-ATCAATAAAAAT-T
1 AAAAAATTATAAAAAAGAT-AATAAAAATCT
* *
33942915 ATAAAAATTAGAAAAAAGATTATAAAAATCCT
1 A-AAAAATTATAAAAAAGATAATAAAAAT-CT
33942947 AAAAAATTATAAA
1 AAAAAATTATAAA
33942960 TATAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.03
30 22 0.58
31 13 0.34
32 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (30 bp):
AAAAAATTATAAAAAAGATAATAAAAATCT
Found at i:33942936 original size:21 final size:20
Alignment explanation
Indices: 33942885--33942979 Score: 81
Period size: 19 Copynumber: 4.8 Consensus size: 20
33942875 GATATGAAGA
33942885 AAAAAAATTATAAAAAAATCA-
1 AAAAAAATTAT--AAAAATCAG
* *
33942906 ATAAAAATTATAAAAATTAG
1 AAAAAAATTATAAAAATCAG
*
33942926 AAAAAAGATTATAAAAATC-C
1 AAAAAA-ATTATAAAAATCAG
* *
33942946 TAAAAAATTATAAATAT-AG
1 AAAAAAATTATAAAAATCAG
33942965 -AAAAAATATATAAAA
1 AAAAAAAT-TATAAAA
33942980 TTTATAAAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
18 7 0.11
19 23 0.38
20 10 0.16
21 21 0.34
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAAAAATTATAAAAATCAG
Found at i:33943084 original size:11 final size:11
Alignment explanation
Indices: 33943068--33943097 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33943058 ATAAGAAGCA
33943068 TTTTATAATTT
1 TTTTATAATTT
33943079 TTTTATAATTT
1 TTTTATAATTT
*
33943090 TTCTATAA
1 TTTTATAA
33943098 CTTCTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:33943253 original size:10 final size:10
Alignment explanation
Indices: 33943240--33943291 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
33943230 TTTTGATGTA
33943240 TTTTATAATT
1 TTTTATAATT
*
33943250 TTTTATGA-T
1 TTTTATAATT
**
33943259 TTTTATAAAA
1 TTTTATAATT
*
33943269 TTTTAGAATT
1 TTTTATAATT
33943279 TTTTATATATT
1 TTTTATA-ATT
33943290 TT
1 TT
33943292 ACAATTTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 8 0.24
10 20 0.61
11 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:33943271 original size:29 final size:28
Alignment explanation
Indices: 33943239--33943378 Score: 112
Period size: 29 Copynumber: 5.0 Consensus size: 28
33943229 TTTTTGATGT
33943239 ATTTTATAATTTTTTATGATTTTTATAAA
1 ATTTTATAATTTTTTAT-ATTTTTATAAA
* * *
33943268 ATTTTAGAATTTTTTATATATTT-TACA
1 ATTTTATAATTTTTTATATTTTTATAAA
33943295 A-TTTATATATTTTTCTA-ATTTTTAGT-AA
1 ATTTTATA-ATTTTT-TATATTTTTA-TAAA
* *
33943323 ATTTTAAATATTCTTTTATATTTTTGTTAAA
1 ATTTTATA-ATT-TTTTATATTTTT-ATAAA
* *
33943354 GTTTAATAA-TTTTTAT-TTTTTATAA
1 ATTTTATAATTTTTTATATTTTTATAA
33943379 TTTTTGTCAC
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
26 8 0.09
27 20 0.22
28 15 0.17
29 29 0.32
30 11 0.12
31 7 0.08
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (28 bp):
ATTTTATAATTTTTTATATTTTTATAAA
Found at i:33943279 original size:19 final size:20
Alignment explanation
Indices: 33943257--33943304 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
33943247 ATTTTTTATG
*
33943257 ATTTTTATA-AAATTTTAGA
1 ATTTTTATATAAATTTTACA
*
33943276 ATTTTT-TATATATTTTACA
1 ATTTTTATATAAATTTTACA
*
33943295 ATTTATATAT
1 ATTTTTATAT
33943305 TTTTCTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 19 0.79
20 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTATATAAATTTTACA
Found at i:33943325 original size:55 final size:55
Alignment explanation
Indices: 33943241--33943347 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 55
33943231 TTTGATGTAT
*
33943241 TTTATAATTTTTTATGATTTTTATAAAATTTTAGA-ATT-TTTTATATATTTTACAA
1 TTTATAATTTTTTA-GATTTTTATAAAATTTTAAATATTCTTTTATAT-TTTTACAA
33943296 TTTATATATTTTTCTA-ATTTTTAGT-AAATTTTAAATATTCTTTTATATTTTT
1 TTTATA-ATTTTT-TAGATTTTTA-TAAAATTTTAAATATTCTTTTATATTTTT
33943348 GTTAAAGTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
55 22 0.48
56 14 0.30
57 10 0.22
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (55 bp):
TTTATAATTTTTTAGATTTTTATAAAATTTTAAATATTCTTTTATATTTTTACAA
Found at i:33943616 original size:89 final size:87
Alignment explanation
Indices: 33943505--33943747 Score: 238
Period size: 89 Copynumber: 2.7 Consensus size: 87
33943495 TGCATTTTTG
* * * * *
33943505 CCAATTGAGTACAAAAAGAGCAGGGGCTTAATTGCTTGTTTTGAAAAATTTTGAGGGTATTTTTG
1 CCAATTGACTGCAAAAAAAGCAGGGGCTTAATTGCTT-TTTTAAAAAATTTTGAGGGCATTTTTG
* *
33943570 ATGCATTTTGACAGTTCAAGTAC
65 ATGCATTTTGAAACTTCAAGTAC
**** * *
33943593 CCAATTGACTAAG-AAAAAAAGCAGGGGCTTAATTGCTTTTTTTTTTAATGTTTGAAGGCCTTTT
1 CCAATTGACT--GCAAAAAAAGCAGGGGCTTAATTGCTTTTTTAAAAAAT-TTTGAGGGCATTTT
*
33943657 TGATGCATTTTGAAACTTCAAGTGC
63 TGATGCATTTTGAAACTTCAAGTAC
* * * *
33943682 CTAATTGAGTGCAAAAAAAGGGAGGGGGGCTTAATTGCTTTTTTAAAAAAAGTTTGAGGGC-TTT
1 CCAATTGACTGCAAAAAAA-GCA--GGGGCTTAATTGCTTTTTT-AAAAAATTTTGAGGGCATTT
33943746 TT
62 TT
33943748 ACACTCTTAA
Statistics
Matches: 125, Mismatches: 22, Indels: 14
0.78 0.14 0.09
Matches are distributed among these distances:
87 1 0.01
88 23 0.18
89 67 0.54
90 5 0.04
91 27 0.22
92 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (87 bp):
CCAATTGACTGCAAAAAAAGCAGGGGCTTAATTGCTTTTTTAAAAAATTTTGAGGGCATTTTTGA
TGCATTTTGAAACTTCAAGTAC
Found at i:33943816 original size:18 final size:17
Alignment explanation
Indices: 33943771--33943816 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
33943761 TTTTAAAATA
33943771 ATTTTTAGAATTTTTTAT
1 ATTTTTA-AATTTTTTAT
*
33943789 TTTTTGTAAATTTTATTAT
1 ATTTT-TAAATTTT-TTAT
33943808 ATTTTTAAA
1 ATTTTTAAA
33943817 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTTAAATTTTTTAT
Found at i:33943818 original size:19 final size:18
Alignment explanation
Indices: 33943771--33943825 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
33943761 TTTTAAAATA
*
33943771 ATTTTTAGAATTTTTTAT
1 ATTTTTAAAATTTTTTAT
*
33943789 -TTTTTGTAAATTTTATTAT
1 ATTTTT-AAAATTTT-TTAT
33943808 ATTTTTAAAATATTTTTA
1 ATTTTTAAAAT-TTTTTA
33943826 ATGGTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.17
18 6 0.20
19 11 0.37
20 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTAAAATTTTTTAT
Found at i:33944383 original size:89 final size:82
Alignment explanation
Indices: 33944222--33944390 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 82
33944212 TCAAAGGGCC
* * * * *
33944222 TTTTTGATTCATTTTGACAGTTCAAGTACTCAATTAAGTAAAAAAATGGGATTAATTGCTTTTTT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTAAAAAAATGGGATTAAATACTTTTTT
33944287 TAAAAAGTTTGAGGGTA
66 TAAAAAGTTTGAGGGTA
* *
33944304 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGATTAAATA
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGT----AAAAAAA-T--GGGATTAAATA
**
33944369 CTTTTTTTTTAAAGTTTGAGGG
59 CTTTTTTTAAAAAGTTTGAGGG
33944391 CTTTTTACAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
82 34 0.48
86 7 0.10
87 1 0.01
89 29 0.41
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (82 bp):
TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTAAAAAAATGGGATTAAATACTTTTTT
TAAAAAGTTTGAGGGTA
Found at i:33947111 original size:49 final size:50
Alignment explanation
Indices: 33947006--33947112 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
33946996 AGTTGAGATG
* * *
33947006 CCAGAAACAAAATATTGTGGTCGAGCCACCAAATAATTGCAAATATACTA
1 CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
* * *
33947056 CCAGATACAAAATATTATGGTCAAGCCATCAGA-AATTGCAAATATACTG
1 CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
*
33947105 CTAGATAC
1 CCAGATAC
33947113 TTCCTCCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 22 0.44
50 28 0.56
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (50 bp):
CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
Found at i:33960842 original size:15 final size:15
Alignment explanation
Indices: 33960796--33960842 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
33960786 GTTTTCAAAA
*
33960796 AAAAATAAAAAAATCG
1 AAAAA-AAAAAAATTG
33960812 AAAAGAAAAAAAATTG
1 AAAA-AAAAAAAATTG
*
33960828 AAAAAAAAAATATTG
1 AAAAAAAAAAAATTG
33960843 CATACGGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 17 0.61
17 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (15 bp):
AAAAAAAAAAAATTG
Found at i:33984933 original size:22 final size:22
Alignment explanation
Indices: 33984886--33984935 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
33984876 ACCACCATAT
*
33984886 CACCACCATACAACCATTATAG
1 CACCACCATACAACCATTATAC
33984908 CACCACCACT-CAACCACTT-TAC
1 CACCACCA-TACAACCA-TTATAC
33984930 CACCAC
1 CACCAC
33984936 TACACCACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.16
Consensus pattern (22 bp):
CACCACCATACAACCATTATAC
Found at i:33990338 original size:66 final size:66
Alignment explanation
Indices: 33990232--33990363 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
33990222 AACACAATAT
33990232 AGTTGAGAAGTGATGATTAAAATATATTAAACTAAATGCAATGATCCCTAATACAAATTATCCTA
1 AGTTGAGAAGTGATGATTAAAATATATTAAACTAAATGCAATGATCCCTAATACAAATTATCCTA
33990297 A
66 A
* * *
33990298 AGTTGAGAAGTGGTGATTGAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCTA
1 AGTTGAGAAGTGATGATTAAAATATATTAAACTAAATGCAATGATCCCTAATACAAATTATCCTA
33990363 A
66 A
33990364 GTATGCAAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (66 bp):
AGTTGAGAAGTGATGATTAAAATATATTAAACTAAATGCAATGATCCCTAATACAAATTATCCTA
A
Found at i:33990877 original size:20 final size:20
Alignment explanation
Indices: 33990852--33990898 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33990842 AGCTCGTTTC
33990852 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
33990872 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
33990892 CAGCTCA
1 CAGCTCA
33990899 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:33999323 original size:20 final size:20
Alignment explanation
Indices: 33999295--33999338 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
33999285 TGAAGTCTAT
*
33999295 TTGTTTGCGAAACTATACTA
1 TTGTATGCGAAACTATACTA
* *
33999315 TTGTATGCGAACCTATGCTA
1 TTGTATGCGAAACTATACTA
33999335 TTGT
1 TTGT
33999339 GTGAACTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGTATGCGAAACTATACTA
Found at i:34025784 original size:51 final size:50
Alignment explanation
Indices: 34025709--34025840 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 50
34025699 ATGAATACGT
* *
34025709 GTGTAGTAGTACTATGTGAAGGCTACTATGTGCACCG-AAAAGCTTTGGTCAC
1 GTGT-GTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAA-C-TTGATCAC
* * *
34025761 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGTAAAACTTGATTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAACTTGATCAC
*
34025811 G-GTGTAGTACTATGTGAAGGCTAATACGTG
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG
34025841 TATCGAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
49 28 0.38
50 7 0.10
51 30 0.41
52 8 0.11
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAACTTGATCAC
Found at i:34025839 original size:49 final size:51
Alignment explanation
Indices: 34025709--34025847 Score: 176
Period size: 49 Copynumber: 2.7 Consensus size: 51
34025699 ATGAATACGT
* * *
34025709 GTGTAGTAGTACTATGTGAAGGCTACTATGTGCACCGAAAAGCTTTGGTCAC
1 GTGT-GTAGTACTATGTGAAGGCTACTACGTGCATCGAAAAGCTTTGATCAC
* *
34025761 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGTAAAA-C-TTGATTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCG-AAAAGCTTTGATCAC
* *
34025811 G-GTGTAGTACTATGTGAAGGCTAATACGTGTATCGAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCGAA
34025848 TGATAATAGT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
48 2 0.03
49 32 0.41
50 7 0.09
51 30 0.38
52 8 0.10
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (51 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCGAAAAGCTTTGATCAC
Found at i:34030743 original size:20 final size:19
Alignment explanation
Indices: 34030708--34030745 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
34030698 AGCTAATAAC
34030708 GAGCTCAATGAACTGAATT
1 GAGCTCAATGAACTGAATT
*
34030727 GAGCTCGAATGACCTGAAT
1 GAGCTC-AATGAACTGAAT
34030746 CAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAACTGAATT
Found at i:34030848 original size:12 final size:11
Alignment explanation
Indices: 34030817--34030861 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
34030807 AAAAAACAAA
*
34030817 CAAAAAAAACT
1 CAAAAAAAATT
34030828 C-AAAAAAATT
1 CAAAAAAAATT
34030838 CAAAAACAAATT
1 CAAAAA-AAATT
34030850 CGAAAAAAAATT
1 C-AAAAAAAATT
34030862 AGTTTCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.30
11 5 0.17
12 11 0.37
13 5 0.17
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:34030914 original size:12 final size:12
Alignment explanation
Indices: 34030897--34030934 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
34030887 GGATATCAAG
34030897 TTGTGAAAAAAA
1 TTGTGAAAAAAA
34030909 TTGTGAAAAAGAAA
1 TTGTG-AAAA-AAA
34030923 TTGTGAAAAAAA
1 TTGTGAAAAAAA
34030935 AAAACTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (12 bp):
TTGTGAAAAAAA
Found at i:34030925 original size:14 final size:13
Alignment explanation
Indices: 34030897--34030935 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
34030887 GGATATCAAG
34030897 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
34030909 TTGTGAAAAAGAAA
1 TTGTGAAAAA-AAA
34030923 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
34030936 AAACTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:34032091 original size:19 final size:18
Alignment explanation
Indices: 34032063--34032108 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
34032053 GAGTTTTTCA
* *
34032063 AAAAACAAAGAGATTGTGG
1 AAAAAGAAAGAGA-AGTGG
*
34032082 AAAAAGAAAGAGAAGTTG
1 AAAAAGAAAGAGAAGTGG
34032100 AAAAAGAAA
1 AAAAAGAAA
34032109 CGAGTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAGAGAAGTGG
Found at i:34032308 original size:9 final size:9
Alignment explanation
Indices: 34032294--34032319 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
34032284 CAAGAGCTTA
34032294 AAGGTAAGC
1 AAGGTAAGC
34032303 AAGGTAAGC
1 AAGGTAAGC
34032312 AAGGTAAG
1 AAGGTAAG
34032320 GAGTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.35, T:0.12
Consensus pattern (9 bp):
AAGGTAAGC
Found at i:34034794 original size:14 final size:13
Alignment explanation
Indices: 34034767--34034806 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
34034757 GGATATCAAG
34034767 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
34034780 TTGTGAAAAAGAAA
1 TTGTGAAAAA-AAA
34034794 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
34034807 AAAACTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:34063131 original size:51 final size:51
Alignment explanation
Indices: 34063071--34063291 Score: 193
Period size: 51 Copynumber: 4.4 Consensus size: 51
34063061 GATGAACACG
*
34063071 TGTGTAGTACTATGTGAAGGCTACTACGTATATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
* * * * * *
34063122 TGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCAAAAAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA--TAATGGTCACA
* * * * * *
34063173 TGTGTAGTACTATGTGAAGGCTACTACGTGGACCG-TAAA-ACTTGATTACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACA
* * *
34063223 TGTGTAGTACTATGTGAAGGCTATTACGTGTATC-A-AATGATAATAGTAACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA--ATAATGGTCACA
* *
34063274 TGGGTGGTACTATGTGAA
1 TGTGTAGTACTATGTGAA
34063292 AACCCCCAAA
Statistics
Matches: 137, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
49 2 0.01
50 43 0.31
51 89 0.65
52 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
Found at i:34069370 original size:10 final size:9
Alignment explanation
Indices: 34069344--34069378 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
34069334 CAAAAAATTC
34069344 AGTCAAAAA
1 AGTCAAAAA
34069353 AGTCAAAAA
1 AGTCAAAAA
*
34069362 ATTCAAAAA
1 AGTCAAAAA
*
34069371 AGACAAAA
1 AGTCAAAA
34069379 TCGAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.11, G:0.09, T:0.11
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:34078706 original size:22 final size:23
Alignment explanation
Indices: 34078658--34078707 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
34078648 TTATTCTTTA
*
34078658 AAAAAGAAAAAACAACAAAAAAG
1 AAAAAGAAAAAACAACAAAAAAC
* *
34078681 AAAAAGAAAAAGC-ACAAAACAC
1 AAAAAGAAAAAACAACAAAAAAC
34078703 AAAAA
1 AAAAA
34078708 AAACCACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAACAACAAAAAAC
Found at i:34078707 original size:23 final size:22
Alignment explanation
Indices: 34078657--34078724 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 22
34078647 CTTATTCTTT
34078657 AAAAAAGAAAAAACAACAAAAA
1 AAAAAAGAAAAAACAACAAAAA
*
34078679 AGAAAAAGAAAAAGC-AC-AAAA
1 A-AAAAAGAAAAAACAACAAAAA
* * * *
34078700 CACAAA-AAAAACCACCAAAAA
1 AAAAAAGAAAAAACAACAAAAA
34078721 AAAA
1 AAAA
34078725 GTTGCCTACC
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 6 0.17
20 5 0.14
21 10 0.28
22 3 0.08
23 12 0.33
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAACAACAAAAA
Found at i:34092766 original size:20 final size:20
Alignment explanation
Indices: 34092715--34092768 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
34092705 TAATTCATGT
*
34092715 TTTAATTTAAGACATACTTAA
1 TTTAA-TTAAGACACACTTAA
** * *
34092736 TAAAATCAAGACACATTTAA
1 TTTAATTAAGACACACTTAA
34092756 TTTAATTAAGACA
1 TTTAATTAAGACA
34092769 AGACAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAATTAAGACACACTTAA
Found at i:34096097 original size:32 final size:31
Alignment explanation
Indices: 34096060--34096121 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
34096050 CCAGATATGT
34096060 AACTTTGCAA-CACTTTTTTTTCTTTTTTTAAC
1 AACTTTG-AATCA-TTTTTTTTCTTTTTTTAAC
*
34096092 AACTTTGAATTATTTTTTTTCTTTTTTTAA
1 AACTTTGAATCATTTTTTTTCTTTTTTTAA
34096122 TTACAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (31 bp):
AACTTTGAATCATTTTTTTTCTTTTTTTAAC
Found at i:34101066 original size:11 final size:10
Alignment explanation
Indices: 34101041--34101101 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
34101031 ACCAATAAAA
34101041 TAAA-TGAGC
1 TAAATTGAGC
*
34101050 TGAATTGTAGC
1 TAAATTG-AGC
34101061 TAAATTGAGC
1 TAAATTGAGC
**
34101071 TCGATTGAGC
1 TAAATTGAGC
34101081 TGAAA-TGAGC
1 T-AAATTGAGC
*
34101091 TCAATTGAGC
1 TAAATTGAGC
34101101 T
1 T
34101102 GGTCGGAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:34101102 original size:20 final size:20
Alignment explanation
Indices: 34101042--34101102 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
34101032 CCAATAAAAT
*
34101042 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
34101062 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
34101083 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
34101103 GTCGGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:34101111 original size:30 final size:30
Alignment explanation
Indices: 34101046--34101122 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
34101036 TAAAATAAAT
* *
34101046 GAGCTGAATTGTAGCTAAATTGAGCTCGATT
1 GAGCTGAAATG-AGCTAAATTGAGCTCGATG
* *
34101077 GAGCTGAAATGAGCTCAATTGAGCT-GGTCG
1 GAGCTGAAATGAGCTAAATTGAGCTCGAT-G
*
34101107 GAGCTGAAACGAGCTA
1 GAGCTGAAATGAGCTA
34101123 GAAAAGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.05
30 27 0.69
31 10 0.26
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (30 bp):
GAGCTGAAATGAGCTAAATTGAGCTCGATG
Found at i:34104706 original size:15 final size:15
Alignment explanation
Indices: 34104669--34104707 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
34104659 ACAACCTCTT
34104669 TTTTTTTATGCACGAA
1 TTTTTTT-TGCACGAA
*
34104685 TTTTTTTTGCATGAA
1 TTTTTTTTGCACGAA
34104700 TTTTTTTT
1 TTTTTTTT
34104708 TTAATTCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.64
Consensus pattern (15 bp):
TTTTTTTTGCACGAA
Found at i:34105879 original size:11 final size:10
Alignment explanation
Indices: 34105854--34105914 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
34105844 ACAAATAAAA
34105854 TAAA-TGAGC
1 TAAATTGAGC
*
34105863 TGAATTGTAGC
1 TAAATTG-AGC
34105874 TAAATTGAGC
1 TAAATTGAGC
**
34105884 TCGATTGAGC
1 TAAATTGAGC
34105894 TGAAA-TGAGC
1 T-AAATTGAGC
*
34105904 TCAATTGAGC
1 TAAATTGAGC
34105914 T
1 T
34105915 GGTCGGAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:34105915 original size:20 final size:20
Alignment explanation
Indices: 34105855--34105915 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
34105845 CAAATAAAAT
*
34105855 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
34105875 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
34105896 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
34105916 GTCGGAACTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:34108812 original size:17 final size:17
Alignment explanation
Indices: 34108787--34108824 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
34108777 ATGCACTAAC
*
34108787 TTGTGTATTTGGTGATG
1 TTGTCTATTTGGTGATG
34108804 TTGTCTATTTGGTGATG
1 TTGTCTATTTGGTGATG
34108821 TTGT
1 TTGT
34108825 ATAGGCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.55
Consensus pattern (17 bp):
TTGTCTATTTGGTGATG
Found at i:34114042 original size:25 final size:24
Alignment explanation
Indices: 34113995--34114081 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 24
34113985 CTACTCATAT
**
34113995 GAGCTTATTGATTTCAGCTCGTAA
1 GAGCTTACCGATTTCAGCTCGTAA
*
34114019 GAGCTTACCGATTCTCAGCTCGTAT
1 GAGCTTACCGATT-TCAGCTCGTAA
** *
34114044 GAGCTTACCGATTTCCAGCTTATGA
1 GAGCTTACCGATTT-CAGCTCGTAA
*
34114069 GAGCATACCGATT
1 GAGCTTACCGATT
34114082 CATAGCTCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 12 0.23
25 41 0.77
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (24 bp):
GAGCTTACCGATTTCAGCTCGTAA
Found at i:34114079 original size:50 final size:49
Alignment explanation
Indices: 34113992--34114093 Score: 125
Period size: 50 Copynumber: 2.1 Consensus size: 49
34113982 CCACTACTCA
** * *
34113992 TATGAGCTTATTGATTTCAGCTCGTAAGAGCTTACCGATTC-TCAGCTCG
1 TATGAGCTTACCGATTTCAGCTCATAAGAGCATACCGATTCAT-AGCTCG
* *
34114041 TATGAGCTTACCGATTTCCAGCTTATGAGAGCATACCGATTCATAGCTCG
1 TATGAGCTTACCGATTT-CAGCTCATAAGAGCATACCGATTCATAGCTCG
34114091 TAT
1 TAT
34114094 AAGCATACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 15 0.33
50 29 0.64
51 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (49 bp):
TATGAGCTTACCGATTTCAGCTCATAAGAGCATACCGATTCATAGCTCG
Found at i:34114098 original size:25 final size:25
Alignment explanation
Indices: 34114010--34114101 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 25
34114000 TATTGATTTC
*
34114010 AGCTCGTA-AGAGCTTACCGATTCT
1 AGCTCGTATAGAGCATACCGATTCT
* *
34114034 CAGCTCGTAT-GAGCTTACCGATTTCC
1 -AGCTCGTATAGAGCATACCGA-TTCT
34114060 AGCT--TATGAGAGCATACCGATTCAT
1 AGCTCGTAT-AGAGCATACCGATTC-T
34114085 AGCTCGTATA-AGCATAC
1 AGCTCGTATAGAGCATAC
34114102 ATGTACAGGA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
23 3 0.05
24 3 0.05
25 44 0.77
26 4 0.07
27 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCTCGTATAGAGCATACCGATTCT
Found at i:34116606 original size:46 final size:46
Alignment explanation
Indices: 34116555--34116648 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
34116545 ATAGTGTGGC
34116555 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
* *
34116601 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
34116647 GT
1 GT
34116649 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
Found at i:34130736 original size:21 final size:22
Alignment explanation
Indices: 34130685--34130751 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
34130675 CAAAAGTGTT
* *
34130685 ATCAGTGGTAGTTTATTTGCAA
1 ATCAGTGGTAGTTTATCTACAA
34130707 ATCAGTGGTAGTTTATCTAC-A
1 ATCAGTGGTAGTTTATCTACAA
* * * *
34130728 ATTAGTGGTGGCTTATCCACAA
1 ATCAGTGGTAGTTTATCTACAA
34130750 AT
1 AT
34130752 GGTGTTTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (22 bp):
ATCAGTGGTAGTTTATCTACAA
Found at i:34131491 original size:21 final size:21
Alignment explanation
Indices: 34131465--34131510 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
34131455 CCGTAATGTC
34131465 TAGGCCTGGTTTGAGGGGTTA
1 TAGGCCTGGTTTGAGGGGTTA
34131486 TAGGCCTGGTTTGAGGGGTTA
1 TAGGCCTGGTTTGAGGGGTTA
34131507 TAGG
1 TAGG
34131511 ACCAATACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.43, T:0.33
Consensus pattern (21 bp):
TAGGCCTGGTTTGAGGGGTTA
Found at i:34134536 original size:24 final size:24
Alignment explanation
Indices: 34134503--34134550 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
34134493 TTTCCTATGT
*
34134503 GGAGAGATAAGGAAGGTGAG-AGAA
1 GGAGAAATAAGG-AGGTGAGTAGAA
34134527 GGAGAAATAAGGAGGTGAGTAGAA
1 GGAGAAATAAGGAGGTGAGTAGAA
34134551 AAGGGTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.44, T:0.10
Consensus pattern (24 bp):
GGAGAAATAAGGAGGTGAGTAGAA
Found at i:34135640 original size:33 final size:33
Alignment explanation
Indices: 34135603--34135704 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
34135593 TTTCTTTAGA
34135603 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
* * * * *
34135636 TTTAG-TTT-ATTTGTTTGTT--GTTTATAGA-
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
34135664 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
34135697 TTTAGTTT
1 TTTAGTTT
34135705 ATTTGTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
28 5 0.09
29 10 0.19
30 8 0.15
31 8 0.15
32 10 0.19
33 13 0.24
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.65
Consensus pattern (33 bp):
TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
Found at i:34135643 original size:28 final size:28
Alignment explanation
Indices: 34135606--34135704 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
34135596 CTTTAGATTT
*
34135606 AGTTTTGTTTTCTTTTTTAGGTTTCTAA
1 AGTTTAGTTTTCTTTTTTAGGTTTCTAA
* *
34135634 AGTTTAGTTTAT-TTGTTTGT-TGTTTATAGA
1 AGTTTAGTTT-TCTT-TTT-TAGGTTTCTA-A
*
34135664 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAA
1 ---AGTTTAGTTTTCTTTTTTAGGTTTCTAA
34135695 AGTTTAGTTT
1 AGTTTAGTTT
34135705 ATTTGTTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
28 20 0.36
29 10 0.18
30 2 0.04
31 2 0.04
32 10 0.18
33 11 0.20
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (28 bp):
AGTTTAGTTTTCTTTTTTAGGTTTCTAA
Found at i:34135694 original size:61 final size:61
Alignment explanation
Indices: 34135599--34135719 Score: 242
Period size: 61 Copynumber: 2.0 Consensus size: 61
34135589 TTTCTTTCTT
34135599 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
1 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
34135660 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTT
1 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTT
34135720 TCTTTTAAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.16, C:0.03, G:0.17, T:0.64
Consensus pattern (61 bp):
TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
Found at i:34138046 original size:11 final size:11
Alignment explanation
Indices: 34138030--34138054 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34138020 TAACATGTCC
34138030 CATAAGTGTAG
1 CATAAGTGTAG
34138041 CATAAGTGTAG
1 CATAAGTGTAG
34138052 CAT
1 CAT
34138055 TAGGCTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (11 bp):
CATAAGTGTAG
Found at i:34143459 original size:137 final size:137
Alignment explanation
Indices: 34143213--34143460 Score: 365
Period size: 137 Copynumber: 1.8 Consensus size: 137
34143203 GAGCCATAAA
*
34143213 TGGGTCTACTCACACAAGCTAACGGTTGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
1 TGGGTCTACTCACACAAGCTAACGGTAGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
* * * *
34143278 AGTATCCACAAAAAATGTCGGAACTCAGCCATCGGTAGGACATTCAGGATCAGCACTTGAAACAT
66 AGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCAGGATCAGCACTTGAAACAT
34143343 GGTAACC
131 GGTAACC
* * * *
34143350 TGGGTCTACTCACACAAGCTGATGGTCAG-AATGTAAGCTGCACGATGCTACTCACACAAGCTGA
1 TGGGTCTACTCACACAAGCTAACGGT-AGAAATGT-AGCTGCACGATGCCACTCACACAAGCTAA
* *
34143414 TGAGTATCCAC-AAAAATGCCAGATCTCAGCCATCAGTAGAACATTCA
64 CGAGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCA
34143461 AGACCAACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
137 60 0.61
138 38 0.39
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (137 bp):
TGGGTCTACTCACACAAGCTAACGGTAGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
AGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCAGGATCAGCACTTGAAACAT
GGTAACC
Found at i:34148680 original size:22 final size:22
Alignment explanation
Indices: 34148653--34148698 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34148643 TAAATAACTA
34148653 TTAGTCTATTTTCCTAAATATT
1 TTAGTCTATTTTCCTAAATATT
34148675 TTAGTCTATTTTCCTAAATATT
1 TTAGTCTATTTTCCTAAATATT
34148697 TT
1 TT
34148699 TAATTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAGTCTATTTTCCTAAATATT
Found at i:34152877 original size:8 final size:8
Alignment explanation
Indices: 34152864--34152914 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
34152854 TATAACACCA
34152864 ATTATTAT
1 ATTATTAT
*
34152872 ATTATTAA
1 ATTATTAT
*
34152880 ATTAATAT
1 ATTATTAT
34152888 ATTA-TAT
1 ATTATTAT
34152895 CATTA-TAT
1 -ATTATTAT
34152903 ATT-TTAT
1 ATTATTAT
34152910 ATTAT
1 ATTAT
34152915 CATTAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 12 0.32
8 25 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTATTAT
Found at i:34157922 original size:22 final size:22
Alignment explanation
Indices: 34157894--34157935 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34157884 AAGGACAAAT
* *
34157894 AGAATAAGATAAGATACATAAC
1 AGAATAACATAAAATACATAAC
34157916 AGAATAACATAAAATACATA
1 AGAATAACATAAAATACATA
34157936 CCTCGTTGCT
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:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (22 bp):
AGAATAACATAAAATACATAAC
Found at i:34160469 original size:18 final size:19
Alignment explanation
Indices: 34160432--34160473 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
34160422 CCTTTCATAA
34160432 TTAAAATAATTTATATTAT
1 TTAAAATAATTTATATTAT
34160451 TTAAATATAATTTAATATT-T
1 TTAAA-ATAATTT-ATATTAT
34160471 TTA
1 TTA
34160474 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAAATAATTTATATTAT
Found at i:34170796 original size:20 final size:20
Alignment explanation
Indices: 34170773--34170812 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34170763 AATGTGTAAT
34170773 CAGAGGCACCAAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
**
34170793 CAGAGGCACTGAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
34170813 TCCCGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAA
Found at i:34176248 original size:19 final size:19
Alignment explanation
Indices: 34176224--34176262 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
34176214 ATAAATTATC
*
34176224 ATTAGAACTTGCCAAACAT
1 ATTAGAACTTCCCAAACAT
34176243 ATTAGAACTTCCCAAACAT
1 ATTAGAACTTCCCAAACAT
34176262 A
1 A
34176263 CTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (19 bp):
ATTAGAACTTCCCAAACAT
Found at i:34179808 original size:26 final size:26
Alignment explanation
Indices: 34179779--34179844 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
34179769 TTCGACCCAT
* **
34179779 AGCTCATGTGAGCAGGCCCATTTCAC
1 AGCTCGTGTGAGCAGAACCATTTCAC
*
34179805 AGCTCGTGTGAGCAGAATCATTTCAC
1 AGCTCGTGTGAGCAGAACCATTTCAC
34179831 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
34179845 ATGATGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGAACCATTTCAC
Found at i:34191103 original size:25 final size:26
Alignment explanation
Indices: 34191074--34191129 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
34191064 TTAATTAGTA
*
34191074 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
34191098 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
34191124 TAAAAT
1 TAAAAT
34191130 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:34191835 original size:22 final size:19
Alignment explanation
Indices: 34191796--34191837 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
34191786 TGTAAAGTTG
34191796 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
34191815 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
34191837 A
1 A
34191838 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:34211354 original size:40 final size:40
Alignment explanation
Indices: 34211309--34211492 Score: 226
Period size: 40 Copynumber: 4.6 Consensus size: 40
34211299 ATGTGTTTTT
**
34211309 AGGGGTACCGAAGTACAAACAGGGGCATGTGTGTGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
* * *
34211349 AGGGGTACTGAAGTACAAACAGAGGCATGTAAATGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
* * *
34211389 AGGGGTGCCAAAGTACAAAACA-GGGCATGTATGTGCATTC
1 AGGGGTACCGAAGTAC-AAACAGGGGCATGTAAGTGCATTC
* * * * *
34211429 AGGGATATCAAAGTACAAACAGGGGAACGTAAGTGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
*
34211469 AGGGGTATCGAAGTACAAACAGGG
1 AGGGGTACCGAAGTACAAACAGGG
34211493 CACATATGTG
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 5 0.04
40 113 0.92
41 5 0.04
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
Found at i:34211443 original size:80 final size:79
Alignment explanation
Indices: 34211309--34211508 Score: 258
Period size: 80 Copynumber: 2.5 Consensus size: 79
34211299 ATGTGTTTTT
* * *
34211309 AGGGGTACCGAAGTACAAACAGGGGCATGTGTGTGCATTCAGGGGTACTGAAGTACAAACAGAGG
1 AGGGGTACCGAAGTACAAACA-GGGCATGTATGTGCATTCAGGGATACTAAAGTACAAACAGAGG
* *
34211374 CATGTAAATGCATTC
65 AACGTAAATGCATTC
* * *
34211389 AGGGGTGCCAAAGTACAAAACAGGGCATGTATGTGCATTCAGGGATA-TCAAAGTACAAACAGGG
1 AGGGGTACCGAAGTAC-AAACAGGGCATGTATGTGCATTCAGGGATACT-AAAGTACAAACAGAG
*
34211453 GAACGTAAGTGCATTC
64 GAACGTAAATGCATTC
* **
34211469 AGGGGTATCGAAGTACAAACAGGGCACATATGTGCATTCA
1 AGGGGTACCGAAGTACAAACAGGGCATGTATGTGCATTCA
34211509 ACAATAATTA
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 23 0.22
80 76 0.73
81 5 0.05
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (79 bp):
AGGGGTACCGAAGTACAAACAGGGCATGTATGTGCATTCAGGGATACTAAAGTACAAACAGAGGA
ACGTAAATGCATTC
Found at i:34211462 original size:20 final size:20
Alignment explanation
Indices: 34211439--34211492 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
34211429 AGGGATATCA
34211439 AAGTACAAACAGGGG-AACG
1 AAGTACAAACAGGGGTAACG
* ** *
34211458 TAAGTGCATTCAGGGGTATCG
1 -AAGTACAAACAGGGGTAACG
34211479 AAGTACAAACAGGG
1 AAGTACAAACAGGG
34211493 CACATATGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.39, C:0.15, G:0.31, T:0.15
Consensus pattern (20 bp):
AAGTACAAACAGGGGTAACG
Found at i:34214689 original size:25 final size:25
Alignment explanation
Indices: 34214661--34214709 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
34214651 AGTTAATAAT
34214661 AATT-CTCATTGAGTTT-TTCTTAAAG
1 AATTGCTC-TTGAGTTTCTT-TTAAAG
34214686 AATTGCTCTTGAGTTTCTTTTAAA
1 AATTGCTCTTGAGTTTCTTTTAAA
34214710 AGCTGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
AATTGCTCTTGAGTTTCTTTTAAAG
Found at i:34215981 original size:28 final size:28
Alignment explanation
Indices: 34215918--34215981 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
34215908 CGTGTGCTAA
** *
34215918 GCCGTGTGGTAGCTGTGTGTGACACATG
1 GCCGTGTGGTAGCCATGTGTGACACACG
* *
34215946 ACCATGTGGTAGCCATGTGTGACACACG
1 GCCGTGTGGTAGCCATGTGTGACACACG
34215974 GCCGTGTG
1 GCCGTGTG
34215982 ACAAGTCGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (28 bp):
GCCGTGTGGTAGCCATGTGTGACACACG
Found at i:34226782 original size:13 final size:13
Alignment explanation
Indices: 34226764--34226790 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34226754 TTCAAGCACT
34226764 CAGAGAGATGCAG
1 CAGAGAGATGCAG
34226777 CAGAGAGATGCAG
1 CAGAGAGATGCAG
34226790 C
1 C
34226791 CTGACTCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.37, T:0.07
Consensus pattern (13 bp):
CAGAGAGATGCAG
Found at i:34227186 original size:19 final size:18
Alignment explanation
Indices: 34227145--34227188 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
34227135 AAACCTATAA
* *
34227145 AAAATAAATACATTAAGT
1 AAAATAAAAACACTAAGT
*
34227163 TAAATAAAAACTACTAAGT
1 AAAATAAAAAC-ACTAAGT
34227182 AAAATAA
1 AAAATAA
34227189 CCAAAACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATAAAAACACTAAGT
Found at i:34230665 original size:30 final size:30
Alignment explanation
Indices: 34230590--34230786 Score: 127
Period size: 30 Copynumber: 6.6 Consensus size: 30
34230580 GATAGCTTCA
* *
34230590 ACTATCG-ATTATGAAAAGGGATGGTGACG
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* *
34230619 ACCATC-AACAATGAAAAGAGATGGTGACG
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* *
34230648 ACTATCGAACTATGAAAAAAGATGGCT-TCG
1 ACTATCGAACTATGAAAAGAGATGG-TGACG
* * * *
34230678 ACTATTGATCTATGAAAA-AGGATAGCT-TCG
1 ACTATCGAACTATGAAAAGA-GAT-GGTGACG
* * * *
34230708 GCTATC-AATTTATGAAAAGGGATGGTGATG
1 ACTATCGAA-CTATGAAAAGAGATGGTGACG
* * * *
34230738 ACCATCGAACAATGAAAAGAGATCGTGACA
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* * *
34230768 ACCATCAAATTATGAAAAG
1 ACTATCGAACTATGAAAAG
34230787 GGATAGCTTC
Statistics
Matches: 129, Mismatches: 30, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
29 33 0.26
30 92 0.71
31 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (30 bp):
ACTATCGAACTATGAAAAGAGATGGTGACG
Found at i:34230753 original size:60 final size:59
Alignment explanation
Indices: 34230579--34230755 Score: 148
Period size: 60 Copynumber: 3.0 Consensus size: 59
34230569 ATACAGAAAG
* * *
34230579 GGATAGCTTCAACTATCGATTATGAAAAGGGATGGTGACGACCATC-AACAATG-AAAA
1 GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAA
* * * ** * * * *
34230636 GAGAT-GGTGACGACTATCGAACTATGAAAAAAGATGGCT--TCGACTATTGATCTATGAAAAA
1 G-GATAGCT-TCGACTATC-AATTATGAAAAGGGATGG-TGAT-GACCATCGAACAATGAAAAA
*
34230697 GGATAGCTTCGGCTATCAATTTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAA
1 GGATAGCTTCGACTATCAA-TTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAA
34230756 GAGATCGTGA
Statistics
Matches: 87, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
57 3 0.03
58 10 0.11
59 22 0.25
60 44 0.51
61 8 0.09
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (59 bp):
GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAA
Found at i:34230796 original size:120 final size:118
Alignment explanation
Indices: 34230551--34230851 Score: 336
Period size: 120 Copynumber: 2.5 Consensus size: 118
34230541 AATGGAAAGG
* * * ** *
34230551 GATAGCTTCAGCTATCGAA-TA-CAGAAAGGGATAGCTTCAACTATCGATTATGAAAAGGGATGG
1 GATAGCTTCAACTATCGAACTATGA-AAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATGG
* * * *
34230614 TGACGACCATCAACAATGAAAAGAGATGGTGACGACTATCGAACTATGAAAAAA
65 TGACGACCATCAACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
* * * *
34230668 GATGGCTTCGACTATTGATCTATGAAAAAGGATAGCTTCGGCTATCAATTTATGAAAAGGGATGG
1 GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAA-TTATGAAAAGGGATGG
* * **
34230733 TGATGACCATCGAACAATGAAAAGAGATCGTGACAACCATCAAATTATGAAAAGG
65 TGACGACCATC-AACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
* * * * **
34230788 GATAGCTTCAACTGTCGAACTATGAAAAGGGATAACTTCGGTTATCAAATTACAAAAAGGGATG
1 GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATC-AATTATGAAAAGGGATG
34230852 TGTCAAGCAT
Statistics
Matches: 151, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
117 14 0.09
118 21 0.14
119 27 0.18
120 87 0.58
121 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (118 bp):
GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGT
GACGACCATCAACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
Found at i:34240511 original size:42 final size:42
Alignment explanation
Indices: 34240451--34240532 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
34240441 GACTGTTGAC
*
34240451 GCCACACGGCTAAGGACATAGGCGTGTGCCCAAGCCGTGTGA
1 GCCACACGGCTAAAGACATAGGCGTGTGCCCAAGCCGTGTGA
* *
34240493 GCCACACGGGC-AAAGACATAGGCGTGTGTCCAGGCCGTGT
1 GCCACAC-GGCTAAAGACATAGGCGTGTGCCCAAGCCGTGT
34240533 AACTCACTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (42 bp):
GCCACACGGCTAAAGACATAGGCGTGTGCCCAAGCCGTGTGA
Found at i:34245604 original size:17 final size:17
Alignment explanation
Indices: 34245561--34245611 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
34245551 TTGGTAGAGT
*
34245561 GGATAGGAAAATTGGAAA
1 GGATAGAAAAATT-GAAA
34245579 -GAT-GAAAAATTGAAA
1 GGATAGAAAAATTGAAA
*
34245594 GGATAGAAAAATAGAAA
1 GGATAGAAAAATTGAAA
34245611 G
1 G
34245612 AAGGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (17 bp):
GGATAGAAAAATTGAAA
Found at i:34246721 original size:17 final size:18
Alignment explanation
Indices: 34246701--34246751 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
34246691 CCATATTAAA
34246701 TTTTTTAT-ATTATTTAT
1 TTTTTTATAATTATTTAT
*
34246718 TTTTAATATAATTA-TTAT
1 TTTT-TTATAATTATTTAT
*
34246736 TCTTTTATAATTATTT
1 TTTTTTATAATTATTT
34246752 TTTAAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 12 0.43
18 12 0.43
19 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTATAATTATTTAT
Found at i:34261449 original size:21 final size:21
Alignment explanation
Indices: 34261402--34261446 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
34261392 ATATTAGAAC
34261402 ATAAA-TATCGATACCCAACT
1 ATAAATTATCGATACCCAACT
34261422 ATAAATTATCGATA-CCAACT
1 ATAAATTATCGATACCCAACT
*
34261442 TTAAA
1 ATAAA
34261447 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAAATTATCGATACCCAACT
Found at i:34263036 original size:131 final size:131
Alignment explanation
Indices: 34262802--34263365 Score: 738
Period size: 131 Copynumber: 4.3 Consensus size: 131
34262792 AGCGATTGGA
* * * *
34262802 AAATCAACTAACACAAATGAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGTGATATTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
34262867 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
66 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
34262932 T
131 T
* *
34262933 AAATCAACTAACTCAAATAAGATTGTTCATGATGTTAAATCAAATGAACTTAGTTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
* * * * *
34262998 AATTAGTGAACCTTAACGATATC-ACTTGTGATCTTAAATCATCGAGATGTTTGGAGTAGCGGTA
66 AATCAGTGAACCTTAACGATATCAAC-TGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATC
34263062 TT
130 TT
** ** *
34263064 AAATCAA-TGAACTCAAATAAGATTGTTCACAATATTAAATTGAATGAACTTAGGTTGTAATCTT
1 AAATCAACT-AACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTT
*** ** * *
34263128 AAATCAGTGAACCTTAACGATATTGGCTGCAATCTTAAATCAACAAATTGTTTGGAGTAGC-ACT
65 AAATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGA-T
34263192 CTT
129 CTT
* * * *
34263195 AAATCAGCTAACTAAAATAATATTGTTCATGATATTAAATCAAATGAGCTTAGGTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
* * * * * * * *
34263260 AATCAGCGAATCTCAATGATATCAACTGTGATATTAAATCAGCGAGCTATTTGGAGTAGCGATCT
66 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
34263325 T
131 T
* *
34263326 AAATCAGCTAACTCAAATAAGATTTTTCATGATATATAAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATAT-TAAA
34263366 GTAAACAATA
Statistics
Matches: 370, Mismatches: 56, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
130 3 0.01
131 360 0.97
132 7 0.02
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (131 bp):
AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
T
Found at i:34277164 original size:72 final size:72
Alignment explanation
Indices: 34277039--34277228 Score: 274
Period size: 72 Copynumber: 2.6 Consensus size: 72
34277029 GTTGAATAAT
* * * * *
34277039 CAGCTTAGAAAAATGCAACAGCAACCTCCTCTCTT-AATGCCGTCCTAAATCCCATGCACACATT
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCT-TTAAATGTCGTCCCAAATCCCATGCACACATT
34277103 AAATTCGG
65 AAATTCGG
* *
34277111 CAGCTTGGAAAAAGGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAGTCCCATGCACACATTA
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAATCCCATGCACACATTA
* *
34277176 CATTTGG
66 AATTCGG
34277183 CAGCTTGGAAAAATGCAGCAGCAACCTTTCTCTTTAAATGTCGTCC
1 CAGCTTGGAAAAATGCAGCAGCAACC-TTCTCTTTAAATGTCGTCC
34277229 ATGTACCTGC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.02
72 85 0.80
73 19 0.18
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (72 bp):
CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAATCCCATGCACACATTA
AATTCGG
Found at i:34281804 original size:14 final size:14
Alignment explanation
Indices: 34281785--34281811 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34281775 ATTCATCTCC
34281785 CATGCATGAATCTA
1 CATGCATGAATCTA
34281799 CATGCATGAATCT
1 CATGCATGAATCT
34281812 GTCCAATGTA
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:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:34288559 original size:72 final size:73
Alignment explanation
Indices: 34288477--34288626 Score: 239
Period size: 72 Copynumber: 2.1 Consensus size: 73
34288467 CTCCTCCCTT
* *
34288477 AATGCCATCCCAAATCCCATGCACACATTAAATTTGGCAGCTTGGAAAAAGGCAACAGCAAC-CT
1 AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
34288541 TCTCTTTA
66 TCTCTTTA
* * * *
34288549 AATGCCATCCCAAGTCCCATGCACACATTAAATTCGGCAGCTTGAAAAAATGCAACAGGAACTTT
1 AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
34288614 TCTCTTTA
66 TCTCTTTA
34288622 AATGC
1 AATGC
34288627 TGTCCATGTA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 57 0.80
73 14 0.20
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (73 bp):
AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
TCTCTTTA
Found at i:34293831 original size:74 final size:74
Alignment explanation
Indices: 34293687--34293824 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 74
34293677 AAATTGACAA
* * * *
34293687 AATTTGCACCCAGCGCTAGTCGGATAAACTGATGAATAATTAGTGAGCCCAGCTCTAGTTGGATA
1 AATTTGCACCCAACACTAGTCGGATAAACTGATGAATAATTAATAAGCCCAGCTCTAGTTGGATA
34293752 TACCAATGG
66 TACCAATGG
* * * *
34293761 AATTTGCGCCCAACACTAGTTGGATGAACTGATGAATTAA-TAATAAGCCTAGCTCTAGTTGGAT
1 AATTTGCACCCAACACTAGTCGGATAAACTGATGAA-TAATTAATAAGCCCAGCTCTAGTTGGAT
34293825 TAACCAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 52 0.95
75 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (74 bp):
AATTTGCACCCAACACTAGTCGGATAAACTGATGAATAATTAATAAGCCCAGCTCTAGTTGGATA
TACCAATGG
Found at i:34297825 original size:58 final size:58
Alignment explanation
Indices: 34297710--34297825 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
34297700 TGTGGCGTTT
* * * * *
34297710 GCTATACCTTTGGTTCTTATCTCGTTAGATAGTGGGTCAAGGTTTATTTGTTGATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
34297768 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
34297826 ACGTTTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (58 bp):
GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
Found at i:34300936 original size:26 final size:24
Alignment explanation
Indices: 34300866--34300938 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 24
34300856 AAGTTTAAGC
34300866 GAGCC-ATATCGGGAAGCTCATGA
1 GAGCCAATATCGGGAAGCTCATGA
*
34300889 GAGCCAATTAATCAGGAAGCTCATGAA
1 GAGCCAA-T-ATCGGGAAGCTCATG-A
*
34300916 GAGCCATATATCGGGACGCTCAT
1 GAGCCA-ATATCGGGAAGCTCAT
34300939 AAAAGCTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 5 0.12
24 1 0.02
25 1 0.02
26 26 0.62
27 8 0.19
28 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCATGA
Found at i:34301404 original size:21 final size:21
Alignment explanation
Indices: 34301378--34301419 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34301368 TAAATTTAAC
34301378 TCAATTCAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
34301399 TCAATTTAATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
34301420 CTTAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:34303251 original size:21 final size:22
Alignment explanation
Indices: 34303227--34303287 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
34303217 TCGATTTTAC
34303227 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
34303248 CTCACTCTTTT-TTTTCTTTTTT
1 CTCACTCTTTTCTTTT-TGTTTT
34303270 CT-A-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
34303288 CTTTTGCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 9 0.26
21 15 0.43
22 11 0.31
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:34303276 original size:20 final size:22
Alignment explanation
Indices: 34303227--34303287 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
34303217 TCGATTTTAC
*
34303227 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTTTTTTTGTTTT
34303248 CTCACTCTTTTTTTTCTT-TTTT
1 CTCACTCTTTTTTTT-TTGTTTT
*
34303270 CT-A-TCTTTTCTTTTTGTT
1 CTCACTCTTTTTTTTTTGTT
34303288 CTTTTGCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 7 0.20
22 13 0.37
23 2 0.06
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (22 bp):
CTCACTCTTTTTTTTTTGTTTT
Found at i:34303284 original size:22 final size:20
Alignment explanation
Indices: 34303227--34303284 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
34303217 TCGATTTTAC
*
34303227 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTCTTTT
34303248 CTCACTCTTT-TTTTTCTTTT
1 CTCACT-TTTCTTTTTCTTTT
*
34303268 TTCTATCTTTTCTTTTT
1 CTC-A-CTTTTCTTTTT
34303285 GTTCTTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 12 0.39
21 12 0.39
22 7 0.23
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (20 bp):
CTCACTTTTCTTTTTCTTTT
Found at i:34314105 original size:18 final size:20
Alignment explanation
Indices: 34314068--34314110 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
34314058 ACATGTATAA
34314068 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
34314088 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
34314106 GTATG
1 GTATG
34314111 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:34315773 original size:50 final size:46
Alignment explanation
Indices: 34315700--34315863 Score: 174
Period size: 44 Copynumber: 3.6 Consensus size: 46
34315690 TTTTAGCCTA
* * *
34315700 CTCCACTGCAACTTCAAGTAGATAAAACTTGTCATGGTAAATTTAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGA--T-T-ATGGTAAATTCAATCTG
* * **
34315750 CTCCACTGCAACTTCAGGGAGATAGGATTA--GTAGCTTCAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
* * *
34315794 CTCCACTGCAACTTCAGGGAGATAAGA-T-TGGTATATTCAACCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
34315838 CTCCACTGCAACTTCAAGGAGATAAG
1 CTCCACTGCAACTTCAAGGAGATAAG
34315864 GTTTGATATG
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 73 0.73
46 1 0.01
47 1 0.01
48 1 0.01
50 23 0.23
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (46 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
Found at i:34315807 original size:44 final size:44
Alignment explanation
Indices: 34315744--34315863 Score: 186
Period size: 44 Copynumber: 2.7 Consensus size: 44
34315734 TGGTAAATTT
* *
34315744 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
* *
34315788 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
* *
34315832 AACCTGCTCCACTGCAACTTCAAGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
34315864 GTTTGATATG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
Found at i:34316023 original size:50 final size:50
Alignment explanation
Indices: 34315952--34316698 Score: 349
Period size: 50 Copynumber: 15.1 Consensus size: 50
34315942 TACGATGTCG
* ** * *
34315952 GGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * * * * *
34316002 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCT-TTTAAATTACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTT-CACTGCACTGCCA
* * * *
34316052 GGGAA-CAAGATTCGCCGTTGTAGCTTCAATTTGATCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * * * * * * * *
34316101 GGAAAGTAAGATTCGCCCTTGCAGCTTCAATCTTCTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
34316151 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
34316201 GGGAAGTAAGATTCGCTGTTGTGGCTTCAACCT--TTAACTGCGA-TGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGC-ACTGCCA
* * * *
34316249 GGGAA-TAAGATTTGTCGTTGTAGCTTTAATCTG-TTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTT-CACTGCACTGCCA
*** ** * * * *
34316298 GGGAAGTAAGATTCGCCGTTACGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
34316347 GGGGAGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCA
1 GGGAAG-TAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
** * ** * * *
34316398 GGGAAGTAAGATTCGCCGTTGCGGGTTCAATCT--TT---TAAAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
** * *
34316443 GGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGGTCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * ** * * * * *
34316493 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCT-CTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGC-TTCACTGCACTGCCA
** * * * * * ** *
34316543 GGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * ** ** * * * * *
34316593 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
34316643 GGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
34316693 GGGAAG
1 GGGAAG
34316699 GTAATTTCAT
Statistics
Matches: 494, Mismatches: 179, Indels: 48
0.69 0.25 0.07
Matches are distributed among these distances:
45 33 0.07
47 22 0.04
48 18 0.04
49 54 0.11
50 357 0.72
51 10 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
Found at i:34316208 original size:100 final size:99
Alignment explanation
Indices: 34315946--34316698 Score: 901
Period size: 100 Copynumber: 7.6 Consensus size: 99
34315936 TTAAACTACG
*** * * **
34315946 ATGTCGGGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* * *
34316011 GATTCACCGTTGTGGCTTCAATCTTTTAAATTACA
66 GATTCGCCGTTGCGGCTTCAATCTTTT-AATTGCA
* * * * *
34316046 ATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATTTGATCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* *
34316110 GATTCGCCCTTGCAGCTTCAATCTTCTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATCTT-TTAATTGCA
* *
34316145 ATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* * * * *
34316210 GATTCGCTGTTGTGGCTTCAA-CCTTTAACTGCG
66 GATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
* *** * *
34316243 ATGTCGGGGAA-TAAGATTTGTCGTTGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
34316307 GATTCGCCGTTACGGCTTCAATCTTTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCA
* * *
34316342 ATGTCGGGG-AGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCAGGGAAGTA
1 ATGTCGGGGAAG-CAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
*
34316406 AGATTCGCCGTTGCGGGTTCAATCTTTTAA----A
65 AGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
* * * * *
34316437 ATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGGTCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
34316502 GATTCACCGTTGCGGCTTCAATCTCTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATCT-TTTAATTGCA
* * * * * ** * *
34316537 ATGTCGGGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
34316602 GATTCACCGTTGCGGCTTCAATCTTTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCA
* * * *
34316637 ATGTCGGGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCAGGGAAG
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAG
34316699 GTAATTTCAT
Statistics
Matches: 560, Mismatches: 80, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
95 78 0.14
96 6 0.01
97 63 0.11
98 20 0.04
99 106 0.19
100 286 0.51
101 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (99 bp):
ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
GATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
Found at i:34316525 original size:392 final size:397
Alignment explanation
Indices: 34315946--34316698 Score: 1072
Period size: 392 Copynumber: 1.9 Consensus size: 397
34315936 TTAAACTACG
** * *
34315946 ATGTCGGGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTAA
*
34316011 GATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCGGGGAACAAGATTCGCCGTTGTAGC
66 GATTCACCGTTGCGGCTTCAATCTTTT-AA-TACAATGTCGGGGAACAAGATTCGCCGTTGTAGC
* *
34316076 TTCAATTTGATCCACTGCATCGCCAGGAAAGTAAGATTCGCCCTTGCAGCTTCAATCT-TCTTAA
129 TTCAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCT-TTAA
* * * ** * *
34316140 TTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCAGGGA
193 TTGCAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAA
* * * * * ***
34316205 AGTAAGATTCGCTGTTGTGGCTTCAA-C-CTTTAACTGCGATGTCGGGGAA-TAAGATTTGTCGT
258 AGTAAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGT
* * *
34316267 TGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTT
323 CGTAACTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTT
34316332 TTTAATTGCA
388 TTTAATTGCA
* *
34316342 ATGTCGGGG-AGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCAGGGAAGTA
1 ATGTCGGGGAAG-CAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTA
* *
34316406 AGATTCGCCGTTGCGGGTTCAATCTTTT-A-A-AATGTCGGGGAAACAAGATTCGCCGTTGTAGC
65 AGATTCACCGTTGCGGCTTCAATCTTTTAATACAATGTCGGGG-AACAAGATTCGCCGTTGTAGC
* * *
34316468 TTCAATCTGGTCCACTGCATCGCCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTCTTTAAT
129 TTCAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCTTTAAT
* *
34316533 TGCAATGTCGGGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCATCGCCAGGAAA
194 TGCAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAAA
* *
34316598 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
259 GTAAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTC
*
34316663 GTAACTTTAATCTGCTCCACTGCACTGCCAGGGAAG
324 GTAACTTTAATCTGCTCCACTGCACCGCCAGGGAAG
34316699 GTAATTTCAT
Statistics
Matches: 314, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
391 10 0.03
392 158 0.50
393 2 0.01
394 20 0.06
395 44 0.14
396 80 0.25
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (397 bp):
ATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTAA
GATTCACCGTTGCGGCTTCAATCTTTTAATACAATGTCGGGGAACAAGATTCGCCGTTGTAGCTT
CAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCTTTAATTG
CAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAAAGT
AAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTCGT
AACTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTTTTT
AATTGCA
Found at i:34317031 original size:24 final size:24
Alignment explanation
Indices: 34316999--34317044 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
34316989 TTGCCCCCAC
*
34316999 TGTAATCTTCAAGGTTCAATCCGT
1 TGTAATCTTCAAGGTTAAATCCGT
*
34317023 TGTAATCTTTAAGGTTAAATCC
1 TGTAATCTTCAAGGTTAAATCC
34317045 ACGGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (24 bp):
TGTAATCTTCAAGGTTAAATCCGT
Found at i:34317051 original size:24 final size:24
Alignment explanation
Indices: 34316995--34317052 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
34316985 CGGATTGCCC
*
34316995 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTAAAT
** *
34317019 CCGTTGTAATCTTTAAGGTTAAAT
1 CCACTGTAATCTTCAAGGTTAAAT
*
34317043 CCACGGTAAT
1 CCACTGTAAT
34317053 TTTGGGACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTAAAT
Found at i:34321362 original size:20 final size:20
Alignment explanation
Indices: 34321306--34321362 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
34321296 AAGAAGTAAA
* *
34321306 ACAC-ATTAATTAACATTTAG
1 ACACAATTAATTAA-GTTAAG
* *
34321326 ACACATTTATTTAAGTTAAG
1 ACACAATTAATTAAGTTAAG
*
34321346 ACACAATTAATTCAGTT
1 ACACAATTAATTAAGTT
34321363 GGACAAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (20 bp):
ACACAATTAATTAAGTTAAG
Found at i:34321506 original size:13 final size:13
Alignment explanation
Indices: 34321488--34321513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34321478 CTATGTATGA
34321488 ACTAAGACACATT
1 ACTAAGACACATT
34321501 ACTAAGACACATT
1 ACTAAGACACATT
34321514 TAAACTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTAAGACACATT
Found at i:34324386 original size:11 final size:12
Alignment explanation
Indices: 34324367--34324397 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34324357 TTTTTTTCAA
34324367 TCAATTTTTTTT
1 TCAATTTTTTTT
34324379 TCAATTTTTTTT
1 TCAATTTTTTTT
*
34324391 TGAATTT
1 TCAATTT
34324398 CCTCTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (12 bp):
TCAATTTTTTTT
Found at i:34325980 original size:13 final size:13
Alignment explanation
Indices: 34325962--34325987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34325952 CTATGTATGA
34325962 ACTAAGACACATT
1 ACTAAGACACATT
34325975 ACTAAGACACATT
1 ACTAAGACACATT
34325988 TAAACTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTAAGACACATT
Found at i:34326083 original size:17 final size:18
Alignment explanation
Indices: 34326051--34326087 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
34326041 TGTTGAGCTG
34326051 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
34326069 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
34326086 AA
1 AA
34326088 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:34328979 original size:222 final size:223
Alignment explanation
Indices: 34328593--34329039 Score: 887
Period size: 222 Copynumber: 2.0 Consensus size: 223
34328583 TTTTTCCTTT
34328593 ATCATTCCCTCCAGCCAATAACTGCTTTAATTGGTTCATCATAGTGTTCTGGGATTCTTGCATGT
1 ATCATTCCCTCCAGCCAATAACTGCTTTAATTGGTTCATCATAGTGTTCTGGGATTCTTGCATGT
34328658 CTTGCTGGATTTTATCCAGTCGTTTCTGCATCTGATCTTGCATCTCCTTTTGTAATTGTTCCAAT
66 CTTGCTGGATTTTATCCAGTCGTTTCTGCATCTGATCTTGCATCTCCTTTTGTAATTGTTCCAAT
34328723 CTTTCTAACCTCTGATCCATTGCTTTTGTTTGGCGACGAGTACCGTAGTGATATTTGATTGGCGA
131 CTTTCTAACCTCTGATCCATTGCTTTTGTTTGGCGACGAGTACCGTAGTGATATTTGATTGGCGA
34328788 ATTCTTGTTGGTTTCCA-GGTAACTGAA
196 ATTCTTGTTGGTTTCCAGGGTAACTGAA
34328815 ATCATTCCCTCCAGCCAATAACTGCTTTAATTGGTTCATCATAGTGTTCTGGGATTCTTGCATGT
1 ATCATTCCCTCCAGCCAATAACTGCTTTAATTGGTTCATCATAGTGTTCTGGGATTCTTGCATGT
34328880 CTTGCTGGATTTTATCCAGTCGTTTCTGCATCTGATCTTGCATCTCCTTTTGTAATTGTTCCAAT
66 CTTGCTGGATTTTATCCAGTCGTTTCTGCATCTGATCTTGCATCTCCTTTTGTAATTGTTCCAAT
34328945 CTTTCTAACCTCTGATCCATTGCTTTTGTTTGGCGACGAGTACCGTAGTGATATTTGATTGGCGA
131 CTTTCTAACCTCTGATCCATTGCTTTTGTTTGGCGACGAGTACCGTAGTGATATTTGATTGGCGA
34329010 ATTCTTGTTGGTTTCCAGGGTAACTGAA
196 ATTCTTGTTGGTTTCCAGGGTAACTGAA
34329038 AT
1 AT
34329040 AATTTTACCT
Statistics
Matches: 224, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
222 212 0.95
223 12 0.05
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (223 bp):
ATCATTCCCTCCAGCCAATAACTGCTTTAATTGGTTCATCATAGTGTTCTGGGATTCTTGCATGT
CTTGCTGGATTTTATCCAGTCGTTTCTGCATCTGATCTTGCATCTCCTTTTGTAATTGTTCCAAT
CTTTCTAACCTCTGATCCATTGCTTTTGTTTGGCGACGAGTACCGTAGTGATATTTGATTGGCGA
ATTCTTGTTGGTTTCCAGGGTAACTGAA
Found at i:34329098 original size:19 final size:20
Alignment explanation
Indices: 34329069--34329120 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
34329059 CACTTCGTGA
* *
34329069 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
34329088 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
34329108 AAATG-AATGCAAA
1 AAATGTAATGCAAA
34329121 AAGAGACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:34331459 original size:18 final size:20
Alignment explanation
Indices: 34331422--34331464 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
34331412 ACATGTATAA
34331422 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
34331442 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
34331460 GTATG
1 GTATG
34331465 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:34334847 original size:22 final size:22
Alignment explanation
Indices: 34334795--34334858 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
34334785 TATTTGGGAA
* *
34334795 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
34334817 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
34334839 TTGGTACGAAATGGAAATGG
1 TTGGTACGAAATGGTAATGG
34334859 TTCAGAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:34335722 original size:10 final size:10
Alignment explanation
Indices: 34335707--34335748 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
34335697 TTTGCAAGTT
34335707 TTGAGCTAAA
1 TTGAGCTAAA
* *
34335717 TTGAGCTGAT
1 TTGAGCTAAA
*
34335727 TTGAGCT-CA
1 TTGAGCTAAA
34335736 TTGAGCTAAA
1 TTGAGCTAAA
34335746 TTG
1 TTG
34335749 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:34382380 original size:13 final size:12
Alignment explanation
Indices: 34382362--34382402 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
34382352 CGTGAGCGAG
34382362 AAAAGAACATTGA
1 AAAAGAA-ATTGA
34382375 AAAAGAAATTG-
1 AAAAGAAATTGA
34382386 -AAAGAAA-TGA
1 AAAAGAAATTGA
34382396 AAAAGAA
1 AAAAGAA
34382403 GAAGAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.27
11 6 0.23
12 4 0.15
13 7 0.27
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:34382562 original size:33 final size:33
Alignment explanation
Indices: 34382493--34382564 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
34382483 AGAAAACGAA
*
34382493 AGTGGAAAAGAAAAAGAGCCTGAAAAGAAATCG
1 AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
* **
34382526 AGTGAAAAAGAAAGAGAGTTTGTAAAAGAAAT-G
1 AGTGAAAAAGAAAAAGAGCCTG-AAAAGAAATCG
34382559 AGTGAA
1 AGTGAA
34382565 GAGAGTAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.28, T:0.14
Consensus pattern (33 bp):
AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
Found at i:34424384 original size:12 final size:12
Alignment explanation
Indices: 34424364--34424403 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
34424354 TTCATCATTT
*
34424364 TTTACTATTTTA
1 TTTAATATTTTA
*
34424376 TTTAATATTTCA
1 TTTAATATTTTA
34424388 TTTAATATTTTA
1 TTTAATATTTTA
34424400 TTTA
1 TTTA
34424404 CTTATTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATATTTTA
Found at i:34424466 original size:18 final size:17
Alignment explanation
Indices: 34424436--34424469 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
34424426 TAAATCCATC
34424436 TTATATTAGTTTTTATT
1 TTATATTAGTTTTTATT
*
34424453 TTATCATTATTTTTTAT
1 TTAT-ATTAGTTTTTAT
34424470 ATTGGCTTGT
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:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATATTAGTTTTTATT
Found at i:34435184 original size:18 final size:17
Alignment explanation
Indices: 34435161--34435202 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
34435151 TGAAAACCCT
34435161 CAAAGGGCACCTTGAGAC
1 CAAAGGGCA-CTTGAGAC
* *
34435179 CAAAGGGGATTTGAGAC
1 CAAAGGGCACTTGAGAC
34435196 CAAAGGG
1 CAAAGGG
34435203 GAATTGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.36, C:0.19, G:0.33, T:0.12
Consensus pattern (17 bp):
CAAAGGGCACTTGAGAC
Found at i:34435194 original size:17 final size:17
Alignment explanation
Indices: 34435172--34435210 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
34435162 AAAGGGCACC
*
34435172 TTGAGACCAAAGGGGAT
1 TTGAGACCAAAGGGGAA
34435189 TTGAGACCAAAGGGGAA
1 TTGAGACCAAAGGGGAA
34435206 TTGAG
1 TTGAG
34435211 TTGAAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.18
Consensus pattern (17 bp):
TTGAGACCAAAGGGGAA
Found at i:34436691 original size:45 final size:45
Alignment explanation
Indices: 34436654--34437058 Score: 483
Period size: 45 Copynumber: 9.0 Consensus size: 45
34436644 TAGGTTGAAA
*
34436654 ATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
34436699 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
34436744 ATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATTGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
34436789 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATTGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * * *
34436834 TTAACAGATCTTGTCTTTCTATATTGGCAGC-AATATAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAA-GTAGATCGAAG
* * *
34436879 TTAGCAGATCTTGTCTTTCTGTATTGGCAGCAAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* *
34436924 ATAGCATATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
* * * * * ** ** * *
34436969 ACATCA-ACCTTGCCTCCCTGGGTTTACAGCGGAGCAGA-CTGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAG
* * * * * *
34437013 ATAGCAGATTTTGCCTTACTGTACTGACAGCGAAGCAGATCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
34437058 A
1 A
34437059 CACCAATCCC
Statistics
Matches: 314, Mismatches: 41, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
43 1 0.00
44 32 0.10
45 278 0.89
46 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAG
Found at i:34438837 original size:12 final size:12
Alignment explanation
Indices: 34438820--34438851 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
34438810 TTTTATTTCC
34438820 TTAATATTTCAG
1 TTAATATTTCAG
34438832 TTAATATTTCAG
1 TTAATATTTCAG
34438844 TTAATATT
1 TTAATATT
34438852 ATTGTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (12 bp):
TTAATATTTCAG
Found at i:34438879 original size:9 final size:9
Alignment explanation
Indices: 34438867--34438892 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
34438857 TATTATCATT
34438867 ATCATTTTC
1 ATCATTTTC
34438876 ATCATTTTC
1 ATCATTTTC
34438885 ATCATTTT
1 ATCATTTT
34438893 TTACTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (9 bp):
ATCATTTTC
Found at i:34448382 original size:13 final size:13
Alignment explanation
Indices: 34448364--34448390 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34448354 TGTTTTAACT
34448364 TATATAATTGTAA
1 TATATAATTGTAA
34448377 TATATAATTGTAA
1 TATATAATTGTAA
34448390 T
1 T
34448391 TAAAGTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TATATAATTGTAA
Found at i:34449807 original size:10 final size:10
Alignment explanation
Indices: 34449792--34449869 Score: 70
Period size: 10 Copynumber: 7.8 Consensus size: 10
34449782 GACGGTATCG
34449792 TAATTTTTTA
1 TAATTTTTTA
34449802 TAATTTTTTTA
1 TAA-TTTTTTA
* *
34449813 CAATTTTTAA
1 TAATTTTTTA
*
34449823 TTA-TTTTTA
1 TAATTTTTTA
* *
34449832 TAATTTCTAA
1 TAATTTTTTA
34449842 TAATTTTTTTA
1 TAA-TTTTTTA
34449853 TAA-TTTTTA
1 TAATTTTTTA
*
34449862 AAATTTTT
1 TAATTTTT
34449870 AATGATATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
9 15 0.28
10 21 0.40
11 17 0.32
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:34449819 original size:9 final size:9
Alignment explanation
Indices: 34449796--34449870 Score: 60
Period size: 9 Copynumber: 7.7 Consensus size: 9
34449786 GTATCGTAAT
34449796 TTTTTATAA
1 TTTTTATAA
*
34449805 TTTTTTTACAA
1 --TTTTTATAA
*
34449816 TTTTTAATTA
1 TTTTT-ATAA
34449826 TTTTTATAA
1 TTTTTATAA
*
34449835 TTTCTAATAA
1 TTT-TTATAA
34449845 TTTTTTTATAA
1 --TTTTTATAA
*
34449856 TTTTTAAAA
1 TTTTTATAA
34449865 TTTTTA
1 TTTTTA
34449871 ATGATATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 25 0.47
10 12 0.23
11 13 0.25
12 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34449819 original size:21 final size:20
Alignment explanation
Indices: 34449796--34449899 Score: 90
Period size: 19 Copynumber: 5.3 Consensus size: 20
34449786 GTATCGTAAT
*
34449796 TTTTTATAATTTTTTTACAA
1 TTTTTATAATTTTTTTATAA
34449816 -TTTT-TAATTATTTTTATAA
1 TTTTTATAATT-TTTTTATAA
*
34449835 TTTCTAATAATTTTTTTATAA
1 TTT-TTATAATTTTTTTATAA
* * *
34449856 TTTTTA-AAATTTTTAATGA
1 TTTTTATAATTTTTTTATAA
* *
34449875 TATTTA-ATTTTTTTTATAA
1 TTTTTATAATTTTTTTATAA
*
34449894 ATTTTA
1 TTTTTA
34449900 AAAAAAACTA
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
18 5 0.07
19 40 0.60
20 4 0.06
21 13 0.19
22 5 0.07
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTTTTTATAA
Found at i:34449836 original size:40 final size:39
Alignment explanation
Indices: 34449792--34449870 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
34449782 GACGGTATCG
* * *
34449792 TAATTTTTTATAATTTTTTTACAATTTTTAATTATTTTTA
1 TAATTTCTAATAATTTTTTTACAATTTTTAA-AATTTTTA
*
34449832 TAATTTCTAATAATTTTTTTATAATTTTTAAAATTTTTA
1 TAATTTCTAATAATTTTTTTACAATTTTTAAAATTTTTA
34449871 ATGATATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (39 bp):
TAATTTCTAATAATTTTTTTACAATTTTTAAAATTTTTA
Found at i:34449850 original size:30 final size:29
Alignment explanation
Indices: 34449796--34449893 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 29
34449786 GTATCGTAAT
* * *
34449796 TTTTTATAATTTTTTTACAATTTTTAATTA
1 TTTTTATAA-TTTCTAATAATTTTTAATTA
* *
34449826 TTTTTATAATTTCTAATAATTTTTTTATAA
1 TTTTTATAATTTCTAATAA-TTTTTAATTA
* * * * *
34449856 TTTTTAAAATTTTTAATGATATTTAATTT
1 TTTTTATAATTTCTAATAATTTTTAATTA
34449885 TTTTTATAA
1 TTTTTATAA
34449894 ATTTTAAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
29 21 0.39
30 33 0.61
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTTATAATTTCTAATAATTTTTAATTA
Done.