Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 24
Found at i:1014094 original size:40 final size:39
Alignment explanation
Indices: 1014027--1014104 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1014017 TTTTACCTTG
* *
1014027 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1014067 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1014105 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1015040 original size:23 final size:23
Alignment explanation
Indices: 1015010--1015065 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
1015000 AGCCTTTGAC
*
1015010 CATGCATTTTTTTTTTTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1015033 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1015055 CATGCATTTTT
1 CATGCATTTTT
1015066 AACATGTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1015072 original size:20 final size:21
Alignment explanation
Indices: 1015027--1015072 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1015017 TTTTTTTTTT
**
1015027 ATGTTTCATGCATTTTTTTATT
1 ATGTTTCATGCA-TTTTTTAAC
1015049 ATGTTTCATGCA-TTTTTAAC
1 ATGTTTCATGCATTTTTTAAC
1015069 ATGT
1 ATGT
1015073 CCAGCATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (21 bp):
ATGTTTCATGCATTTTTTAAC
Found at i:1017527 original size:19 final size:19
Alignment explanation
Indices: 1017505--1017558 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
1017495 TAAATTTTAA
1017505 CATATTTATATTTTCATAT
1 CATATTTATATTTTCATAT
*
1017524 CATATTTCTATTATTTTTATAT
1 CATA-TT-TA-TATTTTCATAT
*
1017546 TATA-TTATATTTT
1 CATATTTATATTTT
1017559 AATTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.20
19 6 0.20
20 3 0.10
21 2 0.07
22 13 0.43
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
CATATTTATATTTTCATAT
Found at i:1017553 original size:16 final size:16
Alignment explanation
Indices: 1017532--1017564 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1017522 ATCATATTTC
1017532 TATTAT-TTTTATATTA
1 TATTATATTTTA-ATTA
1017548 TATTATATTTTAATTA
1 TATTATATTTTAATTA
1017564 T
1 T
1017565 TTTTTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATATTTTAATTA
Found at i:1018174 original size:16 final size:16
Alignment explanation
Indices: 1018150--1018195 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1018140 ATTAAATAAC
* *
1018150 TATTAAATATAATTTA
1 TATTTAATATAATATA
*
1018166 TATTTAATAAAATATA
1 TATTTAATATAATATA
*
1018182 TATTTAATTTAATA
1 TATTTAATATAATA
1018196 GTATGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAATATAATATA
Found at i:1018179 original size:21 final size:21
Alignment explanation
Indices: 1018154--1018195 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1018144 AATAACTATT
1018154 AAATATA-ATTTATATTTAATA
1 AAATATATATTTA-ATTTAATA
1018175 AAATATATATTTAATTTAATA
1 AAATATATATTTAATTTAATA
1018196 GTATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATATATTTAATTTAATA
Found at i:1018881 original size:18 final size:17
Alignment explanation
Indices: 1018851--1018886 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1018841 TATTAATTAT
*
1018851 TATTTTATAATTTTTTA
1 TATTTAATAATTTTTTA
1018868 TATTTAATATATTTTTTA
1 TATTTAATA-ATTTTTTA
1018886 T
1 T
1018887 TAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTAATAATTTTTTA
Found at i:1019097 original size:16 final size:16
Alignment explanation
Indices: 1019076--1019199 Score: 74
Period size: 17 Copynumber: 7.2 Consensus size: 16
1019066 ATTAATTTTT
1019076 TTTATATATTTAATAA
1 TTTATATATTTAATAA
*
1019092 TTTATATATTTTTATTATA
1 TTTATATA--TTTAATA-A
* *
1019111 TTTATATTTTTATTATA
1 TTTATATATTTAATA-A
*
1019128 TTATAATTATATTTAAAAA
1 TT-T-A-TATATTTAATAA
1019147 TTT-TATATTTTAATAAA
1 TTTATATA-TTTAAT-AA
*
1019164 TTTA-ATAACTTAATAA
1 TTTATAT-ATTTAATAA
*
1019180 TTTATATTATATAA-AA
1 TTTATA-TATTTAATAA
1019196 TTTA
1 TTTA
1019200 AAATATATAT
Statistics
Matches: 87, Mismatches: 9, Indels: 24
0.73 0.08 0.20
Matches are distributed among these distances:
15 4 0.05
16 25 0.29
17 28 0.32
18 10 0.11
19 12 0.14
20 8 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATATATTTAATAA
Found at i:1019229 original size:23 final size:22
Alignment explanation
Indices: 1019203--1019270 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
1019193 AAATTTAAAA
1019203 TATATATTTATATTAGATTATAT
1 TATATATTTATATTA-ATTATAT
* * *
1019226 TATAAATATATA-TATTTATAT
1 TATATATTTATATTAATTATAT
*
1019247 TATATAATTATATTTAA-TATAT
1 TATATATTTATA-TTAATTATAT
1019269 TA
1 TA
1019271 AAATATAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.42
22 9 0.25
23 12 0.33
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (22 bp):
TATATATTTATATTAATTATAT
Found at i:1019239 original size:15 final size:15
Alignment explanation
Indices: 1019200--1019282 Score: 54
Period size: 15 Copynumber: 5.9 Consensus size: 15
1019190 ATAAAATTTA
1019200 AAATATATAT-TTAT
1 AAATATATATATTAT
* *
1019214 -ATTAGATTATATTAT
1 AAATATA-TATATTAT
1019229 AAATATATATATT-T
1 AAATATATATATTAT
*
1019243 ATAT-TATATAATTAT
1 AAATATATAT-ATTAT
**
1019258 ATTTA-ATATATTA-
1 AAATATATATATTAT
1019271 AAATATA-ATATT
1 AAATATATATATT
1019283 TTTATAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
13 17 0.31
14 15 0.28
15 18 0.33
16 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
AAATATATATATTAT
Found at i:1019240 original size:31 final size:29
Alignment explanation
Indices: 1019179--1019253 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 29
1019169 TAACTTAATA
*
1019179 ATTTATATTATATAAAATTTAAAATATAT
1 ATTTATATTAGATAAAATTTAAAATATAT
* *
1019208 ATTTATATTAGATTATATTATAAATATATAT
1 ATTTATATTAGATAAAATT-TAAA-ATATAT
*
1019239 ATTTATATTATATAA
1 ATTTATATTAGATAA
1019254 TTATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 16 0.41
30 4 0.10
31 19 0.49
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTTATATTAGATAAAATTTAAAATATAT
Found at i:1019256 original size:29 final size:28
Alignment explanation
Indices: 1019179--1019258 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 28
1019169 TAACTTAATA
1019179 ATTTATATTATATAAAATT-TAAAATATAT
1 ATTTATATTATAT--AATTATAAAATATAT
*
1019208 ATTTATATTAGATTATATTATAAATATATAT
1 ATTTATATTATA-TA-ATTATAAA-ATATAT
1019239 ATTTATATTATATAATTATA
1 ATTTATATTATATAATTATA
1019259 TTTAATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
28 1 0.02
29 20 0.44
30 7 0.16
31 17 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTATATTATATAATTATAAAATATAT
Found at i:1019277 original size:19 final size:21
Alignment explanation
Indices: 1019221--1019292 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
1019211 TATATTAGAT
*
1019221 TATATTATAAATATATATATT
1 TATATTATAAATATATATATA
*
1019242 TATATTATATAAT-TATATTTAA
1 TATATTATA-AATATATATAT-A
1019264 TATATTA-AAATATA-ATAT-
1 TATATTATAAATATATATATA
1019282 T-T-TTATAAATA
1 TATATTATAAATA
1019293 AATAGATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 3 0.07
17 6 0.14
18 1 0.02
20 6 0.14
21 18 0.41
22 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTATAAATATATATATA
Found at i:1020095 original size:2 final size:2
Alignment explanation
Indices: 1020088--1020128 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1020078 TAATCCTCCT
1020088 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
1020129 GAATATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1023451 original size:12 final size:12
Alignment explanation
Indices: 1023434--1023486 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1023424 TATTCGTGTA
1023434 TTTATATTATTT
1 TTTATATTATTT
**
1023446 TTTATATTAAAT
1 TTTATATTATTT
* *
1023458 TATATTTTAATTT
1 TTTATATT-ATTT
*
1023471 TTTATCTTATTT
1 TTTATATTATTT
1023483 TTTA
1 TTTA
1023487 AATTTATCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 24 0.75
13 8 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1024095 original size:17 final size:17
Alignment explanation
Indices: 1024073--1024128 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1024063 GCAATAAATC
1024073 ATAAAAAAATTATTATA
1 ATAAAAAAATTATTATA
* *
1024090 ATAAAATAATTATT-TT
1 ATAAAAAAATTATTATA
* * *
1024106 TTAAAAAAATTAATAAA
1 ATAAAAAAATTATTATA
1024123 ATAAAA
1 ATAAAA
1024129 CATATTTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAAAATTATTATA
Found at i:1025732 original size:18 final size:19
Alignment explanation
Indices: 1025711--1025751 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1025701 TTTTAATATT
1025711 TTTAAATAA-TAAAATAAA
1 TTTAAATAATTAAAATAAA
**
1025729 TTT-AATAATTAATTTAAA
1 TTTAAATAATTAAAATAAA
1025747 TTTAA
1 TTTAA
1025752 TTTATATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 13 0.68
19 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAATAATTAAAATAAA
Found at i:1025747 original size:22 final size:21
Alignment explanation
Indices: 1025722--1025772 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
1025712 TTAAATAATA
*
1025722 AAATAAATTTAATAAT-TAATTT
1 AAATAAATTT-AT-ATCAAATTT
*
1025744 AAATTTAATTTATATCAAATTT
1 AAA-TAAATTTATATCAAATTT
1025766 AAATAAA
1 AAATAAA
1025773 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAAATTTATATCAAATTT
Found at i:1028433 original size:35 final size:33
Alignment explanation
Indices: 1028370--1028440 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
1028360 AATTTTAGTC
**
1028370 TATTTAAATTATTATTTAATAATAAAATAATAT
1 TATTTAAATTATTATAAAATAATAAAATAATAT
*
1028403 TATTTAAATTTAATTATAAAAT-ATATAAATATTAT
1 TATTTAAA-TT-ATTATAAAATAATA-AAATAATAT
1028438 TAT
1 TAT
1028441 AAAACAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 8 0.25
34 5 0.16
35 19 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TATTTAAATTATTATAAAATAATAAAATAATAT
Found at i:1045808 original size:12 final size:12
Alignment explanation
Indices: 1045791--1045849 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
1045781 TATAATCATG
1045791 TATGTATGTATA
1 TATGTATGTATA
1045803 TATGTATG--TA
1 TATGTATGTATA
*
1045813 TATGTATGGATA
1 TATGTATGTATA
*
1045825 TATGTATGCATGA
1 TATGTATGTAT-A
1045838 TATG-A-GTATA
1 TATGTATGTATA
1045848 TA
1 TA
1045850 AATGCATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 13 0.31
11 3 0.07
12 21 0.50
13 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:1045819 original size:22 final size:22
Alignment explanation
Indices: 1045791--1045832 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1045781 TATAATCATG
*
1045791 TATGTATGTATATATGTATGTA
1 TATGTATGGATATATGTATGTA
1045813 TATGTATGGATATATGTATG
1 TATGTATGGATATATGTATG
1045833 CATGATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (22 bp):
TATGTATGGATATATGTATGTA
Found at i:1051887 original size:15 final size:15
Alignment explanation
Indices: 1051867--1051916 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1051857 ATGAAACTTG
1051867 TAAAAAAAATAAAAT
1 TAAAAAAAATAAAAT
*
1051882 TAAAAATTAA-AAAAT
1 TAAAAA-AAATAAAAT
*
1051897 TAAAAAAATTAAAAT
1 TAAAAAAAATAAAAT
1051912 TAAAA
1 TAAAA
1051917 TTAATAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.90
16 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAAAATAAAAT
Found at i:1051894 original size:8 final size:8
Alignment explanation
Indices: 1051877--1051910 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1051867 TAAAAAAAAT
1051877 AAAATT-A
1 AAAATTAA
1051884 AAAATTAA
1 AAAATTAA
1051892 AAAATTAAA
1 AAAATT-AA
1051901 AAAATTAA
1 AAAATTAA
1051909 AA
1 AA
1051911 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.24
8 11 0.44
9 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:1061267 original size:167 final size:167
Alignment explanation
Indices: 1061057--1061569 Score: 622
Period size: 169 Copynumber: 3.1 Consensus size: 167
1061047 AAATTACGGG
* * *
1061057 ATTTTCTTCTCCGTAAA-TTTTTTCAGGAGGATTTTTTTTGGTTTTTAATTTTTAAAATTCATCA
1 ATTTTCTACTCCGTAAATTTTTTTGAGG-GGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * * *
1061121 AATATTGTTATTTAATTCGTA-TAAAATCAATTCTCAAAAATCCATTCATTTTCATAAATGTTTG
65 AATATTGTTATTTAATTCATAGTAAAATCAATTCTCAAAAATTCATTCATTTTCATAAGTTTTTG
* *
1061185 AATTTTTTTCCTTGAAATCTCCTTTTTTCGAAATACGTT
130 -ATTTTTTTCCTTGAAATCTCATTTTTTCGAAATACGAT
* * * *
1061224 ATTTTCTACTTCGTAAATTTTTTTGAGGGGAATTTTCTTGGTTTTTATTTTTTAAATTTCATCAA
1 ATTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
* * * * * * *
1061289 ATGTTATCATTTATTTCATATTAAAA-CAATTTTCAAAAATTCATTCATTTTCATGAGTTTTTGA
66 ATATTGTTATTTAATTCATAGTAAAATCAATTCTCAAAAATTCATTCATTTTCATAAGTTTTTGA
* *
1061353 TTTTTTTCCTTGAAATACTAATTTTTTTTCGAAATACGGT
131 TTTTTTTCCTTGAAAT-CTCA--TTTTTTCGAAATACGAT
* * *
1061393 ATTTTCTACTCCGTAAATTTTTTCGAAGGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAA
1 ATTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
* * * * * *
1061458 ACATCAGTT-TTTGATTCATAGT-AAATCCATTGTCAAAAATTCATTCATTTTCATTAGTTTTTG
66 ATAT-TGTTATTTAATTCATAGTAAAATCAATTCTCAAAAATTCATTCATTTTCATAAGTTTTTG
* *
1061521 ATTTTTTTCCTTGAAACTTTCATTTTTTCAAAATACGAT
130 ATTTTTTTCCTTGAAA-TCTCATTTTTTCGAAATACGAT
*
1061560 GTTTTCTACT
1 ATTTTCTACT
1061570 TCATTGTAGA
Statistics
Matches: 295, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
166 17 0.06
167 121 0.41
168 17 0.06
169 138 0.47
170 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (167 bp):
ATTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
ATATTGTTATTTAATTCATAGTAAAATCAATTCTCAAAAATTCATTCATTTTCATAAGTTTTTGA
TTTTTTTCCTTGAAATCTCATTTTTTCGAAATACGAT
Found at i:1061435 original size:169 final size:164
Alignment explanation
Indices: 1061042--1061569 Score: 596
Period size: 167 Copynumber: 3.2 Consensus size: 164
1061032 GTTTCTCTTG
* * *
1061042 TTTTC-AAATTACGGGATTTTCTTCTCCGTAAATTTTTTC-AGGAGGATTTTTTTTGGTTTTTAA
1 TTTTCGAAA-TACGGTATTTTCTACTCCGTAAATTTTTTCGAGG-GGATTTTTCTTGGTTTTTAA
* * * * *
1061105 TTTTTAAAATTCATCAAATATTGTTATTTAATTCGTATAAAATCAATTCTCAAAAATCCATTCAT
64 TTTTTAAAATTCATCAAAT-TTATCATTTATTTCATATAAAA-CAATTCTCAAAAATTCATTCAT
* *
1061170 TTTCATAAATGTTTGAATTTTTTTCCTTGAAATCTCCTT
127 TTTCATAAGTTTTTG-ATTTTTTTCCTTGAAATCTCCTT
* * * * *
1061209 TTTTCGAAATACGTTATTTTCTACTTCGTAAATTTTTTTGAGGGGAATTTTCTTGGTTTTTATTT
1 TTTTCGAAATACGGTATTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGGTTTTTAATT
* *
1061274 TTTAAATTTCATCAAATGTTATCATTTATTTCATATTAAAACAATTTTCAAAAATTCATTCATTT
66 TTTAAAATTCATCAAAT-TTATCATTTATTTCATA-TAAAACAATTCTCAAAAATTCATTCATTT
* **
1061339 TCATGAGTTTTTGATTTTTTTCCTTGAAATACTAATTTT
129 TCATAAGTTTTTGATTTTTTTCCTTGAAAT-CT--CCTT
* *
1061378 TTTTCGAAATACGGTATTTTCTACTCCGTAAATTTTTTCGAAGGGATTTTTCTTGGTTTTCAATT
1 TTTTCGAAATACGGTATTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGGTTTTTAATT
* * * * *
1061443 TTTAAAATTCATCAAA--CATCAGTTTTTGATTCATAGTAAATCCATTGTCAAAAATTCATTCAT
66 TTTAAAATTCATCAAATTTATCA-TTTAT--TTCATA-TAAAACAATTCTCAAAAATTCATTCAT
* * *
1061506 TTTCATTAGTTTTTGATTTTTTTCCTTGAAACTTTCATT
127 TTTCATAAGTTTTTGATTTTTTTCCTTGAAA-TCTCCTT
* * *
1061545 TTTTCAAAATACGATGTTTTCTACT
1 TTTTCGAAATACGGTATTTTCTACT
1061570 TCATTGTAGA
Statistics
Matches: 309, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
166 21 0.07
167 140 0.45
168 11 0.04
169 136 0.44
170 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (164 bp):
TTTTCGAAATACGGTATTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGGTTTTTAATT
TTTAAAATTCATCAAATTTATCATTTATTTCATATAAAACAATTCTCAAAAATTCATTCATTTTC
ATAAGTTTTTGATTTTTTTCCTTGAAATCTCCTT
Found at i:1061913 original size:33 final size:33
Alignment explanation
Indices: 1061876--1061942 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1061866 TTCAACGATT
1061876 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1061909 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1061942 T
1 T
1061943 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1061914 original size:13 final size:13
Alignment explanation
Indices: 1061896--1061920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1061886 CATAAAATGT
1061896 TGTATCGATACAA
1 TGTATCGATACAA
1061909 TGTATCGATACA
1 TGTATCGATACA
1061921 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1062004 original size:13 final size:13
Alignment explanation
Indices: 1061986--1062010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1061976 ATTACTCACA
1061986 TGTATCGATACAT
1 TGTATCGATACAT
1061999 TGTATCGATACA
1 TGTATCGATACA
1062011 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1062147 original size:52 final size:52
Alignment explanation
Indices: 1062019--1062139 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1062009 CACTGATCTT
*
1062019 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1062071 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1062123 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1062140 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1067773 original size:156 final size:155
Alignment explanation
Indices: 1067489--1068009 Score: 593
Period size: 154 Copynumber: 3.4 Consensus size: 155
1067479 GTTTTTTAAA
* * * * ** * * *
1067489 GGTATCAAGTACTTTTATGTCGAAGATATTCCCTAAAGGCATTTTTGTAATTTCTTAGAATTGAG
1 GGTATCAGGTACTTTTACGTCGAAGGTATTCCTTAGGGGTATTTTTGTAATTTTTTAGAATCGAG
* **
1067554 TTCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGACATTTAGGATAGGTTCACCCCATC
66 TCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCATC
* *
1067619 TATAAATCCTTTGTAAGCCCTTTAGG
131 TAT-AATCCTTTTTAAGTCCTTTAGG
* *
1067645 GGTATCAGGTACTTTTACGTCGAAGGTA-TCCTTTAGGGGTATTTTCGTAATTTTTTAGAACCGA
1 GGTATCAGGTACTTTTACGTCGAAGGTATTCC-TTAGGGGTATTTTTGTAATTTTTTAGAATCGA
* * *
1067709 GTCCTAGGTTGTCACCGGGTTTGCTTTTATGCCAAAGGTGGGTATTTATGATAGGTTCACCCCAT
65 GTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCAT
*
1067774 CCAT-ATCCTTTTTAAGTCCTTTAGG
130 CTATAATCCTTTTTAAGTCCTTTAGG
** * *
1067799 GGTATTGGGCA-TTGTTACGTCGAAGGTATTCCTTAGGGGTATTTTGGTAATTTTTTAGAATCGA
1 GGTATCAGGTACTT-TTACGTCGAAGGTATTCCTTAGGGGTATTTTTGTAATTTTTTAGAATCGA
* * ** * * * * * *
1067863 GTCCTAGATTATCACTTGCTCTGCTTTTATGCCGGAGGTAGGTATTTAGGATAGGTTTATCCCTT
65 GTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCAT
* * *
1067928 TTATAGTCATTTTTAAGTCCTTT-GAG
130 CTATAATCCTTTTTAAGTCCTTTAG-G
* * * *
1067954 GGTACCAGGATGCTTTCACGTCGAAGGTA-TCTTTAGGGGTATTTTTGTAATTTTTT
1 GGTATCAGG-TACTTTTACGTCGAAGGTATTCCTTAGGGGTATTTTTGTAATTTTTT
1068010 TAAACTCAGC
Statistics
Matches: 308, Mismatches: 50, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
153 2 0.01
154 126 0.41
155 54 0.18
156 124 0.40
157 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (155 bp):
GGTATCAGGTACTTTTACGTCGAAGGTATTCCTTAGGGGTATTTTTGTAATTTTTTAGAATCGAG
TCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCATC
TATAATCCTTTTTAAGTCCTTTAGG
Found at i:1071099 original size:13 final size:13
Alignment explanation
Indices: 1071081--1071107 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1071071 TACATAAGTG
1071081 TTGTATCGATACA
1 TTGTATCGATACA
1071094 TTGTATCGATACA
1 TTGTATCGATACA
1071107 T
1 T
1071108 AAGTTTTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1071106 original size:32 final size:32
Alignment explanation
Indices: 1071063--1071125 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1071053 AAACCGTAAC
1071063 TGTATCAATACATAAGTGTTGTATCGATACAT
1 TGTATCAATACATAAGTGTTGTATCGATACAT
* *
1071095 TGTATCGATACATAAGTTTTGTATCGATACA
1 TGTATCAATACATAAGTGTTGTATCGATACA
1071126 ATGCATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAT
Found at i:1071118 original size:19 final size:18
Alignment explanation
Indices: 1071063--1071125 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1071053 AAACCGTAAC
*
1071063 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGT-T
1071082 TGTATCGATAC---A--T
1 TGTATCGATACATAAGTT
1071095 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1071114 TGTATCGATACA
1 TGTATCGATACA
1071126 ATGCATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 12 0.32
16 2 0.05
19 23 0.62
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1084332 original size:37 final size:38
Alignment explanation
Indices: 1084282--1084361 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
1084272 CACTTAAGTG
*
1084282 AAAGCCCACACAAGCTGGTGGCAA-CCTAGTCTGAGTC
1 AAAGCCCACACAAGCTGGTGGCAACCCAAGTCTGAGTC
* *
1084319 AAAGCCCACACAAGTTGGTGGTAACCCAAGTCTGAGTC
1 AAAGCCCACACAAGCTGGTGGCAACCCAAGTCTGAGTC
1084357 AAAGC
1 AAAGC
1084362 TTGCACAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 22 0.56
38 17 0.44
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.16
Consensus pattern (38 bp):
AAAGCCCACACAAGCTGGTGGCAACCCAAGTCTGAGTC
Found at i:1088981 original size:11 final size:12
Alignment explanation
Indices: 1088952--1088984 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1088942 ATTGGATGAA
1088952 ATAAAAATAATT
1 ATAAAAATAATT
1088964 ATAAAAATAA-T
1 ATAAAAATAATT
*
1088975 ATTAAAATAA
1 ATAAAAATAA
1088985 AATAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAAAATAATT
Found at i:1090434 original size:15 final size:15
Alignment explanation
Indices: 1090414--1090460 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 15
1090404 ACATTTTATG
1090414 CATGCATTTTCATTT
1 CATGCATTTTCATTT
1090429 CATGCA-TTTCA---
1 CATGCATTTTCATTT
*
1090440 CAT-AATTTTCATTT
1 CATGCATTTTCATTT
1090454 CATGCAT
1 CATGCAT
1090461 GCATTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
14 8 0.32
15 8 0.32
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (15 bp):
CATGCATTTTCATTT
Found at i:1090448 original size:25 final size:25
Alignment explanation
Indices: 1090419--1090561 Score: 84
Period size: 25 Copynumber: 5.7 Consensus size: 25
1090409 TTATGCATGC
1090419 ATTTTCATTTCATGCATTTCACATA
1 ATTTTCATTTCATGCATTTCACATA
*
1090444 ATTTTCATTTCATGCATGCATT-TCATA
1 ATTTTCATTTCATGCAT---TTCACATA
* *
1090471 A--AT-ATTTCAAGC--TTCATACATGCA
1 ATTTTCATTTCATGCATTTC--ACAT--A
* *
1090495 TTTTTCATTTCATGCATTTCACGTA
1 ATTTTCATTTCATGCATTTCACATA
** *
1090520 ACAATTCA-TGCATGCATTTCACATA
1 A-TTTTCATTTCATGCATTTCACATA
*
1090545 ATTTTTATTTCATGCAT
1 ATTTTCATTTCATGCAT
1090562 GTATTTCATA
Statistics
Matches: 86, Mismatches: 17, Indels: 30
0.65 0.13 0.23
Matches are distributed among these distances:
19 2 0.02
22 3 0.03
24 12 0.14
25 43 0.50
26 5 0.06
27 16 0.19
28 2 0.02
29 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.45
Consensus pattern (25 bp):
ATTTTCATTTCATGCATTTCACATA
Found at i:1090478 original size:29 final size:29
Alignment explanation
Indices: 1090429--1090595 Score: 77
Period size: 29 Copynumber: 5.2 Consensus size: 29
1090419 ATTTTCATTT
*
1090429 CATGCATTTCACATAAT-TTTCATTTCATG
1 CATGCATTTCATA-AATATTTCATTTCATG
* *
1090458 CATGCATTTCATAAATATTTCAAGCTTCATA
1 CATGCATTTCATAAATATTTC-A-TTTCATG
**
1090489 CATGCATTTTTCATTTCATGCATTTCACGTAACAATTCATG
1 CATGCA--TTTCA-TAAAT--ATTTCA--T-----TTCATG
* *
1090530 CATGCATTTCACATAAT-TTTTATTTCATG
1 CATGCATTTCATA-AATATTTCATTTCATG
* *
1090559 CATGTATTTCATAAACATTTCATGCTTCATG
1 CATGCATTTCATAAATATTTCAT--TTCATG
1090590 CATGCA
1 CATGCA
1090596 AATTTTTATT
Statistics
Matches: 104, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
28 5 0.05
29 38 0.37
30 1 0.01
31 22 0.21
33 5 0.05
34 4 0.04
35 1 0.01
36 10 0.10
39 7 0.07
41 11 0.11
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.42
Consensus pattern (29 bp):
CATGCATTTCATAAATATTTCATTTCATG
Found at i:1090540 original size:101 final size:101
Alignment explanation
Indices: 1090429--1090613 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
1090419 ATTTTCATTT
*
1090429 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAATATTTCAAGCTTCATACATGC
1 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATACATGC
1090494 -ATTTTTCATTTCATGCATTTCACGTAACAATTCATG
66 AATTTTT-ATTTCATGCATTTCACGTAACAATTCATG
* * * *
1090530 CATGCATTTCACATAATTTTTATTTCATGCATGTATTTCATAAACATTTCATGCTTCATGCATGC
1 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATACATGC
1090595 AAATTTTTATTTCATGCAT
66 -AATTTTTATTTCATGCAT
1090614 ACATGCATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 60 0.78
102 11 0.14
103 6 0.08
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.43
Consensus pattern (101 bp):
CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATACATGC
AATTTTTATTTCATGCATTTCACGTAACAATTCATG
Found at i:1090606 original size:52 final size:52
Alignment explanation
Indices: 1090443--1090613 Score: 158
Period size: 52 Copynumber: 3.3 Consensus size: 52
1090433 CATTTCACAT
* * * *
1090443 AATTTTCATTTCATGCATGCATTTCATAAATATTTCAAGCTTCATACATGC-
1 AATTTTTATTTCATGCATGTATTTCATAAACATTTCATGCTTCATACATGCA
** * * * *
1090494 -ATTTTTCATTTCATGCAT-T-TCACGT-AACAATTCATGCATGCATTTCA--CA
1 AATTTTT-ATTTCATGCATGTATTTCATAAACATTTCATGC-TTCA-TACATGCA
*
1090543 TAATTTTTATTTCATGCATGTATTTCATAAACATTTCATGCTTCATGCATGCA
1 -AATTTTTATTTCATGCATGTATTTCATAAACATTTCATGCTTCATACATGCA
1090596 AATTTTTATTTCATGCAT
1 AATTTTTATTTCATGCAT
1090614 ACATGCATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
48 10 0.11
49 6 0.06
50 19 0.20
51 21 0.23
52 24 0.26
53 13 0.14
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (52 bp):
AATTTTTATTTCATGCATGTATTTCATAAACATTTCATGCTTCATACATGCA
Found at i:1091230 original size:22 final size:22
Alignment explanation
Indices: 1091197--1091249 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1091187 CAACCTCTAT
*
1091197 CAACTTCCAGCAGCTCCCACGA
1 CAACCTCCAGCAGCTCCCACGA
* *
1091219 CAGCCTCCAGCAGCTCCCACGG
1 CAACCTCCAGCAGCTCCCACGA
1091241 CAACCTCCA
1 CAACCTCCA
1091250 ACTGCTCAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.49, G:0.15, T:0.11
Consensus pattern (22 bp):
CAACCTCCAGCAGCTCCCACGA
Found at i:1091256 original size:22 final size:22
Alignment explanation
Indices: 1091197--1091256 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1091187 CAACCTCTAT
* *
1091197 CAACTTCCAGCAGCTCCCACGA
1 CAACCTCCAACAGCTCCCACGA
* * *
1091219 CAGCCTCCAGCAGCTCCCACGG
1 CAACCTCCAACAGCTCCCACGA
*
1091241 CAACCTCCAACTGCTC
1 CAACCTCCAACAGCTC
1091257 AGCAACCACG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.48, G:0.15, T:0.13
Consensus pattern (22 bp):
CAACCTCCAACAGCTCCCACGA
Found at i:1091565 original size:45 final size:47
Alignment explanation
Indices: 1091456--1091565 Score: 125
Period size: 48 Copynumber: 2.4 Consensus size: 47
1091446 GCTTCCACGG
* * * *
1091456 GCATCCATTATAGCAGCCTCCGATTCTCGATCAAAGAAGTAATCTCCA
1 GCATCCATTCTAGCAGCCTCCCATCCACGATCAAAGAAGT-ATCTCCA
* * *
1091504 GCTTCCATTCTGGCAGCCTCCCATCCACGATCAAAGCAGT-T-TCCA
1 GCATCCATTCTAGCAGCCTCCCATCCACGATCAAAGAAGTATCTCCA
*
1091549 GCATCTATTCTAGCAGC
1 GCATCCATTCTAGCAGC
1091566 TCTGCAACCT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 18 0.35
46 1 0.02
48 33 0.63
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.25
Consensus pattern (47 bp):
GCATCCATTCTAGCAGCCTCCCATCCACGATCAAAGAAGTATCTCCA
Found at i:1094287 original size:14 final size:13
Alignment explanation
Indices: 1094268--1094310 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 13
1094258 TTAATGAAAA
1094268 AATTAATTAAATTT
1 AATTAATT-AATTT
1094282 AATTAAATTAATTT
1 AATT-AATTAATTT
1094296 AATTAATTCAATTT
1 AATTAATT-AATTT
1094310 A
1 A
1094311 TTTTTAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.15
14 19 0.70
15 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:1094292 original size:9 final size:9
Alignment explanation
Indices: 1094267--1094308 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1094257 TTTAATGAAA
1094267 AAATTAATT
1 AAATTAATT
1094276 AAATTTAATT
1 AAA-TTAATT
1094286 AAATTAATT
1 AAATTAATT
*
1094295 TAATTAATT
1 AAATTAATT
*
1094304 CAATT
1 AAATT
1094309 TATTTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
AAATTAATT
Found at i:1094488 original size:23 final size:23
Alignment explanation
Indices: 1094457--1094500 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1094447 TAAACCTATT
* *
1094457 TAAATCTAAACTAGAAGCCCATC
1 TAAACCTAAACTAAAAGCCCATC
1094480 TAAACCTAAACTAAAAGCCCA
1 TAAACCTAAACTAAAAGCCCA
1094501 ATTAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAACCTAAACTAAAAGCCCATC
Found at i:1094506 original size:23 final size:22
Alignment explanation
Indices: 1094456--1094506 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1094446 TTAAACCTAT
* *
1094456 TTAAATCTAAACTAGAAGCCCA
1 TTAAACCTAAACTAAAAGCCCA
1094478 TCTAAACCTAAACTAAAAGCCCAA
1 T-TAAACCTAAACTAAAAGCCC-A
1094502 TTAAA
1 TTAAA
1094507 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.22
Consensus pattern (22 bp):
TTAAACCTAAACTAAAAGCCCA
Found at i:1094967 original size:11 final size:11
Alignment explanation
Indices: 1094951--1094982 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1094941 ATTAAATTCT
*
1094951 ATTTTTATTTA
1 ATTTTTAATTA
1094962 ATTTTTAATTA
1 ATTTTTAATTA
1094973 ATTTTTAATT
1 ATTTTTAATT
1094983 TTTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTAATTA
Found at i:1106997 original size:23 final size:22
Alignment explanation
Indices: 1106956--1107004 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1106946 TTTAATATCG
*
1106956 TTTATGTTTATAATTATTTTAT
1 TTTATGTTTATAATTATTTTAA
*
1106978 TTTATTTTTATCAATTATTTTAA
1 TTTATGTTTAT-AATTATTTTAA
1107001 TTTA
1 TTTA
1107005 ATATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATGTTTATAATTATTTTAA
Found at i:1107011 original size:23 final size:22
Alignment explanation
Indices: 1106963--1107013 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1106953 TCGTTTATGT
* * *
1106963 TTATAATTATTTTATTTTATTT
1 TTATAATTATTTTAATTTAATA
1106985 TTATCAATTATTTTAATTTAATA
1 TTAT-AATTATTTTAATTTAATA
1107008 TTATAA
1 TTATAA
1107014 AAATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATAATTATTTTAATTTAATA
Found at i:1107057 original size:16 final size:15
Alignment explanation
Indices: 1107036--1107100 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
1107026 TTATTTATGA
1107036 ATATAATTTTTATTAC
1 ATATAA-TTTTATTAC
*
1107052 ATATAA-TTTACTTAT
1 ATATAATTTTA-TTAC
*
1107067 ATATAATTTTAATA-
1 ATATAATTTTATTAC
*
1107081 ATAAATATTTTA-TAC
1 ATATA-ATTTTATTAC
1107096 ATATA
1 ATATA
1107101 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.24
15 21 0.51
16 10 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATAATTTTATTAC
Found at i:1109609 original size:26 final size:26
Alignment explanation
Indices: 1109573--1109624 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1109563 ACCGTAGGAC
1109573 TTATACATGGCCTCTAGAACTTTGCA
1 TTATACATGGCCTCTAGAACTTTGCA
1109599 TTATACATGGCCTCTAGAACTTTGCA
1 TTATACATGGCCTCTAGAACTTTGCA
1109625 ACCTTAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (26 bp):
TTATACATGGCCTCTAGAACTTTGCA
Found at i:1110998 original size:13 final size:13
Alignment explanation
Indices: 1110980--1111004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1110970 ATTTTGCTTA
1110980 GTATCGATACATT
1 GTATCGATACATT
1110993 GTATCGATACAT
1 GTATCGATACAT
1111005 AAACTGGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1113713 original size:20 final size:20
Alignment explanation
Indices: 1113688--1113741 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1113678 GTTTGAAGTA
*
1113688 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1113708 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
1113728 ACGTATCGATACAA
1 ATGTATCGATACAA
1113742 ACAATGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1113798 original size:19 final size:20
Alignment explanation
Indices: 1113771--1113827 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
1113761 CTGCCAATTT
*
1113771 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGTA
*
1113791 CA-GTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
1113809 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
1113828 TCATTACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.16
19 25 0.78
20 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:1116367 original size:13 final size:13
Alignment explanation
Indices: 1116349--1116374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1116339 TAATAACCCT
1116349 TGTATCGATACAA
1 TGTATCGATACAA
1116362 TGTATCGATACAA
1 TGTATCGATACAA
1116375 AGAATATTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1120916 original size:3 final size:3
Alignment explanation
Indices: 1120908--1120938 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1120898 TCCAAGTCAC
*
1120908 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1120939 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:1122471 original size:20 final size:20
Alignment explanation
Indices: 1122446--1122499 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1122436 ATTTGAAGCA
1122446 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
*
1122466 ATGTATTGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1122486 ATGTATCGATACAA
1 ATGTATCGATACAA
1122500 ACAGTGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:1122552 original size:20 final size:21
Alignment explanation
Indices: 1122527--1122582 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
1122517 ACTGACAGTT
1122527 TCATGTATCGATACAAT-T-C
1 TCATGTATCGATACAATGTGC
1122546 ATCATGTATCGATACAATGTGC
1 -TCATGTATCGATACAATGTGC
1122568 -CATGTATCGATACAA
1 TCATGTATCGATACAA
1122583 ACAGTGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 32 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (21 bp):
TCATGTATCGATACAATGTGC
Found at i:1122585 original size:83 final size:83
Alignment explanation
Indices: 1122446--1122664 Score: 379
Period size: 83 Copynumber: 2.7 Consensus size: 83
1122436 ATTTGAAGCA
*
1122446 ATGTATCGATACAATTCATCATGTATTGATACAATGTGCCATGTATCGATACAAACAGTGGTAAG
1 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCCATGTATCGATACAAACAGTGGTAAG
1122511 GTAGCTACTGACAGTTTC
66 GTAGCTACTGACAGTTTC
1122529 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCCATGTATCGATACAAACAGTGGTAAG
1 ATGTATCGATACAATTCATCATGTATCGATACAATGTGCCATGTATCGATACAAACAGTGGTAAG
1122594 GTAGCTACTGACAGTTTC
66 GTAGCTACTGACAGTTTC
* **
1122612 ATGTATCGATACAATT-GTGCATGTATCGATACAATG-AACATGTATCGATACAA
1 ATGTATCGATACAATTCAT-CATGTATCGATACAATGTGCCATGTATCGATACAA
1122665 TGTATCGATA
Statistics
Matches: 131, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
82 16 0.12
83 115 0.88
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
ATGTATCGATACAATTCATCATGTATCGATACAATGTGCCATGTATCGATACAAACAGTGGTAAG
GTAGCTACTGACAGTTTC
Found at i:1122655 original size:19 final size:19
Alignment explanation
Indices: 1122611--1122666 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1122601 CTGACAGTTT
**
1122611 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1122631 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1122650 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1122667 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1122669 original size:13 final size:13
Alignment explanation
Indices: 1122651--1122677 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1122641 TACAATGAAC
1122651 ATGTATCGATACA
1 ATGTATCGATACA
1122664 ATGTATCGATACA
1 ATGTATCGATACA
1122677 A
1 A
1122678 AACATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1126324 original size:20 final size:19
Alignment explanation
Indices: 1126297--1126373 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
1126287 GTAAAAAGAT
1126297 AAAATGTATCGAGACATTG
1 AAAATGTATCGAGACATTG
* *
1126316 AAGAATGTATCGATACATTC
1 AA-AATGTATCGAGACATTG
*
1126336 ATACATGTATCGATG-CATTG
1 A-AAATGTATCGA-GACATTG
*
1126356 AAAAATGTATCGATACAT
1 -AAAATGTATCGAGACAT
1126374 CTGGATACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.04
20 42 0.91
21 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (19 bp):
AAAATGTATCGAGACATTG
Found at i:1127335 original size:28 final size:28
Alignment explanation
Indices: 1127271--1127712 Score: 476
Period size: 28 Copynumber: 15.5 Consensus size: 28
1127261 TACTAACTTA
** *
1127271 TGTGGGCTTTGAAAAAAGTGCCATTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
1127300 TGTGGGCTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1127328 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
**
1127356 TGTGGGCTTTGAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
1127385 TGTAGGCTTTAAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
**
1127413 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
1127442 TGTGGGCTTTGAAAATG-TGTCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
1127470 TGTGGGCTTTAAAAAGG-TGCCACTGATT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* *
1127498 TGTGGGCTTTGAAAAGAGTTACCACTGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
*
1127528 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1127556 TGTGGGCTTTGAAAAGAGTTACCACCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT
*
1127586 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
1127617 TGTGAGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1127644 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1127672 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1127700 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1127713 GAGATGAACG
Statistics
Matches: 352, Mismatches: 48, Indels: 27
0.82 0.11 0.06
Matches are distributed among these distances:
27 17 0.05
28 205 0.58
29 74 0.21
30 33 0.09
31 12 0.03
32 11 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1127382 original size:57 final size:57
Alignment explanation
Indices: 1127271--1127712 Score: 525
Period size: 57 Copynumber: 7.7 Consensus size: 57
1127261 TACTAACTTA
** * * *
1127271 TGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGA-TGCTACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
1127328 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * *
1127385 TGTAGGCTTTAAAAGGGTGCCATTGACTTGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
** * * * *
1127442 TGTGGGCTTTGAAAATGTGTCACTAACTTGTGGGCTTTAAAAAG-GTGCCACTGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * *
1127498 TGTGGGCTTTGAAAAGAGTTACCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
1127556 TGTGGGCTTTGAAAAGAGTTACCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
1127617 TGTGAGC-TTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
1127672 TGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAA
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1127713 GAGATGAACG
Statistics
Matches: 332, Mismatches: 44, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
55 21 0.06
56 90 0.27
57 112 0.34
58 70 0.21
59 4 0.01
60 19 0.06
61 16 0.05
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:1127414 original size:85 final size:85
Alignment explanation
Indices: 1127271--1127712 Score: 514
Period size: 85 Copynumber: 5.2 Consensus size: 85
1127261 TACTAACTTA
* * * * *
1127271 TGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGATGCTACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
1127336 TTGAAAGGATGCCACTGACT
66 TTGAAAGGATGCCACTGACT
* * *
1127356 TGTGGGCTTTGAAAATAGTGCCACTGACTTGTAGGCTTTAAAAGGGTGCCATTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
**
1127421 TTGAAAAAAGTGCCACTGACT
66 TTGAAAGGA-TGCCACTGACT
* * * * *
1127442 TGTGGGCTTTGAAAA-TGTGTCACTAACTTGTGGGCTTTAAAAAGGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
* *
1127506 TTGAAAAGAGTTACCACTGACT
66 TTG-AAAG-GATGCCACTGACT
* * * * *
1127528 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTTACCACCGACTCGTGTG
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT-AAAAG-GGTGCCACTGACT--TGTG
*
1127592 GGCTTTGAAAAGAGTGCCACTGACT
62 GGCTTTGAAAGGA-TGCCACTGACT
* * * *
1127617 TGTGAGC-TTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
* *
1127680 TTGAAAGGGTGCCACTAACT
66 TTGAAAGGATGCCACTGACT
*
1127700 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1127713 GAGATGAACG
Statistics
Matches: 300, Mismatches: 45, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
83 15 0.05
84 18 0.06
85 111 0.37
86 82 0.27
87 11 0.04
88 33 0.11
89 19 0.06
90 11 0.04
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCT
TTGAAAGGATGCCACTGACT
Found at i:1128978 original size:9 final size:10
Alignment explanation
Indices: 1128929--1128977 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
1128919 CCCCTTTCTG
1128929 TTTTTTTGTT
1 TTTTTTTGTT
**
1128939 ATTTTTTCCTT
1 -TTTTTTTGTT
1128950 GGTTTTTTTGTT
1 --TTTTTTTGTT
1128962 TTTTTTTGTT
1 TTTTTTTGTT
1128972 TTTTTT
1 TTTTTT
1128978 GGTATGAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 16 0.50
11 8 0.25
12 8 0.25
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:1139955 original size:18 final size:18
Alignment explanation
Indices: 1139932--1140004 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 18
1139922 TATCACTATT
1139932 TGTATCGATACATGTACA
1 TGTATCGATACATGTACA
1139950 TGTATCGATACATAAGTATCGA
1 TGTATCGATACAT--GTA-C-A
*
1139972 TATTATCGATACA--TA-A
1 T-GTATCGATACATGTACA
1139988 TGTATCGATACATGTAC
1 TGTATCGATACATGTAC
1140005 GATACATGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
15 10 0.22
16 2 0.04
17 2 0.04
18 13 0.29
19 2 0.04
20 3 0.07
21 1 0.02
22 2 0.04
23 10 0.22
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (18 bp):
TGTATCGATACATGTACA
Found at i:1140009 original size:11 final size:12
Alignment explanation
Indices: 1139946--1140026 Score: 62
Period size: 15 Copynumber: 6.4 Consensus size: 12
1139936 TCGATACATG
1139946 TACATGTATCGA
1 TACATGTATCGA
1139958 TACATAAGTATCGA
1 TACAT--GTATCGA
1139972 T--AT-TATCGA
1 TACATGTATCGA
1139981 TACATAATGTATCGA
1 TAC---ATGTATCGA
1139996 TACATGTA-CGA
1 TACATGTATCGA
1140007 TACATGAGATATCGA
1 TACAT--G-TATCGA
1140022 TACAT
1 TACAT
1140027 AGCTTGTAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
9 7 0.12
11 8 0.14
12 12 0.21
13 1 0.02
14 12 0.21
15 17 0.30
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (12 bp):
TACATGTATCGA
Found at i:1140019 original size:26 final size:26
Alignment explanation
Indices: 1139946--1140026 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
1139936 TCGATACATG
1139946 TACATGTATCGATACATAAGTATCGA
1 TACATGTATCGATACATAAGTATCGA
1139972 T--AT-TATCGATACATAATGTATCGA
1 TACATGTATCGATACATAA-GTATCGA
*
1139996 TACATGTA-CGATACATGAGATATCGA
1 TACATGTATCGATACATAAG-TATCGA
1140022 TACAT
1 TACAT
1140027 AGCTTGTAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
23 13 0.27
24 10 0.20
25 1 0.02
26 23 0.47
27 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (26 bp):
TACATGTATCGATACATAAGTATCGA
Found at i:1142584 original size:28 final size:28
Alignment explanation
Indices: 1142544--1142613 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1142534 GAAATAAAGC
** *
1142544 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1142572 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1142600 CGAGGTTGGAGTAT
1 CGGGGTTGGAGTAT
1142614 ACTCGATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1142673 original size:52 final size:52
Alignment explanation
Indices: 1142604--1142940 Score: 185
Period size: 52 Copynumber: 6.4 Consensus size: 52
1142594 AAATAACGAG
* *
1142604 GTTGGAGTATACTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
1142656 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
1142709 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
1142760 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
1142815 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
1142869 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
1142920 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1142941 GAGAATTGAT
Statistics
Matches: 215, Mismatches: 43, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.17
52 78 0.36
53 33 0.15
54 28 0.13
55 19 0.09
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:1142819 original size:27 final size:28
Alignment explanation
Indices: 1142756--1142831 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1142746 GCGATAAAAC
***
1142756 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1142784 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1142811 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1142832 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1142910 original size:212 final size:212
Alignment explanation
Indices: 1142537--1142942 Score: 647
Period size: 212 Copynumber: 1.9 Consensus size: 212
1142527 ATGATTAGAA
* *
1142537 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
1142602 AGGTTGGAGTATACTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATACCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* *
1142667 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
1142731 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
1142749 ATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* * *
1142813 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATACCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * *
1142878 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
1142942 A
194 A
1142943 GAATTGATAA
Statistics
Matches: 178, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 31 0.17
212 108 0.61
213 39 0.22
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATACCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:1142915 original size:51 final size:53
Alignment explanation
Indices: 1142819--1142937 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1142809 AACGGGGTTG
* * *
1142819 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1142873 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1142924 GAATATCCCCGATT
1 GAGTATCCCCGATT
1142938 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1145321 original size:13 final size:13
Alignment explanation
Indices: 1145303--1145328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1145293 ACAAAGATCC
1145303 ATGTATCGATACA
1 ATGTATCGATACA
1145316 ATGTATCGATACA
1 ATGTATCGATACA
1145329 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1145324 original size:33 final size:33
Alignment explanation
Indices: 1145282--1145348 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1145272 AAAATTTCCA
***
1145282 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1145315 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1145348 A
1 A
1145349 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1145392 original size:19 final size:18
Alignment explanation
Indices: 1145368--1145467 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
1145358 CAGTAGCTAA
1145368 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1145387 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1145402 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1145419 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1145434 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1145451 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1145468 TCGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1145408 original size:13 final size:13
Alignment explanation
Indices: 1145390--1145446 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1145380 ACAATACTTA
1145390 TGTATCGATACAT
1 TGTATCGATACAT
1145403 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
1145421 ATGTATCGATACAT
1 -TGTATCGATACAT
1145435 TGTATCGATACA
1 TGTATCGATACA
1145447 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1145412 original size:32 final size:32
Alignment explanation
Indices: 1145371--1145465 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
1145361 TAGCTAATTA
*
1145371 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1145403 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1145435 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1145466 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1145546 original size:20 final size:21
Alignment explanation
Indices: 1145503--1145580 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1145493 GTTGGGACCC
1145503 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
1145524 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
1145544 TGTATCAATACATTT-TACAAA
1 TGTATCGATACATTTGTA-GAA
1145565 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1145581 GAATTTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.02
20 17 0.33
21 33 0.65
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:1145567 original size:41 final size:40
Alignment explanation
Indices: 1145503--1145584 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
1145493 GTTGGGACCC
* *
1145503 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCAATACATTTGTAAAATGTATCGATACATTTG-GAA
1145544 TGTATCAATACATTT-TACAAATGTATCGATACATTTGGAA
1 TGTATCAATACATTTGTA-AAATGTATCGATACATTTGGAA
1145584 T
1 T
1145585 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 6 0.16
41 32 0.84
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (40 bp):
TGTATCAATACATTTGTAAAATGTATCGATACATTTGGAA
Found at i:1150398 original size:13 final size:13
Alignment explanation
Indices: 1150380--1150408 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1150370 ACAACATTCC
1150380 TTGTATCGATACA
1 TTGTATCGATACA
1150393 TTGTATCGATACA
1 TTGTATCGATACA
1150406 TTG
1 TTG
1150409 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1152305 original size:35 final size:34
Alignment explanation
Indices: 1152261--1152335 Score: 123
Period size: 35 Copynumber: 2.2 Consensus size: 34
1152251 AAGGGGGAGA
*
1152261 AGATAATCGTTTAAGGGGGAGAATTTTTTTAGAGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTA-AGG
1152296 AGATAATCGTTTAAGGGGGAGAATATTTTTAAGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTAAGG
*
1152330 GGATAA
1 AGATAA
1152336 AAACGACGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 8 0.21
35 30 0.79
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.32
Consensus pattern (34 bp):
AGATAATCGTTTAAGGGGGAGAATATTTTTAAGG
Found at i:1152328 original size:18 final size:18
Alignment explanation
Indices: 1152270--1152331 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
1152260 AAGATAATCG
1152270 TTTAAGGGGGAGAAT-TT
1 TTTAAGGGGGAGAATATT
* * *
1152287 TTTTA-GAGGAG-ATAATCG
1 TTTAAGGGGGAGAAT-AT-T
1152305 TTTAAGGGGGAGAATATT
1 TTTAAGGGGGAGAATATT
1152323 TTTAAGGGG
1 TTTAAGGGG
1152332 ATAAAAACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
15 2 0.06
16 5 0.15
17 5 0.15
18 13 0.38
19 7 0.21
20 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.34
Consensus pattern (18 bp):
TTTAAGGGGGAGAATATT
Found at i:1152935 original size:21 final size:19
Alignment explanation
Indices: 1152889--1152945 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1152879 TGTATTGATA
**
1152889 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
1152908 CATTGTATCGATACATGGC
1 CATTGTATCGATACATGGC
1152927 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
1152946 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:1153000 original size:20 final size:19
Alignment explanation
Indices: 1152975--1153093 Score: 102
Period size: 20 Copynumber: 6.7 Consensus size: 19
1152965 TATCACTATT
1152975 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTA-AA
1152995 TGTATCGATACA---T---
1 TGTATCGATACATGGTAAA
1153008 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTA-AA
1153028 TGTATCGATACA---T---
1 TGTATCGATACATGGTAAA
1153041 TGTATCGATACATGAAG-AAA
1 TGTATCGATACATG--GTAAA
1153061 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTA-AA
1153081 TGTATCGATACAT
1 TGTATCGATACAT
1153094 TGTATCGATA
Statistics
Matches: 82, Mismatches: 0, Indels: 34
0.71 0.00 0.29
Matches are distributed among these distances:
13 24 0.29
16 1 0.01
17 2 0.02
18 1 0.01
19 1 0.01
20 53 0.65
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
TGTATCGATACATGGTAAA
Found at i:1153011 original size:13 final size:12
Alignment explanation
Indices: 1152994--1153126 Score: 77
Period size: 13 Copynumber: 12.2 Consensus size: 12
1152984 ACATGGTACA
1152994 ATGTATCGATAC
1 ATGTATCGATAC
1153006 ATTGTATCGATAC
1 A-TGTATCGATAC
1153019 ATG----G-TAC
1 ATGTATCGATAC
1153026 AATGTATCGATAC
1 -ATGTATCGATAC
1153039 ATTGTATCGATAC
1 A-TGTATCGATAC
*
1153052 ATG-A-AGA-A-
1 ATGTATCGATAC
1153060 ATGTATCGATAC
1 ATGTATCGATAC
1153072 ATG----G-TAC
1 ATGTATCGATAC
1153079 AATGTATCGATAC
1 -ATGTATCGATAC
1153092 ATTGTATCGATAC
1 A-TGTATCGATAC
*
1153105 ATG-A-AGA-A-
1 ATGTATCGATAC
1153113 ATGTATCGATAC
1 ATGTATCGATAC
1153125 AT
1 AT
1153127 AGCTTGTAAC
Statistics
Matches: 94, Mismatches: 4, Indels: 46
0.65 0.03 0.32
Matches are distributed among these distances:
7 6 0.06
8 14 0.15
9 4 0.04
10 8 0.09
11 4 0.04
12 16 0.17
13 42 0.45
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1153016 original size:33 final size:33
Alignment explanation
Indices: 1152974--1153073 Score: 168
Period size: 33 Copynumber: 3.0 Consensus size: 33
1152964 CTATCACTAT
1152974 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
1153007 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
1153040 TTGTATCGATACATGAAG-A-AATGTATCGATACA
1 TTGTATCGATACATG--GTACAATGTATCGATACA
1153073 T
1 T
1153074 GGTACAATGT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 63 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGGTACAATGTATCGATACA
Found at i:1153065 original size:53 final size:53
Alignment explanation
Indices: 1153008--1153126 Score: 238
Period size: 53 Copynumber: 2.2 Consensus size: 53
1152998 ATCGATACAT
1153008 TGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGAAGAAA
1 TGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGAAGAAA
1153061 TGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGAAGAAA
1 TGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGAAGAAA
1153114 TGTATCGATACAT
1 TGTATCGATACAT
1153127 AGCTTGTAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (53 bp):
TGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGAAGAAA
Found at i:1153098 original size:33 final size:32
Alignment explanation
Indices: 1153061--1153126 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
1153051 CATGAAGAAA
1153061 TGTATCGATACATG-GTACAATGTATCGATACAT
1 TGTATCGATACATGAG-A-AATGTATCGATACAT
1153094 TGTATCGATACATGAAGAAATGTATCGATACAT
1 TGTATCGATACATG-AGAAATGTATCGATACAT
1153127 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAAATGTATCGATACAT
Found at i:1157306 original size:20 final size:19
Alignment explanation
Indices: 1157255--1157326 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1157245 AAAAAGATGG
1157255 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* * *
1157274 GAATGCATTGATACATTCATA
1 -AATGTATCGATACATTGA-A
*
1157295 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTG-AA
1157315 AATGTATCGATA
1 AATGTATCGATA
1157327 TATCTAGGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1163487 original size:20 final size:20
Alignment explanation
Indices: 1163449--1163520 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1163439 CGAAAAATTA
** *
1163449 TATCGATACATAAGTAAATG
1 TATCGATACATTTGCAAATG
*
1163469 TATCGATACATTTTCAAATG
1 TATCGATACATTTGCAAATG
* **
1163489 TATCAATACAATTTGC-TTTG
1 TATCGATAC-ATTTGCAAATG
1163509 TATCGATACATT
1 TATCGATACATT
1163521 ATGGGTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
19 3 0.07
20 34 0.81
21 5 0.12
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
TATCGATACATTTGCAAATG
Found at i:1169017 original size:13 final size:13
Alignment explanation
Indices: 1168999--1169023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1168989 TTCAACGATT
1168999 TGTATCGATACAA
1 TGTATCGATACAA
1169012 TGTATCGATACA
1 TGTATCGATACA
1169024 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1169104 original size:13 final size:13
Alignment explanation
Indices: 1169086--1169110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1169076 ATTACTCAAA
1169086 TGTATCGATACAT
1 TGTATCGATACAT
1169099 TGTATCGATACA
1 TGTATCGATACA
1169111 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1169175 original size:52 final size:52
Alignment explanation
Indices: 1169119--1169247 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1169109 CACTGATCTT
* *
1169119 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1169171 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1169223 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1169248 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1172941 original size:21 final size:20
Alignment explanation
Indices: 1172912--1172962 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1172902 ATGAGTGATG
*
1172912 TATCGATACATTGCAAACATA
1 TATCAATACATT-CAAACATA
***
1172933 TATCAATACATTCACTTATA
1 TATCAATACATTCAAACATA
1172953 TATCAATACA
1 TATCAATACA
1172963 ATTTTTTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (20 bp):
TATCAATACATTCAAACATA
Found at i:1174566 original size:29 final size:29
Alignment explanation
Indices: 1174213--1174602 Score: 278
Period size: 29 Copynumber: 13.7 Consensus size: 29
1174203 ACTAGTATTG
* *
1174213 GTGGGCTTTTAAAAAGGTGCCATTGA-TT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* * * ** *
1174241 CATAGGCTTT-AAAAGGGTGTCGCTAACTT
1 -GTGGGCTTTGAAAAGGGTGCCATTGACTT
* **
1174270 ATGGGCTTT-AAAAGGGTGTAATTGACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* **
1174298 GTGGGCTTT-AAAAGGATGGTATTGA-TAT
1 GTGGGCTTTGAAAAGGGTGCCATTGACT-T
* *
1174326 ATAGGCTTTGAAAAGGGTGCCATTGACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
*
1174355 ATGGGCTTTGAAAAGGGTGCCATTGACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* **
1174384 GTGGGCTTTGAAAAGGGTACCACCGACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
*** * ***
1174413 GTGAAATTTG-AAAGGCTGCCATTTTTTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* *
1174441 GTGGACTTT-AAAAGGGTGCCA-TAACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* * *
1174468 GTGGG-TTTTAAAAGGGTGCCACTAACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* * * * *
1174496 GTGGGTTTTGGAAAGGTTGCCACTAACTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* * *
1174525 ATGGACTTTGAAAAGGGTGCCATTGATTT
1 GTGGGCTTTGAAAAGGGTGCCATTGACTT
* * **
1174554 GTGGGCTTGGAAAAAAGGT-CCACCGACTT
1 GTGGGCTTTG-AAAAGGGTGCCATTGACTT
*
1174583 GTGGGCTTTGAAAAGTGTGC
1 GTGGGCTTTGAAAAGGGTGC
1174603 TACCGACTTG
Statistics
Matches: 287, Mismatches: 64, Indels: 20
0.77 0.17 0.05
Matches are distributed among these distances:
26 3 0.01
27 20 0.07
28 108 0.38
29 148 0.52
30 8 0.03
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (29 bp):
GTGGGCTTTGAAAAGGGTGCCATTGACTT
Found at i:1174670 original size:36 final size:37
Alignment explanation
Indices: 1174623--1174698 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
1174613 GTGCCATTAA
1174623 CTTGTGGGCTTT-AAAAAGGTACCACTAACTTATGGG
1 CTTGTGGGCTTTGAAAAAGGTACCACTAACTTATGGG
* * * *
1174659 CTTGTGGGCTTTGAAAAGGGTGCTACTAACTTGTGGG
1 CTTGTGGGCTTTGAAAAAGGTACCACTAACTTATGGG
1174696 CTT
1 CTT
1174699 TGAAAAAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (37 bp):
CTTGTGGGCTTTGAAAAAGGTACCACTAACTTATGGG
Found at i:1174701 original size:29 final size:29
Alignment explanation
Indices: 1174659--1174766 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
1174649 AACTTATGGG
*
1174659 CTTGTGGGCTTTGAAAAGGGTGCTACTAA
1 CTTGTGGGCTTTGAAAAGGGTGCTACTGA
* *
1174688 CTTGTGGGCTTTGAAAA-AGTG-TCATTGA
1 CTTGTGGGCTTTGAAAAGGGTGCT-ACTGA
* *
1174716 CTTGTAGGCTTTGAAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAAGGGTGCTACTGA
*
1174745 CTTGTGCGCTTT-AAAAGGGTGC
1 CTTGTGGGCTTTGAAAAGGGTGC
1174767 AACTCCCTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 32 0.48
29 34 0.51
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (29 bp):
CTTGTGGGCTTTGAAAAGGGTGCTACTGA
Found at i:1175177 original size:13 final size:13
Alignment explanation
Indices: 1175159--1175245 Score: 63
Period size: 13 Copynumber: 6.7 Consensus size: 13
1175149 GAAGAAAGGG
*
1175159 TCTTGACACAAGT
1 TCTTGACAAAAGT
*
1175172 TCTTGACAAAACT
1 TCTTGACAAAAGT
1175185 T-TTGAC-AAAGTT
1 TCTTGACAAAAG-T
*
1175197 TCTAG-CAAAAGT
1 TCTTGACAAAAGT
* *
1175209 TCTTGACGATAGTT
1 TCTTGACAAAAG-T
* *
1175223 TCTTGACAATGATT
1 TCTTGACAA-AAGT
1175237 TCTTGACAA
1 TCTTGACAA
1175246 TGGCCTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
11 3 0.05
12 13 0.22
13 22 0.38
14 19 0.33
15 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (13 bp):
TCTTGACAAAAGT
Found at i:1175199 original size:25 final size:26
Alignment explanation
Indices: 1175159--1175245 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 26
1175149 GAAGAAAGGG
1175159 TCTTGACACAAG-TTCTTGACAAAACT
1 TCTTGACA-AAGTTTCTTGACAAAACT
* *
1175185 T-TTGACAAAGTTTCTAG-CAAAAGT
1 TCTTGACAAAGTTTCTTGACAAAACT
* * *
1175209 TCTTGACGATAGTTTCTTGACAATGATT
1 TCTTGAC-AAAGTTTCTTGACAA-AACT
1175237 TCTTGACAA
1 TCTTGACAA
1175246 TGGCCTTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
24 10 0.20
25 16 0.33
26 10 0.20
27 4 0.08
28 9 0.18
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (26 bp):
TCTTGACAAAGTTTCTTGACAAAACT
Found at i:1175227 original size:14 final size:14
Alignment explanation
Indices: 1175208--1175247 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1175198 CTAGCAAAAG
*
1175208 TTCTTGACGAT-AGT
1 TTCTTGACAATGA-T
1175222 TTCTTGACAATGAT
1 TTCTTGACAATGAT
1175236 TTCTTGACAATG
1 TTCTTGACAATG
1175248 GCCTTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (14 bp):
TTCTTGACAATGAT
Found at i:1181774 original size:20 final size:20
Alignment explanation
Indices: 1181745--1181818 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1181735 AAAAGGACAG
1181745 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* * *
1181765 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
1181785 CATGTATCGCTACATTG-AA
1 AATGTATCGATACATTGAAA
1181804 AATGTATCGATACAT
1 AATGTATCGATACAT
1181819 CTAGGTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1182805 original size:32 final size:31
Alignment explanation
Indices: 1182760--1182872 Score: 156
Period size: 32 Copynumber: 3.6 Consensus size: 31
1182750 TGACATTAGG
*
1182760 TTTAGAAGGGTTGCCACCAACTCATGTGGGC
1 TTTAGAAAGGTTGCCACCAACTCATGTGGGC
*
1182791 TTTAGAGAAGGTTGCCACCAACTCATGTAGGC
1 TTTAGA-AAGGTTGCCACCAACTCATGTGGGC
* *
1182823 TTTAGAATGGTTGCCACCAAC-CTGTGTGGGC
1 TTTAGAAAGGTTGCCACCAACTC-ATGTGGGC
1182854 TTTAGAAGAGGTTGCCACC
1 TTTAGAA-AGGTTGCCACC
1182873 GACTTGCTGG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
30 1 0.01
31 33 0.45
32 39 0.53
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (31 bp):
TTTAGAAAGGTTGCCACCAACTCATGTGGGC
Found at i:1182969 original size:84 final size:85
Alignment explanation
Indices: 1182784--1183400 Score: 604
Period size: 84 Copynumber: 7.2 Consensus size: 85
1182774 CACCAACTCA
* * * * * *
1182784 TGTGGGCTTTAGAGAAGGTTGCCACCAACTCATGTAGGCTTTAGAATGGTTGCCACCAACCTGTG
1 TGTGGGCTTT-GAAAAGG-TGCCACTAACT--TGTGGGCTTT-GAAAGGGTGCCACTAA-CT-TG
* * **
1182849 TGGGCTTTAGAAGAGGTTGCCACCGACT
59 TGGGCTTT-GAAAAGGATGCCACTAACT
* * * *
1182877 TGCT-GGCTTCGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGGGCT
1 TG-TGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
**
1182941 TTGAAAAGG-TGCCACTTGCT
65 TTGAAAAGGATGCCACTAACT
* * ** *
1182961 TGCGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAA-GGTGCCACTGGCTTATGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
*
1183025 TG-AAAGGATGCCACTCACT
66 TGAAAAGGATGCCACTAACT
* * ** * * *
1183044 TGTGGGCTTTGAAAAGCTGCCATTAACTTACGAGCTTTGAAAAGGTGCCATTAACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
*
1183109 TGAAAAGGGTTGCCACTAACT
66 TGAAAA-GGATGCCACTAACT
* * * * *
1183130 TGTGGGCTCTG-AAAGGATGCCATTGACTTGTGGGCTTTGAAAAGGGATGCCATTGACTTGTGGG
1 TGTGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTG-AAAGGG-TGCCACTAACTTGTGGG
*
1183194 CTTTGAAAA-GATGCCACTGACT
63 CTTTGAAAAGGATGCCACTAACT
* * * *
1183216 CGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTCTGAAAGGATGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
*
1183280 CTG-AAAGGATGCCACTAACT
65 TTGAAAAGGATGCCACTAACT
* * * *
1183300 TGTGAGCTTTGAAAGGGTTCAACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
* *
1183365 TGAAAAGG-TACCACTGACT
66 TGAAAAGGATGCCACTAACT
* *
1183384 TATGGGGTTTGAAAAGG
1 TGTGGGCTTTGAAAAGG
1183401 GATGCCATTG
Statistics
Matches: 443, Mismatches: 69, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
82 5 0.01
83 69 0.16
84 171 0.39
85 27 0.06
86 95 0.21
87 7 0.02
88 37 0.08
89 9 0.02
91 9 0.02
92 6 0.01
93 7 0.02
94 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTT
TGAAAAGGATGCCACTAACT
Found at i:1183389 original size:28 final size:28
Alignment explanation
Indices: 1182847--1183432 Score: 594
Period size: 28 Copynumber: 20.7 Consensus size: 28
1182837 CACCAACCTG
* *
1182847 TGTGGGCTTTAGAAGAGGTTGCCACCGACT
1 TGTGGGCTTT-GAAAAGG-TGCCACTGACT
*
1182877 TGCT-GGCTTCGAAAAGGTGCCACTGACT
1 TG-TGGGCTTTGAAAAGGTGCCACTGACT
*
1182905 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1182933 TGCGGGCTTTGAAAAGGTGCCACTTG-CT
1 TGTGGGCTTTGAAAAGGTGCCAC-TGACT
* * *
1182961 TGCGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1182989 TGTGGGCTTTG-AAAGGTGCCACTGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
1183016 TATGGGCTTTG-AAAGGATGCCACTCACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* * *
1183044 TGTGGGCTTTGAAAAGCTGCCATTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
** * * *
1183072 TACGAGCTTTGAAAAGGTGCCATTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1183100 TGTGGGCTTTGAAAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
* *
1183130 TGTGGGCTCTG-AAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
*
1183158 TGTGGGCTTTGAAAAGGGATGCCATTGACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
*
1183188 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1183216 CGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
1183244 TGTGGGCTCTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
1183272 TGTGGGCTCTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * *
1183300 TGTGAGCTTTGAAAGGGTTCAACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
1183328 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
1183356 TGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
1183384 TATGGGGTTTGAAAAGGGATGCCATTGACT
1 TGTGGGCTTTGAAAA-GG-TGCCACTGACT
* * *
1183414 CGGGGGCTTCGAAAAGGTG
1 TGTGGGCTTTGAAAAGGTG
1183433 ATATATTGAC
Statistics
Matches: 482, Mismatches: 60, Indels: 30
0.84 0.10 0.05
Matches are distributed among these distances:
27 34 0.07
28 343 0.71
29 29 0.06
30 75 0.16
31 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:1184035 original size:24 final size:24
Alignment explanation
Indices: 1184007--1184055 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1183997 GGCTCAATTA
1184007 TTTTCTCGACACCGAGAGACATTG
1 TTTTCTCGACACCGAGAGACATTG
*
1184031 TTTTCTCGACTCCGAGAGACATTG
1 TTTTCTCGACACCGAGAGACATTG
1184055 T
1 T
1184056 CAATAATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (24 bp):
TTTTCTCGACACCGAGAGACATTG
Found at i:1184682 original size:11 final size:10
Alignment explanation
Indices: 1184647--1184711 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
1184637 CCCTTTTGTA
1184647 TTGTTTTTTT
1 TTGTTTTTTT
1184657 TT-TTTTGGTTT
1 TTGTTTT--TTT
1184668 TTGTTTTTTT
1 TTGTTTTTTT
1184678 CTTGTTTTTTT
1 -TTGTTTTTTT
*
1184689 ACT-TTTTTTT
1 -TTGTTTTTTT
1184699 TTGTTTTGTTT
1 TTGTTTT-TTT
1184710 TT
1 TT
1184712 TTAGAAGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.11
10 16 0.35
11 21 0.46
12 4 0.09
ACGTcount: A:0.02, C:0.03, G:0.11, T:0.85
Consensus pattern (10 bp):
TTGTTTTTTT
Found at i:1188279 original size:13 final size:13
Alignment explanation
Indices: 1188263--1188287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1188253 GGTAAAAGGG
1188263 TTGATAATAATGC
1 TTGATAATAATGC
1188276 TTGATAATAATG
1 TTGATAATAATG
1188288 ATAGAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGATAATAATGC
Found at i:1198807 original size:20 final size:20
Alignment explanation
Indices: 1198782--1198890 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
1198772 GTAAAAAGAC
*
1198782 AAAATGTATCGATACACTGA
1 AAAATGTATCGATACATTGA
*
1198802 AAAATGTATCGATACATTCA
1 AAAATGTATCGATACATTGA
* * *
1198822 TACATGTATCGATTACACTGA
1 AAAATGTATCGA-TACATTGA
* *
1198843 AAAATGTGTCGATACATTCA
1 AAAATGTATCGATACATTGA
* *
1198863 TACATGTATCGATACATTG-
1 AAAATGTATCGATACATTGA
1198882 AAAATGTAT
1 AAAATGTAT
1198891 TAATACATCT
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
19 7 0.10
20 49 0.69
21 15 0.21
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:1198819 original size:51 final size:51
Alignment explanation
Indices: 1198632--1198818 Score: 241
Period size: 51 Copynumber: 3.7 Consensus size: 51
1198622 TTTTAACTAG
* * * *
1198632 ATGTATCAATACA-TTACAAAATGTATCGATAAATCTGGATAAAAAGATAGA
1 ATGTATCGATACACTGA-AAAATGTATCGATACATCTGGGTAAAAAGATAGA
* * *
1198683 ATGTATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAAGATAGA
1 ATGTATCGATACACTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
* * * * * *
1198734 ATGCATTGATACACTAAAAAATGTATCGATACATTTGGGTAAAAAGACAAA
1 ATGTATCGATACACTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
1198785 ATGTATCGATACACTGAAAAATGTATCGATACAT
1 ATGTATCGATACACTGAAAAATGTATCGATACAT
1198819 TCATACATGT
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
51 116 0.99
52 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACACTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
Found at i:1198844 original size:41 final size:40
Alignment explanation
Indices: 1198785--1198890 Score: 178
Period size: 41 Copynumber: 2.6 Consensus size: 40
1198775 AAAAGACAAA
1198785 ATGTATCGATACACTGAAAAATGTATCGATACATTCATAC
1 ATGTATCGATACACTGAAAAATGTATCGATACATTCATAC
*
1198825 ATGTATCGATTACACTGAAAAATGTGTCGATACATTCATAC
1 ATGTATCGA-TACACTGAAAAATGTATCGATACATTCATAC
*
1198866 ATGTATCGATACATTG-AAAATGTAT
1 ATGTATCGATACACTGAAAAATGTAT
1198891 TAATACATCT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 8 0.13
40 15 0.24
41 39 0.63
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (40 bp):
ATGTATCGATACACTGAAAAATGTATCGATACATTCATAC
Found at i:1211010 original size:20 final size:21
Alignment explanation
Indices: 1210985--1211036 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1210975 ATAATTCCTA
1210985 GTATCGATACATTCACTT-AT
1 GTATCGATACATTCACTTGAT
* * *
1211005 GTATCGATACATTGATTTGTT
1 GTATCGATACATTCACTTGAT
1211026 GTATCGATACA
1 GTATCGATACA
1211037 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTCACTTGAT
Found at i:1211925 original size:2 final size:2
Alignment explanation
Indices: 1211918--1211965 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1211908 TTATTAACTT
* * * * *
1211918 TA TA TA TA TA TA TA TA TG TA TG TT TA TG TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1211960 TA TA TA
1 TA TA TA
1211966 ATTATAGAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1212554 original size:15 final size:15
Alignment explanation
Indices: 1212518--1212565 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1212508 TAAATATTTT
*
1212518 AATA-AAATTCAAT-
1 AATATAAATTAAATA
1212531 AAT-TAAATTAAATA
1 AATATAAATTAAATA
1212545 AATATAAATTATAA-A
1 AATATAAATTA-AATA
1212560 AATATA
1 AATATA
1212566 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.37
14 3 0.10
15 14 0.47
16 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATTAAATA
Found at i:1212939 original size:21 final size:22
Alignment explanation
Indices: 1212910--1212951 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1212900 TTTACCATTG
**
1212910 CTTTCGATTTTGGAAATAGAGC
1 CTTTCGATTTTACAAATAGAGC
1212932 CTTT-GATTTTACAAATAGAG
1 CTTTCGATTTTACAAATAGAG
1212952 TTTTTGACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (22 bp):
CTTTCGATTTTACAAATAGAGC
Found at i:1214231 original size:80 final size:81
Alignment explanation
Indices: 1214086--1214279 Score: 332
Period size: 80 Copynumber: 2.5 Consensus size: 81
1214076 CAGTTCTTCT
1214086 TTGAATTAGATTACTATAATAAATTATGTAAAA-ATAAGATAAATTGAGATATAATAAGAGCATA
1 TTGAATTAGATTACTATAATAAATTATGTAAAATATAAGATAAATTGAGATATAATAAGAGCATA
1214150 TAT-TTTTTTTCTAAA
66 TATATTTTTTTCTAAA
1214165 TTGAATTAGATTACTATAATAAATTATGTAAAATATAAGATAAATTGAGATATAATAAGAGCATA
1 TTGAATTAGATTACTATAATAAATTATGTAAAATATAAGATAAATTGAGATATAATAAGAGCATA
1214230 TATATTTTTTTCTAAA
66 TATATTTTTTTCTAAA
1214246 TTGAATTAG-----TATAATAAATTATGTAAAATA-AAGA
1 TTGAATTAGATTACTATAATAAATTATGTAAAATATAAGA
1214280 ATGAATATAA
Statistics
Matches: 113, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
75 4 0.04
76 21 0.19
79 33 0.29
80 34 0.30
81 21 0.19
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (81 bp):
TTGAATTAGATTACTATAATAAATTATGTAAAATATAAGATAAATTGAGATATAATAAGAGCATA
TATATTTTTTTCTAAA
Found at i:1216106 original size:21 final size:22
Alignment explanation
Indices: 1216079--1216132 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
1216069 AAATGATGAA
1216079 TAGTTTTTAAAATA-AACG-A-G
1 TAGTTTTTAAAATATAA-GTAGG
1216099 TAGTTTTT-AAATATAAGTAGG
1 TAGTTTTTAAAATATAAGTAGG
1216120 TAGTTTTTTAAAA
1 TAG-TTTTTAAAA
1216133 AGTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.21
20 11 0.38
21 4 0.14
22 5 0.17
23 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (22 bp):
TAGTTTTTAAAATATAAGTAGG
Done.