Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1132470 original size:2 final size:2
Alignment explanation
Indices: 1132463--1132552 Score: 101
Period size: 2 Copynumber: 45.5 Consensus size: 2
1132453 TTTTCTAGAT
* *
1132463 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TG TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * **
1132504 TA TA TG TA TA TA TG TA TA TA TA TG TA TA TA TG TA TA TA CG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1132546 TA TA TA T
1 TA TA TA T
1132553 TTAATGCTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1134721 original size:34 final size:34
Alignment explanation
Indices: 1134682--1134749 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1134672 AACGACTTAA
* * *
1134682 TATTAAAATTTATTACTT-TATTTTTATTTTTATT
1 TATTAAAATTT-GTAATTATATTTTCATTTTTATT
1134716 TATTAAAATTTGTAATTATATTTTCATTTTTATT
1 TATTAAAATTTGTAATTATATTTTCATTTTTATT
1134750 GTTTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 26 0.87
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (34 bp):
TATTAAAATTTGTAATTATATTTTCATTTTTATT
Found at i:1137635 original size:121 final size:120
Alignment explanation
Indices: 1137408--1137651 Score: 470
Period size: 121 Copynumber: 2.0 Consensus size: 120
1137398 CTGAAAAGAA
1137408 TCTCAATTGTCTGCAATAAATGCATCAGCAACAACACACATATATAAGAAAAAATAGAATAATAT
1 TCTCAATTGTCTGCAATAAATGCATCAGCAACAACACACATATATAAGAAAAAATAGAATAATAT
1137473 TCCATAGTTAATTGAAAGCAAGACAAATTAGAGGTTCCAAATACTACGGAATGCC
66 TCCATAGTTAATTGAAAGCAAGACAAATTAGAGGTTCCAAATACTACGGAATGCC
1137528 TCTCAATTGTCTGCAATAAATGCATCAGCAACAACACACATATATAAGAAAAAAATAGAATAATA
1 TCTCAATTGTCTGCAATAAATGCATCAGCAACAACACACATATATAAG-AAAAAATAGAATAATA
*
1137593 TTCCATAGTTAATTGAAAGCAAGACAAATTAGAGGTTTCAAATACTACGGAATGCC
65 TTCCATAGTTAATTGAAAGCAAGACAAATTAGAGGTTCCAAATACTACGGAATGCC
1137649 TCT
1 TCT
1137652 GTTATATATA
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 48 0.39
121 74 0.61
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (120 bp):
TCTCAATTGTCTGCAATAAATGCATCAGCAACAACACACATATATAAGAAAAAATAGAATAATAT
TCCATAGTTAATTGAAAGCAAGACAAATTAGAGGTTCCAAATACTACGGAATGCC
Found at i:1139093 original size:2 final size:2
Alignment explanation
Indices: 1139086--1139112 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1139076 TGTTTCCCCA
1139086 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1139113 GCGCGCGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1145868 original size:14 final size:14
Alignment explanation
Indices: 1145849--1145887 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
1145839 AATTTTTATG
1145849 ATTAATATTATAAA
1 ATTAATATTATAAA
*
1145863 ATTAATAATATATAAT
1 ATTAAT-AT-TATAAA
1145879 ATTAATATT
1 ATTAATATT
1145888 TAATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAATATTATAAA
Found at i:1145882 original size:16 final size:17
Alignment explanation
Indices: 1145851--1145885 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1145841 TTTTTATGAT
1145851 TAATATTATAAAATTAA
1 TAATATTATAAAATTAA
*
1145868 TAATA-TATAATATTAA
1 TAATATTATAAAATTAA
1145884 TA
1 TA
1145886 TTTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATATTATAAAATTAA
Found at i:1145908 original size:9 final size:9
Alignment explanation
Indices: 1145883--1145914 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
1145873 TATAATATTA
1145883 ATATTTAAT
1 ATATTTAAT
1145892 AT-TTTAAT
1 ATATTTAAT
1145900 ATATTTAAT
1 ATATTTAAT
1145909 A-ATTTA
1 ATATTTA
1145915 TTAAAATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 13 0.59
9 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTAAT
Found at i:1146085 original size:7 final size:7
Alignment explanation
Indices: 1146051--1146080 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1146041 TTGACATAAA
1146051 TAATTTT
1 TAATTTT
1146058 TAATTTT
1 TAATTTT
1146065 TAATTTT
1 TAATTTT
1146072 TAATATTT
1 TAAT-TTT
1146080 T
1 T
1146081 TTATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TAATTTT
Found at i:1146444 original size:15 final size:15
Alignment explanation
Indices: 1146424--1146465 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
1146414 AAATAATTTT
*
1146424 ATTTTTATTATTAAA
1 ATTTTTACTATTAAA
1146439 ATTTTTACTATTAAA
1 ATTTTTACTATTAAA
1146454 ATTTTTACTATT
1 ATTTTTACTATT
1146466 TTAACTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTACTATTAAA
Found at i:1146855 original size:29 final size:30
Alignment explanation
Indices: 1146818--1146874 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
1146808 CGATTTTAAG
*
1146818 AAAAGTTATTCTA-TAATTTTATTTTTATTT
1 AAAAGTTATTCTAGTAATATT-TTTTTATTT
*
1146848 AAAA-TTATTTTAGTAATATTTTTTTAT
1 AAAAGTTATTCTAGTAATATTTTTTTAT
1146875 GTCTGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (30 bp):
AAAAGTTATTCTAGTAATATTTTTTTATTT
Found at i:1146932 original size:20 final size:22
Alignment explanation
Indices: 1146903--1146962 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1146893 TTCAAATATT
*
1146903 TAATTTTTATATTAAA-A-ATA
1 TAATTATTATATTAAATACATA
1146923 TAATTATTATTATTATAATACATA
1 TAATTATTA-TATTA-AATACATA
*
1146947 TAAATA-TATATTAAAT
1 TAATTATTATATTAAAT
1146963 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 7 0.21
23 3 0.09
24 8 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATTATTATATTAAATACATA
Found at i:1149184 original size:21 final size:21
Alignment explanation
Indices: 1149159--1149207 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1149149 AAAGTATTAA
1149159 TTTAATAA-TTACTTTTAAAAT
1 TTTAATAATTTA-TTTTAAAAT
1149180 TTTAATAATTTATTTTAAAAT
1 TTTAATAATTTATTTTAAAAT
*
1149201 ATTAATA
1 TTTAATA
1149208 GCTAGTAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATAATTTATTTTAAAAT
Found at i:1149333 original size:11 final size:11
Alignment explanation
Indices: 1149317--1149365 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1149307 AAAATAAAGA
1149317 TATATTTATAT
1 TATATTTATAT
*
1149328 TATATTCATAT
1 TATATTTATAT
1149339 TAT-TTT-TA-
1 TATATTTATAT
1149347 TATA-TTATAAT
1 TATATTTAT-AT
1149358 TATATTTA
1 TATATTTA
1149366 AAGTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 3 0.10
11 17 0.55
12 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1149365 original size:19 final size:19
Alignment explanation
Indices: 1149328--1149375 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1149318 ATATTTATAT
*
1149328 TATATTCAT-ATTATTTTTA
1 TATATT-ATAATTATATTTA
1149347 TATATTATAATTATATTTA
1 TATATTATAATTATATTTA
*
1149366 AAGTATTATA
1 TA-TATTATA
1149376 TATTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATATTATAATTATATTTA
Found at i:1149671 original size:19 final size:21
Alignment explanation
Indices: 1149647--1149694 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
1149637 AATTATTAAA
1149647 ATATTAAAAATTTA-A-TTTT
1 ATATTAAAAATTTATATTTTT
*
1149666 ATATT-AATATTTATATTTTT
1 ATATTAAAAATTTATATTTTT
1149686 ATAATTAAA
1 AT-ATTAAA
1149695 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 6 0.25
21 3 0.12
22 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTAAAAATTTATATTTTT
Found at i:1150850 original size:15 final size:15
Alignment explanation
Indices: 1150792--1150865 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 15
1150782 TTTATAAATT
1150792 ATTTA-TTATATTTAA
1 ATTTATTTA-ATTTAA
*
1150807 ATGTATTTAATATTAA
1 ATTTATTTAAT-TTAA
1150823 AGTTT-TTAATAATTTAA
1 A-TTTATT--TAATTTAA
1150840 ATTTATTTAA-TTAA
1 ATTTATTTAATTTAA
*
1150854 ATTAATTTAATT
1 ATTTATTTAATT
1150866 AGATTGATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.27
15 10 0.20
16 13 0.27
17 9 0.18
18 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTATTTAATTTAA
Found at i:1152315 original size:29 final size:27
Alignment explanation
Indices: 1152238--1152337 Score: 81
Period size: 27 Copynumber: 3.8 Consensus size: 27
1152228 TTATTATTTA
1152238 ATAATA-AAAATAATATTTTTATTTAAATT
1 ATAATATAAAATAATA-TTTTA--TAAATT
*
1152267 -TAATTATAAAA-AATA-TATA-AAATT
1 ATAA-TATAAAATAATATTTTATAAATT
1152291 ATAATATAAAATAATATTCTTAT-AA-T
1 ATAATATAAAATAATATT-TTATAAATT
1152317 ATAATAATAAAATAAT-TTTTA
1 ATAAT-ATAAAATAATATTTTA
1152338 ATTAATCTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
24 12 0.20
25 10 0.16
26 9 0.15
27 17 0.28
28 3 0.05
29 6 0.10
30 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAATATAAAATAATATTTTATAAATT
Found at i:1152694 original size:29 final size:30
Alignment explanation
Indices: 1152654--1152774 Score: 91
Period size: 29 Copynumber: 4.2 Consensus size: 30
1152644 TTATACAGAT
* *
1152654 AATAATTT-ATATATT-TATATTATATTT-A
1 AATATTTTAATATATTATA-ATAATATTTAA
*
1152682 TATATTTTAATATATTATAATAATATTTAA
1 AATATTTTAATATATTATAATAATATTTAA
1152712 AATATTTT-ATAT-TTAT-ATAA-ATTTTAA
1 AATATTTTAATATATTATAATAATA-TTTAA
1152739 TAA-ATTATTAATTTATATTATAA-AAT-TTTAA
1 -AATATT-TTAA--TATATTATAATAATATTTAA
1152770 AATAT
1 AATAT
1152775 ATATTTTTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 23
0.74 0.04 0.22
Matches are distributed among these distances:
26 1 0.01
27 12 0.16
28 14 0.18
29 20 0.26
30 12 0.16
31 10 0.13
32 6 0.08
33 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
AATATTTTAATATATTATAATAATATTTAA
Found at i:1152696 original size:10 final size:10
Alignment explanation
Indices: 1152662--1152750 Score: 55
Period size: 10 Copynumber: 9.2 Consensus size: 10
1152652 ATAATAATTT
1152662 ATATATTTATA
1 ATATATTT-TA
*
1152673 TTATA-TTT-
1 ATATATTTTA
1152681 ATATATTTTA
1 ATATATTTTA
*
1152691 ATATATTATA
1 ATATATTTTA
1152701 ATA-ATATTTA
1 ATATAT-TTTA
*
1152711 AAATATTTT-
1 ATATATTTTA
*
1152720 ATAT-TTAT-
1 ATATATTTTA
*
1152728 ATAAATTTTA
1 ATATATTTTA
*
1152738 ATAAATTATTA
1 ATATATT-TTA
1152749 AT
1 AT
1152751 TTATATTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.16
9 12 0.19
10 29 0.47
11 11 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATTTTA
Found at i:1152731 original size:27 final size:27
Alignment explanation
Indices: 1152658--1152756 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
1152648 ACAGATAATA
* *
1152658 ATTTATATATTTATATTATATTT-ATAT
1 ATTT-TATATTTATATAATATTTAAAAT
1152685 ATTTTAATATATTATAATAATATTTAAAAT
1 ATTTT-ATAT-TTAT-ATAATATTTAAAAT
1152715 ATTTTATATTTATATAA-ATTTTAATAA-
1 ATTTTATATTTATATAATA-TTTAA-AAT
1152742 ATTATTA-ATTTATAT
1 ATT-TTATATTTATAT
1152757 TATAAAATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 14
0.80 0.03 0.18
Matches are distributed among these distances:
26 2 0.03
27 28 0.44
28 13 0.21
29 12 0.19
30 8 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTTATATTTATATAATATTTAAAAT
Found at i:1152775 original size:20 final size:20
Alignment explanation
Indices: 1152690--1152776 Score: 51
Period size: 20 Copynumber: 4.3 Consensus size: 20
1152680 TATATATTTT
1152690 AATATATTATAATAATATTTAA
1 AATATATTATAA-AAT-TTTAA
*
1152712 AATAT-TT-T-ATATTTATATA
1 AATATATTATAAAATTT-TA-A
1152731 AAT-T-TTA-ATAAATTATTAA
1 AATATATTATA-AAATT-TTAA
**
1152750 TTTATATTATAAAATTTTAA
1 AATATATTATAAAATTTTAA
1152770 AATATAT
1 AATATAT
1152777 ATTTTTATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
17 2 0.04
18 7 0.14
19 7 0.14
20 17 0.34
21 11 0.22
22 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATATTATAAAATTTTAA
Found at i:1152784 original size:30 final size:29
Alignment explanation
Indices: 1152681--1152784 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 29
1152671 TATTATATTT
1152681 ATATATTTTAATATATTATAATAATATTT-AAA
1 ATATATTTT--TATATTATAA-AAT-TTTAAAA
*
1152713 ATAT-TTTATAT-TTATATAAATTTTAATAA
1 ATATATTTTTATATTATA-AAATTTTAA-AA
1152742 AT-TATTAATTTATATTATAAAATTTTAAAA
1 ATATATT--TTTATATTATAAAATTTTAAAA
1152772 TATATATTTTTAT
1 -ATATATTTTTAT
1152785 CTATCATACT
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
27 3 0.05
28 10 0.16
29 10 0.16
30 7 0.11
31 18 0.30
32 13 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATATTTTTATATTATAAAATTTTAAAA
Found at i:1153473 original size:28 final size:30
Alignment explanation
Indices: 1153433--1153491 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
1153423 AGTTTCATTT
*
1153433 TTTATATATTTTATATAAATTTATATTTAA
1 TTTATATATTTTATATAAATTTATATATAA
*
1153463 TTTAT-TA-TTTATTTAAATTTATATATAA
1 TTTATATATTTTATATAAATTTATATATAA
1153491 T
1 T
1153492 CAATACATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 20 0.74
29 2 0.07
30 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTATATATTTTATATAAATTTATATATAA
Found at i:1154182 original size:23 final size:23
Alignment explanation
Indices: 1154156--1154208 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1154146 CGAAATTAAG
1154156 TATTTATATTAAATA-ATTTATA
1 TATTTATATTAAATATATTTATA
* * *
1154178 TTATTTAAATTTATTATATTTATA
1 -TATTTATATTAAATATATTTATA
1154202 TATTTAT
1 TATTTAT
1154209 GTTATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTATATTAAATATATTTATA
Found at i:1154207 original size:32 final size:32
Alignment explanation
Indices: 1154171--1154231 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1154161 ATATTAAATA
*
1154171 ATTTATATTATTTAAATTTATTATATTTATAT
1 ATTTATATTATTTAAATGTATTATATTTATAT
* **
1154203 ATTTATGTTATTTTTATGTATTATATTTA
1 ATTTATATTATTTAAATGTATTATATTTA
1154232 AAATTATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (32 bp):
ATTTATATTATTTAAATGTATTATATTTATAT
Found at i:1154855 original size:2 final size:2
Alignment explanation
Indices: 1154848--1154876 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1154838 GAATCTTTTA
1154848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1154877 ATTAGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1156088 original size:17 final size:15
Alignment explanation
Indices: 1156067--1156113 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1156057 AAAGATTTTT
1156067 ATTTAGATTTTATTTA
1 ATTTAG-TTTTATTTA
1156083 ATTTTAGTTGTT-TTTA
1 A-TTTAGTT-TTATTTA
*
1156099 AATTAGTTTTATTTA
1 ATTTAGTTTTATTTA
1156114 CTTTCCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.07
15 10 0.37
16 8 0.30
17 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
ATTTAGTTTTATTTA
Found at i:1158455 original size:16 final size:16
Alignment explanation
Indices: 1158446--1158477 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1158436 TTTTTATTTT
1158446 ATTTTATTTTTTTGTA
1 ATTTTATTTTTTTGTA
*
1158462 ATTTTATTTTCTTGTA
1 ATTTTATTTTTTTGTA
1158478 GGCAAATGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (16 bp):
ATTTTATTTTTTTGTA
Found at i:1160084 original size:2 final size:2
Alignment explanation
Indices: 1160077--1160112 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1160067 AAATTGTTAA
1160077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1160113 GGCCATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1161435 original size:22 final size:21
Alignment explanation
Indices: 1161404--1161445 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1161394 ATTTTTTATT
1161404 TAAATTTAAT-TATAAAATATA
1 TAAATTTAATAT-TAAAATATA
1161425 TAAATATTAATATTAAAATAT
1 TAAAT-TTAATATTAAAATAT
1161446 TTTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 13 0.68
23 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTAATATTAAAATATA
Found at i:1162450 original size:21 final size:19
Alignment explanation
Indices: 1162416--1162457 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1162406 TAAATATAAA
1162416 AATATTTTATATTAATATT
1 AATATTTTATATTAATATT
*
1162435 AATATTTTTATAATTAATTTT
1 AATA-TTTTAT-ATTAATATT
1162456 AA
1 AA
1162458 ATAAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 6 0.30
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTTTATATTAATATT
Found at i:1163197 original size:140 final size:140
Alignment explanation
Indices: 1162957--1163223 Score: 453
Period size: 140 Copynumber: 1.9 Consensus size: 140
1162947 ATGTCTGTTT
*
1162957 ATCCATCAATCAGCTTATCTGTCTAGCTTGATAAAGGTTGAATTTTAGACATGATTATTTTTAAT
1 ATCCATCAATCAGCTTATCTGTCTAGCTTGATAAAGGTTGAACTTTAGACATGATTATTTTTAAT
*
1163022 TTAGATTGATTCAATCCACTTGATTTGAATAAAAAATTTAAAAAATTCATACTGTAACCTAATCT
66 TCAGATTGATTCAATCCACTTGATTTGAATAAAAAATTTAAAAAATTCATACTGTAACCTAATCT
1163087 ATGTCGATTG
131 ATGTCGATTG
* * *
1163097 ATCCATCAGTCAGCTTATTTGTCTGGCTTGATAAAGGTTGAACTTTAGACATGATTATTTTTAAT
1 ATCCATCAATCAGCTTATCTGTCTAGCTTGATAAAGGTTGAACTTTAGACATGATTATTTTTAAT
* * * *
1163162 TCAGATTGATTCGATCCACTTGATTTGAATAAAAAATTTAAAAAATTTATATTGTGACCTAA
66 TCAGATTGATTCAATCCACTTGATTTGAATAAAAAATTTAAAAAATTCATACTGTAACCTAA
1163224 CTTAATTTAT
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 118 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (140 bp):
ATCCATCAATCAGCTTATCTGTCTAGCTTGATAAAGGTTGAACTTTAGACATGATTATTTTTAAT
TCAGATTGATTCAATCCACTTGATTTGAATAAAAAATTTAAAAAATTCATACTGTAACCTAATCT
ATGTCGATTG
Found at i:1163741 original size:16 final size:16
Alignment explanation
Indices: 1163702--1163742 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1163692 AAAATAATCC
1163702 AAATTTGAAATAATTT
1 AAATTTGAAATAATTT
* *
1163718 AGAGTTGAAATAATTT
1 AAATTTGAAATAATTT
1163734 AAATTTGAA
1 AAATTTGAA
1163743 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (16 bp):
AAATTTGAAATAATTT
Found at i:1164413 original size:25 final size:22
Alignment explanation
Indices: 1164392--1164437 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1164382 AAATTTATTT
1164392 TATTATTTAATTATTATTTTTATAG
1 TATTATTT-A-TA-TATTTTTATAG
1164417 TATTATTTATATATTTTTATA
1 TATTATTTATATATTTTTATA
1164438 ATGAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 1 0.05
25 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTTATATATTTTTATAG
Found at i:1178730 original size:16 final size:14
Alignment explanation
Indices: 1178698--1178753 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 14
1178688 TTATATACGT
1178698 AAATATAAAATTTTA
1 AAAT-TAAAATTTTA
1178713 AAATTACAAATATTTA
1 AAATTA-AAAT-TTTA
1178729 AAATTTAAAATTTTTA
1 AAA-TTAAAA-TTTTA
1178745 AATATTAAA
1 AA-ATTAAA
1178754 TAAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.06
15 8 0.22
16 21 0.58
17 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAAAATTTTA
Found at i:1179173 original size:6 final size:6
Alignment explanation
Indices: 1179155--1179185 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1179145 CAAATCAGAA
*
1179155 TAAATT TATATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
1179186 TTTTTCGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TAAATT
Found at i:1179482 original size:21 final size:21
Alignment explanation
Indices: 1179446--1179499 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1179436 TGATATAATT
*
1179446 ATATAACAT-AAA-TATTAAA
1 ATATAATATAAAATTATTAAA
1179465 ATATAATATAAAATTATTAAA
1 ATATAATATAAAATTATTAAA
*
1179486 ATATGATATAAAAT
1 ATATAATATAAAAT
1179500 ATAATACGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.26
20 3 0.10
21 20 0.65
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAATATAAAATTATTAAA
Found at i:1180095 original size:2 final size:2
Alignment explanation
Indices: 1180072--1180143 Score: 50
Period size: 2 Copynumber: 38.5 Consensus size: 2
1180062 ATAGATAATT
*
1180072 TA TA T- TA TA TA AA TA T- TA -A TA TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
1180112 GA TA T- TA -A TA T- TA TT TA TA TA TCA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T
1180144 TTTAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
1 7 0.13
2 45 0.82
3 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1180157 original size:29 final size:28
Alignment explanation
Indices: 1180069--1180138 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1180059 TAAATAGATA
*
1180069 ATTTATAT-TATAT-AAATATTAATATAT
1 ATTTATATATATATGAGATATTAATAT-T
*
1180096 ATATATATATATATGAGATATTAATATT
1 ATTTATATATATATGAGATATTAATATT
1180124 ATTTATATATCATAT
1 ATTTATATAT-ATAT
1180139 TATATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 7 0.19
28 15 0.41
29 15 0.41
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (28 bp):
ATTTATATATATATGAGATATTAATATT
Found at i:1180869 original size:81 final size:81
Alignment explanation
Indices: 1180730--1180893 Score: 226
Period size: 81 Copynumber: 2.0 Consensus size: 81
1180720 TAGACCAGAT
* *
1180730 CTCAGTTGATAAGTTTCATGAATATCTGTTTTTCGTGTAAAGGATGTCTCAATCTAAGATAACAA
1 CTCAGTTGATAAGTTTCATGAATATCTGTTTTTCGTGTAAAGGATGTCTCAATATAAGATAAAAA
1180795 GGAGGAAAGATTTGAA
66 GGAGGAAAGATTTGAA
* *
1180811 CTCAGTTGATGAGTTTCATGAATATTTG-TTTTC-TGTACAAAGGATGT-TGCAATATAAGATAA
1 CTCAGTTGATAAGTTTCATGAATATCTGTTTTTCGTGT--AAAGGATGTCT-CAATATAAGATAA
* *
1180873 AAAGGAGTAAAGATTTTAA
63 AAAGGAGGAAAGATTTGAA
1180892 CT
1 CT
1180894 TTAAATCTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
79 3 0.04
80 6 0.08
81 65 0.88
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (81 bp):
CTCAGTTGATAAGTTTCATGAATATCTGTTTTTCGTGTAAAGGATGTCTCAATATAAGATAAAAA
GGAGGAAAGATTTGAA
Found at i:1182542 original size:15 final size:16
Alignment explanation
Indices: 1182521--1182562 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1182511 TTCTTGTTTA
1182521 ATAAAAAATATTT-TT
1 ATAAAAAATATTTATT
*
1182536 TTAAAAAA-ATTTATT
1 ATAAAAAATATTTATT
1182551 ATAAAAATATAT
1 ATAAAAA-ATAT
1182563 AAATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 1 0.05
17 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAAAATATTTATT
Found at i:1182591 original size:28 final size:30
Alignment explanation
Indices: 1182560--1182618 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1182550 TATAAAAATA
*
1182560 TATAAATATT-AATATTAAAATA-ATTTTT
1 TATAAATATTAAATAATAAAATATATTTTT
* *
1182588 TATATATTTTAAATAATAAAATATATTTTT
1 TATAAATATTAAATAATAAAATATATTTTT
1182618 T
1 T
1182619 GTATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
29 11 0.42
30 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATAAATATTAAATAATAAAATATATTTTT
Found at i:1183389 original size:2 final size:2
Alignment explanation
Indices: 1183382--1183407 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1183372 CTATCCTTTA
1183382 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1183408 GTGTGTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1184866 original size:2 final size:2
Alignment explanation
Indices: 1184859--1184887 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1184849 TTCGCTTGCC
1184859 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 T
1184888 TAACACGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1187385 original size:15 final size:15
Alignment explanation
Indices: 1187362--1187422 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
1187352 TAATTATATG
*
1187362 AATATAAATATAATA
1 AATAAAAATATAATA
*
1187377 AATAAAAATAATTATA
1 AATAAAAAT-ATAATA
1187393 ATATAATATAATATAATA
1 A-ATAA-A-AATATAATA
* *
1187411 ATTATAAATATA
1 AATAAAAATATA
1187423 TTATGAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 14 0.38
16 7 0.19
17 6 0.16
18 7 0.19
19 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAAAAATATAATA
Found at i:1187396 original size:24 final size:25
Alignment explanation
Indices: 1187364--1187422 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
1187354 ATTATATGAA
1187364 TATAAATATAATA-AATAAAAATAAT
1 TATAAATATAATATAAT-AAAATAAT
*
1187389 TAT-AATATAATATAATATAATAAT
1 TATAAATATAATATAATAAAATAAT
1187413 TATAAATATA
1 TATAAATATA
1187423 TTATGAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TATAAATATAATATAATAAAATAAT
Found at i:1187399 original size:5 final size:5
Alignment explanation
Indices: 1187349--1187410 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
1187339 ACAAACTTAG
*
1187349 ATATA AT-T- ATATGA ATATAA ATATA ATA-A ATA-A AAATA ATTATA
1 ATATA ATATA ATAT-A ATAT-A ATATA ATATA ATATA ATATA A-TATA
1187393 ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATA
1187411 ATTATAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
3 2 0.04
4 9 0.18
5 25 0.51
6 13 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:1187473 original size:20 final size:20
Alignment explanation
Indices: 1187445--1187488 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1187435 GAACGAATTG
* *
1187445 AAATTTATAAAATTTTATAT
1 AAATATATAAAATTTTAAAT
*
1187465 AAATATATAATATTTTAAAT
1 AAATATATAAAATTTTAAAT
1187485 AAAT
1 AAAT
1187489 TTTATGATAC
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATATAAAATTTTAAAT
Found at i:1187775 original size:21 final size:21
Alignment explanation
Indices: 1187732--1187776 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1187722 TCTTCTTAAT
*
1187732 TTTTTATGTATTATTCATCTA
1 TTTTTATGTATTATTCATATA
*
1187753 TTTTTATGTTTTATT-ATTATA
1 TTTTTATGTATTATTCA-TATA
1187774 TTT
1 TTT
1187777 AAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTATGTATTATTCATATA
Found at i:1194921 original size:5 final size:5
Alignment explanation
Indices: 1194907--1195065 Score: 82
Period size: 5 Copynumber: 32.8 Consensus size: 5
1194897 TTTGTTCGTA
* ** * *
1194907 ATATT ATATT TTATT ATATT ATAATT ATATT -TAAA ATATT TTATA AT-TT
1 ATATT ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT
* * ** * *
1194956 TTATT -TATT TTAAA ATATT A-ATA AT-TT ATATT AT-TT ATATT TTATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * * * *
1195002 ATATT TTATT ATATTT ATATT TTATT TTATT ATATT -TATT -TTTT ATTTT
1 ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
*
1195051 ATTTT ATAATT ATAT
1 ATATT AT-ATT ATAT
1195066 CGTATTTAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
4 25 0.21
5 79 0.67
6 14 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATATT
Found at i:1194921 original size:10 final size:10
Alignment explanation
Indices: 1194908--1195053 Score: 111
Period size: 10 Copynumber: 14.4 Consensus size: 10
1194898 TTGTTCGTAA
1194908 TATTATATTT
1 TATTATATTT
1194918 TATTATATTAT
1 TATTATATT-T
*
1194929 AATTATA-TT
1 TATTATATTT
**
1194938 TAAAATATTT
1 TATTATATTT
*
1194948 TATAAT-TTT
1 TATTATATTT
1194957 TATT-TATTT
1 TATTATATTT
**
1194966 TAAAATATTAAT
1 TATTATATT--T
* *
1194978 AATT-TATAT
1 TATTATATTT
1194987 TATTTATATTT
1 TA-TTATATTT
1194998 TATTATATTT
1 TATTATATTT
1195008 TATTATATTT
1 TATTATATTT
*
1195018 ATATTTTATTT
1 -TATTATATTT
1195029 TATTATATTT
1 TATTATATTT
* *
1195039 ATTTTTTATTT
1 -TATTATATTT
1195050 TATT
1 TATT
1195054 TTATAATTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
8 1 0.01
9 18 0.17
10 53 0.50
11 33 0.31
12 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TATTATATTT
Found at i:1194933 original size:21 final size:21
Alignment explanation
Indices: 1194909--1195065 Score: 88
Period size: 21 Copynumber: 7.3 Consensus size: 21
1194899 TGTTCGTAAT
1194909 ATTATATTTTATTATATTATA
1 ATTATATTTTATTATATTATA
* * *
1194930 ATTATATTTAAAATATTTTATA
1 ATTATATTT-TATTATATTATA
* * **
1194952 ATT-TTTATTTATTTTAAAAT-
1 ATTATAT-TTTATTATATTATA
1194972 ATTAATAATTTATATTAT-TTAT-
1 ATT-AT-ATTT-TATTATATTATA
* * *
1194994 ATTTTATTATATTTTATTATA
1 ATTATATTTTATTATATTATA
* *
1195015 TTTATATTTTATTTTATTATA
1 ATTATATTTTATTATATTATA
* * *
1195036 TTTATTTTTTATTTTATTTTATA
1 ATTATATTTTA--TTATATTATA
1195059 ATTATAT
1 ATTATAT
1195066 CGTATTTAAA
Statistics
Matches: 101, Mismatches: 25, Indels: 18
0.70 0.17 0.12
Matches are distributed among these distances:
19 5 0.05
20 10 0.10
21 45 0.45
22 22 0.22
23 19 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTATATTTTATTATATTATA
Found at i:1194964 original size:27 final size:27
Alignment explanation
Indices: 1194934--1195018 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
1194924 ATTATAATTA
1194934 TATTTAAAATATTTTATAATTTTTATT
1 TATTTAAAATATTTTATAATTTTTATT
* *
1194961 TATTTTAAAATA-TTAATAATTTATA-T
1 TA-TTTAAAATATTTTATAATTTTTATT
*
1194987 TATTT---ATATTTTATTATATTTTATT
1 TATTTAAAATATTTTATAAT-TTTTATT
1195012 ATATTTA
1 -TATTTA
1195019 TATTTTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 3 0.06
23 6 0.13
24 4 0.09
25 4 0.09
26 8 0.17
27 13 0.28
28 9 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTAAAATATTTTATAATTTTTATT
Found at i:1195009 original size:26 final size:26
Alignment explanation
Indices: 1194979--1195053 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
1194969 AATATTAATA
1194979 ATTTATA--TTATTTATATTTTATTAT
1 ATTTATATTTTATTT-TATTTTATTAT
* *
1195004 ATTT-TATTATATTTATATTTTATTTT
1 ATTTATATTTTATTT-TATTTTATTAT
*
1195030 A-TTATATTTATTTTTTATTTTATT
1 ATTTATATTT-TATTTTATTTTATT
1195054 TTATAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.05
25 6 0.14
26 30 0.71
27 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
ATTTATATTTTATTTTATTTTATTAT
Found at i:1195054 original size:26 final size:30
Alignment explanation
Indices: 1194909--1195057 Score: 117
Period size: 31 Copynumber: 4.9 Consensus size: 30
1194899 TGTTCGTAAT
* *
1194909 ATTATATTTTATTATATTATA-ATTATATTT
1 ATTATATTTTATTATATTTTATTTTAT-TTT
** *
1194939 AAAATATTTTATAAT-TTTTA-TTTATTTT
1 ATTATATTTTATTATATTTTATTTTATTTT
** * *
1194967 AAAATATTAATAATT-TATATTATTTATATTTT
1 ATTATATT--TTATTATATTTTATTT-TATTTT
1194999 ATTATATTTTATTATATTTATATTTTATTTT
1 ATTATATTTTATTATATTT-TATTTTATTTT
* *
1195030 ATTATATTTATTTTTTATTTTATTTTAT
1 ATTATATTT-TATTATATTTTATTTTAT
1195058 AATTATATCG
Statistics
Matches: 97, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
28 11 0.11
29 9 0.09
30 23 0.24
31 29 0.30
32 25 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
ATTATATTTTATTATATTTTATTTTATTTT
Found at i:1195063 original size:16 final size:15
Alignment explanation
Indices: 1194980--1195063 Score: 63
Period size: 16 Copynumber: 5.7 Consensus size: 15
1194970 ATATTAATAA
1194980 TTTATATTATTTATAT
1 TTTATATTATTT-TAT
1194996 TTTAT-TATATTTTAT
1 TTTATAT-TATTTTAT
* *
1195011 TATATTTATATTTTA-
1 TTTATAT-TATTTTAT
1195026 TTT-TATTATATTTA-
1 TTTATATTAT-TTTAT
1195040 TTT-T-TTATTTTAT
1 TTTATATTATTTTAT
1195053 TTTATAATTAT
1 TTTAT-ATTAT
1195064 ATCGTATTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
12 4 0.07
13 10 0.17
14 11 0.19
15 10 0.17
16 23 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATATTATTTTAT
Found at i:1195087 original size:17 final size:17
Alignment explanation
Indices: 1195067--1195100 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1195057 TAATTATATC
1195067 GTATTTAAAATTATTAA
1 GTATTTAAAATTATTAA
*
1195084 GTATTTAAAATTTTTAA
1 GTATTTAAAATTATTAA
1195101 AAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
GTATTTAAAATTATTAA
Found at i:1195132 original size:14 final size:13
Alignment explanation
Indices: 1195094--1195130 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1195084 GTATTTAAAA
1195094 TTTTTAAAAAATT
1 TTTTTAAAAAATT
**
1195107 TTTTTTTAAAATT
1 TTTTTAAAAAATT
1195120 TTTTTAAAAAA
1 TTTTTAAAAAA
1195131 ATGTAGAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAAAATT
Found at i:1195328 original size:105 final size:105
Alignment explanation
Indices: 1195218--1195420 Score: 316
Period size: 105 Copynumber: 1.9 Consensus size: 105
1195208 GTTGTTAAAA
* * * * *
1195218 TTAATTAAATAATTATTTATAGTAATATTTTTATATTAAAAATAATAATTGATAGTTAAGTTGAT
1 TTAATTAAATAATTATTTAAAATAATATTTTAATATTAAAAATAATAATTGATAATTAAGTTAAT
* *
1195283 AATTTTTAATGCATTAAAATTATAACTTGACTTAATTAAT
66 AATCTTTAATGCATTAAAATTATAACTTAACTTAATTAAT
* *
1195323 TTAATTAAATTATTATTTAAAATAATATTTTAATATTAAAAATAATAATTGATAATTAATTTAAT
1 TTAATTAAATAATTATTTAAAATAATATTTTAATATTAAAAATAATAATTGATAATTAAGTTAAT
*
1195388 AATCTTTAATGCATTAAAATTGTAACTTAACTT
66 AATCTTTAATGCATTAAAATTATAACTTAACTT
1195421 TAAACCGTGT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (105 bp):
TTAATTAAATAATTATTTAAAATAATATTTTAATATTAAAAATAATAATTGATAATTAAGTTAAT
AATCTTTAATGCATTAAAATTATAACTTAACTTAATTAAT
Found at i:1195578 original size:11 final size:11
Alignment explanation
Indices: 1195562--1195618 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
1195552 TATATATATA
1195562 TATATTTTATT
1 TATATTTTATT
*
1195573 TATATTATA-T
1 TATATTTTATT
*
1195583 TATATTTTAAT
1 TATATTTTATT
1195594 TATTATTTTATAT
1 TA-TATTTTAT-T
*
1195607 CATATTTATATT
1 TATATTT-TATT
1195619 ATTAATCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 9 0.24
11 11 0.29
12 13 0.34
13 5 0.13
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTTATT
Found at i:1195599 original size:24 final size:24
Alignment explanation
Indices: 1195551--1195710 Score: 83
Period size: 24 Copynumber: 6.8 Consensus size: 24
1195541 TAAATTTAAA
1195551 ATATATATATATATATTTT-A-T-TT
1 ATAT-TATAT-TATATTTTAATTATT
1195574 ATATTATATTATATTTTAATTATT
1 ATATTATATTATATTTTAATTATT
* *
1195598 ATTTTATATCATA-TTTATATTATT
1 ATATTATATTATATTTTA-ATTATT
* *
1195622 A-ATCATATAATATTTTAA--ATT
1 ATATTATATTATATTTTAATTATT
* *
1195643 AT-TT-TGTGTATAATTT-ATATATTT
1 ATATTATAT-TATATTTTAAT-TA-TT
*
1195667 ATATTAATATTTATATATT--TTATT
1 ATATT-ATA-TTATATTTTAATTATT
1195691 ATATTATAGTTATAATTTTA
1 ATATTATA-TTAT-ATTTTA
1195711 TATTTATATA
Statistics
Matches: 106, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
20 3 0.03
21 19 0.18
22 6 0.06
23 26 0.25
24 39 0.37
25 4 0.04
26 1 0.01
27 7 0.07
28 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (24 bp):
ATATTATATTATATTTTAATTATT
Found at i:1195620 original size:21 final size:20
Alignment explanation
Indices: 1195558--1195738 Score: 92
Period size: 20 Copynumber: 8.7 Consensus size: 20
1195548 AAAATATATA
*
1195558 TATATATATTT-TATTTATAT
1 TATATATATTTATA-TTATTT
1195578 TATATTATATTTTAATTATTATTT
1 TATA-TATA-TTT-A-TATTATTT
1195602 TATATCATATTTATATTATTAAT
1 TATAT-ATATTTATATTATT--T
* *
1195625 CATATAATATTTTAAATTATTT
1 TATAT-ATA-TTTATATTATTT
* *
1195647 TGTGTATAATTTATA-TA-TT
1 TATATAT-ATTTATATTATTT
1195666 TATATTAATATTTATA-TATTT
1 TATA-T-ATATTTATATTATTT
*
1195687 TAT-TATA-TTATAGTTATAAT
1 TATATATATTTATA-TTAT-TT
*
1195707 T-T-TATATTTATATAAATTT
1 TATATATATTTATAT-TATTT
1195726 T-TATATATTTATA
1 TATATATATTTATA
1195739 ATTTATATTA
Statistics
Matches: 129, Mismatches: 13, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.04
18 3 0.02
19 17 0.13
20 35 0.27
21 25 0.19
22 8 0.06
23 12 0.09
24 22 0.17
25 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATATATTTATATTATTT
Found at i:1195639 original size:16 final size:17
Alignment explanation
Indices: 1195592--1195639 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1195582 TTATATTTTA
*
1195592 ATTATTATTTTATATCAT
1 ATTAATATTTTA-ATCAT
*
1195610 ATTTATATTATTAATCAT
1 ATTAATATT-TTAATCAT
1195628 A-TAATATTTTAA
1 ATTAATATTTTAA
1195640 ATTATTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 6 0.23
18 13 0.50
19 3 0.12
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATATTTTAATCAT
Found at i:1195659 original size:45 final size:45
Alignment explanation
Indices: 1195558--1195678 Score: 112
Period size: 47 Copynumber: 2.7 Consensus size: 45
1195548 AAAATATATA
* *
1195558 TATAT-ATATTT-TAT-TTATATTATATTATATTTTAATTATTATTT
1 TATATCATATTTATATATTA-A-TATATAATATTTTAATTATTATTG
1195602 TATATCATATTTATATTATTAATCATATAATATTTTAAATTATT-TTG
1 TATATCATATTTATA-TATTAAT-ATATAATATTTT-AATTATTATTG
* *
1195649 TGTAT-A-ATTTATATATTTATAT-TAATATTT
1 TATATCATATTTATATATTAATATATAATATTT
1195679 ATATATTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
42 8 0.12
43 2 0.03
44 11 0.16
45 13 0.19
46 4 0.06
47 19 0.28
48 10 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (45 bp):
TATATCATATTTATATATTAATATATAATATTTTAATTATTATTG
Found at i:1195668 original size:8 final size:8
Alignment explanation
Indices: 1195651--1195746 Score: 59
Period size: 7 Copynumber: 12.6 Consensus size: 8
1195641 TTATTTTGTG
1195651 TATA-ATT
1 TATATATT
1195658 TATATA-T
1 TATATATT
1195665 T-TATA-T
1 TATATATT
1195671 TA-ATATT
1 TATATATT
1195678 TATATATT
1 TATATATT
*
1195686 T-TAT-TA
1 TATATATT
*
1195692 TATTATAGT
1 TA-TATATT
1195701 TATA-ATT
1 TATATATT
1195708 T-TATATT
1 TATATATT
1195715 TATATAAATTTT
1 TATAT--A--TT
1195727 TATATATT
1 TATATATT
1195735 TATA-ATT
1 TATATATT
1195742 TATAT
1 TATAT
1195747 TAATTTTAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 27
0.70 0.04 0.26
Matches are distributed among these distances:
6 13 0.18
7 26 0.37
8 21 0.30
9 2 0.03
10 2 0.03
12 7 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (8 bp):
TATATATT
Found at i:1195671 original size:6 final size:6
Alignment explanation
Indices: 1195660--1195747 Score: 54
Period size: 6 Copynumber: 14.0 Consensus size: 6
1195650 GTATAATTTA
* * *
1195660 TATATT TATATT AATATT TATATAT TTTA-T TATA-T TATAGT TATAATTT
1 TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT TAT-A-TT
* * *
1195709 TATATT TATATA AATTTTT ATATATT TATAATT TATATT
1 TATATT TATATT TA-TATT -TATATT TAT-ATT TATATT
1195748 AATTTTAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.14
6 33 0.52
7 17 0.27
8 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:1195683 original size:29 final size:30
Alignment explanation
Indices: 1195651--1195746 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 30
1195641 TTATTTTGTG
1195651 TATAATTTATATAT-TTATA-TTA-ATATTT
1 TATAATTTATATATATTATAGTTATA-ATTT
*
1195679 ATATATTTTAT-TATATTATAGTTATAATTT
1 -TATAATTTATATATATTATAGTTATAATTT
*
1195709 TAT-ATTTATATAAATT-T--TTAT-ATATT
1 TATAATTTATATATATTATAGTTATAAT-TT
1195735 TATAATTTATAT
1 TATAATTTATAT
1195747 TAATTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
25 2 0.03
26 9 0.16
27 8 0.14
28 9 0.16
29 22 0.38
30 7 0.12
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATAATTTATATATATTATAGTTATAATTT
Found at i:1195683 original size:53 final size:50
Alignment explanation
Indices: 1195608--1195732 Score: 128
Period size: 53 Copynumber: 2.5 Consensus size: 50
1195598 ATTTTATATC
* * * *
1195608 ATATTTATATTATTAATCATATAATATT-TTAAATTATTTTGTGTATAATTTAT
1 ATATTTATATTAATATTTATATAATATTATTAAATTA--TAGT-TATAATTT-T
* *
1195661 ATATTTATATTAATATTTATAT-ATTTTATTATATTATAGTTATAATTTT
1 ATATTTATATTAATATTTATATAATATTATTAAATTATAGTTATAATTTT
* *
1195710 ATATTTATATAAATTTTTATATA
1 ATATTTATATTAATATTTATATA
1195733 TTTATAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
49 21 0.34
50 8 0.13
51 3 0.05
52 4 0.06
53 26 0.42
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (50 bp):
ATATTTATATTAATATTTATATAATATTATTAAATTATAGTTATAATTTT
Found at i:1195714 original size:37 final size:33
Alignment explanation
Indices: 1195656--1195747 Score: 107
Period size: 37 Copynumber: 2.7 Consensus size: 33
1195646 TTGTGTATAA
* *
1195656 TTTATATATTTAT-ATTAATATTTATAT-ATTT
1 TTTATATATTTATAATTTATATTTATATAAATT
1195687 TATTATATTATAGTTATAATTTTATATTTATATAAATT
1 T-TTATA-TAT--TTATAA-TTTATATTTATATAAATT
1195725 TTTATATATTTATAATTTATATT
1 TTTATATATTTATAATTTATATT
1195748 AATTTTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
31 1 0.02
32 5 0.10
33 11 0.21
34 6 0.12
35 4 0.08
36 4 0.08
37 17 0.33
38 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
TTTATATATTTATAATTTATATTTATATAAATT
Found at i:1195772 original size:36 final size:34
Alignment explanation
Indices: 1195700--1195774 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
1195690 TATATTATAG
* * *
1195700 TTATAATTTTATATTTATATAAATTTTTATATAT
1 TTATAATTTTATATTTATAAAAATATTTATACAT
1195734 TTATAATTTATATTAATTT-TAAAAATATTTATACAT
1 TTATAATTT-TA-T-ATTTATAAAAATATTTATACAT
1195770 TTATA
1 TTATA
1195775 TTAATTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 9 0.26
35 2 0.06
36 20 0.57
37 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TTATAATTTTATATTTATAAAAATATTTATACAT
Found at i:1196021 original size:3 final size:3
Alignment explanation
Indices: 1196013--1196038 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1196003 TGAGAAATTT
1196013 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1196039 TAAAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1197630 original size:11 final size:12
Alignment explanation
Indices: 1197607--1197652 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
1197597 ATAATCATAA
1197607 AATA-TAAATAT
1 AATATTAAATAT
1197618 AATATTAAA-AT
1 AATATTAAATAT
*
1197629 AAT-TAAAATAT
1 AATATTAAATAT
1197640 AATA-TAAATAT
1 AATATTAAATAT
1197651 AA
1 AA
1197653 CACAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AATATTAAATAT
Found at i:1197670 original size:19 final size:19
Alignment explanation
Indices: 1197641--1197690 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1197631 TTAAAATATA
1197641 ATATAAATATAACACAAATTT
1 ATAT-AATATAACA-AAATTT
*
1197662 AT-TAATATATCAAAATTT
1 ATATAATATAACAAAATTT
1197680 ATATAATATAA
1 ATATAATATAA
1197691 ATTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 1 0.04
21 2 0.08
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATATAACAAAATTT
Found at i:1197696 original size:32 final size:32
Alignment explanation
Indices: 1197660--1197724 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
1197650 TAACACAAAT
1197660 TTATTAATATATCAAAATTTATA-TAATATAAA
1 TTATTAATATATCAAAATTTATATTAA-ATAAA
* *
1197692 TTATTAATTTATTAAAATTTATATTAAATAAA
1 TTATTAATATATCAAAATTTATATTAAATAAA
1197724 T
1 T
1197725 AATATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TTATTAATATATCAAAATTTATATTAAATAAA
Found at i:1198114 original size:22 final size:21
Alignment explanation
Indices: 1198089--1198130 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1198079 AATAAAAAAA
1198089 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1198109 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1198130 A
1 A
1198131 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1198866 original size:16 final size:16
Alignment explanation
Indices: 1198844--1198891 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1198834 TTATTAATAT
1198844 AATAAAATAATATAAA
1 AATAAAATAATATAAA
* * *
1198860 TATAAAATATTTTAAA
1 AATAAAATAATATAAA
*
1198876 AATAATTATAATATAA
1 AATAA-AATAATATAA
1198892 TAAAATATAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAATAATATAAA
Found at i:1199292 original size:16 final size:16
Alignment explanation
Indices: 1199271--1199302 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1199261 TAAGAACACT
*
1199271 GATACAATGAAAGAAG
1 GATACAAGGAAAGAAG
1199287 GATACAAGGAAAGAAG
1 GATACAAGGAAAGAAG
1199303 TTGGTAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (16 bp):
GATACAAGGAAAGAAG
Found at i:1199963 original size:13 final size:13
Alignment explanation
Indices: 1199947--1199977 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1199937 TTTTTTTTTA
1199947 AATATTAATATTT
1 AATATTAATATTT
*
1199960 AATATTTATATTT
1 AATATTAATATTT
1199973 AATAT
1 AATAT
1199978 ATTTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTAATATTT
Found at i:1200846 original size:16 final size:16
Alignment explanation
Indices: 1200780--1200857 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
1200770 CTGATCAATT
*
1200780 ATATTAAA-AAAATTAA
1 ATATTAAATATAA-TAA
1200796 ATATTAAATAT-ATAA
1 ATATTAAATATAATAA
* *
1200811 CT-TTAACA-ATAAATAT
1 ATATTAA-ATAT-AATAA
1200827 ATATTAAATATAATAA
1 ATATTAAATATAATAA
* *
1200843 ATATTTAATAAAATA
1 ATATTAAATATAATA
1200858 TCTATTTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
16 31 0.63
17 7 0.14
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATTAAATATAATAA
Found at i:1200863 original size:16 final size:16
Alignment explanation
Indices: 1200821--1200871 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1200811 CTTTAACAAT
*
1200821 AAATATATATTAAATA
1 AAATATATATTTAATA
* *
1200837 TAATAAATATTTAATA
1 AAATATATATTTAATA
*
1200853 AAATATCTATTTAACTA
1 AAATATATATTTAA-TA
1200870 AA
1 AA
1200872 TATTATAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATATATTTAATA
Found at i:1205939 original size:2 final size:2
Alignment explanation
Indices: 1205932--1205962 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1205922 GAAGCTCAGA
1205932 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1205963 TTTCAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1206172 original size:28 final size:29
Alignment explanation
Indices: 1206140--1206204 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
1206130 TCAAAATAAT
* *
1206140 TAAAAATAT-AATAAAATATAATACGAAA
1 TAAAAATATAAAAAAAATATAATACAAAA
*
1206168 TAAAAA-ATAAAAAAAATATAATATAAAA
1 TAAAAATATAAAAAAAATATAATACAAAA
1206196 TAAAAATAT
1 TAAAAATAT
1206205 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (29 bp):
TAAAAATATAAAAAAAATATAATACAAAA
Found at i:1206211 original size:28 final size:28
Alignment explanation
Indices: 1206140--1206226 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
1206130 TCAAAATAAT
**
1206140 TAAAAATATAATAAAATATAATACGAAA
1 TAAAAATATAATAAAATATAATATAAAA
*
1206168 TAAAAA-ATAAAAAAAATATAATATAAAA
1 TAAAAATAT-AATAAAATATAATATAAAA
** * *
1206196 TAAAAATATTTTAAAAT-TTATATAATA
1 TAAAAATATAATAAAATATAATATAAAA
1206223 TAAA
1 TAAA
1206227 TTATTAATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 14 0.29
28 33 0.67
29 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
TAAAAATATAATAAAATATAATATAAAA
Found at i:1206219 original size:32 final size:32
Alignment explanation
Indices: 1206183--1206263 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
1206173 AATAAAAAAA
*
1206183 ATATAATATAAAATAAAAATATTTTAAAATTT
1 ATATAATATAAAATAAAAATATATTAAAATTT
* **
1206215 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAAATAAAAATATATTAAAATTT
* *
1206247 ACATAAATATATAATAA
1 ATAT-AATATAAAATAA
1206264 TTTAAAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 31 0.77
33 9 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATATAAAATAAAAATATATTAAAATTT
Found at i:1206275 original size:19 final size:20
Alignment explanation
Indices: 1206232--1206281 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1206222 ATAAATTATT
*
1206232 AATATATTAA-AATTTACATA
1 AATATA-TAATAATTTACAAA
1206252 AATATATAATAATTTA-AAA
1 AATATATAATAATTTACAAA
1206271 AATATATAATA
1 AATATATAATA
1206282 CATTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATATAATAATTTACAAA
Found at i:1206385 original size:17 final size:17
Alignment explanation
Indices: 1206363--1206397 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1206353 ATATTAATAC
*
1206363 AAATTACATTAAATTTA
1 AAATTAAATTAAATTTA
1206380 AAATTAAATTAAATTTA
1 AAATTAAATTAAATTTA
1206397 A
1 A
1206398 TTAATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAAATTAAATTTA
Found at i:1206431 original size:38 final size:40
Alignment explanation
Indices: 1206385--1206470 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
1206375 ATTTAAAATT
*
1206385 AAAT-TAAATTT-AA-TT-AATTCATATAATTATTTTTAAA
1 AAATATAAATTTAAATTTCAATACATATAATT-TTTTTAAA
* *
1206422 TAATATAAATTTAAATTTCAATACTTATAATTTTTTTAAA
1 AAATATAAATTTAAATTTCAATACATATAATTTTTTTAAA
1206462 AAATA-AAAT
1 AAATATAAAT
1206471 AAATTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 3 0.07
38 7 0.17
39 6 0.15
40 14 0.34
41 11 0.27
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (40 bp):
AAATATAAATTTAAATTTCAATACATATAATTTTTTTAAA
Found at i:1209468 original size:21 final size:21
Alignment explanation
Indices: 1209430--1209469 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1209420 ATTAAAAAAT
* * *
1209430 TATTTTATATTTATATTTATA
1 TATTTTATAATAAAATTTATA
1209451 TATTTTATAATAAAATTTA
1 TATTTTATAATAAAATTTA
1209470 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATAAAATTTATA
Found at i:1210396 original size:29 final size:29
Alignment explanation
Indices: 1210354--1210410 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1210344 AGATATACTT
* * **
1210354 AATATTTTTTAAAATTTTTATATATTTAA
1 AATATTTTTAAAAAATCATATATATTTAA
1210383 AATATTTTTAAAAAATCATATATATTTA
1 AATATTTTTAAAAAATCATATATATTTA
1210411 TATTCAGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
AATATTTTTAAAAAATCATATATATTTAA
Found at i:1213555 original size:16 final size:17
Alignment explanation
Indices: 1213534--1213569 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1213524 TAAAAAGTAG
1213534 AAAAATATGTATAC-AA
1 AAAAATATGTATACTAA
1213550 AAAAATATGTATACTAA
1 AAAAATATGTATACTAA
1213567 AAA
1 AAA
1213570 TCAAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAAATATGTATACTAA
Found at i:1214085 original size:23 final size:22
Alignment explanation
Indices: 1214043--1214085 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1214033 AAGACAAAAA
1214043 TATTTTTATAACTATATATTTT
1 TATTTTTATAACTATATATTTT
1214065 TATTTTATAATAA-TATATATT
1 TATTTT-T-ATAACTATATATT
1214086 ATAAGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAACTATATATTTT
Found at i:1214447 original size:30 final size:30
Alignment explanation
Indices: 1214413--1214483 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 30
1214403 TCGACTTTTC
1214413 AAATTTTTAAATATTTTAAATAATAAAATA
1 AAATTTTTAAATATTTTAAATAATAAAATA
* *
1214443 AAATTTTTAAATATTTTAAATAGTGAAATA
1 AAATTTTTAAATATTTTAAATAATAAAATA
1214473 AAATATTTTAA
1 AAAT-TTTTAA
1214484 TACTCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 32 0.84
31 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTTTAAATATTTTAAATAATAAAATA
Found at i:1214582 original size:16 final size:16
Alignment explanation
Indices: 1214563--1214598 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1214553 AGTCATTTCG
1214563 AATTCGGATTATTTTA
1 AATTCGGATTATTTTA
*
1214579 AATTTGGATTATTTTA
1 AATTCGGATTATTTTA
1214595 AATT
1 AATT
1214599 AAAGTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTCGGATTATTTTA
Found at i:1215481 original size:3 final size:3
Alignment explanation
Indices: 1215473--1215503 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1215463 TTTTTAAAAA
1215473 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1215504 ATCAAGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1217359 original size:24 final size:24
Alignment explanation
Indices: 1217332--1217399 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 24
1217322 TTTTAACATC
1217332 ATCATTATAATATTTAATTTTAT-
1 ATCATTATAATATTTAATTTTATA
* *
1217355 -T-ATCATAATAATTAATTTTATA
1 ATCATTATAATATTTAATTTTATA
* *
1217377 ATTATTATTAT-TTATAATTTTAT
1 ATCATTATAATATT-TAATTTTAT
1217400 CGAAACGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 18 0.50
22 1 0.03
23 2 0.06
24 15 0.42
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
ATCATTATAATATTTAATTTTATA
Found at i:1217359 original size:27 final size:29
Alignment explanation
Indices: 1217313--1217387 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 29
1217303 ATATATATTT
** * *
1217313 TATTAATAATTTTAACATCATCATTA-TAA
1 TATT-ATAATTTTATTATCATAATAATTAA
1217342 TATT-TAATTTTATTATCATAATAATTAA
1 TATTATAATTTTATTATCATAATAATTAA
*
1217370 TTTTATAATTATTATTAT
1 TATTATAATT-TTATTAT
1217388 TTATAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 16 0.42
28 6 0.16
29 9 0.24
30 7 0.18
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTATAATTTTATTATCATAATAATTAA
Found at i:1217528 original size:20 final size:20
Alignment explanation
Indices: 1217503--1217542 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1217493 GAATATTAAC
1217503 ATATATAGTAATAAGATATA
1 ATATATAGTAATAAGATATA
1217523 ATATATAGTAATAAGATATA
1 ATATATAGTAATAAGATATA
1217543 GGAACAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (20 bp):
ATATATAGTAATAAGATATA
Found at i:1218625 original size:26 final size:28
Alignment explanation
Indices: 1218566--1218628 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
1218556 TTGAATTATA
*
1218566 AAATT-ATTTATTTAAATTTATTAAGTT
1 AAATTAATTTATTTAAATTTATTAAGAT
1218593 AAA-TAATTTATTT-AATTTA-TAA-AT
1 AAATTAATTTATTTAAATTTATTAAGAT
1218617 AATATTAATTTA
1 AA-ATTAATTTA
1218629 AATATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 14 0.44
27 11 0.34
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
AAATTAATTTATTTAAATTTATTAAGAT
Found at i:1218661 original size:20 final size:20
Alignment explanation
Indices: 1218638--1218699 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1218628 AAATATTTAA
1218638 ATTAAATATATTATATATTT
1 ATTAAATATATTATATATTT
* *
1218658 ATTATAT-TATTTTTATATTT
1 ATTAAATATA-TTATATATTT
*
1218678 ATTAAATATATTATATTTTT
1 ATTAAATATATTATATATTT
1218698 AT
1 AT
1218700 ATAGTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTAAATATATTATATATTT
Found at i:1218707 original size:20 final size:19
Alignment explanation
Indices: 1218643--1218708 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 19
1218633 TTTAAATTAA
*
1218643 ATATATTATATATTTATTAT
1 ATATATTATATTTTTA-TAT
*
1218663 ATTATTTTTATATTTATTA-A-
1 A-TA-TATTATATTT-TTATAT
1218683 ATATATTATATTTTTATAT
1 ATATATTATATTTTTATAT
1218702 AGTATAT
1 A-TATAT
1218709 AAAATTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
17 3 0.08
18 10 0.27
19 3 0.08
20 7 0.19
21 3 0.08
22 8 0.22
23 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATATATTATATTTTTATAT
Found at i:1218729 original size:46 final size:40
Alignment explanation
Indices: 1218639--1218727 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
1218629 AATATTTAAA
* *
1218639 TTAAATATATTATATATTTATTATATTATTTTTATATTTA
1 TTAAATATATTATATATTTATTATATTATTATTAAATTTA
* * *
1218679 TTAAATATATTATATTTTTA-TATAGTA-TA-TAAAATTA
1 TTAAATATATTATATATTTATTATATTATTATTAAATTTA
*
1218716 TTAAATTTATTA
1 TTAAATATATTA
1218728 AACGTTTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
37 17 0.40
38 1 0.02
39 6 0.14
40 19 0.44
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (40 bp):
TTAAATATATTATATATTTATTATATTATTATTAAATTTA
Found at i:1219558 original size:20 final size:22
Alignment explanation
Indices: 1219530--1219569 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1219520 TACATAATAT
1219530 ATTTAAAAAATAAA-AAAATTA
1 ATTTAAAAAATAAATAAAATTA
1219551 ATTT-AAAAATAAATAAAAT
1 ATTTAAAAAATAAATAAAAT
1219570 ATATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATTTAAAAAATAAATAAAATTA
Found at i:1220029 original size:20 final size:21
Alignment explanation
Indices: 1220001--1220039 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1219991 ATTTAATTTT
1220001 AATAATAATA-AAAATATATA
1 AATAATAATATAAAATATATA
*
1220021 AATATTAATATAAAATATA
1 AATAATAATATAAAATATA
1220040 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAATATAAAATATATA
Found at i:1220040 original size:19 final size:20
Alignment explanation
Indices: 1220001--1220050 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1219991 ATTTAATTTT
* *
1220001 AATAATAATAAAAATATATA
1 AATATTAATATAAATATATA
1220021 AATATTAATATAAA-ATATA
1 AATATTAATATAAATATATA
* *
1220040 ATTTTTAATAT
1 AATATTAATAT
1220051 TTTATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATTAATATAAATATATA
Found at i:1220754 original size:24 final size:22
Alignment explanation
Indices: 1220727--1220772 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
1220717 TATTTATATA
*
1220727 TTCGTATCATATTTATATTATTTT
1 TTCGTATAATATTT-T-TTATTTT
1220751 TTCGTATAATATTTTTTATTTT
1 TTCGTATAATATTTTTTATTTT
1220773 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (22 bp):
TTCGTATAATATTTTTTATTTT
Found at i:1227234 original size:14 final size:14
Alignment explanation
Indices: 1227215--1227246 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1227205 GAATAACGGC
1227215 TTTTTTTA-TTTTA
1 TTTTTTTATTTTTA
1227228 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
1227242 TTTTT
1 TTTTT
1227247 AAATTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:1227405 original size:22 final size:19
Alignment explanation
Indices: 1227362--1227409 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1227352 ATTTTAGATA
*
1227362 AATATTAAATATAATAAAT
1 AATAATAAATATAATAAAT
*
1227381 AATTAATAAATATATATGAAGT
1 AA-TAATAAATATA-AT-AAAT
1227403 AATAATA
1 AATAATA
1227410 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 7 0.29
22 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AATAATAAATATAATAAAT
Found at i:1227515 original size:19 final size:18
Alignment explanation
Indices: 1227486--1227522 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1227476 CAGATCGATT
*
1227486 AATTTTTATAATTTTTTA
1 AATTTTTATAATCTTTTA
1227504 AATTTTTCATAATCTTTTA
1 AATTTTT-ATAATCTTTTA
1227523 TTGTTGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTTATAATCTTTTA
Found at i:1228036 original size:14 final size:14
Alignment explanation
Indices: 1227992--1228037 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
1227982 GACTAAATAT
*
1227992 TTAAATTTATTAAA
1 TTAAATTTATAAAA
* *
1228006 TT-ATTTTTTAAAA
1 TTAAATTTATAAAA
1228019 -TAAATTTATAAAA
1 TTAAATTTATAAAA
1228032 TTAAAT
1 TTAAAT
1228038 AGATAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 1 0.04
13 17 0.68
14 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTTATAAAA
Found at i:1228767 original size:22 final size:22
Alignment explanation
Indices: 1228739--1228781 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1228729 ATTTTAAAAA
1228739 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
1228761 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
1228782 AATAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:1232533 original size:2 final size:2
Alignment explanation
Indices: 1232526--1232555 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1232516 TGGTGTGAAG
1232526 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1232556 TTCAAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1234817 original size:19 final size:19
Alignment explanation
Indices: 1234793--1234834 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1234783 ATTTAATTTT
* *
1234793 TTTAAATTTTTTTTATATA
1 TTTAAAATTTTTTTAAATA
1234812 TTTAAAATTTTTTTAAATA
1 TTTAAAATTTTTTTAAATA
1234831 TTTA
1 TTTA
1234835 TATTCGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAAAATTTTTTTAAATA
Found at i:1235540 original size:21 final size:21
Alignment explanation
Indices: 1235499--1235541 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1235489 ATGTATTATT
* *
1235499 AATATATCAAATTTTATATAA
1 AATATATCAAATTATAAATAA
1235520 AATATAT-AATATTATAAATAA
1 AATATATCAA-ATTATAAATAA
1235541 A
1 A
1235542 TAAAGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATCAAATTATAAATAA
Found at i:1235708 original size:173 final size:175
Alignment explanation
Indices: 1235341--1235712 Score: 621
Period size: 173 Copynumber: 2.1 Consensus size: 175
1235331 TTTCCATCCA
*
1235341 AAAATATGT-ATA-TATAAATAAATAAAGGGAATGAAAAAAGGGATAGTGAAGGGTGGACTTGGC
1 AAAATATATAATATTATAAATAAATAAAGGGAATGAAAAAAGGGATAGTGAAGGGTGGACTTGGC
*
1235404 AGCTTTTCATACAATACAATTATATTATTAAAAAAATAATTAAAAATAATATAAATAATATAAAA
66 AGCTTTTCATACAATACAATTATATAATTAAAAAAATAATT--AAATAATAT--ATAATATAAAA
1235469 TACGTTAAAATTTATATAATATGTATTATTAATATATCAAATTTTATAT
127 TACGTTAAAATTTATATAATATGTATTATTAATATATCAAATTTTATAT
1235518 AAAATATATAATATTATAAATAAATAAAGGGAAATGAAAAAAAGGGATAGTGAAGGGTGGACTTG
1 AAAATATATAATATTATAAATAAATAAAGGG-AATG-AAAAAAGGGATAGTGAAGGGTGGACTTG
1235583 GCAGCTTTTCATACAATACAATTATATAATTAAAAAAATAATT-AA-AA-AT-TAATATAAAATA
64 GCAGCTTTTCATACAATACAATTATATAATTAAAAAAATAATTAAATAATATATAATATAAAATA
*
1235644 TGTTAAAATTTATATAATATGTATTATTAATATATCAAATTTTATAT
129 CGTTAAAATTTATATAATATGTATTATTAATATATCAAATTTTATAT
1235691 AAAATATATAATATTATAAATA
1 AAAATATATAATATTATAAATA
1235713 TAAATAAAAA
Statistics
Matches: 188, Mismatches: 3, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
173 80 0.43
176 2 0.01
177 10 0.05
178 5 0.03
179 17 0.09
180 4 0.02
181 70 0.37
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (175 bp):
AAAATATATAATATTATAAATAAATAAAGGGAATGAAAAAAGGGATAGTGAAGGGTGGACTTGGC
AGCTTTTCATACAATACAATTATATAATTAAAAAAATAATTAAATAATATATAATATAAAATACG
TTAAAATTTATATAATATGTATTATTAATATATCAAATTTTATAT
Found at i:1236419 original size:265 final size:266
Alignment explanation
Indices: 1235946--1236478 Score: 1023
Period size: 265 Copynumber: 2.0 Consensus size: 266
1235936 TTTGCTCAAA
1235946 TTAGTTTGGTCGATAGATTTGATTTAAATTTAAGTATTAATTTTTATAATTTAAGTTGATTTAAT
1 TTAGTTTGGTCGATAGATTTGATTTAAATTTAAGTATTAATTTTTATAATTTAAGTTGATTTAAT
1236011 TTATTTTGAATTAATTGTTAAATTATTAAAATAATATTTTTATTTAAATTTAATTATAAAAATAT
66 TTATTTTGAATTAATTGTTAAATTATTAAAATAATATTTTTATTTAAATTTAATTATAAAAATAT
*
1236076 AAATATTAATATAATTTTTTAATATTTTAATATTTTTAAATAATAATTTTAGTCATCAGACTTGA
131 AAATATTAATATAATTTTTTAATATTTTAATATTTTTAAATAATAATTTTAGTCATCAGACTTAA
1236141 ACTTAACTTTCAAAATATTTCAAGTCGCATCCAATCAGGCCCATAAAT-AATATATTTATAAAAC
196 ACTTAACTTTCAAAATATTTCAAGTCGCATCCAATCAGGCCCATAAATAAATATATTTATAAAAC
1236205 ATTTTT
261 ATTTTT
1236211 TTAGTTTGGTCGATAGATTTGATTTAAATTTAAGTATTAATTTTTATAATTTAAGTTGATTTAAT
1 TTAGTTTGGTCGATAGATTTGATTTAAATTTAAGTATTAATTTTTATAATTTAAGTTGATTTAAT
*
1236276 TTGTTTTGAATTAATTGTTAAATTATTAAAATAATATTTTTATTTAAATTTAATTATAAAAATAT
66 TTATTTTGAATTAATTGTTAAATTATTAAAATAATATTTTTATTTAAATTTAATTATAAAAATAT
*
1236341 AAATATTAATATAATTTTTTAATATTTTAATATTTTTAAATAATGATTTTAGTCATCAGACTTAA
131 AAATATTAATATAATTTTTTAATATTTTAATATTTTTAAATAATAATTTTAGTCATCAGACTTAA
*
1236406 ACTTAACTTTCAAAATATTTCAAGTCGCATCCAATCCGGCCCATAAATAAATATATTTATAAAAC
196 ACTTAACTTTCAAAATATTTCAAGTCGCATCCAATCAGGCCCATAAATAAATATATTTATAAAAC
1236471 ATTTTT
261 ATTTTT
1236477 TT
1 TT
1236479 GGTATATTTC
Statistics
Matches: 263, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
265 239 0.91
266 24 0.09
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (266 bp):
TTAGTTTGGTCGATAGATTTGATTTAAATTTAAGTATTAATTTTTATAATTTAAGTTGATTTAAT
TTATTTTGAATTAATTGTTAAATTATTAAAATAATATTTTTATTTAAATTTAATTATAAAAATAT
AAATATTAATATAATTTTTTAATATTTTAATATTTTTAAATAATAATTTTAGTCATCAGACTTAA
ACTTAACTTTCAAAATATTTCAAGTCGCATCCAATCAGGCCCATAAATAAATATATTTATAAAAC
ATTTTT
Found at i:1237282 original size:21 final size:21
Alignment explanation
Indices: 1237252--1237298 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1237242 AAAAATAAAA
1237252 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1237272 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
*
1237293 AAATAT
1 ATATAT
1237299 AAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1237476 original size:21 final size:21
Alignment explanation
Indices: 1237452--1237496 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1237442 ATAAAAAAAT
*
1237452 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTAAA
*
1237473 TATTTTTTAATTAAATTTAAA
1 TATTTTATAATTAAATTTAAA
1237494 TAT
1 TAT
1237497 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTAAA
Found at i:1238286 original size:21 final size:22
Alignment explanation
Indices: 1238240--1238286 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1238230 TAACAATAAC
* *
1238240 CAAATCAAATTCATATTTTTTA
1 CAAATCAAATTCATAATATTTA
*
1238262 -AAATCAAATTTA-AATATTTA
1 CAAATCAAATTCATAATATTTA
1238282 CAAAT
1 CAAAT
1238287 AAAAATATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
CAAATCAAATTCATAATATTTA
Found at i:1238562 original size:22 final size:22
Alignment explanation
Indices: 1238534--1238580 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1238524 TCAGCTCCAT
*
1238534 TATTTTTA-AATTAATATTTATA
1 TATTTTTATAATTAA-ATTTAAA
1238556 TATTTTTATAATTAAATTTAAA
1 TATTTTTATAATTAAATTTAAA
1238578 TAT
1 TAT
1238581 AAAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTAAA
Found at i:1239089 original size:4 final size:4
Alignment explanation
Indices: 1239080--1239110 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1239070 TGGAAATTAA
1239080 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1239111 AAGTCAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.