Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 9 of 121
Found at i:1247753 original size:33 final size:33
Alignment explanation
Indices: 1247708--1247842 Score: 130
Period size: 33 Copynumber: 4.1 Consensus size: 33
1247698 TATTAATAAA
* * *
1247708 TTATTAATAATTTACTACTAAATTACTATTGAT
1 TTATTACTAATTTACTACTAATTTACTATTAAT
* * * *
1247741 TTAATACTAATTTA-TAAATGATTTACTACTAAT
1 TTATTACTAATTTACT-ACTAATTTACTATTAAT
* * *
1247774 TTATTACTAATTTACTACTAAGTTACTAATGAT
1 TTATTACTAATTTACTACTAATTTACTATTAAT
* * *
1247807 TGATTA-TAAGTTACAACTAATTTACTATTAAT
1 TTATTACTAATTTACTACTAATTTACTATTAAT
1247839 TTAT
1 TTAT
1247843 CGGTAATTTA
Statistics
Matches: 80, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
32 25 0.31
33 54 0.68
34 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (33 bp):
TTATTACTAATTTACTACTAATTTACTATTAAT
Found at i:1247787 original size:44 final size:43
Alignment explanation
Indices: 1247712--1247842 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 43
1247702 AATAAATTAT
* * * *
1247712 TAATAATTTACTACTAAATTACTATTGATTTAATACTAATTTA
1 TAATGATTTACTACTAAATTACTACTAATTTACTACTAATTTA
* * *
1247755 TAAATGATTTACTACTAATTTATTACTAATTTACTACTAAGTTA
1 T-AATGATTTACTACTAAATTACTACTAATTTACTACTAATTTA
* * * * *
1247799 CTAATGATTGATTA-TAAGTTACAACTAATTTACTATTAATTTA
1 -TAATGATTTACTACTAAATTACTACTAATTTACTACTAATTTA
1247842 T
1 T
1247843 CGGTAATTTA
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
42 1 0.01
43 25 0.35
44 45 0.62
45 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (43 bp):
TAATGATTTACTACTAAATTACTACTAATTTACTACTAATTTA
Found at i:1247871 original size:22 final size:22
Alignment explanation
Indices: 1247663--1247877 Score: 112
Period size: 22 Copynumber: 9.8 Consensus size: 22
1247653 TTATTATTAT
* * *
1247663 GTTATCAATGATTTATTACTAA
1 GTTATTAATAATTTACTACTAA
* * * * * *
1247685 ATTATCAATGATATATTAATAA
1 GTTATTAATAATTTACTACTAA
*
1247707 ATTATTAATAATTTACTACTAA
1 GTTATTAATAATTTACTACTAA
* * * * *
1247729 ATTACTATTGATTTAATACTAA
1 GTTATTAATAATTTACTACTAA
* * *
1247751 TTTATAAATGATTTACTACTAA
1 GTTATTAATAATTTACTACTAA
* *
1247773 TTTATTACTAATTTACTACTAA
1 GTTATTAATAATTTACTACTAA
* * * *
1247795 GTTACTAATGATTGATTA-TAA
1 GTTATTAATAATTTACTACTAA
* *
1247816 GTTA-CAACTAATTTACTATTAA
1 GTTATTAA-TAATTTACTACTAA
* ***
1247838 TTTATCGGTAATTTACTA-TAAA
1 GTTATTAATAATTTACTACT-AA
*
1247860 GTTATTAATAATTAACTA
1 GTTATTAATAATTTACTA
1247878 ATTAGCTACT
Statistics
Matches: 151, Mismatches: 38, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
20 2 0.01
21 15 0.10
22 133 0.88
23 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (22 bp):
GTTATTAATAATTTACTACTAA
Found at i:1247926 original size:22 final size:20
Alignment explanation
Indices: 1247901--1247992 Score: 76
Period size: 22 Copynumber: 4.2 Consensus size: 20
1247891 TTATCACTTT
1247901 TTTATCACTAAATTATTAGTAA
1 TTTA-CACTAAATTATTA-TAA
*
1247923 TTTACTACTAAGTTATTAATAA
1 TTTAC-ACTAAATTATT-ATAA
*
1247945 TTTACATCTAAATTATCATTAA
1 TTTACA-CTAAATTATTA-TAA
* *
1247967 TTTACTATTAAGTTATTATACA
1 TTTAC-ACTAAATTATTATA-A
1247989 TTTA
1 TTTA
1247993 TTACTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.09
22 51 0.88
23 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (20 bp):
TTTACACTAAATTATTATAA
Found at i:1247983 original size:44 final size:44
Alignment explanation
Indices: 1247907--1248018 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 44
1247897 CTTTTTTATC
* *
1247907 ACTAAATTATTAGTAATTTACTACTAAGTTATTAATA-ATTTACAT
1 ACTAAATTATCATTAATTTACTACTAAGTTATT-ATACATTTA-AT
* *
1247952 -CTAAATTATCATTAATTTACTATTAAGTTATTATACATTTATT
1 ACTAAATTATCATTAATTTACTACTAAGTTATTATACATTTAAT
* *
1247995 ACTATATTATCATTGATTTACTAC
1 ACTAAATTATCATTAATTTACTAC
1248019 ATAGCTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
43 4 0.07
44 54 0.93
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (44 bp):
ACTAAATTATCATTAATTTACTACTAAGTTATTATACATTTAAT
Found at i:1248015 original size:19 final size:19
Alignment explanation
Indices: 1247980--1248017 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1247970 ACTATTAAGT
*
1247980 TATTATACATTTATTACTA
1 TATTATACATTGATTACTA
1247999 TATTAT-CATTGATTTACTA
1 TATTATACATTGA-TTACTA
1248018 CATAGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTATACATTGATTACTA
Found at i:1248113 original size:21 final size:22
Alignment explanation
Indices: 1248089--1248389 Score: 124
Period size: 22 Copynumber: 13.8 Consensus size: 22
1248079 CGTTATCAAG
1248089 TTATCATTGATTTA-TATTAAA
1 TTATCATTGATTTACTATTAAA
*
1248110 TTATCCA-TGATTTACTCTTAAA
1 TTAT-CATTGATTTACTATTAAA
* * *
1248132 TTATCATTGATTAACTCTTAAG
1 TTATCATTGATTTACTATTAAA
** *
1248154 TT-TTTTATGATTAACTACTATTAAG
1 TTATCAT-TGATT---TACTATTAAA
* * * *
1248179 TAAT-GTTGATTTACTTTTAAG
1 TTATCATTGATTTACTATTAAA
* * * *
1248200 TTTTCAATGATTAACTACTAAA
1 TTATCATTGATTTACTATTAAA
**
1248222 TTATCATTGATTTACTATTACG
1 TTATCATTGATTTACTATTAAA
* * *
1248244 TTAT-TTATGATTAACTACTAAA
1 TTATCAT-TGATTTACTATTAAA
*
1248266 TTA--ATT-AATTACTATTAAA
1 TTATCATTGATTTACTATTAAA
* * *
1248285 TTGA-AACTGATTTACCATTAAA
1 TT-ATCATTGATTTACTATTAAA
* * *
1248307 TTATCACTAATTTACTCTTAAA
1 TTATCATTGATTTACTATTAAA
*
1248329 TTATCAGTT--TTTACCTA-AAAA
1 TTATCA-TTGATTTA-CTATTAAA
** *
1248350 GTTATCACTT-ATTTTTTATTAAC
1 -TTATCA-TTGATTTACTATTAAA
*
1248373 CTATCATTGATTTACTA
1 TTATCATTGATTTACTA
1248390 ATATGTTGTT
Statistics
Matches: 209, Mismatches: 51, Indels: 39
0.70 0.17 0.13
Matches are distributed among these distances:
19 12 0.06
20 2 0.01
21 40 0.19
22 133 0.64
23 6 0.03
24 5 0.02
25 10 0.05
26 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (22 bp):
TTATCATTGATTTACTATTAAA
Found at i:1248254 original size:44 final size:44
Alignment explanation
Indices: 1248089--1248283 Score: 179
Period size: 44 Copynumber: 4.5 Consensus size: 44
1248079 CGTTATCAAG
* ** *
1248089 TTATCATTGATTTA-TATTAAATTATCCATGATTTACT-CTTAAA
1 TTATCATTGATTTACTATTAAGTTATTTATGATTAACTAC-TAAA
* * *
1248132 TTATCATTGATTAACTCTTAAGTTTTTTATGATTAACTACTATTAA
1 TTATCATTGATTTACTATTAAGTTATTTATGATTAACTACTA--AA
* * * *
1248178 GTAAT-GTTGATTTACTTTTAAGTT-TTCAATGATTAACTACTAAA
1 -TTATCATTGATTTACTATTAAGTTATT-TATGATTAACTACTAAA
*
1248222 TTATCATTGATTTACTATTACGTTATTTATGATTAACTACTAAA
1 TTATCATTGATTTACTATTAAGTTATTTATGATTAACTACTAAA
*
1248266 TTA--ATT-AATTACTATTAA
1 TTATCATTGATTTACTATTAA
1248284 ATTGAAACTG
Statistics
Matches: 125, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
41 10 0.08
42 3 0.02
43 16 0.13
44 56 0.45
45 5 0.04
46 32 0.26
47 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (44 bp):
TTATCATTGATTTACTATTAAGTTATTTATGATTAACTACTAAA
Found at i:1248813 original size:18 final size:18
Alignment explanation
Indices: 1248792--1248826 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1248782 TCATTTTTCT
1248792 TTTAAATTTTAATTTTAA
1 TTTAAATTTTAATTTTAA
*
1248810 TTTAATTTTTAATTTTA
1 TTTAAATTTTAATTTTA
1248827 TTATTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAATTTTAATTTTAA
Found at i:1248842 original size:3 final size:3
Alignment explanation
Indices: 1248824--1248931 Score: 64
Period size: 3 Copynumber: 35.3 Consensus size: 3
1248814 ATTTTTAATT
* *
1248824 TTA TTA TTT TTCA TTA TTA TTA TGA TTA TTA TTA TTA TTTA TCTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
* * *
1248872 ATA TT- TTT TTA GTTA TCTA TTA ATA -TA TT- TTA TTA TTTA TCTA TTA
1 TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
*
1248918 TT- TT- TTA TTT TTA T
1 TTA TTA TTA TTA TTA T
1248932 CTTTTTTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
2 10 0.12
3 54 0.64
4 20 0.24
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1248911 original size:24 final size:23
Alignment explanation
Indices: 1248828--1248933 Score: 116
Period size: 22 Copynumber: 4.8 Consensus size: 23
1248818 TTAATTTTAT
* *
1248828 TATTTTTCATTA-TTAT-TATGAT
1 TATTTTT-ATTATTTATCTATTAA
*
1248850 TATTATTATTATTTATCTATTAA
1 TATTTTTATTATTTATCTATTAA
*
1248873 TATTTTT-TTAGTTATCTATTAA
1 TATTTTTATTATTTATCTATTAA
1248895 TATATTTTATTATTTATCTATT-A
1 TAT-TTTTATTATTTATCTATTAA
1248918 T-TTTTTATT-TTTATCT
1 TATTTTTATTATTTATCT
1248934 TTTTTTTCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.09
21 11 0.15
22 28 0.38
23 16 0.22
24 12 0.16
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTATTATTTATCTATTAA
Found at i:1249788 original size:12 final size:13
Alignment explanation
Indices: 1249766--1249815 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1249756 CGATTCAAGG
1249766 TTTATTTTATTTA
1 TTTATTTTATTTA
1249779 TTTA-TTTATTTA
1 TTTATTTTATTTA
*
1249791 TTTGTTATTA-TTA
1 TTTATT-TTATTTA
*
1249804 TTT-TTTAATTTA
1 TTTATTTTATTTA
1249816 GAATTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 16 0.50
13 11 0.34
14 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1249844 original size:6 final size:6
Alignment explanation
Indices: 1249833--1249863 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1249823 TTGGTATTCC
1249833 TTAATT TTAATT TT-ATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TT
1249864 TTTTCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTAATT
Found at i:1249852 original size:11 final size:12
Alignment explanation
Indices: 1249833--1249863 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1249823 TTGGTATTCC
1249833 TTAATTTTAATT
1 TTAATTTTAATT
1249845 TT-ATTTTAATT
1 TTAATTTTAATT
1249856 TTAATTTT
1 TTAATTTT
1249864 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTAATTTTAATT
Found at i:1249855 original size:17 final size:16
Alignment explanation
Indices: 1249833--1249867 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1249823 TTGGTATTCC
1249833 TTAATTTTAATTTTATT
1 TTAATTTTAATTTT-TT
1249850 TTAATTTTAATTTTTT
1 TTAATTTTAATTTTTT
1249866 TT
1 TT
1249868 CTTTCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTAATTTTAATTTTTT
Found at i:1250079 original size:55 final size:54
Alignment explanation
Indices: 1249910--1250079 Score: 128
Period size: 55 Copynumber: 3.0 Consensus size: 54
1249900 AAAAATTTCC
* * * * *
1249910 AAAAAAAAATATTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAATTTTA
1 AAAAAAAAAAATTTTAAGAGAAAATTGAAAGTATCAATTTCTCTT-GAAATAAA----A
* * * * **
1249969 AAAAATATATATTTTTAA-AGGAAAGTTGATTGTATCAATTTC-CTTTGAACATAAAA
1 AAAAA-AAAAAATTTTAAGA-GAAAATTGAAAGTATCAATTTCTC-TTGAA-ATAAAA
*
1250025 AAAAAAAAAAATTTTAAGAGAAAATTGAAAGTATCAATTTCTCTGGAAAGTAAAA
1 AAAAAAAAAAATTTTAAGAGAAAATTGAAAGTATCAATTTCTCTTGAAA-TAAAA
1250080 GGTTTTAAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
54 1 0.01
55 37 0.43
56 8 0.09
59 9 0.10
60 31 0.36
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (54 bp):
AAAAAAAAAAATTTTAAGAGAAAATTGAAAGTATCAATTTCTCTTGAAATAAAA
Found at i:1250126 original size:119 final size:115
Alignment explanation
Indices: 1249910--1250128 Score: 280
Period size: 115 Copynumber: 1.9 Consensus size: 115
1249900 AAAAATTTCC
* * * *
1249910 AAAAAAAAATATTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAATTTTAAAAAAT
1 AAAAAAAAAAATTTTAAGAAAAAATTGAAAGTATCAATTTCTCTGAAAAATAAATTTTAAAAAAT
**
1249975 ATATATTTTTAAAGGAAAGTTGATTGTATCAATTTCCTTTGAACATAAAA
66 ATATATTTTTAAAGGAAAGTTGAAAGTATCAATTTCCTTTGAACATAAAA
* * *
1250025 AAAAAAAAAAATTTTAAGAGAAAATTGAAAGTATCAATTTCTCTGGAAAGTAAAAGGTTTTAAAA
1 AAAAAAAAAAATTTTAAGAAAAAATTGAAAGTATCAATTTCTCTGAAAAAT-AAA--TTTTAAAA
*
1250090 AA-ATATATGTTTGT-AGGGAAAAGTTGAAAGTATCAATTT
63 AATATATAT-TTT-TAAAGG-AAAGTTGAAAGTATCAATTT
1250129 TTCTTAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
115 44 0.50
116 3 0.03
117 6 0.07
118 16 0.18
119 19 0.22
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (115 bp):
AAAAAAAAAAATTTTAAGAAAAAATTGAAAGTATCAATTTCTCTGAAAAATAAATTTTAAAAAAT
ATATATTTTTAAAGGAAAGTTGAAAGTATCAATTTCCTTTGAACATAAAA
Found at i:1260849 original size:10 final size:9
Alignment explanation
Indices: 1260797--1260839 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1260787 AAAAAAGCAA
1260797 AAAAAAAAT
1 AAAAAAAAT
*
1260806 -AAAGAAAT
1 AAAAAAAAT
*
1260814 AAAAGAAAT
1 AAAAAAAAT
*
1260823 AAAAAGAAT
1 AAAAAAAAT
1260832 AAAAAAAA
1 AAAAAAAA
1260840 GGAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1260851 original size:14 final size:13
Alignment explanation
Indices: 1260823--1260856 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1260813 TAAAAGAAAT
1260823 AAAAA-GAATAAA
1 AAAAAGGAATAAA
1260835 AAAAAGGAATAAA
1 AAAAAGGAATAAA
1260848 AAAAGAGGA
1 AAAA-AGGA
1260857 CTCAATGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
AAAAAGGAATAAA
Found at i:1261894 original size:41 final size:41
Alignment explanation
Indices: 1261848--1262183 Score: 223
Period size: 41 Copynumber: 8.0 Consensus size: 41
1261838 TCGAAAAACC
* * *
1261848 ATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAAAGGAGCA
1 ATTTATTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCA
* * **
1261889 ATTTATTTCTCAAAG-T-TCATTGCCTCTGTTTAGAGGAGTT
1 ATTTATTTTTCAAAGTTGTGA-TGCCTCTGTTTAGAGGAGCA
* * * * * * *
1261929 ATTTATTTTTTAAAAAAATTGTTAAGTCTGTATTTAGAGGAGCA
1 ATTTA-TTTTT--CAAAGTTGTGATGCCTCTGTTTAGAGGAGCA
* * *
1261973 ATTTATTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGTAGCA
1 ATTTATTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCA
* * **
1262014 ATTTA-CTTTCAAAAGTTATGATGCCTCTGTTTAGAGGAGTT
1 ATTTATTTTTC-AAAGTTGTGATGCCTCTGTTTAGAGGAGCA
* * * ** *
1262055 ATTTATTTCTTCAAAAGTTGTTAAGCCTCTGCTTAGAAAAGCTTT
1 ATTTATTT-TTC-AAAGTTGTGATGCCTCTGTTTAGAGGAGC--A
* *
1262100 GTTTATTTTTTAAAAAGTTGTGGA-GCCTCTGTTTAGAGGAGCA
1 ATTTA-TTTTT-CAAAGTTGT-GATGCCTCTGTTTAGAGGAGCA
* * *
1262143 ATTTACTTTCCAAAAGTTTTTGA-GCCTCTGTTTAGAGGAGC
1 ATTTATTTTTC-AAAG-TTGTGATGCCTCTGTTTAGAGGAGC
1262184 TTTGTTTATT
Statistics
Matches: 225, Mismatches: 54, Indels: 31
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.00
40 25 0.11
41 75 0.33
42 28 0.12
43 40 0.18
44 20 0.09
45 32 0.14
46 4 0.02
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (41 bp):
ATTTATTTTTCAAAGTTGTGATGCCTCTGTTTAGAGGAGCA
Found at i:1262076 original size:125 final size:127
Alignment explanation
Indices: 1261848--1262251 Score: 392
Period size: 125 Copynumber: 3.1 Consensus size: 127
1261838 TCGAAAAACC
* * * *
1261848 ATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAAAGGAGCAATTTA-TTTCTCAAAGTTCAT--T
1 ATTTATTTTACAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTC-AAAAGTT-ATGAT
* * * * **
1261910 GCCTCTGTTTAGAGGAGTTATTTATTTTTTAAAAAAATTGTTAAGTCTGTATTTAGAGGAGC-A
64 GCCTCTGTTTAGAGGAGTTATTTATTTCTTAAAAAAATTGTTAAGCCTCTACTTAGAAAAGCTA
* *
1261973 ATTTATTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGTAGCAATTTACTTTCAAAAGTTATGATGC
1 ATTTATTTTACAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTATGATGC
* * * *
1262038 CTCTGTTTAGAGGAGTTATTTATTTCTT-CAAAAGTTGTTAAGCCTCTGCTTAGAAAAGCTTT
66 CTCTGTTTAGAGGAGTTATTTATTTCTTAAAAAAATTGTTAAGCCTCTACTTAGAAAAGC-TA
* * * *
1262100 GTTTATTTTTTAAAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTTTTTG
1 ATTTA--TTTTACAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAAG-TTATG
* * * * * *
1262165 A-GCCTCTGTTTAGAGGAGCTTTGTTTATTT-TT-TAAAAGTCGTTGAGCCTCTACTTAAAAAAG
62 ATGCCTCTGTTTAGAGGAG--TTATTTATTTCTTAAAAAAATTGTTAAGCCTCTACTTAGAAAAG
*
1262227 CTTT
125 C-TA
*
1262231 GTTTATTTTATTCAAAGTTGT
1 ATTTATTTTA--CAAAGTTGT
1262252 TGAGCATCTA
Statistics
Matches: 238, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
124 2 0.01
125 71 0.30
126 34 0.14
127 4 0.02
129 46 0.19
130 23 0.10
131 49 0.21
132 9 0.04
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (127 bp):
ATTTATTTTACAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTATGATGC
CTCTGTTTAGAGGAGTTATTTATTTCTTAAAAAAATTGTTAAGCCTCTACTTAGAAAAGCTA
Found at i:1262116 original size:45 final size:44
Alignment explanation
Indices: 1262036--1262276 Score: 220
Period size: 45 Copynumber: 5.5 Consensus size: 44
1262026 AAGTTATGAT
* * * *
1262036 GCCTCTGTTTAGAGGAG--TTATTTATTTCTTCAAAAGTTGTTAA
1 GCCTCTGCTTAGAGGAGCTTTGTTTATTT-TTTAAAAGTTGTTGA
** *
1262079 GCCTCTGCTTAGAAAAGCTTTGTTTATTTTTTAAAAAGTTGTGGA
1 GCCTCTGCTTAGAGGAGCTTTGTTTATTTTTT-AAAAGTTGTTGA
* ** * ** *
1262124 GCCTCTGTTTAGAGGAGC--AATTTACTTTCCAAAAGTTTTTGA
1 GCCTCTGCTTAGAGGAGCTTTGTTTATTTTTTAAAAGTTGTTGA
* *
1262166 GCCTCTGTTTAGAGGAGCTTTGTTTATTTTTTAAAAGTCGTTGA
1 GCCTCTGCTTAGAGGAGCTTTGTTTATTTTTTAAAAGTTGTTGA
* * ** *
1262210 GCCTCTACTTAAAAAAGCTTTGTTTATTTTATTCAAAGTTGTTGA
1 GCCTCTGCTTAGAGGAGCTTTGTTTATTTT-TTAAAAGTTGTTGA
* *
1262255 GCATCTACTTAGAGGAGCTTTG
1 GCCTCTGCTTAGAGGAGCTTTG
1262277 ATTAAAATTT
Statistics
Matches: 157, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
42 28 0.18
43 21 0.13
44 44 0.28
45 64 0.41
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (44 bp):
GCCTCTGCTTAGAGGAGCTTTGTTTATTTTTTAAAAGTTGTTGA
Found at i:1262251 original size:131 final size:129
Alignment explanation
Indices: 1261849--1262272 Score: 413
Period size: 131 Copynumber: 3.3 Consensus size: 129
1261839 CGAAAAACCA
* * * *
1261849 TTTA-TTTTT-CAAAGTTGTGGTGCCTCTATTTAAAGGAGCAATTTA-TTTCTCAAAGTTCAT--
1 TTTATTTTTTACAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTC-AAAAGTT-ATGA
* * * * * * * * **
1261909 TGCCTCTGTTTAGAGGAGTTATTTATTTTTTAAAAAAATTGTTAAGTCTGTATTTAGAGGAGC--
64 TGCCTCTGTTTAGAGGAGTTATTTATTTCTT-CAAAAGTCGTTAAGCCTCTACTTAAAAAAGCTT
**
1261972 AA
128 TG
* * *
1261974 TTTA--TTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGTAGCAATTTACTTTCAAAAGTTATGATG
1 TTTATTTTTTACAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTATGATG
* * *
1262037 CCTCTGTTTAGAGGAGTTATTTATTTCTTCAAAAGTTGTTAAGCCTCTGCTTAGAAAAGCTTTG
66 CCTCTGTTTAGAGGAGTTATTTATTTCTTCAAAAGTCGTTAAGCCTCTACTTAAAAAAGCTTTG
* *
1262101 TTTATTTTTTAAAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTTTTTGA
1 TTTATTTTTTACAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAAG-TTATGA
* * *
1262166 -GCCTCTGTTTAGAGGAGCTTTGTTTATTT-TTTAAAAGTCGTTGAGCCTCTACTTAAAAAAGCT
64 TGCCTCTGTTTAGAGGAG--TTATTTATTTCTTCAAAAGTCGTTAAGCCTCTACTTAAAAAAGCT
1262229 TTG
127 TTG
* * **
1262232 TTTATTTTATT-CAAAGTTGTTGAGCATCTACTTAGAGGAGC
1 TTTATTTT-TTACAAAGTTGTGGAGCCTCTGTTTAGAGGAGC
1262273 TTTGATTAAA
Statistics
Matches: 255, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
124 6 0.02
125 66 0.26
126 34 0.13
127 4 0.02
129 41 0.16
130 23 0.09
131 70 0.27
132 11 0.04
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (129 bp):
TTTATTTTTTACAAAGTTGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTATGATG
CCTCTGTTTAGAGGAGTTATTTATTTCTTCAAAAGTCGTTAAGCCTCTACTTAAAAAAGCTTTG
Found at i:1262518 original size:3 final size:3
Alignment explanation
Indices: 1262510--1262617 Score: 64
Period size: 3 Copynumber: 35.0 Consensus size: 3
1262500 TAATTTTTAA
* *
1262510 TAT TAT TAT TTT TCAT TAT TAT TAT GAT TAT TAT TAT TATT TAT CTAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT
* *
1262558 TAAT T-T TTT TAGT TAT CTAT TAA TA- TAT T-T TAT TATT TAT CTAT
1 T-AT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TA-T TAT -TAT
*
1262602 TAT T-T T-T TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT
1262618 CTTTTTTTCT
Statistics
Matches: 85, Mismatches: 8, Indels: 24
0.73 0.07 0.21
Matches are distributed among these distances:
2 10 0.12
3 52 0.61
4 23 0.27
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1262522 original size:16 final size:16
Alignment explanation
Indices: 1262502--1262534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1262492 ATTTAATTTA
1262502 ATTTTT-AATATTATT
1 ATTTTTCAATATTATT
*
1262517 ATTTTTCATTATTATT
1 ATTTTTCAATATTATT
1262533 AT
1 AT
1262535 GATTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTCAATATTATT
Found at i:1262618 original size:44 final size:43
Alignment explanation
Indices: 1262513--1262619 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 43
1262503 TTTTTAATAT
* *
1262513 TATTATTTTTCATTATTAT-TATGATTATTATTATTATTTATC
1 TATTATTTTTTATTATTATCTATAATTATTATTATTATTTATC
*
1262555 TATTAATTTTT-TTAGTTATCTATTAATATATT-TTATTATTTATC
1 TATTATTTTTTATTA-TTATCTA-TAAT-TATTATTATTATTTATC
*
1262599 TATTATTTTTTATTTTTATCT
1 TATTATTTTTTATTATTATCT
1262620 TTTTTTCTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 3 0.05
42 13 0.24
43 2 0.04
44 31 0.56
45 6 0.11
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (43 bp):
TATTATTTTTTATTATTATCTATAATTATTATTATTATTTATC
Found at i:1262625 original size:18 final size:21
Alignment explanation
Indices: 1262513--1262619 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 21
1262503 TTTTTAATAT
*
1262513 TATTATTTTTCATTA-TTAT-
1 TATTATTTTTTATTATTTATC
*
1262532 TATGATTATTATTATTATTTATC
1 TATTATT-TT-TTATTATTTATC
* *
1262555 TATTAATTTTT-TTAGTTATC
1 TATTATTTTTTATTATTTATC
1262575 TATTAATATATTTTATTATTTATC
1 TATT-AT-T-TTTTATTATTTATC
1262599 TATTATTTTTTATT-TTTATC
1 TATTATTTTTTATTATTTATC
1262619 T
1 T
1262620 TTTTTTCTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.08
20 21 0.29
21 15 0.21
22 8 0.11
23 11 0.15
24 12 0.16
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTATTTTTTATTATTTATC
Found at i:1262931 original size:24 final size:23
Alignment explanation
Indices: 1262895--1262939 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
1262885 GATTTTAGGA
1262895 ATTTTTTTGGGGAATTTTTGGTG
1 ATTTTTTTGGGGAATTTTTGGTG
*
1262918 ATTTTTTTCTGGGAATTTTTGG
1 ATTTTTTT-GGGGAATTTTTGG
1262940 AAATTCTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.13, C:0.02, G:0.27, T:0.58
Consensus pattern (23 bp):
ATTTTTTTGGGGAATTTTTGGTG
Found at i:1263673 original size:49 final size:50
Alignment explanation
Indices: 1263610--1263705 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 50
1263600 TAAATTTTTA
*
1263610 AAAATATATATTTTTGAA-GGAAAGTT-AATTGTATCAATTTCCTTTGAACAC
1 AAAATATATATTTTT-AAGGGAAAGTTGAA-AGTATCAATTT-CTTTGAACAC
1263661 AAAATAT-T-TTTTTAAGGGAAAGTTGAAAGTATCAATTTCTTTGAA
1 AAAATATATATTTTTAAGGGAAAGTTGAAAGTATCAATTTCTTTGAA
1263706 AAGTAAAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
48 9 0.21
49 23 0.55
50 3 0.07
51 7 0.17
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (50 bp):
AAAATATATATTTTTAAGGGAAAGTTGAAAGTATCAATTTCTTTGAACAC
Found at i:1263898 original size:66 final size:67
Alignment explanation
Indices: 1263719--1263913 Score: 198
Period size: 71 Copynumber: 2.9 Consensus size: 67
1263709 TAAAAGGTTT
* * * * *
1263719 TAAAAAATATATATTTTTAGGAAAAAGTTGAAAGTATCATTTTTTCTTAAAAATAAAATTTCTAA
1 TAAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCTAA
*
1263784 GA
66 AA
* * * * *
1263786 TAAAATTTTCAAAAAGTA-TTTTGAGG-AAAAGTTAAAAGTATCAATTTTCCTCAAAATTAGAAT
1 TAAAA-----AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAT
1263849 TTC-AAAA
60 TTCTAAAA
* *
1263856 TAAAAAAAAAATATTTTTGGGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAA
1 TAAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAA
1263914 ATTATCAAGA
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
65 9 0.09
66 35 0.34
67 5 0.05
70 8 0.08
71 38 0.37
72 7 0.07
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (67 bp):
TAAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCTAA
AA
Found at i:1263927 original size:66 final size:65
Alignment explanation
Indices: 1263720--1263927 Score: 179
Period size: 66 Copynumber: 3.1 Consensus size: 65
1263710 AAAAGGTTTT
* * * * * *
1263720 AAAAAATATATATTTTTAGGAAAAAGTTGAAAGTATCATTTTTTCTTAAAAATAAAATTTCTAAG
1 AAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAG
* * * *
1263785 ATAAAATTTTCAAAAAGTA-TTTTGAGG-AAAAGTTAAAAGTATCAATTTTCCTCAAAATTAGAA
1 A-AAAA-----AAAAA-TATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAA
*
1263848 TTTCAAAAT
58 TTTC-AAAG
* *
1263857 AAAAAAAAAATATTTTTGGGAAAAAGTTGGAAGTACCAATTTTCCTTAAAAATAAAAATTATC-A
1 AAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATT-TCAA
1263921 AG
64 AG
1263923 AAAAA
1 AAAAA
1263928 CATTTTAAGG
Statistics
Matches: 112, Mismatches: 18, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
65 5 0.04
66 48 0.43
67 5 0.04
68 2 0.02
71 45 0.40
72 7 0.06
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (65 bp):
AAAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAG
Found at i:1264678 original size:22 final size:22
Alignment explanation
Indices: 1264614--1264687 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 22
1264604 ATTATTGATA
* *
1264614 ATTTATTATAAAGTTAT-AATTG
1 ATTTACTACAAAGTTATCAA-TG
* * *
1264636 ATTTACTACTAATTTACCAATG
1 ATTTACTACAAAGTTATCAATG
*
1264658 ATTTACT-CAAAAGTTATCAATA
1 ATTTACTAC-AAAGTTATCAATG
*
1264680 ATTAACTA
1 ATTTACTA
1264688 ATTTATTAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.92
23 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTTACTACAAAGTTATCAATG
Found at i:1265517 original size:12 final size:12
Alignment explanation
Indices: 1265500--1265533 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1265490 TCTGTCAGAA
1265500 ATTTAATTAATT
1 ATTTAATTAATT
1265512 ATTTAATTAATT
1 ATTTAATTAATT
*
1265524 TTTTAATTAA
1 ATTTAATTAA
1265534 AATTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTAATTAATT
Found at i:1267111 original size:23 final size:23
Alignment explanation
Indices: 1267076--1267124 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1267066 ATTTTGTTTC
*
1267076 TTTTGTTTGTTTATT-ATATTTT
1 TTTTGTTTGTTTATTAATAATTT
1267098 TTTTGTTTTGTTTATTAATAATTT
1 TTTTG-TTTGTTTATTAATAATTT
1267122 TTT
1 TTT
1267125 ATTAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (23 bp):
TTTTGTTTGTTTATTAATAATTT
Found at i:1267390 original size:49 final size:49
Alignment explanation
Indices: 1267278--1267896 Score: 944
Period size: 47 Copynumber: 12.9 Consensus size: 49
1267268 TTTAAAAGGA
* *
1267278 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTCATC-TGGAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1267325 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1267374 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAA-TCTCATC-TGAAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
* *
1267421 CTCCTCTCAGCAGA-GCTCTACAACTTTAAAA-TCTCATC-TGAAAATG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1267467 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
* *
1267516 CTCCTCTCAGTAGAGGCTCCACAACTTTAAAATT-TCATC-TGAAAATG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
*
1267563 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATT-TTATC-T-AAAAATG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAA-G
*
1267610 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATT-TCATC-TGAAAATG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1267657 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
* ** *
1267706 CTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TTTTCTTGAAAATG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
*
1267754 CTCCTCTCAGCAGAGGCTCTACAACTTTTAAAATTCTCATCTTGGAAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAAC-TTTAAAATTCTCATCTT-GAAAAAG
* * * *
1267805 CTCCTCTTAGCAGAGGTTCTACAACTTTAAAATTCTCATCTTGGAAAAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
*
1267854 CTCCTCTCAGCAGAGGCTCTACAACTTTAAAATTCTCATCTTG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTG
1267897 TTTTCAAATT
Statistics
Matches: 532, Mismatches: 28, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
46 48 0.09
47 189 0.36
48 69 0.13
49 175 0.33
50 22 0.04
51 29 0.05
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (49 bp):
CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAG
Found at i:1267570 original size:96 final size:97
Alignment explanation
Indices: 1267278--1267896 Score: 965
Period size: 96 Copynumber: 6.4 Consensus size: 97
1267268 TTTAAAAGGA
* *
1267278 CTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTCATC-TGGAAAAGCTCCTCTCAGCAGAGG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGG
*
1267341 CTCCACAACTTTAAAATTCTCATCTTGAAAAAG
66 CTCCACAACTTTAAAATT-TCATCTTGAAAATG
1267374 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAA-TCTCATC-TGAAAAAGCTCCTCTCAGCAGA-G
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGG
* *
1267436 CTCTACAACTTTAAAATCTCATC-TGAAAATG
66 CTCCACAACTTTAAAATTTCATCTTGAAAATG
*
1267467 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGTAGAGG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGG
1267532 CTCCACAACTTTAAAATTTCATC-TGAAAATG
66 CTCCACAACTTTAAAATTTCATCTTGAAAATG
*
1267563 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATT-TTATC-T-AAAAATGCTCCTCTCAGCAGAG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAA-GCTCCTCTCAGCAGAG
1267625 GCTCCACAACTTTAAAATTTCATC-TGAAAATG
65 GCTCCACAACTTTAAAATTTCATCTTGAAAATG
*
1267657 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAACAGAGG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGG
**
1267722 CTCCACAACTTTAAAATTTTTTCTTGAAAATG
66 CTCCACAACTTTAAAATTTCATCTTGAAAATG
* *
1267754 CTCCTCTCAGCAGAGGCTCTACAACTTTTAAAATTCTCATCTTGGAAAAAGCTCCTCTTAGCAGA
1 CTCCTCTCAGCAGAGGCTCCACAAC-TTTAAAATTCTCATCTT-GAAAAAGCTCCTCTCAGCAGA
* *
1267819 GGTTCTACAACTTTAAAATTCTCATCTTGGAAAA-G
64 GGCTCCACAACTTTAAAATT-TCATCTT-GAAAATG
*
1267854 CTCCTCTCAGCAGAGGCTCTACAACTTTAAAATTCTCATCTTG
1 CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTG
1267897 TTTTCAAATT
Statistics
Matches: 490, Mismatches: 21, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
93 44 0.09
94 94 0.19
95 46 0.09
96 161 0.33
97 37 0.08
98 18 0.04
99 54 0.11
100 31 0.06
101 5 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (97 bp):
CTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGG
CTCCACAACTTTAAAATTTCATCTTGAAAATG
Found at i:1278979 original size:17 final size:17
Alignment explanation
Indices: 1278956--1279000 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1278946 TGTGTGTGAA
*
1278956 TTTTTTTGTTTTGTT-T
1 TTTTTTTGTTTTATTAT
*
1278972 TATTTTTTGATTTATTAT
1 T-TTTTTTGTTTTATTAT
1278990 TTTTTTTGTTT
1 TTTTTTTGTTT
1279001 ACCCTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTTTTGTTTTATTAT
Found at i:1279730 original size:12 final size:12
Alignment explanation
Indices: 1279713--1279746 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1279703 TTTGTCAAAA
1279713 ATTTTATTAATT
1 ATTTTATTAATT
1279725 ATTTTATTAATT
1 ATTTTATTAATT
1279737 -TTTTAATTAA
1 ATTTT-ATTAA
1279747 AATTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:1280281 original size:19 final size:17
Alignment explanation
Indices: 1280257--1280295 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1280247 CATAAATATT
*
1280257 AATAAAATAATATATAAAA
1 AATAAAA-AA-ATAAAAAA
1280276 AATAAAAAAATAAAAAA
1 AATAAAAAAATAAAAAA
1280293 AAT
1 AAT
1280296 TTTTACCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAAAATAAAAAA
Found at i:1280631 original size:41 final size:42
Alignment explanation
Indices: 1280553--1280640 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
1280543 AACGACGTCG
1280553 TTTTGCTTTTAATTTTTTCTATAAATAACTTGAAAAAAATTT
1 TTTTGCTTTTAATTTTTTCTATAAATAACTTGAAAAAAATTT
*
1280595 TTTTGCTTTTAATTTTTTCTATAAATAACTTG-AAAAATTTT
1 TTTTGCTTTTAATTTTTTCTATAAATAACTTGAAAAAAATTT
1280636 TTTTG
1 TTTTG
1280641 TTCATTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.56
Consensus pattern (42 bp):
TTTTGCTTTTAATTTTTTCTATAAATAACTTGAAAAAAATTT
Found at i:1281622 original size:44 final size:44
Alignment explanation
Indices: 1281574--1281660 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
1281564 TAAACTGAAA
* * ** * *
1281574 TTGATTTACTATTAAATTATCACTAATTTACTATTGAGTTATTC
1 TTGATTAACTACTAAATTATCAAAAATTAACTATTAAGTTATTC
* *
1281618 TTGATTAATTACTAAGTTATCAAAAATTAACTATTAAGTTATT
1 TTGATTAACTACTAAATTATCAAAAATTAACTATTAAGTTATT
1281661 ACCCTTAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (44 bp):
TTGATTAACTACTAAATTATCAAAAATTAACTATTAAGTTATTC
Found at i:1281912 original size:22 final size:22
Alignment explanation
Indices: 1281869--1281912 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1281859 TTGATTATGT
* *
1281869 TTAAGTTTTTAATGATTAATTA
1 TTAAGTTATTAATGATCAATTA
* *
1281891 TTAAGTTATTAATTATCCATTA
1 TTAAGTTATTAATGATCAATTA
1281913 CTATATTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (22 bp):
TTAAGTTATTAATGATCAATTA
Found at i:1286519 original size:216 final size:215
Alignment explanation
Indices: 1286146--1286562 Score: 681
Period size: 216 Copynumber: 1.9 Consensus size: 215
1286136 GTCAAACACA
**** * * *
1286146 GGTTTCTCACGGGTAGTTCGTTGCTTTTGCGAACCACCAATGGGGTTAGTTGGGCGATTTTGAAG
1 GGTTTCTCACGGGTAGTTCGTTGCTCCCACAAACCACCAATGGGGTTAGTTAGACGATTTTGAAG
* * *
1286211 TTTGGGGTAGGTTGAGTGTTAGGACTATACATGGTATTTTGAGGCCTATGAGGGGTTTGACACGT
66 TTTGGGGTAGGCTGAGTGTTAGGACTATACATGGTATTTTGAGGCCTAGGAGGGGTTTGACAAGT
* *
1286276 TTGGGGGTATGGTGATTGTACAAATGGTTGATATGGGTAAGGGGAAGTGTTATTTACAGTAGGGT
131 TTGGGGGTATGGTGATTGTACAAATGGTTGATATGGGTAAGGGGAAGTGTTATTTACAGTAAGAT
1286341 AATATGGTGATTGTACAAAT
196 AATATGGTGATTGTACAAAT
* *
1286361 GGTTTCTCACGGGTAGTTCGTTGCTCCCACAAACCACTAATGGGGTTAGTTAGACGATTTTGAGG
1 GGTTTCTCACGGGTAGTTCGTTGCTCCCACAAACCACCAATGGGGTTAGTTAGACGATTTTGAAG
* *
1286426 TCTTGGGGTAGGCTGAGTGTTAGGATTGTACATGGTATTTTGAGGCCTAGGAGGGGTTTGACAAG
66 T-TTGGGGTAGGCTGAGTGTTAGGACTATACATGGTATTTTGAGGCCTAGGAGGGGTTTGACAAG
1286491 TTTGGGGGTATGGTGATTGTACAAATGGTTGATATGGGTAAGGGGAAGTGTTATTTACAGTAAGA
130 TTTGGGGGTATGGTGATTGTACAAATGGTTGATATGGGTAAGGGGAAGTGTTATTTACAGTAAGA
1286556 TAATATG
195 TAATATG
1286563 ACAGATATCT
Statistics
Matches: 185, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
215 57 0.31
216 128 0.69
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.34
Consensus pattern (215 bp):
GGTTTCTCACGGGTAGTTCGTTGCTCCCACAAACCACCAATGGGGTTAGTTAGACGATTTTGAAG
TTTGGGGTAGGCTGAGTGTTAGGACTATACATGGTATTTTGAGGCCTAGGAGGGGTTTGACAAGT
TTGGGGGTATGGTGATTGTACAAATGGTTGATATGGGTAAGGGGAAGTGTTATTTACAGTAAGAT
AATATGGTGATTGTACAAAT
Found at i:1291258 original size:59 final size:58
Alignment explanation
Indices: 1291014--1291349 Score: 414
Period size: 59 Copynumber: 5.8 Consensus size: 58
1291004 TGCTTTTGTA
* *
1291014 CAAGGAAAAATTGATACTTTCAACTTTTCCCCCAAAAA-A-ATTTTGGAAACTTTAATTT
1 CAAGG-AAAATTGATACTTTCAACTTTT-CCCCAAAAATATTTTTTGGAAACTTTATTTT
* * * * **
1291072 CGAGGAAAATTGATACTTTTAACTTTTCCTCAAAAA-CTTTTTT-GAAAAGTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTT
* * *
1291128 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTAGAAAGTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTT
* * * *
1291185 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAACTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAACTTTATTTT
* *
1291244 CAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTGGAAAGC-TTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAA-CTTTATTTT
* *
1291303 CAAGGAAAATTGATACTTTCAACCTTTCCCCAAAAATTTTTTTTGGA
1 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGA
1291350 TTTTATTTAA
Statistics
Matches: 243, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
56 55 0.23
57 73 0.30
58 13 0.05
59 101 0.42
60 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (58 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTT
Found at i:1291390 original size:6 final size:6
Alignment explanation
Indices: 1291381--1291441 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
1291371 ATACTATAAC
* * * *
1291381 AAAATA AAAAAA AAAAGA AAAGT- AAAACA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
1291427 AAGATA AAAATA AAA
1 AAAATA AAAATA AAA
1291442 GAATATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
5 8 0.18
6 36 0.82
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.11
Consensus pattern (6 bp):
AAAATA
Found at i:1291407 original size:17 final size:17
Alignment explanation
Indices: 1291381--1291441 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1291371 ATACTATAAC
1291381 AAAATAAAAAAAAAAAGA
1 AAAAT-AAAAAAAAAAGA
* * *
1291399 AAAGTAAAACAAAAATA
1 AAAATAAAAAAAAAAGA
* * *
1291416 AAAATAAAATAAAGATA
1 AAAATAAAAAAAAAAGA
1291433 AAAATAAAA
1 AAAATAAAA
1291442 GAATATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 33 0.89
18 4 0.11
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAATAAAAAAAAAAGA
Found at i:1292402 original size:22 final size:24
Alignment explanation
Indices: 1292374--1292421 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
1292364 TAAAAATTAT
*
1292374 AATAGATAAATTATAG-C-ATATA
1 AATAGATAAATAATAGTCAATATA
1292396 AATAGATAAATAATAGTCAATATA
1 AATAGATAAATAATAGTCAATATA
1292420 AA
1 AA
1292422 AAAAGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (24 bp):
AATAGATAAATAATAGTCAATATA
Found at i:1292553 original size:18 final size:17
Alignment explanation
Indices: 1292532--1292572 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1292522 AAGGAAAAAG
*
1292532 AAAATATATATAAAATAT
1 AAAATAAATAT-AAATAT
1292550 AAAATAAATATAAATAT
1 AAAATAAATATAAATAT
1292567 AAAATA
1 AAAATA
1292573 CAAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAATATAAATAT
Found at i:1292564 original size:6 final size:6
Alignment explanation
Indices: 1292533--1292569 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1292523 AGGAAAAAGA
*
1292533 AAATAT ATATA- AAATAT AAA-AT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAA
1292570 ATACAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:1295969 original size:48 final size:49
Alignment explanation
Indices: 1295909--1296220 Score: 373
Period size: 48 Copynumber: 6.4 Consensus size: 49
1295899 TGGAGAACAT
* * *
1295909 ATGAGATTTTTAAAGTTGTCAAGCCTCTACTGAAAAGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
* **
1295958 ATGA-ATTTTTAAAATTGTCGAGCCTCTGCTGAAAGGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
* ** * *
1296006 AT-AAATTTTTAAAGTTGTTAAGCCTCTATTGAGATGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
* * *
1296054 ATGAGAATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTC-AG
1 ATGAG-ATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
* * * *
1296103 ATAAGATTTTTAAAGTTGTTGAGCCTTTGCT-AAGAAGAGCTTTTTCAA-
1 ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAA-AGGAGCTTTTTCAAG
* * *
1296151 ATGAGATTTTTAAAGTTGTTAAGTCTTTGCTGAGAGGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
1296200 ATGAGGATTTTTAAAGTTGTT
1 ATGA-GATTTTTAAAGTTGTT
1296221 GGATAAGGAT
Statistics
Matches: 230, Mismatches: 25, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.01
48 159 0.69
49 17 0.07
50 52 0.23
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (49 bp):
ATGAGATTTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAG
Found at i:1296112 original size:98 final size:99
Alignment explanation
Indices: 1295912--1296220 Score: 432
Period size: 98 Copynumber: 3.2 Consensus size: 99
1295902 AGAACATATG
* * *
1295912 AGATTTTTAAAGTTGTCAAGCCTCTACTGAAAAGAGCTTTTTCAAGAT--GAATTTTTAAAATTG
1 AGATTTTTAAAGTTGTTAAGCCTCTACTGAGAAGAGCTTTTTCAAGATGAGAATTTTTAAAGTTG
* * *
1295975 TCGAGCCTCTGCTGAAAGGAGCTTTTTCAAGATA
66 TTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATA
* *
1296009 A-ATTTTTAAAGTTGTTAAGCCTCTATTGAGATGAGCTTTTTCAAGATGAGAATTTTTAAAGTTG
1 AGATTTTTAAAGTTGTTAAGCCTCTACTGAGAAGAGCTTTTTCAAGATGAGAATTTTTAAAGTTG
1296073 TTGAGCCTTTGCTGAGAGGAGCTTTTTC-AGATA
66 TTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATA
* * * *
1296106 AGATTTTTAAAGTTGTTGAGCCTTTGCTAAGAAGAGCTTTTTCAA-ATGAG-ATTTTTAAAGTTG
1 AGATTTTTAAAGTTGTTAAGCCTCTACTGAGAAGAGCTTTTTCAAGATGAGAATTTTTAAAGTTG
* *
1296169 TTAAGTCTTTGCTGAGAGGAGCTTTTTCAAGATGA
66 TTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGAT-A
*
1296204 GGATTTTTAAAGTTGTT
1 AGATTTTTAAAGTTGTT
1296221 GGATAAGGAT
Statistics
Matches: 190, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
96 81 0.43
97 16 0.08
98 93 0.49
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (99 bp):
AGATTTTTAAAGTTGTTAAGCCTCTACTGAGAAGAGCTTTTTCAAGATGAGAATTTTTAAAGTTG
TTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATA
Found at i:1296127 original size:146 final size:145
Alignment explanation
Indices: 1295909--1296221 Score: 407
Period size: 146 Copynumber: 2.1 Consensus size: 145
1295899 TGGAGAACAT
** *
1295909 ATGAGATTTTTAAAGTTGTCAAGCCTCTACTGAAAAGAGCTTTTTCAAGATGAATTTTTAAAATT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAAAAGAGCTTTTTCAAGATAAATTTTTAAAATT
* *
1295974 GTCGAGCCTCTGCTGAA-AGGAGCTTTTTCAAGAT-AAATTTTTAAAGTTGTTAAGCCTCTATTG
66 GTCGAGCCTCTGCT-AAGAAGAGCTTTTTCAA-ATGAAATTTTTAAAGTTGTTAAGCCTCTACTG
*
1296037 AGATGAGCTTTTTCAAG
129 AGAGGAGCTTTTTCAAG
* * * * *
1296054 ATGAGAATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTC-AGATAAGATTTTTAAAG
1 ATGAG-ATTTTTAAAGTTGTTGAGCCTCTACTGAAAAGAGCTTTTTCAAGATAA-ATTTTTAAAA
* * * * * *
1296118 TTGTTGAGCCTTTGCTAAGAAGAGCTTTTTCAAATGAGATTTTTAAAGTTGTTAAGTCTTTGCTG
64 TTGTCGAGCCTCTGCTAAGAAGAGCTTTTTCAAATGAAATTTTTAAAGTTGTTAAGCCTCTACTG
1296183 AGAGGAGCTTTTTCAAG
129 AGAGGAGCTTTTTCAAG
1296200 ATGAGGATTTTTAAAGTTGTTG
1 ATGA-GATTTTTAAAGTTGTTG
1296222 GATAAGGATT
Statistics
Matches: 146, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
145 14 0.10
146 131 0.90
147 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (145 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAAAAGAGCTTTTTCAAGATAAATTTTTAAAATT
GTCGAGCCTCTGCTAAGAAGAGCTTTTTCAAATGAAATTTTTAAAGTTGTTAAGCCTCTACTGAG
AGGAGCTTTTTCAAG
Found at i:1296274 original size:73 final size:71
Alignment explanation
Indices: 1296155--1296292 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 71
1296145 TTTCAAATGA
* * * * *
1296155 GATTTTTAAAGTTGTTAAGTCTTTGCTGAGAGGAGCTTTTTCAAGATGAGGATTTTTAAAGTTGT
1 GATTTTTAAAGTTGTTAAGTCTTTGCTGAAAGAAACTTTTTCAAGAT-A-AAATTTTAAAGTTGT
1296220 TGGATAAG
64 TGGATAAG
* *
1296228 GATTTTTAAAGTTGTTGAG-CTTCTGCTTAAAGAAACTTTTTCAAGATAAAATTTTAAAGTTGTT
1 GATTTTTAAAGTTGTTAAGTCTT-TGCTGAAAGAAACTTTTTCAAGATAAAATTTTAAAGTTGTT
1296292 G
65 G
1296293 AGCCTCTGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 15 0.26
72 4 0.07
73 38 0.67
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (71 bp):
GATTTTTAAAGTTGTTAAGTCTTTGCTGAAAGAAACTTTTTCAAGATAAAATTTTAAAGTTGTTG
GATAAG
Found at i:1296374 original size:50 final size:50
Alignment explanation
Indices: 1296276--1296374 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 50
1296266 TTTCAAGATA
* *
1296276 AAATTTTAAAGTTGTTGAGCCTCTGATGAGAAGAGTCTATTTTAGATTTT
1 AAATTTTAAAGTTGTCGAGCCTCAGATGAGAAGAGTCTATTTTAGATTTT
*
1296326 AAATTTTCAAAAGTTGTCGAGCCTCA-AGTGAGAAGAG-C-ATTTTCGATTT
1 AAATTTT--AAAGTTGTCGAGCCTCAGA-TGAGAAGAGTCTATTTTAGATTT
1296375 GACGAGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
50 17 0.40
51 2 0.05
52 24 0.56
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (50 bp):
AAATTTTAAAGTTGTCGAGCCTCAGATGAGAAGAGTCTATTTTAGATTTT
Found at i:1296634 original size:28 final size:28
Alignment explanation
Indices: 1296567--1296634 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1296557 CATGCCAATA
* *
1296567 CTCGATTTCAATTCAATTGGGCTTCAGG
1 CTCGATTTCAATACAATTGGGCTTCAAG
* * *
1296595 CACAATTTCAATACAATTGGGTTTCAAG
1 CTCGATTTCAATACAATTGGGCTTCAAG
*
1296623 CTCGATTCCAAT
1 CTCGATTTCAAT
1296635 TCGACTGGGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (28 bp):
CTCGATTTCAATACAATTGGGCTTCAAG
Found at i:1297813 original size:22 final size:21
Alignment explanation
Indices: 1297780--1297825 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
1297770 TGTTCAAGTA
1297780 AAAAATATTTTTTATT-TTTT
1 AAAAATATTTTTTATTATTTT
*
1297800 AAAAATATTATTTTTGTTATTTT
1 AAAAATA-T-TTTTTATTATTTT
1297823 AAA
1 AAA
1297826 TTTTGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 1 0.05
22 7 0.32
23 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AAAAATATTTTTTATTATTTT
Found at i:1302074 original size:40 final size:40
Alignment explanation
Indices: 1302016--1302093 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
1302006 TCGATTAGGA
1302016 CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTT
1 CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTT
*
1302056 CTTAGCCAATCATTAGACTGGTTCTCAAGGCTTTTATT
1 CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATT
1302094 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (40 bp):
CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTT
Found at i:1303657 original size:6 final size:6
Alignment explanation
Indices: 1303646--1303676 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1303636 TGGTGATAGT
*
1303646 TAAATA TAAATA TAAATA TAAATA TATATA T
1 TAAATA TAAATA TAAATA TAAATA TAAATA T
1303677 TTATATAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATA
Found at i:1306021 original size:3 final size:3
Alignment explanation
Indices: 1306013--1306037 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1306003 GAACAGAGAA
1306013 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1306038 GAGTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1308381 original size:40 final size:40
Alignment explanation
Indices: 1308292--1308371 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1308282 GATTAGGACT
* *
1308292 TAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTTCA
1 TAGCAAATCATGAGACTGGTTCTCAAGGCTTTTATTTACA
* *
1308332 TAGCCAATCATTAGACTGGTTCTCAAGGCTTTTATGTTAC
1 TAGCAAATCATGAGACTGGTTCTCAAGGCTTTTAT-TTAC
1308372 TTTTAAATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (40 bp):
TAGCAAATCATGAGACTGGTTCTCAAGGCTTTTATTTACA
Found at i:1312661 original size:40 final size:40
Alignment explanation
Indices: 1312577--1312653 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1312567 GGACTTCGCC
* *
1312577 AATCATTAGACTGGTTCTCAAGGCTTTTATTTTCTTAGCC
1 AATCATTAGACTGGTTCTCAAGGCTTTTATTTACTTAGCA
1312617 AATCATTAGACTGGTTCTCAAGGCTTTTATGTTACTT
1 AATCATTAGACTGGTTCTCAAGGCTTTTAT-TTACTT
1312654 TTAAATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 30 0.86
41 5 0.14
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (40 bp):
AATCATTAGACTGGTTCTCAAGGCTTTTATTTACTTAGCA
Found at i:1313338 original size:2 final size:2
Alignment explanation
Indices: 1313326--1313363 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1313316 TATAAATTAA
1313326 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1313364 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1315676 original size:2 final size:2
Alignment explanation
Indices: 1315658--1315696 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1315648 ATATTATCAG
*
1315658 TA TA TA TG TA TA CTA TA TA TA TA TA TA 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
1315697 CATACATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1315748 original size:17 final size:17
Alignment explanation
Indices: 1315722--1315754 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1315712 TGAATCACAT
1315722 AATTATATTTTATAAATA
1 AATTATATTTTA-AAATA
1315740 AATTA-ATTTTAAAAT
1 AATTATATTTTAAAAT
1315755 TTAAAATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTATATTTTAAAATA
Found at i:1317548 original size:40 final size:40
Alignment explanation
Indices: 1317490--1317567 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
1317480 TCGAGTAGGA
*
1317490 CTTAGCCAATCATGAGACTGGTTCTCAATGCTTTTATTTT
1 CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTT
** *
1317530 CTTAGCCTGTCATTAGACTGGTTCTCAAGGCTTTTATT
1 CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATT
1317568 ATACTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (40 bp):
CTTAGCCAATCATGAGACTGGTTCTCAAGGCTTTTATTTT
Found at i:1317970 original size:13 final size:13
Alignment explanation
Indices: 1317952--1317983 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1317942 TAAAATATTT
1317952 ATATATTTATATA
1 ATATATTTATATA
1317965 ATATA-TTATATA
1 ATATATTTATATA
1317977 A-ATATTT
1 ATATATTT
1317984 TTTAGGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 10 0.56
13 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATTTATATA
Found at i:1322110 original size:2 final size:2
Alignment explanation
Indices: 1322103--1322135 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1322093 ATTGTATGGA
*
1322103 AT AT AT AT AG 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 AT AT A
1322136 GTTAGAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1322994 original size:119 final size:119
Alignment explanation
Indices: 1322779--1323056 Score: 441
Period size: 119 Copynumber: 2.3 Consensus size: 119
1322769 TTTTTTAGGG
*
1322779 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTCGATTTTCAAGGAAAAT
* *
1322843 TGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAAGA
66 TGATACTTTCAACTTTTCCCCAAAAACACTTTTTTTGAAAATTTATTTCTAAGA
*
1322897 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTCGATTTTCAAGGAAAAT
* * * * *
1322962 TGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTGGAAATTTATTTTTGAGG
66 TGATACTTTCAACTTTTCCCCAAAAACACTTTTTTTGAAAATTTATTTCTAAGA
* * *
1323016 AAAATTGATACTTTCAACTTTTCCCTAAAATTTTTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT
1323057 TTGGAAATTT
Statistics
Matches: 147, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
118 33 0.22
119 114 0.78
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.45
Consensus pattern (119 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTCGATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAACACTTTTTTTGAAAATTTATTTCTAAGA
Found at i:1323055 original size:59 final size:59
Alignment explanation
Indices: 1322770--1323072 Score: 396
Period size: 59 Copynumber: 5.1 Consensus size: 59
1322760 AAGAATGATT
*
1322770 TTTTTAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTCGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTT--A
* * *** *
1322829 TTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTA
* *
1322888 TTTCTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT-GAAATTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAA-TTT-A
* *
1322948 TTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTGGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTA
* * * *
1323007 TTTTTGAGGAAAATTGATACTTTCAACTTTTCCCTAAAATTTTTTTTTTTTTGGAAATTTA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAA--ATATTTTTTTTGGAAATTTA
1323068 TTTTT
1 TTTTT
1323073 CTTTTAAGAA
Statistics
Matches: 213, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
58 3 0.01
59 121 0.57
60 50 0.23
61 39 0.18
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (59 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTA
Found at i:1323554 original size:19 final size:20
Alignment explanation
Indices: 1323514--1323559 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1323504 GAACACCGGT
* *
1323514 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTAGAAATTTTC
1323534 GCCGGAATCTAGAAA-TTTC
1 GCCGGAATCTAGAAATTTTC
1323553 GCCGGAA
1 GCCGGAA
1323560 GTTGGCCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (20 bp):
GCCGGAATCTAGAAATTTTC
Found at i:1323650 original size:30 final size:31
Alignment explanation
Indices: 1323612--1323681 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
1323602 ACTGGGCTGG
*
1323612 TCGCCGGAAACTTC-AATGTTCGCCGGAATTA
1 TCGCCGGAAAATTCAAAT-TTCGCCGGAATTA
*
1323643 T-GCCGGAAAATTCAAATTTCGCCGGAATTT
1 TCGCCGGAAAATTCAAATTTCGCCGGAATTA
1323673 TCGCCGGAA
1 TCGCCGGAA
1323682 TCTGAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAATTTCGCCGGAATTA
Found at i:1323691 original size:31 final size:30
Alignment explanation
Indices: 1323630--1323693 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
1323620 AACTTCAATG
**
1323630 TTCGCCGGAATTATGCCGGAAAATTCAAAT
1 TTCGCCGGAATTATGCCGGAAAATGAAAAT
* **
1323660 TTCGCCGGAATTTTCGCCGGAATCTGAAAAT
1 TTCGCCGGAATTAT-GCCGGAAAATGAAAAT
1323691 TTC
1 TTC
1323694 CCAAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (30 bp):
TTCGCCGGAATTATGCCGGAAAATGAAAAT
Found at i:1324057 original size:42 final size:44
Alignment explanation
Indices: 1324009--1324117 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 44
1323999 AAATCAAAAA
* * *
1324009 TAAAAAAATACTAGATAATAATCA-GATAAATCA-AA-AGATATT
1 TAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
* * *
1324051 TAAAAAAAAAATATCTGATAATCAGGAAAAATCAGAACAGATAAT
1 TAAAAAAATAATA-ATAATAATCAGGAAAAATCAGAACAGATAAT
1324096 TAAAAATAATAATAATAATAAT
1 TAAAAA-AATAATAATAATAAT
1324118 AATAATAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 19 0.36
43 8 0.15
44 2 0.04
45 18 0.34
46 6 0.11
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.25
Consensus pattern (44 bp):
TAAAAAAATAATAATAATAATCAGGAAAAATCAGAACAGATAAT
Found at i:1324108 original size:3 final size:3
Alignment explanation
Indices: 1324100--1324278 Score: 65
Period size: 3 Copynumber: 58.3 Consensus size: 3
1324090 GATAATTAAA
* **
1324100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
1324143 AAGT ATAT ATT ACA- AA- AAA AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AA-T A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1324189 AAAT ATAT AACT ATAT ACAT -AT AA- ATCT AAT -CT AAT AA- AAA AAT
1 -AAT A-AT AA-T A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
1324233 AAAT AAAT ATAT ACAT AAT AAT AAT AAT AAT AA- AAT ACAT AA- AAT
1 -AAT -AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
1324278 A
1 A
1324279 CAAAAGAAGA
Statistics
Matches: 137, Mismatches: 17, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
2 17 0.12
3 85 0.62
4 33 0.24
5 2 0.01
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1324353 original size:20 final size:21
Alignment explanation
Indices: 1324330--1324369 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1324320 GCCTTACCCG
1324330 TTTGGGCCAGG-CCCAATTGA
1 TTTGGGCCAGGACCCAATTGA
*
1324350 TTTGGGCCCGGACCCAATTG
1 TTTGGGCCAGGACCCAATTG
1324370 GGTGTCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (21 bp):
TTTGGGCCAGGACCCAATTGA
Found at i:1329318 original size:28 final size:28
Alignment explanation
Indices: 1329287--1329341 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1329277 CTTCCGCTCT
*
1329287 TGTTG-TTCAATCTTTTTTTCGGTTCCAC
1 TGTTGCTTCAA-CTATTTTTCGGTTCCAC
*
1329315 TGTTGCCTTCCACTATTTTTCGGTTCC
1 TGTTG-CTTCAACTATTTTTCGGTTCC
1329342 TGCTAGCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 14 0.61
30 4 0.17
ACGTcount: A:0.09, C:0.25, G:0.15, T:0.51
Consensus pattern (28 bp):
TGTTGCTTCAACTATTTTTCGGTTCCAC
Found at i:1329362 original size:74 final size:74
Alignment explanation
Indices: 1329236--1329379 Score: 234
Period size: 74 Copynumber: 1.9 Consensus size: 74
1329226 GTGGTTCCCC
* *
1329236 TCCACTGTTGCCTTCCACTATTTTTCAGTTCCTACTAGCTTCTTCCGCTCTTGTTGTTCAATCTT
1 TCCACTGTTGCCTTCCACTATTTTTCAGTTCCTACTAGCTTCTTCCGCTCTTGCTGCTCAATCTT
1329301 TTTTTCGGT
66 TTTTTCGGT
* * * *
1329310 TCCACTGTTGCCTTCCACTATTTTTCGGTTCCTGCTAGCTTCTTTCGTTCTTGCTGCTCAATCTT
1 TCCACTGTTGCCTTCCACTATTTTTCAGTTCCTACTAGCTTCTTCCGCTCTTGCTGCTCAATCTT
1329375 TTTTT
66 TTTTT
1329380 TCAGTTCTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.10, C:0.28, G:0.12, T:0.49
Consensus pattern (74 bp):
TCCACTGTTGCCTTCCACTATTTTTCAGTTCCTACTAGCTTCTTCCGCTCTTGCTGCTCAATCTT
TTTTTCGGT
Found at i:1329963 original size:41 final size:41
Alignment explanation
Indices: 1329844--1330039 Score: 245
Period size: 41 Copynumber: 4.8 Consensus size: 41
1329834 TCTTCTAAAC
* *
1329844 AGAGGCAACAAACTTTGAG-AAATAAATGGCTTATCTGAAT
1 AGAGGCAACGAACTTTGAGAAAATAAATGGCTCATCTGAAT
* * *
1329884 AGAGGCAATGAACTTT--GAAAATAAATGGCTCCTTTGAAT
1 AGAGGCAACGAACTTTGAGAAAATAAATGGCTCATCTGAAT
* *
1329923 AGAGACAACAAACTTTGAGAAAATAAATGGCTCATCTGAAT
1 AGAGGCAACGAACTTTGAGAAAATAAATGGCTCATCTGAAT
* * * *
1329964 AGAGGCAATGAATTTTGAGAAAATAAATGGCTCCTTTGAAT
1 AGAGGCAACGAACTTTGAGAAAATAAATGGCTCATCTGAAT
*
1330005 AAAGGCAAACGAACTTTTGAGAAAATAAATGGCTC
1 AGAGGC-AACGAAC-TTTGAGAAAATAAATGGCTC
1330040 CTTAACAATC
Statistics
Matches: 132, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 31 0.23
40 14 0.11
41 61 0.46
42 5 0.04
43 20 0.15
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (41 bp):
AGAGGCAACGAACTTTGAGAAAATAAATGGCTCATCTGAAT
Found at i:1329964 original size:80 final size:81
Alignment explanation
Indices: 1329844--1330039 Score: 306
Period size: 80 Copynumber: 2.4 Consensus size: 81
1329834 TCTTCTAAAC
*
1329844 AGAGGCAACAAACTTTGAG-AAATAAATGGCTTATCTGAATAGAGGCAATGAACTTT-GAAAATA
1 AGAGGCAACAAACTTTGAGAAAATAAATGGCTCATCTGAATAGAGGCAATGAACTTTAGAAAATA
1329907 AATGGCTCCTTTGAAT
66 AATGGCTCCTTTGAAT
* *
1329923 AGAGACAACAAACTTTGAGAAAATAAATGGCTCATCTGAATAGAGGCAATGAATTTTGAGAAAAT
1 AGAGGCAACAAACTTTGAGAAAATAAATGGCTCATCTGAATAGAGGCAATGAACTTT-AGAAAAT
1329988 AAATGGCTCCTTTGAAT
65 AAATGGCTCCTTTGAAT
* *
1330005 AAAGGCAAACGAACTTTTGAGAAAATAAATGGCTC
1 AGAGGC-AACAAAC-TTTGAGAAAATAAATGGCTC
1330040 CTTAACAATC
Statistics
Matches: 106, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
79 18 0.17
80 35 0.33
82 27 0.25
83 6 0.06
84 20 0.19
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (81 bp):
AGAGGCAACAAACTTTGAGAAAATAAATGGCTCATCTGAATAGAGGCAATGAACTTTAGAAAATA
AATGGCTCCTTTGAAT
Found at i:1342488 original size:74 final size:74
Alignment explanation
Indices: 1342367--1342513 Score: 208
Period size: 74 Copynumber: 2.0 Consensus size: 74
1342357 GTTCCCTTCT
* *
1342367 ACTGTTGCCTTCCACTATTTTTCGATTCCTGCGAGCTTATTCCGTTCTTGCTGGTGAATCTTCTT
1 ACTGTTGCCTTCCACTATTTTTCGATTCCTGCGAGCTTATTCCGTTCTTGCTGCTCAATCTT-TT
1342432 TTT-GGTTCC
65 TTTCGGTTCC
* * * *
1342441 ACTGTTGCCTTTCACTATTTTTC-AGTTCCTGCTAGCTTCTTTCGTTCTTGCTGCTCAATCTTTT
1 ACTGTTGCCTTCCACTATTTTTCGA-TTCCTGCGAGCTTATTCCGTTCTTGCTGCTCAATCTTTT
1342505 TTTCGGTTC
65 TTTCGGTTC
1342514 TTCTTTTTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
73 6 0.09
74 59 0.91
ACGTcount: A:0.10, C:0.26, G:0.16, T:0.48
Consensus pattern (74 bp):
ACTGTTGCCTTCCACTATTTTTCGATTCCTGCGAGCTTATTCCGTTCTTGCTGCTCAATCTTTTT
TTCGGTTCC
Found at i:1345443 original size:28 final size:29
Alignment explanation
Indices: 1345411--1345467 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1345401 ATAATAATAA
* *
1345411 AATTTATTATAATTGAGATT-AAAAAAAT
1 AATTTACTATAACTGAGATTGAAAAAAAT
*
1345439 AATTTACTATAACTGTGATTGAAAAAAAT
1 AATTTACTATAACTGAGATTGAAAAAAAT
1345468 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (29 bp):
AATTTACTATAACTGAGATTGAAAAAAAT
Found at i:1351539 original size:2 final size:2
Alignment explanation
Indices: 1351532--1351564 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1351522 ATTGAGATTT
1351532 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 T
1351565 TTGAGATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1356538 original size:12 final size:12
Alignment explanation
Indices: 1356521--1356545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1356511 TATTATATAA
1356521 AAATAATTTTTT
1 AAATAATTTTTT
1356533 AAATAATTTTTT
1 AAATAATTTTTT
1356545 A
1 A
1356546 TTTATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:1356557 original size:8 final size:8
Alignment explanation
Indices: 1356544--1356588 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
1356534 AATAATTTTT
1356544 TATTTATA
1 TATTTATA
1356552 TATTTATA
1 TATTTATA
*
1356560 TAATTATA
1 TATTTATA
*
1356568 TATTTAAA
1 TATTTATA
1356576 TATTTATA
1 TATTTATA
1356584 T-TTTA
1 TATTTA
1356589 AAAAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
7 4 0.12
8 29 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:1356566 original size:16 final size:15
Alignment explanation
Indices: 1356547--1356603 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
1356537 AATTTTTTAT
*
1356547 TTATATATTTATATAA
1 TTATAT-TTTAAATAA
*
1356563 TTATATATTTAAATAT
1 TTATAT-TTTAAATAA
*
1356579 TTATATTTTAAAAAA
1 TTATATTTTAAATAA
*
1356594 TAATATTTTA
1 TTATATTTTA
1356604 TTAATTTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 16 0.44
16 20 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATATTTTAAATAA
Found at i:1357290 original size:2 final size:2
Alignment explanation
Indices: 1357283--1357316 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1357273 AAATTTCAAC
1357283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1357317 AGAGATAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1362123 original size:11 final size:11
Alignment explanation
Indices: 1362107--1362131 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1362097 ATTATGTGAA
1362107 AAAAAAAAAAC
1 AAAAAAAAAAC
1362118 AAAAAAAAAAC
1 AAAAAAAAAAC
1362129 AAA
1 AAA
1362132 GCTATGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1364140 original size:3 final size:3
Alignment explanation
Indices: 1364134--1364177 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1364124 TGCTTATTAT
*
1364134 ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1364178 TACTCACCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1364902 original size:24 final size:24
Alignment explanation
Indices: 1364879--1364933 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1364869 TAAACAAAAT
1364879 TTAA-AATAATAATAATAATGAAA
1 TTAATAATAATAATAATAATGAAA
*
1364902 TTAATTATTATAATAATAA-AATTAAA
1 TTAA-TA--ATAATAATAATAATGAAA
1364928 TTAATA
1 TTAATA
1364934 GTGAAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
25 3 0.11
26 10 0.37
27 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTAATAATAATAATAATAATGAAA
Found at i:1365028 original size:13 final size:14
Alignment explanation
Indices: 1364985--1365028 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1364975 GATGAATTAA
1364985 AATAAAAAATTATT
1 AATAAAAAATTATT
*
1364999 -ATTAAAAATTATAT
1 AATAAAAAATTAT-T
1365013 AATAAAAAATT-TT
1 AATAAAAAATTATT
1365026 AAT
1 AAT
1365029 TATTTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAAAAATTATT
Found at i:1365128 original size:23 final size:23
Alignment explanation
Indices: 1365083--1365135 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1365073 ATATTAAATT
**
1365083 AATAAAATTATTTTATATTTTTA
1 AATAAAATTATTTTATAAATTTA
* *
1365106 AATAAATTTTTTTTATAAATTTA
1 AATAAAATTATTTTATAAATTTA
*
1365129 AAAAAAA
1 AATAAAA
1365136 AAAAGTTATC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAAAATTATTTTATAAATTTA
Found at i:1366094 original size:15 final size:16
Alignment explanation
Indices: 1366070--1366106 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1366060 TTATCAATTT
1366070 TTATTATTT-AAAATA
1 TTATTATTTAAAAATA
*
1366085 TTATTCTTTAAAAATA
1 TTATTATTTAAAAATA
1366101 TT-TTAT
1 TTATTAT
1366107 AATTGATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTATTTAAAAATA
Found at i:1366499 original size:11 final size:11
Alignment explanation
Indices: 1366483--1366511 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1366473 TAAATATATC
1366483 AAAATTTTTTT
1 AAAATTTTTTT
1366494 AAAA-TTTTTT
1 AAAATTTTTTT
1366504 AAAATTTT
1 AAAATTTT
1366512 ACATGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
AAAATTTTTTT
Found at i:1367139 original size:23 final size:23
Alignment explanation
Indices: 1367080--1367140 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
1367070 TTATATAAAA
*
1367080 TATTAATAATTTAT-ATATTTATG
1 TATT-ATAATTTATAAAATTTATG
*
1367103 --TTATATTTTATATAAAATTTATG
1 TATTATA-ATT-TATAAAATTTATG
1367126 TATTATAATTTATAA
1 TATTATAATTTATAA
1367141 TGTAGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 3 0.10
23 13 0.43
24 2 0.07
25 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TATTATAATTTATAAAATTTATG
Found at i:1367224 original size:15 final size:15
Alignment explanation
Indices: 1367194--1367246 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1367184 TTTATTAAAA
*
1367194 TTTTATATTGTATTAT
1 TTTTATATT-TTTTAT
1367210 TTTTATATTTTTTAT
1 TTTTATATTTTTTAT
*
1367225 TTATATCA-TTTTTA-
1 TTTTAT-ATTTTTTAT
1367239 TTTTATAT
1 TTTTATAT
1367247 CATTATATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 16 0.50
16 10 0.31
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTATATTTTTTAT
Found at i:1367247 original size:16 final size:16
Alignment explanation
Indices: 1367210--1367250 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1367200 ATTGTATTAT
1367210 TTTTATAT--TTTTTA
1 TTTTATATCATTTTTA
1367224 -TTTATATCATTTTTA
1 TTTTATATCATTTTTA
1367239 TTTTATATCATT
1 TTTTATATCATT
1367251 ATATTGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
15 6 0.25
16 11 0.46
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATATCATTTTTA
Found at i:1367308 original size:22 final size:22
Alignment explanation
Indices: 1367282--1367324 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1367272 AGCCTACTCT
*
1367282 TAAATTTAT-TTTTTATGATATA
1 TAAATATATATTTTT-TGATATA
1367304 TAAATATATATTTTTTGATAT
1 TAAATATATATTTTTTGATAT
1367325 TTTGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TAAATATATATTTTTTGATATA
Found at i:1367334 original size:2 final size:2
Alignment explanation
Indices: 1367329--1367354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1367319 TGATATTTTG
1367329 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
1367355 TGGAATAAGG
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:1374820 original size:129 final size:129
Alignment explanation
Indices: 1374590--1374846 Score: 444
Period size: 129 Copynumber: 2.0 Consensus size: 129
1374580 GGACAGCAAT
* *
1374590 GAGTTCGAGTCACTCAAGTGAAGTGGGTCCCGCTTGATCTAATTAGGTTGGGTCAATTGGGTGAG
1 GAGTTCAAGTCACTCAAGTGAAGTGGGTCCCGCTGGATCTAATTAGGTTGGGTCAATTGGGTGAG
* *
1374655 TGAGTGAGTGCTGCCTTTTCGAGTGCGCAGGCGCTCCGT-CCCTTTTGTGTAAAATCATGAAAAC
66 TGAGTGAGTGCGGCCTTTTCGAGTGCGCAGCCGCTCC-TACCCTTTTGTGTAAAATCATGAAAAC
* *
1374719 GAGTTCAAGTCTCTCAAGTGAAGTGGGTCCCGCTGGATCTGATTAGGTTGGGTCAATTGGGTGAG
1 GAGTTCAAGTCACTCAAGTGAAGTGGGTCCCGCTGGATCTAATTAGGTTGGGTCAATTGGGTGAG
1374784 TGAGTGAGTGCGGCCTTTTCGAGTGCGCAGCCGCTCCTACCCTTTTGTGTAAAATCATGAAAA
66 TGAGTGAGTGCGGCCTTTTCGAGTGCGCAGCCGCTCCTACCCTTTTGTGTAAAATCATGAAAA
1374847 TGGGGCTGGT
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
128 1 0.01
129 120 0.99
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (129 bp):
GAGTTCAAGTCACTCAAGTGAAGTGGGTCCCGCTGGATCTAATTAGGTTGGGTCAATTGGGTGAG
TGAGTGAGTGCGGCCTTTTCGAGTGCGCAGCCGCTCCTACCCTTTTGTGTAAAATCATGAAAAC
Found at i:1381651 original size:23 final size:25
Alignment explanation
Indices: 1381619--1381668 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1381609 ATTTAGCTTG
1381619 AAACTTC-TTTGGTTAACCATGCTC
1 AAACTTCTTTTGGTTAACCATGCTC
*
1381643 AAAC-TCTTTTGGTTAACCGTGCTC
1 AAACTTCTTTTGGTTAACCATGCTC
1381667 AA
1 AA
1381669 GTTACTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (25 bp):
AAACTTCTTTTGGTTAACCATGCTC
Found at i:1381961 original size:14 final size:15
Alignment explanation
Indices: 1381930--1381961 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1381920 TAAAATTTAC
*
1381930 AAAAGTTAGAAACAA
1 AAAAGTTAAAAACAA
1381945 AAAAGTTAAAAACAA
1 AAAAGTTAAAAACAA
1381960 AA
1 AA
1381962 TAATCATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAGTTAAAAACAA
Found at i:1384642 original size:9 final size:9
Alignment explanation
Indices: 1384628--1384688 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
1384618 TTCTATCTGG
1384628 TATTATTTT
1 TATTATTTT
1384637 TATTATTTT
1 TATTATTTT
*
1384646 T-TTCTTTCT
1 TATTATTT-T
*
1384655 TTTGTATTTT
1 TAT-TATTTT
1384665 TATGTA-TTT
1 TAT-TATTTT
*
1384674 TATTATTAT
1 TATTATTTT
1384683 TATTAT
1 TATTAT
1384689 GTATTAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.16
9 26 0.59
10 7 0.16
11 4 0.09
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:1384739 original size:25 final size:24
Alignment explanation
Indices: 1384711--1384776 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
1384701 GTATATCTGT
*
1384711 ATTTATTTTTTTTTATTTAGAATAG
1 ATTTATTTTATTTTATTTA-AATAG
* *
1384736 ATTTATATGTATTTTATTTATATAG
1 ATTTAT-TTTATTTTATTTAAATAG
*
1384761 ATATA-TTTATTATTAT
1 ATTTATTTTATT-TTAT
1384777 ATTATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 14 0.41
26 11 0.32
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
ATTTATTTTATTTTATTTAAATAG
Found at i:1384781 original size:29 final size:30
Alignment explanation
Indices: 1384722--1384782 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
1384712 TTTATTTTTT
* *
1384722 TTTATTTAGAATAGATTTATATGTATTTTA
1 TTTATATAGAATAGATTTATATGTATATTA
*
1384752 TTTATATAG-ATATATTTATTAT-TATATTA
1 TTTATATAGAATAGATTTA-TATGTATATTA
1384781 TT
1 TT
1384783 ATTATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (30 bp):
TTTATATAGAATAGATTTATATGTATATTA
Found at i:1385224 original size:26 final size:25
Alignment explanation
Indices: 1385178--1385226 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1385168 TCATCAAAAA
**
1385178 TTTTTTGGGAATTTTTCAAAATTTT
1 TTTTTTGGGAATTTTGAAAAATTTT
1385203 TTTTTTGGGAATTTCTGAAAAATT
1 TTTTTTGGGAATTT-TGAAAAATT
1385227 CCAGATTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (25 bp):
TTTTTTGGGAATTTTGAAAAATTTT
Found at i:1385772 original size:20 final size:21
Alignment explanation
Indices: 1385732--1385774 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1385722 AGGTTTTTTT
*
1385732 TTTTTTTCATTCATTTGTTTA
1 TTTTTTTCATTCATTTATTTA
*
1385753 TTTTTTTCATT-TTTTATTTA
1 TTTTTTTCATTCATTTATTTA
1385773 TT
1 TT
1385775 AGATTAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTCATTCATTTATTTA
Found at i:1385818 original size:6 final size:6
Alignment explanation
Indices: 1385797--1385879 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 6
1385787 TTTAATATTC
* * * * *
1385797 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTAT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1385842 TTTTTA TTTTTA TTTATTTA TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA -TT-TTTA TTTTTA TT-TT-TA TTTT
1385880 CTTTAAATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
5 12 0.19
6 34 0.55
7 8 0.13
8 8 0.13
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:1385819 original size:17 final size:17
Alignment explanation
Indices: 1385797--1385868 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 17
1385787 TTTAATATTC
1385797 TTTTTATCTTTATTTTA
1 TTTTTATCTTTATTTTA
* *
1385814 TTTTTATTTTTGTTTTA
1 TTTTTATCTTTATTTTA
*
1385831 -CTTT-TCTTTATTTTTTA
1 TTTTTATCTTTA--TTTTA
1385848 TTTTTA--TTTA-TTTA
1 TTTTTATCTTTATTTTA
1385862 TTTTTAT
1 TTTTTAT
1385869 TATTCTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.23
15 4 0.09
16 3 0.07
17 24 0.55
18 3 0.07
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTTATCTTTATTTTA
Found at i:1385834 original size:27 final size:26
Alignment explanation
Indices: 1385797--1385879 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 26
1385787 TTTAATATTC
1385797 TTTTTATCTTTATTTTATTTTTATTTT
1 TTTTTA-CTTTATTTTATTTTTATTTT
1385824 TGTTTTACTTT-TCTTTATTTTTTATTTT
1 T-TTTTACTTTAT-TTTA-TTTTTATTTT
*
1385852 TATTTA-TTTATTTTTATTATTCTATTTT
1 TTTTTACTTTA-TTTTATT-TT-TATTTT
1385880 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
26 6 0.12
27 19 0.40
28 23 0.48
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTTACTTTATTTTATTTTTATTTT
Found at i:1385863 original size:14 final size:14
Alignment explanation
Indices: 1385837--1385879 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1385827 TTTACTTTTC
1385837 TTTATTT-TTTATT
1 TTTATTTATTTATT
1385850 TTTATTTATTTATT
1 TTTATTTATTTATT
1385864 TTTA-TTATTCTATT
1 TTTATTTATT-TATT
1385878 TT
1 TT
1385880 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:1385871 original size:17 final size:16
Alignment explanation
Indices: 1385728--1385878 Score: 53
Period size: 17 Copynumber: 8.9 Consensus size: 16
1385718 CTTAAGGTTT
* *
1385728 TTTTTTTTTTTCATTCA
1 TTTTTTTATTT-ATTTA
* *
1385745 TTTGTTTATTTTTTTCA
1 TTTTTTTATTTATTT-A
*
1385762 -TTTTTTATTTATTAGA
1 TTTTTTTATTTATT-TA
** *
1385778 TTAGGTTTATTTA-ATA
1 TT-TTTTTATTTATTTA
1385794 TTCTTTTTATCTTTATTTTA
1 TT-TTTTTA--TTTA-TTTA
*
1385814 TTTTTATT-TTTGTTTTA
1 TTTTT-TTATTT-ATTTA
1385831 CTTTTCTTTATTT-TTTA
1 -TTTT-TTTATTTATTTA
1385848 --TTTTTATTTATTTA
1 TTTTTTTATTTATTTA
1385862 TTTTTATTATTCTATTT
1 TTTTT-TTATT-TATTT
1385879 TCTTTAAATA
Statistics
Matches: 100, Mismatches: 16, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
13 7 0.07
14 6 0.06
16 24 0.24
17 27 0.27
18 23 0.23
19 7 0.07
20 6 0.06
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTATTTATTTA
Found at i:1386057 original size:56 final size:56
Alignment explanation
Indices: 1385907--1386085 Score: 225
Period size: 58 Copynumber: 3.1 Consensus size: 56
1385897 AATTTCCAAA
* * * *
1385907 AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
* * *
1385964 AAAAAGGGAT-TTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTCC
1 AAAAA---ATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
*
1386022 AAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCC
1 AAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTCC
1386080 AAAAAA
1 AAAAAA
1386086 AAAAAACATT
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
55 2 0.02
56 36 0.34
57 8 0.08
58 57 0.54
60 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.34
Consensus pattern (56 bp):
AAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
Found at i:1388606 original size:17 final size:17
Alignment explanation
Indices: 1388559--1388616 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1388549 NNNNNNNNTA
1388559 TTTATTTTTATTT-TTGT
1 TTTATTTTTATTTATT-T
* *
1388576 TTTACTTTTCTTTATTT
1 TTTATTTTTATTTATTT
1388593 TTTATTTTTATTTATTT
1 TTTATTTTTATTTATTT
1388610 ATTTATT
1 -TTTATT
1388617 ATTCTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 27 0.77
18 8 0.23
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTATTT
Found at i:1388631 original size:21 final size:20
Alignment explanation
Indices: 1388576--1388631 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1388566 TTATTTTTGT
*
1388576 TTTACTTTTCTTTATTTTTTA
1 TTTA-TTTTCTTTATTTATTA
* *
1388597 TTTTTATTTATTTATTTATTA
1 TTTAT-TTTCTTTATTTATTA
1388618 TTCTATTTTCTTTA
1 TT-TATTTTCTTTA
1388632 AATAAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTTCTTTATTTATTA
Found at i:1388731 original size:43 final size:42
Alignment explanation
Indices: 1388671--1388759 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 42
1388661 TTTTTTAGGG
* *
1388671 AAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTTCA
1 AAAAGTTGAAAGAATCAATTTTCCTTGA-AAATCAAAGTTTCA
1388712 AAAAGGTTGAAAGGAATCAATTTTCCTTGAAAATCAAAGTTTCA
1 AAAA-GTTGAAA-GAATCAATTTTCCTTGAAAATCAAAGTTTCA
1388756 AAAA
1 AAAA
1388760 AAATATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 4 0.10
42 7 0.17
43 18 0.43
44 13 0.31
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (42 bp):
AAAAGTTGAAAGAATCAATTTTCCTTGAAAATCAAAGTTTCA
Found at i:1388776 original size:103 final size:111
Alignment explanation
Indices: 1388636--1388918 Score: 323
Period size: 103 Copynumber: 2.5 Consensus size: 111
1388626 TCTTTAAATA
* *
1388636 AAAATCAAAATTTCCAAAAAAAATATTTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGA
1 AAAATCAAAGTTTCCAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAG-
*
1388700 AATAAATTTTC-AAAA-AGGTT-G-AAAG-G-A-ATCAATTTTCCTTG
64 AATAAATTTCCAAAAATAGGTTGGAAAAGTGAAGATCAATTTTCCTTG
*
1388741 AAAATCAAAGTTT-CAAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTAAGAA
1 AAAATCAAAGTTTCCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA
**
1388805 TAAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTG
66 TAAATTTCC-AAAAATAGGTT--GGAAAAG-TG-AAG-ATCAATTTTCCTTG
* *
1388857 AAAATCAAAGTTTCCAAAAAAAAAAATATTTTTGGGGAAAAAGTTAAAAGTATCAATTTTCC
1 AAAATCAAAGTTTCC---AAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCC
1388919 CTACACAAGA
Statistics
Matches: 150, Mismatches: 9, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
103 37 0.25
104 19 0.13
105 16 0.11
106 3 0.02
109 1 0.01
110 4 0.03
112 1 0.01
114 1 0.01
116 27 0.18
117 1 0.01
120 18 0.12
121 22 0.15
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (111 bp):
AAAATCAAAGTTTCCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA
TAAATTTCCAAAAATAGGTTGGAAAAGTGAAGATCAATTTTCCTTG
Found at i:1388835 original size:56 final size:59
Alignment explanation
Indices: 1388727--1388918 Score: 241
Period size: 56 Copynumber: 3.2 Consensus size: 59
1388717 GTTGAAAGGA
* *
1388727 ATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAAT
1 ATCAATTTTCCTTGAAAATCAAAGTTTC-CAAAAAATATTTTTGGGGAAAAGTTGAAAAT
*
1388787 ATCAATTTTCCTT-AAGAAT-AAA-TTTCCAAAAAATA-TTTTGGGGAAAAGTTGAAAGT
1 ATCAATTTTCCTTGAA-AATCAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAAT
1388843 ATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAAAAAAATATTTTTGGGGAAAAAGTT-AAAAG
1 ATCAATTTTCCTTGAAAATCAAAGTTTCC-----AAAAAATATTTTTGGGG-AAAAGTTGAAAA-
1388907 T
59 T
1388908 ATCAATTTTCC
1 ATCAATTTTCC
1388919 CTACACAAGA
Statistics
Matches: 116, Mismatches: 4, Indels: 19
0.83 0.03 0.14
Matches are distributed among these distances:
56 35 0.30
57 13 0.11
58 9 0.08
59 5 0.04
60 16 0.14
63 8 0.07
64 11 0.09
65 19 0.16
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (59 bp):
ATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAAT
Found at i:1391037 original size:22 final size:22
Alignment explanation
Indices: 1391009--1391050 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1390999 GATGTATATG
* *
1391009 ATACTTTGGACAAGTCCTTTCT
1 ATACTTTGAACAAATCCTTTCT
1391031 ATACTTTGAACAAATCCTTT
1 ATACTTTGAACAAATCCTTT
1391051 TTTTGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (22 bp):
ATACTTTGAACAAATCCTTTCT
Found at i:1394642 original size:24 final size:24
Alignment explanation
Indices: 1394610--1394658 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1394600 ATATGAACTT
1394610 ACACACGTCTCCTTAGGCCTTCCA
1 ACACACGTCTCCTTAGGCCTTCCA
1394634 ACACACGTCTCCTTAGGCCTTCCA
1 ACACACGTCTCCTTAGGCCTTCCA
1394658 A
1 A
1394659 ACGTCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.12, T:0.24
Consensus pattern (24 bp):
ACACACGTCTCCTTAGGCCTTCCA
Found at i:1395354 original size:27 final size:27
Alignment explanation
Indices: 1395324--1395377 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1395314 CTATAAGTAA
* * *
1395324 ATTTTGAAAATTTTTTATATAATTTTG
1 ATTTTGAAAATCTTTGATAAAATTTTG
*
1395351 ATTTTGATAATCTTTGATAAAATTTTG
1 ATTTTGAAAATCTTTGATAAAATTTTG
1395378 GTAACCTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (27 bp):
ATTTTGAAAATCTTTGATAAAATTTTG
Done.