Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 14 of 21
Found at i:2107892 original size:16 final size:16
Alignment explanation
Indices: 2107868--2107901 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2107858 GGAAAATTTT
2107868 TAAAGTTATTATATAA
1 TAAAGTTATTATATAA
* *
2107884 TAAATTTATTATTTAA
1 TAAAGTTATTATATAA
2107900 TA
1 TA
2107902 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAAAGTTATTATATAA
Found at i:2108559 original size:22 final size:23
Alignment explanation
Indices: 2108531--2108575 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2108521 ATAAAAATTA
*
2108531 ATAATAAATTTAAA-TGATTTTT
1 ATAATAAAATTAAAGTGATTTTT
*
2108553 ATAATAAAATTAAAGTTATTTTT
1 ATAATAAAATTAAAGTGATTTTT
2108576 GGACTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATAATAAAATTAAAGTGATTTTT
Found at i:2109956 original size:16 final size:15
Alignment explanation
Indices: 2109935--2109976 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2109925 TAATAATCTA
2109935 AATTTTGTAAAAATAT
1 AATTTT-TAAAAATAT
2109951 AA-TTTTAAAAA-AT
1 AATTTTTAAAAATAT
*
2109964 AATTATTAAAAAT
1 AATTTTTAAAAAT
2109977 TTTTAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 4 0.17
14 14 0.61
15 3 0.13
16 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTTTTAAAAATAT
Found at i:2109965 original size:13 final size:15
Alignment explanation
Indices: 2109942--2109976 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2109932 CTAAATTTTG
2109942 TAAAAATATAATT-T
1 TAAAAATATAATTAT
2109956 TAAAAA-ATAATTAT
1 TAAAAATATAATTAT
2109970 TAAAAAT
1 TAAAAAT
2109977 TTTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAATATAATTAT
Found at i:2110165 original size:14 final size:15
Alignment explanation
Indices: 2110138--2110183 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
2110128 TTTTAAAAAA
2110138 TAAAATTTAATAATTT
1 TAAAATTT-ATAATTT
2110154 TAAAATTT-TAATTT
1 TAAAATTTATAATTT
*
2110168 TAATATTTATAATTT
1 TAAAATTTATAATTT
2110183 T
1 T
2110184 CTACCTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAATTTATAATTT
Found at i:2112082 original size:3 final size:3
Alignment explanation
Indices: 2112074--2112100 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2112064 AGACATTGAG
2112074 ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA
2112101 GGAACACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2112776 original size:14 final size:14
Alignment explanation
Indices: 2112746--2112820 Score: 50
Period size: 14 Copynumber: 5.3 Consensus size: 14
2112736 ATTTATTAAT
*
2112746 TTAAAT-TAATATAA
1 TTAAATATAA-ATTA
2112760 TTAAATATAAATTA
1 TTAAATATAAATTA
2112774 TTATTTAATAATAAATT-
1 TTA---AAT-ATAAATTA
* *
2112791 TTTAAT-TAATTTA
1 TTAAATATAAATTA
2112804 TTAAATATAAA-TA
1 TTAAATATAAATTA
2112817 TTAA
1 TTAA
2112821 CGTAAAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
12 5 0.10
13 11 0.22
14 18 0.37
15 3 0.06
17 5 0.10
18 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAATATAAATTA
Found at i:2112787 original size:18 final size:18
Alignment explanation
Indices: 2112747--2112800 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2112737 TTTATTAATT
2112747 TAAATTAATATAATTAA-ATA
1 TAAATT-AT-TAATTAATA-A
*
2112767 TAAATTATTATTTAATAA
1 TAAATTATTAATTAATAA
*
2112785 TAAATTTTTAATTAAT
1 TAAATTATTAATTAAT
2112801 TTATTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 21 0.70
19 3 0.10
20 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTATTAATTAATAA
Found at i:2112838 original size:45 final size:45
Alignment explanation
Indices: 2112749--2112881 Score: 116
Period size: 44 Copynumber: 3.0 Consensus size: 45
2112739 TATTAATTTA
**
2112749 AATTAATATAATTAAATATAAATTATTATTTAATAATAAATTTTT
1 AATTAATATAATTAAATATAAATTATTACGTAATAATAAATTTTT
*
2112794 AATTAAT-TTATTAAATATAAA-TATTAACGTAA-AATTAAATTTTTT
1 AATTAATATAATTAAATATAAATTATT-ACGTAATAA-TAAA-TTTTT
* * *
2112839 AAAATTATTTAAAAATAAA-ATAAATTATTAC--AATAATAAATTT
1 --AATTA-ATATAATTAAATATAAATTATTACGTAATAATAAATTT
2112882 AAATTTAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
43 6 0.08
44 21 0.29
45 15 0.21
46 6 0.08
47 7 0.10
48 8 0.11
49 9 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (45 bp):
AATTAATATAATTAAATATAAATTATTACGTAATAATAAATTTTT
Found at i:2112904 original size:22 final size:22
Alignment explanation
Indices: 2112879--2112934 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2112869 CAATAATAAA
2112879 TTTAAATTTAAAT-AAATTACTT
1 TTTAAATTTAAATCAAATTA-TT
* *
2112901 TTTAAATAATAACTCAAATTATT
1 TTTAAAT-TTAAATCAAATTATT
2112924 TTTAAATTTAA
1 TTTAAATTTAA
2112935 TTTAAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATTTAAATCAAATTATT
Found at i:2113100 original size:23 final size:23
Alignment explanation
Indices: 2113074--2113141 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 23
2113064 TACTTTAACG
2113074 ATAATTTTTTTTTAATTTTATAA
1 ATAATTTTTTTTTAATTTTATAA
*
2113097 ATAAATTTTATTTT-ATTTTA-AA
1 AT-AATTTTTTTTTAATTTTATAA
* * * *
2113119 TTAAATTTTATTCAA-TTTATAA
1 ATAATTTTTTTTTAATTTTATAA
2113141 A
1 A
2113142 ATATATGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 11 0.31
22 6 0.17
23 8 0.23
24 10 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (23 bp):
ATAATTTTTTTTTAATTTTATAA
Found at i:2113123 original size:22 final size:24
Alignment explanation
Indices: 2113076--2113130 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 24
2113066 CTTTAACGAT
*
2113076 AATTTTTTTTTAATTTTATAAATA
1 AATTTTATTTTAATTTTATAAATA
*
2113100 AATTTTATTTT-ATTTTA-AATTA
1 AATTTTATTTTAATTTTATAAATA
2113122 AATTTTATT
1 AATTTTATT
2113131 CAATTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 13 0.45
23 6 0.21
24 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
AATTTTATTTTAATTTTATAAATA
Found at i:2113136 original size:22 final size:22
Alignment explanation
Indices: 2113087--2113144 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
2113077 ATTTTTTTTT
*
2113087 AATTTTATAAATAAATTTTATTT
1 AATTTTA-AAATAAATTTTATTC
* *
2113110 TATTTTAAATTAAATTTTATTC
1 AATTTTAAAATAAATTTTATTC
2113132 AATTTATAAAATA
1 AATTT-TAAAATA
2113145 TATGTTATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTAAAATAAATTTTATTC
Found at i:2113718 original size:22 final size:23
Alignment explanation
Indices: 2113692--2113735 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2113682 CTTTAAAATA
2113692 TTAAAA-AAATATTTA-ATTTTTT
1 TTAAAATAAAT-TTTATATTTTTT
2113714 TTAAAATAAATTTTATATTTTT
1 TTAAAATAAATTTTATATTTTT
2113736 ATCGTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAAATAAATTTTATATTTTTT
Found at i:2113787 original size:30 final size:29
Alignment explanation
Indices: 2113748--2113819 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
2113738 CGTACTAAAA
*
2113748 TAAAATTTTATTATTTAATTTATATCAAAT
1 TAAATTTTTATT-TTTAATTTATATCAAAT
* *
2113778 TAAATTTTTATTTTTTATTTATATTAAAT
1 TAAATTTTTATTTTTAATTTATATCAAAT
2113807 TAAATTTTTATTT
1 TAAATTTTTATTT
2113820 ATGTTAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TAAATTTTTATTTTTAATTTATATCAAAT
Found at i:2113875 original size:30 final size:29
Alignment explanation
Indices: 2113829--2113911 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
2113819 TATGTTAACT
* * * *
2113829 ATTTTTTTAGATATAAATTACAGATTAAAA
1 ATTTATTTAAATATAAATTAAAAATT-AAA
*
2113859 ATTTATTTAAATATAAATAAAAAATTAAA
1 ATTTATTTAAATATAAATTAAAAATTAAA
* *
2113888 ATATATTTTAATATAAATTAAAAA
1 ATTTATTTAAATATAAATTAAAAA
2113912 ATTATTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.53
30 21 0.47
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (29 bp):
ATTTATTTAAATATAAATTAAAAATTAAA
Found at i:2113900 original size:23 final size:24
Alignment explanation
Indices: 2113872--2113926 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
2113862 TATTTAAATA
*
2113872 TAAATAAAAAATTAAAATA-TATT
1 TAAATAAAAAATTAAAAAATTATT
* *
2113895 TTAAT-ATAAATTAAAAAATTATT
1 TAAATAAAAAATTAAAAAATTATT
2113918 TAAATAAAA
1 TAAATAAAA
2113927 TGAAAGTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 11 0.44
23 12 0.48
24 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATAAAAAATTAAAAAATTATT
Found at i:2113908 original size:22 final size:21
Alignment explanation
Indices: 2113879--2113936 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2113869 ATATAAATAA
*
2113879 AAAATTAAAATATATTTTAAT
1 AAAATTAAAATATATTTAAAT
*
2113900 ATAAATTAAAAAATTATTTAAAT
1 A-AAATTAAAATA-TATTTAAAT
* *
2113923 AAAATGAAAGTATA
1 AAAATTAAAATATA
2113937 AATATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.10
22 18 0.60
23 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAATTAAAATATATTTAAAT
Found at i:2113912 original size:30 final size:30
Alignment explanation
Indices: 2113833--2113915 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
2113823 TTAACTATTT
* * *
2113833 TTTTAGATATAAATT-ACAGATTAAAAATTTA
1 TTTTA-ATATAAATTAAAAAATT-AAAATATA
*
2113864 TTTAAATATAAA-TAAAAAATTAAAATATA
1 TTTTAATATAAATTAAAAAATTAAAATATA
2113893 TTTTAATATAAATTAAAAAATTA
1 TTTTAATATAAATTAAAAAATTA
2113916 TTTAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 19 0.42
30 22 0.49
31 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTTAATATAAATTAAAAAATTAAAATATA
Found at i:2115359 original size:21 final size:20
Alignment explanation
Indices: 2115329--2115370 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2115319 TAATAATTAA
2115329 ATATTATATAAATAAAATAAT
1 ATATTATATAAATAAAA-AAT
* *
2115350 ATATTTTATAATTAAAAAAT
1 ATATTATATAAATAAAAAAT
2115370 A
1 A
2115371 GATCGGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTATATAAATAAAAAAT
Found at i:2115426 original size:17 final size:16
Alignment explanation
Indices: 2115406--2115439 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2115396 TATTTAATTT
2115406 TTATATAATATGATAAA
1 TTATATAATAT-ATAAA
2115423 TTATATAATATATAAA
1 TTATATAATATATAAA
2115439 T
1 T
2115440 AAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTATATAATATATAAA
Found at i:2115429 original size:19 final size:17
Alignment explanation
Indices: 2115386--2115439 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2115376 GATCAACTTG
*
2115386 ATTATATATATATTTAA
1 ATTATATATATATATAA
* *
2115403 TTTTTATATAATATGATAA
1 ATTATATAT-ATAT-ATAA
2115422 ATTATATA-ATATATAA
1 ATTATATATATATATAA
2115438 AT
1 AT
2115440 AAAAATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 6 0.20
17 11 0.37
18 4 0.13
19 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTATATATATATATAA
Found at i:2115498 original size:99 final size:97
Alignment explanation
Indices: 2115301--2115483 Score: 215
Period size: 99 Copynumber: 1.9 Consensus size: 97
2115291 ATAATTATCT
* * **
2115301 TTTAATTTTTATATGATATAATAATTAAATATTATATAAATAAAATAATATATTTTATAATTAAA
1 TTTAATTTTTATATAATATAATAATTAAATAATATATAAATAAAATAATATATCATATAATTAAA
* ** * * *
2115366 AAATAGATCGGATCAACTTGATTATATATATA
66 AAAAAGATAAGATAAACTTCATAATATATATA
* *
2115398 TTTAATTTTTATATAATATGATAAATTATATAATATATAAATAAAAATAATATATCATATAATTA
1 TTTAATTTTTATATAATATAAT-AATTAAATAATATATAAAT-AAAATAATATATCATATAATTA
2115463 AAAATAAAG-TAAGATTAAACT
64 AAAA-AAAGATAAGA-TAAACT
2115484 CAAATCATGA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
97 20 0.28
98 17 0.24
99 27 0.38
100 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (97 bp):
TTTAATTTTTATATAATATAATAATTAAATAATATATAAATAAAATAATATATCATATAATTAAA
AAAAAGATAAGATAAACTTCATAATATATATA
Found at i:2115585 original size:14 final size:15
Alignment explanation
Indices: 2115554--2115597 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2115544 TAAATTAAAA
2115554 TTTTAAATATAATAT
1 TTTTAAATATAATAT
* *
2115569 TTTTATATA-AATTT
1 TTTTAAATATAATAT
*
2115583 TTTTAAATATTATAT
1 TTTTAAATATAATAT
2115598 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTAAATATAATAT
Found at i:2115597 original size:21 final size:20
Alignment explanation
Indices: 2115570--2115621 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
2115560 ATATAATATT
2115570 TTTATATAAATTTTTTTAAA
1 TTTATATAAATTTTTTTAAA
*
2115590 TATTATATAAAATTTTTTAAA
1 T-TTATATAAATTTTTTTAAA
*
2115611 TTTAAATAAAT
1 TTTATATAAAT
2115622 AATTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATATAAATTTTTTTAAA
Found at i:2115621 original size:19 final size:19
Alignment explanation
Indices: 2115570--2115635 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
2115560 ATATAATATT
*
2115570 TTTATATAAATTTTTTTAAA
1 TTTAAATAAA-TTTTTTAAA
*
2115590 TATTATATAAAATTTTTTAAA
1 T-TTAAAT-AAATTTTTTAAA
** *
2115611 TTTAAATAAATAATTTAAT
1 TTTAAATAAATTTTTTAAA
2115630 TTTAAA
1 TTTAAA
2115636 ATAATTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.38
20 6 0.15
21 16 0.40
22 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATAAATTTTTTAAA
Found at i:2116356 original size:3 final size:3
Alignment explanation
Indices: 2116348--2116390 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2116338 AAATACCCAA
*
2116348 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT ACT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2116391 AGGAGATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2123999 original size:19 final size:19
Alignment explanation
Indices: 2123984--2124019 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2123974 TAATTAAATT
2123984 TAATATT-A-TAAATTAAA
1 TAATATTAAGTAAATTAAA
2124001 TAATATTAAGTAAATTAAA
1 TAATATTAAGTAAATTAAA
2124020 AATTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 1 0.06
19 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAATATTAAGTAAATTAAA
Found at i:2127448 original size:17 final size:17
Alignment explanation
Indices: 2127436--2127472 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2127426 TAAATAAATA
2127436 ATTATATTTAATATAAT
1 ATTATATTTAATATAAT
*
2127453 ATTATATTTACAAATAAT
1 ATTATATTTA-ATATAAT
2127471 AT
1 AT
2127473 GTTGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATATTTAATATAAT
Found at i:2129296 original size:9 final size:9
Alignment explanation
Indices: 2129273--2129313 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2129263 ATCAATTTTA
2129273 AAATATAATT
1 AAATA-AATT
*
2129283 GAATAAATT
1 AAATAAATT
2129292 AAATAAATT
1 AAATAAATT
2129301 AAATTAAATT
1 AAA-TAAATT
2129311 AAA
1 AAA
2129314 GCTCTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
AAATAAATT
Found at i:2133053 original size:38 final size:38
Alignment explanation
Indices: 2132971--2133054 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
2132961 ATTATTATTT
* * *
2132971 AATAATAAAATAATTTTTTATTTAAATTTAATTATATAA
1 AATAA-AAAATAATATTTTATATAAATTTAAATATATAA
*
2133010 TATAAAAAATAATATTTTA-ATAATATTATAAATA-ATAA
1 AATAAAAAATAATATTTTATATAA-ATT-TAAATATATAA
2133048 AATAAAA
1 AATAAAA
2133055 TTTTAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
37 3 0.08
38 26 0.68
39 9 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (38 bp):
AATAAAAAATAATATTTTATATAAATTTAAATATATAA
Found at i:2138355 original size:22 final size:24
Alignment explanation
Indices: 2138327--2138374 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2138317 TTCTCAATTC
2138327 AAATTA-TT-ATTTAATAATAAAA
1 AAATTATTTAATTTAATAATAAAA
*
2138349 AAATTATTTAAATTTAATTATAAAA
1 AAATTATTT-AATTTAATAATAAAA
2138374 A
1 A
2138375 TATATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
25 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTATTTAATTTAATAATAAAA
Found at i:2138382 original size:22 final size:23
Alignment explanation
Indices: 2138341--2138393 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
2138331 TATTATTTAA
* *
2138341 TAATAAAAAAATTATTTAAAT-T
1 TAATATAAAAATTATATAAATAT
2138363 TAATTATAAAAA-TATATAAATAT
1 TAA-TATAAAAATTATATAAATAT
2138386 TAATATAA
1 TAATATAA
2138394 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATATAAAAATTATATAAATAT
Found at i:2139016 original size:20 final size:20
Alignment explanation
Indices: 2138991--2139028 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2138981 AGAAGATAGA
2138991 TAATATAAACCTCCAATATC
1 TAATATAAACCTCCAATATC
2139011 TAATATAAACCTCCAATA
1 TAATATAAACCTCCAATA
2139029 ACTAGATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATATAAACCTCCAATATC
Found at i:2144744 original size:30 final size:30
Alignment explanation
Indices: 2144692--2144766 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2144682 TATAAGTTTT
2144692 TATTTAAATTTATTTATATTTATAAATA-AA
1 TATTT-AATTTATTTATATTTATAAATATAA
**
2144722 TAATTTAATTTATTTA-AGTTTATTTATATAA
1 T-ATTTAATTTATTTATA-TTTATAAATATAA
*
2144753 TTTTTAATTTATTT
1 TATTTAATTTATTT
2144767 TTTAAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 1 0.03
30 31 0.79
31 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTTAATTTATTTATATTTATAAATATAA
Found at i:2144764 original size:16 final size:15
Alignment explanation
Indices: 2144725--2144802 Score: 56
Period size: 16 Copynumber: 5.3 Consensus size: 15
2144715 AAATAAATAA
*
2144725 TTTAATTTATTTAA-G
1 TTTAATTTA-TTAATT
2144740 TTT-ATTTATATAATT
1 TTTAATTTAT-TAATT
2144755 TTTAATTTATT--TT
1 TTTAATTTATTAATT
* **
2144768 TTAAATTTATTTTTT
1 TTTAATTTATTAATT
*
2144783 TTGTAATTTAATAATT
1 TT-TAATTTATTAATT
2144799 TTTA
1 TTTA
2144803 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 13 0.25
14 8 0.16
15 13 0.25
16 17 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATTTATTAATT
Found at i:2144770 original size:12 final size:13
Alignment explanation
Indices: 2144753--2144782 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2144743 ATTTATATAA
2144753 TTTTT-AATTTAT
1 TTTTTAAATTTAT
2144765 TTTTTAAATTTAT
1 TTTTTAAATTTAT
2144778 TTTTT
1 TTTTT
2144783 TTGTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTAAATTTAT
Found at i:2144895 original size:18 final size:17
Alignment explanation
Indices: 2144855--2144906 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
2144845 TACAATATAA
* *
2144855 TTTTATATAAATATATAT
1 TTTTATAT-AATAAAAAT
2144873 TTTTATATAATAAAAAT
1 TTTTATATAATAAAAAT
2144890 TATTTAATATATATAAA
1 T-TTT-ATATA-ATAAA
2144907 TATAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.28
18 11 0.38
19 5 0.17
20 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATATAATAAAAAT
Found at i:2145014 original size:27 final size:28
Alignment explanation
Indices: 2144983--2145040 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
2144973 ATTAAAACTT
*
2144983 AATTTATT-TTTTCAACAAATTTTTTTA
1 AATTTATTGTTTTCAACAAAATTTTTTA
* *
2145010 AATTTATTGTTTTTATCAAAATTTTTTA
1 AATTTATTGTTTTCAACAAAATTTTTTA
2145038 AAT
1 AAT
2145041 ATTAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (28 bp):
AATTTATTGTTTTCAACAAAATTTTTTA
Found at i:2147052 original size:50 final size:52
Alignment explanation
Indices: 2146976--2147077 Score: 131
Period size: 50 Copynumber: 2.0 Consensus size: 52
2146966 AATCATTATT
*
2146976 TATAAAATAAAATATTTATATTTATATTTAATTACAAATATTATAAA-TATTAA
1 TATAAAATAAAATATTTATATTTATATTTAAATA-AAA-ATTATAAACTATTAA
* *
2147029 TATAAAA-ATAATA-TTATA-TTATATTTAAATAAAAATTTTAAACTATTAA
1 TATAAAATAAAATATTTATATTTATATTTAAATAAAAATTATAAACTATTAA
2147078 ATTAGATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
48 7 0.16
49 9 0.20
50 12 0.27
51 5 0.11
52 5 0.11
53 7 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (52 bp):
TATAAAATAAAATATTTATATTTATATTTAAATAAAAATTATAAACTATTAA
Found at i:2147060 original size:27 final size:26
Alignment explanation
Indices: 2147012--2147064 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2147002 TTTAATTACA
2147012 AATATTATAAATATTAATATAAAAAT
1 AATATTATAAATATTAATATAAAAAT
*
2147038 AATATTATATTATATTTAA-ATAAAAAT
1 AATATTATA-AATA-TTAATATAAAAAT
2147065 TTTAAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 11 0.46
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATTATAAATATTAATATAAAAAT
Found at i:2147228 original size:26 final size:26
Alignment explanation
Indices: 2147198--2147257 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
2147188 ACCAAAGCAC
2147198 CACTAATGCATACATTATTGCTTCAG
1 CACTAATGCATACATTATTGCTTCAG
* *
2147224 CACTAATGCATAGATTATTGCTTTAG
1 CACTAATGCATACATTATTGCTTCAG
*
2147250 TACTAATG
1 CACTAATG
2147258 GGTTGCTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (26 bp):
CACTAATGCATACATTATTGCTTCAG
Found at i:2148699 original size:21 final size:22
Alignment explanation
Indices: 2148675--2148715 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2148665 AAATATAACT
2148675 ATTTATAATA-TAAAAATAATA
1 ATTTATAATATTAAAAATAATA
* *
2148696 ATTTTTAATATTATAAATAA
1 ATTTATAATATTAAAAATAA
2148716 AAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTATAATATTAAAAATAATA
Found at i:2148702 original size:23 final size:24
Alignment explanation
Indices: 2148663--2148712 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2148653 ATTTTTTTAA
2148663 AAAAATATAACTATTT-ATAATAT
1 AAAAATATAACTATTTAATAATAT
* *
2148686 AAAAATAATAA-TTTTTAATATTAT
1 AAAAAT-ATAACTATTTAATAATAT
2148710 AAA
1 AAA
2148713 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATATAACTATTTAATAATAT
Found at i:2154527 original size:20 final size:20
Alignment explanation
Indices: 2154502--2154554 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2154492 TTTCATTTTT
**
2154502 TTATTTTTAATAAATTTAAA
1 TTATTTTTAATAAACATAAA
* *
2154522 TTATTTTTATTTAACATAAA
1 TTATTTTTAATAAACATAAA
2154542 TATATTTTTAATA
1 T-TATTTTTAATA
2154555 TAAATATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTTTAATAAACATAAA
Found at i:2154557 original size:17 final size:17
Alignment explanation
Indices: 2154531--2154606 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 17
2154521 ATTATTTTTA
*
2154531 TTTAACATAAATATATT
1 TTTAATATAAATATATT
2154548 TTTAATATAAATATTATT
1 TTTAATATAAATA-TATT
*
2154566 TTATACATATACAA-A-AAT
1 TT-TA-ATATA-AATATATT
*
2154584 TTTAATTTAACATATAATT
1 TTTAATATAA-ATAT-ATT
2154603 TTTA
1 TTTA
2154607 TATCATCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
15 1 0.02
16 5 0.11
17 15 0.32
18 10 0.21
19 8 0.17
20 6 0.13
21 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATATAAATATATT
Found at i:2156746 original size:22 final size:20
Alignment explanation
Indices: 2156720--2156762 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
2156710 ATTTATAACT
2156720 ATAAATTTTACATGATATTTTA
1 ATAAATTTTACAT-A-ATTTTA
2156742 ATAAATTTTACATAATTTTA
1 ATAAATTTTACATAATTTTA
2156762 A
1 A
2156763 ATTATCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAAATTTTACATAATTTTA
Found at i:2156751 original size:10 final size:11
Alignment explanation
Indices: 2156720--2156761 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
2156710 ATTTATAACT
2156720 ATAAATTTTAC
1 ATAAATTTTAC
*
2156731 ATGATATTTTA-
1 AT-AAATTTTAC
2156742 ATAAATTTTAC
1 ATAAATTTTAC
2156753 AT-AATTTTA
1 ATAAATTTTA
2156762 AATTATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 14 0.52
11 6 0.22
12 7 0.26
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (11 bp):
ATAAATTTTAC
Found at i:2157285 original size:18 final size:20
Alignment explanation
Indices: 2157262--2157314 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 20
2157252 AGTATGTATT
2157262 ATATTTAAATATAT-AA-TA
1 ATATTTAAATATATAAATTA
* *
2157280 ATATTTATATAAATAAATTA
1 ATATTTAAATATATAAATTA
2157300 A-ATTTAAATAT-TAAA
1 ATATTTAAATATATAAA
2157315 AATTATTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.55
19 10 0.34
20 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTTAAATATATAAATTA
Found at i:2158664 original size:2 final size:2
Alignment explanation
Indices: 2158657--2158694 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2158647 GTTAATGAGG
2158657 AT 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 AT
2158695 TAAGTGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2159317 original size:7 final size:7
Alignment explanation
Indices: 2159307--2159338 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2159297 GAGCCATGAG
*
2159307 GCAGAAA
1 GCAGAGA
2159314 GCAGAGA
1 GCAGAGA
2159321 GCAGAGA
1 GCAGAGA
2159328 GCAGAGA
1 GCAGAGA
2159335 GCAG
1 GCAG
2159339 GTGAGATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.41, T:0.00
Consensus pattern (7 bp):
GCAGAGA
Found at i:2165784 original size:20 final size:17
Alignment explanation
Indices: 2165733--2165812 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 17
2165723 TTTAAATTAT
*
2165733 TATTATTTAACATAAATA
1 TATT-TTTAATATAAATA
2165751 TATTTTTAATATAAATA
1 TATTTTTAATATAAATA
2165768 TTATTTTATACATATAAA-A
1 -TATTTT-TA-ATATAAATA
* * *
2165787 AAATTTTAATTTAACATA
1 TATTTTTAATATAA-ATA
2165805 TAATTTTT
1 T-ATTTTT
2165813 TTACTATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.10
17 15 0.30
18 15 0.30
19 8 0.16
20 7 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTTAATATAAATA
Found at i:2165807 original size:23 final size:24
Alignment explanation
Indices: 2165763--2165807 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2165753 TTTTTAATAT
*
2165763 AAATATTATTTTATACATATAAAA
1 AAATATTAATTTATACATATAAAA
*
2165787 AAATTTTAATTTA-ACATATAA
1 AAATATTAATTTATACATATAA
2165808 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTAATTTATACATATAAAA
Found at i:2165903 original size:30 final size:30
Alignment explanation
Indices: 2165867--2165932 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2165857 CACATAATTT
2165867 TTATATCATCATTTTAACGTTTAATCTCAC
1 TTATATCATCATTTTAACGTTTAATCTCAC
2165897 TTATATCATCATTTTAACGTTTAATCTCAC
1 TTATATCATCATTTTAACGTTTAATCTCAC
2165927 TCTATA
1 T-TATA
2165933 ACCATTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
TTATATCATCATTTTAACGTTTAATCTCAC
Found at i:2166842 original size:50 final size:50
Alignment explanation
Indices: 2166783--2167041 Score: 394
Period size: 50 Copynumber: 5.2 Consensus size: 50
2166773 TATACTTAGA
* *
2166783 GTCAACAATTATGACCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2166833 GTCAACAATTATGGCCACCTCCTTTTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2166883 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2166933 GTCAACAATTATGGTCACCTCCTTTTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2166983 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
2167033 GTCAACAAT
1 GTCAACAAT
2167042 GACAACAACT
Statistics
Matches: 190, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 189 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2166929 original size:100 final size:100
Alignment explanation
Indices: 2166783--2167041 Score: 448
Period size: 100 Copynumber: 2.6 Consensus size: 100
2166773 TATACTTAGA
*
2166783 GTCAACAATTATGACCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
2166848 CACCTCCTTTTATTATCAAAGGTTGGTGAAGAATC
66 CACCTCCTTTTATTATCAAAGGTTGGTGAAGAATC
* *
2166883 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
*
2166948 CACCTCCTTTTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCTTTTATTATCAAAGGTTGGTGAAGAATC
* *
2166983 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATAGTCAACAAT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATTGTCAACAAT
2167042 GACAACAACT
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
100 150 0.99
101 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (100 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGC
CACCTCCTTTTATTATCAAAGGTTGGTGAAGAATC
Found at i:2171144 original size:50 final size:50
Alignment explanation
Indices: 2171082--2171340 Score: 369
Period size: 50 Copynumber: 5.2 Consensus size: 50
2171072 TATACTTAGA
*
2171082 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
2171132 GTAAACAATTATGGTCACCTCCTTCTATTGTTAAAGGTTGGTGAA-ATATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGA-ATC
* * *
2171182 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAATGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2171232 GTCAACAATTATGGCTACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
2171282 GTCAACAATTATAGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
2171332 GTCAACAAT
1 GTCAACAAT
2171341 GACAACAATT
Statistics
Matches: 184, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 181 0.98
51 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2171255 original size:100 final size:100
Alignment explanation
Indices: 2171082--2171340 Score: 416
Period size: 100 Copynumber: 2.6 Consensus size: 100
2171072 TATACTTAGA
* *
2171082 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTAAACAATTATGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGT
*
2171147 CACCTCCTTCTATTGTTAAAGGTTGGTGAA-ATATC
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGA-ATC
*
2171182 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAATGTTGGTGAAGAATTGTCAACAATTATGG-
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGT
2171246 CTACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
66 C-ACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2171282 GTCAACAATTATAGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATAGTCAACAAT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA-GAATTGTCAACAAT
2171341 GACAACAATT
Statistics
Matches: 149, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
99 1 0.01
100 146 0.98
101 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (100 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGT
CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2173542 original size:15 final size:14
Alignment explanation
Indices: 2173522--2173563 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2173512 ATTAAAATAA
2173522 ATTTAAATATTAATT
1 ATTTAAATATT-ATT
*
2173537 ATTTAAAAATTATT
1 ATTTAAATATTATT
*
2173551 ACTTAAAT-TTATT
1 ATTTAAATATTATT
2173564 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 5 0.21
14 9 0.38
15 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATATTATT
Found at i:2173546 original size:33 final size:34
Alignment explanation
Indices: 2173470--2173548 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
2173460 AATAAATTAA
* * *
2173470 ATTTAAATAATTAATATAAATATTTAAATTATTTG
1 ATTTAAA-AATTAAAATAAATATTAAAATTAATTG
2173505 ATTT-AAAATTAAAATAAAT-TTAAATATTAATT-
1 ATTTAAAAATTAAAATAAATATTAAA-ATTAATTG
2173537 ATTTAAAAATTA
1 ATTTAAAAATTA
2173549 TTACTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 8 0.21
33 25 0.64
34 2 0.05
35 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
ATTTAAAAATTAAAATAAATATTAAAATTAATTG
Found at i:2175008 original size:14 final size:14
Alignment explanation
Indices: 2174980--2175027 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2174970 ATTTTTAATT
2174980 TTATT-AAATTATA
1 TTATTAAAATTATA
*
2174993 TTATTAAAATTTTA
1 TTATTAAAATTATA
*
2175007 TTATTATTAAATTAAA
1 TTATTA--AAATTATA
2175023 TTATT
1 TTATT
2175028 TATATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.17
14 13 0.45
16 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTAAAATTATA
Found at i:2175014 original size:30 final size:30
Alignment explanation
Indices: 2174960--2175046 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
2174950 AATTTTTATA
*
2174960 TAAATTA-TAAATTTTTAATTTTATTAAAT
1 TAAATTATTAAAATTTTAATTTTATTAAAT
*
2174989 TATATTATTAAAATTTT-ATTATTATTAAAT
1 TAAATTATTAAAATTTTAATT-TTATTAAAT
* *
2175019 TAAATTATT--TATATTAATTTTATTAAAT
1 TAAATTATTAAAATTTTAATTTTATTAAAT
2175047 AATTTTAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 13 0.26
29 12 0.24
30 25 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAAATTATTAAAATTTTAATTTTATTAAAT
Found at i:2175244 original size:24 final size:24
Alignment explanation
Indices: 2175200--2175274 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
2175190 AATTTATTAA
2175200 TAATAAAAATTT--AATTATATAATT
1 TAAT-AAAATTTAAAATT-TATAATT
*
2175224 TAATAAAATTTAAAATTTATAAAT
1 TAATAAAATTTAAAATTTATAATT
* *
2175248 TATATAAAAATTAATA-TTA-AATT
1 TA-ATAAAATTTAAAATTTATAATT
2175271 TAAT
1 TAAT
2175275 TATTTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 2 0.05
23 12 0.27
24 15 0.34
25 15 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAAAATTTAAAATTTATAATT
Found at i:2175307 original size:15 final size:16
Alignment explanation
Indices: 2175231--2175300 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 16
2175221 ATTTAATAAA
2175231 ATTTAAAATTTATAAATT
1 ATTTAAAA--TATAAATT
* *
2175249 ATATAAAA-ATTAA-T
1 ATTTAAAATATAAATT
*
2175263 A-TT-AAAT-TTAATT
1 ATTTAAAATATAAATT
2175276 ATTTAAAATATAAATT
1 ATTTAAAATATAAATT
2175292 ATTTCAAAA
1 ATTT-AAAA
2175301 AAAATTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
12 7 0.17
13 3 0.07
14 4 0.10
15 8 0.19
16 9 0.21
17 4 0.10
18 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAATATAAATT
Found at i:2175910 original size:34 final size:34
Alignment explanation
Indices: 2175870--2176011 Score: 151
Period size: 34 Copynumber: 4.2 Consensus size: 34
2175860 TATCATTGTT
*
2175870 GATTTGGTGATTTGTCATTATTGATTAAATAAGA
1 GATTTGGTGATTTGTCATTGTTGATTAAATAAGA
* * * * *
2175904 AATTTGGTAATTTATCATTGTTGATTAAATAGGT
1 GATTTGGTGATTTGTCATTGTTGATTAAATAAGA
* * *
2175938 GATTTGGTGGTTTGTCATTGTTGACTAAATGAGA
1 GATTTGGTGATTTGTCATTGTTGATTAAATAAGA
* * * *
2175972 GATTTAGT-AGTTTGTTATTGTTGATTAAATAGGT
1 GATTTGGTGA-TTTGTCATTGTTGATTAAATAAGA
2176006 GATTTG
1 GATTTG
2176012 ATGGTTTTTA
Statistics
Matches: 85, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
34 85 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (34 bp):
GATTTGGTGATTTGTCATTGTTGATTAAATAAGA
Found at i:2175992 original size:68 final size:68
Alignment explanation
Indices: 2175869--2176018 Score: 210
Period size: 68 Copynumber: 2.2 Consensus size: 68
2175859 TTATCATTGT
* * *
2175869 TGATTTGGTGATTTGTCATTATTGATTAAATAAGAAATTTGGTAATTTATCATTGTTGATTAAAT
1 TGATTTGGTGGTTTGTCATTATTGACTAAATAAGAAATTTAGTAATTTATCATTGTTGATTAAAT
2175934 AGG
66 AGG
* * * * * *
2175937 TGATTTGGTGGTTTGTCATTGTTGACTAAATGAGAGATTTAGTAGTTTGTTATTGTTGATTAAAT
1 TGATTTGGTGGTTTGTCATTATTGACTAAATAAGAAATTTAGTAATTTATCATTGTTGATTAAAT
2176002 AGG
66 AGG
*
2176005 TGATTTGATGGTTT
1 TGATTTGGTGGTTT
2176019 TTACTAAACC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (68 bp):
TGATTTGGTGGTTTGTCATTATTGACTAAATAAGAAATTTAGTAATTTATCATTGTTGATTAAAT
AGG
Found at i:2176343 original size:19 final size:19
Alignment explanation
Indices: 2176319--2176367 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2176309 TCGAGGCATC
*
2176319 ATTCACGTATATAGGTATT
1 ATTCACGTATATAGGTACT
2176338 ATTCACGTATATAGGTACT
1 ATTCACGTATATAGGTACT
2176357 ATTCACGTATA
1 ATTCACGTATA
2176368 CGGTACGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
ATTCACGTATATAGGTACT
Found at i:2176367 original size:17 final size:18
Alignment explanation
Indices: 2176319--2176373 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
2176309 TCGAGGCATC
*
2176319 ATTCACGTATATAGGTATT
1 ATTCACG-ATATAGGTACT
2176338 ATTCACGTATATAGGTACT
1 ATTCACG-ATATAGGTACT
2176357 ATTCACG-TATACGGTAC
1 ATTCACGATATA-GGTAC
2176374 GGTGCACGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 25 0.74
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
ATTCACGATATAGGTACT
Found at i:2180513 original size:34 final size:33
Alignment explanation
Indices: 2180442--2180539 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 33
2180432 AAGTGGGAGA
* * *
2180442 ATTGTTGATTAAATGGTGATTTGGTGGTTTGCT
1 ATTGTTGATTAAATGGTGATTTGATGGTTTACC
* * *
2180475 ATTGTTGACTAAATAGGAGATTTGATAGTTTACC
1 ATTGTTGATTAAAT-GGTGATTTGATGGTTTACC
2180509 ATTGTTGATTAAATGTGTGATTTGATGGTTT
1 ATTGTTGATTAAATG-GTGATTTGATGGTTT
2180540 TTACCAAACC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
33 14 0.26
34 40 0.74
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGATGGTTTACC
Found at i:2180631 original size:24 final size:24
Alignment explanation
Indices: 2180596--2180651 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
2180586 TCTAACCAAC
*
2180596 TCAAGTAT-GGTTATAAATAGCTAT
1 TCAAGT-TCGGTTATAAATAGCCAT
2180620 TCAAGTTCGGTTATAAATAGCCAT
1 TCAAGTTCGGTTATAAATAGCCAT
2180644 TCAAGTTC
1 TCAAGTTC
2180652 ATTCAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (24 bp):
TCAAGTTCGGTTATAAATAGCCAT
Found at i:2182829 original size:36 final size:39
Alignment explanation
Indices: 2182789--2182861 Score: 107
Period size: 36 Copynumber: 1.9 Consensus size: 39
2182779 TCGATATAAT
* *
2182789 TTAAATTATTAAT-TATTA-ATAAAAT-TTTTATTTAAA
1 TTAAATTATAAATATATAACATAAAATATTTTATTTAAA
2182825 TTAAATTATAAATATATAACATAAAATATTTTATTTA
1 TTAAATTATAAATATATAACATAAAATATTTTATTTA
2182862 GTTTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 12 0.38
37 4 0.12
38 7 0.22
39 9 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TTAAATTATAAATATATAACATAAAATATTTTATTTAAA
Found at i:2182973 original size:25 final size:26
Alignment explanation
Indices: 2182945--2183002 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
2182935 CTTATAAAAA
* *
2182945 AATTTAATTTTCTTTTATTAT-TTTT
1 AATTTAATTATCTTTTAATATATTTT
*
2182970 AATTTTATTATCTTTTAATATATTTT
1 AATTTAATTATCTTTTAATATATTTT
2182996 -ATTTAAT
1 AATTTAAT
2183003 CGTTATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
AATTTAATTATCTTTTAATATATTTT
Found at i:2182977 original size:15 final size:16
Alignment explanation
Indices: 2182957--2182988 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2182947 TTTAATTTTC
2182957 TTTTATTAT-TTTTAA
1 TTTTATTATCTTTTAA
2182972 TTTTATTATCTTTTAA
1 TTTTATTATCTTTTAA
2182988 T
1 T
2182989 ATATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTATCTTTTAA
Found at i:2183618 original size:3 final size:3
Alignment explanation
Indices: 2183606--2183639 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2183596 ACGTCGGCAT
2183606 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2183640 CTTGAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2184028 original size:11 final size:12
Alignment explanation
Indices: 2184013--2184045 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2184003 AATTAATATT
2184013 TATTTTTAAAAA
1 TATTTTTAAAAA
2184025 -ATTTTTAAAAA
1 TATTTTTAAAAA
2184036 TATTATTTAA
1 TATT-TTTAA
2184046 TAATTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 3 0.16
13 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTTTTAAAAA
Found at i:2193678 original size:22 final size:24
Alignment explanation
Indices: 2193628--2193680 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
2193618 ATAAAAGGTA
2193628 TAAATAT-AATATTGTATTAAATTT
1 TAAATATAAATATTGTATT-AATTT
2193652 T--ATATAAATATT-TATT-ATTT
1 TAAATATAAATATTGTATTAATTT
2193672 TAAATATAA
1 TAAATATAA
2193681 TAATGATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 5 0.19
22 14 0.54
23 6 0.23
24 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAAATATAAATATTGTATTAATTT
Found at i:2196972 original size:2 final size:2
Alignment explanation
Indices: 2196965--2197004 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2196955 CACATAGGAC
2196965 AT AT 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 AT AT
2197005 TGGACGGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2208429 original size:36 final size:38
Alignment explanation
Indices: 2208367--2208470 Score: 99
Period size: 41 Copynumber: 2.7 Consensus size: 38
2208357 AATTTAATAT
* * *
2208367 TATATT-TAATA-ATTAAAATATGATATAAATTTTTTAA
1 TATATTATAATATAATAAAATA-AATATAAATATTTTAA
* *
2208404 -AT-TTATAATATATTAATATAAATATAAAATATTTTAA
1 TATATTATAATATAATAAAATAAATAT-AAATATTTTAA
2208441 TTATAATTATAATATAATAAAATAAATATA
1 -TAT-ATTATAATATAATAAAATAAATATA
2208471 TGAATTATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
35 2 0.04
36 11 0.20
37 18 0.33
39 2 0.04
40 1 0.02
41 21 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TATATTATAATATAATAAAATAAATATAAATATTTTAA
Found at i:2208451 original size:22 final size:21
Alignment explanation
Indices: 2208401--2208470 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
2208391 ATAAATTTTT
* *
2208401 TAAATTTATAATATATTAATA
1 TAAATATAAAATATATTAATA
*
2208422 TAAATATAAAATATTTTAAT-
1 TAAATATAAAATATATTAATA
* * *
2208442 TATAAT-TATAATATAATAAAA
1 TA-AATATAAAATATATTAATA
2208463 TAAATATA
1 TAAATATA
2208471 TGAATTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATATAAAATATATTAATA
Found at i:2209444 original size:5 final size:5
Alignment explanation
Indices: 2209434--2209466 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
2209424 TGAACTCTGA
2209434 AGTAT AGTAT AAGTAT AGTAT AGTAT AGTAT AG
1 AGTAT AGTAT -AGTAT AGTAT AGTAT AGTAT AG
2209467 GATACCGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (5 bp):
AGTAT
Found at i:2209449 original size:11 final size:11
Alignment explanation
Indices: 2209433--2209465 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2209423 CTGAACTCTG
2209433 AAGTATAGTAT
1 AAGTATAGTAT
2209444 AAGTATAGTAT
1 AAGTATAGTAT
2209455 -AGTATAGTAT
1 AAGTATAGTAT
2209465 A
1 A
2209466 GGATACCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (11 bp):
AAGTATAGTAT
Found at i:2209455 original size:16 final size:15
Alignment explanation
Indices: 2209434--2209466 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2209424 TGAACTCTGA
2209434 AGTATAGTATAAGTAT
1 AGTATAGTAT-AGTAT
2209450 AGTATAGTATAGTAT
1 AGTATAGTATAGTAT
2209465 AG
1 AG
2209467 GATACCGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (15 bp):
AGTATAGTATAGTAT
Found at i:2209959 original size:17 final size:17
Alignment explanation
Indices: 2209936--2209975 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2209926 ATAAAATAAA
2209936 ATTTAAGTTTATTGTTT
1 ATTTAAGTTTATTGTTT
*
2209953 CTTTAAGTTTATTGTTT
1 ATTTAAGTTTATTGTTT
2209970 ATTTAA
1 ATTTAA
2209976 AACAACATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (17 bp):
ATTTAAGTTTATTGTTT
Found at i:2211193 original size:23 final size:23
Alignment explanation
Indices: 2211148--2211195 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2211138 TTTTTTATTA
* *
2211148 TTAATTAATTTTAAATTTAATAT
1 TTAATTAATTTAAAATATAATAT
2211171 TTAATATAATTTAAAATAT-ATAT
1 TTAAT-TAATTTAAAATATAATAT
2211194 TT
1 TT
2211196 TATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTAATTTAAAATATAATAT
Found at i:2211244 original size:20 final size:19
Alignment explanation
Indices: 2211195--2211253 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2211185 AATATATATT
*
2211195 TTATTTTATTTTTTAGGTA
1 TTATTTTATTTTTTAGATA
**
2211214 TTATTACATTTTTTAGTATA
1 TTATTTTATTTTTTAG-ATA
*
2211234 TTTTTTTATTTTTTA-ATA
1 TTATTTTATTTTTTAGATA
2211252 TT
1 TT
2211254 TGATGAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 5 0.15
19 14 0.42
20 14 0.42
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (19 bp):
TTATTTTATTTTTTAGATA
Found at i:2211252 original size:18 final size:19
Alignment explanation
Indices: 2211198--2211254 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
2211188 ATATATTTTA
* *
2211198 TTTTATTTTTTAGGTATTA
1 TTTTATTTTTTAGATATTT
**
2211217 TTACATTTTTTAGTATATTT
1 TTTTATTTTTTAG-ATATTT
2211237 TTTTATTTTTTA-ATATTT
1 TTTTATTTTTTAGATATTT
2211255 GATGAGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 14 0.45
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTTTTAGATATTT
Found at i:2211961 original size:13 final size:13
Alignment explanation
Indices: 2211945--2211974 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2211935 TTTTACTATA
*
2211945 TTTCACCGTCACT
1 TTTCACCATCACT
2211958 TTTCACCATCACT
1 TTTCACCATCACT
2211971 TTTC
1 TTTC
2211975 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.37, G:0.03, T:0.43
Consensus pattern (13 bp):
TTTCACCATCACT
Found at i:2217510 original size:22 final size:24
Alignment explanation
Indices: 2217474--2217519 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
2217464 AATTGAACAT
2217474 ATTTTTTAATATTTA-A-AATATA
1 ATTTTTTAATATTTATATAATATA
2217496 ATTTTTT-ATACTTTATATAATATA
1 ATTTTTTAATA-TTTATATAATATA
2217520 TAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.14
22 11 0.52
23 1 0.05
24 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTTAATATTTATATAATATA
Found at i:2217533 original size:15 final size:16
Alignment explanation
Indices: 2217510--2217542 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2217500 TTTATACTTT
2217510 ATATAATATATA-AAA
1 ATATAATATATACAAA
*
2217525 ATATTATATATACAAA
1 ATATAATATATACAAA
2217541 AT
1 AT
2217543 TAAAATGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAATATATACAAA
Found at i:2217621 original size:18 final size:18
Alignment explanation
Indices: 2217594--2217636 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2217584 AAGTTTTTAT
* *
2217594 TTATAATTTAAATAGAGC
1 TTATATTTTAAATAGAAC
2217612 TTATATTTTAAATAGAAC
1 TTATATTTTAAATAGAAC
2217630 TTATATT
1 TTATATT
2217637 CTTTTATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (18 bp):
TTATATTTTAAATAGAAC
Found at i:2219952 original size:26 final size:27
Alignment explanation
Indices: 2219914--2219970 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
2219904 TTCTCCCTCT
*
2219914 ATCTCTATTTG-TTTCATAAATTGGGA
1 ATCTCTATATGTTTTCATAAATTGGGA
*
2219940 ATCTCTATATGTTTTCATATATTGGGA
1 ATCTCTATATGTTTTCATAAATTGGGA
2219967 ATCT
1 ATCT
2219971 TTTTGTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (27 bp):
ATCTCTATATGTTTTCATAAATTGGGA
Found at i:2221754 original size:7 final size:7
Alignment explanation
Indices: 2221742--2221770 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2221732 GCTATCTAGT
2221742 TGATTGC
1 TGATTGC
2221749 TGATTGC
1 TGATTGC
2221756 TGATTGC
1 TGATTGC
2221763 TGATTGC
1 TGATTGC
2221770 T
1 T
2221771 TCATCTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (7 bp):
TGATTGC
Found at i:2236730 original size:18 final size:18
Alignment explanation
Indices: 2236707--2236741 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2236697 TCAAATATAT
*
2236707 ATATATATATAAAAATTA
1 ATATATAAATAAAAATTA
*
2236725 ATATATAAATATAAATT
1 ATATATAAATAAAAATT
2236742 TATTTAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATAAATAAAAATTA
Found at i:2236797 original size:18 final size:19
Alignment explanation
Indices: 2236745--2236800 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
2236735 ATAAATTTAT
*
2236745 TTAATATTAATTATTAATATA
1 TTAA-ATTAATTA-TAATAAA
*
2236766 TTAAAATTTA-TATAA-AAA
1 TT-AAATTAATTATAATAAA
2236784 TTAAATTAATTATAATA
1 TTAAATTAATTATAATA
2236801 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 4 0.14
20 2 0.07
21 6 0.21
22 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATTAATTATAATAAA
Found at i:2243539 original size:18 final size:20
Alignment explanation
Indices: 2243507--2243550 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
2243497 AATAAAATTG
2243507 TATTTTTTAAATTTTAA-AT
1 TATTTTTTAAATTTTAATAT
*
2243526 TATTTTTT-ATTTTTAATAT
1 TATTTTTTAAATTTTAATAT
2243545 TATTTT
1 TATTTT
2243551 AAATAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTTAAATTTTAATAT
Found at i:2245948 original size:18 final size:18
Alignment explanation
Indices: 2245883--2245948 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 18
2245873 AACATAATAT
* *
2245883 AAATATATAAATATATTA
1 AAATTTATAAAAATATTA
2245901 AAATTTAT-AAAATA-T-
1 AAATTTATAAAAATATTA
* * **
2245916 GAA-TTATTATTATATTA
1 AAATTTATAAAAATATTA
2245933 AAATTTATAAAAATAT
1 AAATTTATAAAAATAT
2245949 AAATATTAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
14 4 0.11
15 6 0.17
16 2 0.06
17 7 0.20
18 16 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AAATTTATAAAAATATTA
Found at i:2245956 original size:32 final size:31
Alignment explanation
Indices: 2245878--2245957 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
2245868 ATACGAACAT
2245878 AATATAAATATATAAATATATTAAAATTTATAA
1 AATATAAATAT-T-AATATATTAAAATTTATAA
* *
2245911 AATATGAATTATTATTATATTAAAATTTATAAA
1 AATAT-AAATATTAATATATTAAAATTTAT-AA
2245944 AATATAAATATTAA
1 AATATAAATATTAA
2245958 CTATTGTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 23 0.56
33 13 0.32
34 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AATATAAATATTAATATATTAAAATTTATAA
Found at i:2248090 original size:27 final size:28
Alignment explanation
Indices: 2248060--2248112 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2248050 ATCAAATAAG
*
2248060 CTTTCTTTTGATTTG-TATTT-TTTTCTA
1 CTTTCTTCT-ATTTGTTATTTATTTTCTA
2248087 CTTTCTTCTATTTGTTATTTATTTTC
1 CTTTCTTCTATTTGTTATTTATTTTC
2248113 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 13 0.57
28 5 0.22
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (28 bp):
CTTTCTTCTATTTGTTATTTATTTTCTA
Found at i:2248125 original size:27 final size:26
Alignment explanation
Indices: 2248061--2248130 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 26
2248051 TCAAATAAGC
* *
2248061 TTTCTTTTGATTTGTATTTTTTTCTAC
1 TTTCTTAT-ATTTGTATTTTTTTCTAA
*
2248088 TTTCTTCTATTTGTTATTTATTTTC-AA
1 TTTCTTATATTTG-TATTT-TTTTCTAA
*
2248115 TTTTTTATATTT-TATT
1 TTTCTTATATTTGTATT
2248131 CAAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 23 0.62
28 5 0.14
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTCTTATATTTGTATTTTTTTCTAA
Found at i:2249148 original size:22 final size:23
Alignment explanation
Indices: 2249109--2249154 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2249099 TAGTTTCACA
* *
2249109 ATTTTAAATATTTTTTTAAATAT
1 ATTTTAAATATATATTTAAATAT
2249132 ATTTT-AATATATATTTAAATAT
1 ATTTTAAATATATATTTAAATAT
2249154 A
1 A
2249155 AATATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTAAATATATATTTAAATAT
Found at i:2249154 original size:10 final size:11
Alignment explanation
Indices: 2249109--2249154 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
2249099 TAGTTTCACA
2249109 ATTTTAAATATT
1 ATTTTAAATA-T
*
2249121 TTTTTAAATAT
1 ATTTTAAATAT
2249132 ATTTT-AATAT
1 ATTTTAAATAT
2249142 ATATTTAAATAT
1 AT-TTTAAATAT
2249154 A
1 A
2249155 AATATAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 7 0.23
11 8 0.27
12 15 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAATAT
Found at i:2249154 original size:12 final size:12
Alignment explanation
Indices: 2249111--2249194 Score: 57
Period size: 12 Copynumber: 7.0 Consensus size: 12
2249101 GTTTCACAAT
* *
2249111 TTTAAATATTTT
1 TTTAAATATATA
2249123 TTTAAATATAT-
1 TTTAAATATATA
2249134 TTT-AATATATA
1 TTTAAATATATA
*
2249145 TTTAAATATAAA
1 TTTAAATATATA
* *
2249157 TATAAGAATATAATT
1 T-TTA-AATAT-ATA
* *
2249172 TTTAAAT-TTTT
1 TTTAAATATATA
2249183 TTTAAATATATA
1 TTTAAATATATA
2249195 AAAAATTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 7 0.12
11 15 0.26
12 21 0.37
13 5 0.09
14 7 0.12
15 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATATATA
Found at i:2254371 original size:2 final size:2
Alignment explanation
Indices: 2254364--2254390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2254354 TATTTGCACT
2254364 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 T
2254391 GTTTTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2254975 original size:16 final size:16
Alignment explanation
Indices: 2254956--2255008 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2254946 TTTTCAATTT
*
2254956 TTATTAATTTTTGTTC
1 TTATTAATTTATGTTC
* *
2254972 TTATTGATTAAT-TT-
1 TTATTAATTTATGTTC
2254986 TTATTAATTTATGTTC
1 TTATTAATTTATGTTC
2255002 TTATTAA
1 TTATTAA
2255009 CCTTAAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.33
15 4 0.13
16 16 0.53
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (16 bp):
TTATTAATTTATGTTC
Found at i:2255026 original size:34 final size:30
Alignment explanation
Indices: 2254951--2255026 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 30
2254941 TAAAGTTTTC
* *
2254951 AATTTTTATTAATTTTTGTTCTTATTGATT
1 AATTTTTATTAATTTATGTTCTTATTAATT
2254981 AATTTTTATTAATTTATGTTCTTATTAACCTT
1 AATTTTTATTAATTTATGTTCTTATTAA--TT
2255013 AAACTTTTTATTAA
1 -AA-TTTTTATTAA
2255027 AGTAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 26 0.65
32 2 0.05
33 2 0.05
34 10 0.25
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
AATTTTTATTAATTTATGTTCTTATTAATT
Found at i:2255442 original size:7 final size:7
Alignment explanation
Indices: 2255430--2255460 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2255420 AGCGATATGG
2255430 GCAGGCT
1 GCAGGCT
2255437 GCAGGCT
1 GCAGGCT
2255444 GCAGGCT
1 GCAGGCT
2255451 GCAGGCT
1 GCAGGCT
2255458 GCA
1 GCA
2255461 ATCTCTGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.42, T:0.13
Consensus pattern (7 bp):
GCAGGCT
Found at i:2258613 original size:9 final size:9
Alignment explanation
Indices: 2258601--2258728 Score: 65
Period size: 9 Copynumber: 14.4 Consensus size: 9
2258591 TTTTAATATG
*
2258601 ATATCTTTA
1 ATATATTTA
2258610 ATATATTTA
1 ATATATTTA
*
2258619 ATAAATATTA
1 ATATAT-TTA
2258629 A-A-A--TA
1 ATATATTTA
* *
2258634 ATATAATAA
1 ATATATTTA
*
2258643 ATA-ATTAA
1 ATATATTTA
2258651 ATATAATTTA
1 ATAT-ATTTA
2258661 TTATATATTTA
1 --ATATATTTA
*
2258672 A-AT-TTAA
1 ATATATTTA
*
2258679 ATAAATTTA
1 ATATATTTA
2258688 ATATATATTA
1 ATATAT-TTA
*
2258698 TTTATATTTA
1 -ATATATTTA
2258708 ATAT-TTTA
1 ATATATTTA
*
2258716 ATAAATTTA
1 ATATATTTA
2258725 ATAT
1 ATAT
2258729 TATATCATGT
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 5 0.05
8 18 0.20
9 37 0.40
10 14 0.15
11 10 0.11
12 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
ATATATTTA
Found at i:2258642 original size:20 final size:22
Alignment explanation
Indices: 2258609--2258657 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
2258599 TGATATCTTT
*
2258609 AATAT-ATTTAATAAAT-ATTA
1 AATATAATATAATAAATAATTA
2258629 AA-ATAATATAATAAATAATTA
1 AATATAATATAATAAATAATTA
2258650 AATATAAT
1 AATATAAT
2258658 TTATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 6 0.24
22 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATAATATAATAAATAATTA
Found at i:2258672 original size:22 final size:21
Alignment explanation
Indices: 2258583--2258674 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 21
2258573 TTTTTTTAAT
*
2258583 TTTAAATAT-TTTAATATGATA
1 TTTAAATATATTTAATA-AATA
*
2258604 TCTTTAATATATTTAATAAATA
1 T-TTAAATATATTTAATAAATA
* *
2258626 TTAAAATA-ATATAATAAATA
1 TTTAAATATATTTAATAAATA
* * *
2258646 ATTAAATATAATTTATTATATA
1 TTTAAATAT-ATTTAATAAATA
2258668 TTTAAAT
1 TTTAAAT
2258675 TTAAATAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 17 0.30
21 6 0.11
22 26 0.46
23 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
TTTAAATATATTTAATAAATA
Found at i:2258699 original size:37 final size:37
Alignment explanation
Indices: 2258640--2258756 Score: 123
Period size: 37 Copynumber: 3.1 Consensus size: 37
2258630 AATAATATAA
*
2258640 TAAAT-AATTAAATATA-ATTTATTATATATTTAA-ATT
1 TAAATAAATTTAATATATA-TTATT-TATATTTAATATT
2258676 TAAATAAATTTAATATATATTATTTATATTTAATATT
1 TAAATAAATTTAATATATATTATTTATATTTAATATT
* * *
2258713 TTAATAAATTTAATATTATATCATGTTTATATTTATATAAT
1 TAAATAAATTTAATA-TATAT--TATTTATATTTA-ATATT
2258754 TAA
1 TAA
2258757 CATATTAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
36 14 0.20
37 32 0.46
38 6 0.09
40 11 0.16
41 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
TAAATAAATTTAATATATATTATTTATATTTAATATT
Found at i:2259002 original size:20 final size:21
Alignment explanation
Indices: 2258977--2259036 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
2258967 TTAAGATTAA
2258977 AATTAAATAAA-AATATTT-TT
1 AATTAAATAAATAA-ATTTATT
2258997 AATTAAA-AAATTAAATTTATT
1 AATTAAATAAA-TAAATTTATT
2259018 AAGTTAAATAAAT-AATTTA
1 AA-TTAAATAAATAAATTTA
2259037 ACTTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.09
20 11 0.31
21 12 0.34
22 6 0.17
23 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTAAATAAATAAATTTATT
Found at i:2259012 original size:22 final size:23
Alignment explanation
Indices: 2258979--2259030 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 23
2258969 AAGATTAAAA
2258979 TTAAATAAA--AATATTT-TTAA-
1 TTAAATAAATTAA-ATTTATTAAG
2258999 TTAAA-AAATTAAATTTATTAAG
1 TTAAATAAATTAAATTTATTAAG
2259021 TTAAATAAAT
1 TTAAATAAAT
2259031 AATTTAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.11
20 9 0.33
21 6 0.22
22 5 0.19
23 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAAATAAATTAAATTTATTAAG
Found at i:2261054 original size:14 final size:14
Alignment explanation
Indices: 2261003--2261060 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
2260993 AAATTAAAAA
*
2261003 ATATTATAAATATT
1 ATATTTTAAATATT
* *
2261017 ATATTTTTAATTTT
1 ATATTTTAAATATT
2261031 A-ATTTATTAAATATT
1 ATA-TT-TTAAATATT
*
2261046 ATATTTTAAAAATT
1 ATATTTTAAATATT
2261060 A
1 A
2261061 CTAAATTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.03
14 23 0.66
15 10 0.29
16 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTAAATATT
Found at i:2261068 original size:29 final size:29
Alignment explanation
Indices: 2261009--2261069 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2260999 AAAAATATTA
* ** **
2261009 TAAATATTATATTTTTAATTTTAATTTAT
1 TAAATATTATATTTTAAAAATTAATAAAT
*
2261038 TAAATATTATATTTTAAAAATTACTAAAT
1 TAAATATTATATTTTAAAAATTAATAAAT
2261067 TAA
1 TAA
2261070 TTAATCAAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TAAATATTATATTTTAAAAATTAATAAAT
Found at i:2261471 original size:21 final size:21
Alignment explanation
Indices: 2261446--2261486 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261436 TATCAATTAA
*
2261446 TAATTTATATTATAT-ATATTT
1 TAATTT-TATTAAATAATATTT
2261467 TAATTTTATTAAATAATATT
1 TAATTTTATTAAATAATATT
2261487 AGATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTATTAAATAATATTT
Found at i:2262708 original size:32 final size:32
Alignment explanation
Indices: 2262573--2262719 Score: 103
Period size: 32 Copynumber: 4.6 Consensus size: 32
2262563 AAAATAAGTT
* *
2262573 TTTTTTAAAAATATAATAATAATATAAAAATTATTT
1 TTTTTT-AAATTA-AATAAT-ATATAAAAATTA-TA
2262609 TTATTTTAAATTAAATAATAT-TAAGATAAATGT-TA
1 TT-TTTTAAATTAAATAATATAT-A-A-AAAT-TATA
* * *
2262644 -TATTT-AATTTAATAATAT-TAAAAAAT-TA
1 TTTTTTAAATTAAATAATATATAAAAATTATA
*
2262672 TTTTTTAAATTAAATAATATATTAAAATTATA
1 TTTTTTAAATTAAATAATATATAAAAATTATA
2262704 TTTTTTAAA--AAATAAT
1 TTTTTTAAATTAAATAAT
2262720 TTTTTATATT
Statistics
Matches: 93, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
28 3 0.03
29 7 0.08
30 20 0.22
31 7 0.08
32 24 0.26
33 4 0.04
34 4 0.04
35 8 0.09
36 11 0.12
37 5 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
TTTTTTAAATTAAATAATATATAAAAATTATA
Found at i:2266372 original size:22 final size:24
Alignment explanation
Indices: 2266347--2266396 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2266337 ATGCCAATTT
2266347 ATATTTAT-TTA-TGTTTTATATA
1 ATATTTATATTATTGTTTTATATA
* *
2266369 ATATTTATATTATTTTTTTATATC
1 ATATTTATATTATTGTTTTATATA
2266393 ATAT
1 ATAT
2266397 AATTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 3 0.12
24 13 0.54
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATTTATATTATTGTTTTATATA
Found at i:2266401 original size:18 final size:18
Alignment explanation
Indices: 2266375--2266414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2266365 TATAATATTT
* *
2266375 ATATTATTTTTTTATATC
1 ATATAATTTTTTAATATC
*
2266393 ATATAATTTTTTAATATG
1 ATATAATTTTTTAATATC
2266411 ATAT
1 ATAT
2266415 GTAATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
ATATAATTTTTTAATATC
Found at i:2266455 original size:25 final size:24
Alignment explanation
Indices: 2266426--2266504 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
2266416 TAATAATTTT
*
2266426 AATATTTATACAATATAAAGTTTAA
1 AATATTTATA-AATATAAAATTTAA
* *
2266451 AATATTACATAAATTTAAAATTTAA
1 AATATT-TATAAATATAAAATTTAA
* *
2266476 TA-ATTTATATTATATAAAATTTAA
1 AATATTTATA-AATATAAAATTTAA
2266500 AATAT
1 AATAT
2266505 CATAATTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
23 3 0.07
24 16 0.37
25 21 0.49
26 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (24 bp):
AATATTTATAAATATAAAATTTAA
Found at i:2266499 original size:31 final size:30
Alignment explanation
Indices: 2266452--2266513 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
2266442 AAAGTTTAAA
*
2266452 ATATTACATAAATTTAAAATTTAATAATTT
1 ATATTACATAAATTTAAAATATAATAATTT
* *
2266482 ATATTATATAAAATTTAAAATATCATAATTT
1 ATATTACAT-AAATTTAAAATATAATAATTT
2266513 A
1 A
2266514 ATTTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATTACATAAATTTAAAATATAATAATTT
Done.