Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 25 of 28
Found at i:3845816 original size:16 final size:16
Alignment explanation
Indices: 3845726--3845816 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
3845716 ATATTATTTA
*
3845726 ATATATTTTATTTTAT
1 ATATATTTTATATTAT
*
3845742 -TATA-ATTATATT-T
1 ATATATTTTATATTAT
*
3845755 AAAATATTTTATATTTAT
1 -ATATATTTTATA-TTAT
*
3845773 ATAAATTTTA-ATATAT
1 ATATATTTTATAT-TAT
* *
3845789 AAATAATTTATATTAT
1 ATATATTTTATATTAT
*
3845805 ATATATTATATA
1 ATATATTTTATA
3845817 AATTTTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
13 1 0.02
14 6 0.11
15 8 0.14
16 28 0.50
17 12 0.21
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATATTTTATATTAT
Found at i:3847027 original size:20 final size:20
Alignment explanation
Indices: 3846985--3847027 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3846975 TATTTAATTT
***
3846985 TTTATAAATTTTTTTATGTA
1 TTTATAAATTTTTTTAAAAA
3847005 TTTATAAATTTTTTTAAAAA
1 TTTATAAATTTTTTTAAAAA
3847025 TTT
1 TTT
3847028 TATCTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTATAAATTTTTTTAAAAA
Found at i:3847039 original size:32 final size:31
Alignment explanation
Indices: 3846982--3847042 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
3846972 GGATATTTAA
*
3846982 TTTTTTATAAATTTTTTTATGTATTTATAAAT
1 TTTTTTAAAAATTTTTTTA-GTATTTATAAAT
3847014 TTTTTTAAAAATTTTATCTTA-TATTTATA
1 TTTTTTAAAAATTTT-T-TTAGTATTTATA
3847043 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 22 0.85
33 1 0.04
34 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (31 bp):
TTTTTTAAAAATTTTTTTAGTATTTATAAAT
Found at i:3850812 original size:69 final size:69
Alignment explanation
Indices: 3850733--3850869 Score: 220
Period size: 69 Copynumber: 2.0 Consensus size: 69
3850723 ATTTTTTAAA
* * * * * *
3850733 TTTTTTATTTTTTAAAAGATTTTATTTTTATGCCTATTTTTATATATGTGTTGAATGAAGGTATC
1 TTTTTTATTTTTTAAAAGATTTTATCTCTATGCCTATTTTCAGATATGTGTTGAACGAAGATATC
3850798 AAAT
66 AAAT
3850802 TTTTTTATTTTTTAAAAGATTTTATCTCTATGCCTATTTTCAGATATGTGTTGAACGAAGATATC
1 TTTTTTATTTTTTAAAAGATTTTATCTCTATGCCTATTTTCAGATATGTGTTGAACGAAGATATC
3850867 AAA
66 AAA
3850870 GATTGATGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (69 bp):
TTTTTTATTTTTTAAAAGATTTTATCTCTATGCCTATTTTCAGATATGTGTTGAACGAAGATATC
AAAT
Found at i:3851088 original size:17 final size:16
Alignment explanation
Indices: 3851062--3851094 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3851052 AATGTATTGT
3851062 AATTTAAAAATAAAAA
1 AATTTAAAAATAAAAA
3851078 AATTATAAAAATAAAAA
1 AATT-TAAAAATAAAAA
3851095 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATTTAAAAATAAAAA
Found at i:3853475 original size:14 final size:14
Alignment explanation
Indices: 3853447--3853487 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3853437 TAATTTTTTT
* *
3853447 TTTAAATAATCATA
1 TTTAAATATTTATA
*
3853461 TTTCAATATTTATA
1 TTTAAATATTTATA
3853475 TTTAAATATTTAT
1 TTTAAATATTTAT
3853488 CAGATAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTAAATATTTATA
Found at i:3856186 original size:80 final size:80
Alignment explanation
Indices: 3856053--3856228 Score: 271
Period size: 80 Copynumber: 2.2 Consensus size: 80
3856043 AGTTTGGTGA
* *
3856053 AAACCACCAAATCACCTTTGCACCCATTTTCAACATTAAGTTTGGTGGCTTTATCTTTTAACCAT
1 AAACCACCAAATCACCTTTGCACCCATTTTCAACATTAAGTTTGGTGACTTTATCTTTTAACAAT
3856118 TTAATCAACAATGGT
66 TTAATCAACAATGGT
* *
3856133 AAACCACCAAATTACCTTTGCACTCATTTTCAACATTAAGTTTGGTGACTTTATCTTTTAACAAT
1 AAACCACCAAATCACCTTTGCACCCATTTTCAACATTAAGTTTGGTGACTTTATCTTTTAACAAT
* **
3856198 TTAGTCAACAATGAC
66 TTAATCAACAATGGT
* *
3856213 AAACTACTAAATCACC
1 AAACCACCAAATCACC
3856229 CATTTAGTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 86 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (80 bp):
AAACCACCAAATCACCTTTGCACCCATTTTCAACATTAAGTTTGGTGACTTTATCTTTTAACAAT
TTAATCAACAATGGT
Found at i:3862648 original size:21 final size:21
Alignment explanation
Indices: 3862592--3862648 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3862582 GTTGGGACCT
*
3862592 TGTATCGATACATTCTAAAAA
1 TGTATCGATACATTTTAAAAA
*
3862613 TGTATCGATACATTTTAGAAA
1 TGTATCGATACATTTTAAAAA
3862634 TGTATCGATACATTT
1 TGTATCGATACATTT
3862649 GGACAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTTAAAAA
Found at i:3865102 original size:17 final size:17
Alignment explanation
Indices: 3865082--3865125 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
3865072 AATATAAATT
3865082 TAATTTAAATTTTAAAA
1 TAATTTAAATTTTAAAA
3865099 TAATTTAAA-TTTAAAA
1 TAATTTAAATTTTAAAA
* *
3865115 TTATTCAAATT
1 TAATTTAAATT
3865126 ACAAAGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTAAATTTTAAAA
Found at i:3866058 original size:12 final size:12
Alignment explanation
Indices: 3866043--3866067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3866033 ATATTATTTT
3866043 TATTTTATGTTA
1 TATTTTATGTTA
3866055 TATTTTATGTTA
1 TATTTTATGTTA
3866067 T
1 T
3866068 GTAATTTTAT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTATGTTA
Found at i:3866060 original size:17 final size:17
Alignment explanation
Indices: 3866029--3866077 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
3866019 AATATTTATT
*
3866029 TTTTATATTAT-TTTTA
1 TTTTATGTTATATTTTA
3866045 TTTTATGTTATATTTTA
1 TTTTATGTTATATTTTA
*
3866062 TGTTATG-TA-ATTTTA
1 TTTTATGTTATATTTTA
3866077 T
1 T
3866078 AGTATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 7 0.23
16 12 0.40
17 11 0.37
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTATGTTATATTTTA
Found at i:3866159 original size:36 final size:36
Alignment explanation
Indices: 3866114--3866205 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 36
3866104 AATATAAAAT
*
3866114 AATTAAAAATAATTAATAATATTTTTAAA-ATTATTA
1 AATTAAAAATAA-TAATAATATTTTTAAATATAATTA
*
3866150 AATTAAAAATAAT-AT-TTA-TTTTAAATATAATTA
1 AATTAAAAATAATAATAATATTTTTAAATATAATTA
* *
3866183 AATTTAAAATAAAAATAATATTT
1 AATTAAAAATAATAATAATATTT
3866206 ATTTTTATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
32 7 0.15
33 19 0.40
34 4 0.09
35 3 0.06
36 14 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
AATTAAAAATAATAATAATATTTTTAAATATAATTA
Found at i:3866168 original size:21 final size:20
Alignment explanation
Indices: 3866144--3866208 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 20
3866134 ATTTTTAAAA
3866144 TTATTAAATTAAAAATAATAT
1 TTATTAAA-TAAAAATAATAT
* *
3866165 TTATTTTAAATATAATTAA-AT
1 TTA--TTAAATAAAAATAATAT
3866186 TTA--AAATAAAAATAATAT
1 TTATTAAATAAAAATAATAT
3866204 TTATT
1 TTATT
3866209 TTTATCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
17 10 0.29
18 5 0.14
21 8 0.23
22 7 0.20
23 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATTAAATAAAAATAATAT
Found at i:3869634 original size:9 final size:9
Alignment explanation
Indices: 3869593--3869650 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
3869583 ATTGAATGTA
3869593 ATTTATTAT
1 ATTTATTAT
3869602 ATTTAAGTTAT
1 ATTT-A-TTAT
*
3869613 ATTTGATGA-
1 ATTT-ATTAT
3869622 ATTTATTAT
1 ATTTATTAT
3869631 ATTTA--AT
1 ATTTATTAT
3869638 ATTTATTA-
1 ATTTATTAT
3869646 ATTTA
1 ATTTA
3869651 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
7 7 0.17
8 8 0.20
9 14 0.34
10 3 0.07
11 9 0.22
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (9 bp):
ATTTATTAT
Found at i:3869643 original size:16 final size:15
Alignment explanation
Indices: 3869622--3869651 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3869612 TATTTGATGA
3869622 ATTTATTATATTTAAT
1 ATTTATTA-ATTTAAT
3869638 ATTTATTAATTTAA
1 ATTTATTAATTTAA
3869652 AATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTAATTTAAT
Found at i:3871177 original size:12 final size:14
Alignment explanation
Indices: 3871154--3871189 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3871144 TTTTTTTAAA
3871154 AAAAAATAATTTT-
1 AAAAAATAATTTTC
3871167 AAAAAAT-ATTTTC
1 AAAAAATAATTTTC
3871180 AAAAAA-AATT
1 AAAAAATAATT
3871190 GATTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAATAATTTTC
Found at i:3872812 original size:21 final size:21
Alignment explanation
Indices: 3872788--3872827 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3872778 TTGTATTCAT
3872788 TTTTA-TAATTTACATTTGTAC
1 TTTTATTAATTTA-ATTTGTAC
*
3872809 TTTTATTTATTTAATTTGT
1 TTTTATTAATTTAATTTGT
3872828 TCTTATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTATTAATTTAATTTGTAC
Found at i:3873282 original size:108 final size:110
Alignment explanation
Indices: 3873104--3873382 Score: 370
Period size: 108 Copynumber: 2.6 Consensus size: 110
3873094 TATATATATC
* * * * *
3873104 TTACATCATGGCTTATATAAAGCTTGCAATTTCAAATATAAGGATCAACATTCAAATTAACCGTA
1 TTACATCATGACTTATATAAAGTTTGCAATTTCAAATATAAGAATCAACAGTCAAATTAACCGCA
* *
3873169 AGATCAGGAAATTGAAGCATTATATATACGTATAATCTGATTTTTG
66 AGATCAGGAAATTGAAGCATCATATATACATATAATCTGA-TTTTG
* * *
3873215 TTACATCATCACTTAT-TAAAGTTTGCAATTTCAAATGTACGAAT-AA-AGTCAAATTAACCGCA
1 TTACATCATGACTTATATAAAGTTTGCAATTTCAAATATAAGAATCAACAGTCAAATTAACCGCA
* *
3873277 AGATCAGGAAATTTAAGCATCATATATATATATAATCTGATTTTG
66 AGATCAGGAAATTGAAGCATCATATATACATATAATCTGATTTTG
* * * *
3873322 TTACATCATGACTTATATAAAGTTTGTAATTT-TAA-ATAAGAATCAAGATTCAAATTAACCG
1 TTACATCATGACTTATATAAAGTTTGCAATTTCAAATATAAGAATCAACAGTCAAATTAACCG
3873383 TAATTTATAT
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
106 6 0.04
107 24 0.16
108 77 0.52
109 2 0.01
110 24 0.16
111 14 0.10
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (110 bp):
TTACATCATGACTTATATAAAGTTTGCAATTTCAAATATAAGAATCAACAGTCAAATTAACCGCA
AGATCAGGAAATTGAAGCATCATATATACATATAATCTGATTTTG
Found at i:3874472 original size:2 final size:2
Alignment explanation
Indices: 3874465--3874491 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3874455 AATTAATTGC
3874465 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
3874492 GCTTTCATGT
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:3876567 original size:2 final size:2
Alignment explanation
Indices: 3876555--3876589 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3876545 CAATTTTTGC
*
3876555 AT AT A- AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3876590 TGCTCCTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3882140 original size:4 final size:4
Alignment explanation
Indices: 3882131--3882157 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3882121 CTTTTTAAGG
3882131 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
3882158 GCCTATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:3883033 original size:23 final size:23
Alignment explanation
Indices: 3882978--3883041 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
3882968 TTTATTAAAA
*
3882978 ATATTAAAAA-T-TATTTTAATT
1 ATATTAAAAATTATATTTTAATC
**
3882999 AT-TTAATTATTATATTTTAATC
1 ATATTAAAAATTATATTTTAATC
*
3883021 ATATTAAAAATTAAATTTTAA
1 ATATTAAAAATTATATTTTAA
3883042 CTTAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.15
21 3 0.09
22 11 0.32
23 15 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTAAAAATTATATTTTAATC
Found at i:3883075 original size:50 final size:45
Alignment explanation
Indices: 3882960--3883076 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 45
3882950 AATTATGAAT
3882960 ATTATAATT-TTATTAAA-AATATTAAAAATTATTTTAATTATTTA
1 ATTAT-ATTATTATTAAATAATATTAAAAATTATTTTAATTATTTA
*
3883004 ATTAT-TATATT-TT-AATCATATTAAAAATTAAATTTTAACTTAATTTA
1 ATTATAT-TATTATTAAATAATATTAAAAATT--ATTTTAA-TT-ATTTA
3883051 ATTATATTATTATTAATATAATATTA
1 ATTATATTATTATTAA-ATAATATTA
3883077 GAATTATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
42 3 0.05
43 15 0.25
44 7 0.12
45 7 0.12
46 2 0.03
47 14 0.23
48 3 0.05
49 1 0.02
50 8 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (45 bp):
ATTATATTATTATTAAATAATATTAAAAATTATTTTAATTATTTA
Found at i:3883113 original size:18 final size:19
Alignment explanation
Indices: 3883074--3883113 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3883064 TAATATAATA
* *
3883074 TTAGAATTATAAAAATTCT
1 TTAGAATTATAAAAACTAT
3883093 TTAGAATTAT-AAAACTAT
1 TTAGAATTATAAAAACTAT
3883111 TTA
1 TTA
3883114 TATATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TTAGAATTATAAAAACTAT
Found at i:3883172 original size:20 final size:20
Alignment explanation
Indices: 3883125--3883192 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
3883115 ATATAAATAT
3883125 TATTTATATTTTTT-TATATC
1 TATTTATATTTTTTCTAT-TC
* *
3883145 TTAATTATATTTTTTCTGTTC
1 -TATTTATATTTTTTCTATTC
3883166 TATTTAT-TATTTTTCTATTC
1 TATTTATAT-TTTTTCTATTC
3883186 TATTTAT
1 TATTTAT
3883193 TATAATATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.02
20 23 0.56
21 15 0.37
22 2 0.05
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.69
Consensus pattern (20 bp):
TATTTATATTTTTTCTATTC
Found at i:3883492 original size:2 final size:2
Alignment explanation
Indices: 3883480--3883557 Score: 61
Period size: 2 Copynumber: 39.0 Consensus size: 2
3883470 GGAGATTCAC
* * * * *
3883480 TA TA TA AA TA TA TA TA TA TA TA TA TT TT TA TA TA TA T- TT TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3883521 GA GA T- TCA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3883558 CACTGTGGGC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.03
2 60 0.94
3 1 0.02
4 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3883499 original size:50 final size:50
Alignment explanation
Indices: 3883445--3883549 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 50
3883435 TTAGATTTAA
3883445 ATATACAAAAAGAAAGAGATATTTTGGAGATTCACTATATAAATATATAT
1 ATATACAAAAAGAAAGAGATATTTTGGAGATTCACTATATAAATATATAT
* * ***** * * *
3883495 ATATATATATTTTTATATATATTTTGGAGATTCACTATATATATATATAT
1 ATATACAAAAAGAAAGAGATATTTTGGAGATTCACTATATAAATATATAT
3883545 ATATA
1 ATATA
3883550 TATATATACA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (50 bp):
ATATACAAAAAGAAAGAGATATTTTGGAGATTCACTATATAAATATATAT
Found at i:3884512 original size:16 final size:16
Alignment explanation
Indices: 3884488--3884518 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3884478 TTTATCCTTA
3884488 AAATATAATATTTAAT
1 AAATATAATATTTAAT
*
3884504 AAATTTAATATTTAA
1 AAATATAATATTTAA
3884519 AATTTCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATAATATTTAAT
Found at i:3885644 original size:28 final size:23
Alignment explanation
Indices: 3885591--3885635 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3885581 TCAAGAACTG
3885591 TTGGATGTTGCTCTGTCTTTCTT
1 TTGGATGTTGCTCTGTCTTTCTT
3885614 TTGGATGTTGCTCTGTCTTTCT
1 TTGGATGTTGCTCTGTCTTTCT
3885636 CTTCTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.18, G:0.22, T:0.56
Consensus pattern (23 bp):
TTGGATGTTGCTCTGTCTTTCTT
Found at i:3886619 original size:12 final size:12
Alignment explanation
Indices: 3886600--3886647 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
3886590 AATTAATAAT
3886600 TTTATATTTAAA
1 TTTATATTTAAA
* *
3886612 TATATATTTATA
1 TTTATATTTAAA
3886624 TTTAATATTTAAA
1 TTT-ATATTTAAA
*
3886637 TTTAAATTTAA
1 TTTATATTTAA
3886648 GCAATTATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTATATTTAAA
Found at i:3886626 original size:25 final size:25
Alignment explanation
Indices: 3886589--3886646 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3886579 AAAATTATAA
* *
3886589 AAATTAATAATTTTATATTTAAATAT
1 AAATTTAT-ATTTAATATTTAAATAT
* *
3886615 ATATTTATATTTAATATTTAAATTT
1 AAATTTATATTTAATATTTAAATAT
3886640 AAATTTA
1 AAATTTA
3886647 AGCAATTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATTTATATTTAATATTTAAATAT
Found at i:3886647 original size:6 final size:6
Alignment explanation
Indices: 3886600--3886647 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
3886590 AATTAATAAT
* * * *
3886600 TTTATA TTTAAA TATATA TTTATA TTTAATA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
3886648 GCAATTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:3887312 original size:26 final size:24
Alignment explanation
Indices: 3887255--3887312 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3887245 ATATTAAATA
3887255 AAAATATATTTATTAAAATATTAT
1 AAAATATATTTATTAAAATATTAT
*** *
3887279 ATTTTATATTTATATTAAATATGTAT
1 AAAATATATTTAT-TAAAATAT-TAT
3887305 AAAATATA
1 AAAATATA
3887313 AATATCAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
24 10 0.40
25 7 0.28
26 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAAATATATTTATTAAAATATTAT
Found at i:3887322 original size:13 final size:13
Alignment explanation
Indices: 3887306--3887339 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3887296 AATATGTATA
3887306 AAATATAAATATC
1 AAATATAAATATC
*
3887319 AAATATAAATATT
1 AAATATAAATATC
3887332 AAA-ATAAA
1 AAATATAAA
3887340 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:3887857 original size:22 final size:22
Alignment explanation
Indices: 3887832--3887896 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
3887822 ATTAGGACAC
3887832 ATATAATAAATTTATTATATTT
1 ATATAATAAATTTATTATATTT
* *
3887854 ATAT-TTAAAATTT-TTA-ATAT
1 ATATAAT-AAATTTATTATATTT
*
3887874 ATTTAATAAATTTTATTATATTT
1 ATATAATAAA-TTTATTATATTT
3887897 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
20 9 0.27
21 8 0.24
22 13 0.39
23 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATAATAAATTTATTATATTT
Found at i:3887876 original size:18 final size:19
Alignment explanation
Indices: 3887853--3887896 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3887843 TTATTATATT
*
3887853 TATATTTAA-AATTTTTAA
1 TATATTTAATAAATTTTAA
*
3887871 TATATTTAATAAATTTTAT
1 TATATTTAATAAATTTTAA
3887890 TATATTT
1 TATATTT
3887897 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTTAATAAATTTTAA
Found at i:3892859 original size:5 final size:6
Alignment explanation
Indices: 3892844--3892877 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3892834 AAAATACGTC
3892844 AAAAAG AAAAAG AAAAAG -AAAAG AAAATAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAA
3892878 GAGGACCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:3892859 original size:12 final size:12
Alignment explanation
Indices: 3892844--3892877 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
3892834 AAAATACGTC
3892844 AAAAAGAAAAAG
1 AAAAAGAAAAAG
3892856 AAAAAG-AAAAG
1 AAAAAGAAAAAG
3892867 AAAATAGAAAA
1 AAAA-AGAAAA
3892878 GAGGACCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 8 0.40
13 3 0.15
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:3893706 original size:35 final size:33
Alignment explanation
Indices: 3893667--3893749 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 33
3893657 AAAAAATAAT
3893667 TTAATTTTTATTT-TAATAAATAAATCTAAATAAAA
1 TTAATTTTTATTTGT--TAAATAAAT-TAAATAAAA
*
3893702 TTAATATTTATTTGTTAAATAAATTAAATAAAA
1 TTAATTTTTATTTGTTAAATAAATTAAATAAAA
3893735 TATATATTTTTATTT
1 T-TA-ATTTTTATTT
3893750 ATTTATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 10 0.23
34 11 0.26
35 21 0.49
36 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TTAATTTTTATTTGTTAAATAAATTAAATAAAA
Found at i:3893735 original size:33 final size:36
Alignment explanation
Indices: 3893683--3893749 Score: 104
Period size: 34 Copynumber: 1.9 Consensus size: 36
3893673 TTTATTTTAA
3893683 TAAATAAATCTAAATAAAAT-TA-ATATTTATTTGT
1 TAAATAAATCTAAATAAAATATATATATTTATTTGT
*
3893717 TAAATAAAT-TAAATAAAATATATATTTTTATTT
1 TAAATAAATCTAAATAAAATATATATATTTATTT
3893750 ATTTATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.33
34 11 0.37
35 9 0.30
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
TAAATAAATCTAAATAAAATATATATATTTATTTGT
Found at i:3893795 original size:22 final size:21
Alignment explanation
Indices: 3893768--3893821 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
3893758 TTATGAATAG
3893768 TTTAAATTTATTTAATAAATTA
1 TTTAAATTTATTT-ATAAATTA
* *
3893790 TTTAAAATTTGTTTTTAAATTA
1 TTT-AAATTTATTTATAAATTA
* *
3893812 ATTATATTTA
1 TTTAAATTTA
3893822 ATAATAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.19
22 12 0.46
23 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAATTTATTTATAAATTA
Found at i:3893840 original size:12 final size:12
Alignment explanation
Indices: 3893823--3893880 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
3893813 TTATATTTAA
3893823 TAATAATATAAT
1 TAATAATATAAT
*
3893835 TAATAATATTAT
1 TAATAATATAAT
* * *
3893847 TACTATTTAATATT
1 TAATA-AT-ATAAT
3893861 TAA-AATATAAT
1 TAATAATATAAT
3893872 TAATAATAT
1 TAATAATAT
3893881 TCCTATTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
11 7 0.20
12 21 0.60
13 2 0.06
14 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAATATAAT
Found at i:3893995 original size:21 final size:22
Alignment explanation
Indices: 3893955--3893998 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3893945 ATATTATTTT
*
3893955 TTCATAAATATATCTTTAATTA
1 TTCATAAATATATATTTAATTA
3893977 TTCATAAATA-ATATTTAATTA
1 TTCATAAATATATATTTAATTA
3893998 T
1 T
3893999 ATATTATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTCATAAATATATATTTAATTA
Found at i:3894060 original size:29 final size:30
Alignment explanation
Indices: 3894028--3894092 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
3894018 TTTATTATTC
* *
3894028 ATAAATAAATTTTAA-TTTAAATAAA-AAAT
1 ATAAATAAA-CTTAACTTAAAATAAATAAAT
*
3894057 ATAAATACACTTAACTTAAAATAAATAAAT
1 ATAAATAAACTTAACTTAAAATAAATAAAT
3894087 ATAAAT
1 ATAAAT
3894093 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 17 0.55
30 10 0.32
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (30 bp):
ATAAATAAACTTAACTTAAAATAAATAAAT
Found at i:3894126 original size:11 final size:10
Alignment explanation
Indices: 3894110--3894146 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
3894100 TAAAATTTTT
3894110 AATAAATATA
1 AATAAATATA
3894120 AATTAAATATA
1 AA-TAAATATA
3894131 AAT-AA-ATA
1 AATAAATATA
3894139 AATAAATA
1 AATAAATA
3894147 ATTTCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.25
9 4 0.17
10 4 0.17
11 10 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAAATATA
Found at i:3895427 original size:24 final size:20
Alignment explanation
Indices: 3895400--3895470 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 20
3895390 TCTTAACCAG
*
3895400 ATAATAAAATTAAATATAAATTTA
1 ATAATATAA-TAAATATAAA---A
3895424 ATAAGTATAATAAATATAAAA
1 ATAA-TATAATAAATATAAAA
3895445 ATAATATAATAAATAT-AAA
1 ATAATATAATAAATATAAAA
3895464 ATAATAT
1 ATAATAT
3895471 TTTAAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
19 10 0.22
20 12 0.27
21 5 0.11
24 14 0.31
25 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
ATAATATAATAAATATAAAA
Found at i:3895434 original size:9 final size:9
Alignment explanation
Indices: 3895415--3895462 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
3895405 AAAATTAAAT
*
3895415 ATAAATTTA
1 ATAAATATA
*
3895424 ATAAGTATA
1 ATAAATATA
3895433 ATAAATATAA
1 ATAAATAT-A
*
3895443 AAATAATATA
1 ATA-AATATA
3895453 ATAAATATA
1 ATAAATATA
3895462 A
1 A
3895463 AATAATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 21 0.66
10 6 0.19
11 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAATATA
Found at i:3895482 original size:20 final size:19
Alignment explanation
Indices: 3895423--3895470 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 19
3895413 ATATAAATTT
3895423 AATAAGTATAATAAATATAAA
1 AATAA-TATAATAAATAT-AA
3895444 AATAATATAATAAATATAA
1 AATAATATAATAAATATAA
3895463 AATAATAT
1 AATAATAT
3895471 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 10 0.37
20 12 0.44
21 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAATATAATAAATATAA
Found at i:3895484 original size:15 final size:15
Alignment explanation
Indices: 3895411--3895503 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 15
3895401 TAATAAAATT
3895411 AAATATAA-AT-TTA
1 AAATATAATATATTA
*
3895424 ATAAGTATAATAAATATA
1 A-AA-TATAATATAT-TA
*
3895442 AAA-ATAATATAATA
1 AAATATAATATATTA
*
3895456 AATATAAAATAATATTTTA
1 AA-AT---ATAATATATTA
3895475 AAATATAATATATTA
1 AAATATAATATATTA
* *
3895490 ATATATATTATATT
1 AAATATAATATATT
3895504 TATATTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 6 0.10
15 35 0.56
16 1 0.02
17 3 0.05
18 5 0.08
19 11 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (15 bp):
AAATATAATATATTA
Found at i:3895508 original size:15 final size:15
Alignment explanation
Indices: 3895464--3895524 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
3895454 TAAATATAAA
*
3895464 ATAATAT-TTTAAAAT
1 ATAATATATTT-ATAT
*
3895479 ATAATATATTAATAT
1 ATAATATATTTATAT
*
3895494 ATATTATATTTATAT
1 ATAATATATTTATAT
* *
3895509 TTAAAATATTTATAT
1 ATAATATATTTATAT
3895524 A
1 A
3895525 ATTAATATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 35 0.95
16 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATATATTTATAT
Found at i:3895541 original size:16 final size:18
Alignment explanation
Indices: 3895520--3895554 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3895510 TAAAATATTT
3895520 ATATAAT-T-AATATAAA
1 ATATAATGTAAATATAAA
3895536 ATATAATGTAAATATAAA
1 ATATAATGTAAATATAAA
3895554 A
1 A
3895555 ATTGATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATAATGTAAATATAAA
Found at i:3896109 original size:15 final size:15
Alignment explanation
Indices: 3896089--3896161 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 15
3896079 AGAAACCATT
*
3896089 TTTATAATATATATA
1 TTTATAATATATAAA
*
3896104 TTTAT-ATTTA-AAA
1 TTTATAATATATAAA
3896117 TATTATATATTTATATAAA
1 T-TTATA-A--TATATAAA
*
3896136 TTTATATTATATAAA
1 TTTATAATATATAAA
3896151 TTT-TAATATAT
1 TTTATAATATAT
3896162 TTTTATATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.06
14 15 0.32
15 16 0.34
16 1 0.02
18 8 0.17
19 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATATATAAA
Found at i:3896126 original size:22 final size:21
Alignment explanation
Indices: 3896089--3896132 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
3896079 AGAAACCATT
*
3896089 TTTATAATATATATATTTATA
1 TTTAAAATATATATATTTATA
3896110 TTTAAAATATTATATATTTATA
1 TTTAAAATA-TATATATTTATA
3896132 T
1 T
3896133 AAATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAATATATATATTTATA
Found at i:3896159 original size:17 final size:15
Alignment explanation
Indices: 3896089--3896153 Score: 69
Period size: 15 Copynumber: 4.2 Consensus size: 15
3896079 AGAAACCATT
* *
3896089 TTTATAATATATATA
1 TTTATATTATATAAA
*
3896104 TTTATATT-TAAAATA
1 TTTATATTATATAA-A
3896119 TTATATATTTATATAAA
1 TT-TATA-TTATATAAA
3896136 TTTATATTATATAAA
1 TTTATATTATATAAA
3896151 TTT
1 TTT
3896154 TAATATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.07
15 22 0.52
16 8 0.19
17 5 0.12
18 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:3896161 original size:37 final size:39
Alignment explanation
Indices: 3896120--3896193 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
3896110 TTTAAAATAT
*
3896120 TATATATTTATATAAAT-TTATA-TTATATAAATTTTAA
1 TATATATTTATATAAATATAATAGTTATATAAATTTTAA
* * *
3896157 TATATTTTTATATCAATATAATAGTTATATTAATTTT
1 TATATATTTATATAAATATAATAGTTATATAAATTTT
3896194 TTTATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 15 0.48
38 4 0.13
39 12 0.39
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TATATATTTATATAAATATAATAGTTATATAAATTTTAA
Found at i:3902132 original size:22 final size:21
Alignment explanation
Indices: 3902101--3902141 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3902091 TTTTTTAATT
3902101 TAAATTTAATTATA-AAATATA
1 TAAATTTAA-TATAGAAATATA
3902122 TAAATATTAATATAGAAATA
1 TAAAT-TTAATATAGAAATA
3902142 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAATTTAATATAGAAATATA
Found at i:3903516 original size:22 final size:22
Alignment explanation
Indices: 3903491--3903533 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3903481 CAAAAAGGTA
*
3903491 AAATGATAAATTAATATTTAAT
1 AAATAATAAATTAATATTTAAT
**
3903513 AAATAATAAATTGTTATTTAA
1 AAATAATAAATTAATATTTAA
3903534 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATAATAAATTAATATTTAAT
Found at i:3903973 original size:17 final size:16
Alignment explanation
Indices: 3903938--3903976 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3903928 ACACTTTATT
*
3903938 TATTTATTTTATTAAA
1 TATTTATTTTAATAAA
*
3903954 TATTTATATTTAATATA
1 TATTTAT-TTTAATAAA
3903971 TATTTA
1 TATTTA
3903977 AAAATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTATTTTAATAAA
Found at i:3910232 original size:27 final size:27
Alignment explanation
Indices: 3910183--3910268 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
3910173 ATTTATAATT
* *
3910183 TATTTTATA-TTATAATTATATTTAAAA
1 TATTTTATATTTAT-ATAAAATTTAAAA
*
3910210 TATTTTATATTTATATAAAATTTAATA
1 TATTTTATATTTATATAAAATTTAAAA
3910237 TATTATTA-ATTTATATTATAAATTTTAAAA
1 TATT-TTATATTTATA-TA-AAA-TTTAAAA
3910267 TA
1 TA
3910269 ACAACTGGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
27 30 0.60
28 9 0.18
29 3 0.06
30 8 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTTATATTTATATAAAATTTAAAA
Found at i:3915438 original size:29 final size:27
Alignment explanation
Indices: 3915397--3915451 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
3915387 TATTTAATTT
*
3915397 ATAAATTAATTTATTTTTATATTATTAAA
1 ATAAATTAATTTAATTTTA-ATT-TTAAA
3915426 ATAAA-TAATTTTAATTTTAATTTTAA
1 ATAAATTAA-TTTAATTTTAATTTTAA
3915452 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
28 6 0.25
29 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATAAATTAATTTAATTTTAATTTTAAA
Found at i:3915442 original size:6 final size:6
Alignment explanation
Indices: 3915431--3915457 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3915421 TTAAAATAAA
3915431 TAATTT TAATTT TAATTT TAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
3915458 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:3916334 original size:2 final size:2
Alignment explanation
Indices: 3916327--3916361 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3916317 TATCTAACAT
3916327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3916362 GTATGTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3919709 original size:12 final size:13
Alignment explanation
Indices: 3919687--3919718 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3919677 ATTTTTTAAA
3919687 TAAATAAAAAATT
1 TAAATAAAAAATT
3919700 TAAA-AAAAAA-T
1 TAAATAAAAAATT
3919711 TAAATAAA
1 TAAATAAA
3919719 TATATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 9 0.50
13 4 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAATAAAAAATT
Found at i:3923772 original size:2 final size:2
Alignment explanation
Indices: 3923767--3923795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3923757 AAAAGCGCAC
3923767 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3923796 CAATATACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3930484 original size:24 final size:23
Alignment explanation
Indices: 3930439--3930486 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
3930429 TTTTCCTTAA
*
3930439 ATTTTAATTTTAAATTTAAATTT
1 ATTTTAATTTTAAATATAAATTT
3930462 ATTTTAATTTATAAATA-ATAATTT
1 ATTTTAATTT-TAAATATA-AATTT
3930486 A
1 A
3930487 AATCGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTAATTTTAAATATAAATTT
Found at i:3931509 original size:31 final size:31
Alignment explanation
Indices: 3931471--3931534 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
3931461 GGATTTGCTT
*
3931471 ATTTCTATGTTCGACTTTTACTTACAGATTA
1 ATTTCTATGTTCAACTTTTACTTACAGATTA
3931502 ATTTCTATGTTCAACTTTTACTTACAGATTA
1 ATTTCTATGTTCAACTTTTACTTACAGATTA
3931533 AT
1 AT
3931535 AAAGATAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (31 bp):
ATTTCTATGTTCAACTTTTACTTACAGATTA
Found at i:3931604 original size:2 final size:2
Alignment explanation
Indices: 3931599--3931641 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3931589 TGTGTGTGTG
3931599 TA TA TA TA 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 TA TA TA TA
3931641 T
1 T
3931642 GGGAAATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3931880 original size:26 final size:25
Alignment explanation
Indices: 3931832--3931880 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3931822 TTTAAGGTCA
*
3931832 ATTTTATTTTTTAATTATATAATAT
1 ATTTTATTTTTTAAATATATAATAT
*
3931857 ATTTTATTTTTATAAATATGTAAT
1 ATTTTATTTTT-TAAATATATAAT
3931881 TTATATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTTATTTTTTAAATATATAATAT
Found at i:3934081 original size:15 final size:16
Alignment explanation
Indices: 3934061--3934094 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3934051 GTTAAATACG
*
3934061 ATTTAAAT-TAAATAA
1 ATTTAAATAAAAATAA
3934076 ATTTAAATAAAAATAA
1 ATTTAAATAAAAATAA
3934092 ATT
1 ATT
3934095 AATACATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAATAAAAATAA
Found at i:3936767 original size:15 final size:17
Alignment explanation
Indices: 3936749--3936791 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3936739 TTAAAATCTT
3936749 AAAATTA-AAA-TCAAA
1 AAAATTACAAATTCAAA
*
3936764 AAAATTACAAATTTAAA
1 AAAATTACAAATTCAAA
3936781 AAAATTACAAA
1 AAAATTACAAA
3936792 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 15 0.60
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATTACAAATTCAAA
Found at i:3936798 original size:17 final size:17
Alignment explanation
Indices: 3936755--3936799 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3936745 TCTTAAAATT
*
3936755 AAAATCAAAAAAATTAC
1 AAAATAAAAAAAATTAC
* *
3936772 AAATTTAAAAAAATTAC
1 AAAATAAAAAAAATTAC
3936789 AAAATAAAAAA
1 AAAATAAAAAA
3936800 TTCGGCCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATAAAAAAAATTAC
Found at i:3937747 original size:2 final size:2
Alignment explanation
Indices: 3937740--3937770 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3937730 CTGAAGCAAA
3937740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3937771 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3941130 original size:41 final size:42
Alignment explanation
Indices: 3941073--3941176 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 42
3941063 GTTTAAAATG
* *
3941073 TTGATTTGCAATATATTAATTAGTATATGCTCAAACGAA-TA
1 TTGATTTGTAATATATTAATTAGTATATGCTCAAACGAAGCA
* * * *
3941114 TTGATTTGTAATATATTAATTAGTATATGTTTATACTAAGCA
1 TTGATTTGTAATATATTAATTAGTATATGCTCAAACGAAGCA
3941156 TTGATTTTGTAATATATTAAT
1 TTGA-TTTGTAATATATTAAT
3941177 GCTTAGTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 34 0.62
42 5 0.09
43 16 0.29
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.46
Consensus pattern (42 bp):
TTGATTTGTAATATATTAATTAGTATATGCTCAAACGAAGCA
Found at i:3948701 original size:28 final size:28
Alignment explanation
Indices: 3948668--3948737 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
3948658 ATTTTACTTG
* * * *
3948668 AAAATTTTATATTTTTATTATATTTAAAT
1 AAAATTTTATATTTTAATT-TATATCAAC
*
3948697 AAATTTTTATATTTTAATTTATATCAAC
1 AAAATTTTATATTTTAATTTATATCAAC
3948725 AAAATTTTATATT
1 AAAATTTTATATT
3948738 AAATAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
AAAATTTTATATTTTAATTTATATCAAC
Found at i:3948844 original size:17 final size:16
Alignment explanation
Indices: 3948811--3948842 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3948801 TTAATTAAAA
*
3948811 ATTAAAATTAAAATTT
1 ATTAAAAATAAAATTT
3948827 ATTAAAAATAAAATTT
1 ATTAAAAATAAAATTT
3948843 TAATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAAAATAAAATTT
Found at i:3948845 original size:24 final size:23
Alignment explanation
Indices: 3948799--3948895 Score: 67
Period size: 23 Copynumber: 4.2 Consensus size: 23
3948789 TTACGAGTTT
3948799 ATTTAATTAAAAATTAAAA-TT-AAA
1 ATTT-ATT-AAAA-TAAAATTTAAAA
*
3948823 ATTTATTAAAAATAAAATTT-TAA
1 ATTTATT-AAAATAAAATTTAAAA
* *
3948846 TTTTA-TATAATAAAATTATAAAA
1 ATTTATTAAAATAAAATT-TAAAA
* * *
3948869 ATTCATTTAAATAAAATTAAAAA
1 ATTTATTAAAATAAAATTTAAAA
3948892 ATTT
1 ATTT
3948896 TAAAGGTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
21 10 0.17
22 7 0.12
23 28 0.47
24 14 0.24
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTTATTAAAATAAAATTTAAAA
Found at i:3949753 original size:18 final size:18
Alignment explanation
Indices: 3949726--3949761 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3949716 TTTAATTTTT
3949726 TAAAAATATTTTTAATTA
1 TAAAAATATTTTTAATTA
*
3949744 TAAAATTATTTTTAATTA
1 TAAAAATATTTTTAATTA
3949762 CTATCAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAAATATTTTTAATTA
Found at i:3950531 original size:30 final size:29
Alignment explanation
Indices: 3950496--3950587 Score: 102
Period size: 26 Copynumber: 3.2 Consensus size: 29
3950486 AAATAATAAC
3950496 TTAAAAAATAAATATATTTTTAATTAAATA
1 TTAAAAAATAAATATATTTTT-ATTAAATA
3950526 TTAAAAAA-ATAA-ATA-TTTT-TTAAATA
1 TTAAAAAATA-AATATATTTTTATTAAATA
* *
3950552 TTAAAAAGATAAATATATTTTTTATAAAATT
1 TTAAAAA-ATAAATATA-TTTTTATTAAATA
3950583 TTAAA
1 TTAAA
3950588 TAAAAATCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
26 14 0.26
27 3 0.06
28 8 0.15
29 4 0.08
30 14 0.26
31 10 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TTAAAAAATAAATATATTTTTATTAAATA
Found at i:3952902 original size:23 final size:23
Alignment explanation
Indices: 3952871--3952931 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 23
3952861 TTGCGTTTAA
3952871 AAAAGTAACATAATTAAAAAAGAT
1 AAAA-TAACATAATTAAAAAAGAT
*
3952895 AAAATAACAT-A-T-AAAAATAT
1 AAAATAACATAATTAAAAAAGAT
*
3952915 AAAATAATAATAATTAA
1 AAAATAA-CATAATTAA
3952932 TAGTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 2 0.06
23 7 0.23
24 5 0.16
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (23 bp):
AAAATAACATAATTAAAAAAGAT
Found at i:3956603 original size:13 final size:13
Alignment explanation
Indices: 3956585--3956650 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 13
3956575 TTTTTAAAAA
3956585 ATATTTATATTTT
1 ATATTTATATTTT
3956598 ATATTTAT-TTTT
1 ATATTTATATTTT
3956610 AAAAAATATTTATATTTT
1 -----ATATTTATATTTT
3956628 ATATTTAT-TTTT
1 ATATTTATATTTT
*
3956640 A-ATATATATTT
1 ATATTTATATTT
3956651 AAATTTAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
11 5 0.11
12 12 0.27
13 16 0.36
17 8 0.18
18 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTT
Found at i:3956609 original size:30 final size:30
Alignment explanation
Indices: 3956570--3956656 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
3956560 ACACGAATTT
3956570 TTTATTTTTTAAAAAATATTTATATTTTATA
1 TTTA-TTTTTAAAAAATATTTATATTTTATA
3956601 TTTATTTTTAAAAAATATTTATATTTTATA
1 TTTATTTTTAAAAAATATTTATATTTTATA
* * *
3956631 TTTATTTTTAATATATATTTAAATTT
1 TTTATTTTTAAAAAATATTTATATTT
3956657 AAATATATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTATTTTTAAAAAATATTTATATTTTATA
Found at i:3956663 original size:18 final size:17
Alignment explanation
Indices: 3956627--3956665 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3956617 ATTTATATTT
* *
3956627 TATATTTATTTTTAATA
1 TATATTTAATTTAAATA
3956644 TATATTTAAATTTAAATA
1 TATATTT-AATTTAAATA
3956662 TATA
1 TATA
3956666 AAATATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTAATTTAAATA
Found at i:3956927 original size:23 final size:26
Alignment explanation
Indices: 3956908--3956958 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3956898 GGATAATATA
3956908 TAAATT-TA-TATATTATTAATAAAT
1 TAAATTATATTATATTATTAATAAAT
* *
3956932 TAAATTATATTATTTTATTAAAAAAT
1 TAAATTATATTATATTATTAATAAAT
3956958 T
1 T
3956959 TTAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAAATTATATTATATTATTAATAAAT
Found at i:3957006 original size:20 final size:21
Alignment explanation
Indices: 3956968--3957006 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3956958 TTTAAATATA
* *
3956968 AATATAAATAATTTTATTTTT
1 AATATAAATAATATCATTTTT
3956989 AATA-AAATAATATCATTT
1 AATATAAATAATATCATTT
3957007 AATTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATAAATAATATCATTTTT
Found at i:3957006 original size:25 final size:26
Alignment explanation
Indices: 3956965--3957017 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3956955 AATTTTAAAT
*
3956965 ATAAATATAAATAATTTTATTT-TTA
1 ATAAATATAAATAATTTAATTTATTA
*
3956990 ATAAA-ATAATATCATTTAATTTATTA
1 ATAAATATAA-ATAATTTAATTTATTA
3957016 AT
1 AT
3957018 CGAGTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAAATATAAATAATTTAATTTATTA
Found at i:3961645 original size:2 final size:2
Alignment explanation
Indices: 3961634--3961666 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3961624 ATAATAACTC
3961634 AT AT -T 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
3961667 GTGTGTGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3962927 original size:16 final size:17
Alignment explanation
Indices: 3962896--3962929 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3962886 AAAGACTAAT
*
3962896 TAAAACAATATTTATAA
1 TAAAAAAATATTTATAA
3962913 TAAAAAAAT-TTTATAA
1 TAAAAAAATATTTATAA
3962929 T
1 T
3962930 TAATTGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAAATATTTATAA
Found at i:3963610 original size:16 final size:17
Alignment explanation
Indices: 3963563--3963616 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
3963553 TTATATTCAT
*
3963563 ATTTAAAATTTTAATAA
1 ATTTAAAATTATAATAA
*
3963580 ATTTAATAATTTATAAAAA
1 ATTTAA-AA-TTATAATAA
3963599 ATTTAAAA-TATAATAA
1 ATTTAAAATTATAATAA
3963615 AT
1 AT
3963617 ATACACAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.28
17 6 0.19
18 4 0.12
19 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATTATAATAA
Found at i:3964148 original size:45 final size:47
Alignment explanation
Indices: 3964067--3964155 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 47
3964057 TGTAATGGAT
3964067 ATAATATTTTTTATAAAAAATTATAATTTAAAAATTTAAAATTATTAA
1 ATAATATTTTTTATAAAAAATTATAA-TTAAAAATTTAAAATTATTAA
3964115 ATAAT-TTTTTTA-AAAATAATTAT-A-TAAATAATTTAAAATTA
1 ATAATATTTTTTATAAAA-AATTATAATTAAA-AATTTAAAATTA
3964156 AGCTTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
44 4 0.10
45 12 0.31
46 5 0.13
47 13 0.33
48 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (47 bp):
ATAATATTTTTTATAAAAAATTATAATTAAAAATTTAAAATTATTAA
Found at i:3965068 original size:4 final size:4
Alignment explanation
Indices: 3965059--3965084 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3965049 TGTTCATAGT
3965059 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
3965085 GCAGAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3967553 original size:2 final size:2
Alignment explanation
Indices: 3967546--3967570 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3967536 AAGATAACTT
3967546 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 T
3967571 TTGAGGACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3967937 original size:2 final size:2
Alignment explanation
Indices: 3967930--3967960 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3967920 GAATCAGCAA
3967930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3967961 ATAGGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3981020 original size:2 final size:2
Alignment explanation
Indices: 3981013--3981055 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3981003 ATTCAGACAA
3981013 AT 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 AT
3981055 A
1 A
3981056 GGTTAAGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3987271 original size:14 final size:14
Alignment explanation
Indices: 3987252--3987281 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3987242 ACATGAATGT
*
3987252 AAATTGTTTGAATA
1 AAATTGTCTGAATA
3987266 AAATTGTCTGAATA
1 AAATTGTCTGAATA
3987280 AA
1 AA
3987282 TGACAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (14 bp):
AAATTGTCTGAATA
Found at i:3988557 original size:175 final size:176
Alignment explanation
Indices: 3988266--3988620 Score: 604
Period size: 175 Copynumber: 2.0 Consensus size: 176
3988256 TAATCTCAAA
* * * *
3988266 TTCACATTGCTATATCTTTAAGTATAGTTAGATGTCTTATGTAGTGCAATCCATAACTCGAAGTT
1 TTCACATTGCTATATCTTCAAGTATAGTCAGATATCTTATGTAGTGCAATCCATAACTCGAAATT
3988331 TATCTCGGATATCTGAGCTCTCTTCCAATAGTCTTTTAATGTTCCTTTCCAAAA-TACTCGTGAA
66 TATCTCGGATATCTGAGCTCTCTTCCAATAGTCTTTTAATGTTCCTTTCCAAAATTACTCGTGAA
* *
3988395 TCTATTTAGTTTGCTTATTGAGAAGGCTATGTCCGATCTTGTACAG
131 TCTATTTAGTTTGCTTACTGAGAAAGCTATGTCCGATCTTGTACAG
* * *
3988441 TTCACATTGCTATATCTTCAGGTATAGTCGGATATCTTATGTAGTGCAGTCCATAACTCGAAATT
1 TTCACATTGCTATATCTTCAAGTATAGTCAGATATCTTATGTAGTGCAATCCATAACTCGAAATT
*
3988506 TATCTCGGATATCTGAGCTCTCTTCCAATGGTCTTTTAATGTTCCTTTCCAAAATTACTCGTGAA
66 TATCTCGGATATCTGAGCTCTCTTCCAATAGTCTTTTAATGTTCCTTTCCAAAATTACTCGTGAA
*
3988571 TCTATTTAGTTTGCTTACTGAGAAAGCTATGTTCGATCTTGTACAG
131 TCTATTTAGTTTGCTTACTGAGAAAGCTATGTCCGATCTTGTACAG
3988617 TTCA
1 TTCA
3988621 TCAGATACAT
Statistics
Matches: 168, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
175 111 0.66
176 57 0.34
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (176 bp):
TTCACATTGCTATATCTTCAAGTATAGTCAGATATCTTATGTAGTGCAATCCATAACTCGAAATT
TATCTCGGATATCTGAGCTCTCTTCCAATAGTCTTTTAATGTTCCTTTCCAAAATTACTCGTGAA
TCTATTTAGTTTGCTTACTGAGAAAGCTATGTCCGATCTTGTACAG
Found at i:3992023 original size:8 final size:8
Alignment explanation
Indices: 3992010--3992055 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
3992000 TGTTTATGTA
3992010 TTATATAT
1 TTATATAT
3992018 TTATATA-
1 TTATATAT
*
3992025 TGATA-AT
1 TTATATAT
3992032 TTATATAT
1 TTATATAT
*
3992040 TAATATAT
1 TTATATAT
*
3992048 ATATATAT
1 TTATATAT
3992056 ATTTCATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
6 1 0.03
7 8 0.26
8 22 0.71
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (8 bp):
TTATATAT
Found at i:3992043 original size:12 final size:13
Alignment explanation
Indices: 3992011--3992064 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 13
3992001 GTTTATGTAT
3992011 TATAT-ATTTATA
1 TATATAATTTATA
3992023 TATGATAATTTATA
1 TAT-ATAATTTATA
*
3992037 TAT-TAATATATA
1 TATATAATTTATA
3992049 TATATATATTTCATA
1 TATATA-ATTT-ATA
3992064 T
1 T
3992065 TTACATACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 14 0.40
13 4 0.11
14 13 0.37
15 4 0.11
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (13 bp):
TATATAATTTATA
Found at i:3993886 original size:17 final size:18
Alignment explanation
Indices: 3993864--3993903 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
3993854 TTTTTATATT
3993864 TATATT-TAAAAATTTTA
1 TATATTATAAAAATTTTA
3993881 TATATTTATAAAAATTTTA
1 TATA-TTATAAAAATTTTA
3993900 -ATAT
1 TATAT
3993904 GTAATAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATAAAAATTTTA
Found at i:3993910 original size:19 final size:19
Alignment explanation
Indices: 3993870--3993910 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3993860 TATTTATATT
*
3993870 TAAAAATTTTATATATTTA
1 TAAAAATTTTATATATTAA
3993889 TAAAAATTTTA-ATATGTAA
1 TAAAAATTTTATATAT-TAA
3993908 TAA
1 TAA
3993911 TTCATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAAAATTTTATATATTAA
Found at i:4004489 original size:16 final size:16
Alignment explanation
Indices: 4004468--4004518 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
4004458 GAAGTGAAAC
4004468 AAACAGAGCAAAGAGA
1 AAACAGAGCAAAGAGA
*
4004484 AAACAGAGCAAACAAGA
1 AAACAGAGCAAA-GAGA
* * *
4004501 AAAAAGAGAAAAGCGA
1 AAACAGAGCAAAGAGA
4004517 AA
1 AA
4004519 GAGAAGAGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.67, C:0.12, G:0.22, T:0.00
Consensus pattern (16 bp):
AAACAGAGCAAAGAGA
Found at i:4004995 original size:22 final size:23
Alignment explanation
Indices: 4004970--4005013 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4004960 AAATTTATTC
*
4004970 ATTTAATAAAATATTT-TATTAG
1 ATTTAATAAAAAATTTATATTAG
4004992 ATTTAATAAAAAATTTATATTA
1 ATTTAATAAAAAATTTATATTA
4005014 ATTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAATAAAAAATTTATATTAG
Found at i:4005012 original size:23 final size:22
Alignment explanation
Indices: 4004958--4005013 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4004948 TTATAATTTT
*
4004958 AAAAA-TTTATT-CATTTAATA
1 AAAAATTTTATTAGATTTAATA
*
4004978 AAATATTTTATTAGATTTAATA
1 AAAAATTTTATTAGATTTAATA
4005000 AAAAATTTATATTA
1 AAAAATTT-TATTA
4005014 ATTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 15 0.50
23 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAAATTTTATTAGATTTAATA
Found at i:4009507 original size:17 final size:16
Alignment explanation
Indices: 4009484--4009524 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4009474 TAAATATTAA
4009484 TTTAATTATTTTAAAT
1 TTTAATTATTTTAAAT
*
4009500 TGTTAATTA-TTTATAT
1 T-TTAATTATTTTAAAT
4009516 TTTAATTAT
1 TTTAATTAT
4009525 AATAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAATTATTTTAAAT
Found at i:4009508 original size:37 final size:39
Alignment explanation
Indices: 4009449--4009527 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 39
4009439 TATATATAAA
4009449 AATTATTTACAAATTATAAATTATGTAAATATTAATT-T
1 AATTATTTACAAATTATAAATTATGTAAATATTAATTAT
* * * * * *
4009487 AATTATTT-TAAATTGTTAATTATTTATATTTTAATTAT
1 AATTATTTACAAATTATAAATTATGTAAATATTAATTAT
4009525 AAT
1 AAT
4009528 AATATTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (39 bp):
AATTATTTACAAATTATAAATTATGTAAATATTAATTAT
Found at i:4018469 original size:2 final size:2
Alignment explanation
Indices: 4018462--4018494 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4018452 TTCTTAATTA
*
4018462 AT AT AT AT A- AT AA 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
4018495 CCCCTTGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4020840 original size:71 final size:72
Alignment explanation
Indices: 4020737--4020870 Score: 170
Period size: 71 Copynumber: 1.9 Consensus size: 72
4020727 TTTATAAATA
* *
4020737 TAATATAAATTATTAAATATATTATTTTATTATGAAA-AAA-ATAATTAAACTC-AAATAATTAT
1 TAATATAAATTATTAAATATATTACTTAATTAT-AAATAAATATAATTAAACTCGAAA-AATTAT
4020799 ACATATATT
64 ACATATATT
*
4020808 TAATAT-AATTAATATAAA-ATATTACTTAATTATAAATAAATTTAATTAAACTCGAAAAATTAT
1 TAATATAAATT-AT-TAAATATATTACTTAATTATAAATAAATATAATTAAACTCGAAAAATTAT
4020871 TTTTAATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
70 7 0.13
71 24 0.44
72 21 0.38
73 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (72 bp):
TAATATAAATTATTAAATATATTACTTAATTATAAATAAATATAATTAAACTCGAAAAATTATAC
ATATATT
Found at i:4026344 original size:92 final size:92
Alignment explanation
Indices: 4026187--4026369 Score: 366
Period size: 92 Copynumber: 2.0 Consensus size: 92
4026177 TTTTTCCTTC
4026187 TATTACTAAAACTTTTTAAAAGTTGTTAATATCTCGTCTGCGTGACATGTCAGGGTATAGCAAAA
1 TATTACTAAAACTTTTTAAAAGTTGTTAATATCTCGTCTGCGTGACATGTCAGGGTATAGCAAAA
4026252 AGTTTGCACCAGAATTGTGTCAGTAGT
66 AGTTTGCACCAGAATTGTGTCAGTAGT
4026279 TATTACTAAAACTTTTTAAAAGTTGTTAATATCTCGTCTGCGTGACATGTCAGGGTATAGCAAAA
1 TATTACTAAAACTTTTTAAAAGTTGTTAATATCTCGTCTGCGTGACATGTCAGGGTATAGCAAAA
4026344 AGTTTGCACCAGAATTGTGTCAGTAG
66 AGTTTGCACCAGAATTGTGTCAGTAG
4026370 AATGGAACCG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (92 bp):
TATTACTAAAACTTTTTAAAAGTTGTTAATATCTCGTCTGCGTGACATGTCAGGGTATAGCAAAA
AGTTTGCACCAGAATTGTGTCAGTAGT
Found at i:4028483 original size:25 final size:26
Alignment explanation
Indices: 4028455--4028505 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4028445 CATTCCTTTG
* *
4028455 TCTTCTC-TTTCTTTTTTTTTTTTTT
1 TCTTCTCTTTTCTTTTATTCTTTTTT
*
4028480 TCTTTTCTTTTCTTTTATTCTTTTTT
1 TCTTCTCTTTTCTTTTATTCTTTTTT
4028506 CTCTCTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (26 bp):
TCTTCTCTTTTCTTTTATTCTTTTTT
Found at i:4028506 original size:25 final size:27
Alignment explanation
Indices: 4028457--4028507 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
4028447 TTCCTTTGTC
* *
4028457 TTCTCTTTCTTTTTTTTTTTTTTTCTT
1 TTCTCTTTCTTTTTATTCTTTTTTCTT
4028484 TTCT-TTTC-TTTTATTCTTTTTTCT
1 TTCTCTTTCTTTTTATTCTTTTTTCT
4028508 CTCTGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 4 0.18
27 4 0.18
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (27 bp):
TTCTCTTTCTTTTTATTCTTTTTTCTT
Found at i:4034516 original size:11 final size:11
Alignment explanation
Indices: 4034500--4034551 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
4034490 AATTATAATT
4034500 ATATAAATATA
1 ATATAAATATA
4034511 ATATAAATA-A
1 ATATAAATATA
* *
4034521 A-ATAATTAAA
1 ATATAAATATA
4034531 ATATAAA-ATA
1 ATATAAATATA
4034541 ATATAAATATA
1 ATATAAATATA
4034552 TATTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 6 0.17
10 13 0.37
11 16 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:4034536 original size:16 final size:16
Alignment explanation
Indices: 4034500--4034553 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
4034490 AATTATAATT
*
4034500 ATATAAATATAA-TATA
1 ATATAAA-ATAATTAAA
4034516 A-ATAAAATAATTAAA
1 ATATAAAATAATTAAA
4034531 ATATAAAATAATATAAA
1 ATATAAAATAAT-TAAA
4034548 TATATA
1 -ATATA
4034554 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 11 0.33
17 4 0.12
18 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAATAATTAAA
Found at i:4034592 original size:32 final size:34
Alignment explanation
Indices: 4034498--4034618 Score: 87
Period size: 32 Copynumber: 3.7 Consensus size: 34
4034488 GTAATTATAA
* * * *
4034498 TTATATAAATATAATATAAATAAAATAATTAAAA-
1 TTATATAAATA-AAAATATATTAAATTATTAAAAT
*
4034532 -TATA-AAATAATATAA-ATA-TATATT-TTAAAAT
1 TTATATAAATAA-A-AATATATTAAATTATTAAAAT
*
4034563 TTATAT-AATAAAAAT-TATTAAATTATTAAATT
1 TTATATAAATAAAAATATATTAAATTATTAAAAT
* *
4034595 TTATGTAAATATAAATATATTAAA
1 TTATATAAATAAAAATATATTAAA
4034619 CACCGTACGG
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
30 10 0.15
31 10 0.15
32 28 0.41
33 13 0.19
34 7 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (34 bp):
TTATATAAATAAAAATATATTAAATTATTAAAAT
Found at i:4035628 original size:23 final size:24
Alignment explanation
Indices: 4035598--4035654 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
4035588 AAAGTAGCCA
4035598 TGGCTGTTGCCTATC-GAAAATCT
1 TGGCTGTTGCCTATCAGAAAATCT
*
4035621 TGGCTGTTGCCTATCAGCAAATCT
1 TGGCTGTTGCCTATCAGAAAATCT
4035645 TGGCTGTTGC
1 TGGCTGTTGC
4035655 AGCAATGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (24 bp):
TGGCTGTTGCCTATCAGAAAATCT
Found at i:4038362 original size:32 final size:30
Alignment explanation
Indices: 4038296--4038375 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 30
4038286 TTATTTAAAA
* *
4038296 TTAAATTTAAATTAAA--AAAATTTTAATT
1 TTAAATTTAAATTAAATTTAAACTTTAATT
4038324 TT--ATTTAAATTAAACTTTAAACTTTAATTT
1 TTAAATTTAAATTAAA-TTTAAACTTTAA-TT
*
4038354 TTAAATTTAACTTAAATTTAAA
1 TTAAATTTAAATTAAATTTAAA
4038376 TATTATAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 12 0.28
28 2 0.05
29 8 0.19
30 4 0.09
31 6 0.14
32 11 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAATTTAAATTAAATTTAAACTTTAATT
Found at i:4038365 original size:19 final size:21
Alignment explanation
Indices: 4038333--4038372 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
4038323 TTTATTTAAA
*
4038333 TTAAACTTTAAACTTTAATTT
1 TTAAACTTTAAACTTAAATTT
4038354 TTAAA-TTT-AACTTAAATTT
1 TTAAACTTTAAACTTAAATTT
4038373 AAATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAACTTTAAACTTAAATTT
Found at i:4038374 original size:6 final size:6
Alignment explanation
Indices: 4038288--4038376 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
4038278 TTTGATTTTT
* * * *
4038288 ATTTAA AATTAA ATTTAA A-TTAA A--AAA ATTTTA ATTT-T ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
4038332 A-TTAA ACTTTAA ACTTTAA TTTTTAA ATTT-A ACTTAA ATTTAA AT
1 ATTTAA A-TTTAA A-TTTAA -ATTTAA ATTTAA ATTTAA ATTTAA AT
4038377 ATTATAATAT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.05
5 18 0.28
6 28 0.43
7 16 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:4042432 original size:14 final size:14
Alignment explanation
Indices: 4042413--4042439 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4042403 GACAATAGGT
4042413 TAAAACTACCATGA
1 TAAAACTACCATGA
4042427 TAAAACTACCATG
1 TAAAACTACCATG
4042440 CTTTTCTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (14 bp):
TAAAACTACCATGA
Found at i:4043562 original size:2 final size:2
Alignment explanation
Indices: 4043555--4043581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4043545 ATTCACAACA
4043555 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4043582 GATGTAGCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4045493 original size:40 final size:40
Alignment explanation
Indices: 4045437--4045516 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
4045427 CCTGAGTTAT
*
4045437 TCTCCCATCAATTTCATTTTACATTTAGCAAAGTGTCCCA
1 TCTCCCATCAACTTCATTTTACATTTAGCAAAGTGTCCCA
4045477 TCTCCCATCAACTTCATTTTACATTTAGCAAAGTGTCCCA
1 TCTCCCATCAACTTCATTTTACATTTAGCAAAGTGTCCCA
4045517 AAGGATTACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.29, G:0.07, T:0.36
Consensus pattern (40 bp):
TCTCCCATCAACTTCATTTTACATTTAGCAAAGTGTCCCA
Found at i:4051484 original size:15 final size:15
Alignment explanation
Indices: 4051457--4051504 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
4051447 TTATTTTTTA
*
4051457 AAAAAATTTTAAATT
1 AAAAAATTATAAATT
** *
4051472 AAAATTTTATAAATA
1 AAAAAATTATAAATT
4051487 AAAAAATTAT-AATT
1 AAAAAATTATAAATT
4051501 AAAA
1 AAAA
4051505 GAGCTACACT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATTATAAATT
Done.