Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 7 of 344
Found at i:2593872 original size:30 final size:28
Alignment explanation
Indices: 2593837--2593918 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
2593827 ATAATTTATG
2593837 AAATTTTAAATTAATAATAAAATTAT-ATTTT
1 AAATTTTAAA--AATAATAAAATT-TGA-TTT
*
2593868 AATTTTTTAAAAATAATAAAATTTGATTT
1 AA-ATTTTAAAAATAATAAAATTTGATTT
*
2593897 AAATTTTAAAAAAATATAAAAT
1 AAATTTTAAAAATA-ATAAAAT
2593919 ATAAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 10 0.22
29 13 0.29
30 13 0.29
31 2 0.04
32 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTTTAAAAATAATAAAATTTGATTT
Found at i:2593931 original size:8 final size:7
Alignment explanation
Indices: 2593907--2593941 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2593897 AAATTTTAAA
2593907 AAAATAT
1 AAAATAT
2593914 AAAATAT
1 AAAATAT
2593921 AAAATATT
1 AAAATA-T
2593929 AAAATAAT
1 AAAAT-AT
2593937 AAAAT
1 AAAAT
2593942 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.50
8 12 0.46
9 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:2593931 original size:25 final size:24
Alignment explanation
Indices: 2593897--2593945 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2593887 AATTTGATTT
*
2593897 AAATTTTAAAAAAATATAAAATATA
1 AAATATTAAAAAAATA-AAAATATA
* *
2593922 AAATATTAAAATAATAAAATTATA
1 AAATATTAAAAAAATAAAAATATA
2593946 TATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATATTAAAAAAATAAAAATATA
Found at i:2593938 original size:16 final size:14
Alignment explanation
Indices: 2593907--2593941 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2593897 AAATTTTAAA
2593907 AAAATATAAAATAT
1 AAAATATAAAATAT
2593921 AAAATATTAAAATAAT
1 AAAATA-TAAAAT-AT
2593937 AAAAT
1 AAAAT
2593942 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 6 0.32
16 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATAAAATAT
Found at i:2597036 original size:19 final size:18
Alignment explanation
Indices: 2597008--2597043 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2596998 ATGCTTCACA
2597008 TTAAATCTAAACTAACAT
1 TTAAATCTAAACTAACAT
*
2597026 TTAACATCTAACCTAACA
1 TTAA-ATCTAAACTAACA
2597044 ATCAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATCTAAACTAACAT
Found at i:2602469 original size:33 final size:33
Alignment explanation
Indices: 2602432--2602494 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2602422 TCGCTGCATT
* *
2602432 GGATTAGAGGCGTATTGGATTAGAGGTGTATTG
1 GGATTAGAGGCGTATTGAATTAGAGATGTATTG
*
2602465 GGATTAGAGGTGTATTGAATTAGAGATGTA
1 GGATTAGAGGCGTATTGAATTAGAGATGTA
2602495 ATAGCTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (33 bp):
GGATTAGAGGCGTATTGAATTAGAGATGTATTG
Found at i:2602470 original size:17 final size:16
Alignment explanation
Indices: 2602429--2602494 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
2602419 GGTTCGCTGC
*
2602429 ATTGGATTAGAGGCGT
1 ATTGGATTAGAGGTGT
2602445 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
2602461 ATTGGGATTAGAGGTGT
1 ATT-GGATTAGAGGTGT
* *
2602478 ATTGAATTAGAGATGT
1 ATTGGATTAGAGGTGT
2602494 A
1 A
2602495 ATAGCTAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
16 30 0.65
17 16 0.35
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (16 bp):
ATTGGATTAGAGGTGT
Found at i:2603054 original size:119 final size:120
Alignment explanation
Indices: 2602713--2603656 Score: 1817
Period size: 119 Copynumber: 7.9 Consensus size: 120
2602703 ATCATATTTA
*
2602713 AACATAATTATTATTAAATATATTTTAATTACAA-TATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTA-AACTATATAATTTAAAAAAATTCTTAATAATTA
*
2602777 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2602833 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2602898 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2602953 AACATAATTATTATTAAATATATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603017 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603072 AACATAATTATTATTAAATATATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603136 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603191 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603256 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603311 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603375 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603430 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603495 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603550 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
2603614 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
2603657 TGATGCTAGT
Statistics
Matches: 818, Mismatches: 3, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
119 421 0.51
120 397 0.49
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:2603228 original size:239 final size:239
Alignment explanation
Indices: 2602713--2603656 Score: 1813
Period size: 239 Copynumber: 3.9 Consensus size: 239
2602703 ATCATATTTA
*
2602713 AACATAATTATTATTAAATATATTTTAATTACAA-TATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTA-AACTATATAATTTAAAAAAATTCTTAATAATTA
*
2602777 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
2602842 ATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTAT
130 ATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAATATTCTTAT
2602907 ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
194 ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2602953 AACATAATTATTATTAAATATATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603017 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
2603082 TTATTAAATATATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATA
131 TTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAATATTCTTATA
2603146 TTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
195 TTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603191 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603256 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
2603321 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
131 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
2603386 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
196 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2603430 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
2603495 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
*
2603560 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATGTTCTTATAT
131 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
2603625 TAATTTACTCAAATCATAATATATGATACTGT
196 TAATTTACTCAAATCATAATATATGATACTGT
2603657 TGATGCTAGT
Statistics
Matches: 698, Mismatches: 3, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
238 121 0.17
239 534 0.77
240 43 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (239 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:2603371 original size:358 final size:358
Alignment explanation
Indices: 2602713--2603656 Score: 1811
Period size: 358 Copynumber: 2.6 Consensus size: 358
2602703 ATCATATTTA
* *
2602713 AACATAATTATTATTAAATATATTTTAATTACAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTA-ACTATATAATTTAAAAAAATTCTTAATAATTAA
*
2602778 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
65 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
2602843 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATA
130 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATA
2602908 TTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATA
195 TTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATA
2602973 TATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATATTAATTTACTC
260 TATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATATTAATTTACTC
2603038 AAATCATAATATATGATACTGTAAAATATAAATT
325 AAATCATAATATATGATACTGTAAAATATAAATT
2603072 AACATAATTATTATTAAATATATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAAT
1 AACATAATTATTATTAAATATATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAAT
2603137 ATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTAT
66 ATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTAT
2603202 TATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATAT
131 TATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATAT
2603267 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATAT
196 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATAT
2603332 ATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAATATTCTTATATTAATTTACTC
261 ATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATATTAATTTACTC
2603396 AAATCATAATATATGATACTGTAAAATATAAATT
325 AAATCATAATATATGATACTGTAAAATATAAATT
2603430 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATT-AACTATATAATTTAAAAAAATTCTTAATAATTAA
2603495 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
65 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
*
2603560 TTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAATGTTCTTATA
130 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATA
2603624 TTAATTTACTCAAATCATAATATATGATACTGT
195 TTAATTTACTCAAATCATAATATATGATACTGT
2603657 TGATGCTAGT
Statistics
Matches: 579, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
358 402 0.69
359 177 0.31
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (358 bp):
AACATAATTATTATTAAATATATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAAT
ATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTAT
TATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATAT
TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATAT
ATTTTAATTAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATATTAATTTACTCA
AATCATAATATATGATACTGTAAAATATAAATT
Found at i:2617392 original size:31 final size:31
Alignment explanation
Indices: 2617357--2617433 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
2617347 ATGGACTTAG
*
2617357 TTGTCAAGTTTAAGGACTTATGTGAACCTAC
1 TTGTCAAGTTCAAGGACTTATGTGAACCTAC
2617388 TTGTCAAGTTCAAGGACTTATGTGAACCTAC
1 TTGTCAAGTTCAAGGACTTATGTGAACCTAC
2617419 TTGTCAAGTTCAAGG
1 TTGTCAAGTTCAAGG
2617434 GCCAAAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (31 bp):
TTGTCAAGTTCAAGGACTTATGTGAACCTAC
Found at i:2621122 original size:27 final size:27
Alignment explanation
Indices: 2621068--2621119 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2621058 AAGATAGCTT
* * *
2621068 TTTTTTAATAATATATTCAGATTATTA
1 TTTTTAAATAATATATTAAAATTATTA
2621095 TTTTTAAATAATAT-TTAAAATTATT
1 TTTTTAAATAATATATTAAAATTATT
2621120 TATAATTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTAAATAATATATTAAAATTATTA
Found at i:2623617 original size:20 final size:21
Alignment explanation
Indices: 2623592--2623634 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2623582 GTTTGTAAGA
**
2623592 TTAAAAAGCAAATTAATT-TT
1 TTAAAAAAAAAATTAATTATT
2623612 TTAAAAAAAAAATTAATTATT
1 TTAAAAAAAAAATTAATTATT
2623633 TT
1 TT
2623635 TATCATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAAAAAAATTAATTATT
Found at i:2624142 original size:5 final size:5
Alignment explanation
Indices: 2624132--2624157 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2624122 AAAATTTTTA
2624132 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2624158 TCATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2628333 original size:25 final size:29
Alignment explanation
Indices: 2628284--2628355 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 29
2628274 TGTTGAGTTG
2628284 TATTTATTTTAATATTATTTAAATAAAAA
1 TATTTATTTTAATATTATTTAAATAAAAA
2628313 TATTT-TTTTAAT-TT-TTT-AAT--AAA
1 TATTTATTTTAATATTATTTAAATAAAAA
*
2628336 TATCTATTTTAATATT-TTTA
1 TATTTATTTTAATATTATTTA
2628356 GTAATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 7 0.18
24 7 0.18
25 8 0.21
26 3 0.08
27 2 0.05
28 7 0.18
29 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTTATTTTAATATTATTTAAATAAAAA
Found at i:2628345 original size:26 final size:28
Alignment explanation
Indices: 2628284--2628355 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 28
2628274 TGTTGAGTTG
2628284 TATTTATTTTAATATTATTTAAATAAAAA
1 TATTT-TTTTAATATTATTTAAATAAAAA
2628313 TATTTTTTTAAT-TT-TTT-AAT--AAA
1 TATTTTTTTAATATTATTTAAATAAAAA
*
2628336 TATCTATTTTAATATT-TTTA
1 TAT-TTTTTTAATATTATTTA
2628356 GTAATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 6 0.15
24 8 0.21
25 8 0.21
26 3 0.08
27 2 0.05
28 7 0.18
29 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTTTTTAATATTATTTAAATAAAAA
Found at i:2635611 original size:14 final size:14
Alignment explanation
Indices: 2635572--2635613 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2635562 CAAGTTTTTA
2635572 GTTTAGGGTTTGA-
1 GTTTAGGGTTTGAG
*
2635585 GTTTAAGGTTTTGAG
1 GTTT-AGGGTTTGAG
2635600 GTTTAGGGTTTGAG
1 GTTTAGGGTTTGAG
2635614 ATTCTGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTGAG
Found at i:2635936 original size:20 final size:20
Alignment explanation
Indices: 2635891--2635938 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2635881 AAATTCTATT
*
2635891 TGTATTTTATAATAATTAAT
1 TGTATTTTATAATAATTAAA
*
2635911 TCTATTTT-TAATAATTTAAA
1 TGTATTTTATAATAA-TTAAA
2635931 TGTATTTT
1 TGTATTTT
2635939 CTTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TGTATTTTATAATAATTAAA
Found at i:2636231 original size:3 final size:3
Alignment explanation
Indices: 2636223--2636261 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2636213 AAATTTTTAA
2636223 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
2636262 AAGAAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2636997 original size:31 final size:33
Alignment explanation
Indices: 2636935--2636997 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
2636925 TACTATAAAA
* *
2636935 ATTTATTATTAAACATTTATAAATTTTAATATAT
1 ATTTATTATTAAACA-TTATAAATATAAATATAT
*
2636969 ATTTATTATTAAA-A-TATGAATATAAATAT
1 ATTTATTATTAAACATTATAAATATAAATAT
2636998 TTTCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 12 0.46
33 1 0.04
34 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTTATTATTAAACATTATAAATATAAATATAT
Found at i:2637031 original size:12 final size:11
Alignment explanation
Indices: 2636972--2637096 Score: 55
Period size: 11 Copynumber: 11.2 Consensus size: 11
2636962 AATATATATT
2636972 TATTATTAAAA
1 TATTATTAAAA
* *
2636983 TATGAATATAAA
1 TATTATTA-AAA
2636995 TATT-TTCAAAA
1 TATTATT-AAAA
2637006 -ATATATTAAGAA
1 TAT-TATTAA-AA
2637018 TATTATTTAAAA
1 TATTA-TTAAAA
* *
2637030 TA-TAATAATAT
1 TATTATTAA-AA
* *
2637041 TATTTTTAAATTT
1 TATTATTAAA--A
2637054 TATTATTAAAA
1 TATTATTAAAA
** *
2637065 TAAAATTATAA
1 TATTATTAAAA
2637076 TATTA--AAAA
1 TATTATTAAAA
2637085 -ATTATTAAAA
1 TATTATTAAAA
2637095 TA
1 TA
2637097 ATAGATTATA
Statistics
Matches: 84, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 9 0.11
11 31 0.37
12 21 0.25
13 16 0.19
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:2637044 original size:23 final size:22
Alignment explanation
Indices: 2636972--2637050 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
2636962 AATATATATT
*
2636972 TATTATTAAAATATGAAT-ATAAA
1 TATTTTTAAAATAT-AATAAT-AA
* * *
2636995 TATTTTCAAAAATATATTAAGAA
1 TATTTT-TAAAATATAATAATAA
*
2637018 TATTATTTAAAATATAATAATAT
1 TATT-TTTAAAATATAATAATAA
2637041 TATTTTTAAA
1 TATTTTTAAA
2637051 TTTTATTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 6 0.13
23 29 0.64
24 10 0.22
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTTAAAATATAATAATAA
Found at i:2637089 original size:30 final size:32
Alignment explanation
Indices: 2637055--2637114 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
2637045 TTTAAATTTT
2637055 ATTATTAAAATAA-A-ATTATAATATTAAAAA
1 ATTATTAAAATAATAGATTATAATATTAAAAA
*
2637085 ATTATTAAAATAATAGATTATATTATTAAA
1 ATTATTAAAATAATAGATTATAATATTAAA
2637115 TATAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.48
31 1 0.04
32 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTATTAAAATAATAGATTATAATATTAAAAA
Found at i:2647022 original size:12 final size:12
Alignment explanation
Indices: 2647007--2647032 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2646997 GCAAACATTA
2647007 ATGACCAAATTT
1 ATGACCAAATTT
2647019 ATGACCAAATTT
1 ATGACCAAATTT
2647031 AT
1 AT
2647033 AATTAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATGACCAAATTT
Found at i:2647250 original size:17 final size:17
Alignment explanation
Indices: 2647230--2647269 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2647220 AAAAAATCCT
2647230 AAAATTAAAATAATTTA
1 AAAATTAAAATAATTTA
* *
2647247 AAAATTAAATTTATTTA
1 AAAATTAAAATAATTTA
2647264 ATAAAT
1 A-AAAT
2647270 ATACTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTAAAATAATTTA
Found at i:2648803 original size:13 final size:13
Alignment explanation
Indices: 2648787--2648817 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2648777 CCTTCTCCTT
2648787 CCCTTTCCCCTAC
1 CCCTTTCCCCTAC
*
2648800 CCCTTTCCCTTAC
1 CCCTTTCCCCTAC
2648813 CCCTT
1 CCCTT
2648818 CCCTTTCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.58, G:0.00, T:0.35
Consensus pattern (13 bp):
CCCTTTCCCCTAC
Found at i:2648803 original size:31 final size:31
Alignment explanation
Indices: 2648768--2648826 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2648758 CCATTCTTCT
*
2648768 CCCCTTTCCCCTT-CTCCTTCCCTTTCCCCTA
1 CCCCTTT-CCCTTACCCCTTCCCTTTCCCCTA
2648799 CCCCTTTCCCTTACCCCTTCCCTTTCCC
1 CCCCTTTCCCTTACCCCTTCCCTTTCCC
2648827 GTTTTGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.37
Consensus pattern (31 bp):
CCCCTTTCCCTTACCCCTTCCCTTTCCCCTA
Found at i:2648819 original size:12 final size:12
Alignment explanation
Indices: 2648769--2648822 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
2648759 CATTCTTCTC
*
2648769 CCCTTTCCCCTT
1 CCCTTACCCCTT
*
2648781 CTCCTT-CCCTTT
1 C-CCTTACCCCTT
*
2648793 CCCCTACCCCTTT
1 CCCTTACCCC-TT
2648806 CCCTTACCCCTT
1 CCCTTACCCCTT
2648818 CCCTT
1 CCCTT
2648823 TCCCGTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 15 0.43
ACGTcount: A:0.04, C:0.57, G:0.00, T:0.39
Consensus pattern (12 bp):
CCCTTACCCCTT
Found at i:2648823 original size:18 final size:18
Alignment explanation
Indices: 2648769--2648826 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
2648759 CATTCTTCTC
2648769 CCCTTTCCCCTTCTCC-TT
1 CCCTTTCCCCTTC-CCTTT
*
2648787 CCCTTTCCCCTACCCCTTT
1 CCCTTTCCCCT-TCCCTTT
*
2648806 CCCTTACCCCTTCCCTTT
1 CCCTTTCCCCTTCCCTTT
2648824 CCC
1 CCC
2648827 GTTTTGAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (18 bp):
CCCTTTCCCCTTCCCTTT
Found at i:2651681 original size:22 final size:22
Alignment explanation
Indices: 2651625--2651681 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
2651615 ATATAAGTAT
2651625 ATATATATTATA-AGAATAATGC
1 ATATATA-TATACAGAATAATGC
* *
2651647 ATGTATGTCATACA-AATATATGC
1 ATATATAT-ATACAGAATA-ATGC
2651670 ATATATATATAC
1 ATATATATATAC
2651682 GTACCAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 11 0.39
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
ATATATATATACAGAATAATGC
Found at i:2651773 original size:3 final size:3
Alignment explanation
Indices: 2651724--2651761 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2651714 AATAGGAAGA
* *
2651724 AAT AAT AAT AAT GAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2651762 CCTCAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2653903 original size:14 final size:15
Alignment explanation
Indices: 2653881--2653957 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2653871 CAATCAAACA
2653881 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2653895 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2653910 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2653930 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2653944 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
2653958 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2653922 original size:20 final size:20
Alignment explanation
Indices: 2653897--2653936 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2653887 AATATTTTCC
*
2653897 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2653917 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2653937 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2653942 original size:34 final size:35
Alignment explanation
Indices: 2653885--2653951 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2653875 CAAACACCAG
*
2653885 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2653920 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2653952 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2653958 original size:14 final size:14
Alignment explanation
Indices: 2653920--2653959 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2653910 ACAGAAAAGT
*
2653920 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
2653934 AAATCATTTTACGG
1 AAAACATTTTACAG
2653948 AAAACATTTTAC
1 AAAACATTTTAC
2653960 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:2655046 original size:3 final size:3
Alignment explanation
Indices: 2655038--2655077 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
2655028 TGTTTTTCTT
*
2655038 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2655078 TAATGTATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2656383 original size:16 final size:15
Alignment explanation
Indices: 2656364--2656403 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2656354 AATTTTCAAT
2656364 AAATAAAAAATATATA
1 AAATAAAAAATAT-TA
*
2656380 AAATAATTAAATATTA
1 AAATAA-AAAATATTA
2656396 AAATAAAA
1 AAATAAAA
2656404 TGATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:2656593 original size:28 final size:28
Alignment explanation
Indices: 2656562--2656618 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2656552 AACCCGGCCC
*
2656562 ATTATTACCTCTGCATCAAATTAAGATT
1 ATTATCACCTCTGCATCAAATTAAGATT
2656590 ATTATCACCTCTGCATCAAATTAAGATT
1 ATTATCACCTCTGCATCAAATTAAGATT
2656618 A
1 A
2656619 GGACTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (28 bp):
ATTATCACCTCTGCATCAAATTAAGATT
Found at i:2660427 original size:23 final size:23
Alignment explanation
Indices: 2660393--2660438 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2660383 ACTAGGAGTC
*
2660393 AGTTTTATTATTAAAAATTGGTT
1 AGTTTTACTATTAAAAATTGGTT
2660416 AGTTTTACTATTAAAAATTGGTT
1 AGTTTTACTATTAAAAATTGGTT
2660439 CTCATACACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (23 bp):
AGTTTTACTATTAAAAATTGGTT
Found at i:2662467 original size:18 final size:20
Alignment explanation
Indices: 2662430--2662472 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2662420 GATTGGAAAA
2662430 TGAAATATACTTGTTTTGGTT
1 TGAAATATACTTGTTTTGG-T
2662451 TGAAATA-A-TTG-TTTGGT
1 TGAAATATACTTGTTTTGGT
2662468 TGAAA
1 TGAAA
2662473 ATTTTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 3 0.14
20 1 0.05
21 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (20 bp):
TGAAATATACTTGTTTTGGT
Found at i:2662474 original size:18 final size:20
Alignment explanation
Indices: 2662430--2662474 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
2662420 GATTGGAAAA
*
2662430 TGAAATATACTTGTTTTGGTT
1 TGAAA-ATAATTGTTTTGGTT
2662451 TG-AAATAATTG-TTTGG-T
1 TGAAAATAATTGTTTTGGTT
2662468 TGAAAAT
1 TGAAAAT
2662475 TTTTAGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 6 0.27
20 2 0.09
21 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (20 bp):
TGAAAATAATTGTTTTGGTT
Found at i:2662732 original size:20 final size:20
Alignment explanation
Indices: 2662707--2662758 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2662697 CAGCTGCAGG
* * *
2662707 ACACGGGCATGTTCTAGGCC
1 ACACGGGCATGTCCCAAGCC
*
2662727 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCATGTCCCAAGCC
2662747 ACACGGGCATGT
1 ACACGGGCATGT
2662759 GCCCCTATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (20 bp):
ACACGGGCATGTCCCAAGCC
Found at i:2663592 original size:28 final size:29
Alignment explanation
Indices: 2663539--2663606 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
2663529 TTTTATTTTA
2663539 TTATTAAAATTTAAATATTAAATAAT-TGT
1 TTATTAAAA-TTAAATATTAAATAATATGT
*
2663568 TTATTAAAATTAAA-ATTAATTTAATGATGT
1 TTATTAAAATTAAATATTAA-ATAAT-ATGT
2663598 TT-TTAAAAT
1 TTATTAAAAT
2663607 CATTCAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 5 0.14
28 9 0.26
29 16 0.46
30 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATTAAAATTAAATATTAAATAATATGT
Found at i:2665935 original size:26 final size:26
Alignment explanation
Indices: 2665896--2665957 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
2665886 GTAACTTATA
2665896 ATTATTATAAATATGATTATAATTAAT
1 ATTA-TATAAATATGATTATAATTAAT
*
2665923 ATTATATACATATGATTATAATTAAT
1 ATTATATAAATATGATTATAATTAAT
2665949 ATTATATAA
1 ATTATATAA
2665958 TTTTAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (26 bp):
ATTATATAAATATGATTATAATTAAT
Found at i:2670149 original size:23 final size:23
Alignment explanation
Indices: 2670123--2670166 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2670113 AATATTAGTA
2670123 AGTAAAG-AAAAAGGAATAATAAT
1 AGTAAAGTAAAAA-GAATAATAAT
* *
2670146 AGTATAGTAAAAATAATAATA
1 AGTAAAGTAAAAAGAATAATA
2670167 TGTTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23
Consensus pattern (23 bp):
AGTAAAGTAAAAAGAATAATAAT
Found at i:2672398 original size:122 final size:122
Alignment explanation
Indices: 2672174--2672401 Score: 278
Period size: 122 Copynumber: 1.9 Consensus size: 122
2672164 AGGTTAAAAC
* * * * *
2672174 GTTTTGTTAGTCCCTGTACTTAGACAAACTTTAAAATTTAGTTCCTGTAACATCATTAGTATTTT
1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT
* * * * *
2672239 CTGCCAAATTTTGCCATGAGATGTTAATTACACTGCCTCATTTCATATTGCATAAAT
66 CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT
* * * *
2672296 GTTTTTTTAGTCCTTGTACTTGGACAAAATTGAAAATGTA-ATCCATGTAACATTAGTAGTATTT
1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCC-TGTAACATCAGTAGTATTT
* * * *
2672360 TCTACCAAAATTTATCATGACATCTTGATTAGATTGCCTCAT
65 TCTACCAAAATTTACCATGACATCTTAATTACACTGCCTCAT
2672402 ATAACATTAG
Statistics
Matches: 87, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
121 3 0.03
122 84 0.97
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (122 bp):
GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT
CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT
Found at i:2674282 original size:59 final size:59
Alignment explanation
Indices: 2674190--2674307 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
2674180 ATTTCAACTG
2674190 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
2674249 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
2674308 TTTGGTTACC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (59 bp):
CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
Found at i:2685236 original size:28 final size:28
Alignment explanation
Indices: 2685204--2685260 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2685194 ATATATGTTG
2685204 AATCAGTGAATTAATTGAGGTATTTACC
1 AATCAGTGAATTAATTGAGGTATTTACC
2685232 AATCAGTGAATTAATTGAGGTATTTACC
1 AATCAGTGAATTAATTGAGGTATTTACC
2685260 A
1 A
2685261 TTAACTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
AATCAGTGAATTAATTGAGGTATTTACC
Found at i:2691837 original size:19 final size:19
Alignment explanation
Indices: 2691813--2691854 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2691803 AAAAATAAAA
2691813 TAAAGGTAAGGTTAAGTAC
1 TAAAGGTAAGGTTAAGTAC
2691832 TAAAGGTAAGGTTAAGTAC
1 TAAAGGTAAGGTTAAGTAC
2691851 TAAA
1 TAAA
2691855 TATATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (19 bp):
TAAAGGTAAGGTTAAGTAC
Found at i:2703318 original size:11 final size:11
Alignment explanation
Indices: 2703302--2703332 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2703292 AAGTATGGGT
2703302 AGGTATGGGAA
1 AGGTATGGGAA
*
2703313 AGGTATGGGCA
1 AGGTATGGGAA
2703324 AGGTATGGG
1 AGGTATGGG
2703333 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:2707410 original size:18 final size:18
Alignment explanation
Indices: 2707387--2707443 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
2707377 CCCAACTACT
*
2707387 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
2707405 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
2707423 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
2707441 GTA
1 GTA
2707444 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2715235 original size:32 final size:33
Alignment explanation
Indices: 2715168--2715239 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
2715158 ATTGTAGAAA
* * *
2715168 AAACTTTAAATCAAACATTTGAATAAAAATTTT
1 AAACTTTAAATCAAACAATAGAATAAAAATATT
2715201 AAACTTTAAATCAAACAAATAGAA-AAAAA-ATT
1 AAACTTTAAATCAAAC-AATAGAATAAAAATATT
2715233 AAACTTT
1 AAACTTT
2715240 TTAGAGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 9 0.26
33 21 0.60
34 5 0.14
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31
Consensus pattern (33 bp):
AAACTTTAAATCAAACAATAGAATAAAAATATT
Found at i:2725711 original size:20 final size:20
Alignment explanation
Indices: 2725686--2725725 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2725676 TCTGATCTGA
2725686 TCCTTTATTATCCCATAAAC
1 TCCTTTATTATCCCATAAAC
2725706 TCCTTTATTATCCCATAAAC
1 TCCTTTATTATCCCATAAAC
2725726 AAGTGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (20 bp):
TCCTTTATTATCCCATAAAC
Found at i:2738929 original size:212 final size:199
Alignment explanation
Indices: 2738599--2739215 Score: 781
Period size: 212 Copynumber: 3.0 Consensus size: 199
2738589 TTAATTTTAA
* * * * *
2738599 TGAGTGAGTGGATAATTC-TTCAATTTTCAATCATCTCATGTTTTAAAATTGTTTATTGGATGCA
1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA
* * *
2738663 TGAGTCCACTTCACAGTCATTTTTTTATTTGTTAGCCTGTACATTGGATCTGTTGCAGGTTGGAT
66 --AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGAT
* *
2738728 GATTTTGATTTTGATTCAGCCCTGAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGTAA
129 GATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAA
2738793 AGACGC
194 AGACGC
* ** *
2738799 TGAGTGAGTGGATTATTCTTTTATTTTTCAGTTATCTCATGTACAATCTTTTGCTTTGAAATTGT
1 TGAGTGAGTGGATAATTCTTTTATTTTT-A---A----A--T-C-ATCTCATGCTTTAAAATTGT
*
2738864 TTACTGGACATGCAAGTCAACTTCACATTCA-TTTTTTATTTGTTAGCCTGTATATTGTATCTGT
54 TTACTGG--ATGCAAGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGT
*
2738928 TGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA
117 TGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA
** * *
2738993 TAAGGAATGCAAAGCCGC
182 CCAGGAAAGCAAAGACGC
*
2739011 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTGCTGGATGCA
1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGC-
* *
2739076 TAAGTCAACTTAACATTCATTTTTTTTAATTTATTAGCCTGTACATTGTATCTGTTGCAGGTTGG
65 -AAGTCAACTTCACATTCA-TTTTTTT-ATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGG
** *
2739141 ATGATTTTGATTTTGATTC-GACCCTAAATATTGGAGAGAAGACTAGTAAGAAAAACCAGGAAGG
127 ATGATTTTGATTTTGATTCAG-CCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAG
*
2739205 CAAAGCCGC
191 CAAAGACGC
2739214 TG
1 TG
2739216 CTTCTGAGAG
Statistics
Matches: 362, Mismatches: 34, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
198 4 0.01
200 57 0.16
201 8 0.02
202 7 0.02
203 103 0.28
204 1 0.00
205 1 0.00
208 1 0.00
209 1 0.00
211 2 0.01
212 135 0.37
213 37 0.10
215 5 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (199 bp):
TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA
AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGATGA
TTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAAAG
ACGC
Found at i:2739179 original size:203 final size:199
Alignment explanation
Indices: 2738850--2739215 Score: 572
Period size: 203 Copynumber: 1.8 Consensus size: 199
2738840 TACAATCTTT
* * *
2738850 TGCTTTGAAATTGTTTACTGGACATGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGT
1 TGCTTTAAAATTGTTTACTGGACAT-CAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGT
*
2738915 ATATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA
65 ACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA
* *
2738980 CTAGTAAGAAAAATAAGGAATGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA
130 CTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA
2739045 TCTCA
195 TCTCA
*
2739050 TGCTTTAAAATTGTTTGCTGGATGCAT-AAGTCAACTTAACATTCATTTTTTTTAATTTATTAGC
1 TGCTTTAAAATTGTTTACTGGA--CATCAAGTCAACTTAACATTCA--TTTTTT-ATTTATTAGC
* **
2739114 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCGACCCTAAATATTGGAGAG
61 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAG
*
2739179 AAGACTAGTAAGAAAAACCAGGAAGGCAAAGCCGCTG
126 AAGACTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTG
2739216 CTTCTGAGAG
Statistics
Matches: 150, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
200 37 0.25
202 9 0.06
203 104 0.69
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (199 bp):
TGCTTTAAAATTGTTTACTGGACATCAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGTA
CATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGAC
TAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCAT
CTCA
Found at i:2743901 original size:15 final size:15
Alignment explanation
Indices: 2743883--2743912 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2743873 CTCTCTGCCC
2743883 TTCTCCTCCACCTCT
1 TTCTCCTCCACCTCT
*
2743898 TTCTCCTCCCCCTCT
1 TTCTCCTCCACCTCT
2743913 CTCAGTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCTCCTCCACCTCT
Found at i:2745045 original size:23 final size:24
Alignment explanation
Indices: 2745000--2745047 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2744990 AAATAATTTA
*
2745000 TTTTTAGAAATTTAAAATTTATAT
1 TTTTTAGAAATTTAAAATATATAT
2745024 TTTTTA-AAATTTAAAGAATATATA
1 TTTTTAGAAATTT-AA-AATATATA
2745048 AAGAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTTAGAAATTTAAAATATATAT
Found at i:2748677 original size:4 final size:4
Alignment explanation
Indices: 2748660--2748690 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2748650 CAATGACAAG
*
2748660 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2748691 AAACCCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:2757548 original size:5 final size:5
Alignment explanation
Indices: 2757538--2757563 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2757528 TTGCTATGAT
2757538 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
2757564 ATATGTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2758834 original size:44 final size:44
Alignment explanation
Indices: 2758771--2758856 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
2758761 TGATTGAATT
* *
2758771 GAATTGACTCGAATAAAAAATATTTGAGTTAGTCAAGTTGACAA
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
2758815 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
2758857 GAGTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (44 bp):
GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
Found at i:2759236 original size:20 final size:20
Alignment explanation
Indices: 2759204--2759256 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2759194 AACCTTTATT
2759204 TTTTA-AAATTTTTATAAAAA
1 TTTTAGAAA-TTTTATAAAAA
*
2759224 TTTTAGAAATTTTATAAATA
1 TTTTAGAAATTTTATAAAAA
*
2759244 TTTT-GAAAATTTA
1 TTTTAGAAATTTTA
2759257 AGGTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTAGAAATTTTATAAAAA
Found at i:2759240 original size:45 final size:45
Alignment explanation
Indices: 2759153--2759240 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 45
2759143 TTTATCATTT
* * *
2759153 TTTATTTTTTTAATTTTTTAAAGATTTTTAGAATTTTATATAACC
1 TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
2759198 TTTATTTTTTAAAATTTTTATAAA-AATTTTAGAAATTT-TATAA
1 TTTATTTTTT-AAATTTTT-TAAAGAATTTTAGAAATTTATATAA
2759241 ATATTTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 15 0.39
46 19 0.50
47 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (45 bp):
TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
Found at i:2766347 original size:12 final size:12
Alignment explanation
Indices: 2766330--2766354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2766320 AATTTCTATA
2766330 TATATATATATT
1 TATATATATATT
2766342 TATATATATATT
1 TATATATATATT
2766354 T
1 T
2766355 TAAATGTCAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Found at i:2772478 original size:16 final size:16
Alignment explanation
Indices: 2772457--2772491 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2772447 AAAATTCAAA
*
2772457 ATATTTATAAAAATTT
1 ATATTTATAAAAAATT
*
2772473 ATATTTTTAAAAAATT
1 ATATTTATAAAAAATT
2772489 ATA
1 ATA
2772492 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTATAAAAAATT
Found at i:2772497 original size:19 final size:19
Alignment explanation
Indices: 2772446--2772506 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
2772436 AATAAGGTTC
* *
2772446 AAAAATTCAAAATATTTAT-
1 AAAAATT-ATAATATTTTTA
2772465 AAAAATT-T-ATATTTTTA
1 AAAAATTATAATATTTTTA
2772482 AAAAATTATAATATTTTTTA
1 AAAAATTATAATA-TTTTTA
2772502 AAAAA
1 AAAAA
2772507 ATTAAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 1 0.03
19 10 0.28
20 11 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATTATAATATTTTTA
Found at i:2774034 original size:15 final size:15
Alignment explanation
Indices: 2774014--2774043 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2774004 AAAACGTAAC
2774014 ATTTCAAACATAATT
1 ATTTCAAACATAATT
2774029 ATTTCAAACATAATT
1 ATTTCAAACATAATT
2774044 GATTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTCAAACATAATT
Found at i:2778325 original size:55 final size:55
Alignment explanation
Indices: 2778264--2778373 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
2778254 TGATATGTCT
* * *
2778264 GGTAATGCCTCGTAACCCTATTTCGGA-GACGGTTTGGGGTTAAAAGGGTGTTACA
1 GGTAATGCCTCGTAACCCTATTTC-AACGACGATTTGCGGTTAAAAGGGTGTTACA
*
2778319 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAGGGGTGTTACA
1 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA
2778374 ATATTCTGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.02
55 49 0.98
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (55 bp):
GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA
Found at i:2779945 original size:6 final size:6
Alignment explanation
Indices: 2779934--2779960 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2779924 AGCAATAGTT
2779934 TGAATG TGAATG TGAATG TGAATG TGA
1 TGAATG TGAATG TGAATG TGAATG TGA
2779961 GGTGAAGTGG
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAATG
Found at i:2781456 original size:63 final size:63
Alignment explanation
Indices: 2781316--2781764 Score: 376
Period size: 63 Copynumber: 7.1 Consensus size: 63
2781306 AAACCGGGCT
* * * * *
2781316 ACACCGAAAAGCA-ATACAAAC-AAAGACCACTGTTGTCTTC-AATGAGAAAGCAATGAAACCCT
1 ACACCCAAAAGCATA-ACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCT
2781378 AA
62 AA
* * *
2781380 ACACCCAAAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * * * *
2781443 ACACTCAAAAGCATTACAAAC-AAATACCAGTATTGTCTTC-AATGAGAAAGAAATGAAACCCTA
1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA
2781506 A
63 A
* * * *
2781507 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * * * *
2781570 ACACTCAAAAGCATTACAAAC-AAAGACCAGTATTGTCTTC-AATTAGAAAGCAATGAAACCCTA
1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA
2781633 A
63 A
* * * * *
2781634 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * *
2781697 ACACCCAAAAGCATTACAAACAAAAACCAC-GTTGATCAGC-AATGAAAAAGCAATCAACCCTAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTG-TCTGCAAATAAAAAAG-AGTAAACCCTAA
2781760 ACACC
1 ACACC
2781765 AATTGAGTTA
Statistics
Matches: 303, Mismatches: 67, Indels: 31
0.76 0.17 0.08
Matches are distributed among these distances:
62 33 0.11
63 129 0.43
64 109 0.36
65 32 0.11
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (63 bp):
ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
Found at i:2781548 original size:127 final size:127
Alignment explanation
Indices: 2781322--2781764 Score: 658
Period size: 127 Copynumber: 3.5 Consensus size: 127
2781312 GGCTACACCG
* * *
2781322 AAAAGCAATACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * *
2781387 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
* *
2781449 AAAAGCATTACAAACAAATACCAGTATTGTCTTCAATGAGAAAGAAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
*
2781514 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAAACACTC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
*
2781576 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATTAGAAAGCAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * * *
2781641 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAAACACCC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
* ** * *
2781703 AAAAGCATTACAAACAAAAACCACG--TTGATCAGCAATGAAAAAGCAAT-CAACCCTAAACACC
1 AAAAGCATTACAAACAAAGACCA-GTATTG-TCTTCAATGAGAAAGCAATGAAACCCTAAACACC
2781765 AATTGAGTTA
Statistics
Matches: 289, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
126 16 0.06
127 272 0.94
128 1 0.00
ACGTcount: A:0.49, C:0.23, G:0.12, T:0.15
Consensus pattern (127 bp):
AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
Found at i:2782121 original size:10 final size:10
Alignment explanation
Indices: 2782108--2782186 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
2782098 TTTTTAAGAC
2782108 TTATTAAAAA
1 TTATTAAAAA
2782118 TTA-TAAAAA
1 TTATTAAAAA
* *
2782127 -TATTTGAACA
1 TTA-TTAAAAA
2782137 -TATTAAAAA
1 TTATTAAAAA
2782146 TT-TGT-AAAA
1 TTAT-TAAAAA
2782155 TTATTAAAAA
1 TTATTAAAAA
* *
2782165 ATAATAAAAA
1 TTATTAAAAA
2782175 TT-TTAAACAA
1 TTATTAAA-AA
2782185 TT
1 TT
2782187 GTGAAAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 2 0.04
9 23 0.43
10 29 0.54
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:2782159 original size:19 final size:19
Alignment explanation
Indices: 2782114--2782267 Score: 67
Period size: 19 Copynumber: 8.2 Consensus size: 19
2782104 AGACTTATTA
*
2782114 AAAATTATAAAAATATTTG-
1 AAAATTATTAAAA-ATTTGT
*
2782133 AACA-TATTAAAAATTTGT
1 AAAATTATTAAAAATTTGT
* **
2782151 AAAATTATTAAAAAATAAT
1 AAAATTATTAAAAATTTGT
2782170 AAAAATT-TTAAACAA-TTGT
1 -AAAATTATTAAA-AATTTGT
* *
2782189 GAAAATCATTTAAAAAATT-T
1 -AAAATTA-TTAAAAATTTGT
*
2782209 -AAATTGATTAAAAA-ATGT
1 AAAATT-ATTAAAAATTTGT
** *
2782227 AAGAATTATTTGAAATTTAT
1 AA-AATTATTAAAAATTTGT
2782247 AAGAATT-TT-AAAATTT-T
1 AA-AATTATTAAAAATTTGT
2782264 AAAA
1 AAAA
2782268 AATTATAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.02
17 9 0.08
18 28 0.26
19 36 0.34
20 24 0.23
21 7 0.07
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (19 bp):
AAAATTATTAAAAATTTGT
Found at i:2782159 original size:29 final size:28
Alignment explanation
Indices: 2782109--2782181 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 28
2782099 TTTTAAGACT
* ** *
2782109 TATTAAAAATTATAAAAATATTTGAACA
1 TATTAAAAATTTTAAAAATATTAAAAAA
*
2782137 TATTAAAAATTTGTAAAATTATTAAAAAA
1 TATTAAAAATTT-TAAAAATATTAAAAAA
*
2782166 TAATAAAAATTTTAAA
1 TATTAAAAATTTTAAA
2782182 CAATTGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
TATTAAAAATTTTAAAAATATTAAAAAA
Found at i:2782181 original size:9 final size:9
Alignment explanation
Indices: 2782111--2782268 Score: 54
Period size: 9 Copynumber: 16.8 Consensus size: 9
2782101 TTAAGACTTA
2782111 TTAAAAATT
1 TTAAAAATT
*
2782120 ATAAAAATAT
1 TTAAAAAT-T
* * *
2782130 TTGAACATA
1 TTAAAAATT
2782139 TTAAAAATT
1 TTAAAAATT
2782148 TGT-AAAATT
1 T-TAAAAATT
*
2782157 ATTAAAAAATA
1 -TT-AAAAATT
*
2782168 ATAAAAATT
1 TTAAAAATT
2782177 TTAAACAATT
1 TTAAA-AATT
* *
2782187 GTGAAAATCAT
1 TTAAAAAT--T
*
2782198 TTAAAAAAT
1 TTAAAAATT
2782207 TT--AAATT
1 TTAAAAATT
*
2782214 GATTAAAAAAT
1 --TTAAAAATT
* *
2782225 GTAAGAATT
1 TTAAAAATT
**
2782234 ATTTGAAATT
1 -TTAAAAATT
*
2782244 TATAAGAATT
1 T-TAAAAATT
2782254 TT-AAAATT
1 TTAAAAATT
2782262 TTAAAAA
1 TTAAAAA
2782269 ATTATAATAT
Statistics
Matches: 104, Mismatches: 30, Indels: 30
0.63 0.18 0.18
Matches are distributed among these distances:
7 4 0.04
8 7 0.07
9 51 0.49
10 27 0.26
11 15 0.14
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (9 bp):
TTAAAAATT
Found at i:2783535 original size:9 final size:9
Alignment explanation
Indices: 2783523--2783575 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
2783513 TTTTAATACC
2783523 TTTTATTAT
1 TTTTATTAT
2783532 TTTTATTAT
1 TTTTATTAT
*
2783541 TTTATATGAT
1 TTT-TATTAT
*
2783551 TTTATGATTTT
1 TTT-T-ATTAT
*
2783562 TTTTTTTAT
1 TTTTATTAT
2783571 TTTTA
1 TTTTA
2783576 CCCATGTGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 19 0.53
10 11 0.31
11 6 0.17
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2785885 original size:7 final size:7
Alignment explanation
Indices: 2785875--2785970 Score: 51
Period size: 7 Copynumber: 13.9 Consensus size: 7
2785865 AGGTTTATAG
2785875 TTTAAGA
1 TTTAAGA
2785882 TTTAAGA
1 TTTAAGA
2785889 TTTAA-A
1 TTTAAGA
*
2785895 TTTTAGA
1 TTTAAGA
2785902 GTTTAAG-
1 -TTTAAGA
* *
2785909 TTTAGGTT
1 TTTAAG-A
*
2785917 TTTAACA
1 TTTAAGA
2785924 -TT-AGA
1 TTTAAGA
*
2785929 GTTTAGGA
1 -TTTAAGA
2785937 TTTATAG-
1 TTTA-AGA
2785944 TTTAAGA
1 TTTAAGA
2785951 TTTAAG-
1 TTTAAGA
*
2785957 TTTTAGA
1 TTTAAGA
2785964 GTTTAAG
1 -TTTAAG
2785971 TTGAGATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
5 2 0.03
6 19 0.28
7 29 0.43
8 17 0.25
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (7 bp):
TTTAAGA
Found at i:2785885 original size:14 final size:13
Alignment explanation
Indices: 2785863--2785972 Score: 73
Period size: 14 Copynumber: 8.0 Consensus size: 13
2785853 TTATTTCGTG
*
2785863 TAAGGTTTATAGTT
1 TAAGATTTA-AGTT
2785877 TAAGATTTAAGATT
1 TAAGATTTAAG-TT
2785891 TAA-ATTTTAGAGTT
1 TAAGA-TTTA-AGTT
*
2785905 TAAG-TTTAGGTTTT
1 TAAGATTTAAG--TT
*
2785919 TAACA-TTAGAGTT
1 TAAGATTTA-AGTT
*
2785932 TAGGATTTATAGTT
1 TAAGATTTA-AGTT
2785946 TAAGATTTAAGTT
1 TAAGATTTAAGTT
*
2785959 TTAGAGTTTAAGTT
1 TAAGA-TTTAAGTT
2785973 GAGATTTTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.01
13 20 0.26
14 53 0.69
15 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (13 bp):
TAAGATTTAAGTT
Found at i:2785919 original size:21 final size:20
Alignment explanation
Indices: 2785895--2785972 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
2785885 AAGATTTAAA
2785895 TTTTAGAGTTTAAGTTTAGG
1 TTTTAGAGTTTAAGTTTAGG
**
2785915 TTTTTA-ACATTAGAGTTTAGG
1 -TTTTAGAGTTTA-AGTTTAGG
* * *
2785936 ATTTATAGTTTAAGATTTAAG
1 TTTTAGAGTTTAAG-TTTAGG
2785957 TTTTAGAGTTTAAGTT
1 TTTTAGAGTTTAAGTT
2785973 GAGATTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTTAGAGTTTAAGTTTAGG
Found at i:2790360 original size:6 final size:6
Alignment explanation
Indices: 2790351--2790378 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2790341 GACAAGAACC
2790351 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
2790379 ATAATAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:2792172 original size:31 final size:31
Alignment explanation
Indices: 2792137--2792199 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2792127 ACAACTCGAC
* *
2792137 TTTTTAAAAAAAATTAATAGTTAAATTTAAT
1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
***
2792168 TTTTTTTTAAAAATTAAGAGTAAAATTTAAT
1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
2792199 T
1 T
2792200 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
Found at i:2795686 original size:17 final size:17
Alignment explanation
Indices: 2795666--2795732 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
2795656 CAATAAATAA
2795666 AAATATATAAAAATATT
1 AAATATATAAAAATATT
*
2795683 AAATAT-T-AAAATAAT
1 AAATATATAAAAATATT
* *
2795698 ATAATATA-AATAATTTT
1 A-AATATATAAAAATATT
*
2795715 AAA-AAATCAAAAATATT
1 AAATATAT-AAAAATATT
2795732 A
1 A
2795733 TAGGAGGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
15 10 0.26
16 8 0.21
17 20 0.53
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATATAAAAATATT
Found at i:2795703 original size:16 final size:15
Alignment explanation
Indices: 2795660--2795707 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2795650 AAATTTCAAT
*
2795660 AAATAAAAATATATAA
1 AAATAATAA-ATATAA
* *
2795676 AAATATTAAATATTA
1 AAATAATAAATATAA
2795691 AAATAATATAATATAA
1 AAATAATA-AATATAA
2795707 A
1 A
2795708 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAAATATAA
Found at i:2800240 original size:12 final size:12
Alignment explanation
Indices: 2800223--2800251 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2800213 CAGTGCTTGT
2800223 TTGTTTGTTTGC
1 TTGTTTGTTTGC
2800235 TTGTTTGTTTGC
1 TTGTTTGTTTGC
2800247 TTGTT
1 TTGTT
2800252 CTCATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.24, T:0.69
Consensus pattern (12 bp):
TTGTTTGTTTGC
Found at i:2804080 original size:8 final size:8
Alignment explanation
Indices: 2804067--2804097 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
2804057 GCCAAGGGAC
2804067 AAAAAATAA
1 AAAAAAT-A
2804076 AAAAAATA
1 AAAAAATA
2804084 AAAAAATA
1 AAAAAATA
2804092 AAAAAA
1 AAAAAA
2804098 AAGCTGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:2804081 original size:9 final size:9
Alignment explanation
Indices: 2804067--2804098 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2804057 GCCAAGGGAC
2804067 AAAAAATAA
1 AAAAAATAA
2804076 AAAAAAT-A
1 AAAAAATAA
2804084 AAAAAATAA
1 AAAAAATAA
2804093 AAAAAA
1 AAAAAA
2804099 AGCTGCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2804253 original size:3 final size:3
Alignment explanation
Indices: 2804245--2804274 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2804235 GAACTCTTAA
*
2804245 ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2804275 TAACATAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:2806703 original size:19 final size:19
Alignment explanation
Indices: 2806678--2806729 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2806668 GAAATGGATT
2806678 ACTTGTTAAACAAAACTCT-
1 ACTTGTTAAACAAAACT-TA
* *
2806697 GCTTGTT-TACAAAACTTA
1 ACTTGTTAAACAAAACTTA
2806715 ACTTGTTAAACAAAA
1 ACTTGTTAAACAAAA
2806730 ATGGTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 14 0.52
19 12 0.44
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (19 bp):
ACTTGTTAAACAAAACTTA
Found at i:2811986 original size:132 final size:131
Alignment explanation
Indices: 2811593--2811989 Score: 374
Period size: 131 Copynumber: 3.0 Consensus size: 131
2811583 AGTATTCATT
* * * ** * *
2811593 TAAAAATTCTTTAAAACGAATGCAATACTCGGTGTTTGACAATTCGGGAATCA-TGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTCGGGAAT-AGTGCCCTATCGT
* * * *
2811657 GCTGGGTTGTGATTTCTCGTTTGCTCAAAACAATCGAATAT-TCCTATAGG-TTTTCACTCATGT
65 GCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCT-CT-TCGGAATTTCACTCATGT
2811720 TTAT-
128 TT-TC
* * * * * *
2811724 TAAAAAC-CTTTCAAAACG-AAGATGATGTTCGATGATTGGCGATTTGAGAATCGTGCCCTATCG
1 TAAAAACTCTTT-AAAACGAAAGA-AATGTTCGATGTTTGGCAATTCGGGAATAGTGCCCTATCG
* * * * * * * * * * *
2811787 TGCTAGGTTGCGCTTTTTCATTTGTTCTAAACGATCGAAGATCCCTTCGGAACTTCATTCACGTT
64 TGCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCGGAATTTCACTCATGTT
2811852 TTC
129 TTC
*
2811855 TAAAAACTCTTTAAAATGAAAGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTC-GGGAATAGTGCCCTATCGT
* * * * * *
2811920 GCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATCTCTTCGGAATTTCACTCGTATTT
65 GCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCGGAATTTCACTCATGTTT
2811985 TC
130 TC
2811987 TAA
1 TAA
2811990 GGCAAGGCAA
Statistics
Matches: 205, Mismatches: 52, Indels: 17
0.75 0.19 0.06
Matches are distributed among these distances:
130 10 0.05
131 117 0.57
132 78 0.38
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (131 bp):
TAAAAACTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTCGGGAATAGTGCCCTATCGTG
CTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCGAATATCTCTTCGGAATTTCACTCATGTTTT
C
Found at i:2837225 original size:11 final size:11
Alignment explanation
Indices: 2837209--2837244 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2837199 TGCTCTCCGG
2837209 CACGGCGGAGC
1 CACGGCGGAGC
2837220 CACGGCGGAGC
1 CACGGCGGAGC
* *
2837231 TACGGCAGAGC
1 CACGGCGGAGC
2837242 CAC
1 CAC
2837245 CGCGCGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.22, C:0.36, G:0.39, T:0.03
Consensus pattern (11 bp):
CACGGCGGAGC
Found at i:2837241 original size:22 final size:23
Alignment explanation
Indices: 2837210--2837254 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2837200 GCTCTCCGGC
* *
2837210 ACGGCGGAGCCACGGCG-GAGCT
1 ACGGCAGAGCCACCGCGCGAGCT
2837232 ACGGCAGAGCCACCGCGCGAGCT
1 ACGGCAGAGCCACCGCGCGAGCT
2837255 CGCTGGTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.20, C:0.36, G:0.40, T:0.04
Consensus pattern (23 bp):
ACGGCAGAGCCACCGCGCGAGCT
Found at i:2837970 original size:29 final size:28
Alignment explanation
Indices: 2837909--2837972 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2837899 ATTTTGAATA
* * * *
2837909 GTTTTATATTCATTTTGTTTTAAATATT
1 GTTTTATATACATTATATTTTAAAAATT
*
2837937 TTTTTATATACATATATATTTTAAAAATT
1 GTTTTATATACAT-TATATTTTAAAAATT
2837966 GTTTTAT
1 GTTTTAT
2837973 TATTTGTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (28 bp):
GTTTTATATACATTATATTTTAAAAATT
Found at i:2838046 original size:34 final size:33
Alignment explanation
Indices: 2837999--2838065 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
2837989 TGTTATTTGT
*
2837999 ATATTATTATTTTAAAC-TTTTATGTATATATTA
1 ATATTATTATTTTAAACGTTTT-TATATATATTA
2838032 ATATTATCTATTTTAAACGTTTTTATATATATTA
1 ATATTAT-TATTTTAAACGTTTTTATATATATTA
2838066 TTTATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 20 0.65
35 4 0.13
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (33 bp):
ATATTATTATTTTAAACGTTTTTATATATATTA
Found at i:2838089 original size:14 final size:15
Alignment explanation
Indices: 2838051--2838097 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2838041 ATTTTAAACG
*
2838051 TTTTTATATATATTA
1 TTTTTATATATATCA
* *
2838066 TTTATATATA-ATCC
1 TTTTTATATATATCA
2838080 TTTTTATATATATACA
1 TTTTTATATATAT-CA
2838096 TT
1 TT
2838098 ATTCTATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 11 0.44
16 3 0.12
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTATATATATCA
Found at i:2838163 original size:32 final size:32
Alignment explanation
Indices: 2838126--2838196 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
2838116 TTTTATATAT
2838126 TATATTTTG-AACTATT-TATATTTTATTTTAAA
1 TATATTTTGAAACT-TTATATA-TTTATTTTAAA
* *
2838158 TATATTTTTAAACTTTATTTATTTATTTTAAA
1 TATATTTTGAAACTTTATATATTTATTTTAAA
2838190 -ATATTTT
1 TATATTTT
2838197 ATTTATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 7 0.20
32 21 0.60
33 7 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (32 bp):
TATATTTTGAAACTTTATATATTTATTTTAAA
Found at i:2838346 original size:21 final size:25
Alignment explanation
Indices: 2838302--2838347 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 25
2838292 ATTTACCACT
2838302 TATTTCTTATATATATCTTATCATA
1 TATTTCTTATATATATCTTATCATA
2838327 TATTT-TTAT-TAT-TCTT-TCATA
1 TATTTCTTATATATATCTTATCATA
2838348 ATAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 4 0.19
23 3 0.14
24 4 0.19
25 5 0.24
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTCTTATATATATCTTATCATA
Found at i:2838926 original size:76 final size:76
Alignment explanation
Indices: 2838800--2838951 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
2838790 GTACATTATC
* *
2838800 CCATATCATTGTTTTTCACTTGGTTTACGAAATGTTGTTTTATAAGGTCCAAATCTTTAAGATTA
1 CCATATCATTGTTTTCCACTTGGTTTACGAAATGTGGTTTTATAAGGTCCAAATCTTTAAGATTA
2838865 ATTTCGTTTTA
66 ATTTCGTTTTA
*
2838876 CCATATCATTGTTTTCCACTTGGTTTATGAAATGTGGTTTTATAAGGTCCAAATCTTTAAGATTA
1 CCATATCATTGTTTTCCACTTGGTTTACGAAATGTGGTTTTATAAGGTCCAAATCTTTAAGATTA
2838941 ATTTCGTTTTA
66 ATTTCGTTTTA
2838952 TTTCAAGTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (76 bp):
CCATATCATTGTTTTCCACTTGGTTTACGAAATGTGGTTTTATAAGGTCCAAATCTTTAAGATTA
ATTTCGTTTTA
Found at i:2839235 original size:131 final size:131
Alignment explanation
Indices: 2838998--2839256 Score: 365
Period size: 131 Copynumber: 2.0 Consensus size: 131
2838988 TAATTATTTA
* * * *
2838998 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAAATTGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTAGGGAAATCGTGCCCTATC
* * * * *
2839063 GTGCTGAGTTGCAATTTTCCGTTTGTTCAAAATAATTGAATATTCCTCTAGAATTTCACTCATGT
66 GTGCTGAGTTACAATTTTCCGTTTGTCCAAAATAATCGAATATCCCTCTAAAATTTCACTCATGT
2839128 C
131 C
** * *
2839129 TTTAAAAATTCTTTAAGGCGAAAGAAATGTTCGATGTTTGGCAATTAGGGGAATCGTGCCTTATC
1 TTTAAAAATTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTAGGGAAATCGTGCCCTATC
* * * *
2839194 GTGCTGGGTTACAATTTTCCGTTTGTCCAAAATAGTCGAATATCCCTTTAAAATTTTACTCAT
66 GTGCTGAGTTACAATTTTCCGTTTGTCCAAAATAATCGAATATCCCTCTAAAATTTCACTCAT
2839257 AATTTCTAAT
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 111 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACGAAAGAAATGTTCGATGTTTGGCAATTAGGGAAATCGTGCCCTATC
GTGCTGAGTTACAATTTTCCGTTTGTCCAAAATAATCGAATATCCCTCTAAAATTTCACTCATGT
C
Found at i:2846083 original size:74 final size:74
Alignment explanation
Indices: 2845956--2846103 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
2845946 GCCTTGTGTT
* *
2845956 GAAGATGTCAAGTGAAGTGTCACCAAGGAAGCATAAGCCCCATCGGTTATATTCATCAACGCATC
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCAGTTATATTCATCAACGCATC
*
2846021 GTTTCTACC
66 GTGTCTACC
* *
2846030 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCAG-TAGTATTCATCAATGTAT
1 GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCAGTTA-TATTCATCAACGCAT
2846094 CGTGTCTACC
65 CGTGTCTACC
2846104 TTTCTCAACA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 2 0.03
74 66 0.97
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (74 bp):
GAAGATGTCAAGTGAAGTGCCACCAAGGAAGCATAAGCCCCATCAGTTATATTCATCAACGCATC
GTGTCTACC
Found at i:2849407 original size:26 final size:26
Alignment explanation
Indices: 2849371--2849423 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2849361 AAACAAGAAA
2849371 AACTTGGCAAACATACATATAAATTT
1 AACTTGGCAAACATACATATAAATTT
2849397 AACTTGGCAAACATACATATAAATTT
1 AACTTGGCAAACATACATATAAATTT
2849423 A
1 A
2849424 CTTACATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (26 bp):
AACTTGGCAAACATACATATAAATTT
Found at i:2850734 original size:25 final size:25
Alignment explanation
Indices: 2850697--2850757 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
2850687 CGAAGCAGAA
2850697 ATTGAATAAGAAGTCAAATACAATCT
1 ATTGAA-AAGAAGTCAAATACAATCT
2850723 ATTGAAAAGAAGTCAAATACAATCT
1 ATTGAAAAGAAGTCAAATACAATCT
2850748 ATTGAAAAGA
1 ATTGAAAAGA
2850758 CCCTCAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 29 0.83
26 6 0.17
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (25 bp):
ATTGAAAAGAAGTCAAATACAATCT
Found at i:2851677 original size:26 final size:26
Alignment explanation
Indices: 2851610--2851682 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
2851600 TTTTTTTTAA
*
2851610 TTTAATATGTTA-AATATATATATTCC
1 TTTAATATCTTATAATAT-TATATTCC
* *
2851636 TTTAA-ATTTTATTAATATTATATGT-T
1 TTTAATATCTTA-TAATATTATAT-TCC
*
2851662 TTTAATATCTTATAATTTTAT
1 TTTAATATCTTATAATATTAT
2851683 TTAGGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 5 0.13
26 23 0.59
27 11 0.28
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (26 bp):
TTTAATATCTTATAATATTATATTCC
Found at i:2852280 original size:24 final size:24
Alignment explanation
Indices: 2852248--2852297 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2852238 TCTAATTAAT
2852248 TAATGAAGTTTTTATGTTTATATG
1 TAATGAAGTTTTTATGTTTATATG
2852272 TAATGAAGTTTTTATGTTTATATG
1 TAATGAAGTTTTTATGTTTATATG
2852296 TA
1 TA
2852298 CCAAGACACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (24 bp):
TAATGAAGTTTTTATGTTTATATG
Found at i:2856993 original size:46 final size:46
Alignment explanation
Indices: 2856943--2857115 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
2856933 TTGAGCATCT
*
2856943 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * * *
2856989 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
* * *
2857036 GAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* *
2857082 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2857116 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:2857096 original size:93 final size:93
Alignment explanation
Indices: 2856937--2857108 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
2856927 GGATGGTTGA
* * * **
2856937 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
2857002 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
2857030 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
2857095 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2857109 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:2860915 original size:17 final size:18
Alignment explanation
Indices: 2860890--2860926 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2860880 ATTTTTAAAA
2860890 ATTATAAATACAT-AAATT
1 ATTATAAATA-ATAAAATT
2860908 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
2860925 AT
1 AT
2860927 ATTTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:2861434 original size:33 final size:33
Alignment explanation
Indices: 2861396--2861468 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
2861386 TATTTTCATG
2861396 ATTTTTTTA-ATTATTTAATA-AT-ATTTTAGTA
1 ATTTTTTTATATTA-TTAATACATAATTTTAGTA
2861427 ATTTTTTTATATTATTAATACATAATTTTAGTA
1 ATTTTTTTATATTATTAATACATAATTTTAGTA
2861460 ATTTTTTTA
1 ATTTTTTTA
2861469 CCCGAATCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 15 0.38
32 6 0.15
33 18 0.46
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (33 bp):
ATTTTTTTATATTATTAATACATAATTTTAGTA
Found at i:2863111 original size:20 final size:20
Alignment explanation
Indices: 2863086--2863135 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2863076 TGGCTTAAAA
2863086 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2863106 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2863123 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2863136 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2867750 original size:20 final size:20
Alignment explanation
Indices: 2867725--2867774 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2867715 TGGCTTAAAA
2867725 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2867745 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2867762 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2867775 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2874694 original size:19 final size:20
Alignment explanation
Indices: 2874666--2874704 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2874656 TTTTAAATTA
2874666 TAAAAAAATT-AAATAAAAT
1 TAAAAAAATTCAAATAAAAT
* *
2874685 TAAAATAATTCAATTAAAAT
1 TAAAAAAATTCAAATAAAAT
2874705 AACCAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAAAATTCAAATAAAAT
Found at i:2875286 original size:20 final size:21
Alignment explanation
Indices: 2875254--2875297 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2875244 TTTTAGTTTT
* *
2875254 TATATATTATAAATTATATAA
1 TATATATTATAAATAACATAA
2875275 TATATA-TATAAATAACATAA
1 TATATATTATAAATAACATAA
2875295 TAT
1 TAT
2875298 GCGGAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATATTATAAATAACATAA
Found at i:2878776 original size:30 final size:31
Alignment explanation
Indices: 2878742--2878805 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2878732 ATTTATTTTA
*
2878742 TTGTTAA-TTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTTATTATTATTTTAGAA-GCAT
2878772 TTGTTAATTTTTATTATTATTTTAGAAGCAT
1 TTGTTAATTTTTATTATTATTTTAGAAGCAT
2878803 TTG
1 TTG
2878806 CTTATTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 7 0.23
31 22 0.71
32 2 0.06
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTTATTATTATTTTAGAAGCAT
Found at i:2882381 original size:18 final size:19
Alignment explanation
Indices: 2882344--2882390 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2882334 TTATGTGTAA
2882344 TTTTATTGCTAGCATGAAAG
1 TTTTA-TGCTAGCATGAAAG
*
2882364 TTTTATGCTA-CTTGAAAG
1 TTTTATGCTAGCATGAAAG
2882382 TTTTATGCT
1 TTTTATGCT
2882391 TAATTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 16 0.62
19 5 0.19
20 5 0.19
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTTATGCTAGCATGAAAG
Found at i:2885358 original size:17 final size:17
Alignment explanation
Indices: 2885336--2885370 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2885326 TATTTTGTTT
2885336 TATAATTATTTACACAA
1 TATAATTATTTACACAA
*
2885353 TATAATTATTTATACAA
1 TATAATTATTTACACAA
2885370 T
1 T
2885371 CTTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATTATTTACACAA
Found at i:2889631 original size:5 final size:5
Alignment explanation
Indices: 2889621--2889666 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
2889611 TTTGATTATT
* * *
2889621 TTTTA TTTTA TTTTA TTTTA TTTTA TGTTA TATTA TATTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
2889667 ATTAAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
5 34 0.92
6 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:2889761 original size:15 final size:15
Alignment explanation
Indices: 2889737--2889783 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2889727 ATAACTTAAA
*
2889737 TTCAACACTTATTTT
1 TTCAATACTTATTTT
2889752 TTCAATACTTATTTT
1 TTCAATACTTATTTT
* *
2889767 TTTAATATTTATTTT
1 TTCAATACTTATTTT
2889782 TT
1 TT
2889784 TAACACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCAATACTTATTTT
Found at i:2889784 original size:15 final size:15
Alignment explanation
Indices: 2889743--2889792 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
2889733 TAAATTCAAC
*
2889743 ACTTATTTTTTCAAT
1 ACTTATTTTTTTAAT
2889758 ACTTATTTTTTTAAT
1 ACTTATTTTTTTAAT
* *
2889773 ATTTATTTTTTTAAC
1 ACTTATTTTTTTAAT
2889788 ACTTA
1 ACTTA
2889793 ATGTTTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
ACTTATTTTTTTAAT
Found at i:2890389 original size:10 final size:11
Alignment explanation
Indices: 2890366--2890417 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2890356 TAAGTGTGGT
2890366 AAAATTTATAA
1 AAAATTTATAA
2890377 AAAATTTATAA
1 AAAATTTATAA
* *
2890388 AATTATTAATAA
1 AA-AATTTATAA
2890400 TATAAA-TTATAA
1 -A-AAATTTATAA
2890412 AAAATT
1 AAAATT
2890418 ATATCCAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.09
11 15 0.45
12 12 0.36
13 2 0.06
14 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:2897927 original size:27 final size:25
Alignment explanation
Indices: 2897878--2897936 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
2897868 ATATTTACAT
* *
2897878 TATAATATTATAAATTACTATAAATTA
1 TATAATATTAAAAATAACTAT-AA-TA
2897905 TATAATATATAAAAATAAC-ATAATA
1 TATAATAT-TAAAAATAACTATAATA
2897930 TATAATA
1 TATAATA
2897937 AATACAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
26 2 0.07
27 10 0.34
28 8 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
TATAATATTAAAAATAACTATAATA
Found at i:2898772 original size:31 final size:31
Alignment explanation
Indices: 2898702--2898772 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
2898692 AAAAGATTAG
* * *
2898702 ATACTAAATTAAGAAAAAAAGTAAAATTTAG
1 ATACCAAATTAAGAAAAAAAGTAAAATTCAA
* * *
2898733 GTATCAAATTAA-AAAAAAGAGTCAAATTCAA
1 ATACCAAATTAAGAAAAAA-AGTAAAATTCAA
2898764 ATACCAAAT
1 ATACCAAAT
2898773 ATTATATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (31 bp):
ATACCAAATTAAGAAAAAAAGTAAAATTCAA
Found at i:2926581 original size:19 final size:20
Alignment explanation
Indices: 2926550--2926587 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2926540 AAAAATTTAA
*
2926550 TTTAAATATATAAACTATAT
1 TTTAAATATATAAAATATAT
2926570 TTTAAATA-ATAAAATATA
1 TTTAAATATATAAAATATA
2926588 ACCAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Done.