Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 38 of 171
Found at i:17153804 original size:39 final size:39
Alignment explanation
Indices: 17153750--17153827 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
17153740 GGTAAATAAA
17153750 TCTGACTTCATATCATATGATCAAAATTAGTGATTTAAG
1 TCTGACTTCATATCATATGATCAAAATTAGTGATTTAAG
17153789 TCTGACTTCATATCATATGATCAAAATTAGTGATTTAAG
1 TCTGACTTCATATCATATGATCAAAATTAGTGATTTAAG
17153828 GAGTATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (39 bp):
TCTGACTTCATATCATATGATCAAAATTAGTGATTTAAG
Found at i:17160437 original size:21 final size:21
Alignment explanation
Indices: 17160412--17160454 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17160402 ATATTTTAAA
*
17160412 TTGAGTCTAG-TGAAATGAAAT
1 TTGAGTCGAGTTG-AATGAAAT
17160433 TTGAGTCGAGTTGAATGAAAT
1 TTGAGTCGAGTTGAATGAAAT
17160454 T
1 T
17160455 ATTCGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGAGTCGAGTTGAATGAAAT
Found at i:17165336 original size:57 final size:57
Alignment explanation
Indices: 17165274--17165382 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
17165264 TTTATATATA
17165274 AAAAAAACACTCTCATATTAATATTTGTTATTTTACAAGAA-ATTTTTAATTATTTTTT
1 AAAAAAA-ACTCTCATATTAATATTTGTTATTTTACAAGAATA-TTTTAATTATTTTTT
* * *
17165332 AAAAAAAATTCTCATGTTAATATTTGTTATTTTATAAGAATATTTTAATTA
1 AAAAAAAACTCTCATATTAATATTTGTTATTTTACAAGAATATTTTAATTA
17165383 ATTTCTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 39 0.83
58 8 0.17
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (57 bp):
AAAAAAAACTCTCATATTAATATTTGTTATTTTACAAGAATATTTTAATTATTTTTT
Found at i:17176976 original size:19 final size:18
Alignment explanation
Indices: 17176944--17176985 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
17176934 TTTTACCACA
* *
17176944 ATTAAAATTTTATAAATTT
1 ATTAAAAATATAT-AATTT
17176963 ATTAAAAATATATAATTT
1 ATTAAAAATATATAATTT
17176981 -TTAAA
1 ATTAAA
17176986 TTTCCTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAAAAATATATAATTT
Found at i:17179427 original size:15 final size:16
Alignment explanation
Indices: 17179389--17179479 Score: 83
Period size: 14 Copynumber: 6.2 Consensus size: 16
17179379 AGAAAAATAT
*
17179389 TCGAATC-TACC-TTT
1 TCGAATCATACCGTTA
17179403 TCG-ATCATACCGTTA
1 TCGAATCATACCGTTA
*
17179418 TCGAAT-ATACC-TTT
1 TCGAATCATACCGTTA
17179432 TCG-ATCATACCGTTA
1 TCGAATCATACCGTTA
* *
17179447 TCGAAT-TTACC-TTT
1 TCGAATCATACCGTTA
17179461 TC-AATCATACCGTTA
1 TCGAATCATACCGTTA
17179476 TCGA
1 TCGA
17179480 CACGTGATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.13
14 25 0.41
15 23 0.38
16 5 0.08
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (16 bp):
TCGAATCATACCGTTA
Found at i:17179431 original size:29 final size:29
Alignment explanation
Indices: 17179389--17179479 Score: 155
Period size: 29 Copynumber: 3.1 Consensus size: 29
17179379 AGAAAAATAT
*
17179389 TCGAATCTACCTTTTCGATCATACCGTTA
1 TCGAATATACCTTTTCGATCATACCGTTA
17179418 TCGAATATACCTTTTCGATCATACCGTTA
1 TCGAATATACCTTTTCGATCATACCGTTA
* *
17179447 TCGAATTTACCTTTTCAATCATACCGTTA
1 TCGAATATACCTTTTCGATCATACCGTTA
17179476 TCGA
1 TCGA
17179480 CACGTGATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (29 bp):
TCGAATATACCTTTTCGATCATACCGTTA
Found at i:17180813 original size:22 final size:21
Alignment explanation
Indices: 17180773--17180813 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17180763 TAATTCATCA
*
17180773 AAAAAATTAAAAATTTTAAGG
1 AAAAAATGAAAAATTTTAAGG
*
17180794 AAAAAATGAAATATTGTTAA
1 AAAAAATGAAAAATT-TTAA
17180814 AATAGATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (21 bp):
AAAAAATGAAAAATTTTAAGG
Found at i:17194234 original size:36 final size:37
Alignment explanation
Indices: 17194177--17194323 Score: 192
Period size: 36 Copynumber: 4.0 Consensus size: 37
17194167 TATTGTTATT
*
17194177 AGATCGATAGCGCGTCAATTCCAAACACAACATAA-A
1 AGATCGATAGCGCGTCAATTCCAAACACAAAATAATA
* *
17194213 AGATTGATAACGCGTCAATTCCAAACACAAAATAATA
1 AGATCGATAGCGCGTCAATTCCAAACACAAAATAATA
*
17194250 A-ATCGATAGCGCGTCAATTTCAAACACAAAATAATA
1 AGATCGATAGCGCGTCAATTCCAAACACAAAATAATA
* *
17194286 GATATTTC-ATAGCGCGTCAATTCCAAACACAAAGTAAT
1 -AGA--TCGATAGCGCGTCAATTCCAAACACAAAATAAT
17194324 TACTTTTATA
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
36 64 0.65
37 3 0.03
38 1 0.01
39 28 0.29
40 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (37 bp):
AGATCGATAGCGCGTCAATTCCAAACACAAAATAATA
Found at i:17194265 original size:72 final size:75
Alignment explanation
Indices: 17194179--17194323 Score: 215
Period size: 72 Copynumber: 2.0 Consensus size: 75
17194169 TTGTTATTAG
* *
17194179 ATCGATAGCGCGTCAATTCCAAACACAACATAA-A-AGA-TTGATAACGCGTCAATTCCAAACAC
1 ATCGATAGCGCGTCAATTCCAAACACAAAATAATAGAGATTTCATAACGCGTCAATTCCAAACAC
17194241 AAAATAATAA
66 AAAATAATAA
* * *
17194251 ATCGATAGCGCGTCAATTTCAAACACAAAATAATAGATATTTCATAGCGCGTCAATTCCAAACAC
1 ATCGATAGCGCGTCAATTCCAAACACAAAATAATAGAGATTTCATAACGCGTCAATTCCAAACAC
*
17194316 AAAGTAAT
66 AAAATAAT
17194324 TACTTTTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 31 0.48
73 1 0.02
74 2 0.03
75 30 0.47
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (75 bp):
ATCGATAGCGCGTCAATTCCAAACACAAAATAATAGAGATTTCATAACGCGTCAATTCCAAACAC
AAAATAATAA
Found at i:17198531 original size:11 final size:11
Alignment explanation
Indices: 17198517--17198586 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
17198507 TTTAAATGGG
17198517 TTTTAAATTTA
1 TTTTAAATTTA
17198528 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
17198540 ATTT-ATTTTAA
1 TTTTAAATTT-A
*
17198551 ATTTAAATTTA
1 TTTTAAATTTA
17198562 CTTATTTAAATTTA
1 --T-TTTAAATTTA
*
17198576 CTTTAAATTTA
1 TTTTAAATTTA
17198587 AGTTTAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
11 31 0.63
12 8 0.16
14 10 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:17198538 original size:6 final size:6
Alignment explanation
Indices: 17198518--17198593 Score: 68
Period size: 6 Copynumber: 12.8 Consensus size: 6
17198508 TTAAATGGGT
* * *
17198518 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
* *
17198566 TTTAAA TTT-AC TTTAAA TTTAAG TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
17198594 TCAAATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 12 0.21
6 39 0.70
8 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:17198538 original size:17 final size:17
Alignment explanation
Indices: 17198518--17198592 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
17198508 TTAAATGGGT
17198518 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
17198535 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
17198552 TTTAAATTTA-CTT--A
1 TTTAAATTTATTTTAAA
*
17198566 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
17198583 TTTAAGTTTA
1 TTTAAATTTA
17198593 ATCAAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 2 0.04
17 37 0.71
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:17198570 original size:14 final size:14
Alignment explanation
Indices: 17198551--17198578 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17198541 TTTATTTTAA
17198551 ATTTAAATTTACTT
1 ATTTAAATTTACTT
17198565 ATTTAAATTTACTT
1 ATTTAAATTTACTT
17198579 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:17198572 original size:31 final size:31
Alignment explanation
Indices: 17198534--17198592 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
17198524 TTTATTTTAA
*
17198534 ATTTAAATTTATTTTAAATTTAAATTTACTT
1 ATTTAAATTTACTTTAAATTTAAATTTACTT
*
17198565 ATTTAAATTTACTTTAAATTTAAGTTTA
1 ATTTAAATTTACTTTAAATTTAAATTTA
17198593 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTACTT
Found at i:17200697 original size:90 final size:90
Alignment explanation
Indices: 17200554--17200963 Score: 551
Period size: 90 Copynumber: 4.5 Consensus size: 90
17200544 TAAACTGCCC
* *
17200554 AAAAATTATATTTTAACCCC-AAACTTTTTAAAAATTACATTTTAACCCTAAAACATTTCTAAAA
1 AAAAATTATATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTTTCTAAAA
17200618 TTACATTTTAACCCTAAAACTTTCT
66 TTACATTTTAACCCTAAAACTTTCT
* *
17200643 AAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTTCTAAAA
1 AAAAATTATATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTTTCTAAAA
*
17200708 TTACATTTTGACCCTAAAACTTTCT
66 TTACATTTTAACCCTAAAACTTTCT
* ** * * * *
17200733 AAAAATTATATTTTGACCTTAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTATCCAAAA
1 AAAAATTATATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTTTCTAAAA
* * *
17200798 TTACATTTTAACCTTAAAATTTTTCC
66 TTACATTTTAACCCTAAAA-CTTTCT
* *
17200824 AAAAATTATATTTTAACCCAAAAAC-TTTCTAAAAATTACATTTTAACCTTAAAA-TTTTCTAAA
1 AAAAATTATATTTTAACCCCAAAACTTTTC-AAAAATTACATTTTAACCCTAAAACTTTTCT-AA
*
17200887 AATTACATTTTAACCTTAAAACTTTTCT
64 AATTACATTTTAACCCTAAAAC-TTTCT
**
17200915 -AAAATTATATTTTTAACCCCAAAAC-TTTCTAAAAATTGTATTTTAACCC
1 AAAAATTATA-TTTTAACCCCAAAACTTTTC-AAAAATTACATTTTAACCC
17200964 CGATTTTGCC
Statistics
Matches: 285, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
89 19 0.07
90 157 0.55
91 109 0.38
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (90 bp):
AAAAATTATATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTTTCTAAAA
TTACATTTTAACCCTAAAACTTTCT
Found at i:17200964 original size:30 final size:30
Alignment explanation
Indices: 17200554--17200963 Score: 483
Period size: 30 Copynumber: 13.6 Consensus size: 30
17200544 TAAACTGCCC
* * *
17200554 AAAAATTATATTTTAACCC-CAAACTTTTT
1 AAAAATTACATTTTAACCCTAAAACTTTCT
17200583 AAAAATTACATTTTAACCCTAAAACATTTCT
1 AAAAATTACATTTTAACCCTAAAAC-TTTCT
17200614 -AAAATTACATTTTAACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCTAAAACTTTCT
*
17200643 AAAAATTACATTTTAACCCCAAAACTTT-T
1 AAAAATTACATTTTAACCCTAAAACTTTCT
*
17200672 CCAAAATTACATTTTAACCCTAAAACTTTTCT
1 -AAAAATTACATTTTAACCCTAAAAC-TTTCT
*
17200704 -AAAATTACATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCTAAAACTTTCT
* * *
17200733 AAAAATTATATTTTGACCTTAAAACTTT-T
1 AAAAATTACATTTTAACCCTAAAACTTTCT
* *
17200762 CCAAAATTACATTTTGACCCTAAAACTTATC-
1 -AAAAATTACATTTTAACCCTAAAACTT-TCT
* * * *
17200793 CAAAATTACATTTTAACCTTAAAATTTTTCC
1 AAAAATTACATTTTAACCCTAAAA-CTTTCT
* *
17200824 AAAAATTATATTTTAACCCAAAAACTTTCT
1 AAAAATTACATTTTAACCCTAAAACTTTCT
* *
17200854 AAAAATTACATTTTAACCTTAAAATTTTCT
1 AAAAATTACATTTTAACCCTAAAACTTTCT
*
17200884 AAAAATTACATTTTAACCTTAAAACTTTTCT
1 AAAAATTACATTTTAACCCTAAAAC-TTTCT
* *
17200915 -AAAATTATATTTTTAACCCCAAAACTTTCT
1 AAAAATTACA-TTTTAACCCTAAAACTTTCT
**
17200945 AAAAATTGTATTTTAACCC
1 AAAAATTACATTTTAACCC
17200964 CGATTTTGCC
Statistics
Matches: 336, Mismatches: 30, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
29 30 0.09
30 249 0.74
31 56 0.17
32 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTAAAACTTTCT
Found at i:17203755 original size:23 final size:23
Alignment explanation
Indices: 17203729--17203873 Score: 126
Period size: 23 Copynumber: 6.4 Consensus size: 23
17203719 AGTGCTGGGC
17203729 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
17203752 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
17203771 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
17203791 ATCAGAGAGCACACACACAGTGCTAA
1 AACAGAGAGCACACA-A-AGTGCT-A
* *
17203817 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
17203841 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
17203864 ATCAGAGAGC
1 AACAGAGAGC
17203874 GCGCTAGTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
16 10 0.10
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 52 0.54
24 2 0.02
25 11 0.11
26 2 0.02
27 11 0.11
28 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:17206550 original size:17 final size:17
Alignment explanation
Indices: 17206502--17206572 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
17206492 GGGCCCAACA
17206502 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* * *
17206519 AAAATTAAGTCTATTTT
1 AAATTTAAATTTATTTT
**
17206536 AAATTTAAATTTATTGG
1 AAATTTAAATTTATTTT
*
17206553 GAATTTAAATTTA-TTT
1 AAATTTAAATTTATTTT
17206569 AAAT
1 AAAT
17206573 AATATCTAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
16 4 0.10
17 38 0.90
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:17207282 original size:3 final size:3
Alignment explanation
Indices: 17207231--17207265 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17207221 TTAATAAATG
17207231 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17207266 ATAGGTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17208523 original size:30 final size:30
Alignment explanation
Indices: 17208458--17208752 Score: 85
Period size: 30 Copynumber: 10.0 Consensus size: 30
17208448 TTTGACCCCC
** ** *
17208458 AAACTTTTTAAAAATTA-CATTTCGACCCA
1 AAACTTTACAAAAATTACCATTTTAACCCT
***
17208487 AAACTTTACAAAAATTATGTTTTTAACCCT
1 AAACTTTACAAAAATTACCATTTTAACCCT
* * *
17208517 AAACTTTTCCAAAATTACCATTTTACCCCT
1 AAACTTTACAAAAATTACCATTTTAACCCT
* *
17208547 AAAC-TT-CGAAAAATT-TCATTTTTGACTCC-
1 AAACTTTAC-AAAAATTACCA-TTTTAAC-CCT
* * * **
17208576 AAATTTTCCAAAAATCACCATTTTGTCCCT
1 AAACTTTACAAAAATTACCATTTTAACCCT
* * * ** ** *
17208606 AAAC-TTCCAAGAGTT-TTATTTTTGGCCCC
1 AAACTTTACAAAAATTACCA-TTTTAACCCT
*
17208635 AAACTTTCCAAAAATTACCATTTT-ACCCT
1 AAACTTTACAAAAATTACCATTTTAACCCT
* * * * *
17208664 TAATTTTTCAAAAAATT--CATTTTTGACCTT
1 AAACTTTAC-AAAAATTACCA-TTTTAACCCT
* * * * *
17208694 GAACTTTCCAAAAATCACCATTTTACCCCC
1 AAACTTTACAAAAATTACCATTTTAACCCT
*
17208724 AAA-TATT-C-AAAATTTCCATTTTTAACCCT
1 AAACT-TTACAAAAATTACCA-TTTTAACCCT
17208753 GAGCCTCAAA
Statistics
Matches: 196, Mismatches: 52, Indels: 36
0.69 0.18 0.13
Matches are distributed among these distances:
28 14 0.07
29 82 0.42
30 94 0.48
31 6 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (30 bp):
AAACTTTACAAAAATTACCATTTTAACCCT
Found at i:17208559 original size:59 final size:59
Alignment explanation
Indices: 17208487--17208722 Score: 210
Period size: 59 Copynumber: 4.0 Consensus size: 59
17208477 TTTCGACCCA
* * * *
17208487 AAACTTTACAAAAATTATGTTTTTAACCCTAAACTTTTCC-AAAATTACCATTTTACCCCT
1 AAACTTCA-AAAAATTATATTTTTGACCCTAAAC-TTTCCAAAAATCACCATTTTACCCCT
* * **
17208547 AAACTTCGAAAAATT-TCATTTTTGACTCC-AAATTTTCCAAAAATCACCATTTTGTCCCT
1 AAACTTCAAAAAATTAT-ATTTTTGAC-CCTAAACTTTCCAAAAATCACCATTTTACCCCT
* * * * * * * *
17208606 AAACTTCCAAGAGTTTTATTTTTGGCCCCAAACTTTCCAAAAATTACCATTTTACCCTT
1 AAACTTCAAAAAATTATATTTTTGACCCTAAACTTTCCAAAAATCACCATTTTACCCCT
** * * *
17208665 AATTTTTCAAAAAATT-CATTTTTGACCTTGAACTTTCCAAAAATCACCATTTTACCCC
1 AA-ACTTCAAAAAATTATATTTTTGACCCTAAACTTTCCAAAAATCACCATTTTACCCC
17208723 CAAATATTCA
Statistics
Matches: 141, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
58 8 0.06
59 116 0.82
60 17 0.12
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (59 bp):
AAACTTCAAAAAATTATATTTTTGACCCTAAACTTTCCAAAAATCACCATTTTACCCCT
Found at i:17208676 original size:29 final size:30
Alignment explanation
Indices: 17208636--17208721 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
17208626 TTTGGCCCCA
17208636 AACTTTCCAAAAATTACCATTTTACCCTT-
1 AACTTTCCAAAAATTACCATTTTACCCTTG
* *
17208665 AATTTTTCAAAAAATT--CATTTTTGA-CCTTG
1 AA-CTTTCCAAAAATTACCA-TTTT-ACCCTTG
*
17208695 AACTTTCCAAAAATCACCATTTTACCC
1 AACTTTCCAAAAATTACCATTTTACCC
17208722 CCAAATATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
28 2 0.04
29 21 0.47
30 20 0.44
31 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTTCCAAAAATTACCATTTTACCCTTG
Found at i:17208733 original size:59 final size:58
Alignment explanation
Indices: 17208517--17208746 Score: 214
Period size: 59 Copynumber: 3.9 Consensus size: 58
17208507 TTTTAACCCT
* *
17208517 AAACTTTTCC-AAAATTACCATTTTACCCCTAAACTTCGAAAAATTTCATTTTTGA-CTCC
1 AAAC-TTTCCAAAAATCACCATTTTACCCCTAAATTTC-AAAAATTTCATTTTTGACCT-C
* ** * * * * * *
17208576 AAATTTTCCAAAAATCACCATTTTGTCCCTAAACTTCCAAGAGTTTTATTTTTGGCCCC
1 AAACTTTCCAAAAATCACCATTTTACCCCTAAA-TTTCAAAAATTTCATTTTTGACCTC
* * * * *
17208635 AAACTTTCCAAAAATTACCATTTTACCCTTAATTTTTCAAAAAATTCATTTTTGACCTT
1 AAACTTTCCAAAAATCACCATTTTACCCCTAA-ATTTCAAAAATTTCATTTTTGACCTC
* *
17208694 GAACTTTCCAAAAATCACCATTTTACCCCCAAATATTC-AAAATTTCCATTTTT
1 AAACTTTCCAAAAATCACCATTTTACCCCTAAAT-TTCAAAAATTT-CATTTTT
17208747 AACCCTGAGC
Statistics
Matches: 134, Mismatches: 31, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
58 12 0.09
59 119 0.89
60 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
AAACTTTCCAAAAATCACCATTTTACCCCTAAATTTCAAAAATTTCATTTTTGACCTC
Found at i:17211724 original size:21 final size:23
Alignment explanation
Indices: 17211686--17211731 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
17211676 AAAAAATGAG
*
17211686 TTTTATAAGAAATTACTTGGGTTT
1 TTTTATAAGAAA-TACTTGGATTT
17211710 TTTTAT-AGAAA-ACTTGGATTT
1 TTTTATAAGAAATACTTGGATTT
17211731 T
1 T
17211732 GCAGGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
23 5 0.24
24 6 0.29
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (23 bp):
TTTTATAAGAAATACTTGGATTT
Found at i:17217244 original size:18 final size:18
Alignment explanation
Indices: 17217216--17217266 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
17217206 CGCAAGACTC
*
17217216 AATTCATTTTTTAAACG-
1 AATTTATTTTTTAAACGA
* *
17217233 AATCTTATTTTTTTATCGA
1 AAT-TTATTTTTTAAACGA
17217252 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
17217267 TCTCTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (18 bp):
AATTTATTTTTTAAACGA
Found at i:17219813 original size:12 final size:12
Alignment explanation
Indices: 17219796--17219821 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17219786 CTGATCTAAT
17219796 TCGGTTAATCGA
1 TCGGTTAATCGA
17219808 TCGGTTAATCGA
1 TCGGTTAATCGA
17219820 TC
1 TC
17219822 TAATTTTGTC
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:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (12 bp):
TCGGTTAATCGA
Found at i:17224781 original size:13 final size:13
Alignment explanation
Indices: 17224763--17224809 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
17224753 ATTATTTTTT
17224763 ATAAAATATTTAA
1 ATAAAATATTTAA
* *
17224776 ATAAAACAATTAA
1 ATAAAATATTTAA
*
17224789 ATATCAATATTTAA
1 ATA-AAATATTTAA
17224803 A-AAAATA
1 ATAAAATA
17224810 AAAAAAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
12 4 0.15
13 15 0.56
14 8 0.30
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATATTTAA
Found at i:17225288 original size:15 final size:15
Alignment explanation
Indices: 17225263--17225302 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
17225253 AAATTGTGAG
17225263 ATTTAAATTTAAAAT-
1 ATTT-AATTTAAAATC
17225278 ATTATAATTTAAAATC
1 ATT-TAATTTAAAATC
17225294 ATTTAATTT
1 ATTTAATTT
17225303 TATCATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAATTTAAAATC
Found at i:17229655 original size:3 final size:3
Alignment explanation
Indices: 17229649--17229674 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17229639 CAATGATGAT
17229649 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
17229675 CAATGGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17235541 original size:20 final size:20
Alignment explanation
Indices: 17235516--17235553 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17235506 TCCATTGCAT
17235516 TGCTGAAGCAAATGACTCAC
1 TGCTGAAGCAAATGACTCAC
17235536 TGCTGAAGCAAATGACTC
1 TGCTGAAGCAAATGACTC
17235554 GATGAGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
TGCTGAAGCAAATGACTCAC
Found at i:17236164 original size:12 final size:12
Alignment explanation
Indices: 17236147--17236171 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17236137 TATTATCTTT
17236147 AAATATAAATAA
1 AAATATAAATAA
17236159 AAATATAAATAA
1 AAATATAAATAA
17236171 A
1 A
17236172 TAAAGATGAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:17237689 original size:816 final size:813
Alignment explanation
Indices: 17236121--17238961 Score: 3060
Period size: 816 Copynumber: 3.5 Consensus size: 813
17236111 ACGCGATCTA
* * * *
17236121 AATGTAAATATAAATTTATTATCTTTAAATATAAATAAAAATATAAATAAATAA-AGATGAAATG
1 AATGTAAATATAAATTTGTTATCTTTAAAAACAAATAAAAATATAAATAAATAAGAGATGAAAAG
* * * *
17236185 AGTATAAATGTCAAAAATAATTATCAATAGAGAGTATAAAAAAGAGAGAGACTAATACTGACATA
66 AGTATAAATGTCAAAAATAATTATCAACAGAGAGTATAAAAAAAAAAGAGAC-AATA-TGAGATA
* * * * * * *
17236250 AAAAATGAACGTGAAAAACACAAAACCAAATAAAATCGGTTAAGGGATCGTTCCCCCTCATGATT
129 AAAAATGAACAT-AAACACAC-AAACCAAACAAAATCAGTTGAGGGATCGTT-TCCCTCGTGATT
* * * * * * *
17236315 CTCT-CCCTCAACCTCAACCAATAAATATATTTAACTCCATTAATTGTATTTTATCAAATGTTAT
191 CTCTCCCCTCAACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAAATGTCAT
* * * * *
17236379 TTTATATATCTCGTGTCAGATATTATATCAGAAATAATGAAAAGAAATATAATGTATTTCCATTC
256 TTTACATATCACGTGTCAGATATTATATCAGAAATCAT-AAAA-AAACATAAAGTATTTCCATTC
* * * *
17236444 TAACCTTCACTCCACCTTCCAAACTAGTCATTTGAGTTTCCTAAGCAATGCTAAATCTAAATTTA
319 TAACCTTCACTCCACCTTCCAAACTTGTCATTTGAATTTCCTAA-CAATACTAAATCCAAATTTA
* * *
17236509 TGAATTTAAATTCCAAAATCTATAATACTTTGAGGAATTATTGCATTGAAATAGGGAGTCAAAGA
383 TGAATTTAAATTCCAAAATATATAATACTTTGAGGAATTATTACATTGAAATAGAGAGTCAAAGA
* * * * *
17236574 AAAATGATATATAGCGTACATATGCTTCATGTTGCGAAGAAGGCAAATAGTTTTTCTAAGACATA
448 AAAATG--ACATAGCATACATATGCTTCATGTTGTGAAGAGGGCAAATAGTTTCTCTAAGACATA
* *
17236639 AACAATGATTATAATGCCCTTTTAAGACATAAGACATTTCTCCTATACAAAGAGAAGTCACCAAG
511 AACAATGATTATAATGCCCTTTTAAGACATAA-ACCTTTCT--TATACAAAGAGAAGTCACTAAG
* * * *
17236704 TTTTTGGAGACATTGTTGAAGACATATTTGCGTGAGAAGCGAAGGAAGTGATGGCCTCAGCATTC
573 -TTTTGGAGACATT-TTGAAGACA-ATTTGTGTGAG-TGTGAAGGAAATGAT-GCCTCAGCATTC
* * ** *
17236769 TCTTTCTAGCTAGTTTCTACTGGTTCTTTAATCTTTGCTCTTGTTTTGTTTTTTTTCCACTACTA
633 TCTTTCTAGCTAGTTCCTACAGGTTCTTTAATCTTTGCTCTTCATTTG-TTTTTTTCCACTACTT
* * * * *
17236834 CATATGTAATTAAAGATATACAATCTTTATTAT-ATTGATATAGTCTACAAATATTTTTTTATGA
697 CATATATAATCAAAGACATACAATGTTTCTTATAATTGATATAGTCTACAAATATTTTTTTATGA
* * *
17236898 TCAAATTTCTTATAACTGATGTTTCGGTGATTTAAGTGTTTCATC-CATTATG
762 TCAAATTTTTTATAACTGATATTTCAGTGATTTAAGTGTTTCA-CACATTATG
* *
17236950 AATGTAAATAT-AATTTGTTTTCTTTAAAAACAAATATAAATATAAATAAATAAGAGATGAAAAG
1 AATGTAAATATAAATTTGTTATCTTTAAAAACAAATAAAAATATAAATAAATAAGAGATGAAAAG
* **
17237014 AGTATAAATGTCAAAAATAATTATCAGCAGAGAGTATAAAAAAAAAAGAAGA-AA-A-GAGACGA
66 AGTATAAATGTCAAAAATAATTATCAACAGAGAGTATAAAAAAAAAAG-AGACAATATGAGATAA
* * ** *
17237076 ATACT-AACAT-TTCACACAAACCAAACAAAATCAGTTGAGGAATCGTTTCCCTCGTGATTCTCT
130 AAAATGAACATAAACACACAAACCAAACAAAATCAGTTGAGGGATCGTTTCCCTCGTGATTCTCT
* * *
17237139 CTCCTCAACCTAAACCAACAAATATCTTCAACTCCATCAATTACATTTTACCAAATG-CTATTTT
195 CCCCTCAACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAAATGTC-ATTTT
* * * *
17237203 ACATATCATGTGTCAGATAGTATATCAGAAATCATAAAAAAACATAAAGTATTTCTATTTTAACC
259 ACATATCACGTGTCAGATATTATATCAGAAATCATAAAAAAACATAAAGTATTTCCATTCTAACC
* * * *
17237268 TTCACGT-CACCTGCCAAACTTGTCATTTGAATTTCCTAACAATACGATATCCAAATGTATGAAT
324 TTCAC-TCCACCTTCCAAACTTGTCATTTGAATTTCCTAACAATACTAAATCCAAATTTATGAAT
* * *
17237332 TTAAATTCCAAAATTTATAATACTTTGAGGACTTATTACATTGAAATAGAGAGTCAAAGGAAAAT
388 TTAAATTCCAAAATATATAATACTTTGAGGAATTATTACATTGAAATAGAGAGTCAAAGAAAAAT
*
17237397 GACATAGCATACATATACTTCATGTTGTGAAGAGGGCAAATAGTTTCTCTAAGACATAAACAATG
453 GACATAGCATACATATGCTTCATGTTGTGAAGAGGGCAAATAGTTTCTCTAAGACATAAACAATG
* * * * * *
17237462 ATTATAATGCCCTATTAAGACATAAACCTTTCTGTTATTCAAATAGAAATCATTAAATTTTGGGA
518 ATTATAATGCCCTTTTAAGACATAAACCTTTC--TTATACAAAGAGAAGTCACTAAGTTTT-GGA
*
17237527 GACATTATTGAAGACAGATTTGTGTGAGTTGTGAAGGAAATGATGACCTCAGCATTTTTCTTT-T
580 GACATT-TTGAAGACA-ATTTGTGTGAG-TGTGAAGGAAATGATG-CCTCAGCA-TTCTCTTTCT
17237591 GAGCTAGTTCCTACAGGTTCTTTAATCTTTGCTCTTCATTTGTTTTTTTCCACTACTTCATATAT
640 -AGCTAGTTCCTACAGGTTCTTTAATCTTTGCTCTTCATTTGTTTTTTTCCACTACTTCATATAT
* * * *
17237656 AATCAAACACATACAATGTTTCTTATAATTGATATGGTCTACAAATATCTTTTTATGGTCAAATT
704 AATCAAAGACATACAATGTTTCTTATAATTGATATAGTCTACAAATATTTTTTTATGATCAAATT
* * * * * *
17237721 TTTTATAATTGATATTTAAGTGATTTAAGTGTTTTACGCGTTCTG
769 TTTTATAACTGATATTTCAGTGATTTAAGTGTTTCACACATTATG
* * * * * *
17237766 AATATAAATAT-GATTTCGTTATCTTTAAAAACAAATAAAAATATCAATAATTAAGAGGTGAAAC
1 AATGTAAATATAAATTT-GTTATCTTTAAAAACAAATAAAAATATAAATAAATAAGAGATGAAAA
* * * * * * * * * * *
17237830 GAGTATAGATGT-TAAAACAGTTATCAGCAGAGAGTGTAAAAAATATATAGA-TAT-TG-GCGTA
65 GAGTATAAATGTCAAAAATAATTATCAACAGAGAGTATAAAAAAAAAAGAGACAATATGAG-ATA
**** * * *
17237891 AAAAATGGGTGTGAAAGACACAAAAGCCAAGCAAAATCGGTTGAGGGATCGTTTCCCCTCGTGAT
129 AAAAATGAACAT-AAACACAC-AAA-CCAAACAAAATCAGTTGAGGGATCGTTT-CCCTCGTGAT
* * *
17237956 TCTCTCCCCTCGACCTCAACCAACAAATATCTTCAACTCCATCCATTGTATTTTACCAAATGTCA
190 TCTCTCCCCTCAACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAAATGTCA
* * *
17238021 TTTTACATATCACGTGTCAGATATTATATTAAAAATCATAAAAAGAA-ATGTAAAGTATTACCAT
255 TTTTACATATCACGTGTCAGATATTATATCAGAAATCATAAAAA-AACA--TAAAGTATTTCCAT
* * * * *
17238085 TCTAACTTTCGCTCCATCTTCCAAACTTATCATTTG-AGTTCTCTAAACAATACTAAATCCAAAT
317 TCTAACCTTCACTCCACCTTCCAAACTTGTCATTTGAATTTC-CT-AACAATACTAAATCCAAAT
* * * * * *
17238149 TTATAAATTTAAATTCCAAAATATATAACACTTTTAAGATTTATTACATTTAAATAGAGAGTC-A
380 TTATGAATTTAAATTCCAAAATATATAATACTTTGAGGAATTATTACATTGAAATAGAGAGTCAA
* * * *
17238213 AGAAAAAAGACATAGCATACGTATGCTTCATGTTGTGAAGAGGGCAAATAGTTTCTATAAGACAG
445 AGAAAAATGACATAGCATACATATGCTTCATGTTGTGAAGAGGGCAAATAGTTTCTCTAAGACAT
* * *
17238278 AAACAATGATTATAATTCCCTTTTAAGACATAAAACCTTTC---TCCTAAGAGAAGTCACTAAGT
510 AAACAATGATTATAATGCCCTTTTAAGACAT-AAACCTTTCTTATACAAAGAGAAGTCACTAAGT
17238340 TTT-G-G-------G-AGAC-A----T-T--GT-T----G--ATG--GCCTCAGCATTCTCTTTC
574 TTTGGAGACATTTTGAAGACAATTTGTGTGAGTGTGAAGGAAATGATGCCTCAGCATTCTCTTTC
* * *
17238378 TAGCTAGTTCCTATATGTTCTTTAGT-TTGTGCTCTTCATTTG-TTTTTTCCTACTACTTCATAT
639 TAGCTAGTTCCTACAGGTTCTTTAATCTT-TGCTCTTCATTTGTTTTTTTCC-ACTACTTCATAT
* *
17238441 ATAATCAAAGACATACAATGTTTCTTATAACTGATATAGTTTACAAATATTTTTTTATGATCAAA
702 ATAATCAAAGACATACAATGTTTCTTATAATTGATATAGTCTACAAATATTTTTTTATGATCAAA
* * *
17238506 TTTTTTATAACTGATATTTCAGTTATTCATGTGTTTCACACATTATG
767 TTTTTTATAACTGATATTTCAGTGATTTAAGTGTTTCACACATTATG
* * *
17238553 AATGTAAATATGAATTTGTTATCTTTAAAAACAAATAAAAATATCAATAAATAAGAGGTGAAATA
1 AATGTAAATATAAATTTGTTATCTTTAAAAACAAATAAAAATATAAATAAATAAGAGATGAAA-A
* * * * * * *
17238618 -AGTATACAGGTAAAAAAATAGTTATCAATAGCGAACGTA-AAAAAATAAAGAGACAATATTG-G
65 GAGTATAAATGT-CAAAAATAATTATCAACAGAG-A-GTATAAAAAAAAAAGAGACAATA-TGAG
* * * *
17238680 TATAAAAAATAGGA-GTGAAAGACATAAAACCAAACAAAATCAGTTGAGGGATCGTTTCACCTCG
126 -ATAAAAAAT-GAACAT-AAACACA-CAAACCAAACAAAATCAGTTGAGGGATCGTTTC-CCTCG
** *
17238744 TGATTCTCTCCCCTGGACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAATT
186 TGATTCTCTCCCCTCAACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAAAT
* * * *
17238809 GTCATTTTACATATCACGTGTAAGATACTATATCAGAAATCAGTAAGAAAAACGTAAAGTATTTT
251 GTCATTTTACATATCACGTGTCAGATATTATATCAGAAATCA-TAA-AAAAACATAAAGTATTTC
* * * * * * * * *
17238874 CATTCTAGCTTTCACTCCACCTTCCAAAGTTATCATTTGAGTTTTCTAAGTACTACTAAATTCAA
314 CATTCTAACCTTCACTCCACCTTCCAAACTTGTCATTTGAATTTCCTAA-CAATACTAAATCCAA
* *
17238939 ATTTATGAATTCAAAATCCAAAA
378 ATTTATGAATTTAAATTCCAAAA
17238962 CAACTTATTG
Statistics
Matches: 1721, Mismatches: 240, Indels: 139
0.82 0.11 0.07
Matches are distributed among these distances:
786 10 0.01
787 215 0.12
788 13 0.01
789 16 0.01
790 13 0.01
791 10 0.01
792 208 0.12
793 32 0.02
794 5 0.00
797 1 0.00
798 1 0.00
799 1 0.00
801 1 0.00
802 1 0.00
806 1 0.00
808 4 0.00
809 1 0.00
814 5 0.00
815 119 0.07
816 244 0.14
817 55 0.03
818 82 0.05
819 60 0.03
820 40 0.02
821 133 0.08
822 112 0.07
823 8 0.00
824 135 0.08
825 88 0.05
827 1 0.00
828 39 0.02
829 64 0.04
830 3 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (813 bp):
AATGTAAATATAAATTTGTTATCTTTAAAAACAAATAAAAATATAAATAAATAAGAGATGAAAAG
AGTATAAATGTCAAAAATAATTATCAACAGAGAGTATAAAAAAAAAAGAGACAATATGAGATAAA
AAATGAACATAAACACACAAACCAAACAAAATCAGTTGAGGGATCGTTTCCCTCGTGATTCTCTC
CCCTCAACCTCAACCAACAAATATCTTCAACTCCATCAATTATATTTTACCAAATGTCATTTTAC
ATATCACGTGTCAGATATTATATCAGAAATCATAAAAAAACATAAAGTATTTCCATTCTAACCTT
CACTCCACCTTCCAAACTTGTCATTTGAATTTCCTAACAATACTAAATCCAAATTTATGAATTTA
AATTCCAAAATATATAATACTTTGAGGAATTATTACATTGAAATAGAGAGTCAAAGAAAAATGAC
ATAGCATACATATGCTTCATGTTGTGAAGAGGGCAAATAGTTTCTCTAAGACATAAACAATGATT
ATAATGCCCTTTTAAGACATAAACCTTTCTTATACAAAGAGAAGTCACTAAGTTTTGGAGACATT
TTGAAGACAATTTGTGTGAGTGTGAAGGAAATGATGCCTCAGCATTCTCTTTCTAGCTAGTTCCT
ACAGGTTCTTTAATCTTTGCTCTTCATTTGTTTTTTTCCACTACTTCATATATAATCAAAGACAT
ACAATGTTTCTTATAATTGATATAGTCTACAAATATTTTTTTATGATCAAATTTTTTATAACTGA
TATTTCAGTGATTTAAGTGTTTCACACATTATG
Found at i:17243639 original size:61 final size:60
Alignment explanation
Indices: 17243574--17243711 Score: 152
Period size: 61 Copynumber: 2.3 Consensus size: 60
17243564 TAAATATAAG
* ** ** * * *
17243574 AAATTCAATAAATTTAATTCTCAATGTTTACAAAATTTGT-AATTTTAGTTCTAATTCTAAA
1 AAATTAAATAAATTTAACCCTCAACATTTACAAAATCTATCAA-TTTAGTTCTAACTCT-AA
* *
17243635 AAATTAAATAAATTTGACCCTCGACATTTACAAAATCTATCAATTTAGTTCTAACTCTAA
1 AAATTAAATAAATTTAACCCTCAACATTTACAAAATCTATCAATTTAGTTCTAACTCTAA
*
17243695 AAATTAAAAAAATTTAA
1 AAATTAAATAAATTTAA
17243712 AAAAATTCAT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 17 0.27
61 45 0.70
62 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.38
Consensus pattern (60 bp):
AAATTAAATAAATTTAACCCTCAACATTTACAAAATCTATCAATTTAGTTCTAACTCTAA
Found at i:17248722 original size:24 final size:22
Alignment explanation
Indices: 17248695--17248741 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
17248685 AAGAAAATAT
*
17248695 TTTTAAATATAATATAATTTAAAA
1 TTTTAAACAT-AT-TAATTTAAAA
*
17248719 TTTTAAACATGTTAATTTAAAA
1 TTTTAAACATATTAATTTAAAA
17248741 T
1 T
17248742 ATTTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAACATATTAATTTAAAA
Found at i:17248757 original size:24 final size:24
Alignment explanation
Indices: 17248688--17248757 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
17248678 AATTTTAAAG
*
17248688 AAAATATTTTTAAATATAATATAATTT
1 AAAATA-TTTTAAACAT-AT-TAATTT
*
17248715 -AAA-ATTTTAAACATGTTAATTT
1 AAAATATTTTAAACATATTAATTT
17248737 AAAATATTTTCAAA-ATATTAA
1 AAAATATTTT-AAACATATTAA
17248758 CAACATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.16
23 4 0.11
24 20 0.54
25 4 0.11
26 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (24 bp):
AAAATATTTTAAACATATTAATTT
Found at i:17249845 original size:18 final size:19
Alignment explanation
Indices: 17249810--17249884 Score: 93
Period size: 18 Copynumber: 3.9 Consensus size: 19
17249800 AATTATACTG
17249810 TTGTTTTTGTGATT-TTTTA
1 TTGTTTTTGTG-TTGTTTTA
*
17249829 TTGTTTTGGTTGCTT-TTTTA
1 TTGTTTTTG-TG-TTGTTTTA
17249849 TTGTTTTTGTGTT-TTTTA
1 TTGTTTTTGTGTTGTTTTA
17249867 TTGTTTTTGTGTTGTTTT
1 TTGTTTTTGTGTTGTTTT
17249885 TTTACTGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 20 0.39
19 14 0.27
20 17 0.33
ACGTcount: A:0.05, C:0.01, G:0.19, T:0.75
Consensus pattern (19 bp):
TTGTTTTTGTGTTGTTTTA
Found at i:17249885 original size:12 final size:11
Alignment explanation
Indices: 17249852--17249939 Score: 69
Period size: 11 Copynumber: 8.3 Consensus size: 11
17249842 TTTTTTATTG
17249852 TTTTTG-TG-T
1 TTTTTGTTGTT
*
17249861 TTTTTATTGTT
1 TTTTTGTTGTT
*
17249872 TTTGTGTTGTT
1 TTTTTGTTGTT
**
17249883 TTTTTACTG--
1 TTTTTGTTGTT
*
17249892 TTTTGGTTGTT
1 TTTTTGTTGTT
*
17249903 TTTTCG-TGTT
1 TTTTTGTTGTT
17249913 GTTTTTGTTGTT
1 -TTTTTGTTGTT
17249925 ATTTTTGTTGTT
1 -TTTTTGTTGTT
17249937 TTT
1 TTT
17249940 AATATTGTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
9 11 0.18
10 6 0.10
11 29 0.48
12 15 0.25
ACGTcount: A:0.03, C:0.02, G:0.19, T:0.75
Consensus pattern (11 bp):
TTTTTGTTGTT
Found at i:17249894 original size:60 final size:64
Alignment explanation
Indices: 17249822--17249939 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 64
17249812 GTTTTTGTGA
*
17249822 TTTTTTATTGTTTTGGTTGCTTTTT-TATTGTTTTTG-TG-T-TTTTTATTGTTTTTGTGTTGT
1 TTTTTTACTGTTTTGGTTGCTTTTTCTATTGTTTTTGTTGTTATTTTTATTGTTTTTGTGTTGT
* * *
17249882 TTTTTTACTGTTTTGGTTGTTTTTTCGTGTTGTTTTTGTTGTTATTTTTGTTGTTTTT
1 TTTTTTACTGTTTTGGTTGCTTTTTC-TATTGTTTTTGTTGTTATTTTTATTGTTTTT
17249940 AATATTGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
60 23 0.47
62 10 0.20
63 2 0.04
64 1 0.02
65 13 0.27
ACGTcount: A:0.04, C:0.03, G:0.19, T:0.75
Consensus pattern (64 bp):
TTTTTTACTGTTTTGGTTGCTTTTTCTATTGTTTTTGTTGTTATTTTTATTGTTTTTGTGTTGT
Found at i:17249921 original size:9 final size:9
Alignment explanation
Indices: 17249808--17249939 Score: 58
Period size: 9 Copynumber: 14.1 Consensus size: 9
17249798 AAAATTATAC
17249808 TGTTGTTTT
1 TGTTGTTTT
17249817 TG-TGATTTTT
1 TGTTG--TTTT
*
17249827 TATTGTTTT
1 TGTTGTTTT
*
17249836 GGTTGCTTTTT
1 TGTTG--TTTT
*
17249847 TATTGTTTT
1 TGTTGTTTT
17249856 TG-TGTTTTT
1 TGTTG-TTTT
*
17249865 TATTGTTTTT
1 TGTTG-TTTT
17249875 GTGTTGTTTT
1 -TGTTGTTTT
*
17249885 TTTACTGTTTT
1 TGT--TGTTTT
*
17249896 GGTTGTTTT
1 TGTTGTTTT
* *
17249905 T-TCG-TGT
1 TGTTGTTTT
17249912 TGTT-TTTGT
1 TGTTGTTT-T
*
17249921 TGTTATTTT
1 TGTTGTTTT
17249930 TGTTGTTTT
1 TGTTGTTTT
17249939 T
1 T
17249940 AATATTGTTT
Statistics
Matches: 92, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
7 3 0.03
8 8 0.09
9 42 0.46
10 19 0.21
11 20 0.22
ACGTcount: A:0.05, C:0.02, G:0.20, T:0.73
Consensus pattern (9 bp):
TGTTGTTTT
Found at i:17249939 original size:22 final size:20
Alignment explanation
Indices: 17249810--17249939 Score: 131
Period size: 20 Copynumber: 6.4 Consensus size: 20
17249800 AATTATACTG
*
17249810 TTGTTTTTG-TGATTTTTTA
1 TTGTTTTTGTTGTTTTTTTA
* *
17249829 TTGTTTTGGTTGCTTTTTTA
1 TTGTTTTTGTTGTTTTTTTA
17249849 TTGTTTTTG-TG-TTTTTTA
1 TTGTTTTTGTTGTTTTTTTA
17249867 TTGTTTTTGTGTTGTTTTTTTA
1 TTG-TTTT-TGTTGTTTTTTTA
* * *
17249889 CTGTTTTGGTTGTTTTTTCGTG
1 TTGTTTTTGTTGTTTTTT--TA
*
17249911 TTGTTTTTGTTGTTATTTTTG
1 TTGTTTTTGTTGTT-TTTTTA
17249932 TTGTTTTT
1 TTGTTTTT
17249940 AATATTGTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.11
19 14 0.15
20 29 0.31
21 16 0.17
22 22 0.23
23 4 0.04
ACGTcount: A:0.05, C:0.02, G:0.19, T:0.74
Consensus pattern (20 bp):
TTGTTTTTGTTGTTTTTTTA
Found at i:17249939 original size:54 final size:54
Alignment explanation
Indices: 17249861--17249992 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 54
17249851 GTTTTTGTGT
* * * *
17249861 TTTTTATTGTT-TTTGTGTTGTTTTT-TTACTGTTTTGGTTGTT-TTTT-CGTGTTG
1 TTTTTGTTGTTATTTTTGTTGTTTTTAATACTG-TTT-GTTGTTATTTTGC-TGATG
*
17249914 TTTTTGTTGTTATTTTTGTTGTTTTTAATATTGTTTGTTGTTATTTTGCTGATG
1 TTTTTGTTGTTATTTTTGTTGTTTTTAATACTGTTTGTTGTTATTTTGCTGATG
17249968 -TTTTGATTGTTATTTTTGTTGTTTT
1 TTTTTG-TTGTTATTTTTGTTGTTTT
17249993 GATGTTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
53 21 0.30
54 43 0.62
55 5 0.07
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (54 bp):
TTTTTGTTGTTATTTTTGTTGTTTTTAATACTGTTTGTTGTTATTTTGCTGATG
Found at i:17249990 original size:21 final size:21
Alignment explanation
Indices: 17249947--17250004 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
17249937 TTTAATATTG
17249947 TTTG-TTGTTATTTTGCTGATGT
1 TTTGATTGTTATTTT--TGATGT
*
17249969 TTTGATTGTTATTTTTGTTGT
1 TTTGATTGTTATTTTTGATGT
17249990 TTTGA-TGTTATTTTT
1 TTTGATTGTTATTTTT
17250005 TTTATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.29
21 10 0.29
22 4 0.12
23 10 0.29
ACGTcount: A:0.10, C:0.02, G:0.19, T:0.69
Consensus pattern (21 bp):
TTTGATTGTTATTTTTGATGT
Found at i:17250163 original size:12 final size:11
Alignment explanation
Indices: 17250145--17250174 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
17250135 AATTTATTTA
17250145 TTTTTAATGTT
1 TTTTTAATGTT
17250156 TGTTTTAATGTT
1 T-TTTTAATGTT
17250168 TTTTTAA
1 TTTTTAA
17250175 GTGTATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (11 bp):
TTTTTAATGTT
Found at i:17250614 original size:18 final size:16
Alignment explanation
Indices: 17250577--17250625 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
17250567 TTCAAATGGG
17250577 ATTAGAATAAATTTTTA
1 ATTA-AATAAATTTTTA
17250594 ATTAAATAAA--TTTA
1 ATTAAATAAATTTTTA
*
17250608 ATTAATTAAAATTTTTA
1 ATTAAAT-AAATTTTTA
17250625 A
1 A
17250626 ACCTAAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 6 0.21
17 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTAAATAAATTTTTA
Found at i:17250971 original size:14 final size:14
Alignment explanation
Indices: 17250954--17250983 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17250944 AGGGTTTAAA
17250954 AATTTTAATTAATT
1 AATTTTAATTAATT
17250968 AATTTTAATTAATT
1 AATTTTAATTAATT
17250982 AA
1 AA
17250984 AGATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTAATTAATT
Found at i:17251608 original size:21 final size:21
Alignment explanation
Indices: 17251575--17251619 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17251565 GAATTTAGAG
*
17251575 TTTTAAATTTAGGGATTAAGA
1 TTTTAAATCTAGGGATTAAGA
* * *
17251596 TTTTGAATCTAGGGTTTAGGA
1 TTTTAAATCTAGGGATTAAGA
17251617 TTT
1 TTT
17251620 ATGATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (21 bp):
TTTTAAATCTAGGGATTAAGA
Found at i:17251620 original size:35 final size:36
Alignment explanation
Indices: 17251540--17251620 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
17251530 GGTATCTAAA
* * *
17251540 TTTAGGATTTAGGGTATAAGGTTTTGAATTTAGAGT
1 TTTAGGATTTAGGGTATAAGATTTTGAATCTAGAGG
*
17251576 TTTA-AATTTAGGG-ATTAAGATTTTGAATCTAG-GG
1 TTTAGGATTTAGGGTA-TAAGATTTTGAATCTAGAGG
17251610 TTTAGGATTTA
1 TTTAGGATTTA
17251621 TGATTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 6 0.16
35 28 0.74
36 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (36 bp):
TTTAGGATTTAGGGTATAAGATTTTGAATCTAGAGG
Found at i:17252092 original size:23 final size:22
Alignment explanation
Indices: 17252066--17252151 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 22
17252056 AATAATAACC
* *
17252066 AAAATAGCAGCAAAAATAATAGA
1 AAAATAGCACCAAAAATAA-AAA
* *
17252089 AAAATAGTAACAAAAATAACAATA
1 AAAATAGCACCAAAAATAA-AA-A
*
17252113 AAAACAGCACCAAAATAGTAAAAA
1 AAAATAGCACCAAAA-A-TAAAAA
17252137 AAAATAGCACCAAAA
1 AAAATAGCACCAAAA
17252152 CAGCAATCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 18 0.35
24 28 0.54
25 3 0.06
26 3 0.06
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAATAGCACCAAAAATAAAAA
Found at i:17252128 original size:35 final size:34
Alignment explanation
Indices: 17252089--17252173 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 34
17252079 AAATAATAGA
*
17252089 AAAATAGTAACAAAAATAACAATAAAAACAGC-ACC
1 AAAATAGTAA-AAAAATAAC-ACAAAAACAGCAACC
* * *
17252124 AAAATAGTAAAAAAAAATAGCACCAAAACAGCAATC
1 AAAATAGT--AAAAAAATAACACAAAAACAGCAACC
17252160 AAAATAGTAAAAAA
1 AAAATAGTAAAAAA
17252174 GCACCAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 6 0.14
35 17 0.40
36 18 0.42
37 2 0.05
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (34 bp):
AAAATAGTAAAAAAATAACACAAAAACAGCAACC
Found at i:17252163 original size:24 final size:23
Alignment explanation
Indices: 17252108--17252163 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
17252098 ACAAAAATAA
*
17252108 CAATAAAAACAGCACCAAAATAG
1 CAATAAAAACAGCACCAAAACAG
* * *
17252131 TAAAAAAAAATAGCACCAAAACAG
1 -CAATAAAAACAGCACCAAAACAG
*
17252155 CAATCAAAA
1 CAATAAAAA
17252164 TAGTAAAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.64, C:0.20, G:0.07, T:0.09
Consensus pattern (23 bp):
CAATAAAAACAGCACCAAAACAG
Found at i:17252203 original size:22 final size:20
Alignment explanation
Indices: 17252168--17252248 Score: 99
Period size: 22 Copynumber: 3.9 Consensus size: 20
17252158 TCAAAATAGT
*
17252168 AAAAAAGCACCAAAACAGTA
1 AAAAAAGCACCAAAACAGCA
* *
17252188 AAAACACAACACCAAAACAACA
1 AAAA-A-AGCACCAAAACAGCA
17252210 AAAAATAGCAACCAAAACAGCA
1 AAAAA-AGC-ACCAAAACAGCA
17252232 AAAAAAGCACCAAAACA
1 AAAAAAGCACCAAAACA
17252249 ACAATATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.25
21 7 0.13
22 32 0.62
ACGTcount: A:0.67, C:0.25, G:0.06, T:0.02
Consensus pattern (20 bp):
AAAAAAGCACCAAAACAGCA
Found at i:17252244 original size:42 final size:42
Alignment explanation
Indices: 17252168--17252252 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
17252158 TCAAAATAGT
*
17252168 AAAAAAGCACCAAAACAGTAAAAACACAACACCAAAACAACA
1 AAAAAAGCACCAAAACAGCAAAAACACAACACCAAAACAACA
*
17252210 AAAAATAGCAACCAAAACAGCAAAAA-A-AGCACCAAAACAACA
1 AAAAA-AGC-ACCAAAACAGCAAAAACACAACACCAAAACAACA
17252252 A
1 A
17252253 TATAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 20 0.51
43 4 0.10
44 15 0.38
ACGTcount: A:0.67, C:0.25, G:0.06, T:0.02
Consensus pattern (42 bp):
AAAAAAGCACCAAAACAGCAAAAACACAACACCAAAACAACA
Found at i:17252488 original size:14 final size:14
Alignment explanation
Indices: 17252465--17252532 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
17252455 ATTAGGCCTA
*
17252465 GTTTAAGGTTTAAG
1 GTTTAGGGTTTAAG
17252479 GTTTAGGGTTT-AG
1 GTTTAGGGTTTAAG
*
17252492 GTTTTAGTGTTTTGAA-
1 G-TTTAG-GGTTT-AAG
*
17252508 -TTTAGGGTTTAAA
1 GTTTAGGGTTTAAG
*
17252521 GTTTAGTGTTTA
1 GTTTAGGGTTTA
17252533 TGTTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.05
13 7 0.16
14 30 0.68
15 4 0.09
17 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:17252503 original size:28 final size:26
Alignment explanation
Indices: 17252480--17252532 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
17252470 AGGTTTAAGG
*
17252480 TTTAGGGTTT-AGGTTTTAGTGTTTTGAA
1 TTTAGGGTTTAAAG-TTTAGTG-TTT-AA
17252508 TTTAGGGTTTAAAGTTTAGTGTTTA
1 TTTAGGGTTTAAAGTTTAGTGTTTA
17252533 TGTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 3 0.13
28 17 0.74
29 2 0.09
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (26 bp):
TTTAGGGTTTAAAGTTTAGTGTTTAA
Found at i:17252517 original size:35 final size:35
Alignment explanation
Indices: 17252473--17252566 Score: 84
Period size: 35 Copynumber: 2.7 Consensus size: 35
17252463 TAGTTTAAGG
* *
17252473 TTTAAGGTTTAGGGTTTAGGTTTTA-GTGTTTTGAA
1 TTTAGGGTTTAGGGTTTAGGTTTTATGT-TTTTAAA
**
17252508 TTTAGGGTTTAAAGTTTA-GTGTTTATGTTTTTAAA
1 TTTAGGGTTTAGGGTTTAGGT-TTTATGTTTTTAAA
** *
17252543 TTTAGAATTTAAGGCTTTAGGTTT
1 TTTAGGGTTT-AGGGTTTAGGTTT
17252567 AGGGATTAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
34 2 0.04
35 33 0.72
36 9 0.20
37 2 0.04
ACGTcount: A:0.23, C:0.01, G:0.23, T:0.52
Consensus pattern (35 bp):
TTTAGGGTTTAGGGTTTAGGTTTTATGTTTTTAAA
Found at i:17252567 original size:35 final size:36
Alignment explanation
Indices: 17252486--17252567 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 36
17252476 AAGGTTTAGG
* **
17252486 GTTTAGGTTT-TAGTGTTTTGAATTTAGGGTTTAAA
1 GTTTAGGTTTATAGTGTTTTAAATTTAGAATTTAAA
*
17252521 GTTTAGTGTTTAT-GT-TTTTAAATTTAGAATTTAAG
1 GTTTAG-GTTTATAGTGTTTTAAATTTAGAATTTAAA
17252556 GCTTTAGGTTTA
1 G-TTTAGGTTTA
17252568 GGGATTAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 28 0.70
36 11 0.28
37 1 0.03
ACGTcount: A:0.24, C:0.01, G:0.22, T:0.52
Consensus pattern (36 bp):
GTTTAGGTTTATAGTGTTTTAAATTTAGAATTTAAA
Found at i:17252832 original size:21 final size:21
Alignment explanation
Indices: 17252808--17252851 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
17252798 TAGGGTCTAT
* *
17252808 TTGCCCCGGAGGAGTGGAGTA
1 TTGCCCAGGAGGAGTAGAGTA
17252829 TTGCCCAGGAGGAGTAGAGTA
1 TTGCCCAGGAGGAGTAGAGTA
17252850 TT
1 TT
17252852 ACGGTGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.23
Consensus pattern (21 bp):
TTGCCCAGGAGGAGTAGAGTA
Found at i:17254936 original size:5 final size:5
Alignment explanation
Indices: 17254920--17254957 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
17254910 ACTACTAACA
* *
17254920 AAATA AAATT AATTT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
17254958 AATAACCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:17256837 original size:15 final size:15
Alignment explanation
Indices: 17256817--17256876 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
17256807 AATAAACTGC
*
17256817 ATAATCTGCTCTTGA
1 ATAATCTGCTATTGA
17256832 ATAATCTGCTATTGA
1 ATAATCTGCTATTGA
* *
17256847 ATAAGCTGCTATAG-
1 ATAATCTGCTATTGA
*
17256861 A-AATCTGCTAGTGA
1 ATAATCTGCTATTGA
17256875 AT
1 AT
17256877 TCTCTGAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 26 0.70
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (15 bp):
ATAATCTGCTATTGA
Found at i:17262570 original size:58 final size:58
Alignment explanation
Indices: 17262482--17262627 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 58
17262472 ATATATTATA
* *
17262482 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
17262539 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
17262599 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
17262628 CATTAAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.62
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:17262818 original size:16 final size:16
Alignment explanation
Indices: 17262797--17262868 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
17262787 TGAATTACTG
17262797 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
17262813 ATTACAGCTATATTCC
1 ATTACAGCTCTATTCC
*
17262829 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
17262845 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
17262861 ATTACAGC
1 ATTACAGC
17262869 GAACCAAACG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17267108 original size:59 final size:59
Alignment explanation
Indices: 17266969--17267232 Score: 358
Period size: 58 Copynumber: 4.5 Consensus size: 59
17266959 TGGGGTTAAT
* * * *
17266969 AATGGAATTTTGAAAAGTTTG-GAGGTAAAATGGTAATTTTTGGTGAAATTGAGGT-TAA
1 AATGGAATTTTGGAAAGTTCGAG-GGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAA
* * * * *
17267027 AATAGAATTTTGGATAGTTCGAGGATAAAATGGTAATTTTTGATAAAA-TCAGGGTCAAA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGA-GGTCAAA
*
17267086 AATGGAATTTTGGAAAGCTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTC-AA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAA
* *
17267144 AATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTAAAATCG-GGATCAAA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGG-TCAAA
17267203 AATGGAATTTTGGAAAGTTCGAGGGTAAAA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAA
17267233 ACATATTTTT
Statistics
Matches: 181, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
57 4 0.02
58 94 0.52
59 81 0.45
60 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.32
Consensus pattern (59 bp):
AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAA
Found at i:17267113 original size:117 final size:117
Alignment explanation
Indices: 17266969--17267232 Score: 406
Period size: 117 Copynumber: 2.3 Consensus size: 117
17266959 TGGGGTTAAT
* * * *
17266969 AATGGAATTTTGAAAAGTTTG-GAGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAATAGA
1 AATGGAATTTTGGAAAGTTCGAG-GGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAAATAGA
*
17267033 ATTTTGGATAGTTCGAGGATAAAATGGTAATTTTTGATAAAATCAGGG-TCAAA
65 ATTTTGGAAAGTTCGAGGATAAAATGGTAATTTTTGATAAAATC-GGGATCAAA
* *
17267086 AATGGAATTTTGGAAAGCTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAAATGGAA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAAATAGAA
* * *
17267151 TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGATCAAA
66 TTTTGGAAAGTTCGAGGATAAAATGGTAATTTTTGATAAAATCGGGATCAAA
17267203 AATGGAATTTTGGAAAGTTCGAGGGTAAAA
1 AATGGAATTTTGGAAAGTTCGAGGGTAAAA
17267233 ACATATTTTT
Statistics
Matches: 134, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
116 3 0.02
117 130 0.97
118 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.32
Consensus pattern (117 bp):
AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTCAAAATAGAA
TTTTGGAAAGTTCGAGGATAAAATGGTAATTTTTGATAAAATCGGGATCAAA
Found at i:17267212 original size:30 final size:29
Alignment explanation
Indices: 17267053--17267213 Score: 124
Period size: 30 Copynumber: 5.5 Consensus size: 29
17267043 GTTCGAGGAT
*
17267053 AAAATGGTAATTTTTGATAAAATCAGGGTC
1 AAAATGGTAATTTTTGGTAAAATC-GGGTC
*
17267083 AAAAATGG-AA-TTTTGG-AAAGCTCGAGGGT-
1 -AAAATGGTAATTTTTGGTAAA-ATC--GGGTC
*
17267112 AAAATGGTAATTTTTGGTAAAATTGAGGTC
1 AAAATGGTAATTTTTGGTAAAATCG-GGTC
*
17267142 AAAATGG-AA-TTTTGG-AAAGTTCGGGGGT-
1 AAAATGGTAATTTTTGGTAAA-ATC--GGGTC
17267170 AAAATGGTAATTTTTGGTAAAATCGGGATC
1 AAAATGGTAATTTTTGGTAAAATCGGG-TC
17267200 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
17267214 GGAAAGTTCG
Statistics
Matches: 107, Mismatches: 7, Indels: 33
0.73 0.05 0.22
Matches are distributed among these distances:
27 3 0.03
28 28 0.26
29 20 0.19
30 36 0.34
31 20 0.19
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGTAAAATCGGGTC
Found at i:17267232 original size:29 final size:29
Alignment explanation
Indices: 17266930--17267337 Score: 202
Period size: 29 Copynumber: 14.0 Consensus size: 29
17266920 TTTTTGACTC
* * *
17266930 TCGATGGTAAAAGTGAAATTTTGGAAA-T
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
* * *
17266958 TTG-GGGTTAATAATGGAATTTTGAAAAGT
1 TCGAGGG-TAAAAATGGAATTTTGGAAAGT
*
17266987 TTG-GAGGT-AAAATGGTAATTTTTGGTGAAA-T
1 TCGAG-GGTAAAAATGG-AA-TTTT-G-GAAAGT
* * *
17267018 T-GA-GGTTAAAATAGAATTTTGGATAGT
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
* * **
17267045 TCGAGGAT-AAAATGGTAATTTTTGATAAAA
1 TCGAGGGTAAAAATGG-AATTTTGGA-AAGT
*
17267075 TC-AGGGTCAAAAATGGAATTTTGGAAAGC
1 TCGAGGGT-AAAAATGGAATTTTGGAAAGT
*
17267104 TCGAGGGT-AAAATGGTAATTTTTGGTAAAAT
1 TCGAGGGTAAAAATGG-AA-TTTTGG-AAAGT
*
17267135 T-GA-GGTCAAAATGGAATTTTGGAAAGT
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
* *
17267162 TCGGGGGT-AAAATGGTAATTTTTGGTAAA-A
1 TCGAGGGTAAAAATGG-AA-TTTTGG-AAAGT
*
17267192 TCG-GGATCAAAAATGGAATTTTGGAAAGT
1 TCGAGGGT-AAAAATGGAATTTTGGAAAGT
*** * * *
17267221 TCGAGGGTAAAAACATATTTTTGAAAAGC
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
**
17267250 TCGAGGGTAAAAATATAATTTTTGG-AAGT
1 TCGAGGGTAAAAATGGAA-TTTTGGAAAGT
* * * ** *
17267279 T-TAGGGGTAAAAATGTATTTTTAAAAAGC
1 TCGA-GGGTAAAAATGGAATTTTGGAAAGT
** *
17267308 TCGAGGGTAAAAATATAATTTTTGAAAGT
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
17267337 T
1 T
17267338 TTGAGGTCAA
Statistics
Matches: 296, Mismatches: 50, Indels: 67
0.72 0.12 0.16
Matches are distributed among these distances:
26 3 0.01
27 10 0.03
28 65 0.22
29 127 0.43
30 64 0.22
31 24 0.08
32 3 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
TCGAGGGTAAAAATGGAATTTTGGAAAGT
Found at i:17267263 original size:117 final size:117
Alignment explanation
Indices: 17267002--17267290 Score: 345
Period size: 117 Copynumber: 2.5 Consensus size: 117
17266992 GGTAAAATGG
* * * * * *
17267002 TAATTTTTGGTGAAATTGAGGTTAAAATAGAATTTTGGATAGTTCGAGGATAAAATGGTAATTTT
1 TAATTTTTGGTAAAATCGAGGTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
***
17267067 TGATAAAATCAGGGTCAAAAATGGAATTTTGGAAAGCTCGAGGGTAAAATGG
66 TGATAAAATCAGGGTCAAAAATGGAATTTTGGAAAGCTCGAGGGTAAAAACA
* * *
17267119 TAATTTTTGGTAAAATTGAGGTCAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
1 TAATTTTTGGTAAAATCGAGGTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
* *
17267184 TGGTAAAATC-GGGATCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAACA
66 TGATAAAATCAGGG-TCAAAAATGGAATTTTGGAAAGCTCGAGGGTAAAAACA
* **
17267236 T-ATTTTT-G-AAAAGCTCGAGGGTAAAAATATAATTTTTGG-AAGTTTAGGGGTAAAA
1 TAATTTTTGGTAAAA--TCGA-GGTAAAAATAGAA-TTTTGGAAAGTTCGGGGGTAAAA
17267291 ATGTATTTTT
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
114 4 0.03
115 1 0.01
116 12 0.08
117 127 0.85
118 6 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (117 bp):
TAATTTTTGGTAAAATCGAGGTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
TGATAAAATCAGGGTCAAAAATGGAATTTTGGAAAGCTCGAGGGTAAAAACA
Found at i:17267270 original size:58 final size:57
Alignment explanation
Indices: 17266973--17267337 Score: 291
Period size: 58 Copynumber: 6.3 Consensus size: 57
17266963 GTTAATAATG
* * * * *
17266973 GAATTTTGAAAAGTTTG-GAGGTAAAATGGTAATTTTTGGTGAAATTGA-GGTTAAAATA
1 GAATTTTGGAAAGTTCGAG-GGTAAAATGGTAATTTTT-G-AAAATCGAGGGTAAAAATA
* * *
17267031 GAATTTTGGATAGTTCGAGGATAAAATGGTAATTTTTGATAAAATC-AGGGTCAAAAATG
1 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTG--AAAATCGAGGGT-AAAAATA
* * * *
17267090 GAATTTTGGAAAGCTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGA-GGTCAAAATG
1 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT-G-AAAATCGAGGGTAAAAATA
* * *
17267148 GAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTAAAATCG-GGATCAAAAATG
1 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT-G-AAAATCGAGGGT-AAAAATA
***
17267207 GAATTTTGGAAAGTTCGAGGGTAAAAACAT-ATTTTTGAAAAGCTCGAGGGTAAAAATA
1 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAA--TCGAGGGTAAAAATA
* * *
17267265 TAATTTTTGG-AAGTT-TAGGGGTAAAAAT-GT-ATTTTTAAAAAGCTCGAGGGTAAAAATA
1 GAA-TTTTGGAAAGTTCGA-GGGT-AAAATGGTAATTTTTGAAAA--TCGAGGGTAAAAATA
* *
17267323 TAATTTTTGAAAGTT
1 GAATTTTGGAAAGTT
17267338 TTGAGGTCAA
Statistics
Matches: 262, Mismatches: 30, Indels: 30
0.81 0.09 0.09
Matches are distributed among these distances:
56 4 0.02
57 9 0.03
58 153 0.58
59 94 0.36
60 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (57 bp):
GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATCGAGGGTAAAAATA
Found at i:17267338 original size:58 final size:59
Alignment explanation
Indices: 17267208--17267360 Score: 195
Period size: 58 Copynumber: 2.6 Consensus size: 59
17267198 TCAAAAATGG
* * *
17267208 AATTTTGGAAAG-TTCGAGGGTAAAAACATATTTTTGAAAAGCTCGAGGGTAAAAATAT
1 AATTTTTGAAAGTTTAGAGGGTAAAAACATATTTTTAAAAAGCTCGAGGGTAAAAATAT
* **
17267266 AATTTTTGGAAGTTTAG-GGGTAAAAATGTATTTTTAAAAAGCTCGAGGGTAAAAATAT
1 AATTTTTGAAAGTTTAGAGGGTAAAAACATATTTTTAAAAAGCTCGAGGGTAAAAATAT
* * *
17267324 AATTTTTGAAAGTTTTGA-GGTCAAAATATAATTTTTA
1 AATTTTTGAAAGTTTAGAGGGTAAAAACAT-ATTTTTA
17267361 GGAAGTTTAG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 72 0.88
59 10 0.12
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (59 bp):
AATTTTTGAAAGTTTAGAGGGTAAAAACATATTTTTAAAAAGCTCGAGGGTAAAAATAT
Found at i:17267349 original size:29 final size:30
Alignment explanation
Indices: 17267255--17267370 Score: 114
Period size: 29 Copynumber: 4.0 Consensus size: 30
17267245 AAAGCTCGAG
* *
17267255 GGTAAAAATATAATTTTT-GGAAGTTTAGG
1 GGTAAAAATATAATTTTTAGAAAGTTTAGA
* * * *
17267284 GGTAAAAATGT-ATTTTTAAAAAG-CTCGA
1 GGTAAAAATATAATTTTTAGAAAGTTTAGA
*
17267312 GGGTAAAAATATAATTTTT-GAAAGTTTTGA
1 -GGTAAAAATATAATTTTTAGAAAGTTTAGA
* *
17267342 GGTCAAAATATAATTTTTAGGAAGTTTAG
1 GGTAAAAATATAATTTTTAGAAAGTTTAG
17267371 GGACTAGAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 8 0.12
29 44 0.64
30 17 0.25
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
GGTAAAAATATAATTTTTAGAAAGTTTAGA
Found at i:17278506 original size:29 final size:29
Alignment explanation
Indices: 17278474--17278535 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
17278464 TCTTGATGGC
*
17278474 AAAAA-TGAAATTTCGGAAAATTTAGGGTT
1 AAAAATTG-AATTTCGGAAAATTTAGGGGT
* *
17278503 AAAAATTGAATTTTGGAAAGTTTAGGGGT
1 AAAAATTGAATTTCGGAAAATTTAGGGGT
17278532 AAAA
1 AAAA
17278536 TGGTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.31
Consensus pattern (29 bp):
AAAAATTGAATTTCGGAAAATTTAGGGGT
Found at i:17278543 original size:29 final size:30
Alignment explanation
Indices: 17278474--17278728 Score: 110
Period size: 30 Copynumber: 8.7 Consensus size: 30
17278464 TCTTGATGGC
* * * *
17278474 AAAAAT-GAAATTTCGGAAAATTTAGGGTT
1 AAAAATGGTAATTTTGGAAAGTTTAGGGGT
*
17278503 AAAAATTG-AATTTTGGAAAGTTTAGGGGT
1 AAAAATGGTAATTTTGGAAAGTTTAGGGGT
* *
17278532 -AAAATGGTAATTTTTTGGTGAAA---TCGAGGT
1 AAAAATGGTAA--TTTT-G-GAAAGTTTAGGGGT
* * **
17278562 TAAAATGG-AATTTTGGAAAGCTCGGGGGT
1 AAAAATGGTAATTTTGGAAAGTTTAGGGGT
* *
17278591 -AAAATGGTAATTTTTGGTAAA--ATCGGGGT
1 AAAAATGGTAA-TTTTGG-AAAGTTTAGGGGT
* **
17278620 CAAAAATGG-GATTTTGGAAAGTTCGGGGGT
1 -AAAAATGGTAATTTTGGAAAGTTTAGGGGT
* * *
17278650 AAAAA-CGTAATTTTTGAAAAGCTT-GAGGGT
1 AAAAATGGTAA-TTTTGGAAAGTTTAG-GGGT
*
17278680 AAAAAT-GTAATTTTTGG-AAGTTTCGAGGGT
1 AAAAATGGTAA-TTTTGGAAAGTTTAG-GGGT
*
17278710 AAAAAT-GTAATTTTTGAAA
1 AAAAATGGTAATTTTGGAAA
17278729 AGCTCGAGGT
Statistics
Matches: 179, Mismatches: 24, Indels: 45
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.02
27 1 0.01
28 21 0.12
29 60 0.34
30 67 0.37
31 21 0.12
32 1 0.01
33 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAAATGGTAATTTTGGAAAGTTTAGGGGT
Found at i:17278617 original size:30 final size:30
Alignment explanation
Indices: 17278513--17278757 Score: 145
Period size: 30 Copynumber: 8.3 Consensus size: 30
17278503 AAAAATTGAA
* **
17278513 TTTTGGAAAGTTTAGGGGTAAAATGGTAATT
1 TTTTGGAAAGATCGGGGGTAAAATGGTAA-T
* * *
17278544 TTTTGGTGAA-ATCGAGGTTAAAATGG-AA-
1 TTTTGG-AAAGATCGGGGGTAAAATGGTAAT
*
17278572 TTTTGGAAAGCTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAGATCGGGGGTAAAATGGTAAT
*
17278602 TTTTGGTAAA-ATC-GGGGTCAAAAATGG-GA-
1 TTTTGG-AAAGATCGGGGGT--AAAATGGTAAT
* **
17278631 TTTTGGAAAGTTCGGGGGTAAAAACGTAAT
1 TTTTGGAAAGATCGGGGGTAAAATGGTAAT
* * * *
17278661 TTTTGAAAAGCTTGAGGGTAAAAAT-GTAAT
1 TTTTGGAAAGATCGGGGGT-AAAATGGTAAT
* *
17278691 TTTTGG-AAGTTTCGAGGGTAAAAAT-GTAAT
1 TTTTGGAAAG-ATCGGGGGT-AAAATGGTAAT
* * *
17278721 TTTTGAAAAGCTC-GAGGTATAAAT-GTAAT
1 TTTTGGAAAGATCGGGGGTA-AAATGGTAAT
17278750 TTTTGGAA
1 TTTTGGAA
17278758 GTTTCAAGGT
Statistics
Matches: 170, Mismatches: 29, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
27 2 0.01
28 28 0.16
29 38 0.22
30 66 0.39
31 34 0.20
32 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (30 bp):
TTTTGGAAAGATCGGGGGTAAAATGGTAAT
Found at i:17278665 original size:59 final size:58
Alignment explanation
Indices: 17278502--17278725 Score: 229
Period size: 59 Copynumber: 3.8 Consensus size: 58
17278492 AATTTAGGGT
* ** * * *
17278502 TAAAAATTGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTTGGTGAAATCGAGG
1 TAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAGGTAA-TTTTTGGTAAAATCGGGG
* * *
17278561 TTAAAATGGAATTTTGGAAAGCTCGGGGGTAAAATGGTAATTTTTGGTAAAATCGGGG
1 TAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAGGTAATTTTTGGTAAAATCGGGG
* * *
17278619 TCAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAAACGTAATTTTT-G-AAAAGCTTGAGGG
1 T-AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAGGTAATTTTTGGTAAAA--TCG-GGG
* * *
17278679 TAAAAATGTAATTTTTGG-AAGTTTCGAGGGTAAAAATGTAATTTTTG
1 TAAAAATGGAA-TTTTGGAAAG-TTCGGGGGTAAAAAGGTAATTTTTG
17278726 AAAAGCTCGA
Statistics
Matches: 141, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
57 4 0.03
58 18 0.13
59 87 0.62
60 32 0.23
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (58 bp):
TAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAGGTAATTTTTGGTAAAATCGGGG
Found at i:17278724 original size:60 final size:59
Alignment explanation
Indices: 17278555--17278783 Score: 213
Period size: 59 Copynumber: 3.9 Consensus size: 59
17278545 TTTGGTGAAA
* * * *
17278555 TCGAGGTTAAAATGGAA-TTTTGGAAAG-CTCGGGGGT-AAAATGGTAATTTTTGGTAAAA--
1 TCGAGGTAAAAATGTAATTTTTGG-AAGTTTCGAGGGTAAAAAT-GTAATTTTT-G-AAAAGC
* ** * *
17278613 TCGGGGTCAAAAATGGGA-TTTTGGAAAG-TTCGGGGGTAAAAACGTAATTTTTGAAAAGC
1 TCGAGGT-AAAAATGTAATTTTTGG-AAGTTTCGAGGGTAAAAATGTAATTTTTGAAAAGC
*
17278672 TTGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAAGC
1 TCGA-GGTAAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAAGC
* * * *
17278732 TCGAGGTATAAATGTAATTTTTGGAAGTTTC-AAGGTCAAAATATAATTTTTG
1 TCGAGGTAAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGTAATTTTTG
17278784 GGAAGTTTAG
Statistics
Matches: 148, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
57 4 0.03
58 25 0.17
59 74 0.50
60 45 0.30
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (59 bp):
TCGAGGTAAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAATGTAATTTTTGAAAAGC
Found at i:17278767 original size:29 final size:29
Alignment explanation
Indices: 17278647--17278791 Score: 139
Period size: 30 Copynumber: 4.9 Consensus size: 29
17278637 AAAGTTCGGG
* * * * *
17278647 GGTAAAAACGTAATTTTTGAAAAGCTTGAG
1 GGTAAAAATGTAATTTTTG-GAAGTTTCAA
*
17278677 GGTAAAAATGTAATTTTTGGAAGTTTCGAG
1 GGTAAAAATGTAATTTTTGGAAGTTTC-AA
* * *
17278707 GGTAAAAATGTAATTTTTGAAAAG-CTCGA
1 GGTAAAAATGTAATTTTTG-GAAGTTTCAA
*
17278736 GGTATAAATGTAATTTTTGGAAGTTTCAA
1 GGTAAAAATGTAATTTTTGGAAGTTTCAA
* *
17278765 GGTCAAAATATAATTTTTGGGAAGTTT
1 GGTAAAAATGTAATTTTT-GGAAGTTT
17278792 AGGGACTAGA
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
28 3 0.03
29 41 0.43
30 49 0.51
31 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.36
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGGAAGTTTCAA
Found at i:17278790 original size:30 final size:28
Alignment explanation
Indices: 17278681--17278791 Score: 116
Period size: 29 Copynumber: 3.8 Consensus size: 28
17278671 CTTGAGGGTA
*
17278681 AAAATGTAATTTTTGGAAGTTTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTTC-AAGGT
* * *
17278710 AAAAATGTAATTTTTGAAAAG-CTCGAGGT
1 -AAAATGTAATTTTTG-GAAGTTTCAAGGT
17278739 ATAAATGTAATTTTTGGAAGTTTCAAGGT
1 A-AAATGTAATTTTTGGAAGTTTCAAGGT
*
17278768 CAAAATATAATTTTTGGGAAGTTT
1 -AAAATGTAATTTTT-GGAAGTTT
17278792 AGGGACTAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
28 4 0.06
29 35 0.51
30 26 0.38
31 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTCAAGGT
Found at i:17279982 original size:24 final size:24
Alignment explanation
Indices: 17279954--17280004 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
17279944 AAATGTTATT
17279954 AATACTCATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
*
17279978 AATACTTATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
17280002 AAT
1 AAT
17280005 GCAATGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (24 bp):
AATACTCATTAATGCATTTAAAAC
Found at i:17280722 original size:11 final size:12
Alignment explanation
Indices: 17280701--17280729 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
17280691 AAAAATGAAT
17280701 TTTAAATTTAAA
1 TTTAAATTTAAA
17280713 TTTAAA-TTAAA
1 TTTAAATTTAAA
17280724 TTTAAA
1 TTTAAA
17280730 CTTAGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:17280722 original size:17 final size:18
Alignment explanation
Indices: 17280702--17280749 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
17280692 AAAATGAATT
*
17280702 TTAAATTTAAATTTA-AA
1 TTAAATTTAAACTTAGAA
17280719 TTAAATTTAAACTTAGAA
1 TTAAATTTAAACTTAGAA
*
17280737 ATAAATTTGAAAC
1 TTAAATTT-AAAC
17280750 CAAATCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 14 0.52
18 9 0.33
19 4 0.15
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
TTAAATTTAAACTTAGAA
Found at i:17280724 original size:5 final size:6
Alignment explanation
Indices: 17280701--17280729 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
17280691 AAAAATGAAT
17280701 TTTAAA TTTAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
17280730 CTTAGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:17284303 original size:17 final size:17
Alignment explanation
Indices: 17284281--17284319 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17284271 AGGTGGAGAA
* *
17284281 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
17284298 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
17284315 CTTGT
1 CTTGT
17284320 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:17289831 original size:58 final size:60
Alignment explanation
Indices: 17289680--17289843 Score: 251
Period size: 62 Copynumber: 2.7 Consensus size: 60
17289670 TACCAAAAAA
*
17289680 AATGTAATGAAAAAGACTAATCCCAATATTCATTTATTAGTTTACGTACTTCAAATTAATAT
1 AATGTAATGAAAAAGACTAATCCCAATATTCATTTATTAATTTACGTACTTC-AA-TAATAT
* *
17289742 AATGTAATGAAAAAGACTAATCCCAATATTCATTTATGAATTTACGTATTTC-A-AATAT
1 AATGTAATGAAAAAGACTAATCCCAATATTCATTTATTAATTTACGTACTTCAATAATAT
* *
17289800 AATGTAATGAAAAAGACTAATCCCAACATTCACTTATTAATTTA
1 AATGTAATGAAAAAGACTAATCCCAATATTCATTTATTAATTTA
17289844 AAGTATATAA
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
58 46 0.48
60 1 0.01
62 49 0.51
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (60 bp):
AATGTAATGAAAAAGACTAATCCCAATATTCATTTATTAATTTACGTACTTCAATAATAT
Found at i:17291616 original size:14 final size:14
Alignment explanation
Indices: 17291572--17291616 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
17291562 TAAAAAGTAG
17291572 AAAAATTAAATTCTT
1 AAAAATTAAATTC-T
* *
17291587 AAAAA-TAAAATAT
1 AAAAATTAAATTCT
17291600 AAAAATTAAATTCT
1 AAAAATTAAATTCT
17291614 AAA
1 AAA
17291617 TTTTTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 6 0.24
14 14 0.56
15 5 0.20
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTAAATTCT
Found at i:17293742 original size:18 final size:18
Alignment explanation
Indices: 17293712--17293757 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
17293702 AAAAAACATG
*
17293712 TTTAAAGAAT-AAATCAA
1 TTTAAAGAATAAAATAAA
17293729 TTTAAAGCAATAAAATAAA
1 TTTAAAG-AATAAAATAAA
17293748 TTTAAA-AATA
1 TTTAAAGAATA
17293758 GAATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
19 12 0.46
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
TTTAAAGAATAAAATAAA
Found at i:17293764 original size:69 final size:69
Alignment explanation
Indices: 17293679--17293965 Score: 330
Period size: 73 Copynumber: 4.0 Consensus size: 69
17293669 TACCCAAAAA
* *
17293679 TTAAAAATATATATTTAAATTAAAAAAAACATGTTTAAAG-AATAAATCAATTTAAAGCAATAAA
1 TTAAAAATAGA-ATTT-AATTAAAAAAAACATATTTAAAGAAATAAATCAATTTAAAGCAATAAA
*
17293743 ATAAAT
64 TTAAAT
*
17293749 TTAAAAATAGAATTTAATT--AAAAAACATATTTAAAGAATAATAAATCAATTTAAAACAATAAA
1 TTAAAAATAGAATTTAATTAAAAAAAACATATTTAAAG-A-AATAAATCAATTTAAAGCAATAAA
17293812 TTAAAATT
64 TT-AAA-T
* * * *
17293820 TTAAAAAATATAATCTAAATTTAAAAAAGACATATTTAAA-AAAGAAATCAATTTAAAGCAATAA
1 TT-AAAAATAGAAT-TTAA-TTAAAAAAAACATATTTAAAGAAATAAATCAATTTAAAGCAATAA
17293884 ATTAAAT
63 ATTAAAT
* *
17293891 TTAAAAAAAGAATTTAATTAAAAAAATTACATATTTAAAGAATAATAAATTAATTTAAAGCAATA
1 TTAAAAATAGAATTTAATTAAAAAAA--ACATATTTAAAG-A-AATAAATCAATTTAAAGCAATA
*
17293956 AATTTAAT
62 AATTAAAT
17293964 TT
1 TT
17293966 TTTTTAAAAT
Statistics
Matches: 186, Mismatches: 16, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
66 16 0.09
68 12 0.06
69 31 0.17
70 33 0.18
71 6 0.03
72 14 0.08
73 56 0.30
74 3 0.02
76 15 0.08
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (69 bp):
TTAAAAATAGAATTTAATTAAAAAAAACATATTTAAAGAAATAAATCAATTTAAAGCAATAAATT
AAAT
Found at i:17293819 original size:20 final size:20
Alignment explanation
Indices: 17293796--17293847 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
17293786 ATAATAAATC
17293796 AATTTAAAACAATA-AAT-TAA
1 AATTTAAAA-AATATAATCT-A
17293816 AATTTTAAAAAATATAATCTA
1 AA-TTTAAAAAATATAATCTA
17293837 AATTTAAAAAA
1 AATTTAAAAAA
17293848 GACATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 15 0.52
21 13 0.45
22 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTAAAAAATATAATCTA
Found at i:17293832 original size:22 final size:19
Alignment explanation
Indices: 17293796--17293847 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
17293786 ATAATAAATC
*
17293796 AATTTAAAACAATAAAT-TAA
1 AATTTAAAAAAAT-AATCT-A
17293816 AATTTTAAAAAATATAATCTA
1 AA-TTTAAAAAA-ATAATCTA
17293837 AATTTAAAAAA
1 AATTTAAAAAA
17293848 GACATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 11 0.39
21 14 0.50
22 3 0.11
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTTAAAAAAATAATCTA
Found at i:17293882 original size:142 final size:144
Alignment explanation
Indices: 17293681--17293959 Score: 429
Period size: 142 Copynumber: 1.9 Consensus size: 144
17293671 CCCAAAAATT
* * * *
17293681 AAAAATATATATTTAAATTAAAAAAAACATGTTTAAAGAATAAATCAATTTAAAGCAATAAAATA
1 AAAAATATATATCTAAATTAAAAAAAACATATTTAAAAAAGAAATCAATTTAAAGCAATAAAATA
*
17293746 AATTTAAAAATAGAATTTAATT-AAAAA-ACATATTTAAAGAATAATAAATCAATTTAAAACAAT
66 AATTTAAAAAAAGAATTTAATTAAAAAATACATATTTAAAGAATAATAAATCAATTTAAAACAAT
17293809 AAATTAAAATTTTA
131 AAATTAAAATTTTA
* *
17293823 AAAAATATA-ATCTAAATTTAAAAAAGACATATTTAAAAAAGAAATCAATTTAAAGCAATAAATT
1 AAAAATATATATCTAAA-TTAAAAAAAACATATTTAAAAAAGAAATCAATTTAAAGCAATAAAAT
* *
17293887 AAATTTAAAAAAAGAATTTAATTAAAAAAATTACATATTTAAAGAATAATAAATTAATTTAAAGC
65 AAATTTAAAAAAAGAATTTAATT-AAAAAA-TACATATTTAAAGAATAATAAATCAATTTAAAAC
17293952 AATAAATT
128 AATAAATT
17293960 TAATTTTTTT
Statistics
Matches: 123, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
141 6 0.05
142 73 0.59
144 5 0.04
146 39 0.32
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (144 bp):
AAAAATATATATCTAAATTAAAAAAAACATATTTAAAAAAGAAATCAATTTAAAGCAATAAAATA
AATTTAAAAAAAGAATTTAATTAAAAAATACATATTTAAAGAATAATAAATCAATTTAAAACAAT
AAATTAAAATTTTA
Found at i:17293964 original size:19 final size:18
Alignment explanation
Indices: 17293712--17293965 Score: 65
Period size: 17 Copynumber: 14.2 Consensus size: 18
17293702 AAAAAACATG
*
17293712 TTTAAAGAATAAA-TCAA
1 TTTAAAGAATAAATTTAA
* *
17293729 TTTAAAGCAATAAAATAAA
1 TTTAAAG-AATAAATTTAA
17293748 TTTAAA-AATAGAATTTAA
1 TTTAAAGAATA-AATTTAA
*
17293766 -TTAAA-AA-ACA--T-A
1 TTTAAAGAATAAATTTAA
* *
17293778 TTTAAAGAATAATAAATCAA
1 TTTAAAGAAT-A-AATTTAA
* *
17293798 TTTAAAACAATAAATTAAAA
1 TTT-AAAGAATAAATT-TAA
* *
17293818 TTTTAAAAAATATAATCTAAA
1 -TTTAAAGAATA-AAT-TTAA
* **
17293839 TTTAAA-AA-AGACAT-A
1 TTTAAAGAATAAATTTAA
* * *
17293854 TTTAAAAAAGAAA-TCAA
1 TTTAAAGAATAAATTTAA
*
17293871 TTTAAAGCAATAAATTAAA
1 TTTAAAG-AATAAATTTAA
*
17293890 TTTAAA-AAAAGAATTTAA
1 TTTAAAGAATA-AATTTAA
*
17293908 -TT-AA-AA-AAATTACATA
1 TTTAAAGAATAAATT-TA-A
*
17293924 TTTAAAGAATAATAAATTAA
1 TTTAAAGAAT-A-AATTTAA
17293944 TTTAAAGCAATAAATTTAA
1 TTTAAAG-AATAAATTTAA
17293963 TTT
1 TTT
17293966 TTTTTAAAAT
Statistics
Matches: 180, Mismatches: 26, Indels: 60
0.68 0.10 0.23
Matches are distributed among these distances:
12 1 0.01
13 6 0.03
14 6 0.03
15 10 0.06
16 9 0.05
17 36 0.20
18 25 0.14
19 34 0.19
20 29 0.16
21 20 0.11
22 4 0.02
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
TTTAAAGAATAAATTTAA
Found at i:17294014 original size:73 final size:69
Alignment explanation
Indices: 17293696--17294013 Score: 277
Period size: 73 Copynumber: 4.4 Consensus size: 69
17293686 TATATATTTA
** * *
17293696 AATTAAAAAAAACATGTTTAAAGAATAAATCAATTTAAAGCAATAAAATAA-ATTTAAAAATAGA
1 AATTAAAAATGACATATTTAAAGAATAAATCAATTTAAAGCAATAAATTAATATTTAAAAATAGA
*
17293760 ATTT
66 AATT
* *
17293764 AATTAAAAA--ACATATTTAAAGAATAATAAATCAATTTAAAACAATAAATTAAAATTTTAAAAA
1 AATTAAAAATGACATATTTAAAG---AATAAATCAATTTAAAGCAATAAATTAATA-TTT-AAAA
*
17293827 ATA-TAATCT
61 ATAGAAAT-T
* * * *
17293836 AAATTTAAAAAAGACATATTTAAAAAAGAAATCAATTTAAAGCAATAAATTAA-ATTTAAAAAAA
1 -AA-TTAAAAATGACATATTTAAAGAATAAATCAATTTAAAGCAATAAATTAATATTTAAAAATA
*
17293900 GAATTT
64 GAAATT
* * * *
17293906 AATTAAAAAAATTACATATTTAAAGAATAATAAATTAATTTAAAGCAATAAATTTAATTTTTTTT
1 AATT--AAAAATGACATATTTAAAG---AATAAATCAATTTAAAGCAATAAA-TTAA--TATTTA
17293971 AAAATAGAAATT
58 AAAATAGAAATT
* *
17293983 AATTAAAAGATGAAATAATTAAAGAATAAAT
1 AATTAAAA-ATGACATATTTAAAGAATAAAT
17294014 TTAAAGTAAT
Statistics
Matches: 205, Mismatches: 23, Indels: 39
0.77 0.09 0.15
Matches are distributed among these distances:
66 11 0.05
68 11 0.05
69 28 0.14
70 24 0.12
71 10 0.05
72 9 0.04
73 57 0.28
74 11 0.05
75 4 0.02
76 23 0.11
77 17 0.08
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (69 bp):
AATTAAAAATGACATATTTAAAGAATAAATCAATTTAAAGCAATAAATTAATATTTAAAAATAGA
AATT
Found at i:17294015 original size:142 final size:140
Alignment explanation
Indices: 17293722--17294036 Score: 370
Period size: 142 Copynumber: 2.2 Consensus size: 140
17293712 TTTAAAGAAT
* * *
17293722 AAATCAATTTAAAGCAATAAAATAAATTTAAAAATAGAATTTAATTAAAAAACATATTTAAAGAA
1 AAATAAATTTAAAGCAATAAATTAAATTTAAAAAAAGAATTTAATTAAAAAACATATTTAAAGAA
* *
17293787 TAATAAATCAATTTAAAACAATAAATTAAAATTTTAAAAAATATAATCTAAATTTAAAAAAGACA
66 TAATAAATCAATTTAAAACAATAAATTAAAATTTTAAAAAATAAAATCTAAATTTAAAAAAGAAA
*
17293852 TATTTAAAAAAG
131 TAATT--AAAAG
*
17293864 AAATCAATTTAAAGCAATAAATTAAATTTAAAAAAAGAATTTAATTAAAAAAATTACATATTTAA
1 AAATAAATTTAAAGCAATAAATTAAATTTAAAAAAAGAATTTAATT--AAAAA--ACATATTTAA
* * ** **
17293929 AGAATAATAAATTAATTTAAAGCAATAAATTTAATTTTTTTTAAAATAGAAAT-T-AA-TTAAAA
62 AGAATAATAAATCAATTTAAAACAATAAA-TTAAAATTTTAAAAAATA-AAATCTAAATTTAAAA
*
17293991 GATGAAATAATT-AAAG
125 -AAGAAATAATTAAAAG
* *
17294007 -AATAAATTTAAAGTAATAAATTTAATTTAA
1 AAATAAATTTAAAGCAATAAATTAAATTTAA
17294037 TTTTAAATTA
Statistics
Matches: 151, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
142 71 0.47
143 4 0.03
144 5 0.03
145 6 0.04
146 47 0.31
147 15 0.10
148 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (140 bp):
AAATAAATTTAAAGCAATAAATTAAATTTAAAAAAAGAATTTAATTAAAAAACATATTTAAAGAA
TAATAAATCAATTTAAAACAATAAATTAAAATTTTAAAAAATAAAATCTAAATTTAAAAAAGAAA
TAATTAAAAG
Found at i:17294037 original size:14 final size:14
Alignment explanation
Indices: 17294001--17294031 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
17293991 GATGAAATAA
17294001 TTAAAG-AATAAAT
1 TTAAAGTAATAAAT
17294014 TTAAAGTAATAAAT
1 TTAAAGTAATAAAT
17294028 TTAA
1 TTAA
17294032 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TTAAAGTAATAAAT
Found at i:17294280 original size:21 final size:21
Alignment explanation
Indices: 17294254--17294298 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
17294244 ATATTTATTC
*
17294254 TTTAAA-TATATCTTTTCTTAA
1 TTTAAATTATATATTTT-TTAA
17294275 TTTAAATTATATATTTTTTAA
1 TTTAAATTATATATTTTTTAA
17294296 TTT
1 TTT
17294299 GTGGATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAAATTATATATTTTTTAA
Found at i:17296342 original size:3 final size:3
Alignment explanation
Indices: 17296334--17296366 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17296324 ATAATTAAAG
17296334 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
17296367 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:17303790 original size:13 final size:13
Alignment explanation
Indices: 17303772--17303796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17303762 ACCCTACGAA
17303772 AACATCATTTTTG
1 AACATCATTTTTG
17303785 AACATCATTTTT
1 AACATCATTTTT
17303797 ATTATGGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
AACATCATTTTTG
Found at i:17310547 original size:14 final size:14
Alignment explanation
Indices: 17310515--17310556 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
17310505 AAAAATATAA
*
17310515 ATTTAAT-TTTTAG
1 ATTTAATATTTAAG
*
17310528 ATTTAATATTTAAT
1 ATTTAATATTTAAG
*
17310542 ATTTAAAATTTAAG
1 ATTTAATATTTAAG
17310556 A
1 A
17310557 GTTATTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
ATTTAATATTTAAG
Found at i:17317078 original size:7 final size:7
Alignment explanation
Indices: 17317066--17317095 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
17317056 AAACGAAATG
17317066 AACCCTA
1 AACCCTA
17317073 AACCCTA
1 AACCCTA
17317080 AACCCTA
1 AACCCTA
17317087 AACCCTA
1 AACCCTA
17317094 AA
1 AA
17317096 AGAGTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCTA
Found at i:17320830 original size:2 final size:2
Alignment explanation
Indices: 17320823--17320879 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
17320813 ATCTAGCTTT
17320823 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
17320865 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
17320880 TTAACATTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17331472 original size:329 final size:329
Alignment explanation
Indices: 17330874--17331533 Score: 1214
Period size: 329 Copynumber: 2.0 Consensus size: 329
17330864 AGCTGCTAAG
*
17330874 ATATTGATTCAGTGATGGTGATATGCTACATCACTTGGAGTGTTTAATACGAGTATGTGTCTAGA
1 ATATTGATTCAGTGATGGTGATATGCTACATCACTAGGAGTGTTTAATACGAGTATGTGTCTAGA
17330939 CATGAGTTTACTTATTCTAAGTTTGTTGGTATATTTTGAGGATATTATTTCGTACTCATGTCCGA
66 CATGAGTTTACTTATTCTAAGTTTGTTGGTATATTTTGAGGATATTATTTCGTACTCATGTCCGA
* *
17331004 ATGTATATTGAATGAAGAGTCCAGAATCCAAATGACTTCTTGTTCCACACCAAACCAAGGCCAGG
131 ATATATATTGAATGAAGAGTCCAGAATCCAAATGACTTCTTATTCCACACCAAACCAAGGCCAGG
*
17331069 TTAGCTTATGATTTGGCCTTAGACCTTGGAAGATGCAATTTGGTGAATGGGGTTTAGTGCTACAC
196 TTAGCTCATGATTTGGCCTTAGACCTTGGAAGATGCAATTTGGTGAATGGGGTTTAGTGCTACAC
*
17331134 ACACTATTCACCTGCCTTTGGGATTTGTATTAGAAAAGGAATTTTCTCAAAAGAAAGGCCAATTA
261 ACACTATTCACCTGCCTTTGGGATTTGCATTAGAAAAGGAATTTTCTCAAAAGAAAGGCCAATTA
17331199 ACCA
326 ACCA
17331203 ATATTGATTCAGTGATGGTGATATGCTACATCACTAGGAGTGTTTAATACGAGTATGTGTCTAGA
1 ATATTGATTCAGTGATGGTGATATGCTACATCACTAGGAGTGTTTAATACGAGTATGTGTCTAGA
* *
17331268 CATG-GATTTACTTATTCTAAGTTTTTTGTTATATTTTGAGGATATTATTTCGTACTCATGTCCG
66 CATGAG-TTTACTTATTCTAAGTTTGTTGGTATATTTTGAGGATATTATTTCGTACTCATGTCCG
*
17331332 AATATATATTGAATGAAGAGTCCTGAATCCAAATGACTTCTTATTCCACACCAAACCAAGGCCAG
130 AATATATATTGAATGAAGAGTCCAGAATCCAAATGACTTCTTATTCCACACCAAACCAAGGCCAG
*
17331397 GTTAGCTCATGATTTGGCCTTAGACCTTGGAAGATGCAATTTGGTGAATGGGGTTTAGTGCTATA
195 GTTAGCTCATGATTTGGCCTTAGACCTTGGAAGATGCAATTTGGTGAATGGGGTTTAGTGCTACA
*
17331462 CACACTATTCACCTGCCTTTGGGATTTGCATTAGAAAAGGAATTTTCTCAAAAGAAAGGGCAATT
260 CACACTATTCACCTGCCTTTGGGATTTGCATTAGAAAAGGAATTTTCTCAAAAGAAAGGCCAATT
17331527 AACCA
325 AACCA
17331532 AT
1 AT
17331534 GTTTAACTTA
Statistics
Matches: 320, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
328 1 0.00
329 319 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (329 bp):
ATATTGATTCAGTGATGGTGATATGCTACATCACTAGGAGTGTTTAATACGAGTATGTGTCTAGA
CATGAGTTTACTTATTCTAAGTTTGTTGGTATATTTTGAGGATATTATTTCGTACTCATGTCCGA
ATATATATTGAATGAAGAGTCCAGAATCCAAATGACTTCTTATTCCACACCAAACCAAGGCCAGG
TTAGCTCATGATTTGGCCTTAGACCTTGGAAGATGCAATTTGGTGAATGGGGTTTAGTGCTACAC
ACACTATTCACCTGCCTTTGGGATTTGCATTAGAAAAGGAATTTTCTCAAAAGAAAGGCCAATTA
ACCA
Found at i:17332672 original size:82 final size:81
Alignment explanation
Indices: 17332576--17332807 Score: 254
Period size: 82 Copynumber: 2.8 Consensus size: 81
17332566 TATGAAGGGA
* *
17332576 TTTAAACAAAATGATCAGTTTGCATTTTGATCTTACATATGTAGATTAATTTATCCATTTTTTAA
1 TTTAAACAAAATGATCAATTTGCTTTTTGATCTTACATATG-AGATTAATTTATCCATTTTTTAA
* *
17332641 GTAAAAATGGATGTGAT
65 GTAAAAATAGATGTAAT
* * * * * *
17332658 TTTAAACAAAATGATCATTTTGCTTTTTTATCGTACAGATGGGAATTAATTTA-CCTATTTTTTG
1 TTTAAACAAAATGATCAATTTGCTTTTTGATCTTACATATGAG-ATTAATTTATCC-ATTTTTTA
17332722 AGTAAAAATAGATGTAAT
64 AGTAAAAATAGATGTAAT
* * * * *
17332740 TTTAAACAAAATAATTAATTTACTTTTTTGATCTTATATA-GAGGGATTAATTTATCTA-TTTTT
1 TTTAAACAAAATGATCAATTTGC-TTTTTGATCTTACATATGA--GATTAATTTATCCATTTTTT
17332803 AAGTA
63 AAGTA
17332808 GAGAGAGTAA
Statistics
Matches: 124, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
81 3 0.02
82 97 0.78
83 22 0.18
84 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (81 bp):
TTTAAACAAAATGATCAATTTGCTTTTTGATCTTACATATGAGATTAATTTATCCATTTTTTAAG
TAAAAATAGATGTAAT
Found at i:17340285 original size:4 final size:4
Alignment explanation
Indices: 17340276--17340306 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
17340266 GTGTCAACTT
17340276 CCTG CCTG CCTG CCTG CCTG CCTG CCTG CCT
1 CCTG CCTG CCTG CCTG CCTG CCTG CCTG CCT
17340307 AAAATTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.23, T:0.26
Consensus pattern (4 bp):
CCTG
Found at i:17340524 original size:2 final size:2
Alignment explanation
Indices: 17340519--17340558 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17340509 TAATATATAC
17340519 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
17340559 TTAACAGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:17347856 original size:19 final size:21
Alignment explanation
Indices: 17347832--17347872 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
17347822 GAATCTTGAA
17347832 TGAGGTTCGAG-TTTG-GATT
1 TGAGGTTCGAGATTTGAGATT
17347851 TGAGGTTCGAGATTTGAGATT
1 TGAGGTTCGAGATTTGAGATT
17347872 T
1 T
17347873 AGAATTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.20, C:0.05, G:0.34, T:0.41
Consensus pattern (21 bp):
TGAGGTTCGAGATTTGAGATT
Found at i:17349696 original size:23 final size:23
Alignment explanation
Indices: 17349670--17349783 Score: 126
Period size: 23 Copynumber: 5.0 Consensus size: 23
17349660 TTACCATTCA
*
17349670 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
*
17349693 GCACTTTGTGTGCCTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
17349716 GCACT-TCGTGTGCCTACTGATTT-
1 GCACTGT-GTGTGCCTACTG-TTTC
* * * *
17349739 GCGCTATGTGCGCCTACTGATT-
1 GCACTGTGTGTGCCTACTGTTTC
*
17349761 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGTTTC
17349784 CCCAGCACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 20 0.26
23 53 0.69
24 4 0.05
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (23 bp):
GCACTGTGTGTGCCTACTGTTTC
Found at i:17349754 original size:46 final size:45
Alignment explanation
Indices: 17349670--17349783 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 45
17349660 TTACCATTCA
* * *
17349670 GCACTGTGTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGTTT
1 GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
* *
17349715 CGCACT-TCGTGTGCCTACTGATTT-GCGCTATGTGCGCCTACTGATT
1 -GCACTGT-GTGTGCTTACTG-TTTCGCACTATGTGCGCCTACTGATT
17349761 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCTTACTGTTTC
17349784 CCCAGCACTT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
44 3 0.05
45 17 0.29
46 35 0.60
47 3 0.05
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40
Consensus pattern (45 bp):
GCACTGTGTGTGCTTACTGTTTCGCACTATGTGCGCCTACTGATT
Found at i:17354085 original size:16 final size:16
Alignment explanation
Indices: 17354064--17354097 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17354054 AGATACTAGC
* *
17354064 TTGAGAAGTGAAAGAA
1 TTGAGAAATAAAAGAA
17354080 TTGAGAAATAAAAGAA
1 TTGAGAAATAAAAGAA
17354096 TT
1 TT
17354098 CCTCTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (16 bp):
TTGAGAAATAAAAGAA
Found at i:17357467 original size:14 final size:13
Alignment explanation
Indices: 17357448--17357499 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
17357438 CCAGCCCGCC
17357448 TATATTAATTTTTT
1 TATATT-ATTTTTT
17357462 TATATTATCTTTTT
1 TATATTAT-TTTTT
*
17357476 GA-A-TACTTTTTT
1 TATATTA-TTTTTT
17357488 TATATTATTTTT
1 TATATTATTTTT
17357500 AAATGTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.25
13 10 0.31
14 14 0.44
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (13 bp):
TATATTATTTTTT
Found at i:17357656 original size:30 final size:30
Alignment explanation
Indices: 17357620--17357678 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
17357610 CTTAACAAAC
*
17357620 AAATGCCTCTAAAATATTAACAAAATTAAT
1 AAATGCCTCTAAAATACTAACAAAATTAAT
*
17357650 AAATGCCTTTAAAATACTAACAAAATTAA
1 AAATGCCTCTAAAATACTAACAAAATTAA
17357679 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATACTAACAAAATTAAT
Found at i:17357736 original size:22 final size:22
Alignment explanation
Indices: 17357711--17357753 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17357701 TATCCAAACA
17357711 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
** *
17357733 ATAATAATGAAATCGTAGCAA
1 ATAATAACAAAATAGTAGCAA
17357754 AATAGGGAGA
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:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:17364019 original size:29 final size:29
Alignment explanation
Indices: 17363987--17364044 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
17363977 TTAACCCTAA
* * *
17363987 TTATCATATTAGGTCATTTTTAAAAAAAT
1 TTATCAGACTAGGTCAATTTTAAAAAAAT
* *
17364016 TTATTAGACTAGGTCAATTTTAAGAAAAT
1 TTATCAGACTAGGTCAATTTTAAAAAAAT
17364045 ATTTTTGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (29 bp):
TTATCAGACTAGGTCAATTTTAAAAAAAT
Found at i:17366123 original size:16 final size:16
Alignment explanation
Indices: 17366102--17366138 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
17366092 TCTAAGTAAG
17366102 ATCTATAAGAAAATTT
1 ATCTATAAGAAAATTT
17366118 ATCTATAAGAAAATTT
1 ATCTATAAGAAAATTT
17366134 ATCTA
1 ATCTA
17366139 GAACCTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (16 bp):
ATCTATAAGAAAATTT
Found at i:17366961 original size:23 final size:21
Alignment explanation
Indices: 17366934--17366990 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
17366924 AAATTTTTTT
17366934 ATTTAATCTTTAAAAAATTATA
1 ATTTAAT-TTTAAAAAATTATA
* *
17366956 TTTTTATTATTATAAAAATTATA
1 ATTTAATT-TTA-AAAAATTATA
17366979 ATTTAATTTTAA
1 ATTTAATTTTAA
17366991 TCTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.07
22 11 0.38
23 16 0.55
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATTTTAAAAAATTATA
Found at i:17369161 original size:24 final size:25
Alignment explanation
Indices: 17369114--17369162 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
17369104 AAATTATTGA
17369114 AATTTGATATTTAATTTATACATTTT
1 AATTTGATA-TTAATTTATACATTTT
17369140 AATTTGATA-TAATTTGAT-CATTT
1 AATTTGATATTAATTT-ATACATTT
17369163 ATTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 2 0.09
26 9 0.41
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (25 bp):
AATTTGATATTAATTTATACATTTT
Found at i:17387696 original size:18 final size:18
Alignment explanation
Indices: 17387673--17387715 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17387663 GAATAGATTT
17387673 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
17387691 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
17387709 TTAATTA
1 TTAATTA
17387716 CACTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:17392900 original size:2 final size:2
Alignment explanation
Indices: 17392893--17392918 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17392883 TTCTGTTTAC
17392893 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
17392919 GGTGTGCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17395115 original size:57 final size:59
Alignment explanation
Indices: 17395040--17395183 Score: 168
Period size: 57 Copynumber: 2.5 Consensus size: 59
17395030 TGAACTTGAC
* ** *
17395040 ACTTTTTTTTGACCCAATTTGGTACCTAAACTTGACATTTTTT-TAAGTTGGTACTTAA
1 ACTTTTTTTAGATTCAATTTGGTACCTAAACTTGACATTTTTTCTAAGTTGGTACCTAA
* * * *
17395098 AC-TTTTTTATG-TTCAATTTGGTATCTGAACTTGATATTTTTTCCTAATTTGGTACCTAA
1 ACTTTTTTTA-GATTCAATTTGGTACCTAAACTTGACATTTTTT-CTAAGTTGGTACCTAA
*
17395157 ACTTTTTTTAGATTCAATTTGGAACCT
1 ACTTTTTTTAGATTCAATTTGGTACCT
17395184 CAATTTATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
57 32 0.45
58 3 0.04
59 16 0.23
60 20 0.28
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (59 bp):
ACTTTTTTTAGATTCAATTTGGTACCTAAACTTGACATTTTTTCTAAGTTGGTACCTAA
Found at i:17403544 original size:38 final size:39
Alignment explanation
Indices: 17403500--17403587 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 39
17403490 AAAAATTATA
*
17403500 TTTAATATAATAAAATATTTATTATATTTAT-TTGTGTT
1 TTTAATATAATAAAATATTTATTATATTTATGTAGTGTT
17403538 TTTAATATAATAAAATATTTATTATATTTATGGTAGTGTT
1 TTTAATATAATAAAATATTTATTATATTTAT-GTAGTGTT
17403578 TTTAATATAA
1 TTTAATATAA
17403588 ATGTTTTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 31 0.66
40 16 0.34
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (39 bp):
TTTAATATAATAAAATATTTATTATATTTATGTAGTGTT
Found at i:17403668 original size:15 final size:15
Alignment explanation
Indices: 17403648--17403691 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
17403638 TTTAATTTAT
17403648 TATTTTAAAAAAAAA
1 TATTTTAAAAAAAAA
*
17403663 TATTTTTAAATAAAAAT
1 TA-TTTTAAA-AAAAAA
*
17403680 TAATTTAAAAAA
1 TATTTTAAAAAA
17403692 TTAAATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 13 0.52
17 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTTTAAAAAAAAA
Found at i:17404330 original size:13 final size:13
Alignment explanation
Indices: 17404292--17404334 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
17404282 ATTTAAAAAG
17404292 AAAATAACATTAT
1 AAAATAACATTAT
* *
17404305 AAACTTACA-TAT
1 AAAATAACATTAT
17404317 AAAATAACATTAT
1 AAAATAACATTAT
17404330 AAAAT
1 AAAAT
17404335 TAAAAATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAACATTAT
Found at i:17404442 original size:15 final size:16
Alignment explanation
Indices: 17404402--17404445 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
17404392 TTTTAAGAGT
17404402 ATTTAATTTTTTATGA
1 ATTTAATTTTTTATGA
17404418 ATTT-ATTTTTTA-G-
1 ATTTAATTTTTTATGA
17404431 ATTTAATATTTTTAT
1 ATTTAAT-TTTTTAT
17404446 TTAAATCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.16
14 3 0.12
15 14 0.56
16 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
ATTTAATTTTTTATGA
Done.