Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 27 of 31
Found at i:5404923 original size:3 final size:3
Alignment explanation
Indices: 5404915--5404943 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5404905 AAACTATGTA
5404915 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5404944 GTTTTGAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5405580 original size:27 final size:28
Alignment explanation
Indices: 5405550--5405621 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
5405540 AAAAAAAAAA
5405550 TTTAAAATATGTATATTGAGAAATA-TT
1 TTTAAAATATGTATATTGAGAAATATTT
* * *
5405577 TTTAAAGTATGTTTTTTGAGAAATATTT
1 TTTAAAATATGTATATTGAGAAATATTT
*
5405605 TTTAAAATATATATATT
1 TTTAAAATATGTATATT
5405622 TTTTGAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 22 0.59
28 15 0.41
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (28 bp):
TTTAAAATATGTATATTGAGAAATATTT
Found at i:5407860 original size:2 final size:2
Alignment explanation
Indices: 5407853--5407897 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5407843 TTAGGTAAGG
5407853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5407895 AT A
1 AT A
5407898 GTGGGTGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5408080 original size:12 final size:12
Alignment explanation
Indices: 5408065--5408094 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5408055 CCAATGATGA
5408065 TCTTTTTTTTTT
1 TCTTTTTTTTTT
5408077 TCTTTTTTTTTT
1 TCTTTTTTTTTT
5408089 T-TTTTT
1 TCTTTTT
5408095 GGTGTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:5411765 original size:2 final size:2
Alignment explanation
Indices: 5411758--5411794 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5411748 ATCTTTATCC
5411758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5411795 GAAACAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5411889 original size:2 final size:2
Alignment explanation
Indices: 5411884--5411915 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5411874 TATGAGTGTG
5411884 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
5411916 GCTTTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5413496 original size:29 final size:27
Alignment explanation
Indices: 5413463--5413530 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
5413453 GTCAAAAGTC
*
5413463 AAATTATAAAATTTTTTTGGAATTAAATAA
1 AAATT-TAAAATTTTGTTGG-ATTAAA-AA
* * *
5413493 AATTTTATACTTTTGTTGGATTAAAAA
1 AAATTTAAAATTTTGTTGGATTAAAAA
5413520 ACAATTTAAAA
1 A-AATTTAAAA
5413531 ATTAAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
27 3 0.10
28 12 0.40
29 11 0.37
30 4 0.13
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (27 bp):
AAATTTAAAATTTTGTTGGATTAAAAA
Found at i:5415678 original size:13 final size:13
Alignment explanation
Indices: 5415655--5415687 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5415645 CTATATTATT
5415655 TAAAT-TTAAATA
1 TAAATATTAAATA
5415667 TAAATATTAAATA
1 TAAATATTAAATA
5415680 TAAATATT
1 TAAATATT
5415688 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:5416985 original size:18 final size:19
Alignment explanation
Indices: 5416935--5416985 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
5416925 TTAATTTAAA
*
5416935 ATTTTTTTATTTAAATTTG
1 ATTTTATTATTTAAATTTG
*
5416954 ATTTTA--ATCATAAATTT-
1 ATTTTATTAT-TTAAATTTG
5416971 ATTTTATTATTTAAA
1 ATTTTATTATTTAAA
5416986 AATAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 8 0.31
18 11 0.42
19 7 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTATTATTTAAATTTG
Found at i:5417034 original size:26 final size:27
Alignment explanation
Indices: 5416985--5417037 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5416975 TATTATTTAA
*
5416985 AAATAAAATATTTTTATAATTAAATTT
1 AAATAAAATAATTTTATAATTAAATTT
5417012 AAATAAAA-AATTTTAT-ATGTAAATTT
1 AAATAAAATAATTTTATAAT-TAAATTT
5417038 GACTTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 2 0.08
26 14 0.58
27 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATAAAATAATTTTATAATTAAATTT
Found at i:5417930 original size:3 final size:3
Alignment explanation
Indices: 5417922--5417951 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5417912 TAAAATGTTG
5417922 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5417952 ATGAAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:5418324 original size:13 final size:14
Alignment explanation
Indices: 5418300--5418330 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5418290 TTTTAGTTGG
5418300 ATTTATATATAAAT
1 ATTTATATATAAAT
5418314 ATTTA-ATATAAAT
1 ATTTATATATAAAT
5418327 ATTT
1 ATTT
5418331 TTTCTACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTATATATAAAT
Found at i:5419856 original size:12 final size:12
Alignment explanation
Indices: 5419819--5419860 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5419809 TTATTTAATT
*
5419819 TTAATTTTAAAA
1 TTAATTTAAAAA
* *
5419831 TT-ATATAAATA
1 TTAATTTAAAAA
5419842 TTAATTTAAAAA
1 TTAATTTAAAAA
5419854 TTAATTT
1 TTAATTT
5419861 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATTTAAAAA
Found at i:5420032 original size:12 final size:13
Alignment explanation
Indices: 5420015--5420043 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5420005 TTGATATTTC
5420015 TAAAGAT-TTAAA
1 TAAAGATATTAAA
5420027 TAAAGATATTAAA
1 TAAAGATATTAAA
5420040 TAAA
1 TAAA
5420044 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAAGATATTAAA
Found at i:5420266 original size:18 final size:17
Alignment explanation
Indices: 5420243--5420277 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5420233 TTTTAAAAAT
5420243 TATTAATAAAAAAATTTA
1 TATTAA-AAAAAAATTTA
*
5420261 TATTAAAAAAAGATTTA
1 TATTAAAAAAAAATTTA
5420278 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TATTAAAAAAAAATTTA
Found at i:5420600 original size:19 final size:21
Alignment explanation
Indices: 5420551--5420601 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
5420541 TTATAATTAA
5420551 ATTT-AAA-TAAAAATATATC
1 ATTTAAAATTAAAAATATATC
* *
5420570 ATTTTAATTTAAAAATAT-T-
1 ATTTAAAATTAAAAATATATC
5420589 ATTTAAAATTAAA
1 ATTTAAAATTAAA
5420602 TTAACTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.56
20 3 0.11
21 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTAAAATTAAAAATATATC
Found at i:5429120 original size:16 final size:17
Alignment explanation
Indices: 5429099--5429131 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5429089 GTTTGGAGGG
5429099 TTTGAT-AAAAAAATTA
1 TTTGATCAAAAAAATTA
*
5429115 TTTGATCTAAAAAATTA
1 TTTGATCAAAAAAATTA
5429132 GTTAGGAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
TTTGATCAAAAAAATTA
Found at i:5429368 original size:26 final size:27
Alignment explanation
Indices: 5429327--5429385 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
5429317 TATTTATATT
* *
5429327 TTAAAATTTAATAAAATTTATTAAAAA
1 TTAAAATTTAATAAAATATATAAAAAA
*
5429354 TTAAATTTTAA-AAAATATATAAAAAA
1 TTAAAATTTAATAAAATATATAAAAAA
*
5429380 TAAAAA
1 TTAAAA
5429386 ATAATATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TTAAAATTTAATAAAATATATAAAAAA
Found at i:5429404 original size:21 final size:19
Alignment explanation
Indices: 5429361--5429404 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
5429351 AAATTAAATT
5429361 TTAAAAAATATATAAAAAA
1 TTAAAAAATATATAAAAAA
5429380 -TAAAAAATAATATAATAAAA
1 TTAAAAAAT-ATATAA-AAAA
5429400 TTAAA
1 TTAAA
5429405 TAATTTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 4 0.18
21 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAAAATATATAAAAAA
Found at i:5429436 original size:10 final size:10
Alignment explanation
Indices: 5429423--5429497 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 10
5429413 CCCTATTTAA
5429423 AAATATAAAT
1 AAATATAAAT
5429433 AAATATAAAT
1 AAATATAAAT
*
5429443 AAAATTTAATATTT
1 -AAATATAA-A--T
*
5429457 AAAT-T--TT
1 AAATATAAAT
5429464 AAAT-TAAATT
1 AAATATAAA-T
*
5429474 AAATTTAAAT
1 AAATATAAAT
5429484 AAATATAAAT
1 AAATATAAAT
5429494 AAAT
1 AAAT
5429498 TAATATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
7 6 0.11
10 29 0.55
11 11 0.21
12 2 0.04
13 4 0.08
14 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATATAAAT
Found at i:5429472 original size:5 final size:5
Alignment explanation
Indices: 5429462--5429520 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
5429452 TATTTAAATT
*
5429462 TTAAA TTAAA TTAAA TTTAAA -TAAA TATAAA -TAAA TTAATA TTATAT
1 TTAAA TTAAA TTAAA -TTAAA TTAAA T-TAAA TTAAA TTAA-A TTA-AA
*
5429509 TTAAA TTCAA TT
1 TTAAA TTAAA TT
5429521 TACATTCAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 8 0.18
5 20 0.44
6 16 0.36
7 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:5429955 original size:9 final size:10
Alignment explanation
Indices: 5429934--5429963 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5429924 AGATTAAACC
5429934 AAAATTTTAA
1 AAAATTTTAA
5429944 AAAATTTTAA
1 AAAATTTTAA
*
5429954 AAAATGTTAA
1 AAAATTTTAA
5429964 TATCATCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:5430519 original size:21 final size:21
Alignment explanation
Indices: 5430485--5430531 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5430475 ATTAAAATTT
*
5430485 TATTTTTATTTTTAT-ATTAA
1 TATTTATATTTTTATAATTAA
5430505 TATTTATATTTTTTATAATTAA
1 TATTTATA-TTTTTATAATTAA
5430527 -ATTTA
1 TATTTA
5430532 AATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 12 0.50
22 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTATATTTTTATAATTAA
Found at i:5437799 original size:28 final size:30
Alignment explanation
Indices: 5437723--5437799 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 30
5437713 CTAATAATAA
*
5437723 TTTATAT-ATTTACATTATATTTATATTATTT
1 TTTATATCATATA-ATTAT-TTTATATTATTT
*
5437754 TTTATATCGTATAA-TATTTTA-ATTATTT
1 TTTATATCATATAATTATTTTATATTATTT
5437782 TTTA-AT-ATATAAATTATT
1 TTTATATCATAT-AATTATT
5437800 ACCACCTCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 3 0.08
27 4 0.10
28 15 0.38
29 4 0.10
30 3 0.08
31 8 0.20
32 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTATATCATATAATTATTTTATATTATTT
Found at i:5438412 original size:22 final size:21
Alignment explanation
Indices: 5438368--5438414 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5438358 AAATTGAATT
5438368 AATTTAAATTATTAAAATATA
1 AATTTAAATTATTAAAATATA
*
5438389 AATTTAAA-TATATATATATATA
1 AATTTAAATTAT-TA-AAATATA
5438411 AATT
1 AATT
5438415 GAAGAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTAAATTATTAAAATATA
Found at i:5441470 original size:17 final size:19
Alignment explanation
Indices: 5441442--5441476 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5441432 TTTTGTGATT
5441442 TGAAATTGACTTT-TTATA
1 TGAAATTGACTTTATTATA
5441460 TGAAA-TGACTTTATTAT
1 TGAAATTGACTTTATTAT
5441477 TTTCACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (19 bp):
TGAAATTGACTTTATTATA
Found at i:5442215 original size:3 final size:3
Alignment explanation
Indices: 5442209--5442250 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5442199 TCTTCTAAGC
5442209 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5442251 TCTATACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5442361 original size:14 final size:14
Alignment explanation
Indices: 5442342--5442393 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
5442332 GGCATGGGAG
5442342 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
5442356 AAAAAGAGAAAAAAA
1 AAAAAGA-AAAAAAA
* *
5442371 GGAAAAAGAAAGAAAG
1 --AAAAAGAAAAAAAA
5442387 AAAAAGA
1 AAAAAGA
5442394 TTTTCTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 14 0.42
15 7 0.21
16 5 0.15
17 7 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:5442375 original size:25 final size:23
Alignment explanation
Indices: 5442342--5442391 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
5442332 GGCATGGGAG
5442342 AAAAAGAAAAAAAAAAAAAGAGAA
1 AAAAAGAAAAAAAAAAAAAGA-AA
* *
5442366 AAAAAGGAAAAAGAAAGAAAGAAA
1 AAAAA-GAAAAAAAAAAAAAGAAA
5442390 AA
1 AA
5442392 GATTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAAAAAAAGAAA
Found at i:5442376 original size:21 final size:21
Alignment explanation
Indices: 5442352--5442392 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5442342 AAAAAGAAAA
5442352 AAAAAAAAAGAGAA-AAAAAGG
1 AAAAAAAAAGA-AAGAAAAAGG
*
5442373 AAAAAGAAAGAAAGAAAAAG
1 AAAAAAAAAGAAAGAAAAAG
5442393 ATTTTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAAGAAAAAGG
Found at i:5443402 original size:14 final size:14
Alignment explanation
Indices: 5443378--5443424 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5443368 TCAGCTGAGT
5443378 AAAAAAGAAAGAAAG
1 AAAAAA-AAAGAAAG
*
5443393 AAAAATAAAG-AAG
1 AAAAAAAAAGAAAG
*
5443406 AAAAAAAAAAAAAG
1 AAAAAAAAAGAAAG
5443420 AAAAA
1 AAAAA
5443425 GAGAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.39
14 12 0.43
15 5 0.18
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:5443406 original size:21 final size:20
Alignment explanation
Indices: 5443377--5443436 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
5443367 TTCAGCTGAG
*
5443377 TAAAAAAGAAAGAAAGAAAAA
1 TAAAGAAGAAAGAAA-AAAAA
5443398 TAAAGAAG-AA-AAAAAAAA
1 TAAAGAAGAAAGAAAAAAAA
*
5443416 -AAAGAAAAAGAGAAAAAAAA
1 TAAAGAAGAA-AGAAAAAAAA
5443436 T
1 T
5443437 TTATGAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 4 0.12
20 10 0.30
21 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (20 bp):
TAAAGAAGAAAGAAAAAAAA
Found at i:5443408 original size:17 final size:17
Alignment explanation
Indices: 5443378--5443435 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
5443368 TCAGCTGAGT
5443378 AAAAAAGAAAGAAAGAAA
1 AAAAAAG-AAGAAAGAAA
* *
5443396 AATAAAGAAGAAAAAAA
1 AAAAAAGAAGAAAGAAA
5443413 AAAAAAGAA-AAAGAGAA
1 AAAAAAGAAGAAAGA-AA
5443430 AAAAAA
1 AAAAAA
5443436 TTTATGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.11
17 25 0.71
18 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAGAAAGAAA
Found at i:5443431 original size:14 final size:13
Alignment explanation
Indices: 5443379--5443432 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
5443369 CAGCTGAGTA
5443379 AAAAAGAAAGAAAG
1 AAAAAGAAA-AAAG
* *
5443393 AAAAATAAAGAAG
1 AAAAAGAAAAAAG
*
5443406 AAAAAAAAAAAAAG
1 -AAAAAGAAAAAAG
5443420 AAAAAGAGAAAAA
1 AAAAAGA-AAAAA
5443433 AAATTTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 9 0.27
14 24 0.73
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:5443524 original size:32 final size:32
Alignment explanation
Indices: 5443447--5443531 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 32
5443437 TTATGAATTC
5443447 ATATTTTTAT-TATTTTTATAT-TTAAAATATT
1 ATATTTTTATAT-TTTTTATATATTAAAATATT
5443478 ATATTTTTATATTTTTTATATATTAATAAT-TT
1 ATATTTTTATATTTTTTATATATTAA-AATATT
5443510 AT-TTTATTATATTTTTT-TATAT
1 ATATTT-TTATATTTTTTATATAT
5443532 GTATGTATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
31 27 0.54
32 20 0.40
33 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (32 bp):
ATATTTTTATATTTTTTATATATTAAAATATT
Found at i:5443923 original size:488 final size:481
Alignment explanation
Indices: 5443395--5444287 Score: 1176
Period size: 488 Copynumber: 1.8 Consensus size: 481
5443385 AAAGAAAGAA
*
5443395 AAATAAAGAAGAAAAAAAAAAAAAGAAAAAGAGAAAAAAAATTTATGAATTCATATTTTTATTAT
1 AAATAAAGAAGAAAAAAAAAAAAAGAAAAAGAGAAAAAAAATTTATGAATT--TATATTTA-TA-
* * *
5443460 TTTTATATTTAAAATATTATATTTTTATA-TTTTTTATATATTAATAATTTATTTTA-TT-A-TA
62 TTTT-TATTTAAAATATTACATTTTTATATTTTTTTACATATTAATAATTCATTTTATTTCAGTA
* * ** * * *
5443521 TTTTTTTATATGTATGTATATTTTTGTTATGTACATATTATTTTCAAGTTATGTTTTAAATATTT
126 TATTTTTATATGTACGTATATTCGTGTTATATACATATCATTTTCAAGTTATATTTTAAATATTT
**
5443586 TTTATAAACATCATGTTTATG-TAATTTTTTATG-T-AATAAATTTATATAAATTTTTGTACGTT
191 TTTATAAACATCATGTTTATGTTAATTTTTTATGATAAATAAATTTATATAAATTTTTACACGTT
*
5443648 AATTATTTATTTATCTATA-TTTGACATATTCGTGTATTCATACAGTATTTATATTATTTTTCAT
256 AATTATTTATTTATCTATATTTTGACATATTCATGTATTCATACAGTATTTATATTATTTTTCAT
*
5443712 GCTGTGTTTTAATTTTTTTATATATATTAAGTTTGTATTATATCTCAATTCATGTTATATTTTAC
321 GCTGTG-TTT-A-----TT-TATATATTAAGTTTGTACTATATCTCAATTCATGTTATATTTTAC
*
5443777 ATTGCTAAAT-ACTGTGATTCATATAAAATTAACTACACAAACTCACCTGATGCTGACACGTGAT
378 ATAGCTAAATAAC-GTGATTCATATAAAATTAACTACACAAACTCACCTGATGCTGACACGTGAT
5443841 TTTTTTTTTTTGCGTTCAGCAAGGCAAGGCTAAAAAAAAG
442 TTTTTTTTTTTGCGTTCAGCAAGGCAAGGCTAAAAAAAAG
* ** *
5443881 AAATAAAGGAGAAAAAAATGAAAGAAAGAAAAAGAG-AAAAAAATTTATGTGTTTGTATTTATAT
1 AAATAAAGAAGAAAAAAA--AAA-AAAGAAAAAGAGAAAAAAAATTTATGAATTTATATTTATAT
* *
5443945 TTTTATTTAAAATATTACATTTTTATATTTTTTTACATATTGATAATTCGTTTTATTTCATGTAT
63 TTTTATTTAAAATATTACATTTTTATATTTTTTTACATATTAATAATTCATTTTATTTCA-GTAT
* * *
5444010 ATTTTTATATGTACGTGTATTCGTGTTATATGCATATCATTTTCATGTTATATTTTAAATATTTT
127 ATTTTTATATGTACGTATATTCGTGTTATATACATATCATTTTCAAGTTATATTTTAAATATTTT
* * *
5444075 TTATAAACATCGTGTTTATGTTATTTTTTTATGTTAAAATAAAATAAATTTTTATAAATTTTTAC
192 TTATAAACATCATGTTTATGTTAATTTTTTATG-----AT-AAATAAATTTATATAAATTTTTAC
* * *
5444140 ACGTTAATTATTTATTTATCTATATTTTGATATATTCATGTATTCATACCGTGTTTATATTATTT
251 ACGTTAATTATTTATTTATCTATATTTTGACATATTCATGTATTCATACAGTATTTATATTATTT
* * * *
5444205 TTTATGTTGTGTTTATTTATATGTTGAGTTTGTACTATATCTCAATTCATGTTATATTTTACATA
316 TTCATGCTGTGTTTATTTATATATTAAGTTTGTACTATATCTCAATTCATGTTATATTTTACATA
*
5444270 GCTAATTAACGTGATTCA
381 GCTAAATAACGTGATTCA
5444288 ATTTATAAAA
Statistics
Matches: 352, Mismatches: 36, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
483 23 0.07
484 27 0.08
485 4 0.01
486 24 0.07
488 95 0.27
489 23 0.07
490 58 0.16
491 4 0.01
495 1 0.00
496 1 0.00
497 47 0.13
498 45 0.13
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (481 bp):
AAATAAAGAAGAAAAAAAAAAAAAGAAAAAGAGAAAAAAAATTTATGAATTTATATTTATATTTT
TATTTAAAATATTACATTTTTATATTTTTTTACATATTAATAATTCATTTTATTTCAGTATATTT
TTATATGTACGTATATTCGTGTTATATACATATCATTTTCAAGTTATATTTTAAATATTTTTTAT
AAACATCATGTTTATGTTAATTTTTTATGATAAATAAATTTATATAAATTTTTACACGTTAATTA
TTTATTTATCTATATTTTGACATATTCATGTATTCATACAGTATTTATATTATTTTTCATGCTGT
GTTTATTTATATATTAAGTTTGTACTATATCTCAATTCATGTTATATTTTACATAGCTAAATAAC
GTGATTCATATAAAATTAACTACACAAACTCACCTGATGCTGACACGTGATTTTTTTTTTTTGCG
TTCAGCAAGGCAAGGCTAAAAAAAAG
Found at i:5444988 original size:17 final size:18
Alignment explanation
Indices: 5444953--5444991 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5444943 GCCTTAATTT
* *
5444953 ATTTTTTATTTTATATAA
1 ATTTTTTATATGATATAA
5444971 ATTTTTTATATGAT-TAA
1 ATTTTTTATATGATATAA
5444988 ATTT
1 ATTT
5444992 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTTATATGATATAA
Found at i:5448226 original size:4 final size:4
Alignment explanation
Indices: 5448217--5448242 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5448207 CTCCTTTTTC
5448217 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
5448243 CAGTATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:5450651 original size:2 final size:2
Alignment explanation
Indices: 5450644--5450683 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5450634 GACTCTGAAG
5450644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5450684 CCCTTCTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5458415 original size:28 final size:28
Alignment explanation
Indices: 5458313--5458587 Score: 246
Period size: 28 Copynumber: 9.8 Consensus size: 28
5458303 AACTTTAGAG
* *
5458313 AAAGTTGCCACCGACTTGTGTGAGCTTT-A
1 AAAGATGCCACTGACTTGTG-G-GCTTTGA
* * ** * *
5458342 AAAGGATACCCCTGACTCATGGGTTTTGG
1 AAA-GATGCCACTGACTTGTGGGCTTTGA
* * * *
5458371 AAGGATGTCACAGACTTATGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* *
5458399 AGAGATGCCACTAACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
5458427 AAGGATGCCACTAACTCGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* *
5458455 AAAGATGCCATTGATTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* *
5458483 AGAGATGCTACTGACTTGTGGGCTTTGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * * * *
5458511 AAGGATGTCACTGACTTATGGGCTATAA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
* * *
5458539 AAAGGTGTCACTGACTTGTGGGCTTAGA
1 AAAGATGCCACTGACTTGTGGGCTTTGA
*
5458567 AAAGATGCCACAGACTTGTGG
1 AAAGATGCCACTGACTTGTGG
5458588 ACTTAAAAGG
Statistics
Matches: 194, Mismatches: 50, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
28 177 0.91
29 6 0.03
30 11 0.06
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (28 bp):
AAAGATGCCACTGACTTGTGGGCTTTGA
Found at i:5458615 original size:27 final size:27
Alignment explanation
Indices: 5458536--5459110 Score: 605
Period size: 27 Copynumber: 21.0 Consensus size: 27
5458526 TTATGGGCTA
* * * * *
5458536 TAAAAAGGTGTCACTGACTTGTGGGCT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * * *
5458563 TAGAAAAGATGCCACAGACTTGTGGACT
1 TA-AAAGGGTGCCACGGAGTTGTGGACT
* *
5458591 TAAAAGGGTGCCACGGAGTTATGGAAT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
*
5458618 TAAAAAGGGCTGCCACGGAGTTATGGACT
1 T-AAAAGGG-TGCCACGGAGTTGTGGACT
*
5458647 TAAAAGGGTACCACGGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * *
5458674 TAAAAGGGTGCTACAGAGTTATGGACTT
1 TAAAAGGGTGCCACGGAGTTGTGGAC-T
*
5458702 TAAAAGGGTGCCACAGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
5458729 TAAAAAGGGCTGCCACGGAGTTGTGGACT
1 T-AAAAGGG-TGCCACGGAGTTGTGGACT
* *
5458758 TAAACGGGTGCCAC-GAGTTGTGGATTT
1 TAAAAGGGTGCCACGGAGTTGTGGA-CT
* * * *
5458785 TAAAAAGGTGTCACAGAGTTGTGGATT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * *
5458812 TAAAA-GATGCCACGGAGCTGTGGATT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * *
5458838 TTAAAGGTTGCCACGGAGCTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
*
5458865 TAAAAGGTTGCCACGGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * *
5458892 TAAAAGGTTGTCACAGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
*
5458919 TAAAAGGGTGCCACGGAGTTGTGAACTT
1 TAAAAGGGTGCCACGGAGTTGTGGAC-T
* **
5458947 TAAAAGGATGCCAAAGAGTTGTGGACTT
1 TAAAAGGGTGCCACGGAGTTGTGGAC-T
* *
5458975 TAAACGGGTGCCACAGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* *
5459002 TAAAATGGTACCACGGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
*
5459029 TAAAAGGGTGTCACGGAGTTGTGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* ** * *
5459056 TAAAAGGATGTTATGGAGTTGTGAACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
* * *
5459083 TAAAAGGTTACCACGGAGTTGTGAACT
1 TAAAAGGGTGCCACGGAGTTGTGGACT
5459110 T
1 T
5459111 TGAAAAGAAA
Statistics
Matches: 475, Mismatches: 63, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
26 31 0.07
27 273 0.57
28 133 0.28
29 38 0.08
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.26
Consensus pattern (27 bp):
TAAAAGGGTGCCACGGAGTTGTGGACT
Found at i:5459046 original size:164 final size:162
Alignment explanation
Indices: 5458536--5459117 Score: 634
Period size: 164 Copynumber: 3.5 Consensus size: 162
5458526 TTATGGGCTA
* * * * * * *
5458536 TAAAAAGGTGTCACTGACTTGTGGGCTTAGAAAAGATGCCACAGACTTGTGGACTTAAAAGGGTG
1 TAAAAGGGTGCCACGGAGTTGTGGACTTA-AAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTG
* * * * *
5458601 CCACGGAGTTATGGAA--TTAAAAAGGGCTGCCACGGAGTTATGGACTTAAAAGGGTACCACGGA
65 CCACGGAGTTGT-GAACTTTAAAAA-GG-TGCCACAGAGTTGTGGACTTTAAAGGGTGCCACGGA
* * *
5458664 GTTGTGGACTTAAAAGGGTGCTACAGAGTTATGGACTT
127 GTTGTGGACTTAAAA-GGTGCCACGGAGTTGTGGAC-T
* * * *
5458702 TAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGCTGCCACGGAGTTGTGGACTTAAACGGGT
1 TAAAAGGGTGCCACGGAGTTGTGGACTT-AAAA-GGATGCCACAGAGTTGTGGACTTAAAAGGGT
* * * * * *
5458767 GCCAC-GAGTTGTGGATTTTAAAAAGGTGTCACAGAGTTGTGGA-TTTAAAAGATGCCACGGAGC
64 GCCACGGAGTTGTGAACTTTAAAAAGGTGCCACAGAGTTGTGGACTTTAAAGGGTGCCACGGAGT
* * *
5458830 TGTGGATTTTAAAGGTTGCCACGGAGCTGTGGACT
129 TGTGGACTTAAAAGG-TGCCACGGAGTTGTGGACT
* * *
5458865 TAAAAGGTTGCCACGGAGTTGTGGACTTAAAAGGTTGTCACAGAGTTGTGGACTTAAAAGGGTGC
1 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGC
* *
5458930 CACGGAGTTGTGAACTTT-AAAAGGATGCCAAAGAGTTGTGGACTTTAAACGGGTGCCACAGAGT
66 CACGGAGTTGTGAACTTTAAAAAGG-TGCCACAGAGTTGTGGACTTTAAA-GGGTGCCACGGAGT
*
5458994 TGTGGACTTAAAATGGTACCACGGAGTTGTGGACT
129 TGTGGACTTAAAA-GGTGCCACGGAGTTGTGGACT
* ** ** * * *
5459029 TAAAAGGGTGTCACGGAGTTGTGGACTTAAAAGGATGTTATGGAGTTGTGAACTTAAAAGGTTAC
1 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGC
*
5459094 CACGGAGTTGTGAACTTTGAAAAG
66 CACGGAGTTGTGAACTTTAAAAAG
5459118 AAATGTCACT
Statistics
Matches: 352, Mismatches: 53, Indels: 23
0.82 0.12 0.05
Matches are distributed among these distances:
161 38 0.11
162 31 0.09
163 35 0.10
164 152 0.43
165 23 0.07
166 34 0.10
167 39 0.11
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (162 bp):
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGC
CACGGAGTTGTGAACTTTAAAAAGGTGCCACAGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTG
TGGACTTAAAAGGTGCCACGGAGTTGTGGACT
Found at i:5459091 original size:245 final size:247
Alignment explanation
Indices: 5458536--5459110 Score: 726
Period size: 245 Copynumber: 2.3 Consensus size: 247
5458526 TTATGGGCTA
* * * * * *
5458536 TAAAAAGGTGTCACTGACTTGTGGGCTTAGAAAAGATGCCACAGACTTGTGGACTTAAAAGGGTG
1 TAAAAAGGTGTCACAGAGTTGTGGACTT--AAAAGATGCCACGGAGTTGTGGACTTAAAAGGTTG
* * *
5458601 CCACGGAGTTATGGAATTAAAAAGGGCTGCCACGGAGTTATGGACTTAAAAGGGTACCACGGAGT
64 CCACGGAGTTGTGGACTTAAAAAGGGCTGCCACGGAGTTATGGACTTAAAAGGGTACCACAGAGT
* * * *
5458666 TGTGGACTTAAAAGGGTGCTACAGAGTTATGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTA
129 TGTGGACTTAAAAGGGTGCCACAGAGTTATGAACTTTAAAAGGATGCCAAAGAGTTGTGGACTTA
* * * *
5458731 AAAAGGGCTGCCACGGAGTTGTGGACTTAAACGGGTGCCACGAGTTGTGGATTT
194 AAAAGGGCTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGAGTTGTGGATCT
* * * *
5458785 TAAAAAGGTGTCACAGAGTTGTGGATTTAAAAGATGCCACGGAGCTGTGGATTTTAAAGGTTGCC
1 TAAAAAGGTGTCACAGAGTTGTGGACTTAAAAGATGCCACGGAGTTGTGGACTTAAAAGGTTGCC
* * * * **
5458850 ACGGAGCTGTGGACTT-AAAA-GGTTGCCACGGAGTTGTGGACTTAAAAGGTTGTCACAGAGTTG
66 ACGGAGTTGTGGACTTAAAAAGGGCTGCCACGGAGTTATGGACTTAAAAGGGTACCACAGAGTTG
* * *
5458913 TGGACTTAAAAGGGTGCCACGGAGTTGTGAACTTTAAAAGGATGCCAAAGAGTTGTGGACTTTAA
131 TGGACTTAAAAGGGTGCCACAGAGTTATGAACTTTAAAAGGATGCCAAAGAGTTGTGGACTTAAA
* *
5458978 ACGGG-TGCCACAGAGTTGTGGACTTAAAATGGTACCACGGAGTTGTGGA-CT
196 AAGGGCTGCCACAGAGTTGTGGACTTAAAAGGGTACCAC-GAGTTGTGGATCT
* * ** * * *
5459029 TAAAAGGGTGTCACGGAGTTGTGGACTTAAAAGGATGTTATGGAGTTGTGAACTTAAAAGGTTAC
1 TAAAAAGGTGTCACAGAGTTGTGGACTTAAAA-GATGCCACGGAGTTGTGGACTTAAAAGGTTGC
*
5459094 CACGGAGTTGTGAACTT
65 CACGGAGTTGTGGACTT
5459111 TGAAAAGAAA
Statistics
Matches: 279, Mismatches: 45, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
244 59 0.21
245 148 0.53
246 4 0.01
247 44 0.16
249 24 0.09
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.26
Consensus pattern (247 bp):
TAAAAAGGTGTCACAGAGTTGTGGACTTAAAAGATGCCACGGAGTTGTGGACTTAAAAGGTTGCC
ACGGAGTTGTGGACTTAAAAAGGGCTGCCACGGAGTTATGGACTTAAAAGGGTACCACAGAGTTG
TGGACTTAAAAGGGTGCCACAGAGTTATGAACTTTAAAAGGATGCCAAAGAGTTGTGGACTTAAA
AAGGGCTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGAGTTGTGGATCT
Found at i:5463852 original size:428 final size:428
Alignment explanation
Indices: 5463050--5463911 Score: 1661
Period size: 428 Copynumber: 2.0 Consensus size: 428
5463040 ATGACAATGA
*
5463050 ATGACTAGTGATGCAGATGCACGATCAAGATAATTAAATGAATAGAGTGGACAACGGAAATGCAA
1 ATGATTAGTGATGCAGATGCACGATCAAGATAATTAAATGAATAGAGTGGACAACGGAAATGCAA
* *
5463115 TTATTGCCCTGATATTCAAGATAAGTGATGCGATGGGGTTACAATAACCAAATGGAGGTAAAATG
66 TTATTGCCCTGATAGTCAAGATAAGTGATGCGATGGGGTTACAATAACCAAATAGAGGTAAAATG
5463180 TGATGATGATGCAGGCTATTGACGAAACAAAGGATGAACAAGATGTGATGATGCATGCAAAAATC
131 TGATGATGATGCAGGCTATTGACGAAACAAAGGATGAACAAGATGTGATGATGCATGCAAAAATC
5463245 ACAAACGCAAAATTTTACAACGTGCAAACAATTGCAAAGAATAAAAAGAATAAGGGTAAAGAATA
196 ACAAACGCAAAATTTTACAACGTGCAAACAATTGCAAAGAATAAAAAGAATAAGGGTAAAGAATA
*
5463310 TACCCTAACAATTGCCCTGAATTAGGCATTACCATGCTTATGGACATGTGTGATGAGGAGAAAAG
261 TACCCTAACAATTGCCCTGAATTAGGCATTACCATGCCTATGGACATGTGTGATGAGGAGAAAAG
5463375 ACAGATAGCAAAACAGTGTGTCTGGTAGTAAATAGCTCCTAATGAGGTAATATGATACCTCGAGG
326 ACAGATAGCAAAACAGTGTGTCTGGTAGTAAATAGCTCCTAATGAGGTAATATGATACCTCGAGG
*
5463440 GCACAAAAAGCGACCGAATAAGTGGTATGCGTTAAGCC
391 GCACAAAAAGCGACCGAATAAGTGGTATGCATTAAGCC
5463478 ATGATTAGTGATGCAGATGCACGATCAAGATAATTAAATGAATAGAGTGGACAACGGAAATGCAA
1 ATGATTAGTGATGCAGATGCACGATCAAGATAATTAAATGAATAGAGTGGACAACGGAAATGCAA
5463543 TTATTGCCCTGATAGTCAAGATAAGTGATGCGATGGGGTTACAATAACCAAATAGAGGTAAAATG
66 TTATTGCCCTGATAGTCAAGATAAGTGATGCGATGGGGTTACAATAACCAAATAGAGGTAAAATG
*
5463608 TGATGATGATGCAGGCTATTGACGAAACAAAGGATGAACATGATGTGATGATGCATGCAAAAATC
131 TGATGATGATGCAGGCTATTGACGAAACAAAGGATGAACAAGATGTGATGATGCATGCAAAAATC
*
5463673 ACAAACGCAAAATTTTACAACGTGCAAACGATTGCAAAGAATAAAAAGAATAAGGGTAAAGAATA
196 ACAAACGCAAAATTTTACAACGTGCAAACAATTGCAAAGAATAAAAAGAATAAGGGTAAAGAATA
5463738 TACCCTAACAATTGCCCTGAATTAGGCATTACCATGCCTATGGACATGTGTGATGAGGAGAAAAG
261 TACCCTAACAATTGCCCTGAATTAGGCATTACCATGCCTATGGACATGTGTGATGAGGAGAAAAG
5463803 ACAGATAGCAAAACAGTGTGTCTGGTAGTAAATAGCTCCTAATGAGGTAATATGATACCTCGAGG
326 ACAGATAGCAAAACAGTGTGTCTGGTAGTAAATAGCTCCTAATGAGGTAATATGATACCTCGAGG
5463868 GCACAAAAAGCGACCGAATAAGTGGTATGCATTAAGCC
391 GCACAAAAAGCGACCGAATAAGTGGTATGCATTAAGCC
5463906 ATGATT
1 ATGATT
5463912 TGGGATAGCA
Statistics
Matches: 427, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
428 427 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (428 bp):
ATGATTAGTGATGCAGATGCACGATCAAGATAATTAAATGAATAGAGTGGACAACGGAAATGCAA
TTATTGCCCTGATAGTCAAGATAAGTGATGCGATGGGGTTACAATAACCAAATAGAGGTAAAATG
TGATGATGATGCAGGCTATTGACGAAACAAAGGATGAACAAGATGTGATGATGCATGCAAAAATC
ACAAACGCAAAATTTTACAACGTGCAAACAATTGCAAAGAATAAAAAGAATAAGGGTAAAGAATA
TACCCTAACAATTGCCCTGAATTAGGCATTACCATGCCTATGGACATGTGTGATGAGGAGAAAAG
ACAGATAGCAAAACAGTGTGTCTGGTAGTAAATAGCTCCTAATGAGGTAATATGATACCTCGAGG
GCACAAAAAGCGACCGAATAAGTGGTATGCATTAAGCC
Found at i:5465660 original size:20 final size:20
Alignment explanation
Indices: 5465635--5465713 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
5465625 AAAAAGACAG
5465635 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
5465655 AATGTATCGATATATTCATACA
1 AATGTATCGATACATTGA-A-A
*
5465677 TGTATCGTGTATCGATACATTGAAA
1 ---A--ATGTATCGATACATTGAAA
5465702 AATGTATCGATA
1 AATGTATCGATA
5465714 TATTTAGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 26 0.57
21 1 0.02
22 2 0.04
25 2 0.04
26 1 0.02
27 14 0.30
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:5465706 original size:27 final size:27
Alignment explanation
Indices: 5465657--5465710 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5465647 CATTGAAAAA
* * *
5465657 TGTATCGATATATTCATACATGTATCG
1 TGTATCGATACATTCAAAAATGTATCG
*
5465684 TGTATCGATACATTGAAAAATGTATCG
1 TGTATCGATACATTCAAAAATGTATCG
5465711 ATATATTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (27 bp):
TGTATCGATACATTCAAAAATGTATCG
Found at i:5466785 original size:17 final size:17
Alignment explanation
Indices: 5466761--5466810 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
5466751 ATAAATATAA
5466761 TTAA-AAAAATTATATT
1 TTAATAAAAATTATATT
5466777 TTAATAAAAATTAT-TT
1 TTAATAAAAATTATATT
**
5466793 AAAATAAAAATT-TATT
1 TTAATAAAAATTATATT
5466809 TT
1 TT
5466811 TAAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 18 0.64
17 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATAAAAATTATATT
Found at i:5466798 original size:16 final size:16
Alignment explanation
Indices: 5466765--5466838 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
5466755 ATATAATTAA
**
5466765 AAAAATTATATTTTAAT
1 AAAAATTAT-TTAAAAT
5466782 AAAAATTATTTAAAAT
1 AAAAATTATTTAAAAT
*
5466798 AAAAATTTATTTTTAAAT
1 AAAAA-TTA-TTTAAAAT
*
5466816 ATAAA-TATTTAAATAT
1 AAAAATTATTTAAA-AT
5466832 ATAAAAT
1 A-AAAAT
5466839 AATTACATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 5 0.11
16 15 0.33
17 15 0.33
18 11 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAAATTATTTAAAAT
Found at i:5466812 original size:33 final size:35
Alignment explanation
Indices: 5466764--5466838 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
5466754 AATATAATTA
*
5466764 AAAAAATTATATTTT-AATAAAAATTATTTAAA-AT
1 AAAAATTTATATTTTAAATAAAAA-TATTTAAATAT
*
5466798 AAAAATTTAT-TTTTAAATATAAATATTTAAATAT
1 AAAAATTTATATTTTAAATAAAAATATTTAAATAT
5466832 ATAAAAT
1 A-AAAAT
5466839 AATTACATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 12 0.33
34 19 0.53
35 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
AAAAATTTATATTTTAAATAAAAATATTTAAATAT
Found at i:5466825 original size:20 final size:19
Alignment explanation
Indices: 5466779--5466826 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5466769 ATTATATTTT
5466779 AATAAAAA-TTA--TTTAA
1 AATAAAAATTTATTTTTAA
5466795 AATAAAAATTTATTTTTAA
1 AATAAAAATTTATTTTTAA
*
5466814 ATATAAATATTTA
1 A-ATAAAAATTTA
5466827 AATATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 3 0.11
19 6 0.22
20 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAAAAATTTATTTTTAA
Found at i:5466923 original size:34 final size:34
Alignment explanation
Indices: 5466885--5466949 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
5466875 ATACTTAAAA
*
5466885 TTAAATTAAATTCAAATCTCAAATAAATTTATAT
1 TTAAATTAAATTCAAATCTCAAAAAAATTTATAT
* * *
5466919 TTAAATTAAATTTAAATTTTAAAAAAATTTA
1 TTAAATTAAATTCAAATCTCAAAAAAATTTA
5466950 ACTCGAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAAATTAAATTCAAATCTCAAAAAAATTTATAT
Found at i:5466928 original size:17 final size:17
Alignment explanation
Indices: 5466879--5466950 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
5466869 ATAAAAATAC
*
5466879 TTAAAATTAAATTAAAT
1 TTAAATTTAAATTAAAT
* *
5466896 TCAAATCTCAAA-TAAAT
1 TTAAAT-TTAAATTAAAT
*
5466913 TTATATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
*
5466930 TTAAATTTTAAA-AAAAT
1 TTAAA-TTTAAATTAAAT
5466947 TTAA
1 TTAA
5466951 CTCGAATACA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.09
17 30 0.68
18 10 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:5468119 original size:20 final size:22
Alignment explanation
Indices: 5468094--5468143 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
5468084 AGGTAATTTT
5468094 TATCATATAAAAAAT-A-TATA
1 TATCATATAAAAAATAAGTATA
*
5468114 TATCATATAAAGAATAAGTATA
1 TATCATATAAAAAATAAGTATA
*
5468136 TATAATAT
1 TATCATAT
5468144 TTAGTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 1 0.04
22 11 0.42
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (22 bp):
TATCATATAAAAAATAAGTATA
Found at i:5468648 original size:13 final size:13
Alignment explanation
Indices: 5468630--5468662 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5468620 AGTTTATTTG
5468630 TAATTTTGTAT-T
1 TAATTTTGTATGT
5468642 ATAATTTTGTATGT
1 -TAATTTTGTATGT
5468656 TAATTTT
1 TAATTTT
5468663 TTTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (13 bp):
TAATTTTGTATGT
Found at i:5468854 original size:17 final size:17
Alignment explanation
Indices: 5468832--5468866 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5468822 TGATAAATTA
5468832 AATTGTTATAATATTTT
1 AATTGTTATAATATTTT
5468849 AATTGTTATAATATTTT
1 AATTGTTATAATATTTT
5468866 A
1 A
5468867 TAAGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
AATTGTTATAATATTTT
Found at i:5468873 original size:17 final size:17
Alignment explanation
Indices: 5468836--5468875 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5468826 AAATTAAATT
*
5468836 GTTATAATATTTTAATT
1 GTTATAATATTTTAATA
5468853 GTTATAATATTTT-ATAA
1 GTTATAATATTTTAAT-A
5468870 GTTATA
1 GTTATA
5468876 TTTTATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
GTTATAATATTTTAATA
Found at i:5468878 original size:14 final size:15
Alignment explanation
Indices: 5468859--5468892 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
5468849 AATTGTTATA
5468859 ATATTTTATAAG-TT
1 ATATTTTATAAGATT
5468873 ATATTTTATAAGATT
1 ATATTTTATAAGATT
5468888 ATATT
1 ATATT
5468893 ATCATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
ATATTTTATAAGATT
Found at i:5469380 original size:23 final size:22
Alignment explanation
Indices: 5469350--5469393 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5469340 ATAAACAAAT
5469350 TAAATTAAATTA-AATATTAACG
1 TAAATTAAATTATAAT-TTAACG
5469372 TAAATTTAAATTATAATTTAAC
1 TAAA-TTAAATTATAATTTAAC
5469394 TTGCATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
TAAATTAAATTATAATTTAACG
Found at i:5469389 original size:12 final size:11
Alignment explanation
Indices: 5469346--5469392 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
5469336 TTAAATAAAC
5469346 AAATTAAA-TT
1 AAATTAAATTT
5469356 AAATTAAATATT
1 AAATTAAAT-TT
**
5469368 AACGTAAATTT
1 AAATTAAATTT
5469379 AAATTATAATTT
1 AAATTA-AATTT
5469391 AA
1 AA
5469393 CTTGCATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 8 0.27
11 6 0.20
12 16 0.53
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:5471227 original size:20 final size:21
Alignment explanation
Indices: 5471202--5471240 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5471192 TCGATCAATT
5471202 ATATTAAA-ATAAAATTTTAA
1 ATATTAAATATAAAATTTTAA
*
5471222 ATATTAAATATATAATTTT
1 ATATTAAATATAAAATTTT
5471241 GATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTAAATATAAAATTTTAA
Found at i:5471405 original size:18 final size:18
Alignment explanation
Indices: 5471372--5471407 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5471362 CACATGATTA
**
5471372 ATGATATGTATTGAATTG
1 ATGATATGTACCGAATTG
5471390 ATGATATGTACCGAATTG
1 ATGATATGTACCGAATTG
5471408 GATAGACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
ATGATATGTACCGAATTG
Found at i:5472984 original size:2 final size:2
Alignment explanation
Indices: 5472977--5473003 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5472967 AAATATAGTG
5472977 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5473004 GAAATAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5476102 original size:25 final size:25
Alignment explanation
Indices: 5476046--5476127 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
5476036 ATTATTTATC
* *
5476046 AAATATTTTAATAAAAGTTAATATTTAG
1 AAATATTTAAAT-AAA-TT-ATATTTAA
5476074 AAATATTTAAATAAATTATATTTAA
1 AAATATTTAAATAAATTATATTTAA
**
5476099 AAATA-TTATTTAGAATTATA-TTAA
1 AAATATTTAAATA-AATTATATTTAA
5476123 AAATA
1 AAATA
5476128 ATACATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.29
25 19 0.39
26 2 0.04
27 3 0.06
28 11 0.22
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATATTTAAATAAATTATATTTAA
Found at i:5476211 original size:22 final size:22
Alignment explanation
Indices: 5476160--5476211 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5476150 TTTTATGTAT
* *
5476160 TAAATATTTAACATATAATATAT
1 TAAATA-TTAACAAATAATATAC
* *
5476183 TACATATTAATAAATAATATAC
1 TAAATATTAACAAATAATATAC
5476205 TAAATAT
1 TAAATAT
5476212 AAGTTTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAACAAATAATATAC
Found at i:5476240 original size:15 final size:15
Alignment explanation
Indices: 5476222--5476250 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5476212 AAGTTTATTA
5476222 AATATATTCAACATT
1 AATATATTCAACATT
5476237 AATATATTCAACAT
1 AATATATTCAACAT
5476251 ACTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATTCAACATT
Found at i:5476276 original size:20 final size:20
Alignment explanation
Indices: 5476253--5476310 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
5476243 TTCAACATAC
* * *
5476253 TAAATATTTATTTTATATAA
1 TAAATATTTAATATATAAAA
*
5476273 TAAATATCTAATATATAAAA
1 TAAATATTTAATATATAAAA
5476293 T-AATATTTAA-ATATAAAA
1 TAAATATTTAATATATAAAA
5476311 ATATTTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 17 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATTTAATATATAAAA
Found at i:5476289 original size:18 final size:17
Alignment explanation
Indices: 5476266--5476314 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
5476256 ATATTTATTT
5476266 TATATAATAAATATCTAA
1 TATATAA-AAATATCTAA
*
5476284 TATATAAAATAATATTTAA
1 TATAT-AAA-AATATCTAA
5476303 -ATATAAAAATAT
1 TATATAAAAATAT
5476315 TTATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 5 0.18
17 3 0.11
18 10 0.36
19 10 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATAAAAATATCTAA
Found at i:5476313 original size:16 final size:17
Alignment explanation
Indices: 5476266--5476321 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 17
5476256 ATATTTATTT
*
5476266 TATATAATAAATATCTAA
1 TATATAA-AAATATTTAA
5476284 TATATAAAATAATATTTAA
1 TATAT-AAA-AATATTTAA
5476303 -ATATAAAAATATTT-A
1 TATATAAAAATATTTAA
5476318 TATA
1 TATA
5476322 AAATATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.03
16 10 0.29
17 3 0.09
18 10 0.29
19 10 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATAAAAATATTTAA
Found at i:5478020 original size:26 final size:27
Alignment explanation
Indices: 5477963--5478020 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
5477953 AGAGTGAGGT
*
5477963 AGAGAATAAAAAGAATTGAAGAAAACA
1 AGAGAAGAAAAAGAATTGAAGAAAACA
* * * *
5477990 TGAGAAGAAAAAG-CTTGCAGAAAATA
1 AGAGAAGAAAAAGAATTGAAGAAAACA
5478016 AGAGA
1 AGAGA
5478021 TTAGGATTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.60, C:0.05, G:0.22, T:0.12
Consensus pattern (27 bp):
AGAGAAGAAAAAGAATTGAAGAAAACA
Found at i:5478364 original size:3 final size:3
Alignment explanation
Indices: 5478356--5478390 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5478346 GATTTGTTTG
5478356 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5478391 TGTGTAATTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5479903 original size:50 final size:50
Alignment explanation
Indices: 5479839--5480193 Score: 523
Period size: 50 Copynumber: 7.1 Consensus size: 50
5479829 GTTGCCATTA
* * ** * *
5479839 TTGACTATTCTTCACCAACCTTTGACAATCGAAAAATATGGTCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
* * * **
5479889 TTAACTATTTTTCACCAACCTTTGACAATCGAGAGAGATGATCG-AATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
5479938 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
*
5479988 TTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
* *
5480038 TTGACGATTCTTCATCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
* * * *
5480088 TTGACGATTCTTCACCAACCTTTGACAATTGAGAGAGGTGGCCATAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
**
5480138 TTGACTATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
5480188 TTGACT
1 TTGACT
5480194 CTAAGCAACT
Statistics
Matches: 281, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
49 44 0.16
50 237 0.84
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTG
Found at i:5482634 original size:128 final size:128
Alignment explanation
Indices: 5482406--5482652 Score: 440
Period size: 128 Copynumber: 1.9 Consensus size: 128
5482396 CCGTCGACAA
* * *
5482406 CAATTGGACTGAAGACTCCAATGGAAATGTGGATAAATAAGCTAGTTGATTACTCTAATATCCAA
1 CAATTGGACTGAAAACTCCAATGAAAATGTGGACAAATAAGCTAGTTGATTACTCTAATATCCAA
5482471 ATATTTGGATGTCCTGCATATGTAATGTATAATGCCCAAGAAAGAACAAAGTTGTATAATGCC
66 ATATTTGGATGTCCTGCATATGTAATGTATAATGCCCAAGAAAGAACAAAGTTGTATAATGCC
* * *
5482534 CAATTGGACTGAAAACTCCAATGAAAATGTGGACAAGTAAGCTAGTTGATTACTCTAATCTCCAC
1 CAATTGGACTGAAAACTCCAATGAAAATGTGGACAAATAAGCTAGTTGATTACTCTAATATCCAA
5482599 ATATTTGGATGTCCTGCATATGTAATGTATAATGCCCAAGAAAGAACAAAGTTG
66 ATATTTGGATGTCCTGCATATGTAATGTATAATGCCCAAGAAAGAACAAAGTTG
5482653 GATCCAAAAT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 113 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (128 bp):
CAATTGGACTGAAAACTCCAATGAAAATGTGGACAAATAAGCTAGTTGATTACTCTAATATCCAA
ATATTTGGATGTCCTGCATATGTAATGTATAATGCCCAAGAAAGAACAAAGTTGTATAATGCC
Found at i:5484786 original size:35 final size:35
Alignment explanation
Indices: 5484740--5484809 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
5484730 ATTGTTGACT
5484740 ATTCTTCACCAACCTTTGATAATCAAGAAAGATGG
1 ATTCTTCACCAACCTTTGATAATCAAGAAAGATGG
5484775 ATTCTTCACCAACCTTTGATAATCAAGAAAGATGG
1 ATTCTTCACCAACCTTTGATAATCAAGAAAGATGG
5484810 TCGTAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (35 bp):
ATTCTTCACCAACCTTTGATAATCAAGAAAGATGG
Found at i:5484906 original size:50 final size:50
Alignment explanation
Indices: 5484775--5484917 Score: 189
Period size: 50 Copynumber: 2.9 Consensus size: 50
5484765 AGAAAGATGG
* * * * **
5484775 ATTCTTCACCAACCTTTGATAATCAAGAAAGATGGTCGTAATTATTAACT
1 ATTCTTCACCAACCTTTGACAATAAAGAGAGGTGACCGTAATTATTAACT
* * *
5484825 ATTCTTCACCAACCTTTGACAATTGAA-AGAGGTAACCATAATTATTAACT
1 ATTCTTCACCAACCTTTGACAA-TAAAGAGAGGTGACCGTAATTATTAACT
5484875 ATTCTTCACCAACCTTTGACAATAAAGAGAGGTGACCGTAATT
1 ATTCTTCACCAACCTTTGACAATAAAGAGAGGTGACCGTAATT
5484918 GTTGACTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.04
50 74 0.93
51 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (50 bp):
ATTCTTCACCAACCTTTGACAATAAAGAGAGGTGACCGTAATTATTAACT
Found at i:5485554 original size:3 final size:3
Alignment explanation
Indices: 5485546--5485588 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5485536 TTTCGTGTGG
*
5485546 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5485589 ATTAGCCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5488143 original size:22 final size:22
Alignment explanation
Indices: 5488118--5488167 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
5488108 AATAATAAAA
*
5488118 AAAATTATTTAAAT-TTAATTAT
1 AAAATTATATAAATATTAA-TAT
5488140 AAAA-TATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
5488161 AAAATTA
1 AAAATTA
5488168 ATATTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:5488169 original size:11 final size:11
Alignment explanation
Indices: 5488118--5488171 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
5488108 AATAATAAAA
*
5488118 AAAATT-ATTT
1 AAAATTAATAT
*
5488128 AAATTTAATTAT
1 AAAATTAA-TAT
5488140 AAAA-T-ATAT
1 AAAATTAATAT
5488149 AAATATTAATAT
1 AAA-ATTAATAT
5488161 AAAATTAATAT
1 AAAATTAATAT
5488172 TTTCATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.17
10 7 0.19
11 11 0.31
12 12 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:5488894 original size:12 final size:12
Alignment explanation
Indices: 5488878--5488916 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
5488868 ATATATTTAA
5488878 TAAATTTATATT
1 TAAATTTATATT
5488890 TAAATTTAAATATT
1 TAAATTT--ATATT
*
5488904 TATATTTATATT
1 TAAATTTATATT
5488916 T
1 T
5488917 TTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTATATT
Found at i:5492967 original size:11 final size:11
Alignment explanation
Indices: 5492953--5492982 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5492943 AAATAAAATA
5492953 ATTATTTTATT
1 ATTATTTTATT
5492964 ATTATTTTATT
1 ATTATTTTATT
5492975 -TTATTTTA
1 ATTATTTTA
5492983 ATAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:5493771 original size:43 final size:43
Alignment explanation
Indices: 5493723--5493809 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
5493713 TTATTAATGT
* * *
5493723 AATTTTATATAATTATTTTTTA-AATATCTTTGATTTG-ATTTAA
1 AATTTTATATAAATATTATTTATAATAT-TGT-ATTTGTATTTAA
*
5493766 AATTTTATTTAAATATTATTTATAATATTGTATTTGTATTTAA
1 AATTTTATATAAATATTATTTATAATATTGTATTTGTATTTAA
5493809 A
1 A
5493810 TATAATAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 5 0.13
43 28 0.74
44 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (43 bp):
AATTTTATATAAATATTATTTATAATATTGTATTTGTATTTAA
Found at i:5495076 original size:2 final size:2
Alignment explanation
Indices: 5495069--5495099 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5495059 CTCTTTCATT
5495069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5495100 TCTTAGGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5495926 original size:3 final size:3
Alignment explanation
Indices: 5495920--5495954 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5495910 TAGGTTGTTG
5495920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5495955 TTTAAGATTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5497334 original size:18 final size:19
Alignment explanation
Indices: 5497300--5497336 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5497290 ATTTTGTTTT
*
5497300 AATATTTAAAATATATTTA
1 AATATTAAAAATATATTTA
5497319 AATATTAAAAAT-TATTTA
1 AATATTAAAAATATATTTA
5497337 TTTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTAAAAATATATTTA
Found at i:5497521 original size:2 final size:2
Alignment explanation
Indices: 5497516--5497553 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5497506 AAAAAAAAAG
5497516 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5497554 ACTTTATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5498052 original size:2 final size:2
Alignment explanation
Indices: 5498045--5498084 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5498035 GAATCACAAA
5498045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5498085 CAAAGAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5499730 original size:22 final size:21
Alignment explanation
Indices: 5499702--5499747 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
5499692 TTAAATTATT
5499702 TTTAAAATATAATATTTAGTAA
1 TTTAAAATATAATATTTA-TAA
*
5499724 TTTAAAATTTAATATTTATAA
1 TTTAAAATATAATATTTATAA
5499745 TTT
1 TTT
5499748 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAAAATATAATATTTATAA
Found at i:5499977 original size:20 final size:19
Alignment explanation
Indices: 5499952--5499989 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5499942 AAAAAACACA
5499952 TTAAATATAAAATAATTTTT
1 TTAAATATAAAAT-ATTTTT
*
5499972 TTAAATATATAATATTTT
1 TTAAATATAAAATATTTT
5499990 AACTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAATATAAAATATTTTT
Found at i:5500479 original size:18 final size:18
Alignment explanation
Indices: 5500458--5500507 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
5500448 AAAAATAATT
5500458 AAAATATAATATA-ATATA
1 AAAATATAATATACA-ATA
5500476 AAAATATAA-ATACAATA
1 AAAATATAATATACAATA
5500493 AAATATATAAATATA
1 AAA-ATAT-AATATA
5500508 TCAAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.32
18 14 0.50
19 2 0.07
20 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATAATATACAATA
Found at i:5500492 original size:24 final size:24
Alignment explanation
Indices: 5500441--5500507 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
5500431 TAGTTATAAT
*
5500441 TATAATA-AAAAATAATTAAAATATAA
1 TATAATATAAAAAT-A-T-AAATACAA
5500467 TATAATATAAAAATATAAATACAA
1 TATAATATAAAAATATAAATACAA
* *
5500491 TAAAATATATAAATATA
1 TATAATATAAAAATATA
5500508 TCAAATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 22 0.59
25 1 0.03
26 8 0.22
27 6 0.16
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (24 bp):
TATAATATAAAAATATAAATACAA
Found at i:5500492 original size:29 final size:28
Alignment explanation
Indices: 5500445--5500499 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5500435 TATAATTATA
* *
5500445 ATAAAAAATAATTAAAATATAATATAAT
1 ATAAAAAATAAATAAAATAAAATATAAT
*
5500473 ATAAAAATATAAATACAATAAAATATA
1 ATAAAAA-ATAAATAAAATAAAATATA
5500500 TAAATATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
ATAAAAAATAAATAAAATAAAATATAAT
Found at i:5501538 original size:20 final size:19
Alignment explanation
Indices: 5501477--5501546 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
5501467 TTTTTACTAT
**
5501477 AATAT-TATATATACTTTA
1 AATATATATATATAAATTA
*
5501495 TATGATATATAT-TAAATTA
1 AAT-ATATATATATAAATTA
*
5501514 GATATATATATATAAATATA
1 AATATATATATATAAAT-TA
5501534 AATAT-TAT-TATAA
1 AATATATATATATAA
5501547 CAAGTCGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.35
19 17 0.40
20 11 0.26
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (19 bp):
AATATATATATATAAATTA
Found at i:5501941 original size:22 final size:22
Alignment explanation
Indices: 5501903--5501946 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5501893 ATAAATTTTT
5501903 AAAAAAATTAAAATTTT-TTCA
1 AAAAAAATTAAAATTTTATTCA
* *
5501924 AAAATAAATTATACTTTTATTCA
1 AAAA-AAATTAAAATTTTATTCA
5501947 CTTAACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAAAATTAAAATTTTATTCA
Found at i:5503946 original size:2 final size:2
Alignment explanation
Indices: 5503939--5503969 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5503929 TAACATTTTC
5503939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5503970 GTTGTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5506285 original size:13 final size:13
Alignment explanation
Indices: 5506233--5506518 Score: 188
Period size: 13 Copynumber: 21.8 Consensus size: 13
5506223 TTAGCACGTA
5506233 TACTTGGCA-AGG
1 TACTTGGCACAGG
* *
5506245 TATTTGGCGCAGG
1 TACTTGGCACAGG
*
5506258 TACTTTGGTACAGG
1 TAC-TTGGCACAGG
*
5506272 TACTTAGCACAGG
1 TACTTGGCACAGG
*
5506285 TACTTGGC-GAGG
1 TACTTGGCACAGG
*
5506297 TACTTGGCATAGG
1 TACTTGGCACAGG
*
5506310 TACTTGACACAGG
1 TACTTGGCACAGG
*
5506323 TACTTGGCATAGG
1 TACTTGGCACAGG
* *
5506336 TATTTAGCACAGG
1 TACTTGGCACAGG
*
5506349 CT-CTTTGGCACA-A
1 -TAC-TTGGCACAGG
* * *
5506362 TACTTTGGTATATG
1 TAC-TTGGCACAGG
*
5506376 TACTTGGCA-AGA
1 TACTTGGCACAGG
* *
5506388 TACTTGGTACAAG
1 TACTTGGCACAGG
*
5506401 TACTTTGGTACAGG
1 TAC-TTGGCACAGG
*
5506415 TACTTGGCATAGG
1 TACTTGGCACAGG
* *
5506428 TA-TCTGACACAAG
1 TACT-TGGCACAGG
*
5506441 TACTTGGCACAAG
1 TACTTGGCACAGG
* *
5506454 TACTTTGACATAGG
1 TAC-TTGGCACAGG
* * *
5506468 TACCTGACACAGA
1 TACTTGGCACAGG
* *
5506481 TACTTTGACATAGG
1 TAC-TTGGCACAGG
5506495 TACTTGGCACAGG
1 TACTTGGCACAGG
*
5506508 TACTTAGCACA
1 TACTTGGCACA
5506519 AATATCTAGC
Statistics
Matches: 213, Mismatches: 48, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
12 29 0.14
13 129 0.61
14 55 0.26
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (13 bp):
TACTTGGCACAGG
Found at i:5506403 original size:25 final size:26
Alignment explanation
Indices: 5506353--5506405 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
5506343 CACAGGCTCT
* *
5506353 TTGGCACAATACTTTGGTATATGTAC
1 TTGGCACAATACTTTGGTACAAGTAC
5506379 TTGGCA-AGATAC-TTGGTACAAGTAC
1 TTGGCACA-ATACTTTGGTACAAGTAC
5506404 TT
1 TT
5506406 TGGTACAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (26 bp):
TTGGCACAATACTTTGGTACAAGTAC
Found at i:5506408 original size:14 final size:14
Alignment explanation
Indices: 5506351--5506419 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 14
5506341 AGCACAGGCT
*
5506351 CTTTGGCACAA-TA
1 CTTTGGTACAAGTA
* *
5506364 CTTTGGTATATGTA
1 CTTTGGTACAAGTA
5506378 C-TTGG--CAAGATA
1 CTTTGGTACAAG-TA
5506390 C-TTGGTACAAGTA
1 CTTTGGTACAAGTA
*
5506403 CTTTGGTACAGGTA
1 CTTTGGTACAAGTA
5506417 CTT
1 CTT
5506420 GGCATAGGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.04
12 7 0.16
13 15 0.33
14 21 0.47
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (14 bp):
CTTTGGTACAAGTA
Found at i:5506466 original size:40 final size:40
Alignment explanation
Indices: 5506396--5506510 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 40
5506386 GATACTTGGT
* * * *
5506396 ACAAGTACTTTGGTACAGGTACTTGGCATAGGTATCTGAC
1 ACAAGTACTTTGGCACAAGTACTTGACATAGGTACCTGAC
5506436 ACAAGTAC-TTGGCACAAGTACTTTGACATAGGTACCTGAC
1 ACAAGTACTTTGGCACAAGTAC-TTGACATAGGTACCTGAC
* * * * *
5506476 AC-AGATACTTTGACATAGGTACTTGGCACAGGTAC
1 ACAAG-TACTTTGGCACAAGTACTTGACATAGGTAC
5506511 TTAGCACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
39 13 0.21
40 40 0.63
41 10 0.16
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (40 bp):
ACAAGTACTTTGGCACAAGTACTTGACATAGGTACCTGAC
Found at i:5506470 original size:27 final size:27
Alignment explanation
Indices: 5506388--5506512 Score: 119
Period size: 27 Copynumber: 4.7 Consensus size: 27
5506378 CTTGGCAAGA
* **
5506388 TACTTGGTACAAGTACTTTGGTACAGG
1 TACTTGGCACAAGTACTTTGACACAGG
* * * *
5506415 TACTTGGCATAGGTA-TCTGACACAAG
1 TACTTGGCACAAGTACTTTGACACAGG
*
5506441 TACTTGGCACAAGTACTTTGACATAGG
1 TACTTGGCACAAGTACTTTGACACAGG
* * *
5506468 TACCTGACAC-AGATACTTTGACATAGG
1 TACTTGGCACAAG-TACTTTGACACAGG
*
5506495 TACTTGGCACAGGTACTT
1 TACTTGGCACAAGTACTT
5506513 AGCACAAATA
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
26 22 0.28
27 55 0.71
28 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (27 bp):
TACTTGGCACAAGTACTTTGACACAGG
Found at i:5509117 original size:67 final size:67
Alignment explanation
Indices: 5509020--5509585 Score: 655
Period size: 67 Copynumber: 8.4 Consensus size: 67
5509010 CATTATGGAA
* * * * **
5509020 AAGTCGACCGTTGTGATCTTATGCGTCACTTTCGTCA-GTTTCCTCAATATAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
5509084 GAG
65 GAG
* * *
5509087 AAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTCATTTTTCC-CAATGCAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTCT-ATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
*
5509151 GGG
65 GAG
* *
5509154 AAGTTGATCGTTGTGGTCATATGCGCCACTTTCGTCACTTTTCCT-AATGTAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
5509218 GAG
65 GAG
* * * *
5509221 AAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTT-TTCTATGCAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
5509285 GAG
65 GAG
* * *
5509288 AAGTCGATCGTTATGGTCTCATGCACCACTTTCGTTACTTTTCC-CAATGCAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTCT-ATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
5509352 GAG
65 GAG
* * ** *
5509355 AAGTCGATCATTGTGGTCATATGTGCCACTTTTATCACTTTTCC-CAATGCAAGTACTGTTAATA
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
*
5509419 GAA
65 GAG
* * * *
5509422 AAGTCGATCTTTGTGGTCGTATGCGTCATTTTCGTCACTTTTTCCT--ATGCAAGTACACTTAAT
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCAC-TTTTCCTCAATGCAAGTACTCTTAAT
5509485 AGAG
64 AGAG
* * * * *
5509489 AAGTCGATTGTTGTGGTCTTATGTGCCACTTCCATTACTTTTCCT-AATGCAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTC-TATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATA
5509553 GAG
65 GAG
* *
5509556 AAGTCGATCATTGTGGTCTTATGCGTCACT
1 AAGTCGATCGTTGTGGTC-TATGCGCCACT
5509586 CTCGCTACTC
Statistics
Matches: 427, Mismatches: 61, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
66 10 0.02
67 404 0.95
68 13 0.03
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (67 bp):
AAGTCGATCGTTGTGGTCTATGCGCCACTTTCGTCACTTTTCCTCAATGCAAGTACTCTTAATAG
AG
Found at i:5509207 original size:134 final size:134
Alignment explanation
Indices: 5509020--5509585 Score: 724
Period size: 134 Copynumber: 4.2 Consensus size: 134
5509010 CATTATGGAA
* * * **
5509020 AAGTCGACCGTTGTGATCTTATGCGTCACTTTCGTCA-GTTTCCTCAATATAAGTACTCTTAATA
1 AAGTCGATCGTTGTGGTCTTATGCGTCACTTTCGTCACTTTTCCT-AATGCAAGTACTCTTAATA
* * *
5509084 GAGAAGTCGATCGTTGTGGTC-TCATGTGCCACTTCCGTCATTTTTCCCAATGCAAGTACTCTTA
65 GAGAAGTCGATCATTGTGGTCAT-ATGTGCCACTTCCATCACTTTTCCCAATGCAAGTACTCTTA
*
5509148 ATAGGG
129 ATAGAG
* * * *
5509154 AAGTTGATCGTTGTGGTCATATGCGCCACTTTCGTCACTTTTCCTAATGTAAGTACTCTTAATAG
1 AAGTCGATCGTTGTGGTCTTATGCGTCACTTTCGTCACTTTTCCTAATGCAAGTACTCTTAATAG
* * * * ** *
5509219 AGAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTTCTATGCAAGTACTCTTAAT
66 AGAAGTCGATCATTGTGGTCATATGTGCCACTTCCATCACTTTTCCCAATGCAAGTACTCTTAAT
5509284 AGAG
131 AGAG
* * ** * *
5509288 AAGTCGATCGTTATGGTCTCATGCACCACTTTCGTTACTTTTCCCAATGCAAGTACTCTTAATAG
1 AAGTCGATCGTTGTGGTCTTATGCGTCACTTTCGTCACTTTTCCTAATGCAAGTACTCTTAATAG
** *
5509353 AGAAGTCGATCATTGTGGTCATATGTGCCACTTTTATCACTTTTCCCAATGCAAGTACTGTTAAT
66 AGAAGTCGATCATTGTGGTCATATGTGCCACTTCCATCACTTTTCCCAATGCAAGTACTCTTAAT
*
5509418 AGAA
131 AGAG
* * * *
5509422 AAGTCGATCTTTGTGGTCGTATGCGTCATTTTCGTCACTTTTTCCT-ATGCAAGTACACTTAATA
1 AAGTCGATCGTTGTGGTCTTATGCGTCACTTTCGTCAC-TTTTCCTAATGCAAGTACTCTTAATA
** * * *
5509486 GAGAAGTCGATTGTTGTGGTCTTATGTGCCACTTCCATTACTTTTCCTAATGCAAGTACTCTTAA
65 GAGAAGTCGATCATTGTGGTCATATGTGCCACTTCCATCACTTTTCCCAATGCAAGTACTCTTAA
5509551 TAGAG
130 TAGAG
*
5509556 AAGTCGATCATTGTGGTCTTATGCGTCACT
1 AAGTCGATCGTTGTGGTCTTATGCGTCACT
5509586 CTCGCTACTC
Statistics
Matches: 374, Mismatches: 55, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
134 361 0.97
135 13 0.03
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (134 bp):
AAGTCGATCGTTGTGGTCTTATGCGTCACTTTCGTCACTTTTCCTAATGCAAGTACTCTTAATAG
AGAAGTCGATCATTGTGGTCATATGTGCCACTTCCATCACTTTTCCCAATGCAAGTACTCTTAAT
AGAG
Found at i:5509289 original size:201 final size:201
Alignment explanation
Indices: 5509070--5509585 Score: 771
Period size: 201 Copynumber: 2.6 Consensus size: 201
5509060 TCCTCAATAT
* *
5509070 AAGTACTCTTAATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTCATTTTTCCCAAT
1 AAGTACTCTTAATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAAT
* * * * *
5509135 GCAAGTACTCTTAATAGGGAAGTTGATCGTTGTGGTCATATGCGCCACTTTCGTCACTTTTCCTA
66 GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCATATGCGCCACTTTCATCACTTTTCCCA
* * *
5509200 ATGTAAGTACTCTTAATAGAGAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTT
131 ATGCAAGTACTCTTAATAGAAAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTC
5509265 CTATGC
196 CTATGC
* ** *
5509271 AAGTACTCTTAATAGAGAAGTCGATCGTTATGGTCTCATGCACCACTTTCGTTACTTTTCCCAAT
1 AAGTACTCTTAATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAAT
* *
5509336 GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCATATGTGCCACTTTTATCACTTTTCCCA
66 GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCATATGCGCCACTTTCATCACTTTTCCCA
* * * * * *
5509401 ATGCAAGTACTGTTAATAGAAAAGTCGATCTTTGTGGTCGTATGCGTCATTTTCGTCACTTTTTC
131 ATGCAAGTACTCTTAATAGAAAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTC
5509466 CTATGC
196 CTATGC
* * * * *
5509472 AAGTACACTTAATAGAGAAGTCGATTGTTGTGGTCTTATGTGCCACTTCCATTACTTTTCCTAAT
1 AAGTACTCTTAATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAAT
* *
5509537 GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCTTATGCGTCACT
66 GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCATATGCGCCACT
5509586 CTCGCTACTC
Statistics
Matches: 281, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
201 281 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (201 bp):
AAGTACTCTTAATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAAT
GCAAGTACTCTTAATAGAGAAGTCGATCATTGTGGTCATATGCGCCACTTTCATCACTTTTCCCA
ATGCAAGTACTCTTAATAGAAAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTC
CTATGC
Found at i:5509611 original size:201 final size:200
Alignment explanation
Indices: 5509017--5509623 Score: 731
Period size: 201 Copynumber: 3.0 Consensus size: 200
5509007 TTACATTATG
* * * * * **
5509017 GAAAAGTCGACCGTTGTGATCTTATGCGTCACTTTCGTCA--GTTTCCTCAATATAAGTACTCTT
1 GAAAAGTCGATCATTGTGGTCATATGCGTCACTTTCGTCACTTTTTCCT--ATGCAAGTACTCTT
* *
5509080 AATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTCATTTTTCCCAATGCAAGTACTC
64 AATAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAATGCAAGTACTC
* * * * *
5509145 TTAATAGGGAAGTTGATCGTTGTGGTCATATGCGCCACTTTCGTCACTTTTCCTAATGT-AAGTA
129 TTAATAGAGAAGTCGATCATTGTGGTCATATGCGCCAC-TTCGTCACTTTT-CTCATATCAAGTA
5509209 CTCTTAATA
192 CTCTTAATA
* * * *
5509218 GAGAAGTCAATCATTGTGGTCATATGCGCCACTTTCGTCACTTTTTTCTATGCAAGTACTCTTAA
1 GAAAAGTCGATCATTGTGGTCATATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTAA
* ** *
5509283 TAGAGAAGTCGATCGTTATGGTCTCATGCACCACTTTCGTTACTTTTCCCAATGCAAGTACTCTT
66 TAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAATGCAAGTACTCTT
* ** *
5509348 AATAGAGAAGTCGATCATTGTGGTCATATGTGCCACTTTTATCACTTTTCCCA-ATGCAAGTACT
131 AATAGAGAAGTCGATCATTGTGGTCATATGCGCCAC-TTCGTCACTTTTCTCATAT-CAAGTACT
*
5509412 GTTAATA
194 CTTAATA
* * * *
5509419 GAAAAGTCGATCTTTGTGGTCGTATGCGTCATTTTCGTCACTTTTTCCTATGCAAGTACACTTAA
1 GAAAAGTCGATCATTGTGGTCATATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTAA
* * * *
5509484 TAGAGAAGTCGATTGTTGTGGTCTTATGTGCCACTTCCATTACTTTTCCTAATGCAAGTACTCTT
66 TAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAATGCAAGTACTCTT
* * * *
5509549 AATAGAGAAGTCGATCATTGTGGTCTTATGCGTCACTCTCG-CTAC-TCTCTCATTTACAAGTAC
131 AATAGAGAAGTCGATCATTGTGGTCATATGCGCCACT-TCGTC-ACTTTTCTCATAT-CAAGTAC
*
5509612 TCTTAATG
193 TCTTAATA
5509620 GAAA
1 GAAA
5509624 GGTTGTCTAT
Statistics
Matches: 345, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
199 1 0.00
200 9 0.03
201 330 0.96
203 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (200 bp):
GAAAAGTCGATCATTGTGGTCATATGCGTCACTTTCGTCACTTTTTCCTATGCAAGTACTCTTAA
TAGAGAAGTCGATCGTTGTGGTCTCATGTGCCACTTCCGTTACTTTTCCCAATGCAAGTACTCTT
AATAGAGAAGTCGATCATTGTGGTCATATGCGCCACTTCGTCACTTTTCTCATATCAAGTACTCT
TAATA
Found at i:5510119 original size:13 final size:13
Alignment explanation
Indices: 5510101--5510519 Score: 285
Period size: 13 Copynumber: 32.2 Consensus size: 13
5510091 CATAGATACT
*
5510101 TTGGCACAGGGAC
1 TTGGCACAGGTAC
5510114 TTGGCA-AGGTAC
1 TTGGCACAGGTAC
*
5510126 TTAGCACAGGTAC
1 TTGGCACAGGTAC
5510139 TTTGGCACAGGTAC
1 -TTGGCACAGGTAC
* *
5510153 TTGACA-AGGTAT
1 TTGGCACAGGTAC
5510165 TTGGCACAGGTAC
1 TTGGCACAGGTAC
*
5510178 TTGGC-GAGGTAC
1 TTGGCACAGGTAC
* *
5510190 TTAGCACGGGTAC
1 TTGGCACAGGTAC
*
5510203 TTAGCA-AGGTAC
1 TTGGCACAGGTAC
*
5510215 TTGGCACAGGTAT
1 TTGGCACAGGTAC
*
5510228 TTGGCACTGGTAC
1 TTGGCACAGGTAC
*
5510241 TTGGC-GAGGTAC
1 TTGGCACAGGTAC
5510253 TTGGCACAGGTAC
1 TTGGCACAGGTAC
* * * *
5510266 CTAGCACAAGTTC
1 TTGGCACAGGTAC
*
5510279 TTTGGCACAGGTATT
1 -TTGGCACAGGTA-C
* * *
5510294 TTAGTATAGGTAC
1 TTGGCACAGGTAC
**
5510307 TTGGCACATATAC
1 TTGGCACAGGTAC
* *
5510320 TTGGCACAAGTTC
1 TTGGCACAGGTAC
5510333 TTTGGCACAGGTAC
1 -TTGGCACAGGTAC
*
5510347 TTTGACACAGGTAC
1 -TTGGCACAGGTAC
* ***
5510361 CTAATACAGGTAC
1 TTGGCACAGGTAC
*
5510374 TTGACA-AGGTAC
1 TTGGCACAGGTAC
*
5510386 TTGGCACAGATAC
1 TTGGCACAGGTAC
*
5510399 TTTGGCATAGGTAC
1 -TTGGCACAGGTAC
* * *
5510413 CTAGCACAGATAC
1 TTGGCACAGGTAC
* * * *
5510426 TTTAGCATAAGTGC
1 -TTGGCACAGGTAC
*
5510440 TTGACA-AGGTAC
1 TTGGCACAGGTAC
5510452 TTGGCACAGGTAC
1 TTGGCACAGGTAC
*
5510465 TTGGCATAGGTAC
1 TTGGCACAGGTAC
* * *
5510478 CTAGCACAAGTAC
1 TTGGCACAGGTAC
* * * * *
5510491 CTAGTATAGGTTC
1 TTGGCACAGGTAC
5510504 TTTGGCACAGGTAC
1 -TTGGCACAGGTAC
5510518 TT
1 TT
5510520 TGACAATAAT
Statistics
Matches: 311, Mismatches: 81, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
12 70 0.23
13 161 0.52
14 80 0.26
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (13 bp):
TTGGCACAGGTAC
Found at i:5510133 original size:25 final size:26
Alignment explanation
Indices: 5510101--5510519 Score: 285
Period size: 25 Copynumber: 16.1 Consensus size: 26
5510091 CATAGATACT
*
5510101 TTGGCACAGGGACTTGGCA-AGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
*
5510126 TTAGCACAGGTACTTTGGCACAGGTAC
1 TTGGCACAGGTAC-TTGGCACAGGTAC
* *
5510153 TTGACA-AGGTATTTGGCACAGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* * *
5510178 TTGGC-GAGGTACTTAGCACGGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* *
5510203 TTAGCA-AGGTACTTGGCACAGGTAT
1 TTGGCACAGGTACTTGGCACAGGTAC
* *
5510228 TTGGCACTGGTACTTGGC-GAGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* * * *
5510253 TTGGCACAGGTACCTAGCACAAGTTC
1 TTGGCACAGGTACTTGGCACAGGTAC
* * * *
5510279 TTTGGCACAGGTATTTTAGTATAGGTAC
1 -TTGGCACAGGTA-CTTGGCACAGGTAC
** * *
5510307 TTGGCACATATACTTGGCACAAGTTC
1 TTGGCACAGGTACTTGGCACAGGTAC
*
5510333 TTTGGCACAGGTACTTTGACACAGGTAC
1 -TTGGCACAGGTAC-TTGGCACAGGTAC
* *** *
5510361 CTAATACAGGTACTTGACA-AGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* *
5510386 TTGGCACAGATACTTTGGCATAGGTAC
1 TTGGCACAGGTAC-TTGGCACAGGTAC
* * * * * * *
5510413 CTAGCACAGATACTTTAGCATAAGTGC
1 TTGGCACAGGTAC-TTGGCACAGGTAC
*
5510440 TTGACA-AGGTACTTGGCACAGGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* * * *
5510465 TTGGCATAGGTACCTAGCACAAGTAC
1 TTGGCACAGGTACTTGGCACAGGTAC
* * * * *
5510491 CTAGTATAGGTTCTTTGGCACAGGTAC
1 TTGGCACAGGTAC-TTGGCACAGGTAC
5510518 TT
1 TT
5510520 TGACAATAAT
Statistics
Matches: 303, Mismatches: 77, Indels: 26
0.75 0.19 0.06
Matches are distributed among these distances:
25 117 0.39
26 74 0.24
27 94 0.31
28 18 0.06
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (26 bp):
TTGGCACAGGTACTTGGCACAGGTAC
Found at i:5510240 original size:38 final size:38
Alignment explanation
Indices: 5510101--5510490 Score: 225
Period size: 38 Copynumber: 10.0 Consensus size: 38
5510091 CATAGATACT
*
5510101 TTGGCACAGGGACTTGGCAAGGTACTTAGCACAGGTAC
1 TTGGCACAGGTACTTGGCAAGGTACTTAGCACAGGTAC
* * *
5510139 TTTGGCACAGGTACTTGACAAGGTATTTGGCACAGGTAC
1 -TTGGCACAGGTACTTGGCAAGGTACTTAGCACAGGTAC
* * *
5510178 TTGGC-GAGGTACTTAGCACGGGTACTTAGCA-AGGTAC
1 TTGGCACAGGTACTTGGCA-AGGTACTTAGCACAGGTAC
* * * *
5510215 TTGGCACAGGTATTTGGCACTGGTACTTGGC-GAGGTAC
1 TTGGCACAGGTACTTGGCA-AGGTACTTAGCACAGGTAC
* * * * * *
5510253 TTGGCACAGGTACCTAGCACAAGTTCTTTGGCACAGGTATT
1 TTGGCACAGGTACTTGGCA-AGGTAC-TTAGCACAGGTA-C
* * * ** * * *
5510294 TTAGTATAGGTACTTGGCACATATACTTGGCACAAGTTC
1 TTGGCACAGGTACTTGGCA-AGGTACTTAGCACAGGTAC
* * **
5510333 TTTGGCACAGGTACTTTGACACAGGTACCTAATACAGGTAC
1 -TTGGCACAGGTAC-TTGGCA-AGGTACTTAGCACAGGTAC
* * * *
5510374 TTGACA-AGGTACTTGGCACAGATACTTTGGCATAGGTAC
1 TTGGCACAGGTACTTGGCA-AGGTAC-TTAGCACAGGTAC
* * * * * *
5510413 CTAGCACAGATACTTTAGCATAAGTGCTT-G-ACAAGGTAC
1 TTGGCACAGGTAC-TTGGCA-AGGTACTTAGCAC-AGGTAC
* *
5510452 TTGGCACAGGTACTTGGCATAGGTACCTAGCACAAGTAC
1 TTGGCACAGGTACTTGGCA-AGGTACTTAGCACAGGTAC
5510491 CTAGTATAGG
Statistics
Matches: 265, Mismatches: 72, Indels: 28
0.73 0.20 0.08
Matches are distributed among these distances:
37 21 0.08
38 83 0.31
39 79 0.30
40 39 0.15
41 43 0.16
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (38 bp):
TTGGCACAGGTACTTGGCAAGGTACTTAGCACAGGTAC
Found at i:5510284 original size:27 final size:27
Alignment explanation
Indices: 5510253--5510348 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
5510243 GGCGAGGTAC
*
5510253 TTGGCACAGGTACCTAGCACAAGTTCT
1 TTGGCACAGGTACTTAGCACAAGTTCT
* * * * *
5510280 TTGGCACAGGTATTTTAGTATAGGTAC-
1 TTGGCACAGGTA-CTTAGCACAAGTTCT
** *
5510307 TTGGCACATATACTTGGCACAAGTTCT
1 TTGGCACAGGTACTTAGCACAAGTTCT
5510334 TTGGCACAGGTACTT
1 TTGGCACAGGTACTT
5510349 TGACACAGGT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
26 8 0.16
27 35 0.69
28 8 0.16
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (27 bp):
TTGGCACAGGTACTTAGCACAAGTTCT
Found at i:5510419 original size:27 final size:27
Alignment explanation
Indices: 5510337--5510428 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 27
5510327 AAGTTCTTTG
* *
5510337 GCACAGGTACTTTGACACAGGTACCTA
1 GCACAGATACTTTGACATAGGTACCTA
** * * *
5510364 ATACAGGTAC-TTGACA-AGGTACTTG
1 GCACAGATACTTTGACATAGGTACCTA
*
5510389 GCACAGATACTTTGGCATAGGTACCTA
1 GCACAGATACTTTGACATAGGTACCTA
5510416 GCACAGATACTTT
1 GCACAGATACTTT
5510429 AGCATAAGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 14 0.26
26 11 0.21
27 28 0.53
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (27 bp):
GCACAGATACTTTGACATAGGTACCTA
Found at i:5514529 original size:16 final size:16
Alignment explanation
Indices: 5514510--5514554 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5514500 TTCAAAAAAC
5514510 TTAAA-TTAAAAGTAAT
1 TTAAACTTAAAA-TAAT
*
5514526 TTAAAATTTAAAATAAT
1 TT-AAACTTAAAATAAT
5514543 TTAAACTTAAAA
1 TTAAACTTAAAA
5514555 CGATTTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 9 0.35
18 6 0.23
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TTAAACTTAAAATAAT
Found at i:5515750 original size:16 final size:16
Alignment explanation
Indices: 5515731--5515781 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5515721 CATAAAAATC
*
5515731 TAAACTTAAAATAACT
1 TAAACTTAAAATAATT
5515747 TAAA-TCTAATAA-AATT
1 TAAACT-TAA-AATAATT
*
5515763 TAAACTCAAAATAATT
1 TAAACTTAAAATAATT
5515779 TAA
1 TAA
5515782 TTCAAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAACTTAAAATAATT
Found at i:5522403 original size:19 final size:19
Alignment explanation
Indices: 5522362--5522404 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5522352 TATATCGAAT
* *
5522362 TTAAATTTAAATTTATTTT
1 TTAAATTTAAAATTATTTA
5522381 TTAAATTTAATAATT-TTTA
1 TTAAATTTAA-AATTATTTA
5522400 TTAAA
1 TTAAA
5522405 ATGTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAATTTAAAATTATTTA
Found at i:5525169 original size:33 final size:34
Alignment explanation
Indices: 5525106--5525173 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
5525096 AGAAGAAGAA
**
5525106 TGGGATGGGTAGTTTTTTTATGATAAGTTAATTT
1 TGGGATGGGTAGGCTTTTTATGATAAGTTAATTT
* *
5525140 TGGGATGGGT-GGCTTTTTATGCTATGTTAATTT
1 TGGGATGGGTAGGCTTTTTATGATAAGTTAATTT
5525173 T
1 T
5525174 CTTCAATGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (34 bp):
TGGGATGGGTAGGCTTTTTATGATAAGTTAATTT
Found at i:5527786 original size:42 final size:43
Alignment explanation
Indices: 5527726--5527811 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
5527716 GTTTAAAAAT
5527726 GTTGCTTAAATGAAAACATAAAT-AAAACTTTTCATTGGATAA
1 GTTGCTTAAATGAAAACATAAATAAAAACTTTTCATTGGATAA
* * * *
5527768 GTTGCTTAAGTGACAACATAAATAAAAACTTTTTATTTGATAA
1 GTTGCTTAAATGAAAACATAAATAAAAACTTTTCATTGGATAA
5527811 G
1 G
5527812 CAATTTGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (43 bp):
GTTGCTTAAATGAAAACATAAATAAAAACTTTTCATTGGATAA
Found at i:5528257 original size:15 final size:16
Alignment explanation
Indices: 5528218--5528256 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5528208 ATTAAAATTG
* *
5528218 ATTAAAAAATAAATAA
1 ATTAAAAATTAAAAAA
5528234 ATTAAAAATTAAAAAA
1 ATTAAAAATTAAAAAA
5528250 ATTAAAA
1 ATTAAAA
5528257 TACTACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAAATTAAAAAA
Found at i:5529008 original size:18 final size:18
Alignment explanation
Indices: 5528976--5529016 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5528966 TATTACATAT
*
5528976 ATTAA-AAAGTTAATTAA
1 ATTAATAAAATTAATTAA
*
5528993 ATTAATAAAATTAATTTA
1 ATTAATAAAATTAATTAA
5529011 ATTAAT
1 ATTAAT
5529017 TTAAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAATAAAATTAATTAA
Found at i:5529305 original size:14 final size:14
Alignment explanation
Indices: 5529285--5529320 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5529275 TATTTTTTTT
5529285 TAATTTTTAAAATAA
1 TAATTTTTAAAA-AA
5529300 -AATTTTTAAAAAA
1 TAATTTTTAAAAAA
5529313 TAATTTTT
1 TAATTTTT
5529321 TACATATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTTTTAAAAAA
Found at i:5532239 original size:18 final size:18
Alignment explanation
Indices: 5532178--5532242 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
5532168 TAAATTTATA
5532178 TTTAATAAATTAAAATGTTT
1 TTTAA-AAATTAAAATG-TT
* *
5532198 TTTAAAAAATAAAAAT-TA
1 TTT-AAAAATTAAAATGTT
* *
5532216 TATAAAAATTAACATGTT
1 TTTAAAAATTAAAATGTT
5532234 TTTAAAAAT
1 TTTAAAAAT
5532243 AGAAAAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 10 0.28
18 12 0.33
20 12 0.33
21 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTAAAAATTAAAATGTT
Found at i:5532575 original size:16 final size:17
Alignment explanation
Indices: 5532533--5532575 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5532523 TTTAATATTT
*
5532533 ATAAAATTTTTAATCAA
1 ATAAAATTTATAATCAA
*
5532550 ATAAAA-TTATAAT-TA
1 ATAAAATTTATAATCAA
5532565 ATAAAATTTAT
1 ATAAAATTTAT
5532576 TCAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATCAA
Found at i:5532820 original size:11 final size:11
Alignment explanation
Indices: 5532793--5532827 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5532783 ATTAATACGC
*
5532793 AACATGAAAACT
1 AACATGAATA-T
5532805 AACATGAATAT
1 AACATGAATAT
5532816 AACATGAATAT
1 AACATGAATAT
5532827 A
1 A
5532828 TGAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (11 bp):
AACATGAATAT
Found at i:5533263 original size:16 final size:17
Alignment explanation
Indices: 5533244--5533276 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5533234 ATAATTAATG
5533244 ATATTTTTAATT-TTTT
1 ATATTTTTAATTATTTT
5533260 ATATTTTTAATTATTTT
1 ATATTTTTAATTATTTT
5533277 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTTAATTATTTT
Found at i:5533274 original size:10 final size:9
Alignment explanation
Indices: 5533244--5533281 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
5533234 ATAATTAATG
5533244 ATATTTTTA
1 ATATTTTTA
5533253 AT-TTTTT-
1 ATATTTTTA
5533260 ATATTTTTA
1 ATATTTTTA
5533269 ATTATTTTTA
1 A-TATTTTTA
5533279 ATA
1 ATA
5533282 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 10 0.38
9 5 0.19
10 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTTA
Done.