Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 35 of 235
Found at i:11337189 original size:32 final size:31
Alignment explanation
Indices: 11337146--11337213 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11337136 GTCATCTTTA
11337146 AAAATAATATATTTAAAAAAAT-AAAAATATTT
1 AAAATAATATA--TAAAAAAATAAAAAATATTT
* * *
11337178 AAAATATTATATAACAAATTAAAAAATATTT
1 AAAATAATATATAAAAAAATAAAAAATATTT
11337209 AAAAT
1 AAAAT
11337214 TTAAAGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 15 0.47
32 10 0.31
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATAATATATAAAAAAATAAAAAATATTT
Found at i:11337406 original size:9 final size:9
Alignment explanation
Indices: 11337394--11337440 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
11337384 AGGAAAAATA
11337394 AAAAAAGTT
1 AAAAAAGTT
*
11337403 AAAAAAATT
1 AAAAAAGTT
*
11337412 TAAAAAGTT
1 AAAAAAGTT
11337421 AAAAAAGTT
1 AAAAAAGTT
*
11337430 AAAAAAATT
1 AAAAAAGTT
11337439 AA
1 AA
11337441 TAGAACAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (9 bp):
AAAAAAGTT
Found at i:11337408 original size:18 final size:18
Alignment explanation
Indices: 11337387--11337440 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
11337377 ATAAATAAGG
11337387 AAAAATAAAAAAAGTTAA
1 AAAAATAAAAAAAGTTAA
**
11337405 AAAAATTTAAAAAGTTAA
1 AAAAATAAAAAAAGTTAA
*
11337423 AAAAGTTAAAAAAA-TTAA
1 AAAA-ATAAAAAAAGTTAA
11337441 TAGAACAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAAATAAAAAAAGTTAA
Found at i:11337467 original size:14 final size:15
Alignment explanation
Indices: 11337447--11337481 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11337437 TTAATAGAAC
11337447 AAATAATAA-AAAAT
1 AAATAATAATAAAAT
*
11337461 CAATAATAATAAAAT
1 AAATAATAATAAAAT
11337476 AAATAA
1 AAATAA
11337482 ATAAGGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAATAATAAAAT
Found at i:11337510 original size:101 final size:103
Alignment explanation
Indices: 11337360--11337558 Score: 280
Period size: 101 Copynumber: 2.0 Consensus size: 103
11337350 TAAAATTAAT
* *
11337360 AATAATAAAATAAATAAATAAATAAGGAAAAATAAAAAAAGTTAAAAAAATTTAAAAAGT-TAAA
1 AATAATAAAATAAATAAATAAATAAGGAAAAATAAAAAAAGTTAAAAAAATTAAAAAAGTAAAAA
**
11337424 AAAGTTAAAAAAATTAATAGAACAAA-TAATAAAAAATC
66 AAAGAGAAAAAAA-TAATAGAACAAAGTAATAAAAAATC
* *
11337462 AATAATAATA-AAATAAATAAATAAGGACAAAT-AAAAAAGTTAAAAAAAATTAAAAAAGTAAAA
1 AATAATAAAATAAATAAATAAATAAGGAAAAATAAAAAAAGTT-AAAAAAATTAAAAAAGTAAAA
* *
11337525 AAAAGAGAAAGAAATAATAGATCAAAGTAATAAA
65 AAAAGAGAAAAAAATAATAGAACAAAGTAATAAA
11337559 GGACAAAACT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
100 9 0.10
101 48 0.56
102 29 0.34
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (103 bp):
AATAATAAAATAAATAAATAAATAAGGAAAAATAAAAAAAGTTAAAAAAATTAAAAAAGTAAAAA
AAAGAGAAAAAAATAATAGAACAAAGTAATAAAAAATC
Found at i:11337517 original size:19 final size:18
Alignment explanation
Indices: 11337493--11337528 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
11337483 TAAGGACAAA
11337493 TAAAAAAGTTAAAAAAAAT
1 TAAAAAAG-TAAAAAAAAT
11337512 TAAAAAAGTAAAAAAAA
1 TAAAAAAGTAAAAAAAA
11337529 GAGAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAAAAAGTAAAAAAAAT
Found at i:11342915 original size:19 final size:18
Alignment explanation
Indices: 11342891--11342926 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11342881 CAAAAGTTTT
*
11342891 ATTTTAATATTTTTTATAC
1 ATTTTAAT-TTTATTATAC
11342910 ATTTTAATTTTATTATA
1 ATTTTAATTTTATTATA
11342927 TAAACTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:11348105 original size:23 final size:22
Alignment explanation
Indices: 11348079--11348130 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
11348069 TAAAAGAACA
11348079 TATATAAATAATAAGAAAAATAT-
1 TATATAAATAAT-A-AAAAATATC
* *
11348102 TATAATAAGTACTAAAAAATATC
1 TAT-ATAAATAATAAAAAATATC
11348125 TATATA
1 TATATA
11348131 TATACATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
TATATAAATAATAAAAAATATC
Found at i:11348681 original size:24 final size:25
Alignment explanation
Indices: 11348650--11348700 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
11348640 GTTTACAACA
11348650 ATAATAATAAGA-AGCAACAA-TAAT
1 ATAATAATAAGATAGCAA-AACTAAT
*
11348674 ATAATAATAATATAGCAAAACTAAT
1 ATAATAATAAGATAGCAAAACTAAT
11348699 AT
1 AT
11348701 TACAAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (25 bp):
ATAATAATAAGATAGCAAAACTAAT
Found at i:11349926 original size:17 final size:16
Alignment explanation
Indices: 11349899--11349949 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
11349889 GGTCTGATGT
11349899 TGGG-TTGGGGTTTAA
1 TGGGTTTGGGGTTTAA
11349914 TGGGTTTGAGGGTTTAAA
1 TGGGTTTG-GGGTTT-AA
* *
11349932 GGGGTTTGGGTTTTAA
1 TGGGTTTGGGGTTTAA
11349948 TG
1 TG
11349950 TAAGTGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.13
16 6 0.20
17 11 0.37
18 9 0.30
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (16 bp):
TGGGTTTGGGGTTTAA
Found at i:11349938 original size:18 final size:17
Alignment explanation
Indices: 11349906--11349939 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11349896 TGTTGGGTTG
*
11349906 GGGTTTAATGGGTTTGA
1 GGGTTTAAGGGGTTTGA
11349923 GGGTTTAAAGGGGTTTG
1 GGGTTT-AAGGGGTTTG
11349940 GGTTTTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (17 bp):
GGGTTTAAGGGGTTTGA
Found at i:11358666 original size:30 final size:30
Alignment explanation
Indices: 11358632--11358702 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
11358622 TATGGCAGCC
* **
11358632 TTGATCATCTCGAGCTCTCCCTTAAGTTCA
1 TTGATCATCTCGAGCTCCCCCTTAAACTCA
11358662 TTGATCATCTCGAGCTCCCCCTTAAACTCA
1 TTGATCATCTCGAGCTCCCCCTTAAACTCA
*
11358692 TTGATCTTCTC
1 TTGATCATCTC
11358703 CTTCAAAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.37
Consensus pattern (30 bp):
TTGATCATCTCGAGCTCCCCCTTAAACTCA
Found at i:11361151 original size:16 final size:16
Alignment explanation
Indices: 11361130--11361161 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11361120 AAATCCAAAT
*
11361130 TTTCCCTTTTTTTTCC
1 TTTCCCTTTTTCTTCC
11361146 TTTCCCTTTTTCTTCC
1 TTTCCCTTTTTCTTCC
11361162 CCTGTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTCCCTTTTTCTTCC
Found at i:11361686 original size:26 final size:27
Alignment explanation
Indices: 11361626--11361687 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
11361616 CCAAAATTTT
* *
11361626 AAATCAAATAATAATAATATTATTAATA
1 AAATCTAATAACAATAATA-TATTAATA
*
11361654 AATTCTAATAACAATAATA-ATTAATA
1 AAATCTAATAACAATAATATATTAATA
11361680 AAATCTAA
1 AAATCTAA
11361688 GAAAAATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.47
28 16 0.53
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATCTAATAACAATAATATATTAATA
Found at i:11362193 original size:117 final size:117
Alignment explanation
Indices: 11362067--11362292 Score: 362
Period size: 117 Copynumber: 1.9 Consensus size: 117
11362057 GTCATTATGA
*
11362067 ATGTTAAGGTATGATTCTCTAAAGATATAAAAGAAATTATTAAAAATTCAAAATATTTGTATCTG
1 ATGTTAAGGTATGATTCTCTAAAAATATAAAAGAAATTATTAAAAATTCAAAATATTTGTATCTG
* * *
11362132 ATCCGATATTCATTCTTAGTCTGAGTAATATAAGCAATAACTGTCATGATCG
66 ATCCAACATTCATTCCTAGTCTGAGTAATATAAGCAATAACTGTCATGATCG
* * * *
11362184 ATGTTAAGGTATGATTTTCTAAAAATATAAAAGAAGTTATTAAAAATTTAAAATATTTGTATTTG
1 ATGTTAAGGTATGATTCTCTAAAAATATAAAAGAAATTATTAAAAATTCAAAATATTTGTATCTG
* *
11362249 ATTCAACATTCATTCCTAGTCTGAGTAATATAGGCAATAACTGT
66 ATCCAACATTCATTCCTAGTCTGAGTAATATAAGCAATAACTGT
11362293 TTTTAAAGAA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (117 bp):
ATGTTAAGGTATGATTCTCTAAAAATATAAAAGAAATTATTAAAAATTCAAAATATTTGTATCTG
ATCCAACATTCATTCCTAGTCTGAGTAATATAAGCAATAACTGTCATGATCG
Found at i:11378503 original size:42 final size:43
Alignment explanation
Indices: 11378396--11378553 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
11378386 CTCATACAAC
** * *
11378396 GCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCGAT
1 GCCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGAT
* * * *
11378439 GCCACTGCCCCATACA-GAGTCTTACACGAAATCATATA-CGAT
1 GCCAATGTCCCAGACATG-GTCTTACACGAAATCAAATATCGAT
*
11378481 GCCAATGTCCCAGACATGGTCTTACACGTAAATCACAA-ATCGAC
1 GCCAATGTCCCAGACATGGTCTTACACG-AAATCA-AATATCGAT
* * *
11378525 GCCAACGTCACAGACGTGGTCTTACACGA
1 GCCAATGTCCCAGACATGGTCTTACACGA
11378554 TAACACATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
42 28 0.30
43 37 0.39
44 29 0.31
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
GCCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGAT
Found at i:11378539 original size:44 final size:42
Alignment explanation
Indices: 11378457--11378553 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 42
11378447 CCCATACAGA
* * * * *
11378457 GTCTTACACGAAATCATATACGATGCCAATGTCCCAGACATG
1 GTCTTACACGAAATCACAAACGACGCCAACGTCACAGACATG
*
11378499 GTCTTACACGTAAATCACAAATCGACGCCAACGTCACAGACGTG
1 GTCTTACACG-AAATCACAAA-CGACGCCAACGTCACAGACATG
11378543 GTCTTACACGA
1 GTCTTACACGA
11378554 TAACACATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 10 0.21
43 9 0.19
44 28 0.60
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (42 bp):
GTCTTACACGAAATCACAAACGACGCCAACGTCACAGACATG
Found at i:11386463 original size:5 final size:5
Alignment explanation
Indices: 11386453--11386484 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
11386443 TTGTGTGTTC
11386453 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
11386485 TTCACAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:11386467 original size:9 final size:9
Alignment explanation
Indices: 11386453--11386483 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
11386443 TTGTGTGTTC
11386453 TTTATTTTA
1 TTTATTTTA
11386462 TTTATTTTA
1 TTTATTTTA
11386471 TTTTATTTTA
1 -TTTATTTTA
11386481 TTT
1 TTT
11386484 TTTCACAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:11400409 original size:35 final size:35
Alignment explanation
Indices: 11400369--11400438 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
11400359 TCTAGGATCA
* *
11400369 CATATCTTTGAAGGTCTCCTTCCATATTTGCCAAG
1 CATATCTTTGAAGATCACCTTCCATATTTGCCAAG
*
11400404 CATATCTTTGAAGATCACTTTCCATATTTGCCAAG
1 CATATCTTTGAAGATCACCTTCCATATTTGCCAAG
11400439 TTCCGGAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (35 bp):
CATATCTTTGAAGATCACCTTCCATATTTGCCAAG
Found at i:11404144 original size:20 final size:19
Alignment explanation
Indices: 11404112--11404150 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
11404102 GTACAACGAT
*
11404112 CTAAAAAGTATAAAAAATA
1 CTAAAAAGGATAAAAAATA
*
11404131 CTAAAAACGGATAAGAAATA
1 CTAAAAA-GGATAAAAAATA
11404151 GTTACCATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (19 bp):
CTAAAAAGGATAAAAAATA
Found at i:11408585 original size:33 final size:34
Alignment explanation
Indices: 11408548--11408626 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 34
11408538 AAAATGCACA
* *
11408548 AAAAAATAACA-CCCAAACAGCAAAAACAGA-AGC
1 AAAAAATAACAGCACAAACAACAAAAACA-ACAGC
* *
11408581 -AAAAATAACAGTACAAATAACAAAAACAACAGC
1 AAAAAATAACAGCACAAACAACAAAAACAACAGC
11408614 AGAAAAATAACAG
1 A-AAAAATAACAG
11408627 AACCAAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 11 0.29
33 16 0.42
35 11 0.29
ACGTcount: A:0.66, C:0.19, G:0.09, T:0.06
Consensus pattern (34 bp):
AAAAAATAACAGCACAAACAACAAAAACAACAGC
Found at i:11411365 original size:22 final size:24
Alignment explanation
Indices: 11411337--11411381 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
11411327 AATTTTTTTC
11411337 TACTTTAAATT-TTAT-TCAAAAA
1 TACTTTAAATTGTTATATCAAAAA
*
11411359 TACTTTAATTTGTTATATCAAAA
1 TACTTTAAATTGTTATATCAAAA
11411382 CATATTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (24 bp):
TACTTTAAATTGTTATATCAAAAA
Found at i:11414446 original size:93 final size:93
Alignment explanation
Indices: 11414277--11414466 Score: 335
Period size: 93 Copynumber: 2.0 Consensus size: 93
11414267 GGATATTTGA
*
11414277 GCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
11414342 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
11414370 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATTTCTGAACTTGTTGAGT
1 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
*
11414435 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
11414463 GCAT
1 GCAT
11414467 TGCGAATGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (93 bp):
GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:11414473 original size:56 final size:56
Alignment explanation
Indices: 11414411--11414708 Score: 222
Period size: 56 Copynumber: 6.0 Consensus size: 56
11414401 CACTTATGGA
* * * *
11414411 TGCGAATTTCTGAACTTGTTGAGTTGAGTCTGAGTTCGTGAAATGTAACTAGGCAT
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
11414467 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA-
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* * *
11414522 T-CCAA-----G--CTCATTGAGTTGAGTCCGAGTTC----ACT-T-A-T-GG-A-
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* *
11414560 TGCGAATGTCCGAACTCGTTGAGTTGAGTTCGAGTTCATGAAATGTAACTA-G---
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* *
11414612 -GC--AT-T-CGAACTCATTGAGTTGAGTCCGAGTTC----ACT-T-A-T-GG-A-
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
*
11414653 TGCGAATGTCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
11414709 CTGAACTCGT
Statistics
Matches: 194, Mismatches: 15, Indels: 66
0.71 0.05 0.24
Matches are distributed among these distances:
38 2 0.01
39 5 0.03
40 3 0.02
41 2 0.01
42 4 0.02
43 4 0.02
44 3 0.02
45 1 0.01
46 48 0.25
47 47 0.24
48 1 0.01
49 3 0.02
50 4 0.02
51 4 0.02
52 2 0.01
53 3 0.02
54 5 0.03
55 2 0.01
56 51 0.26
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (56 bp):
TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
Found at i:11414571 original size:93 final size:92
Alignment explanation
Indices: 11414467--11414783 Score: 510
Period size: 93 Copynumber: 3.4 Consensus size: 92
11414457 AACTAGGCAT
*
11414467 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCAAGCTCA
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCGAA-CTCA
11414532 TTGAGTTGAGTCCGAGTTCACTTATGGA
65 TTGAGTTGAGTCCGAGTTCACTTATGGA
* *
11414560 TGCGAATGTCCGAACTCGTTGAGTTGAGTTCGAGTTCATGAAATGTAACTAGGCATTCGAACTCA
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA-TCGAACTCA
11414625 TTGAGTTGAGTCCGAGTTCACTTATGGA
65 TTGAGTTGAGTCCGAGTTCACTTATGGA
* *
11414653 TGCGAATGTCCGAACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCTGAACTCG
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC-GAACTCA
11414718 TTGAGTTGAGTCCGAGTTCACTTATGGA
65 TTGAGTTGAGTCCGAGTTCACTTATGGA
** * *
11414746 TGCGAA-CACCTGAGCTCGTTGAGTTGAATCCGAGTTCG
1 TGCGAATGTCC-GAACTCGTTGAGTTGAGTCCGAGTTCG
11414784 CTTATGGGCG
Statistics
Matches: 209, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
92 4 0.02
93 201 0.96
94 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (92 bp):
TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCGAACTCAT
TGAGTTGAGTCCGAGTTCACTTATGGA
Found at i:11414581 original size:149 final size:149
Alignment explanation
Indices: 11414318--11414620 Score: 529
Period size: 149 Copynumber: 2.0 Consensus size: 149
11414308 CACTTATGGA
* *
11414318 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCGAGCTCG
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCAAGCTCA
* * *
11414383 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATTTCTGAACTTGTTGAGTTGAG-TCTGAGTT
66 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTTC-GAGTT
*
11414447 CGTGAAATGTAACTAGGCAT
130 CATGAAATGTAACTAGGCAT
11414467 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCAAGCTCA
1 TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCAAGCTCA
11414532 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTTCGAGTTC
66 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTTCGAGTTC
11414597 ATGAAATGTAACTAGGCAT
131 ATGAAATGTAACTAGGCAT
11414616 T-CGAA
1 TGCGAA
11414621 CTCATTGAGT
Statistics
Matches: 147, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
148 4 0.03
149 141 0.96
150 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (149 bp):
TGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCAAGCTCA
TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTTCGAGTTC
ATGAAATGTAACTAGGCAT
Found at i:11422283 original size:13 final size:13
Alignment explanation
Indices: 11422265--11422292 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11422255 AGTCTATTTG
11422265 CAATAGAAACAAA
1 CAATAGAAACAAA
11422278 CAATAGAAACAAA
1 CAATAGAAACAAA
11422291 CA
1 CA
11422293 GGAACATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (13 bp):
CAATAGAAACAAA
Found at i:11427658 original size:21 final size:21
Alignment explanation
Indices: 11427634--11427691 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
11427624 TTTTATGTTT
*
11427634 TATTATATTATTAAATTATTA
1 TATTATATTATTAAATTAATA
* *
11427655 TATTATATTAATATATTAATA
1 TATTATATTATTAAATTAATA
11427676 TATTA-ATTTATTAAAT
1 TATTATA-TTATTAAAT
11427692 ACTAAGTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATATTATTAAATTAATA
Found at i:11427681 original size:8 final size:8
Alignment explanation
Indices: 11427658--11427715 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
11427648 ATTATTATAT
11427658 TATATTAA
1 TATATTAA
11427666 TATATTAA
1 TATATTAA
11427674 TATATTAA
1 TATATTAA
*
11427682 TTTATTAA
1 TATATTAA
*
11427690 -ATACTAA
1 TATATTAA
11427697 GTATA-TAA
1 -TATATTAA
*
11427705 TATATTTA
1 TATATTAA
11427713 TAT
1 TAT
11427716 TATACATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
7 9 0.21
8 31 0.72
9 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:11427689 original size:16 final size:16
Alignment explanation
Indices: 11427632--11427710 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
11427622 TCTTTTATGT
11427632 TTTATT-ATATTATTAA
1 TTTATTAATA-TATTAA
*
11427648 ATTATTATATTATATTAA
1 TTTATTA-A-TATATTAA
*
11427666 TATATTAATATATTAA
1 TTTATTAATATATTAA
*
11427682 TTTATTAA-ATACTAA
1 TTTATTAATATATTAA
*
11427697 -GTATATAATATATT
1 TTTAT-TAATATATT
11427711 TATATTATAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.06
15 9 0.18
16 24 0.47
17 1 0.02
18 12 0.24
19 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
TTTATTAATATATTAA
Found at i:11431375 original size:19 final size:18
Alignment explanation
Indices: 11431353--11431431 Score: 55
Period size: 16 Copynumber: 4.5 Consensus size: 18
11431343 CACATATAAA
11431353 AATAATTAAAATATAATAT
1 AATAA-TAAAATATAATAT
11431372 AAT-A-AAAATAT--TAT
1 AATAATAAAATATAATAT
11431386 AA-AATATAAATATATATAT
1 AATAATA-AAATATA-ATAT
*
11431405 AATAAATCAAAAT-TCATAT
1 AAT-AAT-AAAATATAATAT
11431424 AAT-ATAAA
1 AATAATAAA
11431432 TTATTATCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 21
0.69 0.01 0.29
Matches are distributed among these distances:
14 6 0.12
15 1 0.02
16 16 0.32
17 2 0.04
18 1 0.02
19 15 0.30
20 1 0.02
21 7 0.14
22 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATAAAATATAATAT
Found at i:11431379 original size:16 final size:16
Alignment explanation
Indices: 11431354--11431410 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
11431344 ACATATAAAA
*
11431354 ATAATTAAAATATAAT
1 ATAATAAAAATATAAT
*
11431370 ATAATAAAAATATTAT
1 ATAATAAAAATATAAT
* *
11431386 AAAATATAAATATATAT
1 ATAATAAAAATATA-AT
11431403 ATAATAAA
1 ATAATAAA
11431411 TCAAAATTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
16 25 0.76
17 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAAAAATATAAT
Found at i:11431404 original size:22 final size:22
Alignment explanation
Indices: 11431319--11431410 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 22
11431309 AAAACACTTA
* *
11431319 ATAAATAGTATAAATTATAAAAT
1 ATAAATA-TAAAAATAATAAAAT
* *
11431342 ACACATATAAAAATAATTAAAAT
1 ATAAATATAAAAATAA-TAAAAT
11431365 ATAATATAATAAAAATATTATAAAAT
1 ATAA-AT-ATAAAAATA--ATAAAAT
* *
11431391 ATAAATATATATATAATAAA
1 ATAAATATAAAAATAATAAA
11431411 TCAAAATTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
22 12 0.21
23 13 0.23
24 9 0.16
25 11 0.20
26 10 0.18
27 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (22 bp):
ATAAATATAAAAATAATAAAAT
Found at i:11431417 original size:21 final size:20
Alignment explanation
Indices: 11431363--11431417 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
11431353 AATAATTAAA
11431363 ATATAATATAATAAAA-ATAT
1 ATATAATA-AATAAAATATAT
11431383 -TAT-A-AAATATAAATATAT
1 ATATAATAAATA-AAATATAT
11431401 ATATAATAAATCAAAAT
1 ATATAATAAAT-AAAAT
11431418 TCATATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 5 0.17
19 6 0.21
20 1 0.03
21 8 0.28
22 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAATAAATAAAATATAT
Found at i:11431428 original size:36 final size:32
Alignment explanation
Indices: 11431361--11431463 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 32
11431351 AAAATAATTA
*
11431361 AAATATAATATAATAAAAATATTATAAAATAT
1 AAATATAATATAATAAAAAAATTATAAAATAT
*
11431393 AAATATATATATAATAAATCAAAATTCATATAATAT
1 AAATATA-ATATAATAAA--AAAATT-ATAAAATAT
* * * *
11431429 AAAT-TATTATCATATCAAAATTTATAACAATAT
1 AAATATAATATAATA-AAAAAATTATAA-AATAT
11431462 AA
1 AA
11431464 CACATCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
32 10 0.17
33 22 0.38
34 6 0.10
35 8 0.14
36 12 0.21
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATATAATATAATAAAAAAATTATAAAATAT
Found at i:11433796 original size:43 final size:43
Alignment explanation
Indices: 11433760--11433901 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
11433750 CTTACATGTT
* * * * *
11433760 ATCACATATCGATGCCACTATCCCAGACAGGGTCTTATACAAA
1 ATCACATATCGATGCCAATGTCCCAGACAAGGTCTTACACGAA
* *
11433803 ATCATATAACGATGCCAATGTCCCAGACAAGGTCTTACACGAA
1 ATCACATATCGATGCCAATGTCCCAGACAAGGTCTTACACGAA
* * * * *
11433846 ATCACA-ATACAATGCCAATGTCTCAGACATGGTCTTACATGTA
1 ATCACATAT-CGATGCCAATGTCCCAGACAAGGTCTTACACGAA
*
11433889 ATCACATCTCGAT
1 ATCACATATCGAT
11433902 AATACTAATG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 79 0.98
44 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCCAGACAAGGTCTTACACGAA
Found at i:11441568 original size:32 final size:32
Alignment explanation
Indices: 11441469--11441576 Score: 99
Period size: 33 Copynumber: 3.3 Consensus size: 32
11441459 GGTGTAAATT
* * **
11441469 CCTTTCCAAGTGGTACACACAAAGTATACATTT
1 CCTTTCCAAG-AGTACACATAAAGTATACATAA
* * * * *
11441502 CCTTTTCATATAGTATACATTAAGTATACCTAA
1 CCTTTCCA-AGAGTACACATAAAGTATACATAA
*
11441535 CCTTTCCAAGAGTACACATAAAGTGTACATAA
1 CCTTTCCAAGAGTACACATAAAGTATACATAA
*
11441567 CCTTTTCAAG
1 CCTTTCCAAG
11441577 TTGTACCATT
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
32 28 0.48
33 29 0.50
34 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.32
Consensus pattern (32 bp):
CCTTTCCAAGAGTACACATAAAGTATACATAA
Found at i:11444337 original size:42 final size:42
Alignment explanation
Indices: 11444229--11444398 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 42
11444219 ATCCGATATG
* * * * * *
11444229 TGATTTCGTGTAAGACCACGTTTGGGACGTTGGTATCG-ATT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
11444270 TCAGATTTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
1 T--GA-TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
* * *
11444315 TGATCT-CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGAT-TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATA
* * * * *
11444358 TGATTACATGTAAGACCTTCTCTGGGACGTTGGCATTGTAT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
11444399 GAGTTTACGA
Statistics
Matches: 107, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 35 0.33
43 38 0.36
44 30 0.28
45 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:11444353 original size:86 final size:85
Alignment explanation
Indices: 11444229--11444398 Score: 202
Period size: 86 Copynumber: 2.0 Consensus size: 85
11444219 ATCCGATATG
* * * * *
11444229 TGATTTCGTGTAAGACCACGTTTGGGACGTTGGTATCGAT-TTCAGATTTACGTGTAAGACCATG
1 TGATCTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-AGA-TTACATGTAAGACCATC
11444293 TCTGGGACATTGGCATCGTATA
64 TCTGGGACATTGGCATCGTATA
* *
11444315 TGATCTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTACATGTAAGACCTTC
1 TGATCTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTAGATTACATGTAAGACCATC
* *
11444378 TCTGGGACGTTGGCATTGTAT
64 TCTGGGACATTGGCATCGTAT
11444399 GAGTTTACGA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 34 0.47
86 35 0.49
87 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (85 bp):
TGATCTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTAGATTACATGTAAGACCATCTC
TGGGACATTGGCATCGTATA
Found at i:11444384 original size:43 final size:42
Alignment explanation
Indices: 11444276--11444398 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
11444266 GATTTCAGAT
*
11444276 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGGCATCGTATATGA
* *
11444318 TCT-CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA
1 T-TACGTGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGA
* * * *
11444361 TTACATGTAAGACCTTCTCTGGGAC-GTTGGCATTGTAT
1 TTACGTGTAAGACCATGTCTGGGACAG-TGGCATCGTAT
11444399 GAGTTTACGA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
42 36 0.51
43 34 0.49
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGGCATCGTATATGA
Found at i:11445334 original size:131 final size:131
Alignment explanation
Indices: 11445121--11445376 Score: 354
Period size: 131 Copynumber: 2.0 Consensus size: 131
11445111 TTGTCTTAGA
* * ** *
11445121 ATGAGTGAAATTCTAAAGGAATATTCGATTATTTGGAACAAACAAGAGATCGCAACCCAGCACGA
1 ATGAATGAAATTCCAAAGGAATATTCGATTATTTCAAACAAACAAGAAATCGCAACCCAGCACGA
*
11445186 TAGGGCACGATTCCCCGAATT-ACCAAACATCGAACATTACCTTCGTTTTGAAGAATTTTTAAAG
66 TAGGGCACGATTCCCCGAATTGA-CAAACATCGAACATTACCTTCGTTTTAAAGAATTTTTAAAG
11445250 AC
130 AC
* * ** *
11445252 ATGAATGAAATTCCAAAGGAATATTCGTTTGTTTCAAACAAACGGGGAAATCGCAACCCATCACG
1 ATGAATGAAATTCCAAAGGAATATTCGATTATTTCAAACAAAC-AAGAAATCGCAACCCAGCACG
** *
11445317 ATAGGGCACGATT-CCCGAATTGACAAACATCGAGTATTGCCTTCGTTTTAAAGAATTTTT
65 ATAGGGCACGATTCCCCGAATTGACAAACATCGAACATTACCTTCGTTTTAAAGAATTTTT
11445377 TTAAATGAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
131 78 0.72
132 31 0.28
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (131 bp):
ATGAATGAAATTCCAAAGGAATATTCGATTATTTCAAACAAACAAGAAATCGCAACCCAGCACGA
TAGGGCACGATTCCCCGAATTGACAAACATCGAACATTACCTTCGTTTTAAAGAATTTTTAAAGA
C
Found at i:11449644 original size:13 final size:13
Alignment explanation
Indices: 11449626--11449680 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
11449616 ACAAATGAAC
11449626 ACAAGAAAAGATA
1 ACAAGAAAAGATA
*
11449639 ACAAGAAATGATGAA
1 ACAAGAAAAGAT--A
*
11449654 TACAAGAAAAGATT
1 -ACAAGAAAAGATA
*
11449668 ACAAGAAATGATA
1 ACAAGAAAAGATA
11449681 CTAAAAAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 22 0.65
15 1 0.03
16 11 0.32
ACGTcount: A:0.62, C:0.07, G:0.16, T:0.15
Consensus pattern (13 bp):
ACAAGAAAAGATA
Found at i:11449658 original size:29 final size:29
Alignment explanation
Indices: 11449620--11449679 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
11449610 ACCCAGACAA
11449620 ATGAACACAAGAAAAGATAACAAGAAATG
1 ATGAACACAAGAAAAGATAACAAGAAATG
* *
11449649 ATGAATACAAGAAAAGATTACAAGAAATG
1 ATGAACACAAGAAAAGATAACAAGAAATG
11449678 AT
1 AT
11449680 ACTAAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.17, T:0.15
Consensus pattern (29 bp):
ATGAACACAAGAAAAGATAACAAGAAATG
Found at i:11454857 original size:24 final size:24
Alignment explanation
Indices: 11454805--11454859 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
11454795 ATACATCATC
* *
11454805 ATTAAAAATTGTAAATAAATTCTA
1 ATTAAAAATGGTAAATAAAATCTA
11454829 ATTAAAAATGGTAAA-AAAATCATA
1 ATTAAAAATGGTAAATAAAATC-TA
*
11454853 TTTAAAA
1 ATTAAAA
11454860 CTTAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (24 bp):
ATTAAAAATGGTAAATAAAATCTA
Found at i:11458123 original size:54 final size:52
Alignment explanation
Indices: 11457945--11458149 Score: 232
Period size: 53 Copynumber: 3.9 Consensus size: 52
11457935 TATCATACCA
* * * * * * *
11457945 ATGCCATATCCCGGATATGGTCTTACACGGGAGCACTTATCACTTTTCTCCG
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAATCACTTATCACTTTTATCCG
* *
11457997 ATGCCATAGCCTAGCTATGGTCTTATACGG-ATCACTTGTATCACTTTAATCCG
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAATCAC-T-TATCACTTTTATCCG
* * * **
11458050 AAGCCATAGCCCAGCTATGGTTTTATACGGAAATCACTTATCACTTGTTTTTTG
1 ATGCCATAGCCCAGCTATGGTCTTATACGG-AATCACTTATCACTT-TTATCCG
11458104 ATGCCATAGCCCAGCTATGGTCTTATACGGATATCACTTATCACTT
1 ATGCCATAGCCCAGCTATGGTCTTATACGGA-ATCACTTATCACTT
11458150 GTTGCCATGG
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
51 4 0.03
52 26 0.20
53 49 0.38
54 46 0.35
55 5 0.04
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
ATGCCATAGCCCAGCTATGGTCTTATACGGAATCACTTATCACTTTTATCCG
Found at i:11472369 original size:127 final size:127
Alignment explanation
Indices: 11472143--11472397 Score: 510
Period size: 127 Copynumber: 2.0 Consensus size: 127
11472133 ATTTTGTATG
11472143 TCTCACTCCTTTATTCAATCACGTCACTAAAAAATTCAAAGTTTAGAAGATAAACCAAGAAAAAT
1 TCTCACTCCTTTATTCAATCACGTCACTAAAAAATTCAAAGTTTAGAAGATAAACCAAGAAAAAT
11472208 ACTGGGTTTTTGCCTTAGCAGTTTATGCATTTGCCAATGGCATTACAAAGTGATGGTATTAT
66 ACTGGGTTTTTGCCTTAGCAGTTTATGCATTTGCCAATGGCATTACAAAGTGATGGTATTAT
11472270 TCTCACTCCTTTATTCAATCACGTCACTAAAAAATTCAAAGTTTAGAAGATAAACCAAGAAAAAT
1 TCTCACTCCTTTATTCAATCACGTCACTAAAAAATTCAAAGTTTAGAAGATAAACCAAGAAAAAT
11472335 ACTGGGTTTTTGCCTTAGCAGTTTATGCATTTGCCAATGGCATTACAAAGTGATGGTATTAT
66 ACTGGGTTTTTGCCTTAGCAGTTTATGCATTTGCCAATGGCATTACAAAGTGATGGTATTAT
11472397 T
1 T
11472398 GAACATATGA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (127 bp):
TCTCACTCCTTTATTCAATCACGTCACTAAAAAATTCAAAGTTTAGAAGATAAACCAAGAAAAAT
ACTGGGTTTTTGCCTTAGCAGTTTATGCATTTGCCAATGGCATTACAAAGTGATGGTATTAT
Found at i:11473044 original size:44 final size:44
Alignment explanation
Indices: 11472981--11473069 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
11472971 ATATACAACT
*
11472981 AAAGTTGCGTACTCCTGGCTCATTCTCAAAAAGATAGGCATGGG
1 AAAGTTGCGTACTCCTGGCTCATTCTAAAAAAGATAGGCATGGG
11473025 AAAGTTGCGTACTCCTGGCTCATTCTAAAAAAGATAGGCATGGG
1 AAAGTTGCGTACTCCTGGCTCATTCTAAAAAAGATAGGCATGGG
11473069 A
1 A
11473070 CCTCACCGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
AAAGTTGCGTACTCCTGGCTCATTCTAAAAAAGATAGGCATGGG
Found at i:11475029 original size:19 final size:19
Alignment explanation
Indices: 11475007--11475078 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
11474997 ATTACTAATA
11475007 ATTTTTATATTTTTATTAT
1 ATTTTTATATTTTTATTAT
* *
11475026 A-TTTTACATTTTCTAATA-
1 ATTTTTATATTTT-TATTAT
* *
11475044 ATGTTTATAGTTTTTATAGAT
1 ATTTTTATA-TTTTTAT-TAT
*
11475065 TTTTTTATATTTTT
1 ATTTTTATATTTTT
11475079 TTCCAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
18 11 0.28
19 12 0.30
20 10 0.25
21 7 0.17
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTATATTTTTATTAT
Found at i:11475030 original size:18 final size:17
Alignment explanation
Indices: 11475009--11475060 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
11474999 TACTAATAAT
11475009 TTTTATATTTTTATTATA
1 TTTTATATTTTTATTA-A
* *
11475027 TTTTACATTTTCTAATAA
1 TTTTATATTTT-TATTAA
11475045 TGTTTATAGTTTTTAT
1 T-TTTATA-TTTTTAT
11475061 AGATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.44
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTTATATTTTTATTAA
Found at i:11475619 original size:85 final size:86
Alignment explanation
Indices: 11475489--11475656 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 86
11475479 AGTCCCTCAT
* * *
11475489 TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGTATCAAAAAAGCCCTCAAACTTCTTC
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATC-AAAAAGCCCTCAAAATTCTTC
11475554 AAAAAA-AAATTAAGCCCCAAC
65 AAAAAAGAAATTAAGCCCCAAC
* * * * *
11475575 TTTTTTT-CACTCAATTGGGTACTTAAAGTTTCAAAATGCATCAAAAGGCCCTCAAAATTTTTCA
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGCCCTCAAAATTCTTCA
*
11475639 AAAAAGCAATTAAGCCCC
66 AAAAAGAAATTAAGCCCC
11475657 TGCTCTTATT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 24 0.33
85 41 0.57
86 7 0.10
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (86 bp):
TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGCATCAAAAAGCCCTCAAAATTCTTCA
AAAAAGAAATTAAGCCCCAAC
Found at i:11476038 original size:10 final size:10
Alignment explanation
Indices: 11476025--11476125 Score: 50
Period size: 10 Copynumber: 10.4 Consensus size: 10
11476015 TTTATAAACA
11476025 TTTATAATTT
1 TTTATAATTT
11476035 TTTAT-A-TT
1 TTTATAATTT
* *
11476043 TCTAT-ATAT
1 TTTATAATTT
*
11476052 TTTAAAATTT
1 TTTATAATTT
**
11476062 TTTACGATTT
1 TTTATAATTT
*
11476072 TTTAGAAATTT
1 TTTA-TAATTT
* *
11476083 TTTTTACAATT
1 TTTATA-ATTT
11476094 TTTAT-ATTT
1 TTTATAATTT
*
11476103 TTT-TAATTC
1 TTTATAATTT
* *
11476112 TTAATAAATT
1 TTTATAATTT
11476122 TTTA
1 TTTA
11476126 ATATTTAAAT
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
8 8 0.12
9 16 0.24
10 28 0.42
11 14 0.21
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTATAATTT
Found at i:11481899 original size:40 final size:39
Alignment explanation
Indices: 11481868--11482077 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
11481858 GGACTAAGAT
* *
11481868 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
11481908 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
11481948 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
11481988 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
11482028 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
11482067 CCGAAGGCATT
1 CCGAAGGCATT
11482078 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:11482031 original size:120 final size:120
Alignment explanation
Indices: 11481815--11482077 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
11481805 TTGAATGCTG
* *
11481815 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
11481879 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
11481935 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
11481998 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
11482054 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
11482078 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:11482097 original size:79 final size:80
Alignment explanation
Indices: 11481816--11482112 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
11481806 TGAATGCTGT
* ** * * * **
11481816 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
11481879 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
11481896 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
11481960 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
11481976 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
11482040 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
11482055 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
11482113 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:11491872 original size:10 final size:10
Alignment explanation
Indices: 11491855--11491886 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
11491845 AACAGATGGC
11491855 AAAAAAGAAA
1 AAAAAAGAAA
*
11491865 AGAAAAGAAA
1 AAAAAAGAAA
11491875 AAAAAAGAAA
1 AAAAAAGAAA
11491885 AA
1 AA
11491887 GTACTTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:11492187 original size:28 final size:29
Alignment explanation
Indices: 11492142--11492198 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
11492132 TTTCCTTAAA
11492142 TATCTAAATTAATAAATATATAAGAAATGC
1 TATCTAAA-TAATAAATATATAAGAAATGC
11492172 TATCTAAA-AATAAATATATAAGAAATG
1 TATCTAAATAATAAATATATAAGAAATG
11492199 TAATAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 19 0.70
30 8 0.30
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (29 bp):
TATCTAAATAATAAATATATAAGAAATGC
Found at i:11493957 original size:15 final size:15
Alignment explanation
Indices: 11493937--11493966 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11493927 TATTATTATT
11493937 AAATTTAAAAATAAA
1 AAATTTAAAAATAAA
11493952 AAATTTAAAAATAAA
1 AAATTTAAAAATAAA
11493967 TACTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTTAAAAATAAA
Found at i:11494284 original size:21 final size:22
Alignment explanation
Indices: 11494237--11494285 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
11494227 ATAATTACAA
*
11494237 TTAAAAAAATATTTAAATAACT
1 TTAAAAAAATATTAAAATAACT
* * *
11494259 ATAAATAAA-ATTAAAATAATT
1 TTAAAAAAATATTAAAATAACT
11494280 TTAAAA
1 TTAAAA
11494286 CCCTTCTATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAAAAAATATTAAAATAACT
Found at i:11495045 original size:7 final size:7
Alignment explanation
Indices: 11495033--11495059 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11495023 CTTGTTCAGG
11495033 AATTTTA
1 AATTTTA
11495040 AATTTTA
1 AATTTTA
11495047 AATTTTA
1 AATTTTA
11495054 AATTTT
1 AATTTT
11495060 TATCAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:11502737 original size:35 final size:35
Alignment explanation
Indices: 11502698--11502814 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
11502688 TGCTATCTGT
11502698 TTGGTGTGTTTCAGAGGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGAGGGACTAGCTCTTATGAGCA
** *
11502733 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGACCA
1 TTGGTGTGTTTCAGAGGGACTAGCTCTTATGAGCA
* ** * * *
11502768 TTAGTGTGTTTTGGAGGGATTGGCTCTTGTGAGCA
1 TTGGTGTGTTTCAGAGGGACTAGCTCTTATGAGCA
11502803 TCTGGTGTGTTT
1 T-TGGTGTGTTT
11502815 TGGTTGGACT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 59 0.87
36 9 0.13
ACGTcount: A:0.15, C:0.13, G:0.32, T:0.40
Consensus pattern (35 bp):
TTGGTGTGTTTCAGAGGGACTAGCTCTTATGAGCA
Found at i:11508196 original size:20 final size:20
Alignment explanation
Indices: 11508166--11508216 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
11508156 GTGAAATAAG
* *
11508166 TTATA-ATTTTTATGATTTT
1 TTATATATTTTTATGAATTA
11508185 TTATATATTTTTA-GAATTA
1 TTATATATTTTTATGAATTA
11508204 TTA-ATATTTTTAT
1 TTATATATTTTTAT
11508217 AAAATTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 12 0.43
20 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTATATATTTTTATGAATTA
Found at i:11508360 original size:8 final size:8
Alignment explanation
Indices: 11508349--11508390 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
11508339 TTTTTTGAAT
11508349 TTTTTATA
1 TTTTTATA
11508357 -TTTTA-A
1 TTTTTATA
*
11508363 TTTTTTTA
1 TTTTTATA
11508371 TTTTTATA
1 TTTTTATA
11508379 -TTTTATA
1 TTTTTATA
11508386 TTTTT
1 TTTTT
11508391 GTACTGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 1 0.03
7 16 0.55
8 12 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTATA
Found at i:11508364 original size:15 final size:15
Alignment explanation
Indices: 11508341--11508389 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
11508331 AATACATTTT
11508341 TTTTGAATTTTTTATA
1 TTTT-AATTTTTTATA
11508357 TTTTAATTTTTT-TA
1 TTTTAATTTTTTATA
* *
11508371 TTTTTATATTTTATA
1 TTTTAATTTTTTATA
11508386 TTTT
1 TTTT
11508390 TGTACTGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 12 0.40
15 14 0.47
16 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTAATTTTTTATA
Found at i:11508367 original size:16 final size:16
Alignment explanation
Indices: 11508348--11508382 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11508338 TTTTTTTGAA
11508348 TTTTTTATATTTTA-AT
1 TTTTTTAT-TTTTATAT
11508364 TTTTTTATTTTTATAT
1 TTTTTTATTTTTATAT
11508380 TTT
1 TTT
11508383 ATATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTATAT
Found at i:11508658 original size:3 final size:3
Alignment explanation
Indices: 11508650--11508685 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
11508640 TTGATTAGTT
*
11508650 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11508686 AGGACTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11510003 original size:15 final size:13
Alignment explanation
Indices: 11509982--11510031 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
11509972 ACTATGAGCT
11509982 ACCTCCGCCGCCCC
1 ACCTCCGCC-CCCC
11509996 AGCCTCCG-CCCCC
1 A-CCTCCGCCCCCC
*
11510009 ACCTCCG-CCTCC
1 ACCTCCGCCCCCC
*
11510021 GCCTCCGCCCC
1 ACCTCCGCCCC
11510032 TGCCATATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 16 0.52
13 7 0.23
14 2 0.06
15 6 0.19
ACGTcount: A:0.06, C:0.70, G:0.14, T:0.10
Consensus pattern (13 bp):
ACCTCCGCCCCCC
Found at i:11510006 original size:12 final size:12
Alignment explanation
Indices: 11509989--11510031 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
11509979 GCTACCTCCG
11509989 CCGCCCCAGCCT
1 CCGCCCCAGCCT
11510001 CCGCCCCCA-CCT
1 CCG-CCCCAGCCT
11510013 CCGCCTCC-GCCT
1 CCGCC-CCAGCCT
11510025 CCGCCCC
1 CCGCCCC
11510032 TGCCATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.14
12 19 0.68
13 5 0.18
ACGTcount: A:0.05, C:0.72, G:0.14, T:0.09
Consensus pattern (12 bp):
CCGCCCCAGCCT
Found at i:11511116 original size:17 final size:18
Alignment explanation
Indices: 11511094--11511131 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
11511084 AATATTTATT
*
11511094 ATTTAATATAATAA-ATA
1 ATTTAAAATAATAACATA
*
11511111 ATTTAAAATGATAACATA
1 ATTTAAAATAATAACATA
11511129 ATT
1 ATT
11511132 AATTAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
ATTTAAAATAATAACATA
Found at i:11511884 original size:27 final size:25
Alignment explanation
Indices: 11511854--11511906 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
11511844 ATCTTTCATA
*
11511854 TTTTATTAATGGAATATTTTAATATGT
1 TTTTATTAA-AGAA-ATTTTAATATGT
* *
11511881 TTTTCTTAAAGTAATTTTAATATGT
1 TTTTATTAAAGAAATTTTAATATGT
11511906 T
1 T
11511907 GTAGAACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 2 0.09
27 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTTATTAAAGAAATTTTAATATGT
Found at i:11513096 original size:27 final size:27
Alignment explanation
Indices: 11513065--11513130 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
11513055 GGAAGGTAAG
*
11513065 AGAGGTGACACCAGTGGAGGGTGAGAA
1 AGAGGCGACACCAGTGGAGGGTGAGAA
* *
11513092 AGAGGCGGCTCCAGTGGAGGGTGAGAA
1 AGAGGCGACACCAGTGGAGGGTGAGAA
* *
11513119 AAAGGCAACACC
1 AGAGGCGACACC
11513131 CGTGTTGAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.41, T:0.09
Consensus pattern (27 bp):
AGAGGCGACACCAGTGGAGGGTGAGAA
Found at i:11516293 original size:16 final size:16
Alignment explanation
Indices: 11516274--11516304 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11516264 CTTCTTCACT
11516274 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
11516290 TACTTACTTACTTAA
1 TACTCACTTACTTAA
11516305 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:11516310 original size:20 final size:20
Alignment explanation
Indices: 11516271--11516310 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11516261 AAACTTCTTC
* *
11516271 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
11516291 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
11516311 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:11516626 original size:53 final size:54
Alignment explanation
Indices: 11516497--11516696 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 54
11516487 ACACGGGTAC
* * * *
11516497 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
11516546 CTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * * *
11516599 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* *
11516654 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTT
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTT
11516697 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
49 37 0.29
50 1 0.01
52 2 0.02
53 45 0.36
54 3 0.02
55 36 0.29
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:11520653 original size:16 final size:16
Alignment explanation
Indices: 11520634--11520664 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11520624 CTTCTTCACT
11520634 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
11520650 TACTTACTTACTTAA
1 TACTCACTTACTTAA
11520665 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:11520670 original size:20 final size:20
Alignment explanation
Indices: 11520631--11520670 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11520621 AAACTTCTTC
* *
11520631 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
11520651 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
11520671 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:11521109 original size:55 final size:54
Alignment explanation
Indices: 11520857--11521112 Score: 208
Period size: 55 Copynumber: 4.8 Consensus size: 54
11520847 ACACGGGTAC
** * *
11520857 CTTACC-ATTTCCATGAGTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
* * * *
11520906 CTTACC-ATTTCCATGTCTTAACATGGTCTTACATGGTTTCCTTGCCTTATG-AA
1 CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTA-GAAA
* * * * * * *
11520959 CTCACCAA-TGCCATGCCTTGGCATGGTTTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCC-TTACC-T-TAGAAA
* * * *
11521014 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGATATCCTTACCTTAGAAA
1 CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
* *
11521067 CCTTACCAATTTCCAAGCCTTGGCATGGTCTTACATGGTATCCTTA
1 -CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCCTTA
11521113 AACCCTAATG
Statistics
Matches: 165, Mismatches: 29, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
49 37 0.22
52 4 0.02
53 40 0.24
54 12 0.07
55 70 0.42
56 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
CTTACCAATTTCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTAGAAA
Found at i:11524154 original size:165 final size:165
Alignment explanation
Indices: 11523882--11524205 Score: 549
Period size: 165 Copynumber: 2.0 Consensus size: 165
11523872 TTCGGTTCAG
* *
11523882 GTGCGAGCTCTGGTTCGGGTGCAGAAGGTAGATGTGACATACGTTGGGAGAGATGCCCTAGTCTT
1 GTGCGAGCTCCGGTTCGGGTGCAGAAGGCAGATGTGACATACGTTGGGAGAGATGCCCTAGTCTT
* * *
11523947 TCCATTTGTAAAGGGACTAGCATTGTTTGCCCACCAAATAAAAAAGGTTTCCTACATGCCATGTA
66 TCCATGTATAAAGGGACTAGCATTGTTTGCCCACCAAATAAAAAAGGTTTCCTACACGCCATGTA
*
11524012 CTAGACAATGCATAATCCATCCGAGGTCTCTACCC
131 CTAGACAATACATAATCCATCCGAGGTCTCTACCC
* *
11524047 GTGCGAGCTCCGGTTCGGGTGCAGAAGGCAGATGTGACATGCGTTGGGAGAGGTGCCCTAGTCTT
1 GTGCGAGCTCCGGTTCGGGTGCAGAAGGCAGATGTGACATACGTTGGGAGAGATGCCCTAGTCTT
* * *
11524112 TCCATGTATGAAGGGATTAGCATTGTTTTCCCACCAAATAAAAAAGGTTTCCTACACGCCATGTA
66 TCCATGTATAAAGGGACTAGCATTGTTTGCCCACCAAATAAAAAAGGTTTCCTACACGCCATGTA
11524177 CTAGACAATACATAATCCATCCGAGGTCT
131 CTAGACAATACATAATCCATCCGAGGTCT
11524206 TCGCCCTGTC
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 148 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (165 bp):
GTGCGAGCTCCGGTTCGGGTGCAGAAGGCAGATGTGACATACGTTGGGAGAGATGCCCTAGTCTT
TCCATGTATAAAGGGACTAGCATTGTTTGCCCACCAAATAAAAAAGGTTTCCTACACGCCATGTA
CTAGACAATACATAATCCATCCGAGGTCTCTACCC
Found at i:11528975 original size:44 final size:44
Alignment explanation
Indices: 11528774--11528995 Score: 177
Period size: 44 Copynumber: 4.9 Consensus size: 44
11528764 ATGTGGGCCC
* * * * *
11528774 GTGTAAGACATGTCTGTGACATGCATCGGCTA-TATTATGAAAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATG--TGCTA
* *
11528820 GTGTAAGACCATGTCTGGGGCATGGCATCGGCATTGA-GACGA-GTGCCA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGC--T-ACGA-GATGTGCTA
* * * *
11528868 ATGTAAAACATGTCTAGGACATGCATCGCCT-CGAGATGTAAGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGT--GCTA
*
11528913 GTGTAAGACATGTCTGGGACATGCATTGGCTACGAGATGTGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCTA
* *
11528957 GTGTAGGACATGTTTGGGACATGCATCGGC-ACG-GATGTG
1 GTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTG
11528996 TGAGAGCCAA
Statistics
Matches: 146, Mismatches: 20, Indels: 24
0.77 0.11 0.13
Matches are distributed among these distances:
42 8 0.05
43 7 0.05
44 32 0.22
45 29 0.20
46 23 0.16
47 24 0.16
48 18 0.12
50 2 0.01
51 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (44 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCTA
Found at i:11532011 original size:20 final size:20
Alignment explanation
Indices: 11531952--11532013 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
11531942 TGGCAGTTTA
*
11531952 TCTGCATTACTGGTGACTCG
1 TCTGCATTACTGGTGACTTG
* ** * *
11531972 ACCACATTATTGG-CAGCTTG
1 TCTGCATTACTGGTGA-CTTG
11531992 TCTGCATTACTGGTGACTTG
1 TCTGCATTACTGGTGACTTG
11532012 TC
1 TC
11532014 CACAAATTGA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (20 bp):
TCTGCATTACTGGTGACTTG
Found at i:11537512 original size:16 final size:16
Alignment explanation
Indices: 11537491--11537529 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
11537481 AGTGATCCTT
11537491 AATGCAAATTAACCTA
1 AATGCAAATTAACCTA
11537507 AATGCAAATTAACCTA
1 AATGCAAATTAACCTA
11537523 AATGCAA
1 AATGCAA
11537530 TGTATGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.23
Consensus pattern (16 bp):
AATGCAAATTAACCTA
Found at i:11539234 original size:23 final size:25
Alignment explanation
Indices: 11539208--11539253 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
11539198 TATCATTCAT
*
11539208 TTCATTATAT-CA-ATATTTTATAC
1 TTCATCATATCCATATATTTTATAC
*
11539231 TTCATCATTTCCATATATTTTAT
1 TTCATCATATCCATATATTTTAT
11539254 GTATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.54
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATAC
Found at i:11539575 original size:46 final size:47
Alignment explanation
Indices: 11539515--11539742 Score: 322
Period size: 46 Copynumber: 5.0 Consensus size: 47
11539505 TTTGACGTGA
* * * * * *
11539515 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
** * *
11539561 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
11539607 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
11539653 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
11539699 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
11539743 AGAGCACACT
Statistics
Matches: 169, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.03
46 164 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:11545813 original size:11 final size:11
Alignment explanation
Indices: 11545797--11545822 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11545787 TAGATTAGGG
11545797 TAAATTTTAGC
1 TAAATTTTAGC
11545808 TAAATTTTAGC
1 TAAATTTTAGC
11545819 TAAA
1 TAAA
11545823 GGTAGTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (11 bp):
TAAATTTTAGC
Found at i:11558045 original size:12 final size:11
Alignment explanation
Indices: 11558029--11558063 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11558019 GAAGAAGAAG
11558029 AAGA-AAAACT
1 AAGAGAAAACT
*
11558039 AAGAGAAAACC
1 AAGAGAAAACT
11558050 AAGAGAAAACT
1 AAGAGAAAACT
11558061 AAG
1 AAG
11558064 CCTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.66, C:0.11, G:0.17, T:0.06
Consensus pattern (11 bp):
AAGAGAAAACT
Found at i:11559701 original size:41 final size:41
Alignment explanation
Indices: 11559656--11559741 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
11559646 CTAATTAGTC
11559656 TATACTTAAGAATACCAAATTATCTAGTATCATTTGAAATT
1 TATACTTAAGAATACCAAATTATCTAGTATCATTTGAAATT
11559697 TATACTTAAGAATACCAAATTATCTAGTATCATTTGAAATT
1 TATACTTAAGAATACCAAATTATCTAGTATCATTTGAAATT
11559738 TATA
1 TATA
11559742 AGTTTGGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (41 bp):
TATACTTAAGAATACCAAATTATCTAGTATCATTTGAAATT
Found at i:11560167 original size:24 final size:25
Alignment explanation
Indices: 11560120--11560167 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
11560110 AATAAAAAAC
*
11560120 TTTAAAATACAATAAATCAAATATA
1 TTTAAAATACAATAAAACAAATATA
11560145 TTTAAAA-AC-ATAAAAACAAATAT
1 TTTAAAATACAAT-AAAACAAATAT
11560168 TAAAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.57
25 7 0.33
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TTTAAAATACAATAAAACAAATATA
Found at i:11560409 original size:11 final size:11
Alignment explanation
Indices: 11560395--11560512 Score: 89
Period size: 11 Copynumber: 10.9 Consensus size: 11
11560385 GACAAAAAGT
*
11560395 AGCAGCAAACC
1 AGCAGCAAAAC
11560406 AGCA-CTAAAAC
1 AGCAGC-AAAAC
*
11560417 AGCAGCAAAAT
1 AGCAGCAAAAC
* *
11560428 AGCACCAAAAA
1 AGCAGCAAAAC
11560439 AGCAGCAAAAC
1 AGCAGCAAAAC
*
11560450 AGCAACAAAAC
1 AGCAGCAAAAC
* * *
11560461 ATCACCAAAAT
1 AGCAGCAAAAC
* *
11560472 AGCATCAAAAT
1 AGCAGCAAAAC
* *
11560483 AGCA-CCAAAT
1 AGCAGCAAAAC
*
11560493 AGCAACAAAAC
1 AGCAGCAAAAC
11560504 AGCA-CAAAA
1 AGCAGCAAAA
11560513 AATAGCATCA
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
10 15 0.17
11 73 0.82
12 1 0.01
ACGTcount: A:0.57, C:0.26, G:0.11, T:0.06
Consensus pattern (11 bp):
AGCAGCAAAAC
Found at i:11560449 original size:33 final size:31
Alignment explanation
Indices: 11560406--11560512 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 31
11560396 GCAGCAAACC
11560406 AGCACTAAAACAGCAGCAAAATAGCACCAAAAA
1 AGCAC-AAAACAGCA-CAAAATAGCACCAAAAA
* * *
11560439 AGCAGCAAAACAGCAACAAAACATCACCAAAAT
1 AGCA-CAAAACAGC-ACAAAATAGCACCAAAAA
* * * *
11560472 AGCATCAAAATAGCACCAAATAGCAACAAAAC
1 AGCA-CAAAACAGCACAAAATAGCACCAAAAA
11560504 AGCACAAAA
1 AGCACAAAA
11560513 AATAGCATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 5 0.08
32 17 0.27
33 38 0.61
34 2 0.03
ACGTcount: A:0.58, C:0.25, G:0.10, T:0.07
Consensus pattern (31 bp):
AGCACAAAACAGCACAAAATAGCACCAAAAA
Found at i:11560515 original size:44 final size:44
Alignment explanation
Indices: 11560395--11560522 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 44
11560385 GACAAAAAGT
* *
11560395 AGCAGCAAACCAGC-ACTAAAACAGCAGC-AAAATAGCACCAAAAA
1 AGCAGCAAAACAGCAAC-AAAACAGCA-CAAAAATAGCATCAAAAA
* * *
11560439 AGCAGCAAAACAGCAACAAAACATCACCAAAATAGCATCAAAAT
1 AGCAGCAAAACAGCAACAAAACAGCACAAAAATAGCATCAAAAA
* *
11560483 AGCA-CCAAATAGCAACAAAACAGCACAAAAAATAGCATCA
1 AGCAGCAAAACAGCAACAAAACAGCAC-AAAAATAGCATCA
11560523 CCGACAACAC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 20 0.27
44 51 0.70
45 2 0.03
ACGTcount: A:0.56, C:0.26, G:0.11, T:0.07
Consensus pattern (44 bp):
AGCAGCAAAACAGCAACAAAACAGCACAAAAATAGCATCAAAAA
Found at i:11572176 original size:20 final size:21
Alignment explanation
Indices: 11572153--11572192 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11572143 ATACCTGGTA
11572153 AAAGG-TATCGATACTTTTTG
1 AAAGGATATCGATACTTTTTG
11572173 AAAGGATATCGATACTTTTT
1 AAAGGATATCGATACTTTTT
11572193 ATGATTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
AAAGGATATCGATACTTTTTG
Found at i:11572251 original size:18 final size:18
Alignment explanation
Indices: 11572225--11572259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11572215 AACAAGAATG
*
11572225 CAAAAATGGTATTGATAT
1 CAAAAATGGTATCGATAT
*
11572243 CAAAGATGGTATCGATA
1 CAAAAATGGTATCGATA
11572260 AAAATATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (18 bp):
CAAAAATGGTATCGATAT
Found at i:11573975 original size:41 final size:41
Alignment explanation
Indices: 11573912--11573994 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
11573902 CTAGTTGTTA
* * *
11573912 TATATAAATTTCCCCATTCAAATCCCCGTGAAGGAATACAG
1 TATATAAATTTCCCAATCCAAATCCCCGTGAAAGAATACAG
*
11573953 TATATAAATTTCCCAATCCAAATCCCCGTGAAAGAATGCAG
1 TATATAAATTTCCCAATCCAAATCCCCGTGAAAGAATACAG
11573994 T
1 T
11573995 CTTTATATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (41 bp):
TATATAAATTTCCCAATCCAAATCCCCGTGAAAGAATACAG
Found at i:11586598 original size:52 final size:51
Alignment explanation
Indices: 11586468--11586591 Score: 187
Period size: 50 Copynumber: 2.4 Consensus size: 51
11586458 ATGTGTTCTG
* * *
11586468 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
* *
11586519 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTGCAT
11586570 CATTAAATTAAGTCATGCATTA
1 CATTAAATTAAGTCATGCATTA
11586592 AATAACTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
50 33 0.52
51 14 0.22
52 17 0.27
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
Found at i:11591043 original size:15 final size:15
Alignment explanation
Indices: 11591025--11591059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11591015 ATTCTATGTA
* *
11591025 AAAATATTTATAAAT
1 AAAATATGTAAAAAT
11591040 AAAATATGTAAAAAT
1 AAAATATGTAAAAAT
11591055 AAAAT
1 AAAAT
11591060 GAAAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATATGTAAAAAT
Found at i:11597989 original size:16 final size:16
Alignment explanation
Indices: 11597954--11597991 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
11597944 TTTCAAACAG
11597954 CTTATGTTTTAGAAGT
1 CTTATGTTTTAGAAGT
* *
11597970 -TTATGTTTTTGTAGT
1 CTTATGTTTTAGAAGT
11597985 CTTATGT
1 CTTATGT
11597992 ATTATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.58
Consensus pattern (16 bp):
CTTATGTTTTAGAAGT
Found at i:11598358 original size:33 final size:33
Alignment explanation
Indices: 11598316--11598381 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11598306 GGGTTTGGCA
11598316 AGGAATGGTCACAAAAAAAGAACTCTAAAATTT
1 AGGAATGGTCACAAAAAAAGAACTCTAAAATTT
11598349 AGGAATGGTCACAAAAAAAGAACTCTAAAATTT
1 AGGAATGGTCACAAAAAAAGAACTCTAAAATTT
11598382 GACAATCTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (33 bp):
AGGAATGGTCACAAAAAAAGAACTCTAAAATTT
Found at i:11606803 original size:19 final size:19
Alignment explanation
Indices: 11606772--11606809 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
11606762 TTGCAATTTA
11606772 AATTTTTATTTTATTTTCT
1 AATTTTTATTTTATTTTCT
11606791 AATTCTTTA-TTTATTTTCT
1 AATT-TTTATTTTATTTTCT
11606810 TCTGACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:11611221 original size:13 final size:13
Alignment explanation
Indices: 11611203--11611229 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11611193 GGAGTAATCG
11611203 CACACGGGCGTGT
1 CACACGGGCGTGT
11611216 CACACGGGCGTGT
1 CACACGGGCGTGT
11611229 C
1 C
11611230 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:11613850 original size:9 final size:11
Alignment explanation
Indices: 11613814--11613864 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
11613804 TTACACCATG
*
11613814 TATATAT-TTT
1 TATATATATTA
* *
11613824 TATAAATGTTA
1 TATATATATTA
11613835 TATATATATT-
1 TATATATATTA
11613845 TA-ATATATTA
1 TATATATATTA
11613855 TATATATATT
1 TATATATATT
11613865 GTGTACATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.21
10 10 0.29
11 17 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TATATATATTA
Found at i:11613887 original size:233 final size:233
Alignment explanation
Indices: 11613460--11613888 Score: 720
Period size: 233 Copynumber: 1.8 Consensus size: 233
11613450 TTACATATAT
11613460 TTTATATATATTCATATAGTTGTTTTTTTTATTAATATTCCTAATATATATTTTATATATACACA
1 TTTATATATATTCATATAGTTGTTTTTTTTATTAATATTCCTAATATATATTTTATATATACACA
11613525 TTTAAATACTACATCATACTCCATATTATGCATATACATATTAACATTACACCATGTATATATTT
66 TTTAAATACTACATCATACTCCATATTATGCATATACATATTAACATTACACCATGTATATATTT
* * * * *
11613590 TTATAAATATTATATATATATATATTATTTATTATTCTATCTACTACTTTCGTATTATTATTATC
131 TTATAAATATTATATATATATATAATATTTATTATTATATCTACTACATACGTATTAGTATTATC
11613655 AGCATATTTTACTATTATTTAGACATTTTTAGTTTTAA
196 AGCATATTTTACTATTATTTAGACATTTTTAGTTTTAA
11613693 TTTATATATATTCATATAGTTGTTTTTTTTATTAATATTCCTAATATATATTTTATATATACACA
1 TTTATATATATTCATATAGTTGTTTTTTTTATTAATATTCCTAATATATATTTTATATATACACA
11613758 TTTAAATACTACATCATACTCCATATTATGCATATACATATTAACATTACACCATGTATATATTT
66 TTTAAATACTACATCATACTCCATATTATGCATATACATATTAACATTACACCATGTATATATTT
* * ** *
11613823 TTATAAATGTTATATATATATTTAATATATTA-TATATATAT-TGTGTACATAC-TTTTAGTATT
131 TTATAAATATTATATATATATATAATAT-TTATTAT-TATATCT-ACTACATACGTATTAGTATT
11613885 ATCA
193 ATCA
11613889 TGTATTCATT
Statistics
Matches: 183, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
233 171 0.93
234 12 0.07
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.50
Consensus pattern (233 bp):
TTTATATATATTCATATAGTTGTTTTTTTTATTAATATTCCTAATATATATTTTATATATACACA
TTTAAATACTACATCATACTCCATATTATGCATATACATATTAACATTACACCATGTATATATTT
TTATAAATATTATATATATATATAATATTTATTATTATATCTACTACATACGTATTAGTATTATC
AGCATATTTTACTATTATTTAGACATTTTTAGTTTTAA
Found at i:11616131 original size:23 final size:21
Alignment explanation
Indices: 11616079--11616133 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
11616069 ATTCATATTA
11616079 TATAATAAAGGTTAAATATGT
1 TATAATAAAGGTTAAATATGT
* *
11616100 AATTAAATAATATGTTAATATATGT
1 TA-T-AATAA-AGGTTAA-ATATGT
11616125 TATAATAAA
1 TATAATAAA
11616134 ACATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.04
22 2 0.07
23 10 0.37
24 7 0.26
25 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
TATAATAAAGGTTAAATATGT
Found at i:11617978 original size:15 final size:15
Alignment explanation
Indices: 11617960--11617996 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
11617950 TGGCTATGGT
11617960 TATACATAGATAAAA
1 TATACATAGATAAAA
11617975 TATACATAGATAAAA
1 TATACATAGATAAAA
11617990 TATACAT
1 TATACAT
11617997 GTGAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (15 bp):
TATACATAGATAAAA
Found at i:11622604 original size:32 final size:32
Alignment explanation
Indices: 11622563--11622624 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
11622553 CATCTATTTT
11622563 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
11622595 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
11622625 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:11626775 original size:22 final size:22
Alignment explanation
Indices: 11626749--11626792 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11626739 TTATCTCTTT
11626749 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
11626771 TGATTGAAAAGGAGCAATAAAA
1 TGATTGAAAAGGAGCAATAAAA
11626793 AAATCGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (22 bp):
TGATTGAAAAGGAGCAATAAAA
Found at i:11630402 original size:25 final size:25
Alignment explanation
Indices: 11630373--11630424 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
11630363 TTGATAATTT
11630373 GGATGTGGTTGAAAGGGTCAGACAC
1 GGATGTGGTTGAAAGGGTCAGACAC
*
11630398 GGATGTGGTTGAAAGGGTCGGACAC
1 GGATGTGGTTGAAAGGGTCAGACAC
11630423 GG
1 GG
11630425 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.44, T:0.19
Consensus pattern (25 bp):
GGATGTGGTTGAAAGGGTCAGACAC
Found at i:11653988 original size:3 final size:3
Alignment explanation
Indices: 11653980--11654046 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
11653970 AACTGTTTAC
11653980 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11654028 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
11654047 TTGCCCGAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11658317 original size:38 final size:37
Alignment explanation
Indices: 11658257--11658391 Score: 119
Period size: 38 Copynumber: 3.6 Consensus size: 37
11658247 AAGTATACTA
* ** *
11658257 TTATACAAGCTTCGTGCGTAGTAGGCTTAATGCCGTTG
1 TTATTCAAGCTTTATGCCTAGTAGGCTTAATGCCG-TG
*
11658295 TTATTCAAGCTTTATGCCTAGTAGGCTTAGTGCCAGTG
1 TTATTCAAGCTTTATGCCTAGTAGGCTTAATGCC-GTG
* * * * **
11658333 TTATTCAGGCTTTGTGCCTAGCAGGCTGAATGTTGATG
1 TTATTCAAGCTTTATGCCTAGTAGGCTTAATGCCG-TG
*
11658371 TTATTCAGGC-TTAGTGCCTAG
1 TTATTCAAGCTTTA-TGCCTAG
11658392 CATGCTTCTT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
37 3 0.04
38 77 0.95
39 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (37 bp):
TTATTCAAGCTTTATGCCTAGTAGGCTTAATGCCGTG
Found at i:11660335 original size:12 final size:12
Alignment explanation
Indices: 11660318--11660351 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11660308 TGGCCCGCCC
11660318 ATATTAATTTTT
1 ATATTAATTTTT
*
11660330 ATATTATTTTTT
1 ATATTAATTTTT
11660342 ATA-TAATTTT
1 ATATTAATTTT
11660352 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:11665825 original size:21 final size:21
Alignment explanation
Indices: 11665799--11665839 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11665789 AGACGAGCAA
* *
11665799 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
11665820 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
11665840 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:11671880 original size:28 final size:28
Alignment explanation
Indices: 11671830--11671920 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 28
11671820 GTTCGCACCC
* * * *
11671830 TGCCACTTCGCGGTGCCATCTCGCATCT
1 TGCCACTTCGCAGAGTCAGCTCGCATCT
* * *
11671858 TGCCTCTTTGCAGAGTCAGCTCGCACCT
1 TGCCACTTCGCAGAGTCAGCTCGCATCT
** *
11671886 TGCCACTTCGTGGAGTCAGCTTGCATCT
1 TGCCACTTCGCAGAGTCAGCTCGCATCT
11671914 TG-CACTT
1 TGCCACTT
11671921 TGACACTTCG
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 5 0.10
28 45 0.90
ACGTcount: A:0.13, C:0.34, G:0.22, T:0.31
Consensus pattern (28 bp):
TGCCACTTCGCAGAGTCAGCTCGCATCT
Found at i:11676823 original size:17 final size:18
Alignment explanation
Indices: 11676803--11676836 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11676793 AAGTGAATTG
11676803 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
11676820 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
11676837 ATAAGGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:11677590 original size:20 final size:19
Alignment explanation
Indices: 11677566--11677625 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
11677556 TGAAATTCTA
11677566 AAAGATAAATACAAATAAAT
1 AAAGATAAATA-AAATAAAT
* *
11677586 TAAGATAATTAAAGATAAAT
1 AAAGATAAATAAA-ATAAAT
11677606 AAAGATAAATGAAAATAAAT
1 AAAGATAAAT-AAAATAAAT
11677626 CCTAGAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:11677593 original size:10 final size:10
Alignment explanation
Indices: 11677567--11677625 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
11677557 GAAATTCTAA
11677567 AAGATAAA-T
1 AAGATAAATT
*
11677576 ACAAATAAATT
1 A-AGATAAATT
11677587 AAGAT-AATT
1 AAGATAAATT
*
11677596 AAAGATAAATA
1 -AAGATAAATT
*
11677607 AAGATAAATG
1 AAGATAAATT
*
11677617 AAAATAAAT
1 AAGATAAAT
11677626 CCTAGAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
9 5 0.12
10 31 0.76
11 5 0.12
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAGATAAATT
Found at i:11678268 original size:11 final size:11
Alignment explanation
Indices: 11678247--11678280 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11678237 TACCTCATTC
*
11678247 TTCTTTTTTTT
1 TTCTCTTTTTT
*
11678258 TTTTCTTTTTT
1 TTCTCTTTTTT
11678269 TTCTCTTTTTT
1 TTCTCTTTTTT
11678280 T
1 T
11678281 AAATTCTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTCTTTTTT
Found at i:11679276 original size:6 final size:6
Alignment explanation
Indices: 11679237--11679287 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
11679227 TTAATATCTG
11679237 AAAATA ATAAATTA TAAAATA ATAAGAT- AAAATA AAAATA AAAATA AAAAT
1 AAAATA A-AAA-TA -AAAATA A-AA-ATA AAAATA AAAATA AAAATA AAAAT
11679288 TGGGTTGCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
5 2 0.05
6 21 0.54
7 8 0.21
8 7 0.18
9 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (6 bp):
AAAATA
Found at i:11682279 original size:17 final size:18
Alignment explanation
Indices: 11682259--11682292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11682249 AAGTGAATTG
*
11682259 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAAGTAAAT
11682276 AAATTGCAGAAAGTAAA
1 AAATTGCAGAAAGTAAA
11682293 ATGAGGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (18 bp):
AAATTGCAGAAAGTAAAT
Found at i:11682927 original size:10 final size:10
Alignment explanation
Indices: 11682912--11682971 Score: 72
Period size: 10 Copynumber: 6.2 Consensus size: 10
11682902 ATTCTAAAAG
*
11682912 ATAAATATAA
1 ATAAAGATAA
11682922 AT-AA-ATAA
1 ATAAAGATAA
11682930 ATAAAGATAA
1 ATAAAGATAA
*
11682940 TTAAAGATAA
1 ATAAAGATAA
11682950 ATAAAGATAA
1 ATAAAGATAA
11682960 ATGAAA-ATAA
1 AT-AAAGATAA
11682970 AT
1 AT
11682972 CCTAGAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 6 0.13
9 4 0.09
10 32 0.71
11 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (10 bp):
ATAAAGATAA
Found at i:11682929 original size:14 final size:14
Alignment explanation
Indices: 11682912--11682954 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11682902 ATTCTAAAAG
11682912 ATAAATATAAATAA
1 ATAAATATAAATAA
11682926 ATAAATA-AAGATAA
1 ATAAATATAA-ATAA
* *
11682940 TTAAAGATAAATAA
1 ATAAATATAAATAA
11682954 A
1 A
11682955 GATAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
ATAAATATAAATAA
Found at i:11683513 original size:8 final size:9
Alignment explanation
Indices: 11683495--11683659 Score: 50
Period size: 9 Copynumber: 17.0 Consensus size: 9
11683485 TTTTGGTACG
11683495 ATAATTTTT
1 ATAATTTTT
11683504 ATAATTTTATT
1 ATAA-TTT-TT
*
11683515 ATAAGTTTT
1 ATAATTTTT
11683524 AT-ATTTCTT
1 ATAATTT-TT
11683533 -TAGATTTTCT
1 ATA-ATTTT-T
11683543 ATAATTTTCTT
1 ATAA-TTT-TT
* *
11683554 ATGA-CTTT
1 ATAATTTTT
*
11683562 ATAAACTTTT
1 AT-AATTTTT
11683572 ATAATTTTTTT
1 ATAA--TTTTT
* *
11683583 CTATATTTCT
1 ATA-ATTTTT
11683593 AT-ATATTTT
1 ATAAT-TTTT
11683602 ATAATTTTTTT
1 ATAA--TTTTT
*
11683613 ATGATTTTT
1 ATAATTTTT
* *
11683622 GTAAAATTTT
1 AT-AATTTTT
*
11683632 ATAAATTTT
1 ATAATTTTT
*
11683641 ATTGATTTTT
1 A-TAATTTTT
*
11683651 ATCATTTTT
1 ATAATTTTT
11683660 TTGCCACATG
Statistics
Matches: 117, Mismatches: 19, Indels: 40
0.66 0.11 0.23
Matches are distributed among these distances:
8 10 0.09
9 41 0.35
10 35 0.30
11 28 0.24
12 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Done.