Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 43 of 175
Found at i:12169320 original size:9 final size:10
Alignment explanation
Indices: 12169301--12169329 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
12169291 CATTTCTCTT
12169301 TTTCTATTCA
1 TTTCTATTCA
12169311 TTTC-ATTCA
1 TTTCTATTCA
12169320 TTTCTATTCA
1 TTTCTATTCA
12169330 AACATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:12172510 original size:33 final size:35
Alignment explanation
Indices: 12172466--12172533 Score: 106
Period size: 33 Copynumber: 2.0 Consensus size: 35
12172456 TCATAATGAG
12172466 AAAATATAATATATT-ATATATAAATTTTA-ATTTT
1 AAAATATAATAT-TTGATATATAAATTTTACATTTT
12172500 AAAA-ATAATATTTGATATATAAATTTTACATTTT
1 AAAATATAATATTTGATATATAAATTTTACATTTT
12172534 GAGAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 2 0.06
33 21 0.66
34 9 0.28
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
AAAATATAATATTTGATATATAAATTTTACATTTT
Found at i:12173081 original size:31 final size:32
Alignment explanation
Indices: 12173046--12173106 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
12173036 TTATATTGAG
*
12173046 AATCATTTTTATAATAATTA-ATTATGAGAGA
1 AATCATATTTATAATAATTATATTATGAGAGA
* *
12173077 AATCATATTTATATTAATTATATTTTGAGA
1 AATCATATTTATAATAATTATATTATGAGA
12173107 AAACACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (32 bp):
AATCATATTTATAATAATTATATTATGAGAGA
Found at i:12175040 original size:62 final size:61
Alignment explanation
Indices: 12174933--12175058 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 61
12174923 TATTGCTTCA
* * *
12174933 CACGCCGTGTGGTTTCACACGGCCTAAAGAATTGGGCTGTATGACTCTACACGGTTTGGCC
1 CACGCCGTGTGGTTTCACACGACCTAAAGAATTGGGCTGTATGACTCCACACGGTCTGGCC
* ** * * *
12174994 CACGCCCGTGTGGTTTCACACGACTTGGAGAATTGGTCTGTGTGACTCCACACGGTCTGGTC
1 CACG-CCGTGTGGTTTCACACGACCTAAAGAATTGGGCTGTATGACTCCACACGGTCTGGCC
12175056 CAC
1 CAC
12175059 ACCTGTATGC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
61 4 0.07
62 51 0.93
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (61 bp):
CACGCCGTGTGGTTTCACACGACCTAAAGAATTGGGCTGTATGACTCCACACGGTCTGGCC
Found at i:12178681 original size:30 final size:31
Alignment explanation
Indices: 12178635--12178697 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
12178625 TAAATCACAA
*
12178635 TTCAATTTGGTTGCTATCAATATTTAATATT
1 TTCAATTTGGTCGCTATCAATATTTAATATT
12178666 TTCAA-TTGGTCGCTATCAATATTTAATATT
1 TTCAATTTGGTCGCTATCAATATTTAATATT
12178696 TT
1 TT
12178698 TATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (31 bp):
TTCAATTTGGTCGCTATCAATATTTAATATT
Found at i:12180438 original size:19 final size:21
Alignment explanation
Indices: 12180400--12180438 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12180390 CCTTTTTTAA
*
12180400 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
12180421 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
12180439 AAAGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:12180652 original size:22 final size:23
Alignment explanation
Indices: 12180603--12180647 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12180593 GGGTATCTAC
* *
12180603 AAATTAAATC-TCTAATATTACA
1 AAATCAAATCTTCTAAGATTACA
12180625 AAATCAAATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
12180648 TATCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:12182040 original size:25 final size:23
Alignment explanation
Indices: 12181995--12182041 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12181985 TTGGTTTATT
* *
12181995 TTTAGAAAAAAAAACTTAGTTAA
1 TTTACAAAAAAAAACTGAGTTAA
12182018 TTTACAAAAAAAAATCATGAGTTA
1 TTTACAAAAAAAAA-C-TGAGTTA
12182042 CCAAAACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (23 bp):
TTTACAAAAAAAAACTGAGTTAA
Found at i:12188115 original size:3 final size:3
Alignment explanation
Indices: 12188100--12188205 Score: 86
Period size: 3 Copynumber: 35.0 Consensus size: 3
12188090 TTTAAGATTT
* * ** * * * * * *
12188100 TTA TTA TTG TTA TTA TTA TTA TTA ATA CCA TCA TCA TCA TCA TCA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
12188148 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA CCA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
12188194 TTA TTA TTA TTA
1 TTA TTA TTA TTA
12188206 AATTTTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 86 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:12192533 original size:17 final size:18
Alignment explanation
Indices: 12192499--12192544 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
12192489 CCGTTATGTC
12192499 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
12192514 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
12192531 CGCGACCGCGACCG
1 CGCGACCGCGACCG
12192545 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:12195364 original size:20 final size:19
Alignment explanation
Indices: 12195326--12195364 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
12195316 AATAACTTTT
* *
12195326 AAAATTTAAAATATTTATA
1 AAAATTTAAAAAATATATA
12195345 AAAATTTCAAAAAATATATA
1 AAAATTT-AAAAAATATATA
12195365 TTTTAAAAAT
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:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTTAAAAAATATATA
Found at i:12195366 original size:26 final size:26
Alignment explanation
Indices: 12195336--12195388 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
12195326 AAAATTTAAA
*
12195336 ATATTTATAAAAATT-TCAAAAAATAT
1 ATATTT-TAAAAATTCTAAAAAAATAT
12195362 ATATTTTAAAAATTCTAAAAAAATAT
1 ATATTTTAAAAATTCTAAAAAAATAT
12195388 A
1 A
12195389 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATTTTAAAAATTCTAAAAAAATAT
Found at i:12195372 original size:24 final size:26
Alignment explanation
Indices: 12195336--12195388 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
12195326 AAAATTTAAA
*
12195336 ATATTTATAAAAATTTC-AAAAAATAT
1 ATATTTATAAAAAATTCTAAAAAA-AT
12195362 ATATTT-T-AAAAATTCTAAAAAAAT
1 ATATTTATAAAAAATTCTAAAAAAAT
12195386 ATA
1 ATA
12195389 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 12 0.48
25 7 0.28
26 6 0.24
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATTTATAAAAAATTCTAAAAAAAT
Found at i:12198176 original size:17 final size:16
Alignment explanation
Indices: 12198156--12198276 Score: 57
Period size: 17 Copynumber: 7.0 Consensus size: 16
12198146 CACAGCTTAC
12198156 ACAAGATAACAGTTCAT
1 ACAA-ATAACAGTTCAT
*
12198173 ACAAATTAAACGGTTTACAT
1 ACAAA-T-AACAG-TT-CAT
*
12198193 A-GAATAGACAGTTCGTAT
1 ACAAATA-ACAGTTC--AT
12198211 A-AAATAACAGTTCAT
1 ACAAATAACAGTTCAT
* * *
12198226 GCATAATAATAGATCAT
1 ACA-AATAACAGTTCAT
* **
12198243 TCAATATAGTAGTTCAT
1 ACAA-ATAACAGTTCAT
12198260 ACAATATAACAGTTCAT
1 ACAA-ATAACAGTTCAT
12198277 TCAATATAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.02
16 4 0.05
17 52 0.64
18 15 0.19
19 4 0.05
20 4 0.05
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (16 bp):
ACAAATAACAGTTCAT
Found at i:12198258 original size:34 final size:35
Alignment explanation
Indices: 12198214--12198298 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 35
12198204 TTCGTATAAA
* * *
12198214 ATAACAGTTCATGCATA-ATAATAGATCATTCAAT
1 ATAATAGTTCATACATATATAACAGATCATTCAAT
* *
12198248 ATAGTAGTTCATACA-ATATAACAGTTCATTCAAT
1 ATAATAGTTCATACATATATAACAGATCATTCAAT
* *
12198282 ATAATAATTCATTCATA
1 ATAATAGTTCATACATA
12198299 CAACATCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 1 0.02
34 39 0.95
35 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (35 bp):
ATAATAGTTCATACATATATAACAGATCATTCAAT
Found at i:12198281 original size:17 final size:17
Alignment explanation
Indices: 12198231--12198296 Score: 87
Period size: 17 Copynumber: 3.9 Consensus size: 17
12198221 TTCATGCATA
*
12198231 ATAATAGATCATTCAAT
1 ATAATAGTTCATTCAAT
* *
12198248 ATAGTAGTTCATACAAT
1 ATAATAGTTCATTCAAT
*
12198265 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
12198282 ATAATAATTCATTCA
1 ATAATAGTTCATTCA
12198297 TACAACATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAATAGTTCATTCAAT
Found at i:12198941 original size:18 final size:18
Alignment explanation
Indices: 12198918--12198984 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
12198908 AATTTGACAA
*
12198918 ATTAATACAGTTCACCAT
1 ATTAATACAATTCACCAT
* *
12198936 ATTAATACAAATCACCAA
1 ATTAATACAATTCACCAT
* *
12198954 ATTAACACAATTCGCCAT
1 ATTAATACAATTCACCAT
* *
12198972 AATAATATAATTC
1 ATTAATACAATTC
12198985 GCCAAGTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (18 bp):
ATTAATACAATTCACCAT
Found at i:12205303 original size:22 final size:21
Alignment explanation
Indices: 12205274--12205318 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
12205264 AACTATATGT
* *
12205274 ATATATAGATATATTAGATTG
1 ATATATAGAAATATTAAATTG
*
12205295 ATATGATAGAAATTTTAAATTG
1 ATAT-ATAGAAATATTAAATTG
12205317 AT
1 AT
12205319 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATATAGAAATATTAAATTG
Found at i:12214263 original size:19 final size:18
Alignment explanation
Indices: 12214217--12214275 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
12214207 CAACCTAATT
*
12214217 TTTATGTTTATTTATGTTTA
1 TTTAT-TTTA-TTATTTTTA
12214237 TTCT-TTTTACTTATTTTTA
1 TT-TATTTTA-TTATTTTTA
12214256 TTTATTTTATTATTTATTA
1 TTTATTTTATTATTT-TTA
12214275 T
1 T
12214276 CACTTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.21
19 23 0.68
20 3 0.09
21 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTATTTTATTATTTTTA
Found at i:12214275 original size:15 final size:15
Alignment explanation
Indices: 12214216--12214273 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
12214206 GCAACCTAAT
*
12214216 TTTTATGTTTATTTA
1 TTTTATTTTTATTTA
*
12214231 TGTTTATTCTT-TTTA
1 T-TTTATTTTTATTTA
*
12214246 -CTTATTTTTATTTA
1 TTTTATTTTTATTTA
12214260 TTTTATTATTTATT
1 TTTTATT-TTTATT
12214274 ATCACTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 10 0.29
16 13 0.38
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:12225693 original size:43 final size:43
Alignment explanation
Indices: 12225645--12225742 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
12225635 GTGTGATTTT
* * * *
12225645 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTAC
1 GTGTAAGACCATGCCTGGGACAGTGACATCGATATGAGATAAC
* * *
12225688 GTGTAAGACCCTGCCTGGGACAGTGACATTGATATGTGATAAC
1 GTGTAAGACCATGCCTGGGACAGTGACATCGATATGAGATAAC
*
12225731 ATGTAAGACCAT
1 GTGTAAGACCAT
12225743 ATCTAGGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (43 bp):
GTGTAAGACCATGCCTGGGACAGTGACATCGATATGAGATAAC
Found at i:12237010 original size:22 final size:22
Alignment explanation
Indices: 12236968--12237013 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12236958 AGTCAAAATG
* *
12236968 AAAATGAAAAAAGAGAGAAGAA
1 AAAAGGAAAAAAGAGAAAAGAA
12236990 AAAAGGAAAAAAG-GAAAAAGAA
1 AAAAGGAAAAAAGAG-AAAAGAA
12237012 AA
1 AA
12237014 GGAGAGGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAAGGAAAAAAGAGAAAAGAA
Found at i:12237870 original size:13 final size:13
Alignment explanation
Indices: 12237848--12237884 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12237838 TGATTTCTCA
* *
12237848 AAAAAAGAAAGTG
1 AAAAATGAAAATG
12237861 AAAAATGAAAATG
1 AAAAATGAAAATG
12237874 AAAAATGAAAA
1 AAAAATGAAAA
12237885 ATGGAGAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (13 bp):
AAAAATGAAAATG
Found at i:12237871 original size:7 final size:7
Alignment explanation
Indices: 12237859--12237887 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12237849 AAAAAGAAAG
12237859 TGAAAAA
1 TGAAAAA
12237866 TG-AAAA
1 TGAAAAA
12237872 TGAAAAA
1 TGAAAAA
12237879 TGAAAAA
1 TGAAAAA
12237886 TG
1 TG
12237888 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (7 bp):
TGAAAAA
Found at i:12239389 original size:128 final size:128
Alignment explanation
Indices: 12239161--12240116 Score: 1361
Period size: 128 Copynumber: 7.5 Consensus size: 128
12239151 GATGAAGATT
** * *
12239161 ACAAGTCCTATATCTTTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGT
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * *
12239226 AGTAGCGGAGTAGATCGAAGACGGCTAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * *
12239289 ACAAGTCCTATCTCACTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* *
12239354 AGTAGCGGAGCAGATCGAAA-ATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGCGGAGCAGATC-AAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * *
12239417 ACAAGTCCTATGTCCCTGGTCAGTAGTGGAATAGGTTGGAGATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * *
12239482 TGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * * * * * *
12239545 ACAAGTCTTATGTCCCTAGTTAGCAGTGGAATAGGTTAGAAATTACAGATCTGGTCTTCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * ** *
12239610 AATAGCAGG-GCAGATTAAAGACGGCGGATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
66 AGTAGC-GGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * *
12239673 ACAAGTCCTATTTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAAATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * ** *
12239738 AATAGCGGAGCAGATCAAAGACTGCGGATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* **
12239801 ACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTTCAAAATTACAGATCTTGTCTCCCTAAG
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGG-TTGGAAATTACAGATCTTGTCTCCCTAAG
* *
12239866 CAGTAGCGGATC-G---AAAG-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCC
65 CAGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* * *
12239925 ACAAGTCGTATATCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAAATCTTGTCTCCCTAAGC
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* *
12239990 AATAGCGGAGCAGATCAAAGACGG-AGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGTC
66 AGTAGCGGAGCAGATCAAAGACGGCA-AATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
* *
12240053 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCCTATCTCCCTAA
1 ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAA
12240117 AGTTGTAGTG
Statistics
Matches: 747, Mismatches: 69, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
123 37 0.05
124 71 0.10
125 4 0.01
127 10 0.01
128 562 0.75
129 63 0.08
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (128 bp):
ACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCAAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
Found at i:12240513 original size:44 final size:43
Alignment explanation
Indices: 12240272--12240792 Score: 225
Period size: 44 Copynumber: 11.9 Consensus size: 43
12240262 TCGAAAATGG
* * * * *
12240272 AATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAACCAGA
* * * ** *
12240316 AATCCTATCTCCCTGAGATTATAGTGGAACAGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACCAGA
* * * * ** *** *
12240359 AGATTTTATCTCTCTGAAATTACAGTAGAATAGATCGCATCAG-
1 A-ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACCAGA
* ** * ** ** *
12240402 -GTCTTATCTCCCTTG-GATTACAGTGGAATATACCAAAAAATTTCA
1 AATCTTATCTCCC-TGAGATTACAGTGGAGCAGATTAAACCA---GA
12240447 AATCTTATCTCCCTGA-AGTTACAGTGGAGCAGATTAAAGCCAGA
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA-CCAGA
* * * *
12240491 AATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAACCAGA
* * * **
12240535 AATCCTATTTCCCTGAGATTACAGTGGAGCGGATTAAAATA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACCAGA
* * * * * *** *
12240577 AGGATCTTGTCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG-
1 A--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACCAGA
* * * ****
12240621 -GTCTTATCTCCCTTG-GATTACAGTGGAATAGACCGA-AAAATTTCA
1 AATCTTATCTCCC-TGAGATTACAGTGG---AG-CAGATTAAACCAGA
* *
12240666 TATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAACACCAGA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AA-ACCAGA
* * *
12240711 AATCTTATCTCCCTGAGATTACAGCT-GAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAG-TGGAGCAGATT-AAACCAGA
* * *
12240755 AATCCTATTTCCCTGAGATTACAGTGGAGCGGATTAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
12240793 ATAAAGGATC
Statistics
Matches: 350, Mismatches: 99, Indels: 57
0.69 0.20 0.11
Matches are distributed among these distances:
41 44 0.13
42 8 0.02
43 13 0.04
44 190 0.54
45 46 0.13
46 48 0.14
47 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAACCAGA
Found at i:12240550 original size:219 final size:219
Alignment explanation
Indices: 12240272--12240925 Score: 1019
Period size: 219 Copynumber: 3.0 Consensus size: 219
12240262 TCGAAAATGG
* *
12240272 AATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
* * * * * *
12240337 TAGTGGAACAGATTAAAATAAAAGATTTTATCTCTCTGAAATTACAGTAGAATAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
*
12240402 GTCTTATCTCCCTTGGATTACAGTGGAATATACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
131 GTCTTATCTCCCTTGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
12240467 ACAGTGGAGCAGATTAAAGCCAGA
196 ACAGTGGAGCAGATTAAAGCCAGA
* *
12240491 AATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
*
12240556 CAGTGGAGCGGATTAAAATAAAGGATCTTGTCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
* * *
12240621 GTCTTATCTCCCTTGGATTACAGTGGAATAGACCGAAAAATTTCATATCTTATCTCCCTGAGGTT
131 GTCTTATCTCCCTTGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
12240686 ACAGTGGAGCAGATTGAACA-CCAGA
196 ACAGTGGAGCAGATT-AA-AGCCAGA
*
12240711 AATCTTATCTCCCTGAGATTACAGCTGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
*
12240776 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAATTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
* * **
12240841 GTCTTATCTCCC-TGAGATTACAGGGGAATAGA-CATAAGAATTTCAAATCTTA-CTTCCCTGGC
131 GTCTTATCTCCCTTG-GATTACAGTGGAATAGACCA-AAAAATTTCAAATCTTATC-TCCCTGAA
* * *
12240903 GGTGCAGTGGAACAGATTAAAGC
193 GTTACAGTGGAGCAGATTAAAGC
12240926 TACAATGACG
Statistics
Matches: 400, Mismatches: 29, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
218 1 0.00
219 202 0.50
220 196 0.49
221 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (219 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTTGGATTACAGTGGAATAGACCAAAAAATTTCAAATCTTATCTCCCTGAAGTT
ACAGTGGAGCAGATTAAAGCCAGA
Found at i:12241306 original size:16 final size:16
Alignment explanation
Indices: 12241282--12241321 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
12241272 CCCAAAATTA
12241282 TAACCCAAACCCAAT-
1 TAACCCAAACCCAATC
*
12241297 TAAGCCCAAACCTAATC
1 TAA-CCCAAACCCAATC
12241314 TAACCCAA
1 TAACCCAA
12241322 TACTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (16 bp):
TAACCCAAACCCAATC
Found at i:12244739 original size:21 final size:20
Alignment explanation
Indices: 12244707--12244745 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12244697 TTGAAAATAA
12244707 AATTGTAATATGAAATTGAGG
1 AATTGTAATATG-AATTGAGG
12244728 AATT-TAATTATGAATTGA
1 AATTGTAA-TATGAATTGA
12244746 ATTGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (20 bp):
AATTGTAATATGAATTGAGG
Found at i:12245569 original size:18 final size:18
Alignment explanation
Indices: 12245531--12245566 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12245521 TTATTATTTT
*
12245531 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
12245549 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
12245567 TAATTTATTA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:12245584 original size:16 final size:19
Alignment explanation
Indices: 12245555--12245614 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
12245545 AAAATAAAAT
12245555 TTAA-ATATTAAATAATTTA
1 TTAATATATT-AATAATTTA
12245574 TTAA-A-A-TAATAAATTATA
1 TTAATATATTAAT-AATT-TA
12245592 TTAATTATATTAATAATTTA
1 TTAA-TATATTAATAATTTA
12245612 TTA
1 TTA
12245615 TATGACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 7 0.20
19 5 0.14
20 6 0.17
21 5 0.14
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATATATTAATAATTTA
Found at i:12260276 original size:22 final size:21
Alignment explanation
Indices: 12260227--12260277 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
12260217 TTAAAATAAT
*
12260227 ATTTTTTATTTTTATTTTTAA
1 ATTTTTAATTTTTATTTTTAA
** *
12260248 AAATTTAATTCTTTTTTTTTAA
1 ATTTTTAATT-TTTATTTTTAA
12260270 ATTTTTAA
1 ATTTTTAA
12260278 ATTTAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTAATTTTTATTTTTAA
Found at i:12265015 original size:30 final size:30
Alignment explanation
Indices: 12264979--12265039 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12264969 CGTTGCTCCG
12264979 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
12265009 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
12265039 A
1 A
12265040 TCAATTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (30 bp):
AACTCTGATACAGCAACCTCATAAGTTTCC
Found at i:12281939 original size:18 final size:19
Alignment explanation
Indices: 12281916--12281955 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
12281906 ATGACTTATT
12281916 TTATATTAATTTGAATA-A
1 TTATATTAATTTGAATATA
12281934 TTATATTAATTTGAATATA
1 TTATATTAATTTGAATATA
12281953 TTA
1 TTA
12281956 CAAAACCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATTAATTTGAATATA
Found at i:12303408 original size:16 final size:16
Alignment explanation
Indices: 12303355--12303414 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
12303345 AATACGATTT
12303355 TCCCTAATGCAAATTA
1 TCCCTAATGCAAATTA
* *
12303371 T-CCTAAGTATGC-AGTGA
1 TCCCT-A--ATGCAAATTA
12303388 TCCCTAATGCAAATTA
1 TCCCTAATGCAAATTA
12303404 TCCCTAATGCA
1 TCCCTAATGCA
12303415 TTTAGTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
15 7 0.20
16 16 0.46
17 5 0.14
18 7 0.20
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (16 bp):
TCCCTAATGCAAATTA
Found at i:12308796 original size:24 final size:24
Alignment explanation
Indices: 12308780--12308831 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
12308770 AATCAAAGTC
*
12308780 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
12308804 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
12308828 AAAT
1 AAAT
12308832 CTTTTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:12310998 original size:21 final size:21
Alignment explanation
Indices: 12310972--12311021 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
12310962 CAACGTTAAG
12310972 CATTTTCTGGTTTGTGTTTTA
1 CATTTTCTGGTTTGTGTTTTA
12310993 CATTTTCTGGTTTGTGTTTTA
1 CATTTTCTGGTTTGTGTTTTA
12311014 CATTTTCT
1 CATTTTCT
12311022 TAGGAACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.10, C:0.12, G:0.16, T:0.62
Consensus pattern (21 bp):
CATTTTCTGGTTTGTGTTTTA
Found at i:12311696 original size:35 final size:35
Alignment explanation
Indices: 12311646--12311872 Score: 267
Period size: 35 Copynumber: 6.3 Consensus size: 35
12311636 GCGTGTTTAC
* *
12311646 CCCAACC-TTTTAAGGTTACCGTAGACGGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * **
12311680 CCCAGCCTTTTTAAGGTTGCCTTAGATGGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * *
12311715 CCCAACTTTTTTTAAAGGTTGCCTTAGAAAAGGTCTAT
1 CCCAAC-CTTTTT-AAGGTTACCTTAG-ACAGGTCTAT
*
12311753 CCCAACCTTTTTAAGGTTACCTTAGACAGCTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
* * *
12311788 ACCAACCTTTTTTAAAGGTTGCCTCAGACAAGGTCTAT
1 CCCAACC-TTTTT-AAGGTTACCTTAGAC-AGGTCTAT
12311826 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
1 CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
*
12311861 CCCAACATTTTT
1 CCCAACCTTTTT
12311873 TAAAGGTATG
Statistics
Matches: 166, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
34 6 0.04
35 62 0.37
36 35 0.21
37 36 0.22
38 27 0.16
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (35 bp):
CCCAACCTTTTTAAGGTTACCTTAGACAGGTCTAT
Found at i:12311751 original size:73 final size:73
Alignment explanation
Indices: 12311673--12311886 Score: 329
Period size: 73 Copynumber: 2.9 Consensus size: 73
12311663 ACCGTAGACG
* * ** *
12311673 GGTCTATCCCAGCCTTTTTAAGGTTGCCTTAGATGGGTCTATCCCAACTTTTTTTAAAGGTTGCC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
12311738 TTAGAAAA
66 TTAGAAAA
* * *
12311746 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGCTCTATACCAACCTTTTTTAAAGGTTGCC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
* *
12311811 TCAGACAA
66 TTAGAAAA
12311819 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTATGC
1 GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGT-TGC
12311884 CTT
65 CTT
12311887 GACTAAGTCT
Statistics
Matches: 127, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 122 0.96
74 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (73 bp):
GGTCTATCCCAACCTTTTTAAGGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAAGGTTGCC
TTAGAAAA
Found at i:12319309 original size:19 final size:21
Alignment explanation
Indices: 12319287--12319329 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
12319277 ATAAAAGACC
12319287 ATAAAAATA-TAGAAA-TTAT
1 ATAAAAATATTAGAAATTTAT
*
12319306 ATAAAATTATTAGAAATTTAT
1 ATAAAAATATTAGAAATTTAT
12319327 ATA
1 ATA
12319330 TATTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAAAATATTAGAAATTTAT
Found at i:12319314 original size:10 final size:11
Alignment explanation
Indices: 12319293--12319329 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
12319283 GACCATAAAA
12319293 ATATAGAAATT
1 ATATAGAAATT
12319304 ATATA-AAATT
1 ATATAGAAATT
12319314 AT-TAGAAATTT
1 ATATAGAAA-TT
12319325 ATATA
1 ATATA
12319330 TATTTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.09
10 10 0.43
11 9 0.39
12 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
ATATAGAAATT
Found at i:12319390 original size:22 final size:20
Alignment explanation
Indices: 12319340--12319412 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 20
12319330 TATTTGAGTT
12319340 TTATTAAAAA-ATAGAAAAA
1 TTATTAAAAATATAGAAAAA
*
12319359 CTATTAAAAATATAGAAAAA
1 TTATTAAAAATATAGAAAAA
*
12319379 TTATCTTAAAAATATAGGAAAA
1 TTA--TTAAAAATATAGAAAAA
12319401 -T-TTAAAAATATA
1 TTATTAAAAATATA
12319413 TATATAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.23
19 9 0.19
20 11 0.23
21 1 0.02
22 16 0.33
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
TTATTAAAAATATAGAAAAA
Found at i:12319511 original size:20 final size:20
Alignment explanation
Indices: 12319482--12319519 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12319472 TGACAACATG
*
12319482 ATAAAAAATAATTAAAATCA
1 ATAAAAAATAATAAAAATCA
*
12319502 ATAAATAATAATAAAAAT
1 ATAAAAAATAATAAAAAT
12319520 ATTTTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAAAATAATAAAAATCA
Found at i:12329943 original size:10 final size:10
Alignment explanation
Indices: 12329928--12329957 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12329918 AAGAAAACCG
12329928 AAAGAAAAAA
1 AAAGAAAAAA
*
12329938 AAAGAAAAAG
1 AAAGAAAAAA
12329948 AAAGAAAAAA
1 AAAGAAAAAA
12329958 GAAAACCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:12329947 original size:16 final size:17
Alignment explanation
Indices: 12329928--12329962 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12329918 AAGAAAACCG
12329928 AAAGAAA-AAAAAAGAA
1 AAAGAAAGAAAAAAGAA
12329944 AAAGAAAGAAAAAAGAA
1 AAAGAAAGAAAAAAGAA
12329961 AA
1 AA
12329963 CCAGGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAA
Found at i:12329950 original size:20 final size:21
Alignment explanation
Indices: 12329916--12329957 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
12329906 ATAAACACAG
*
12329916 AAAAGAAAACCGAAAGAAAAA
1 AAAAGAAAACAGAAAGAAAAA
12329937 AAAAGAAAA-AGAAAGAAAAA
1 AAAAGAAAACAGAAAGAAAAA
12329957 A
1 A
12329958 GAAAACCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAGAAAACAGAAAGAAAAA
Found at i:12329970 original size:20 final size:19
Alignment explanation
Indices: 12329916--12329972 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
12329906 ATAAACACAG
12329916 AAAAGAAAACC-GAAAGAA
1 AAAAGAAAACCAGAAAGAA
* **
12329934 AAAAAAAGAAAAAGAAAGAA
1 AAAAGAA-AACCAGAAAGAA
12329954 AAAAGAAAACCAGGAAAGA
1 AAAAGAAAACCA-GAAAGA
12329973 TTTAAAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 19 0.63
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAACCAGAAAGAA
Found at i:12331043 original size:44 final size:44
Alignment explanation
Indices: 12331015--12331248 Score: 134
Period size: 44 Copynumber: 5.1 Consensus size: 44
12331005 CCTTTATTTT
*
12331015 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
* * * * *
12331059 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
* * *
12331103 AATCTGATGCGATCTACTCTACTGTAA-CTTC-AGAGAGATAAGATCCT-TTA-TTTT
1 AATC-----CG--CT-C-C-ACTGTAATC-TCAAG-GAGATAAGAT--TACTAGCTTC
* * * *
12331157 AATCCACTCCACAGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
** * * * * *
12331201 AATCTACTCCGCTGTAATCTCAGGGAGATAATATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
12331245 AATC
1 AATC
12331249 TGCTGCGATC
Statistics
Matches: 145, Mismatches: 27, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 102 0.70
45 3 0.02
46 1 0.01
47 2 0.01
49 2 0.01
51 2 0.01
52 1 0.01
53 3 0.02
54 24 0.17
55 1 0.01
56 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
AATCCGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
Found at i:12331146 original size:142 final size:142
Alignment explanation
Indices: 12330971--12331293 Score: 574
Period size: 142 Copynumber: 2.3 Consensus size: 142
12330961 GACCTAATAT
* * *
12330971 GATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACAGTAATCTC
*
12331036 AAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
66 AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
12331101 TCAATCTGATGC
131 TCAATCTGATGC
12331113 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACAGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACAGTAATCTC
* *
12331178 AGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAATATTTCTGGCT
66 AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
*
12331243 TCAATCTGCTGC
131 TCAATCTGATGC
*
12331255 GATCTACTCTACCGTAACTTCAGAGAGATAAGATCCTTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
12331294 CTCAGTCTCC
Statistics
Matches: 173, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 173 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (142 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACAGTAATCTC
AAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCT
TCAATCTGATGC
Found at i:12331630 original size:87 final size:87
Alignment explanation
Indices: 12331534--12332300 Score: 1165
Period size: 87 Copynumber: 8.8 Consensus size: 87
12331524 CTGTCGACAT
* * ** *
12331534 AGGAGGGCAAGATCTGCTATCTTCAACCAGCTCCACTAAAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* ***
12331599 CGATCTGCTTCGCTGTTAATAT
66 CGATCTGCTTCGCCGTTAACGC
* * *
12331621 AGGAAGGCAAGATCCGCTATCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
12331686 CGATCTGCTTCACCGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
* *
12331708 AGGAAGGCAAGATCTGCAATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
12331773 CGATCTGCTTCGCCGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
*
12331795 AGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* **
12331860 CGATCTGCTTCACCGTTAATAC
66 CGATCTGCTTCGCCGTTAACGC
*
12331882 AGGAAGGCAAGATCTGCTATCTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
12331947 TGATCTGCTTCGCCGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
*
12331969 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCTACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
12332034 CGATCTGTTTTGCTGTTAACGC
66 CGATCTGCTTCGCCGTTAACGC
* * * *
12332056 AGGAAGACAAGATCTGCTATCTTTAACCAACTCCACTACAACTGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
12332121 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCCGTTAACGC
* * * * *
12332143 AGGAAGGCAAGATCTACTATCTTTAACCAGCTTCACTGTAACTGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
12332208 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCCGTTAACGC
* * *
12332230 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGGTAGAGGTAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
12332295 CGATCT
66 CGATCT
12332301 TCACTGATAT
Statistics
Matches: 620, Mismatches: 60, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 620 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCCGTTAACGC
Found at i:12332241 original size:43 final size:43
Alignment explanation
Indices: 12332104--12332241 Score: 140
Period size: 43 Copynumber: 3.2 Consensus size: 43
12332094 CAACTGATGG
*
12332104 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
* * * * * *
12332147 AGGCAAGATCTACTATCTTT-AACCAGCTTCACTG-TAACTG-ATGG-
1 AGGCAAGA-CT-TTGT-TTTCGATCTGCTTCGCTGTTAA-TGCA-GGA
12332191 AGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
12332234 AGGCAAGA
1 AGGCAAGA
12332242 TCTGCTATCT
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
41 3 0.04
42 16 0.22
43 21 0.29
44 14 0.19
45 16 0.22
46 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (43 bp):
AGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
Found at i:12333541 original size:20 final size:18
Alignment explanation
Indices: 12333516--12333568 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
12333506 CCTCTCTATT
12333516 TTTCATTTTCATTTTTTACA
1 TTTCATTTTCATTTTTT--A
*
12333536 TTTCATTCTCATTTTTTA
1 TTTCATTTTCATTTTTTA
12333554 TTT--TTTTCATTTTTT
1 TTTCATTTTCATTTTTT
12333569 TTGAAATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 11 0.35
18 4 0.13
20 16 0.52
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCATTTTCATTTTTTA
Found at i:12333990 original size:27 final size:27
Alignment explanation
Indices: 12333960--12334011 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
12333950 TTTGACTTTG
*
12333960 ATTGA-TTTCTCTTTTTTTGTTTTTGAC
1 ATTGATTTTCTCTTTTCTT-TTTTTGAC
*
12333987 ATTGATTTTTTCTTTTCTTTTTTTG
1 ATTGATTTTCTCTTTTCTTTTTTTG
12334012 TTTCTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (27 bp):
ATTGATTTTCTCTTTTCTTTTTTTGAC
Found at i:12334011 original size:33 final size:33
Alignment explanation
Indices: 12333928--12334034 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
12333918 TTTTCTTTTC
* *
12333928 TTTTTCTCTTTTCATATTTTG-TTTTGACTTTGA
1 TTTTT-TCTTTTCTTTTTTTGTTTTTGACTTTGA
* *
12333961 TTGATTTC---TCTTTTTTTGTTTTTGACATTGA
1 TT-TTTTCTTTTCTTTTTTTGTTTTTGACTTTGA
* *
12333992 TTTTTTCTTTTCTTTTTTTGTTTCTGATTTTGA
1 TTTTTTCTTTTCTTTTTTTGTTTTTGACTTTGA
12334025 TTTTTT-TTTT
1 TTTTTTCTTTT
12334035 GAATCTGAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
30 12 0.20
31 13 0.21
32 4 0.07
33 30 0.49
34 2 0.03
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.72
Consensus pattern (33 bp):
TTTTTTCTTTTCTTTTTTTGTTTTTGACTTTGA
Found at i:12339868 original size:20 final size:21
Alignment explanation
Indices: 12339831--12339870 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12339821 AATAAACACA
*
12339831 GAAAAGAAAACCGAAAAAAAT
1 GAAAAGAAAACAGAAAAAAAT
12339852 GAAAAGAAAA-AGAAAAAAA
1 GAAAAGAAAACAGAAAAAAA
12339871 AAGAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.03
Consensus pattern (21 bp):
GAAAAGAAAACAGAAAAAAAT
Found at i:12339871 original size:21 final size:21
Alignment explanation
Indices: 12339830--12339877 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12339820 AAATAAACAC
*
12339830 AGAAAAGAAAACCGAAAAAAA
1 AGAAAAGAAAACAGAAAAAAA
*
12339851 TGAAAAGAAAA-AGAAAAAAAA
1 AGAAAAGAAAACAG-AAAAAAA
12339872 AGAAAA
1 AGAAAA
12339878 CCAGGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAAAAGAAAACAGAAAAAAA
Found at i:12339873 original size:10 final size:10
Alignment explanation
Indices: 12339844--12339877 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12339834 AAGAAAACCG
*
12339844 AAAAAAATGA
1 AAAAAAAAGA
12339854 AAAGAAAAAGA
1 AAA-AAAAAGA
12339865 AAAAAAAAGA
1 AAAAAAAAGA
12339875 AAA
1 AAA
12339878 CCAGGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:12340572 original size:19 final size:19
Alignment explanation
Indices: 12340527--12340570 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
12340517 ATAACTTTAA
12340527 AATTTTTATATTTTATAAT
1 AATTTTTATATTTTATAAT
*
12340546 AATTTTTATA-TTTCTAAT
1 AATTTTTATATTTTATAAT
12340564 AATTTTT
1 AATTTTT
12340571 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTATATTTTATAAT
Found at i:12340597 original size:28 final size:29
Alignment explanation
Indices: 12340534--12340613 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
12340524 TAAAATTTTT
* * * *
12340534 ATATTTTATAATAATTTTT-ATATTTCTA
1 ATATTTTTTAAAAATTTTTAATATATCAA
12340562 ATAATTTTTTAAAAATTTTTAATATAT-AA
1 AT-ATTTTTTAAAAATTTTTAATATATCAA
12340591 ATATTTTTTATAAAA-TTTTAATA
1 ATATTTTTTA-AAAATTTTTAATA
12340614 ATTTTTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 18 0.40
29 22 0.49
30 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTTTTAAAAATTTTTAATATATCAA
Found at i:12344393 original size:40 final size:40
Alignment explanation
Indices: 12344348--12344692 Score: 539
Period size: 40 Copynumber: 8.6 Consensus size: 40
12344338 CAAGCTCAAT
* * * * *
12344348 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12344388 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
*
12344428 TGCCTTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
12344468 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12344508 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
12344548 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
12344588 TGCCTTCAGGTCTTAGCCTGGATATATCAATTCGTACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12344628 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
12344668 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
12344693 CATTCAAATG
Statistics
Matches: 280, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
39 2 0.01
40 277 0.99
41 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:12351789 original size:40 final size:40
Alignment explanation
Indices: 12351744--12352088 Score: 566
Period size: 40 Copynumber: 8.6 Consensus size: 40
12351734 CAAGCTCAAT
* * * * *
12351744 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12351784 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
12351824 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * *
12351864 CGCCGTCGGGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12351904 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
12351944 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12351984 TGCCTTCAGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
12352024 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
12352064 TGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
12352089 CATTCAAATG
Statistics
Matches: 284, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 2 0.01
40 281 0.99
41 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:12359859 original size:141 final size:141
Alignment explanation
Indices: 12359605--12359878 Score: 539
Period size: 141 Copynumber: 1.9 Consensus size: 141
12359595 AAAAGTATAA
*
12359605 AATTTTTTTCAAACTGTAGAGATCACATAGCTGAGACACATGCCCCTGTCTTAGGCCATGTGGAC
1 AATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGGCCATGTGGAC
12359670 ATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTG
66 ATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTG
12359735 GGTAAAAGTTG
131 GGTAAAAGTTG
12359746 AATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGGCCATGTGGAC
1 AATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGGCCATGTGGAC
12359811 ATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTG
66 ATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTG
12359876 GGT
131 GGT
12359879 CACACGGCCA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 132 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (141 bp):
AATTTTTTTCAAACTGTAGAGATCACACAGCTGAGACACATGCCCCTGTCTTAGGCCATGTGGAC
ATTCGAAGTAGGGACAGACGGCCGTGTCCCAGCCCGTGTCCGTGCCCGTGTAACTCTCTGACTTG
GGTAAAAGTTG
Found at i:12360158 original size:23 final size:23
Alignment explanation
Indices: 12360123--12360173 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
12360113 AAGCATCCAA
12360123 TGTAATATGCCGAAAATTACTAC
1 TGTAATATGCCGAAAATTACTAC
12360146 TGTAATACT-CCGAAAATTACTAC
1 TGTAATA-TGCCGAAAATTACTAC
*
12360169 AGTAA
1 TGTAA
12360174 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (23 bp):
TGTAATATGCCGAAAATTACTAC
Found at i:12385409 original size:23 final size:24
Alignment explanation
Indices: 12385383--12385433 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
12385373 AGGTGTAGTG
*
12385383 ATCAGGGGTGCATA-AGCACGATT
1 ATCAGGGGTGCATATAGCACGAAT
* * *
12385406 ATCATGGGTGTATATAGCATGAAT
1 ATCAGGGGTGCATATAGCACGAAT
12385430 ATCA
1 ATCA
12385434 AGGGCACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (24 bp):
ATCAGGGGTGCATATAGCACGAAT
Found at i:12389342 original size:21 final size:21
Alignment explanation
Indices: 12389318--12389357 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12389308 GCCGTGTATC
*
12389318 TTAGTCACACAGGC-ATGTCAT
1 TTAGCCACAC-GGCTATGTCAT
12389339 TTAGCCACACGGCTATGTC
1 TTAGCCACACGGCTATGTC
12389358 CTCCCTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
TTAGCCACACGGCTATGTCAT
Found at i:12393414 original size:40 final size:40
Alignment explanation
Indices: 12393370--12393463 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
12393360 GCCTGCTAAT
* *
12393370 TACACTGGCACTAAGCCTGT-AAGGCAA-TAAGCCAAATAGA
1 TACACCGGCACAAAGCCT-TCAAGG-AACTAAGCCAAATAGA
* *
12393410 TACACCGGCACAAAGCCTTCTAGGAACTAAGCCCAATAGA
1 TACACCGGCACAAAGCCTTCAAGGAACTAAGCCAAATAGA
*
12393450 TACACCGACACAAA
1 TACACCGGCACAAA
12393464 CCCTGTTAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.06
40 44 0.94
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (40 bp):
TACACCGGCACAAAGCCTTCAAGGAACTAAGCCAAATAGA
Found at i:12396385 original size:34 final size:34
Alignment explanation
Indices: 12396311--12396385 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 34
12396301 CATTGGGATT
12396311 TAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
1 TAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
12396345 TAAGCCCTTTTCAATATCAGTGACAGT-TTGGGCCC
1 T-AGCCCTTTTCAATATCAGTGACAGTCTTGGG-CC
12396380 TAGCCC
1 TAGCCC
12396386 ATCTCAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
34 11 0.28
35 28 0.72
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (34 bp):
TAGCCCTTTTCAATATCAGTGACAGTCTTGGGCC
Found at i:12403403 original size:26 final size:26
Alignment explanation
Indices: 12403344--12403405 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
12403334 TACCTACAGT
* *
12403344 AGTTTCAAAATATCTTAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
12403370 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
12403396 AGTTTCAGAA
1 AGTTTCAGAA
12403406 CACTTACAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:12411640 original size:19 final size:19
Alignment explanation
Indices: 12411616--12411655 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12411606 GAACCACTAA
12411616 TATATGTAAAATATTTATT
1 TATATGTAAAATATTTATT
12411635 TATATGTAAAATATTTATT
1 TATATGTAAAATATTTATT
12411654 TA
1 TA
12411656 ATAAATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TATATGTAAAATATTTATT
Found at i:12414191 original size:23 final size:23
Alignment explanation
Indices: 12414165--12414210 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12414155 TAAAAGAAGC
*
12414165 ATAGTTCTATAGGAATTTTACTT
1 ATAGTTCTACAGGAATTTTACTT
* *
12414188 ATAGTTGTACATGAATTTTACTT
1 ATAGTTCTACAGGAATTTTACTT
12414211 GTATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (23 bp):
ATAGTTCTACAGGAATTTTACTT
Found at i:12419383 original size:8 final size:8
Alignment explanation
Indices: 12419370--12419398 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12419360 TTTTAAATGA
12419370 TATTTTAT
1 TATTTTAT
12419378 TATTTTAT
1 TATTTTAT
12419386 TATTTTAT
1 TATTTTAT
12419394 TATTT
1 TATTT
12419399 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:12420189 original size:24 final size:24
Alignment explanation
Indices: 12420144--12420190 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12420134 GGGTTATAAT
***
12420144 TTATATTTTTAAAATCCTAAAATA
1 TTATATTTTTAAAATAAAAAAATA
*
12420168 TTATATTTTTAATATAAAAAAAT
1 TTATATTTTTAAAATAAAAAAAT
12420191 GGGGATATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATATTTTTAAAATAAAAAAATA
Found at i:12428191 original size:12 final size:12
Alignment explanation
Indices: 12428174--12428207 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12428164 CAGTTACTGG
*
12428174 CCTAGCGCACGA
1 CCTAGCACACGA
12428186 CCTAGCACACGA
1 CCTAGCACACGA
12428198 CCTAGCACAC
1 CCTAGCACAC
12428208 AAGTGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.18, T:0.09
Consensus pattern (12 bp):
CCTAGCACACGA
Found at i:12443883 original size:27 final size:27
Alignment explanation
Indices: 12443839--12444013 Score: 183
Period size: 27 Copynumber: 6.5 Consensus size: 27
12443829 ATACCCCTAG
* * * *
12443839 AGGGTAAAATAATTGAAATACCGTCGG
1 AGGGTAAAATGATCGAAATACCCTCGA
* * *
12443866 GGGGTAAAATGACCGAAATACCCTCAA
1 AGGGTAAAATGATCGAAATACCCTCGA
* *
12443893 AGGGTGAAATGATCGAAATACCCCCGA
1 AGGGTAAAATGATCGAAATACCCTCGA
* *
12443920 AGGGTAAATTGATCGAAATACCCCCGA
1 AGGGTAAAATGATCGAAATACCCTCGA
*
12443947 AGGGT-AAATGGATCGAAATACCCTCAA
1 AGGGTAAAAT-GATCGAAATACCCTCGA
* * *
12443974 AGGGTAAAATGA-CATAAAGACCCACGA
1 AGGGTAAAATGATC-GAAATACCCTCGA
12444001 AGGGTAAAATGAT
1 AGGGTAAAATGAT
12444014 TGTTATACCC
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.03
27 115 0.93
28 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (27 bp):
AGGGTAAAATGATCGAAATACCCTCGA
Found at i:12443886 original size:54 final size:55
Alignment explanation
Indices: 12443818--12443986 Score: 157
Period size: 54 Copynumber: 3.1 Consensus size: 55
12443808 ATTCGTGGGC
* * * * ** **
12443818 AAATGACTGTAATACCCCT-AGAGGGTAAAATAATTGAAATACCGTCGGGGGGTA
1 AAATGACCGAAATACCCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
* *
12443872 AAATGACCGAAATA-CCCTCAAAGGGTGAAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
* * * * * *
12443926 AATTGATCGAAATACCCC-CGAAGGGT-AAATGGATCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCCTCAAAGGGTAAAAT-AATCGAAATACCCCCGAAGGGTA
12443980 AAATGAC
1 AAATGAC
12443987 ATAAAGACCC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 8 0.08
54 84 0.88
55 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (55 bp):
AAATGACCGAAATACCCCTCAAAGGGTAAAATAATCGAAATACCCCCGAAGGGTA
Found at i:12443938 original size:81 final size:81
Alignment explanation
Indices: 12443839--12444013 Score: 210
Period size: 81 Copynumber: 2.2 Consensus size: 81
12443829 ATACCCCTAG
* * ** ** *
12443839 AGGGTAAAATAATTGAAATACCGTCGGGGGGTAAAAT-GACCGAAATACCCTCAAAGGGTGAAAT
1 AGGGTAAAATGATCGAAATACCCCCGAAGGGT-AAATGGACCGAAATACCCTCAAAGGGTAAAAT
* *
12443903 GATC-GAAATACCCCCGA
65 GA-CAGAAAGACCCACGA
* *
12443920 AGGGTAAATTGATCGAAATACCCCCGAAGGGTAAATGGATCGAAATACCCTCAAAGGGTAAAATG
1 AGGGTAAAATGATCGAAATACCCCCGAAGGGTAAATGGACCGAAATACCCTCAAAGGGTAAAATG
*
12443985 ACATAAAGACCCACGA
66 ACAGAAAGACCCACGA
12444001 AGGGTAAAATGAT
1 AGGGTAAAATGAT
12444014 TGTTATACCC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 5 0.06
81 74 0.94
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (81 bp):
AGGGTAAAATGATCGAAATACCCCCGAAGGGTAAATGGACCGAAATACCCTCAAAGGGTAAAATG
ACAGAAAGACCCACGA
Found at i:12444126 original size:20 final size:21
Alignment explanation
Indices: 12444101--12444140 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12444091 TACGTTCAAA
12444101 TATGATATTTT-ACAT-ACATG
1 TATGAT-TTTTGACATGACATG
12444121 TATGATTTTTGACATGACAT
1 TATGATTTTTGACATGACAT
12444141 ATTTCATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGATTTTTGACATGACATG
Found at i:12444214 original size:26 final size:26
Alignment explanation
Indices: 12444185--12444256 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
12444175 TATACTGTTT
*
12444185 CTGGCAGCTTTGCTACTATAATGA-TA
1 CTGGCAGCTTTGCTACGATAAT-ACTA
* * * **
12444211 CTGGCAACTCTGCTGCGATGCTACTA
1 CTGGCAGCTTTGCTACGATAATACTA
12444237 CTGGCAGCTTTGCTACGATA
1 CTGGCAGCTTTGCTACGATA
12444257 TTGGTGTGTT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (26 bp):
CTGGCAGCTTTGCTACGATAATACTA
Found at i:12444399 original size:28 final size:28
Alignment explanation
Indices: 12444367--12444447 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
12444357 ATATTGATAT
* *
12444367 TGTATTGGGCTAAGGCACACACTGTTAC
1 TGTATTGGGCTAAGGCCCACACTATTAC
* *
12444395 TGTATTGGGCTAAGGCCCTCACTATTAT
1 TGTATTGGGCTAAGGCCCACACTATTAC
12444423 TGTATTGGGCTAAGGCCCACACTAT
1 TGTATTGGGCTAAGGCCCACACTAT
12444448 ACTATTACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACACTATTAC
Found at i:12445729 original size:11 final size:11
Alignment explanation
Indices: 12445713--12445755 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
12445703 ATATGCTCGA
12445713 AAAAAAAAGAG
1 AAAAAAAAGAG
12445724 AAAAAAAAGA-
1 AAAAAAAAGAG
12445734 AAAAGAAAA-AG
1 AAAA-AAAAGAG
*
12445745 AAAAGAAAGAG
1 AAAAAAAAGAG
12445756 CATATGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:12445737 original size:21 final size:21
Alignment explanation
Indices: 12445711--12445754 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12445701 TAATATGCTC
12445711 GAAAAA-AAAAGAGAAAAAAAA
1 GAAAAAGAAAA-AGAAAAAAAA
*
12445732 GAAAAAGAAAAAGAAAAGAAA
1 GAAAAAGAAAAAGAAAAAAAA
12445753 GA
1 GA
12445755 GCATATGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAAAAGAAAAAAAA
Found at i:12445738 original size:6 final size:6
Alignment explanation
Indices: 12445712--12445752 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
12445702 AATATGCTCG
*
12445712 AAAA-A AAAAGA GAAA-A AAAAGA AAAAGA AAAAG- AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
12445753 GAGCATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 13 0.42
6 18 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:12445738 original size:17 final size:17
Alignment explanation
Indices: 12445711--12445752 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
12445701 TAATATGCTC
12445711 GAAAA-AAAAAGAGAAAA
1 GAAAAGAAAAAGA-AAAA
12445728 -AAAAGAAAAAGAAAAA
1 GAAAAGAAAAAGAAAAA
12445744 GAAAAGAAA
1 GAAAAGAAA
12445753 GAGCATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAGAAAAA
Found at i:12445740 original size:15 final size:14
Alignment explanation
Indices: 12445712--12445754 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
12445702 AATATGCTCG
*
12445712 AAAAAAAAAGAGAA
1 AAAAAAAAAAAGAA
12445726 AAAAAAGAAAAAGAA
1 AAAAAA-AAAAAGAA
*
12445741 AAAGAAAAGAAAGA
1 AAA-AAAAAAAAGA
12445755 GCATATGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 16 0.64
16 3 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:12445771 original size:33 final size:34
Alignment explanation
Indices: 12445734--12445804 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
12445724 AAAAAAAAGA
*
12445734 AAAAGAAAAAGA-AAAGAAAGAGCATATGTACTC
1 AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
* ** *
12445767 AAAAGAAATAGATGTACAAAGAGCATGTGTACTC
1 AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
12445801 AAAA
1 AAAA
12445805 TGCAAAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15
Consensus pattern (34 bp):
AAAAGAAAAAGATAAACAAAGAGCATATGTACTC
Found at i:12447923 original size:16 final size:17
Alignment explanation
Indices: 12447902--12447935 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12447892 ATTAGAATTT
12447902 TTACTT-TTAATTTTTA
1 TTACTTATTAATTTTTA
12447918 TTACTTAGTTAATTTTTA
1 TTACTTA-TTAATTTTTA
12447936 GTTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
TTACTTATTAATTTTTA
Found at i:12448753 original size:29 final size:29
Alignment explanation
Indices: 12448721--12448796 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
12448711 ACAATAATAG
*
12448721 AATAGAGTGGCACCAAAGGGAAATATCAT
1 AATAGAGTGGCACCAAAGGGAAATATCAA
* * ** ***
12448750 AATAGAATAGCACCAAATTGCTTTATCAA
1 AATAGAGTGGCACCAAAGGGAAATATCAA
12448779 AATAGAGTGGCACCAAAG
1 AATAGAGTGGCACCAAAG
12448797 TGCATTAACA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
AATAGAGTGGCACCAAAGGGAAATATCAA
Found at i:12449066 original size:188 final size:188
Alignment explanation
Indices: 12448753--12449108 Score: 466
Period size: 188 Copynumber: 1.9 Consensus size: 188
12448743 ATATCATAAT
* * * * *
12448753 AGAATAGCACCAAATTGCTTTATCAAAATAGAGTGGCACCAAAGTGCATTAACAGAACTGAGAGC
1 AGAATAACACCAAATTGCTTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
* * *** * *
12448818 ACATTGAATGTTTCCTAATGGCATGCCATCTATATCCCTCTACTTTGTATCTTGTCTACTTGGGA
66 ACATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGAGA
12448883 A-AGTATACCAAAACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
131 AGA-TATACCAAAACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
* *
12448941 AGAATAACACCAAATTGCTTTATCATAACAGAATGGCACTAAAGTGCATTAACA-AAAT-AGAGA
1 AGAATAACACCAAATTGCTTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
* * * *
12449004 ACGTGTTGAATGTTTCCTAATGGCATACCATCTATATCTCACTAGTTCACATATTTTCTACTTGA
66 AC--ATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGA
** * *
12449069 GAAGATATATTAAAATTAGCTTTACATTTACATTTCAAAA
129 GAAGATATACCAAAACTAGCTTCACATTTACATTTCAAAA
12449109 TAGAGCTTAT
Statistics
Matches: 143, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
186 6 0.04
187 3 0.02
188 133 0.93
189 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (188 bp):
AGAATAACACCAAATTGCTTTATCAAAACAGAATGGCACCAAAGTGCATTAACAGAAATGAGAGA
ACATTGAATGTTTCCTAATGGCATACCATCTATATCCCACTACTTCACATATTGTCTACTTGAGA
AGATATACCAAAACTAGCTTCACATTTACATTTCAAAACCAAAGTGCAATATTGGAAC
Found at i:12463416 original size:10 final size:8
Alignment explanation
Indices: 12463394--12463426 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
12463384 ATACAAACTA
12463394 GTATATAG
1 GTATATAG
12463402 GTATATAG
1 GTATATAG
12463410 GTATATAG
1 GTATATAG
12463418 GTTATATAG
1 G-TATATAG
12463427 ATAAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (8 bp):
GTATATAG
Found at i:12469670 original size:9 final size:9
Alignment explanation
Indices: 12469658--12469700 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
12469648 TATTAAAAAC
12469658 GAGAGAGTT
1 GAGAGAGTT
*
12469667 GAGAGACTT
1 GAGAGAGTT
*
12469676 GAGAGGGTTT
1 GAGAGAG-TT
*
12469686 GAAAGAGTT
1 GAGAGAGTT
12469695 GAGAGA
1 GAGAGA
12469701 AGGATGTGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.35, C:0.02, G:0.42, T:0.21
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:12474335 original size:41 final size:41
Alignment explanation
Indices: 12474290--12474379 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
12474280 TTTATTTTAT
*
12474290 CCCGAACCTAAAACCCTAAATATAGAATTCTAAATCCCAAA
1 CCCGAACCTAAAACCCTAAATATAGAATTCTAAACCCCAAA
* *
12474331 CCCGAACTTTAAACCCTAAATATAGAATTCTAAACCCCAAA
1 CCCGAACCTAAAACCCTAAATATAGAATTCTAAACCCCAAA
*
12474372 CCCAAACC
1 CCCGAACC
12474380 CAAACCTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.44, C:0.32, G:0.04, T:0.19
Consensus pattern (41 bp):
CCCGAACCTAAAACCCTAAATATAGAATTCTAAACCCCAAA
Found at i:12474366 original size:21 final size:21
Alignment explanation
Indices: 12474300--12474367 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
12474290 CCCGAACCTA
12474300 AAACCCTAAATATAGAATTCT
1 AAACCCTAAATATAGAATTCT
***
12474321 AAATCCC-AAA-CCCGAACTT-T
1 AAA-CCCTAAATATAGAA-TTCT
12474341 AAACCCTAAATATAGAATTCT
1 AAACCCTAAATATAGAATTCT
12474362 AAACCC
1 AAACCC
12474368 CAAACCCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 18 0.50
22 3 0.08
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (21 bp):
AAACCCTAAATATAGAATTCT
Found at i:12474500 original size:41 final size:39
Alignment explanation
Indices: 12474434--12474511 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 39
12474424 GGAGTTTAGA
*
12474434 GTTTGGGTTTGGATTCGAGTTTAAGGTTTATGGTTTATG
1 GTTTGGGTTTGGATTCGAGTTTAAGGTTTAAGGTTTATG
* *
12474473 GTTTGAGGTTTGGGGTTTGAGTTTAAGGTTTAAGGTTTA
1 GTTTG-GGTTT-GGATTCGAGTTTAAGGTTTAAGGTTTA
12474512 AGATTATGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.15
40 5 0.15
41 24 0.71
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (39 bp):
GTTTGGGTTTGGATTCGAGTTTAAGGTTTAAGGTTTATG
Found at i:12474501 original size:20 final size:20
Alignment explanation
Indices: 12474420--12474503 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
12474410 AATGTTTCAA
* *
12474420 GTTTGGAGTTTAGAGTTT-GG
1 GTTTGGGGTTT-GAGTTTAAG
* *
12474440 GTTT-GGATTCGAGTTTAAG
1 GTTTGGGGTTTGAGTTTAAG
** *
12474459 GTTTATGGTTT-ATGGTTTGAG
1 GTTTGGGGTTTGA--GTTTAAG
12474480 GTTTGGGGTTTGAGTTTAAG
1 GTTTGGGGTTTGAGTTTAAG
12474500 GTTT
1 GTTT
12474504 AAGGTTTAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 6 0.12
19 9 0.19
20 17 0.35
21 15 0.31
22 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.36, T:0.48
Consensus pattern (20 bp):
GTTTGGGGTTTGAGTTTAAG
Found at i:12474511 original size:7 final size:7
Alignment explanation
Indices: 12474452--12474513 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
12474442 TTGGATTCGA
12474452 GTTTAAG
1 GTTTAAG
*
12474459 GTTTATG
1 GTTTAAG
*
12474466 GTTTATG
1 GTTTAAG
*
12474473 GTTTGAG
1 GTTTAAG
**
12474480 GTTTGGG
1 GTTTAAG
*
12474487 GTTTGA-
1 GTTTAAG
12474493 GTTTAAG
1 GTTTAAG
12474500 GTTTAAG
1 GTTTAAG
12474507 GTTTAAG
1 GTTTAAG
12474514 ATTATGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
6 5 0.10
7 43 0.90
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:12474523 original size:34 final size:35
Alignment explanation
Indices: 12474457--12474537 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
12474447 TTCGAGTTTA
* * * * *
12474457 AGGTTTATGGTTTATGGTTTGAGGTTTGGGGTTTG
1 AGGTTTAAGGTTTAAGGTTTAAGATTTGGGGTTCG
12474492 A-GTTTAAGGTTTAAGGTTTAAGATTAT-GGGTTCG
1 AGGTTTAAGGTTTAAGGTTTAAGATT-TGGGGTTCG
*
12474526 AGGTTTAGGGTT
1 AGGTTTAAGGTT
12474538 CTAGTTCGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (35 bp):
AGGTTTAAGGTTTAAGGTTTAAGATTTGGGGTTCG
Found at i:12474531 original size:41 final size:41
Alignment explanation
Indices: 12474450--12474531 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
12474440 GTTTGGATTC
* * * * *
12474450 GAGTTTAAGGTTTATGGTTTATGGTTTGAGGTTTGGGGTTT
1 GAGTTTAAGGTTTAAGGTTTAAGATTTGAGGTTCGAGGTTT
12474491 GAGTTTAAGGTTTAAGGTTTAAGATTATG-GGTTCGAGGTTT
1 GAGTTTAAGGTTTAAGGTTTAAGATT-TGAGGTTCGAGGTTT
12474532 AGGGTTCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.45
Consensus pattern (41 bp):
GAGTTTAAGGTTTAAGGTTTAAGATTTGAGGTTCGAGGTTT
Found at i:12474550 original size:48 final size:48
Alignment explanation
Indices: 12474434--12474556 Score: 121
Period size: 48 Copynumber: 2.6 Consensus size: 48
12474424 GGAGTTTAGA
* * *
12474434 GTTT-GGGTTTG-GATTCGA-GTTTAAGGTTTATGGTTTATGGTTTGAG
1 GTTTAGGGTTTGAG-TTCGAGGTTTAAGGTTTATAGATTATGGTTCGAG
* **
12474480 GTTTGGGGTTTGAGTTTAAGGTTTAAGGTTTA-AGATTATGGGTTCGAG
1 GTTTAGGGTTTGAGTTCGAGGTTTAAGGTTTATAGATTAT-GGTTCGAG
*
12474528 GTTTAGGGTTCT-AGTTCGAGGTTCAAGGT
1 GTTTAGGGTT-TGAGTTCGAGGTTTAAGGT
12474557 AAAAAATTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 4 0.06
47 15 0.24
48 43 0.68
49 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.43
Consensus pattern (48 bp):
GTTTAGGGTTTGAGTTCGAGGTTTAAGGTTTATAGATTATGGTTCGAG
Found at i:12478177 original size:14 final size:14
Alignment explanation
Indices: 12478160--12478190 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12478150 TGACATTTTT
*
12478160 TAATGATATTATTC
1 TAATGATACTATTC
12478174 TAATGATACTATTC
1 TAATGATACTATTC
12478188 TAA
1 TAA
12478191 CATGTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (14 bp):
TAATGATACTATTC
Found at i:12478854 original size:12 final size:12
Alignment explanation
Indices: 12478839--12478868 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
12478829 GCGGAGCCAA
12478839 AGCCCGAGCCTG
1 AGCCCGAGCCTG
12478851 AGCCCGAGCCTG
1 AGCCCGAGCCTG
12478863 AGCCCG
1 AGCCCG
12478869 TCAGGTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.33, T:0.07
Consensus pattern (12 bp):
AGCCCGAGCCTG
Found at i:12479040 original size:33 final size:33
Alignment explanation
Indices: 12478989--12479083 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
12478979 TAGTTCAGTA
**
12478989 CCACCGCAGTACAACACTCCTCCTAGC-CTGTAT
1 CCACCGCAGTACTGCACTCCTCCTAGCTC-GTAT
* *
12479022 CCACCGCATTACTGCACTCCTCCTAGGTCGTAT
1 CCACCGCAGTACTGCACTCCTCCTAGCTCGTAT
*
12479055 CCACCGCAGTACTGCACTCCTCCTGGCTC
1 CCACCGCAGTACTGCACTCCTCCTAGCTC
12479084 AAGTTCATCG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.19, C:0.43, G:0.15, T:0.23
Consensus pattern (33 bp):
CCACCGCAGTACTGCACTCCTCCTAGCTCGTAT
Found at i:12479410 original size:14 final size:14
Alignment explanation
Indices: 12479391--12479419 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12479381 TGGAACAAAC
12479391 TTTGTAATATAAAT
1 TTTGTAATATAAAT
12479405 TTTGTAATATAAAT
1 TTTGTAATATAAAT
12479419 T
1 T
12479420 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:12479459 original size:62 final size:62
Alignment explanation
Indices: 12479362--12479591 Score: 424
Period size: 62 Copynumber: 3.7 Consensus size: 62
12479352 CAACATTACA
12479362 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * *
12479424 ACATTACAATATTAAAACTTGGAACTAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
*
12479486 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
12479548 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
12479592 AGGTACATTG
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 160 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
Found at i:12479534 original size:14 final size:14
Alignment explanation
Indices: 12479515--12479543 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12479505 TGGAACAAAC
12479515 TTTGTAATATAAAT
1 TTTGTAATATAAAT
12479529 TTTGTAATATAAAT
1 TTTGTAATATAAAT
12479543 T
1 T
12479544 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:12483086 original size:218 final size:210
Alignment explanation
Indices: 12482609--12483245 Score: 940
Period size: 218 Copynumber: 3.0 Consensus size: 210
12482599 CAATATATAA
12482609 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* * *
12482674 TTTCTTATC-ATAACCTATTCTATTTGAGAATAACAA-AAAA-AATAATACCTTTTATTTCTTTC
66 TTTCTTA-CAATAATCTATTCTATTTGAAAATAACAATAAAATAATAATACCTTTTCTTTCTTTC
* * *
12482736 TTCTCTTCTCCCTCTCTTATTCTGCTATTTTTTTAACTGATATTTTAAAATTGAGCTGGATGGGG
130 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGATGGGG
*
12482801 GAGTGGCCGAGGGGGG
195 GAGCGGCCGAGGGGGG
* *
12482817 AATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAATTATATAATACTAACAAAATAAATT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* *
12482882 TTTCTTACAATAATATATTCTATTTGAAAATAATAATAAAGATAATAATACCTTCTCTTTCTTTC
66 TTTCTTACAATAATCTATTCTATTTGAAAATAACAATAAA-ATAATAATA-C--CT-TTTCTTTC
* *
12482947 TTCTCTTCTCTTCTCCCTCTCTTGTTCTACTATTTTTTTAATTGATACTTTAAAATTGAGCCGGA
126 TT-TCTTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGA
*
12483012 TGGGGGAGCGGCCGGGGGGGGGG
190 TGGGGGAGCGGCC--GAGGGGGG
*
12483035 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAAAT
1 AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
* ** * *
12483100 TTTCTTATAGCAATCTATTCTATTTGAAAATAACAATATAAATAATAATACATATTCTTTCTTTC
66 TTTCTTACAATAATCTATTCTATTTGAAAATAACAATA-AAATAATAATACCTTTTCTTTCTTTC
* *
12483165 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTAAAACTGATACTTTAAAATTGAGCCGGAAGGG
130 TTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTT-TAACTGATACTTTAAAATTGAGCCGGATGGG
*
12483230 GGAGCGG-GGAGGGGGG
194 GGAGCGGCCGAGGGGGG
12483246 CGAGGGGAAT
Statistics
Matches: 386, Mismatches: 30, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
207 1 0.00
208 93 0.24
209 3 0.01
210 1 0.00
211 14 0.04
212 1 0.00
213 34 0.09
214 46 0.12
215 10 0.03
216 69 0.18
217 1 0.00
218 111 0.29
219 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (210 bp):
AATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACTAACAAAATAAATT
TTTCTTACAATAATCTATTCTATTTGAAAATAACAATAAAATAATAATACCTTTTCTTTCTTTCT
TCTCTTCTCCCTCTCTTGTTCTGCTATTTTTTTAACTGATACTTTAAAATTGAGCCGGATGGGGG
AGCGGCCGAGGGGGG
Found at i:12487146 original size:30 final size:30
Alignment explanation
Indices: 12487112--12487172 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
12487102 GAATTTTAAG
12487112 TATTGGAGTACTTTATGGCATTTATTTAGT
1 TATTGGAGTACTTTATGGCATTTATTTAGT
12487142 TATTGGAGTACTTTATGGCATTTATTTAGT
1 TATTGGAGTACTTTATGGCATTTATTTAGT
12487172 T
1 T
12487173 TATGTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.51
Consensus pattern (30 bp):
TATTGGAGTACTTTATGGCATTTATTTAGT
Found at i:12495826 original size:60 final size:60
Alignment explanation
Indices: 12495718--12495841 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
12495708 CTGGAATATT
* *
12495718 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCTGAATTATAATTAGTGACTTTTAAGTC
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
* * *
12495778 TTCTTCCTGATCTGTTGAAGTTTTTTCTTCATCAG-ATTGATAACTAGTGACTTTTAAGTT
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATT-ATAACTAGTGACTTTTAAGTC
12495838 TTCT
1 TTCT
12495842 GTATTTTAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 3 0.05
60 55 0.95
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (60 bp):
TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
Found at i:12496077 original size:17 final size:18
Alignment explanation
Indices: 12496048--12496096 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
12496038 GGAAATATTT
**
12496048 TTTTTCATATTTTTTTTCG
1 TTTTT-ATATTTTTTTTAA
12496067 TTTTT-TATTTTTTTTAA
1 TTTTTATATTTTTTTTAA
12496084 TTTTTATATTTTT
1 TTTTTATATTTTT
12496097 CATACTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 15 0.56
18 7 0.26
19 5 0.19
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTATATTTTTTTTAA
Found at i:12498256 original size:76 final size:75
Alignment explanation
Indices: 12498174--12498373 Score: 183
Period size: 78 Copynumber: 2.6 Consensus size: 75
12498164 GAAATTAGGG
* *
12498174 ATGTATATATTAGATTCGAATATATATGAGTATACAAGTATAAGTTCATGTTTTG-ATTATGAGT
1 ATGTATATATTAGATTCGAATATATATGAGTATACATGTATAAGTTCATGTATTGAATTA-GA-T
12498238 ATGTAA-TTATAT
64 ATG-AATTTATAT
* * * * * *
12498250 ATGTATATGA-TAAACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAG
1 ATGTATAT-ATTAGATTCG-A-ATATATATGAGTATACATGTATAAGTTCATGTATTG-AATTAG
12498314 ATATGAATTTATAT
62 ATATGAATTTATAT
* * * * *
12498328 ATGTATATGTGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATATTAGATTCGAATATATATGAG-TATACATGTATAAGTT
12498374 TTATATTGAA
Statistics
Matches: 98, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
76 35 0.36
77 5 0.05
78 52 0.53
79 2 0.02
80 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (75 bp):
ATGTATATATTAGATTCGAATATATATGAGTATACATGTATAAGTTCATGTATTGAATTAGATAT
GAATTTATAT
Found at i:12498326 original size:78 final size:78
Alignment explanation
Indices: 12498193--12498336 Score: 186
Period size: 78 Copynumber: 1.8 Consensus size: 78
12498183 TTAGATTCGA
* * * *
12498193 ATATATATGAGTATACAAGTATAAGTTCATGTTTTGATTATGAGTATGTAATTATATATGTATAT
1 ATATATATAAATATACAAGTATAAATTCATGTATTGATTATGAGTATGTAATTATATATGTATAT
12498258 GATAAACTCGAAT
66 GATAAACTCGAAT
* *
12498271 ATATATATAAATATACATGTATAAATTCTTGTATTGAAATTA-GA-TATG-AATTTATATATGTA
1 ATATATATAAATATACAAGTATAAATTCATGTATTG--ATTATGAGTATGTAA-TTATATATGTA
12498333 TATG
63 TATG
12498337 TGAGGTTCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
77 2 0.04
78 49 0.86
79 2 0.04
80 4 0.07
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (78 bp):
ATATATATAAATATACAAGTATAAATTCATGTATTGATTATGAGTATGTAATTATATATGTATAT
GATAAACTCGAAT
Found at i:12498813 original size:41 final size:41
Alignment explanation
Indices: 12498767--12498987 Score: 302
Period size: 41 Copynumber: 5.4 Consensus size: 41
12498757 CAGGCTTAGC
* *
12498767 GCCTAGCAGGCTAAGTGTCGGTAATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGTTATAA
*
12498808 GCCTAGCAGGCTAAGTGCCGGTGAA-CTGAATTAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGT-AATCTGAATCAGGTTATAA
* * * *
12498849 GCCTAGCAGGATAAGTGCCGGTGATCTGAATCAAGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGTTATAA
*
12498890 GCCTAGCAGGCTAAGTGCCGGTGAA-CTGAGTCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGT-AATCTGAATCAGGTTATAA
* * *
12498931 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATCA
1 GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGTTATAA
*
12498972 GCCTAGCAAGCTAAGT
1 GCCTAGCAGGCTAAGT
12498988 ACAGGTGAAT
Statistics
Matches: 158, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
40 2 0.01
41 153 0.97
42 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGTTATAA
Found at i:12498904 original size:82 final size:82
Alignment explanation
Indices: 12498767--12498996 Score: 352
Period size: 82 Copynumber: 2.8 Consensus size: 82
12498757 CAGGCTTAGC
* *
12498767 GCCTAGCAGGCTAAGTGTCGGTAATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
*
12498832 ACTGAATTAGGTTATAA
66 ACTGAATCAGGTTATAA
* *
12498849 GCCTAGCAGGATAAGTGCCGGTGATCTGAATCAAGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
*
12498914 ACTGAGTCAGGTTATAA
66 ACTGAATCAGGTTATAA
* * * * * *
12498931 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATCAGCCTAGCAAGCTAAGTACAGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
12498996 A
66 A
12498997 TTTGTTTAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 134 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (82 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
ACTGAATCAGGTTATAA
Found at i:12498995 original size:123 final size:123
Alignment explanation
Indices: 12498767--12498995 Score: 343
Period size: 123 Copynumber: 1.9 Consensus size: 123
12498757 CAGGCTTAGC
* *
12498767 GCCTAGCAGGCTAAGTGTCGGTAATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
* * * *
12498832 ACTGAATTAGGTTATAAGCCTAGCAGGATAAGTGCCGGTGATCTGAATCAAGCTATAA
66 ACTGAATCAGGTTATAAGCCTAGCAAGATAAGTACAGGTGATCTGAATCAAGCTATAA
* *
12498890 GCCTAGCAGGCTAAGTGCCGGTGAA-CTGAGTCAGGTTATAAGCCTAGCAGGCTAAGTGCCAGTG
1 GCCTAGCAGGCTAAGTGCCGGT-AATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTG
* * *
12498954 ATCTGAATCAGGTTATCAGCCTAGCAAGCTAAGTACAGGTGA
65 AACTGAATCAGGTTATAAGCCTAGCAAGATAAGTACAGGTGA
12498996 ATTTGTTTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
123 92 0.98
124 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (123 bp):
GCCTAGCAGGCTAAGTGCCGGTAATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
ACTGAATCAGGTTATAAGCCTAGCAAGATAAGTACAGGTGATCTGAATCAAGCTATAA
Found at i:12506297 original size:76 final size:76
Alignment explanation
Indices: 12506202--12506401 Score: 194
Period size: 78 Copynumber: 2.6 Consensus size: 76
12506192 GAAATTAGGG
* * *
12506202 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
12506265 TATGTAA-TTATAT
64 TATG-AATTTATAT
* * * * * * *
12506278 ATGTATATGATAGACTCGAATATATATATAAATATACATGTATAAATTCTTGTATTGAAATTAGA
1 ATGTATATGATAGATTCG-A-ATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGA
12506343 TATGAATTTATAT
64 TATGAATTTATAT
* *
12506356 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
12506402 TTATATTGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
76 36 0.36
77 10 0.10
78 54 0.54
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:12506842 original size:41 final size:41
Alignment explanation
Indices: 12506796--12507019 Score: 274
Period size: 41 Copynumber: 5.5 Consensus size: 41
12506786 CAGGCTTAGC
*
12506796 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
*
12506837 GCCTAGCAGGCTAAGTGCCGGTGAAT-TGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGATG-ATCTGAATCAGGTTATAA
* *
12506878 GCCTAGCAGGCTAAGTGCC-AGTGATTTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGTTATAA
** * * * **
12506919 TTCTAGCATGCTAAGTGTC-AGTGAACTGAATCATATTATAA
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGTTATAA
* * *
12506960 GCCTAGCAAGCTATGTGCCGATGATCTAAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
12507001 GCCTAGCAGGCTAAGTGCC
1 GCCTAGCAGGCTAAGTGCC
12507020 AGTGAATTTG
Statistics
Matches: 155, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.01
41 150 0.97
42 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAA
Found at i:12506925 original size:82 final size:82
Alignment explanation
Indices: 12506796--12507027 Score: 331
Period size: 82 Copynumber: 2.8 Consensus size: 82
12506786 CAGGCTTAGC
*
12506796 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
*
12506861 ATTGAATCAGGTTATAA
66 ATTGAATCAGATTATAA
* ** * *
12506878 GCCTAGCAGGCTAAGTGCC-AGTGATTTGAATCAGGCTATAATTCTAGCATGCTAAGTGTCAGTG
1 GCCTAGCAGGCTAAGTGCCGA-TGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTG
* *
12506942 AACTGAATCATATTATAA
65 AATTGAATCAGATTATAA
* * * *
12506960 GCCTAGCAAGCTATGTGCCGATGATCTAAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCAGTGA
1 GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
12507025 ATT
66 ATT
12507028 TGTTTAAATT
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 127 0.98
83 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (82 bp):
GCCTAGCAGGCTAAGTGCCGATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCAGTGA
ATTGAATCAGATTATAA
Found at i:12513529 original size:27 final size:27
Alignment explanation
Indices: 12513499--12513552 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12513489 TTTATTTCTT
* * *
12513499 AGATTTTCTTAACGTTAGAATCAAATA
1 AGATTTTATTAACATAAGAATCAAATA
12513526 AGATTTTATTAACATAAGAATCAAATA
1 AGATTTTATTAACATAAGAATCAAATA
12513553 TTTACCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (27 bp):
AGATTTTATTAACATAAGAATCAAATA
Found at i:12535964 original size:21 final size:21
Alignment explanation
Indices: 12535940--12535983 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12535930 TATTGATAAT
*
12535940 CAATACACAATCTCAAGATAC
1 CAATACACAATCGCAAGATAC
12535961 CAATACACAATCGCAAGATAC
1 CAATACACAATCGCAAGATAC
12535982 CA
1 CA
12535984 TCTTTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.16
Consensus pattern (21 bp):
CAATACACAATCGCAAGATAC
Found at i:12542295 original size:20 final size:20
Alignment explanation
Indices: 12542272--12542310 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12542262 ATTTTGACAA
*
12542272 GTTAAAATAATTTTTACTTT
1 GTTAAAATAATTTTAACTTT
*
12542292 GTTAAAATCATTTTAACTT
1 GTTAAAATAATTTTAACTT
12542311 GATTTTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (20 bp):
GTTAAAATAATTTTAACTTT
Found at i:12558853 original size:17 final size:15
Alignment explanation
Indices: 12558826--12558864 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12558816 ATATAAGAAC
*
12558826 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
12558842 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
12558858 ATTTTAA
1 ATTTTAA
12558865 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Done.