Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 167 of 199
Found at i:54263066 original size:142 final size:142
Alignment explanation
Indices: 54262810--54263308 Score: 863
Period size: 142 Copynumber: 3.5 Consensus size: 142
54262800 CCATCGGTTG
54262810 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * * *
54262875 ATTGAAGCCAAAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAAATTCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
54262940 TCCCTGAGATTA
131 TCCCTGAGATTA
*
54262952 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
54263017 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
54263082 TCCCTGAGATTA
131 TCCCTGAGATTA
* * *
54263094 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATTAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
54263159 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
*
54263224 TCCATGAGATTA
131 TCCCTGAGATTA
* * **
54263236 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTTTGAAGTTACAGCGGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
54263301 AATGAAGC
66 ATTGAAGC
54263309 TACAACAGCA
Statistics
Matches: 340, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 340 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (142 bp):
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
TCCCTGAGATTA
Found at i:54263268 original size:44 final size:44
Alignment explanation
Indices: 54263171--54263269 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
54263161 TGAAGCCAGA
* * * *
54263171 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAACAAGT
* *
54263215 AATCCTATCTCCATGAGATTACAGTGGAGCGGATTAAAACAAAG-
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAAC-AAGT
*
54263259 GATCTTATCTC
1 AATCTTATCTC
54263270 TTTGAAGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAACAAGT
Found at i:54263699 original size:28 final size:27
Alignment explanation
Indices: 54263660--54263730 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 27
54263650 TTACAATAGG
54263660 CCTAATAGCCCAAATCCACTACCCAAA
1 CCTAATAGCCCAAATCCACTACCCAAA
**
54263687 CCTAATTAGCCCAAATCCACTACTTAAA
1 CCTAA-TAGCCCAAATCCACTACCCAAA
*
54263715 CCCAACTAGCCCAAAT
1 CCTAA-TAGCCCAAAT
54263731 GCCCATGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.39, C:0.38, G:0.04, T:0.18
Consensus pattern (27 bp):
CCTAATAGCCCAAATCCACTACCCAAA
Found at i:54265064 original size:19 final size:20
Alignment explanation
Indices: 54265025--54265067 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
54265015 TAATAATAAT
* *
54265025 ATATTTTTTAATTGTTATCA
1 ATATGTTTTAAATGTTATCA
54265045 ATATGTTTTAAATG-TATCA
1 ATATGTTTTAAATGTTATCA
54265064 ATAT
1 ATAT
54265068 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (20 bp):
ATATGTTTTAAATGTTATCA
Found at i:54265073 original size:19 final size:19
Alignment explanation
Indices: 54265029--54265075 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
54265019 AATAATATAT
*
54265029 TTTTTAATTGTTATCAATA
1 TTTTTAAATGTTATCAATA
54265048 TGTTTTAAATG-TATCAATA
1 T-TTTTAAATGTTATCAATA
54265067 TTATTTAAA
1 TT-TTTAAA
54265076 AATACATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTTAAATGTTATCAATA
Found at i:54265169 original size:16 final size:16
Alignment explanation
Indices: 54265148--54265185 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
54265138 CAAATTAACC
54265148 TTTTATTCACATAATT-
1 TTTTATT-ACATAATTG
54265164 TTTTA-TACATAATTG
1 TTTTATTACATAATTG
54265179 TTTTATT
1 TTTTATT
54265186 TCTTAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 6 0.30
16 6 0.30
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTATTACATAATTG
Found at i:54266842 original size:9 final size:9
Alignment explanation
Indices: 54266824--54266857 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
54266814 ATATAAGCCA
54266824 TTTAAAATT
1 TTTAAAATT
*
54266833 TTTAAGATT
1 TTTAAAATT
54266842 TTTAAAA-T
1 TTTAAAATT
54266850 TTTAAAAT
1 TTTAAAAT
54266858 GATAAAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:54270807 original size:8 final size:9
Alignment explanation
Indices: 54270794--54270833 Score: 52
Period size: 8 Copynumber: 4.9 Consensus size: 9
54270784 ATTATTTATT
54270794 ACAAATTTA
1 ACAAATTTA
54270803 A-AAA-TTA
1 ACAAATTTA
54270810 ACAAATTTA
1 ACAAATTTA
54270819 A-AAA-TTA
1 ACAAATTTA
54270826 ACAAATTT
1 ACAAATTT
54270834 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
7 8 0.30
8 12 0.44
9 7 0.26
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (9 bp):
ACAAATTTA
Found at i:54270815 original size:16 final size:16
Alignment explanation
Indices: 54270794--54270833 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
54270784 ATTATTTATT
54270794 ACAAATTTAAAAATTA
1 ACAAATTTAAAAATTA
54270810 ACAAATTTAAAAATTA
1 ACAAATTTAAAAATTA
54270826 ACAAATTT
1 ACAAATTT
54270834 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
ACAAATTTAAAAATTA
Found at i:54271468 original size:27 final size:26
Alignment explanation
Indices: 54271437--54271497 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
54271427 TAAAAATTTA
54271437 AAATTTATATT-GAATTACTTTATACTT
1 AAATTTATATTAGAA--ACTTTATACTT
*
54271464 AAA-TTATTATTAGAAATTTTATACTT
1 AAATTTA-TATTAGAAACTTTATACTT
54271490 AAATTTAT
1 AAATTTAT
54271498 GAGAACCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 17 0.57
27 10 0.33
28 3 0.10
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (26 bp):
AAATTTATATTAGAAACTTTATACTT
Found at i:54271502 original size:24 final size:26
Alignment explanation
Indices: 54271455--54271502 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54271445 ATTGAATTAC
*
54271455 TTTATACTTAAATTATTATTAGAAAT
1 TTTATACTTAAATTATTATGAGAAAT
54271481 TTTATACTTAAA-T-TTATGAGAA
1 TTTATACTTAAATTATTATGAGAA
54271503 CCACAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 12 0.57
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTATACTTAAATTATTATGAGAAAT
Found at i:54272046 original size:15 final size:17
Alignment explanation
Indices: 54272018--54272067 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
54272008 AATTTATAAT
* *
54272018 TGACGAATAAATTTATA
1 TGACTAATATATTTATA
54272035 -GA-TAATATATTTATA
1 TGACTAATATATTTATA
54272050 TGATCTAATATA-TTATA
1 TGA-CTAATATATTTATA
54272067 T
1 T
54272068 TTATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 6 0.21
18 7 0.25
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (17 bp):
TGACTAATATATTTATA
Found at i:54272230 original size:13 final size:13
Alignment explanation
Indices: 54272186--54272241 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
54272176 AAAATTAGTG
*
54272186 ATATATTTTAATT
1 ATATTTTTTAATT
* *
54272199 ATATTTATTATTT
1 ATATTTTTTAATT
*
54272212 AT-TTTTTTAATA
1 ATATTTTTTAATT
54272224 ATATTTTTTTAATT
1 ATA-TTTTTTAATT
54272238 ATAT
1 ATAT
54272242 GAAGTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 9 0.26
13 13 0.38
14 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTTTAATT
Found at i:54272230 original size:14 final size:14
Alignment explanation
Indices: 54272211--54272241 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54272201 ATTTATTATT
54272211 TATTTTTTTAATAA
1 TATTTTTTTAATAA
*
54272225 TATTTTTTTAATTA
1 TATTTTTTTAATAA
54272239 TAT
1 TAT
54272242 GAAGTAAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTTAATAA
Found at i:54273884 original size:596 final size:597
Alignment explanation
Indices: 54272716--54275259 Score: 4664
Period size: 597 Copynumber: 4.3 Consensus size: 597
54272706 CATGCCAAAT
* * *
54272716 GGAATGCTACCAAATAACTCATTGCTATGCAAGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACA
1 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
* * *
54272781 CATATCATTAGG-AAATTACCTGATAGGCTATTTTTGGAGAGATCAATGGTCTTCAGAGAAGAAA
66 CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
* *
54272845 TGTTGAAGATCAAAGTTGGAATCTGACCTGTAAGGCCTTTAATTGCTTGAATATTAAGCAATTCC
131 TGTTGAAGATCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
*
54272910 AAACCATGAAGATTACCAATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
196 AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
*
54272975 TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATGGTAATTTGGA
261 TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
54273040 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
326 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
54273105 TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAAA
391 TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAAA
54273170 TTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATAC
456 TTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATAC
54273235 TTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTTG
521 TTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTTG
54273300 CCCATACTTGAC
586 CCCATACTTGAC
* * *
54273312 GAAATGTTACCAGATAACTCATTGCTCTGCAAGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACA
1 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
* * * *
54273377 CATATCATTAGGTAAACTACCTGGTAGGCTATTGCTGGAGAGATCAATGGTCTTC-GAAGAAGAA
66 CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAG-AGAAGAA
* * *
54273441 ATGTTGGAGACCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTCAATATTAAGCAATTC
130 ATGTTGAAGATCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTC
* *
54273506 CAAACCAAGAAGATTACCGATTTCCTCAGGAATTTGGCCTGCACACATAGTCGAAAAATCAAGGT
195 CAAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGT
*
54273571 GTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAAGTTGG
260 GTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGG
*
54273636 AGATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTTCTT
325 AGATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTT
54273701 TTGTTATCTATTACAAATCAAACTCTTTTAT-AAAAAAATACTTAAAATTCAAGAAATCAAGGAA
390 TTGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAA
54273765 ATTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATA
455 ATTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATA
*
54273830 CTTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTTTTAAGGTTGCTGCACTT
520 CTTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTT
54273895 GCCCATACTTGAC
585 GCCCATACTTGAC
54273908 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
1 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
*
54273973 CATATCATTAGGCAAACTACCTAATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
66 CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
*
54274038 TGTTGAAGATCGAATTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
131 TGTTGAAGATCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
54274103 AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
196 AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
*
54274168 TCAAACTACCTATTTTGTTAGCAGAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
261 TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
54274233 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
326 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
54274298 TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAAA
391 TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAAA
54274363 TTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATAC
456 TTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATAC
54274428 TTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTTG
521 TTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTTG
54274493 CCCATACTTGAC
586 CCCATACTTGAC
54274505 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
1 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
*
54274570 CATATCATTAGGCAAACTACCTAATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
66 CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
*
54274635 TGTTGAAGATCGAATTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
131 TGTTGAAGATCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
54274700 AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
196 AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
54274765 TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
261 TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
54274830 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
326 GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
*
54274895 TGTTATCTATTACAAATCAAACTCTTTTAT-AAAAAAATACATAAAATTCAAGAAATCAAAGGAA
391 TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATC-AAGGAA
54274959 ATTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATA
455 ATTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATA
* *
54275024 CTTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTTTTAAGGTTGCTGCATTT
520 CTTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTT
54275089 GCCCATACTTGAC
585 GCCCATACTTGAC
54275102 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
1 GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
* * ** * *
54275167 CATATCATTAGGCAAACTACCTGATAGGCTATTGCTGGAGAGAATAATAATCTTTAGAGAAGATA
66 CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
* * *
54275232 TGTTGAAGATGGAAGATGGAACCTGACC
131 TGTTGAAGATCGAAGTTGGAATCTGACC
54275260 AGATAATTGA
Statistics
Matches: 1890, Mismatches: 53, Indels: 9
0.97 0.03 0.00
Matches are distributed among these distances:
596 676 0.36
597 1214 0.64
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (597 bp):
GGAATGTTACCAGATAACTCATTGCTATGCAAGTAAAGCACTTCAAGCTTGGGAAGATGTTGACA
CATATCATTAGGCAAACTACCTGATAGGCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAA
TGTTGAAGATCGAAGTTGGAATCTGACCTGTAACGCCTTTAATTGCTTGAATATTAAGCAATTCC
AAACCATGAAGATTACCGATTTCCTCAGGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTG
TCAAACTACCTATTTTGTTAGCATAAGTCAAAGAGGTTTTCTTTTCTGTTCTATAGTAATTTGGA
GATGTTAGATTTTCATATATTTCAGCATATGTTTTTCATCAAATGAAATAAAAACTTTTTCCTTT
TGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATACTTAAAATTCAAGAAATCAAGGAAA
TTGATTACCTTCTAGATTATTAAATCCCAAATATAATTCTCTGAGTTGTGTCAGATTTCCAATAC
TTCTTGGAATGATCCCCGTCAATTGATTCAAGGACAAGGACAAATTATTAAGGTTGCTGCACTTG
CCCATACTTGAC
Found at i:54280006 original size:20 final size:20
Alignment explanation
Indices: 54279981--54280043 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
54279971 TCTAAAAAAA
54279981 AAATTAGAAGAATTAGAATT
1 AAATTAGAAGAATTAGAATT
* **
54280001 AAATT---ATAATCTA-AAAA
1 AAATTAGAAGAAT-TAGAATT
54280018 AAATTAGAAGAATTAGAATT
1 AAATTAGAAGAATTAGAATT
54280038 AAATTA
1 AAATTA
54280044 TAAAACTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.30
Consensus pattern (20 bp):
AAATTAGAAGAATTAGAATT
Found at i:54280017 original size:37 final size:37
Alignment explanation
Indices: 54279976--54280046 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
54279966 GTGAATCTAA
54279976 AAAAAAAATTAGAAGAATTAGAATTAAATTATAATCT
1 AAAAAAAATTAGAAGAATTAGAATTAAATTATAATCT
54280013 AAAAAAAATTAGAAGAATTAGAATTAAATTATAA
1 AAAAAAAATTAGAAGAATTAGAATTAAATTATAA
54280047 AACTTTGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.28
Consensus pattern (37 bp):
AAAAAAAATTAGAAGAATTAGAATTAAATTATAATCT
Found at i:54281617 original size:68 final size:68
Alignment explanation
Indices: 54281508--54281643 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
54281498 TTTCAATCAC
* * * *
54281508 AATCTATTGTATTCAAGAGTACCACATCTTTTTGGATGAAACAAACCTCTCAATCTTAAGATAAA
1 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
54281573 CGG
66 CGG
*
54281576 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAAGCACTCAATATTAAGATAAA
1 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
54281641 CGG
66 CGG
54281644 GTCTTTAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (68 bp):
AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
CGG
Found at i:54282101 original size:17 final size:18
Alignment explanation
Indices: 54282074--54282107 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54282064 GAAATTGGGA
*
54282074 GAAATTTTTAAATTTTAT
1 GAAATTTTTAAAATTTAT
54282092 GAAA-TTTTAAAATTTA
1 GAAATTTTTAAAATTTA
54282108 ACTGTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
GAAATTTTTAAAATTTAT
Found at i:54282676 original size:26 final size:26
Alignment explanation
Indices: 54282646--54282698 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
54282636 TTGGACAAGT
54282646 AGAATTTTCTAACCTATTTTCCATCA
1 AGAATTTTCTAACCTATTTTCCATCA
54282672 AGAATTTTCTAACCTATTTTCCATCA
1 AGAATTTTCTAACCTATTTTCCATCA
54282698 A
1 A
54282699 CTTCACTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAATTTTCTAACCTATTTTCCATCA
Found at i:54284524 original size:23 final size:24
Alignment explanation
Indices: 54284496--54284548 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
54284486 AAAAAAATCA
*
54284496 AAATATGTAATATACA-AAATAAT
1 AAATATGTAATATAAATAAATAAT
* *
54284519 ATATAT-TAATCTAAATAAATAAT
1 AAATATGTAATATAAATAAATAAT
54284542 AAATATG
1 AAATATG
54284549 GAATGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATATGTAATATAAATAAATAAT
Found at i:54284994 original size:24 final size:23
Alignment explanation
Indices: 54284962--54285130 Score: 137
Period size: 24 Copynumber: 7.3 Consensus size: 23
54284952 AAAAAAAAAG
* * *
54284962 TAATTATACATGAAAAACTTAGAA
1 TAATAATACATGATAAATTTA-AA
* * *
54284986 TAATAATACATAAAAAACTTAAAA
1 TAATAATACATGATAAA-TTTAAA
*
54285010 TAATAATACATGATGAATTTAAA
1 TAATAATACATGATAAATTTAAA
*
54285033 TAACAAATACATGATAAATTTAAA
1 TAA-TAATACATGATAAATTTAAA
**
54285057 TAATGTTA-ATGATAAATTTAAAA
1 TAATAATACATGATAAATTT-AAA
* * * *
54285080 TAATAATATATTACAAATTGAAA
1 TAATAATACATGATAAATTTAAA
**
54285103 TAAT-ATTGATGATAAATTTAAA
1 TAATAATACATGATAAATTTAAA
54285125 -AATAAT
1 TAATAAT
54285131 GTTAAGCTTA
Statistics
Matches: 117, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.03
22 26 0.22
23 26 0.22
24 60 0.51
25 2 0.02
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (23 bp):
TAATAATACATGATAAATTTAAA
Found at i:54285077 original size:46 final size:45
Alignment explanation
Indices: 54284984--54285124 Score: 129
Period size: 46 Copynumber: 3.0 Consensus size: 45
54284974 AAAAACTTAG
* * * * * *
54284984 AATAATAATACATAAAAAACTTAAAATAATAATACATGATGAATTTA
1 AATAAAAATACATGACAAA-TTGAAATAATATTA-ATGATAAATTTA
* * *
54285031 AATAACAAATACATGATAAATTTAAATAATGTTAATGATAAATTTAA
1 AATAA-AAATACATGACAAATTGAAATAATATTAATGATAAATTT-A
* * * *
54285078 AATAATAATATATTACAAATTGAAATAATATTGATGATAAATTTA
1 AATAAAAATACATGACAAATTGAAATAATATTAATGATAAATTTA
54285123 AA
1 AA
54285125 AATAATGTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
45 3 0.04
46 42 0.54
47 22 0.28
48 11 0.14
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (45 bp):
AATAAAAATACATGACAAATTGAAATAATATTAATGATAAATTTA
Found at i:54285104 original size:70 final size:69
Alignment explanation
Indices: 54285004--54285135 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 69
54284994 CATAAAAAAC
** *
54285004 TTAAAATAATAATACATGATGAATTTAAATAACAAATACATGATAAATTT-AAATAATGTTAATG
1 TTAAAATAATAATACATGACAAATTGAAAT-A-AAATACATGATAAATTTAAAATAATGTTAATG
54285068 ATAAAT
64 ATAAAT
* * * **
54285074 TTAAAATAATAATATATTACAAATTGAAATAATATTGATGATAAATTTAAAAATAATGTTAA
1 TTAAAATAATAATACATGACAAATTGAAATAAAATACATGATAAATTT-AAAATAATGTTAA
54285136 GCTTAAACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
68 14 0.27
69 1 0.02
70 37 0.71
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (69 bp):
TTAAAATAATAATACATGACAAATTGAAATAAAATACATGATAAATTTAAAATAATGTTAATGAT
AAAT
Found at i:54285172 original size:24 final size:24
Alignment explanation
Indices: 54285070--54285180 Score: 63
Period size: 24 Copynumber: 4.7 Consensus size: 24
54285060 TGTTAATGAT
* * *
54285070 AAATTTAAAATAATAATATA-TTA
1 AAATTAAAAATAATATTAGATTTA
* *
54285093 CAAATT-GAAATAATATT-GATGATA
1 -AAATTAAAAATAATATTAGAT-TTA
* * *
54285117 AATTTAAAAATAATGTTA-AGCTTA
1 AAATTAAAAATAATATTAGA-TTTA
54285141 AACA-TAAAAATAATATTAGATTTA
1 AA-ATTAAAAATAATATTAGATTTA
*
54285165 AAATTAAATAT-ATATT
1 AAATTAAAAATAATATT
54285181 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
22 1 0.02
23 19 0.29
24 45 0.68
25 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (24 bp):
AAATTAAAAATAATATTAGATTTA
Found at i:54288894 original size:15 final size:15
Alignment explanation
Indices: 54288871--54288901 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54288861 CTAATATTTA
*
54288871 AAACTTATTAAAAAT
1 AAACATATTAAAAAT
54288886 AAACATATTAAAAAT
1 AAACATATTAAAAAT
54288901 A
1 A
54288902 CTAAGCTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACATATTAAAAAT
Found at i:54289105 original size:8 final size:8
Alignment explanation
Indices: 54289094--54289118 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54289084 GCCACCTACC
54289094 CCCACTTG
1 CCCACTTG
54289102 CCCACTTG
1 CCCACTTG
54289110 CCCACTTG
1 CCCACTTG
54289118 C
1 C
54289119 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:54289637 original size:13 final size:12
Alignment explanation
Indices: 54289601--54289638 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
54289591 CCTTTCCCCC
54289601 TCCCTTCTCTC-
1 TCCCTTCTCTCT
54289612 TCCCTTCTCTCT
1 TCCCTTCTCTCT
54289624 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
54289637 TC
1 TC
54289639 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:54290126 original size:3 final size:3
Alignment explanation
Indices: 54290103--54290172 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
54290093 AATATCATTG
* * *
54290103 TTA TT- TTA -TA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
54290149 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
54290173 GTACGCGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:54290169 original size:23 final size:22
Alignment explanation
Indices: 54290114--54290175 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
54290104 TATTTTATAT
*
54290114 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
54290135 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
54290157 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
54290176 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:54290182 original size:23 final size:23
Alignment explanation
Indices: 54290138--54290183 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54290128 GTATTACTAT
**
54290138 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
54290161 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
54290184 CATGTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:54301979 original size:46 final size:46
Alignment explanation
Indices: 54301783--54302306 Score: 245
Period size: 44 Copynumber: 11.5 Consensus size: 46
54301773 ATACAGGTCT
* *
54301783 TTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATC
* ** **
54301829 TTATCTCCCTGAGATTACAGTGGAGCGGA-TTAA-AA-TAAAGGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCA-GATC
* ** * * *
54301873 TTATCTCTCTGA-AGTTACAGCAGAGTAGATC---G-A--TCAAGGTC
1 TTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATTTC-AGATC
* * *
54301914 TTATCACCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATC
* ** * *
54301960 TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA---GAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAG-AATTTCAGATC
* * * ** * *
54302004 TTATCTCTCTGAGATTACAGCGGAGTAGATTGAAG-CTAGT-A-ATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAAT-TTCAGATC
* * * ** **
54302048 CTATCTCTCTGA-AGTTACAGTGGAGCGGA-TTAA-AA-TAAAGGATC
1 TTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATTTCA-GATC
* * * *
54302092 TTATCTCTCTGA-AGTTACAGTAGAGTAGATCAC-ATCAG-ATTGAAGCCAGAGATC
1 TTATCTCCCTGAGA-TTACAGTGGAGCAGA-C-CGA--AGAATT----TC--AGATC
* *
54302146 TTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATC
* *
54302192 TTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATC
* * ** *
54302238 TTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG-ATAGT-A-ATC
1 TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAAT-TTCAGATC
* *
54302282 CTATCTGCCTGAGATTACAGTGGAG
1 TTATCTCCCTGAGATTACAGTGGAG
54302307 TGGATTAAAA
Statistics
Matches: 375, Mismatches: 64, Indels: 80
0.72 0.12 0.15
Matches are distributed among these distances:
41 27 0.07
42 3 0.01
43 7 0.02
44 144 0.38
45 7 0.02
46 144 0.38
47 3 0.01
48 3 0.01
49 1 0.00
51 1 0.00
52 4 0.01
53 2 0.01
54 27 0.07
55 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (46 bp):
TTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTTCAGATC
Found at i:54302022 original size:131 final size:132
Alignment explanation
Indices: 54301777--54302033 Score: 367
Period size: 131 Copynumber: 2.0 Consensus size: 132
54301767 TTTATTATAC
*
54301777 AGGTCTTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
1 AGGTCTTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
* *
54301842 ATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGAT
66 ATTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGAT
54301907 CA
131 CA
* ** *
54301909 AGGTC-TTATCACCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 AGGTCTTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
* * * * *
54301973 GTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCTCTG-AGATTACAGCGGAGTAGAT
66 ATTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCTCTGAAG-TTACAGCAGAGTAGAT
54302034 TGAAGCTAGT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
130 4 0.04
131 102 0.92
132 5 0.05
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
AGGTCTTTATCACCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGAT
CA
Found at i:54302319 original size:234 final size:231
Alignment explanation
Indices: 54301912--54302388 Score: 699
Period size: 234 Copynumber: 2.1 Consensus size: 231
54301902 TCGATCAAGG
* * ** * *
54301912 TCTTATCACCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTA
* ** ** * * *
54301977 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAGATTACAGCGGAGTAGATTGAAGCTA
66 CAGTGGAACAGACCGAAGAAACAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATA
54302042 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
131 GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
* ** * *
54302107 TACAGTAGAGTAGATCACATCAGATTGAAGCCAGAGA
196 TACAGTAGAGTAGATCACAGCAGA-CAAAACCACAGA
54302144 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTA
54302209 CAGTGGAACAGACCGAA-AAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG
66 CAGTGGAACAGACCGAAGAAA---CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG
*
54302273 ATAGTAATCCTATCTGC-CTG-AGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCT
128 ATAGTAATCCTATCT-CTCTGAAG-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCT
54302336 GAAGTTACAGTAGAGTAGATCACAGCAGACAAAACCACAGA
191 GAAGTTACAGTAGAGTAGATCACAGCAGACAAAACCACAGA
54302377 TCTTATCTCCCT
1 TCTTATCTCCCT
54302389 AAGCAGTTAG
Statistics
Matches: 220, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
231 1 0.00
232 73 0.33
233 22 0.10
234 123 0.56
235 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (231 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTA
CAGTGGAACAGACCGAAGAAACAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATA
GTAATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
TACAGTAGAGTAGATCACAGCAGACAAAACCACAGA
Found at i:54302331 original size:44 final size:44
Alignment explanation
Indices: 54302142--54302355 Score: 123
Period size: 46 Copynumber: 4.8 Consensus size: 44
54302132 TGAAGCCAGA
* ** ** *
54302142 GATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAA-ATTT
1 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATA-GT
* ** ** *
54302186 CAGATCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAAA-ATTT
1 --GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATA-GT
*
54302232 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGATAGT
1 --GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAGT
* * * * *
54302278 AATCCTATCTGCCTGAGATTACAGTGGAGTGGATT-AAAATAAAG-
1 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAAT--AGT
* **
54302322 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCGGAGTAGAT
54302356 CACAGCAGAC
Statistics
Matches: 145, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
43 5 0.03
44 56 0.39
45 2 0.01
46 81 0.56
47 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAAATAGT
Found at i:54302821 original size:8 final size:8
Alignment explanation
Indices: 54302810--54302836 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54302800 GCCACCTACC
54302810 CCCACTTG
1 CCCACTTG
54302818 CCCACTTG
1 CCCACTTG
54302826 CCCACTTG
1 CCCACTTG
54302834 CCC
1 CCC
54302837 GAACACCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.56, G:0.11, T:0.22
Consensus pattern (8 bp):
CCCACTTG
Found at i:54303810 original size:9 final size:9
Alignment explanation
Indices: 54303787--54303843 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
54303777 AAATATCATT
*
54303787 GTATTTTTA
1 GTATTATTA
54303796 -TATTATTA
1 GTATTATTA
54303804 GTATTATTA
1 GTATTATTA
*
54303813 GTATTACTA
1 GTATTATTA
*
54303822 TTA-TATTA
1 GTATTATTA
*
54303830 TTATGTATTA
1 GTAT-TATTA
54303840 GTAT
1 GTAT
54303844 AATTTATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 14 0.35
9 18 0.45
10 8 0.20
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.58
Consensus pattern (9 bp):
GTATTATTA
Found at i:54303816 original size:26 final size:25
Alignment explanation
Indices: 54303760--54303839 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 25
54303750 CCTTTTTCGT
* *
54303760 TATTTTTATATTTTATTAAATATCATTG
1 TATTTTTATA--TTATT-AGTATTATTG
54303788 TATTTTTATATTATTAGTATTATTAG
1 TATTTTTATATTATTAGTATTATT-G
54303814 TATTACTATTATATTATTATGTATTA
1 TATT--T-TTATATTATTA-GTATTA
54303840 GTATAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
25 7 0.16
26 10 0.22
28 11 0.24
29 11 0.24
30 6 0.13
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (25 bp):
TATTTTTATATTATTAGTATTATTG
Found at i:54303853 original size:20 final size:21
Alignment explanation
Indices: 54303805--54303856 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
54303795 ATATTATTAG
*
54303805 TATTATTA-GTATTACTATTA
1 TATTATTATGTATTACTATAA
*
54303825 TATTATTATGTATTAGTATAA
1 TATTATTATGTATTACTATAA
54303846 T-TTATTATGTA
1 TATTATTATGTA
54303857 CGCGTATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTATTATGTATTACTATAA
Found at i:54304212 original size:25 final size:25
Alignment explanation
Indices: 54304184--54304232 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54304174 ACATACACAT
54304184 ATATATAGTAGACATACATA-TTTTC
1 ATATATA-TAGACATACATAGTTTTC
* *
54304209 ATATATATATACCTACATAGTTTT
1 ATATATATAGACATACATAGTTTT
54304233 TTTTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (25 bp):
ATATATATAGACATACATAGTTTTC
Found at i:54306293 original size:22 final size:19
Alignment explanation
Indices: 54306268--54306316 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
54306258 TATGGAGGCA
*
54306268 GAGGCTGGCGTGGAGCGGCTCG
1 GAGGCTGGC-TGCAGC-GCT-G
54306290 GAGGCGTGGCTGCAGCGCTG
1 GAGGC-TGGCTGCAGCGCTG
54306310 GAGGCTG
1 GAGGCTG
54306317 AATGTTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 3 0.12
22 10 0.40
23 4 0.16
ACGTcount: A:0.10, C:0.22, G:0.53, T:0.14
Consensus pattern (19 bp):
GAGGCTGGCTGCAGCGCTG
Found at i:54307315 original size:16 final size:16
Alignment explanation
Indices: 54307286--54307355 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
54307276 TTTGGTTCGT
* *
54307286 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
54307302 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
54307318 TGTAATGGATTAGAGG
1 TGTAATGGAATAGAGG
54307334 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
54307350 TGTAAT
1 TGTAAT
54307356 AGCAAATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:54307327 original size:32 final size:32
Alignment explanation
Indices: 54307286--54307355 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
54307276 TTTGGTTCGT
*
54307286 TGTATTGGATTAGAGGCGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
*
54307318 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
54307350 TGTAAT
1 TGTAAT
54307356 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATGGAATAGAGG
Found at i:54307389 original size:45 final size:44
Alignment explanation
Indices: 54307334--54307428 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
54307324 GGATTAGAGG
*
54307334 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTAAA
* *** *
54307379 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTAAA
54307423 TGTAAT
1 TGTAAT
54307429 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 21 0.48
45 23 0.52
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTAAA
Found at i:54307722 original size:17 final size:15
Alignment explanation
Indices: 54307672--54307714 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
54307662 ACTATAAAAT
54307672 TAATTAACATA-ATTA
1 TAATTAA-ATATATTA
*
54307687 TTATTAAATATATTA
1 TAATTAAATATATTA
54307702 TAATTAAATATAT
1 TAATTAAATATAT
54307715 AATTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTAAATATATTA
Found at i:54307727 original size:114 final size:116
Alignment explanation
Indices: 54307564--54308005 Score: 592
Period size: 114 Copynumber: 4.0 Consensus size: 116
54307554 ATCATATTTA
* *
54307564 AACATAATTATTATTAAATAT-TTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAT
1 AACATAATTATTATTAAATATATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
54307628 ATT-TTATATGAATTTA-T-AAATCATAATATATGATACTATAAAATTAATT
66 ATTCTTATATGAATTTACTCAAAT-ATAATATATGATACTATAAAATTAATT
54307677 AACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAATAA--AA
1 AACATAATTATTATTAAATATA-TATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
54307739 TATTCTTATATGAATTTACTCAAATATAATATATGATACTGTAAAATTAAATT
65 TATTCTTATATGAATTTACTCAAATATAATATATGATACTATAAAATT-AATT
54307792 -ACATAATTATTATTAAATATATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
1 AACATAATTATTATTAAATATATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
* * * * *
54307856 ATTCTTATATGAATTTACTCAAAT-CAATATATGATACTGTAATATAAATA
66 ATTCTTATATGAATTTACTCAAATATAATATATGATACTATAAAATTAATT
* *
54307906 AAAATAATTATTAATAAAT-TA-ATAA-T--AATATAT-A-TTAAT-AAATT-TTAATAATTAAT
1 AACATAATTATTATTAAATATATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
54307962 A-T-TTATATG-ATTTACT-AAATATAATA-ATGATA-TATAAAA-TAATT
66 ATTCTTATATGAATTTACTCAAATATAATATATGATACTATAAAATTAATT
54308006 TAAAAATTAT
Statistics
Matches: 305, Mismatches: 13, Indels: 35
0.86 0.04 0.10
Matches are distributed among these distances:
100 3 0.01
101 5 0.02
102 10 0.03
103 11 0.04
104 7 0.02
105 1 0.00
106 13 0.04
107 5 0.02
108 5 0.02
109 1 0.00
110 7 0.02
112 7 0.02
113 45 0.15
114 109 0.36
115 49 0.16
116 27 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (116 bp):
AACATAATTATTATTAAATATATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
ATTCTTATATGAATTTACTCAAATATAATATATGATACTATAAAATTAATT
Found at i:54307828 original size:13 final size:14
Alignment explanation
Indices: 54307803--54307837 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
54307793 CATAATTATT
54307803 ATTAAATATATATA
1 ATTAAATATATATA
54307817 ATTAAA-ATATATA
1 ATTAAATATATATA
*
54307830 ATTTAATA
1 ATTAAATA
54307838 AAATTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAAATATATATA
Found at i:54307921 original size:10 final size:11
Alignment explanation
Indices: 54307911--54307956 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
54307901 AAATAAAAAT
54307911 AATTATTAATA
1 AATTATTAATA
*
54307922 AATTAATAATA
1 AATTATTAATA
54307933 ATATATATTAATA
1 A-AT-TATTAATA
54307946 AATT-TTAATA
1 AATTATTAATA
54307956 A
1 A
54307957 TTAATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 7 0.23
11 12 0.39
12 4 0.13
13 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTATTAATA
Found at i:54307930 original size:24 final size:24
Alignment explanation
Indices: 54307902--54307949 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
54307892 CTGTAATATA
54307902 AATAAAAATA-ATTATTAATAAATT
1 AATAAAAATATA-TATTAATAAATT
*
54307926 AATAATAATATATATTAATAAATT
1 AATAAAAATATATATTAATAAATT
54307950 TTAATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAAAAATATATATTAATAAATT
Found at i:54308197 original size:90 final size:91
Alignment explanation
Indices: 54308019--54308225 Score: 301
Period size: 91 Copynumber: 2.3 Consensus size: 91
54308009 AAATTATAAC
* * * * *
54308019 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTACATATAATTTAATAAT
*
54308084 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
*
54308110 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTTAATAG
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAA-TAATTATTACATATAATTTAATAA
*
54308173 TGATATATAATTTCATAAAATTCTTAA
65 TAATATATAATTTCATAAAATTCTTAA
*
54308200 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
54308226 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
90 42 0.40
91 60 0.57
92 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTACATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:54311359 original size:19 final size:19
Alignment explanation
Indices: 54311335--54311374 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
54311325 TAAAATGAAG
54311335 AATGAAGATTTGGTTTAAT
1 AATGAAGATTTGGTTTAAT
54311354 AATGAAGATTTGGTTTAAT
1 AATGAAGATTTGGTTTAAT
54311373 AA
1 AA
54311375 ATAAAATGAA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (19 bp):
AATGAAGATTTGGTTTAAT
Found at i:54311376 original size:51 final size:48
Alignment explanation
Indices: 54311311--54311454 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 48
54311301 AAGGTTTTCT
54311311 AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
1 AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
*** *
54311359 AGATTTGGTTTAATAAATAAAATGAAGAATGAAGATTTGGTTT--T-CT--
1 A-ATTT--CAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
54311405 AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
1 AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
54311453 AA
1 AA
54311455 ATGAAGTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
43 32 0.40
45 5 0.06
46 2 0.03
48 4 0.05
49 5 0.06
51 32 0.40
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (48 bp):
AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGA
Found at i:54311772 original size:13 final size:13
Alignment explanation
Indices: 54311754--54311778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54311744 ATCAAATTTG
54311754 TATGTACTCTTTA
1 TATGTACTCTTTA
54311767 TATGTACTCTTT
1 TATGTACTCTTT
54311779 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:54313457 original size:6 final size:7
Alignment explanation
Indices: 54313436--54313466 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
54313426 GCCGGCCACC
54313436 AACCAAA
1 AACCAAA
54313443 AACCAAA
1 AACCAAA
54313450 AACCAAA
1 AACCAAA
54313457 AACCATAA
1 AACCA-AA
54313465 AA
1 AA
54313467 TGAAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (7 bp):
AACCAAA
Found at i:54323082 original size:10 final size:9
Alignment explanation
Indices: 54323032--54323074 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
54323022 CACTGATAAT
*
54323032 TTTTTATAA
1 TTTTTACAA
54323041 TTTTTACAA
1 TTTTTACAA
*
54323050 TATTTACAA
1 TTTTTACAA
*
54323059 TTTCTAACAA
1 TTT-TTACAA
54323069 TTTTTA
1 TTTTTA
54323075 ATAATTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTACAA
Found at i:54323127 original size:44 final size:46
Alignment explanation
Indices: 54323031--54323127 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 46
54323021 ACACTGATAA
* *
54323031 TTTTTTATAATTTTTACAATATTTACAATTTCTAACAATTTTTAAT
1 TTTTTTATAATTTATACAATATTTACAAATTCTAACAATTTTTAAT
** * *
54323077 AATTTTATTATTTAATACAA-ATTTA-AAATT-TAACAATTTTTTAT
1 TTTTTTATAATTT-ATACAATATTTACAAATTCTAACAATTTTTAAT
54323121 TTTTTTA
1 TTTTTTA
54323128 AAACAATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
44 18 0.43
45 4 0.10
46 15 0.36
47 5 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (46 bp):
TTTTTTATAATTTATACAATATTTACAAATTCTAACAATTTTTAAT
Found at i:54330172 original size:12 final size:12
Alignment explanation
Indices: 54330155--54330181 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54330145 TGCCCATCAC
54330155 TTTAAATATAAA
1 TTTAAATATAAA
54330167 TTTAAATATAAA
1 TTTAAATATAAA
54330179 TTT
1 TTT
54330182 TCTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAATATAAA
Found at i:54333282 original size:3 final size:3
Alignment explanation
Indices: 54333274--54333336 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
54333264 TATTTGTTCG
54333274 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
54333322 TGA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA T
54333337 ACTTATCGGA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54334565 original size:20 final size:19
Alignment explanation
Indices: 54334538--54334592 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
54334528 CTAAAATGAG
54334538 AAAT-TTAAGAATAAATAA
1 AAATATTAAGAATAAATAA
*
54334556 TAAATATTAAAAATAAATAA
1 -AAATATTAAGAATAAATAA
54334576 AGAA-ATTATAGAATAAA
1 A-AATATTA-AGAATAAA
54334593 AAGTGGCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATATTAAGAATAAATAA
Found at i:54339347 original size:20 final size:20
Alignment explanation
Indices: 54339298--54339348 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
54339288 AAAATAACTA
* *
54339298 AAATGAGAAAT-TTAAGAAT
1 AAATAAGAAATATTAAAAAT
*
54339317 AAATAATAAATATTAAAAAT
1 AAATAAGAAATATTAAAAAT
54339337 -AATAAAGAAATA
1 AAAT-AAGAAATA
54339349 AAGAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (20 bp):
AAATAAGAAATATTAAAAAT
Found at i:54345518 original size:34 final size:34
Alignment explanation
Indices: 54345480--54345544 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
54345470 CAAAATGATG
* * * *
54345480 ATGCTCCTAAGCATGAGCTTAAACTGTTCATCTA
1 ATGCTCCTAAGAAGGAGCCTAAACTATTCATCTA
54345514 ATGCTCCTAAGAAGGAGCCTAAACTATTCAT
1 ATGCTCCTAAGAAGGAGCCTAAACTATTCAT
54345545 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (34 bp):
ATGCTCCTAAGAAGGAGCCTAAACTATTCATCTA
Found at i:54345673 original size:46 final size:45
Alignment explanation
Indices: 54345568--54345674 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
54345558 TGATCCAGTG
* *
54345568 AAGCACGAGATTAAACTATTCATACGAAATAAATGATTACCTCCT
1 AAGCATGAGATTAAATTATTCATACGAAATAAATGATTACCTCCT
*
54345613 AAGCATGA-ATTTAAATTGTTCATAC-ATAATAAATGATGATA-CTCCT
1 AAGCATGAGA-TTAAATTATTCATACGA-AATAAATGAT--TACCTCCT
*
54345659 AAGCATGAGCTTAAAT
1 AAGCATGAGATTAAAT
54345675 AGCAGTCCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
44 2 0.04
45 30 0.57
46 19 0.36
47 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (45 bp):
AAGCATGAGATTAAATTATTCATACGAAATAAATGATTACCTCCT
Found at i:54349839 original size:17 final size:17
Alignment explanation
Indices: 54349819--54349868 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
54349809 TTCCATTAGT
54349819 ATATAAATATTT-TATAA
1 ATATAAAT-TTTATATAA
*
54349836 ATATAGATTTTATATAA
1 ATATAAATTTTATATAA
*
54349853 A-A-AAATTTTATGTAA
1 ATATAAATTTTATATAA
54349868 A
1 A
54349869 CTTTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATAAATTTTATATAA
Found at i:54354684 original size:119 final size:119
Alignment explanation
Indices: 54354485--54354707 Score: 383
Period size: 119 Copynumber: 1.9 Consensus size: 119
54354475 TGGTGAGTGA
* * *
54354485 ACTTCTAGTGAAATTATTGTGCTAAGTCCATTGGGGCAGTCTGTTTGAGTAAGTACACTTTATAG
1 ACTTCTAGTGAAATTATTGTACTAAGTCCATTGGGGCAGTCTATTCGAGTAAGTACACTTTATAG
54354550 GAATGTACCTTTGGAAGTACAAGGGATTGTGTTTTCGGCAGATCTGGTGAGGTT
66 GAATGTACCTTTGGAAGTACAAGGGATTGTGTTTTCGGCAGATCTGGTGAGGTT
** * *
54354604 ACTTCTAGTGAAATTATTGTACTAAGTCTGTTGGGGTAGTCTATTCGAGTAAGTAGACTTTATAG
1 ACTTCTAGTGAAATTATTGTACTAAGTCCATTGGGGCAGTCTATTCGAGTAAGTACACTTTATAG
54354669 GAATGTACCTTTGGAAGTACAAGGGATTGTGTTTTCGGC
66 GAATGTACCTTTGGAAGTACAAGGGATTGTGTTTTCGGC
54354708 GTTTTATTCA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 97 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (119 bp):
ACTTCTAGTGAAATTATTGTACTAAGTCCATTGGGGCAGTCTATTCGAGTAAGTACACTTTATAG
GAATGTACCTTTGGAAGTACAAGGGATTGTGTTTTCGGCAGATCTGGTGAGGTT
Found at i:54360766 original size:19 final size:19
Alignment explanation
Indices: 54360736--54360784 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
54360726 TAAATGAATA
54360736 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
54360756 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
54360775 ATTTTTATTT
1 ATTTTTATTT
54360785 GTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:54361151 original size:7 final size:7
Alignment explanation
Indices: 54361139--54361360 Score: 83
Period size: 7 Copynumber: 31.0 Consensus size: 7
54361129 CACTAATTAA
54361139 CCTAAAC
1 CCTAAAC
54361146 CCTAAAC
1 CCTAAAC
54361153 CCTAAACC
1 CCTAAA-C
**
54361161 CCTATCC
1 CCTAAAC
54361168 CCTAAAC
1 CCTAAAC
* * *
54361175 CTTGAAT
1 CCTAAAC
** *
54361182 TATAAAA
1 CCTAAAC
* *
54361189 CATAAAA
1 CCTAAAC
*
54361196 CATAAAC
1 CCTAAAC
54361203 CCTAAATC
1 CCTAAA-C
*
54361211 CCTGAATC
1 CCT-AAAC
54361219 CCT-AAC
1 CCTAAAC
*
54361225 CCTTAACC
1 CC-TAAAC
*
54361233 CCTAACC
1 CCTAAAC
*
54361240 CCTAACC
1 CCTAAAC
54361247 CCTAAAC
1 CCTAAAC
*
54361254 CTTAAAC
1 CCTAAAC
*
54361261 CC-CAAC
1 CCTAAAC
54361267 CCTTAAAC
1 CC-TAAAC
* *
54361275 CATAATC
1 CCTAAAC
54361282 CCTAAAC
1 CCTAAAC
*
54361289 CCATAATC
1 CC-TAAAC
* *
54361297 CATAATC
1 CCTAAAC
*
54361304 CATAAAC
1 CCTAAAC
*
54361311 CTTAAA-
1 CCTAAAC
*
54361317 -ATAGTAAC
1 CCTA--AAC
*
54361325 TCTTAAAC
1 -CCTAAAC
*
54361333 CTTAAAC
1 CCTAAAC
54361340 CCTAAAC
1 CCTAAAC
*
54361347 CATAAAC
1 CCTAAAC
54361354 CCTAAAC
1 CCTAAAC
54361361 TATAATGATA
Statistics
Matches: 167, Mismatches: 35, Indels: 26
0.73 0.15 0.11
Matches are distributed among these distances:
5 2 0.01
6 9 0.05
7 123 0.74
8 29 0.17
9 2 0.01
10 2 0.01
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:54361287 original size:28 final size:29
Alignment explanation
Indices: 54361222--54361365 Score: 85
Period size: 29 Copynumber: 5.0 Consensus size: 29
54361212 CTGAATCCCT
* * *
54361222 AACCCTTAACCCCTAACCCCTAACCCCTA
1 AACCCTAAACCCCTAACCCCTAAACCATA
* *
54361251 AACCTTAAACCCC-AACCCTTAAACCATA
1 AACCCTAAACCCCTAACCCCTAAACCATA
* * * * *
54361279 ATCCCTAAACCCATAATCCATAATCCATA
1 AACCCTAAACCCCTAACCCCTAAACCATA
* **** * * *
54361308 AACCTTAAAATAGTAACTCTTAAACCTTA
1 AACCCTAAACCCCTAACCCCTAAACCATA
* * *
54361337 AACCCTAAA-CCATAAACCCTAAACTATA
1 AACCCTAAACCCCTAACCCCTAAACCATA
54361365 A
1 A
54361366 TGATAATTAA
Statistics
Matches: 83, Mismatches: 31, Indels: 3
0.71 0.26 0.03
Matches are distributed among these distances:
28 34 0.41
29 49 0.59
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.22
Consensus pattern (29 bp):
AACCCTAAACCCCTAACCCCTAAACCATA
Found at i:54361299 original size:22 final size:22
Alignment explanation
Indices: 54361264--54361311 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
54361254 CTTAAACCCC
* *
54361264 AACCCTTAAACCATAATCCCTA
1 AACCCATAAACCATAATCCATA
*
54361286 AACCCATAATCCATAATCCATA
1 AACCCATAAACCATAATCCATA
54361308 AACC
1 AACC
54361312 TTAAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (22 bp):
AACCCATAAACCATAATCCATA
Found at i:54362018 original size:106 final size:107
Alignment explanation
Indices: 54361809--54362033 Score: 319
Period size: 106 Copynumber: 2.1 Consensus size: 107
54361799 CGCCGCTAAT
* *
54361809 GCCACTAAAGCTCAACATAAAACACCAGCATTGAGCTTAATTTTTTTGCGGCGTTTTTCAAAAAG
1 GCCACTAAAGCTCAACATAAAACACCAGCATTGAGCTTAATTTTTTTACGGCATTTTTCAAAAAG
* * *
54361874 AGCCGCTAATGGTAGACCTATAGCGGCGTTTTTCAAAAAG-C
66 AGCCGCTAATGGTAGACCTATAGCAGCGGTTTTAAAAAAGAC
* * *
54361915 GCCACTAAAGCTCAACATAAAACACCGGCGTTGTGCTTAATTTTTTTACGGCATTTTTCAAAAAG
1 GCCACTAAAGCTCAACATAAAACACCAGCATTGAGCTTAATTTTTTTACGGCATTTTTCAAAAAG
* * * *
54361980 CGCCGCTAATGGTCGACTTATAGCAGTGGTTTTAAAAAAGAC
66 AGCCGCTAATGGTAGACCTATAGCAGCGGTTTTAAAAAAGAC
*
54362022 -CCACTAATGCTC
1 GCCACTAAAGCTC
54362034 GATCTATAGC
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
106 104 0.99
107 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (107 bp):
GCCACTAAAGCTCAACATAAAACACCAGCATTGAGCTTAATTTTTTTACGGCATTTTTCAAAAAG
AGCCGCTAATGGTAGACCTATAGCAGCGGTTTTAAAAAAGAC
Found at i:54362092 original size:40 final size:40
Alignment explanation
Indices: 54361968--54362092 Score: 146
Period size: 40 Copynumber: 3.1 Consensus size: 40
54361958 TTTTACGGCA
* *
54361968 TTTTTCAAAAAGCGCCGCTAATGGTCGA-CTTATAGCAGTG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATC-TATAGCAGCG
* * * * *
54362008 GTTTTAAAAAAGAC-CCACTAATGCTCGATCTATAGCGGCA
1 TTTTTCAAAAAG-CGCCGCTAATGCTCGATCTATAGCAGCG
*
54362048 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTAGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCG
54362088 TTTTT
1 TTTTT
54362093 TATCCAAACG
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 66 0.96
41 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAGCG
Found at i:54366752 original size:17 final size:15
Alignment explanation
Indices: 54366725--54366763 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
54366715 ATATAAGAAC
*
54366725 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
54366741 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
54366757 ATTTTAA
1 ATTTTAA
54366764 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
Found at i:54366826 original size:91 final size:91
Alignment explanation
Indices: 54366730--54366975 Score: 440
Period size: 91 Copynumber: 2.7 Consensus size: 91
54366720 AGAACATTTT
*
54366730 ATTATTAAATTATATTTAATATTAATTATTTTAAATTGTATAAATTCATATAAGAAAATTTATTA
1 ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
54366795 TCAAGAATTTTATGAAATTATATATC
66 TCAAGAATTTTATGAAATTATATATC
54366821 ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
1 ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
* *
54366886 TCACGAATTTTATGAAATTATATATT
66 TCAAGAATTTTATGAAATTATATATC
* *
54366912 ATTATT-AATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
54366976 GTTATAATTA
Statistics
Matches: 150, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 56 0.37
91 94 0.63
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
TCAAGAATTTTATGAAATTATATATC
Found at i:54366838 original size:47 final size:47
Alignment explanation
Indices: 54366787--54366928 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 47
54366777 ATATAAGAAA
*
54366787 ATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
* * ** *
54366834 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* *
54366878 ATTTATTATCACGAATTTTATGAAATTATATATTATTATT-AATTAT
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
54366924 ATTTA
1 ATTTA
54366929 ATAATAATTA
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
43 3 0.04
44 24 0.33
45 8 0.11
46 12 0.16
47 23 0.32
48 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (47 bp):
ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
Found at i:54367112 original size:16 final size:15
Alignment explanation
Indices: 54367091--54367120 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54367081 TAAATTCATA
54367091 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
54367107 TAAGAATTTTATTA
1 TAAGAATTTTATTA
54367121 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:54367115 original size:120 final size:120
Alignment explanation
Indices: 54366991--54367526 Score: 862
Period size: 120 Copynumber: 4.5 Consensus size: 120
54366981 AATTATTTTA
* * * * *
54366991 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTA-TGTTAAATTATATTT
* * *
54367055 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
54367111 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATAATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
54367176 ATCGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
54367231 AATTTTACTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
54367296 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
54367350 AATTTTATTAAATTATATATTTTAATT-TAATATATTTAATAATTATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
54367414 ATAGTATCATATATTATGATTTGAGCAAATTCATATAAGAATATTAATTATTAAT
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54367469 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
54367527 ATGATTAAAT
Statistics
Matches: 387, Mismatches: 25, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
118 73 0.19
119 80 0.21
120 228 0.59
121 6 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:54367140 original size:18 final size:17
Alignment explanation
Indices: 54367112--54367146 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54367102 ATTATTAAGA
*
54367112 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54367129 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54367147 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54367266 original size:16 final size:16
Alignment explanation
Indices: 54367245--54367291 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
54367235 TTACTAAATT
54367245 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
54367261 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
54367276 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
54367292 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:54367271 original size:15 final size:15
Alignment explanation
Indices: 54367241--54367291 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
54367231 AATTTTACTA
54367241 AATTAT-ATAT-TTT
1 AATTATAATATATTT
54367254 AATTATAATATATTT
1 AATTATAATATATTT
*
54367269 AATAATAAT-TATGTT
1 AATTATAATATAT-TT
54367284 AAATTATA
1 -AATTATA
54367292 TTTTATAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 13 0.41
16 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTATAATATATTT
Found at i:54367462 original size:238 final size:240
Alignment explanation
Indices: 54366991--54367526 Score: 898
Period size: 238 Copynumber: 2.2 Consensus size: 240
54366981 AATTATTTTA
* * * * *
54366991 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTA-TGTTAAATTATATTT
* *
54367055 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATT
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATT
*
54367120 AAATTATATATTTTAATTAAAATATATTTAATAATAATAATGTTAAATTATCTTTTATCGTATCA
130 AAATTATATATTTTAATTAAAATATATTTAATAATAATAATGTTAAATTATCTTTTATAGTATCA
* *
54367185 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
195 TATATTATGATTTGAGCAAATTCATATAAGAATATTAATTATTAAG
*
54367231 AATTTTACTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
54367296 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAGAATTTTATTA
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
* * *
54367360 AATTATATATTTTAATT-TAATATATTTAATAATTATTATGTTAAATTATCTTTTATAGTATCAT
131 AATTATATATTTTAATTAAAATATATTTAATAATAATAATGTTAAATTATCTTTTATAGTATCAT
*
54367424 ATATTATGATTTGAGCAAATTCATATAAGAATATTAATTATTAAT
196 ATATTATGATTTGAGCAAATTCATATAAGAATATTAATTATTAAG
54367469 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
54367527 ATGATTAAAT
Statistics
Matches: 278, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
238 135 0.49
239 48 0.17
240 95 0.34
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (240 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
AATTATATATTTTAATTAAAATATATTTAATAATAATAATGTTAAATTATCTTTTATAGTATCAT
ATATTATGATTTGAGCAAATTCATATAAGAATATTAATTATTAAG
Found at i:54367503 original size:18 final size:18
Alignment explanation
Indices: 54367457--54367504 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
54367447 TATAAGAATA
*
54367457 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
54367473 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
54367490 TTAATTATAATATAT
1 TTAATTATAATATAT
54367505 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:54367504 original size:16 final size:16
Alignment explanation
Indices: 54367457--54367524 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
54367447 TATAAGAATA
54367457 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
54367473 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
54367490 TTAATTATAATATA-T
1 TTAATTATAATATATT
*
54367505 TTAATAATAAT-TATGT
1 TTAATTATAATATAT-T
54367521 TTAA
1 TTAA
54367525 ATATGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.05
15 14 0.33
16 18 0.42
17 6 0.14
18 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:54367509 original size:15 final size:15
Alignment explanation
Indices: 54367474--54367515 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54367464 TTAATAATTT
*
54367474 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54367488 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54367502 TATTTAATAATAAT
1 TATTTAATTATAAT
54367516 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54367715 original size:16 final size:16
Alignment explanation
Indices: 54367694--54367728 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
54367684 CAAGAATACT
54367694 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54367710 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54367726 ATT
1 ATT
54367729 CAACCAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.34, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54367732 original size:55 final size:56
Alignment explanation
Indices: 54367655--54367784 Score: 201
Period size: 56 Copynumber: 2.3 Consensus size: 56
54367645 CCATTATGCT
54367655 ATTACACCTCTATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTATTCC
1 ATTACACCTCTATTCCATTCAACCAAACA-ATAGATATACTATTACGCCTCTATTCC
* * * *
54367710 ATTACGCCTCTATTCCATTCAACCAAACAATTGATTTGCTATTACGCCTCTATTCC
1 ATTACACCTCTATTCCATTCAACCAAACAATAGATATACTATTACGCCTCTATTCC
54367766 ATTACACCTCTATTCCATT
1 ATTACACCTCTATTCCATT
54367785 ACGCCTCTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.01
55 30 0.44
56 37 0.54
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.34
Consensus pattern (56 bp):
ATTACACCTCTATTCCATTCAACCAAACAATAGATATACTATTACGCCTCTATTCC
Found at i:54367775 original size:16 final size:16
Alignment explanation
Indices: 54367750--54367803 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
54367740 TTGATTTGCT
*
54367750 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
54367766 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
54367782 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
54367798 AATACA
1 ATTACA
54367804 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:54368972 original size:19 final size:17
Alignment explanation
Indices: 54368945--54368997 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
54368935 AATTTGTTTC
*
54368945 TTTGTAATAAAATTAAA
1 TTTGAAATAAAATTAAA
*
54368962 TTATAGAAATAACATTAAAA
1 TT-T-GAAATAAAATT-AAA
*
54368982 TTTTAAATAAAATTAA
1 TTTGAAATAAAATTAA
54368998 TTCACAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 10 0.34
20 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (17 bp):
TTTGAAATAAAATTAAA
Found at i:54369213 original size:21 final size:19
Alignment explanation
Indices: 54369187--54369229 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
54369177 CAATGCTTAA
54369187 AAATTTTATCAAAAAAGTTTT
1 AAATTTTAT-AAAAAA-TTTT
*
54369208 AAATTTTATATAAAATTTT
1 AAATTTTATAAAAAATTTT
54369227 AAA
1 AAA
54369230 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATTTTATAAAAAATTTT
Found at i:54371015 original size:7 final size:7
Alignment explanation
Indices: 54371003--54371052 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
54370993 TTCTATAAAG
54371003 ATTTTGA
1 ATTTTGA
54371010 ATTTTGA
1 ATTTTGA
54371017 ATTTTGA
1 ATTTTGA
54371024 ATTTTGA
1 ATTTTGA
54371031 ATTTTGA
1 ATTTTGA
54371038 ATTTTGA
1 ATTTTGA
54371045 ATTTTGA
1 ATTTTGA
54371052 A
1 A
54371053 GCAGATTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (7 bp):
ATTTTGA
Found at i:54372670 original size:71 final size:71
Alignment explanation
Indices: 54372554--54372695 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
54372544 TCTCGGATTT
*
54372554 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
54372619 CTTGAG
66 CTTGAG
* *
54372625 AAAAAAGGGATCATGCCCAGTAAGTTAGGACATGATCTCTTCTTAATTCCCGAGATCGTTTTAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
54372690 CTTGAG
66 CTTGAG
54372696 TTTGAAAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (71 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAG
Found at i:54375157 original size:41 final size:41
Alignment explanation
Indices: 54375091--54375245 Score: 138
Period size: 41 Copynumber: 3.8 Consensus size: 41
54375081 ATAAAGTGAT
* * * *
54375091 TGAATGTAATACAGACGTTACGTCTAGCAGGCTTGATGCCGG
1 TGAA-GTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
54375133 TGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
1 TGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
* * *
54375174 TG-A-TACATTTCAGACTATATGTCCAGCAGGC-TAAGTGCCGG
1 TGAAGTA-A-TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGG
* * * *
54375215 TGTACTGAA-TCAGGCTTTAAGCCTAGCAGGC
1 TGAAGT-AATTCAGACTTTAAGTCTAGCAGGC
54375246 AAAATGCTAG
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
39 2 0.02
40 5 0.05
41 80 0.84
42 5 0.05
43 2 0.02
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (41 bp):
TGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGG
Found at i:54376986 original size:26 final size:26
Alignment explanation
Indices: 54376938--54376992 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
54376928 GGCCGTCGCA
* *
54376938 CCGCCCACCGACCACCGGCGACGGTG
1 CCGCCCACCGACCACCGACGACGGCG
* *
54376964 CCGCCCACTGACCACCGATGACGGCG
1 CCGCCCACCGACCACCGACGACGGCG
54376990 CCG
1 CCG
54376993 TCGTGCACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.29, T:0.05
Consensus pattern (26 bp):
CCGCCCACCGACCACCGACGACGGCG
Found at i:54380838 original size:9 final size:9
Alignment explanation
Indices: 54380826--54380859 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
54380816 ATTTAAGCTG
54380826 TTTAAAATT
1 TTTAAAATT
*
54380835 TTTAAGATT
1 TTTAAAATT
54380844 TTTAAAA-T
1 TTTAAAATT
54380852 TTTAAAAT
1 TTTAAAAT
54380860 GATAAAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:54380840 original size:18 final size:18
Alignment explanation
Indices: 54380810--54380854 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
54380800 AAAATAAAAA
*
54380810 AAAATTATTTAAGCTGTTT
1 AAAATT-TTTAAGATGTTT
*
54380829 AAAATTTTTAAGATTTTT
1 AAAATTTTTAAGATGTTT
54380847 AAAATTTT
1 AAAATTTT
54380855 AAAATGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
AAAATTTTTAAGATGTTT
Found at i:54384722 original size:10 final size:10
Alignment explanation
Indices: 54384705--54384776 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
54384695 TTTTATCGTC
54384705 TTTT-ATAAT
1 TTTTAATAAT
*
54384714 TTCTAATAAT
1 TTTTAATAAT
*
54384724 TTTTTATAAT
1 TTTTAATAAT
* *
54384734 TTTTTACAAT
1 TTTTAATAAT
* *
54384744 ATTTAACAAT
1 TTTTAATAAT
*
54384754 TTCTAA-AATT
1 TTTTAATAA-T
54384764 TTTTAATAAT
1 TTTTAATAAT
54384774 TTT
1 TTT
54384777 ATTATTTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 5 0.10
10 44 0.86
11 2 0.04
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:54384730 original size:20 final size:19
Alignment explanation
Indices: 54384705--54384775 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
54384695 TTTTATCGTC
54384705 TTTTATAATTTCTAATAATT
1 TTTTATAATTTCTAA-AATT
* * *
54384725 TTTTATAATTTTTTACAATA
1 TTTTATAA-TTTCTAAAATT
* *
54384745 TTTAACAATTTCTAAAATT
1 TTTTATAATTTCTAAAATT
54384764 TTTTAATAATTT
1 TTTT-ATAATTT
54384776 TATTATTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
19 11 0.28
20 23 0.59
21 5 0.13
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATAATTTCTAAAATT
Found at i:54388832 original size:31 final size:31
Alignment explanation
Indices: 54388794--54388864 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
54388784 TTAACTTTTT
54388794 AAGTACAAGGATTAAATTTTAAATGTTGTCA
1 AAGTACAAGGATTAAATTTTAAATGTTGTCA
54388825 AAGTACAAGGATTAAATTTTAAATGTTGTCA
1 AAGTACAAGGATTAAATTTTAAATGTTGTCA
54388856 AAGTACAAG
1 AAGTACAAG
54388865 CACTAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (31 bp):
AAGTACAAGGATTAAATTTTAAATGTTGTCA
Found at i:54391142 original size:14 final size:14
Alignment explanation
Indices: 54391123--54391151 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54391113 TAATTTTGTG
54391123 TCTTGTAATATATT
1 TCTTGTAATATATT
54391137 TCTTGTAATATATT
1 TCTTGTAATATATT
54391151 T
1 T
54391152 AATTACATTT
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:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TCTTGTAATATATT
Found at i:54397143 original size:14 final size:15
Alignment explanation
Indices: 54397124--54397152 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54397114 GTGATAATAA
54397124 TTAAATT-AAAAAAT
1 TTAAATTGAAAAAAT
54397138 TTAAATTGAAAAAAT
1 TTAAATTGAAAAAAT
54397153 AGGGGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TTAAATTGAAAAAAT
Found at i:54400908 original size:36 final size:35
Alignment explanation
Indices: 54400841--54400909 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
54400831 GCATGCAATA
* * **
54400841 TAGGGCTTGATCACATATATAGGTTCACATGATCT
1 TAGGGCTCGATCACATATATAAGCACACATGATCT
*
54400876 TAGGGCTCGCATCACATATATAAGCACGCATGAT
1 TAGGGCTCG-ATCACATATATAAGCACACATGAT
54400910 ACATGGGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (35 bp):
TAGGGCTCGATCACATATATAAGCACACATGATCT
Found at i:54403705 original size:20 final size:20
Alignment explanation
Indices: 54403680--54403719 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54403670 ATAACACATT
*
54403680 TTCTACTCTGCTCTATTCTG
1 TTCTACTCAGCTCTATTCTG
*
54403700 TTCTACTCAGTTCTATTCTG
1 TTCTACTCAGCTCTATTCTG
54403720 CTTGATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.10, T:0.50
Consensus pattern (20 bp):
TTCTACTCAGCTCTATTCTG
Found at i:54405867 original size:23 final size:22
Alignment explanation
Indices: 54405823--54405867 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
54405813 ATTGAATTTA
* *
54405823 TATAAAATAATATATGACAAAT
1 TATAAAATAATACATAACAAAT
*
54405845 TATAATAATAATACATAATAAAT
1 TATAA-AATAATACATAACAAAT
54405868 CTGAAATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
TATAAAATAATACATAACAAAT
Found at i:54409428 original size:11 final size:11
Alignment explanation
Indices: 54409412--54409439 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54409402 GGAATTGGTA
54409412 TGTTTTAAATG
1 TGTTTTAAATG
54409423 TGTTTTAAATG
1 TGTTTTAAATG
54409434 TGTTTT
1 TGTTTT
54409440 GATTATTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (11 bp):
TGTTTTAAATG
Found at i:54410885 original size:20 final size:19
Alignment explanation
Indices: 54410862--54410913 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
54410852 AATGATAAAT
*
54410862 TTAAGAATAAATAATCAATA
1 TTAAGAATAAATAAACAA-A
* *
54410882 TTAAAAAT-AATAAAGAAA
1 TTAAGAATAAATAAACAAA
54410900 TTATAGAATAAATA
1 TTA-AGAATAAATA
54410914 GTGGAAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.15
19 11 0.42
20 11 0.42
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (19 bp):
TTAAGAATAAATAAACAAA
Found at i:54410956 original size:17 final size:16
Alignment explanation
Indices: 54410918--54410960 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
54410908 TAAATAGTGG
54410918 AAGATGGA-ATGAATA
1 AAGATGGATATGAATA
54410933 AACGATGGATATGACATA
1 AA-GATGGATATGA-ATA
*
54410951 TAGATGGATA
1 AAGATGGATA
54410961 AGTGTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 6 0.25
17 12 0.50
18 4 0.17
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (16 bp):
AAGATGGATATGAATA
Found at i:54416003 original size:17 final size:16
Alignment explanation
Indices: 54415965--54416007 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
54415955 TAAATAGTGG
54415965 AAGATGGA-ATGAATA
1 AAGATGGATATGAATA
54415980 AATGATGGATATGACATA
1 AA-GATGGATATGA-ATA
*
54415998 TAGATGGATA
1 AAGATGGATA
54416008 AGTGTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 6 0.25
17 12 0.50
18 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATGGATATGAATA
Found at i:54419178 original size:44 final size:44
Alignment explanation
Indices: 54419124--54419208 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
54419114 ATCTATTTTT
*
54419124 GGAATATCAGAATGGTCATGATTGGACTCTAGCCACATGTCTTC
1 GGAACATCAGAATGGTCATGATTGGACTCTAGCCACATGTCTTC
54419168 GGAACATCAGAATGGTCATGATTGGACTCTAGCCACATGTC
1 GGAACATCAGAATGGTCATGATTGGACTCTAGCCACATGTC
54419209 AAAGAAGCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
GGAACATCAGAATGGTCATGATTGGACTCTAGCCACATGTCTTC
Found at i:54420932 original size:16 final size:15
Alignment explanation
Indices: 54420911--54420954 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54420901 TTAAGTTTTT
*
54420911 ATTTTAAATATGATTA
1 ATTTTAAATAT-AATA
*
54420927 ATTTTATATATAATA
1 ATTTTAAATATAATA
*
54420942 ACTTTAAATATAA
1 ATTTTAAATATAA
54420955 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
ATTTTAAATATAATA
Found at i:54426223 original size:17 final size:17
Alignment explanation
Indices: 54426203--54426252 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
54426193 TTCCATTAGT
54426203 ATATAAATATTT-TATAA
1 ATATAAAT-TTTATATAA
*
54426220 ATATAGATTTTATATAA
1 ATATAAATTTTATATAA
*
54426237 A-A-AAATTTTATGTAA
1 ATATAAATTTTATATAA
54426252 A
1 A
54426253 CTTTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATAAATTTTATATAA
Found at i:54428514 original size:22 final size:21
Alignment explanation
Indices: 54428481--54428524 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
54428471 TTTTCGCACG
*
54428481 CGGTTAGTTTTCGCTTAGTTT
1 CGGTAAGTTTTCGCTTAGTTT
* *
54428502 CGGTAAGTGTTTCTCTTCGTTT
1 CGGTAAGT-TTTCGCTTAGTTT
54428524 C
1 C
54428525 TATCATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.50
Consensus pattern (21 bp):
CGGTAAGTTTTCGCTTAGTTT
Found at i:54432187 original size:15 final size:15
Alignment explanation
Indices: 54432147--54432195 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
54432137 ATATACTTAG
54432147 ATTAAATCTTAATTA
1 ATTAAATCTTAATTA
*
54432162 ATCAAAT-TTAATTA
1 ATTAAATCTTAATTA
54432176 ATTAAATCTTAATTA
1 ATTAAATCTTAATTA
54432191 ATTAA
1 ATTAA
54432196 CCTTAATCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATCTTAATTA
Found at i:54432200 original size:14 final size:14
Alignment explanation
Indices: 54432147--54432202 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
54432137 ATATACTTAG
54432147 ATTAAATCTTAATTA
1 ATTAAA-CTTAATTA
* *
54432162 ATCAAATTTAATTA
1 ATTAAACTTAATTA
54432176 ATTAAATCTTAATTA
1 ATTAAA-CTTAATTA
*
54432191 ATTAACCTTAAT
1 ATTAAACTTAAT
54432203 CACAATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 18 0.51
15 17 0.49
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAACTTAATTA
Found at i:54432201 original size:29 final size:29
Alignment explanation
Indices: 54432147--54432202 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
54432137 ATATACTTAG
*
54432147 ATTAAATCTTAATTAATCAAATTTAATTA
1 ATTAAATCTTAATTAATCAAACTTAATTA
* *
54432176 ATTAAATCTTAATTAATTAACCTTAAT
1 ATTAAATCTTAATTAATCAAACTTAAT
54432203 CACAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTAAATCTTAATTAATCAAACTTAATTA
Found at i:54439845 original size:46 final size:46
Alignment explanation
Indices: 54439776--54440040 Score: 166
Period size: 46 Copynumber: 5.8 Consensus size: 46
54439766 CGACCTAATT
* ** * * **
54439776 TGCGAACTCATATGTTAAAAGTATGTGAACCTATCTATGTTTGTTA
1 TGCGAACTCACATGTTAGCAGTATGTGAACCTATATATATCAGTTA
*
54439822 TGCGAGCTCACATGTTAGCAGTATGTGAACCTATATATATCAGTTA
1 TGCGAACTCACATGTTAGCAGTATGTGAACCTATATATATCAGTTA
* ** * *
54439868 TGCAAACTCACATGTTAGCAGTATACGAACC-ATA-A-GTCTGTTA
1 TGCGAACTCACATGTTAGCAGTATGTGAACCTATATATATCAGTTA
* ** * * * **
54439911 TGCAAACTCACACATTGGCAGTATGCGAACCCTATATACA-CCTTTA
1 TGCGAACTCACATGTTAGCAGTATGTGAA-CCTATATATATCAGTTA
* ** * * *
54439957 TGCAAACTCACACATTAACAGTATGCGAACC-CTATATA-C-GCCTCTA
1 TGCGAACTCACATGTTAGCAGTATGTGAACCTATATATATCAG--T-TA
* * *
54440003 TGCAAACTCACACGTTAGCAGTATGCGAACCCTATATA
1 TGCGAACTCACATGTTAGCAGTATGTGAA-CCTATATA
54440041 CGCCTTCATG
Statistics
Matches: 181, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
43 31 0.17
44 9 0.05
45 9 0.05
46 126 0.70
47 2 0.01
48 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (46 bp):
TGCGAACTCACATGTTAGCAGTATGTGAACCTATATATATCAGTTA
Found at i:54440041 original size:46 final size:45
Alignment explanation
Indices: 54439819--54440058 Score: 249
Period size: 46 Copynumber: 5.3 Consensus size: 45
54439809 TCTATGTTTG
* * * * *
54439819 TTATGCGAGCTCACATGTTAGCAGTATGTGAACCTATATATATCAG--
1 TTATGCAAACTCACACGTTAGCAGTATGCGAACC-CTATATA-C-GCC
* * *
54439865 TTATGCAAACTCACATGTTAGCAGTATACGAA-CC-ATA-A-GTCTG
1 TTATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACG-C-C
* * *
54439908 TTATGCAAACTCACACATTGGCAGTATGCGAACCCTATATACACC
1 TTATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACGCC
* *
54439953 TTTATGCAAACTCACACATTAACAGTATGCGAACCCTATATACGCC
1 -TTATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACGCC
54439999 TCTATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACGCC
1 T-TATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACGCC
54440045 TTCATGCAAACTCA
1 TT-ATGCAAACTCA
54440059 TATGATTTGC
Statistics
Matches: 167, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.01
42 1 0.01
43 31 0.19
44 2 0.01
45 6 0.04
46 126 0.75
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (45 bp):
TTATGCAAACTCACACGTTAGCAGTATGCGAACCCTATATACGCC
Found at i:54452861 original size:43 final size:43
Alignment explanation
Indices: 54452652--54452866 Score: 209
Period size: 43 Copynumber: 5.0 Consensus size: 43
54452642 GCGGCGTTTT
* * * * *
54452652 AGAACATGACCTTTAGCGGCAC-TTTACCCACAAATGCCACTGA
1 AGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACGCCGCTAA
* ** * * *
54452695 AGAACATGATCTTTAGCGGCGC-TTTCCCATAAACACCACTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* * * *
54452737 AGAACTTGATCTTTAGCGACACTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
*
54452780 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTGA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* * * * * *
54452823 AGAGCATGGCCTTTTGTGGTGCTTTTATCACAAACGCCGTTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
54452866 A
1 A
54452867 AGTACCATTC
Statistics
Matches: 144, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 31 0.22
43 113 0.78
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
Found at i:54454596 original size:17 final size:15
Alignment explanation
Indices: 54454566--54454599 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
54454556 AACTAAATAA
54454566 AACCAAAGAAATGAG
1 AACCAAAGAAATGAG
54454581 AACCACAAGTAAATGAG
1 AACCA-AAG-AAATGAG
54454598 AA
1 AA
54454600 AGAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 3 0.18
17 9 0.53
ACGTcount: A:0.59, C:0.15, G:0.18, T:0.09
Consensus pattern (15 bp):
AACCAAAGAAATGAG
Found at i:54456302 original size:20 final size:20
Alignment explanation
Indices: 54456277--54456324 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
54456267 AAATTATAAT
54456277 TTTTTATTTTTTGTATTTCA
1 TTTTTATTTTTTGTATTTCA
54456297 TTTTTA-TTTTTGTATTTCA
1 TTTTTATTTTTTGTATTTCA
54456316 TTTTTATTT
1 TTTTTATTT
54456325 GTTATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTTTGTATTTCA
Found at i:54456713 original size:7 final size:7
Alignment explanation
Indices: 54456703--54456854 Score: 61
Period size: 7 Copynumber: 21.6 Consensus size: 7
54456693 CCCTATCCCC
54456703 TAAACCT
1 TAAACCT
* *
54456710 TAAATCA
1 TAAACCT
* *
54456717 TAAAACA
1 TAAACCT
*
54456724 TAACCCT
1 TAAACCT
*
54456731 TAACCCT
1 TAAACCT
*
54456738 TAACCCT
1 TAAACCT
*
54456745 TAACCCT
1 TAAACCT
*
54456752 TAATCCT
1 TAAACCT
*
54456759 TAATCCT
1 TAAACCT
* *
54456766 TAACCCC
1 TAAACCT
54456773 TAAACCT
1 TAAACCT
*
54456780 TAAACCC
1 TAAACCT
* *
54456787 CAACCCT
1 TAAACCT
*
54456794 TAAACCA
1 TAAACCT
* * *
54456801 AAAATCA
1 TAAACCT
*
54456808 TAAACCA
1 TAAACCT
*
54456815 TAAACCA
1 TAAACCT
* *
54456822 TAATCCC
1 TAAACCT
*
54456829 TAAACCCA
1 TAAA-CCT
* *
54456837 TAATCCA
1 TAAACCT
54456844 TAAACCT
1 TAAACCT
54456851 TAAA
1 TAAA
54456855 ATAGTAACTC
Statistics
Matches: 115, Mismatches: 29, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
7 110 0.96
8 5 0.04
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:54456743 original size:14 final size:14
Alignment explanation
Indices: 54456724--54456796 Score: 85
Period size: 14 Copynumber: 5.2 Consensus size: 14
54456714 TCATAAAACA
54456724 TAACCCTTAACCCT
1 TAACCCTTAACCCT
54456738 TAACCCTTAACCCT
1 TAACCCTTAACCCT
* *
54456752 TAATCCTTAATCCT
1 TAACCCTTAACCCT
* *
54456766 TAACCCCTAAACCT
1 TAACCCTTAACCCT
*
54456780 TAAACCC-CAACCCT
1 T-AACCCTTAACCCT
54456794 TAA
1 TAA
54456797 ACCAAAAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
13 2 0.04
14 44 0.86
15 5 0.10
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (14 bp):
TAACCCTTAACCCT
Found at i:54456748 original size:21 final size:21
Alignment explanation
Indices: 54456724--54456799 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
54456714 TCATAAAACA
*
54456724 TAACCCTTAACCCTTAACCCT
1 TAACCCTTAAACCTTAACCCT
* *
54456745 TAACCCTTAATCCTTAATCCT
1 TAACCCTTAAACCTTAACCCT
*
54456766 TAACCCCTAAACCTTAAACCC-
1 TAACCCTTAAACCTT-AACCCT
*
54456787 CAACCCTTAAACC
1 TAACCCTTAAACC
54456800 AAAAATCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 43 0.91
22 4 0.09
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (21 bp):
TAACCCTTAAACCTTAACCCT
Done.