Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 118 of 345
Found at i:31346177 original size:38 final size:38
Alignment explanation
Indices: 31346050--31346198 Score: 126
Period size: 38 Copynumber: 3.8 Consensus size: 38
31346040 GAAGGTTGCA
* * *
31346050 ATATGAATATTGAGCAAACCGTAAAAATGACAACCGCT
1 ATATGAATATCGAGCGAACCGTAAAAATGACAACCGCG
* * * **
31346088 ATATGAATATCAAGCGAACTGTTAAAACAT-CCAAGGTTGCG
1 ATATGAATATCGAGCGAACCG-TAAAA-ATGACAA--CCGCG
*
31346129 ATAT-AGATATCGAGCGAACCATAAAAATGACAACCGCG
1 ATATGA-ATATCGAGCGAACCGTAAAAATGACAACCGCG
31346167 ATATGAATATC-AG-GTAAACCGTAAAAATGACA
1 ATATGAATATCGAGCG--AACCGTAAAAATGACA
31346199 CTCGTAATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 44 0.51
39 11 0.13
40 11 0.13
41 18 0.21
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (38 bp):
ATATGAATATCGAGCGAACCGTAAAAATGACAACCGCG
Found at i:31349964 original size:18 final size:18
Alignment explanation
Indices: 31349938--31350008 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
31349928 AATTGATCGG
*
31349938 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* *
31349956 TTATTCAGTAAAAATCAA
1 TTATTCAGTAACAGTCAA
* * * *
31349974 ATATACAGTAACAATTAAA
1 TTATTCAGTAAC-AGTCAA
*
31349993 TTATTCAGCAACAGTC
1 TTATTCAGTAACAGTC
31350009 GATCTTTCCA
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
18 26 0.67
19 13 0.33
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:31350188 original size:47 final size:47
Alignment explanation
Indices: 31350135--31350249 Score: 169
Period size: 47 Copynumber: 2.4 Consensus size: 47
31350125 GTAACAGTAA
* * **
31350135 CAGTAACAATACGGTACACAGAGTACCTCGTCGGAACAAATCCGGAG
1 CAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAAAG
*
31350182 CAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCTAAAG
1 CAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAAAG
31350229 CAGTAACAGTAACGGTA-ACAG
1 CAGTAACAGT-ACGGTACACAG
31350250 TAATAATATC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 56 0.90
48 6 0.10
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (47 bp):
CAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCAAAG
Found at i:31350717 original size:2 final size:2
Alignment explanation
Indices: 31350710--31350737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31350700 CACCTACTAC
31350710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31350738 TAAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31351361 original size:16 final size:16
Alignment explanation
Indices: 31351340--31351378 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31351330 AATTTTCCCC
*
31351340 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
31351356 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
31351372 TCTTTCC
1 TTTTTCC
31351379 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:31351453 original size:2 final size:2
Alignment explanation
Indices: 31351446--31351474 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31351436 CCTTTTACTT
31351446 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31351475 ATAACTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31353391 original size:55 final size:55
Alignment explanation
Indices: 31353326--31353445 Score: 170
Period size: 55 Copynumber: 2.2 Consensus size: 55
31353316 AAATAAGCAA
*
31353326 TATTCCAACATAACAATCGATTTAAACATATAAACAATCGATTT-AAAAGAAAAAG
1 TATTCCAACATAACAATCGATTTAAACATATAAAAAATCG-TTTCAAAAGAAAAAG
* * * **
31353381 TATTCTAACATGACAATTGATTTAAACATATAAAAAATCGTTTCAAAAGAAGCAG
1 TATTCCAACATAACAATCGATTTAAACATATAAAAAATCGTTTCAAAAGAAAAAG
31353436 TATTCCAACA
1 TATTCCAACA
31353446 ATTAAGAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 3 0.05
55 54 0.95
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (55 bp):
TATTCCAACATAACAATCGATTTAAACATATAAAAAATCGTTTCAAAAGAAAAAG
Found at i:31355346 original size:19 final size:19
Alignment explanation
Indices: 31355322--31355434 Score: 148
Period size: 19 Copynumber: 6.2 Consensus size: 19
31355312 AATCTTTAAG
31355322 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31355341 GATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATAT
31355360 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31355379 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31355396 GATATG--AT-AT-GATAT
1 GATATGCAATCTTAGATAT
31355411 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
31355432 GAT
1 GAT
31355435 TTTGTAATCT
Statistics
Matches: 82, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
15 11 0.13
16 1 0.01
17 21 0.26
18 1 0.01
19 40 0.49
21 8 0.10
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31355365 original size:38 final size:38
Alignment explanation
Indices: 31355322--31355434 Score: 148
Period size: 36 Copynumber: 3.1 Consensus size: 38
31355312 AATCTTTAAG
*
31355322 GATATGCAATCTTAGATATGATATGCAATCTTAGATGT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
31355360 GATATGCAATCTTAGATATGATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
*
31355396 GATATG--AT-AT-GATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTT--AGATAT
31355432 GAT
1 GAT
31355435 TTTGTAATCT
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
32 9 0.13
33 1 0.01
34 9 0.13
36 27 0.39
38 23 0.33
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:31355379 original size:14 final size:15
Alignment explanation
Indices: 31355360--31355397 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
31355350 TCTTAGATGT
31355360 GATATG-CAATCTTA
1 GATATGACAATCTTA
31355374 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
31355391 GATATGA
1 GATATGA
31355398 TATGATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:31355399 original size:5 final size:5
Alignment explanation
Indices: 31355391--31355416 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31355381 TACAATCTTA
31355391 GATAT GATAT GATAT GATAT GATAT G
1 GATAT GATAT GATAT GATAT GATAT G
31355417 CAATCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:31358648 original size:28 final size:28
Alignment explanation
Indices: 31358608--31358663 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31358598 TCCTAAATAG
31358608 AATAGTTTGTCATAAGGAAACGAATTTC
1 AATAGTTTGTCATAAGGAAACGAATTTC
31358636 AATAGTTTGTCATAAGGAAACGAATTTC
1 AATAGTTTGTCATAAGGAAACGAATTTC
31358664 TTGATAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
AATAGTTTGTCATAAGGAAACGAATTTC
Found at i:31361737 original size:16 final size:15
Alignment explanation
Indices: 31361712--31361745 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
31361702 TTTCAAAAGC
31361712 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
31361727 AAAAAAGAAAAAAGAA
1 AAAAAA-AAAAAAGAA
31361743 AAA
1 AAA
31361746 TGGAGAGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:31362906 original size:84 final size:84
Alignment explanation
Indices: 31362687--31363062 Score: 463
Period size: 84 Copynumber: 4.4 Consensus size: 84
31362677 CAAAATTCAG
* * * * * **
31362687 CGCCTTAATCCCCTAAGCAATAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAATAAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTA
* *
31362752 GCGGAGCAGATCAATAACGACT
66 GTGGAGCAGATC--GAA-GACT
* * * *
31362774 CGCCTTAATCCCCTAAGCAGTAGGGTAACATGTCAAAATTATG--GATCTTATCTTCCTAAGCAG
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGT-TAAATT-TGCAAATCTTATCTCCCTAAGCAG
31362837 TAGTGGAGCAGATCGAAGACT
64 TAGTGGAGCAGATCGAAGACT
* * * *
31362858 CGCTTTAATCTCCTGAGCAGTAAGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTA
*
31362923 GTGGAGCAGATCGAAGCCT
66 GTGGAGCAGATCGAAGACT
* * *
31362942 CACCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAAATCTTAACTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTA
*
31363007 GTGGAGTAGATCGAAGA-T
66 GTGGAGCAGATCGAAGACT
31363025 GCGCCTTAA-CCTCCTAAGCAGTAGGGTAACAGGTTAAA
1 -CGCCTTAATCC-CCTAAGCAGTAGGGTAACAGGTTAAA
31363063 GCATAGCAGA
Statistics
Matches: 252, Mismatches: 31, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
82 2 0.01
83 8 0.03
84 175 0.69
85 2 0.01
87 60 0.24
88 4 0.02
89 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:31363355 original size:175 final size:175
Alignment explanation
Indices: 31363064--31363607 Score: 937
Period size: 175 Copynumber: 3.1 Consensus size: 175
31363054 CAGGTTAAAG
* * * *
31363064 CATAGCAGATCTGACCTTCGGATGTTCTTACACCAAAGCAGATTCAAGATAACAGATCTGGCATC
1 CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCATC
31363129 TCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
66 TCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
31363194 CAAGATGATTTGGCATCCTTT-TGTTCACAAGGAGCAAATCGAAGA
131 CAAGATGATTTGGCAT-CTTTGTGTTCACAAGGAGCAAATCGAAGA
**
31363239 CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAATAGATCCAAGATAACAGATCTGGCATC
1 CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCATC
* *
31363304 TCTATTTCGACGGAGAGCAGATATATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
66 TCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
31363369 CAAGATGATTTGGCATCTTTGTGTTCACAAGGAGCAAATCGAAGA
131 CAAGATGATTTGGCATCTTTGTGTTCACAAGGAGCAAATCGAAGA
* *
31363414 CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAGGATAACAGATTTGGCATC
1 CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCATC
* * * *
31363479 TCCATTTCGACGGAGAGCAGATACATAGCAAATGTAACTTTCAGATAATTTTACTGAAGCAGATC
66 TCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
31363544 CAAGATGATTTGGCATCTTTGTGTTCACAAGGAGCAAATCGAAGA
131 CAAGATGATTTGGCATCTTTGTGTTCACAAGGAGCAAATCGAAGA
*
31363589 CATAGCAGATTTGGCTTTC
1 CATAGCAGATTTGACTTTC
31363608 ACGTGTTTAC
Statistics
Matches: 349, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
174 4 0.01
175 345 0.99
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (175 bp):
CATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCATC
TCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTACTGAAGCAGATC
CAAGATGATTTGGCATCTTTGTGTTCACAAGGAGCAAATCGAAGA
Found at i:31363623 original size:87 final size:86
Alignment explanation
Indices: 31363151--31363648 Score: 332
Period size: 87 Copynumber: 5.7 Consensus size: 86
31363141 GAGAGCAGAT
* * *
31363151 ACATAGCAGATCTAACCTTCAGATGATTTTA-CTGAAGCAGATCCAAGATGATTTGGCATCCTTT
1 ACATAGCAGATTTGACTTTCAGATG--TTTACCTGAAGCAGATCCAAGATGATTTGGCAT-CTTT
31363215 -TGTTCACAAGGAGCAAATCGAAG
63 GTGTTCACAAGGAGCAAATCGAAG
* ** ** *
31363238 ACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAATAGATCCAAGATAACAGATCTGGCAT
1 ACATAGCAGATTTGACTTTCAGATGTT-T-AC-CTGAAGCAGATCCAAGAT----GATTTGGCAT
* * * *
31363303 CTCTAT-TTCGAC--GGAG---AGC-AGAT
59 CTTTGTGTTC-ACAAGGAGCAAATCGA-AG
* * * *
31363326 ATATAGCAGATCTAACCTTCAGATGATTTTA-CTGAAGCAGATCCAAGATGATTTGGCATCTTTG
1 ACATAGCAGATTTGACTTTCAGATG--TTTACCTGAAGCAGATCCAAGATGATTTGGCATCTTTG
31363390 TGTTCACAAGGAGCAAATCGAAG
64 TGTTCACAAGGAGCAAATCGAAG
* ** *
31363413 ACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAGGATAACAGATTTGGCAT
1 ACATAGCAGATTTGACTTTCAGATGTT-T-AC-CTGAAGCAGATCCAAGAT----GATTTGGCAT
*** * *
31363478 CTCCAT-TTCGAC--GGAG---AGC-AGAT
59 CTTTGTGTTC-ACAAGGAGCAAATCGA-AG
* * * *
31363501 ACATAGCAAATGTAACTTTCAGATAATTTTA-CTGAAGCAGATCCAAGATGATTTGGCATCTTTG
1 ACATAGCAGATTTGACTTTCAGAT--GTTTACCTGAAGCAGATCCAAGATGATTTGGCATCTTTG
31363565 TGTTCACAAGGAGCAAATCGAAG
64 TGTTCACAAGGAGCAAATCGAAG
* *
31363588 ACATAGCAGATTTGGCTTTCACG-TGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCT
1 ACATAGCAGATTTGACTTTCA-GATGTTTAC-CTGAAGCAGATCCAAGATGATTTGGCATCT
31363649 CTGTATTGTT
Statistics
Matches: 311, Mismatches: 58, Indels: 84
0.69 0.13 0.19
Matches are distributed among these distances:
82 30 0.10
83 6 0.02
84 8 0.03
85 8 0.03
86 31 0.10
87 98 0.32
88 51 0.16
89 31 0.10
90 4 0.01
91 8 0.03
92 9 0.03
93 27 0.09
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (86 bp):
ACATAGCAGATTTGACTTTCAGATGTTTACCTGAAGCAGATCCAAGATGATTTGGCATCTTTGTG
TTCACAAGGAGCAAATCGAAG
Found at i:31364063 original size:17 final size:18
Alignment explanation
Indices: 31364041--31364101 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
31364031 ATGGAAATAT
31364041 AATCTTTA-AGGATATGC
1 AATCTTTACAGGATATGC
* *
31364058 AATCTTAGACATGATATGC
1 AATCTT-TACAGGATATGC
*
31364077 AAT-TTTAGATGTGATATGC
1 AATCTTTACA-G-GATATGC
31364096 AATCTT
1 AATCTT
31364102 AGATATGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.24
18 3 0.09
19 21 0.62
20 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
AATCTTTACAGGATATGC
Found at i:31364075 original size:19 final size:19
Alignment explanation
Indices: 31364051--31364113 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
31364041 AATCTTTAAG
*
31364051 GATATGCAATCTTAGACAT
1 GATATGCAATCTTAGATAT
* *
31364070 GATATGCAATTTTAGATGT
1 GATATGCAATCTTAGATAT
31364089 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31364108 GATATG
1 GATATG
31364114 ATACGATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31369074 original size:17 final size:18
Alignment explanation
Indices: 31369049--31369087 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
31369039 AAGAGAGAAA
*
31369049 AATATAATTTAACTC-TT
1 AATACAATTTAACTCTTT
*
31369066 AATACAATTTAATTCTTT
1 AATACAATTTAACTCTTT
31369084 AATA
1 AATA
31369088 TTTAAGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (18 bp):
AATACAATTTAACTCTTT
Found at i:31371891 original size:15 final size:15
Alignment explanation
Indices: 31371873--31371902 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31371863 ATGCGACAAA
31371873 CATATTATCATTCGT
1 CATATTATCATTCGT
31371888 CATATTATCATTCGT
1 CATATTATCATTCGT
31371903 GTAATGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
CATATTATCATTCGT
Found at i:31373008 original size:4 final size:4
Alignment explanation
Indices: 31372999--31373025 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31372989 GATTGAGATT
31372999 TGGA TGGA TGGA TGGA TGGA TGGA TGG
1 TGGA TGGA TGGA TGGA TGGA TGGA TGG
31373026 GTGGGTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.52, T:0.26
Consensus pattern (4 bp):
TGGA
Found at i:31379200 original size:27 final size:28
Alignment explanation
Indices: 31379158--31379213 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
31379148 TCTTTTAAGT
*
31379158 TTTATTATAATAA-TTTAAATATTTAAAG
1 TTTATTATAAAAATTTTAAA-ATTTAAAG
*
31379186 TTTA-TATAAAAATTTTAAAATTTTAAG
1 TTTATTATAAAAATTTTAAAATTTAAAG
31379213 T
1 T
31379214 GAGGATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTATTATAAAAATTTTAAAATTTAAAG
Found at i:31392954 original size:50 final size:49
Alignment explanation
Indices: 31392830--31393148 Score: 174
Period size: 46 Copynumber: 6.8 Consensus size: 49
31392820 TGGGTAAAGT
* * * *
31392830 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTATCATCTTTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTATAAG
* * *
31392879 GCTGATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCA-C-ATAACCG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTATAA--G
*
31392928 TTCCGATGCCATGTCCCAGACATGGTCTTACACT-GAC-A-CATCTCAT-A-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTATCATCT-ATAAG
* * * * * *
31392975 GCCGTTG-CATGTCCCAGACAT-ATCTTATACTGGCT-TACGTCT-CAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTATAAG
* * * *
31393021 GCTGATG-CATGTCCCTGACAT-GTCTTACACTAG-TACTCATCT-CAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTATAAG
* * * * * * * *
31393067 GTCGATGTCATGTCCAAAACATGGTCTTACACTGGCTCTCATAATGTAA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCAT-CTATAAG
* *
31393116 -CCGATG-CATGT-CTAGACAT-GTCTTACGCTAGCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
31393149 CACACAAATG
Statistics
Matches: 211, Mismatches: 39, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
44 9 0.04
45 29 0.14
46 54 0.26
47 19 0.09
48 23 0.11
49 41 0.19
50 34 0.16
51 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTATAAG
Found at i:31401827 original size:30 final size:28
Alignment explanation
Indices: 31401765--31401820 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
31401755 TTTTTCAATT
*
31401765 TTTTATATATGAATTTTAGTTTGACATAA
1 TTTTATATATGAATTTTAATTT-ACATAA
31401794 TTTTATATATGAAATTTTAATTT-CATA
1 TTTTATATATG-AATTTTAATTTACATA
31401821 CTATTTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 11 0.44
30 10 0.40
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
TTTTATATATGAATTTTAATTTACATAA
Found at i:31404550 original size:12 final size:12
Alignment explanation
Indices: 31404533--31404561 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31404523 AATATTATTT
31404533 TATTAAATTTAA
1 TATTAAATTTAA
31404545 TATTAAATTTAA
1 TATTAAATTTAA
31404557 T-TTAA
1 TATTAA
31404562 TACTTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTAAATTTAA
Found at i:31404693 original size:17 final size:17
Alignment explanation
Indices: 31404671--31404757 Score: 55
Period size: 17 Copynumber: 5.5 Consensus size: 17
31404661 TAATAAGATT
31404671 TAATATTAAATTTAATA
1 TAATATTAAATTTAATA
*
31404688 TAATATT-TATTT--T-
1 TAATATTAAATTTAATA
31404701 TAATATT-AATTT-A-A
1 TAATATTAAATTTAATA
**
31404715 TAATATTTATTTTTAATA
1 TAATA-TTAAATTTAATA
* * *
31404733 -AATATTAGATTAAATT
1 TAATATTAAATTTAATA
31404749 TAATATTAA
1 TAATATTAA
31404758 TTTGATTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
13 11 0.20
14 6 0.11
15 2 0.04
16 15 0.28
17 19 0.35
18 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
TAATATTAAATTTAATA
Found at i:31404698 original size:21 final size:21
Alignment explanation
Indices: 31404674--31404773 Score: 53
Period size: 21 Copynumber: 4.6 Consensus size: 21
31404664 TAAGATTTAA
31404674 TATTAAATTTAATATAATATT
1 TATTAAATTTAATATAATATT
* * *
31404695 TATTTTTAATATTAATTTAATA-A
1 TA--TTAAAT-TTAATATAATATT
**
31404718 TATTTATTTTTAATA-AATATT
1 TA-TTAAATTTAATATAATATT
*
31404739 AGATTAAATTTAATATTAAT-TT
1 -TATTAAATTTAATA-TAATATT
* *
31404761 GATTAATTTTAAT
1 TATTAAATTTAAT
31404774 TATAGTTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
20 4 0.07
21 29 0.48
22 7 0.12
23 10 0.17
24 10 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTAAATTTAATATAATATT
Found at i:31404703 original size:24 final size:27
Alignment explanation
Indices: 31404653--31404730 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
31404643 ATAAATATTC
* * *
31404653 TATTAATTTAATAAGATTTAATATTAAA
1 TATTAA-TTAATAATATTTATTTTTAAA
31404681 T-TTAA-T-ATAATATTTATTTTT-AA
1 TATTAATTAATAATATTTATTTTTAAA
31404704 TATTAATTTAATAATATTTATTTTTAA
1 TATTAA-TTAATAATATTTATTTTTAA
31404731 TAAATATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 3 0.07
24 16 0.38
25 1 0.02
26 1 0.02
27 19 0.45
28 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TATTAATTAATAATATTTATTTTTAAA
Found at i:31404706 original size:13 final size:13
Alignment explanation
Indices: 31404688--31404732 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
31404678 AAATTTAATA
31404688 TAATATTTATTTT
1 TAATATTTATTTT
* *
31404701 TAATATTAATTTAA
1 TAATATTTATTT-T
31404715 TAATATTTATTTT
1 TAATATTTATTTT
31404728 TAATA
1 TAATA
31404733 AATATTAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATTTATTTT
Found at i:31404717 original size:27 final size:30
Alignment explanation
Indices: 31404669--31404732 Score: 107
Period size: 27 Copynumber: 2.2 Consensus size: 30
31404659 TTTAATAAGA
31404669 TTTAATATTAAATTTAATATAATATTTATT
1 TTTAATATTAAATTTAATATAATATTTATT
31404699 TTTAATATT-AATTT-A-ATAATATTTATT
1 TTTAATATTAAATTTAATATAATATTTATT
31404726 TTTAATA
1 TTTAATA
31404733 AATATTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 19 0.56
28 1 0.03
29 5 0.15
30 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTAATATTAAATTTAATATAATATTTATT
Found at i:31404731 original size:16 final size:15
Alignment explanation
Indices: 31404687--31404738 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 15
31404677 TAAATTTAAT
31404687 ATAATATTTATTTT-
1 ATAATATTTATTTTA
*
31404701 -TAATA-TTAATTTA
1 ATAATATTTATTTTA
31404714 ATAATATTTATTTTTA
1 ATAATATTTA-TTTTA
31404730 ATAAATATT
1 AT-AATATT
31404739 AGATTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 5 0.16
15 3 0.10
16 6 0.19
17 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATATTTATTTTA
Found at i:31405389 original size:40 final size:39
Alignment explanation
Indices: 31405313--31405391 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
31405303 ACCGTCAATT
* * *
31405313 TTTTTTTTTTAAGTTTTAAGTTTTATTATAATAATTTAA
1 TTTTTTTTTTAAGTTTTAAGTTTAAATATAACAATTTAA
*
31405352 TTTTTTTTTTATATTTTTAAAGTTTAAATA-AACAATTTAA
1 TTTTTTTTTTA-AGTTTT-AAGTTTAAATATAACAATTTAA
31405392 AATTTTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 11 0.32
40 14 0.41
41 9 0.26
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (39 bp):
TTTTTTTTTTAAGTTTTAAGTTTAAATATAACAATTTAA
Found at i:31418967 original size:29 final size:29
Alignment explanation
Indices: 31418932--31418992 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
31418922 ATAGGATGTA
31418932 TTTAATAAACCTAAGGAAACCGCGCTAAG
1 TTTAATAAACCTAAGGAAACCGCGCTAAG
31418961 TTTAATAAACCTAAGGAAACCGCGCTAAG
1 TTTAATAAACCTAAGGAAACCGCGCTAAG
31418990 TTT
1 TTT
31418993 TCTGAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (29 bp):
TTTAATAAACCTAAGGAAACCGCGCTAAG
Found at i:31421127 original size:46 final size:46
Alignment explanation
Indices: 31421077--31421252 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
31421067 TGGTTGAGCA
31421077 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
31421123 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
31421168 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
31421216 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31421253 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31421233 original size:93 final size:93
Alignment explanation
Indices: 31421074--31421245 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31421064 GGATGGTTGA
* *
31421074 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31421139 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
31421167 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
31421232 TGAGTTCGAGTTCG
66 TGAGTCCGAGTTCG
31421246 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31424786 original size:2 final size:2
Alignment explanation
Indices: 31424779--31424804 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31424769 TAAATTAAAG
31424779 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31424805 CTTTCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31429687 original size:29 final size:28
Alignment explanation
Indices: 31429643--31429709 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
31429633 AATGAATCTG
* *
31429643 AATTTTAAAATTTAAAAGTCGAGAAATTA
1 AATTTTAAAA-ATAAAAGTAGAGAAATTA
* *
31429672 AATTCTTAAAAATAAAAGTATAGAGATTA
1 AATT-TTAAAAATAAAAGTAGAGAAATTA
31429701 AATTTTAAA
1 AATTTTAAA
31429710 TTTTAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 22 0.67
30 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (28 bp):
AATTTTAAAAATAAAAGTAGAGAAATTA
Found at i:31441431 original size:41 final size:38
Alignment explanation
Indices: 31441386--31441489 Score: 104
Period size: 37 Copynumber: 2.7 Consensus size: 38
31441376 ACTTCAAGTC
*
31441386 GATGAGACACTAGGTGTTAATTTACTACTTCGGATTAATCA
1 GATGAGACACTAGGTGTCAATTTA-T--TTCGGATTAATCA
* * * *
31441427 GATGACG-CACTGGGTGCCAATTTATTTCGGTTTAGTCA
1 GATGA-GACACTAGGTGTCAATTTATTTCGGATTAATCA
*
31441465 -ATGAGACACTTGGTGTCAATTTATT
1 GATGAGACACTAGGTGTCAATTTATT
31441490 ATTTTAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
36 1 0.02
37 21 0.39
38 11 0.20
40 1 0.02
41 19 0.35
42 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (38 bp):
GATGAGACACTAGGTGTCAATTTATTTCGGATTAATCA
Found at i:31442424 original size:15 final size:15
Alignment explanation
Indices: 31442404--31442433 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31442394 CCCTAATCAG
31442404 CCCCCACTTGCCTTC
1 CCCCCACTTGCCTTC
31442419 CCCCCACTTGCCTTC
1 CCCCCACTTGCCTTC
31442434 TGCCGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.60, G:0.07, T:0.27
Consensus pattern (15 bp):
CCCCCACTTGCCTTC
Found at i:31443732 original size:16 final size:16
Alignment explanation
Indices: 31443711--31443762 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
31443701 ATTTTTAGTA
31443711 CTTATTATAATATTTT
1 CTTATTATAATATTTT
*
31443727 CTTATTAT--TA-TGT
1 CTTATTATAATATTTT
*
31443740 -ATATTATAATATTTT
1 CTTATTATAATATTTT
31443755 CTTATTAT
1 CTTATTAT
31443763 TATGTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 4 0.14
15 2 0.07
16 14 0.50
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (16 bp):
CTTATTATAATATTTT
Found at i:31443748 original size:28 final size:28
Alignment explanation
Indices: 31443713--31443774 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
31443703 TTTTAGTACT
31443713 TATTATAATATTTTCTTATTATTATGTA
1 TATTATAATATTTTCTTATTATTATGTA
31443741 TATTATAATATTTTCTTATTATTATGTA
1 TATTATAATATTTTCTTATTATTATGTA
31443769 TATTAT
1 TATTAT
31443775 TTTTACTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
TATTATAATATTTTCTTATTATTATGTA
Found at i:31443786 original size:25 final size:27
Alignment explanation
Indices: 31443713--31443788 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
31443703 TTTTAGTACT
* *
31443713 TATTATAATATTTTCTTATTATTATGTA
1 TATTAT-ATATTTACTCATTATTATGTA
* *
31443741 TATTATAATATTTTCTTATTATTATGTA
1 TATTAT-ATATTTACTCATTATTATGTA
31443769 TATTAT-T-TTTACTCATTATT
1 TATTATATATTTACTCATTATT
31443789 TTTACTCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 11 0.24
26 1 0.02
28 34 0.74
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTATATATTTACTCATTATTATGTA
Found at i:31443788 original size:13 final size:13
Alignment explanation
Indices: 31443770--31443798 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31443760 TATTATGTAT
31443770 ATTATTTTTACTC
1 ATTATTTTTACTC
31443783 ATTATTTTTACTC
1 ATTATTTTTACTC
31443796 ATT
1 ATT
31443799 TCTTCACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTTTTACTC
Found at i:31443943 original size:23 final size:22
Alignment explanation
Indices: 31443917--31443967 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
31443907 TCATGTTTTT
31443917 TATATAT-GTATATATCTTTAATG
1 TATATATAG-ATATATCTTT-ATG
*
31443940 TATATATAGGTATATCTTTATG
1 TATATATAGATATATCTTTATG
31443962 TA-ATAT
1 TATATAT
31443968 TAGTATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 16 0.62
24 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (22 bp):
TATATATAGATATATCTTTATG
Found at i:31444068 original size:21 final size:20
Alignment explanation
Indices: 31444020--31444068 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
31444010 ATTATGTATA
*
31444020 TATATATTATGTAAATGTTT
1 TATATATTATATAAATGTTT
31444040 TA-ATATTATATATAA-GTTTT
1 TATATATTATATA-AATG-TTT
31444060 TATATATTA
1 TATATATTA
31444069 CGAGTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 9 0.36
21 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
TATATATTATATAAATGTTT
Found at i:31456707 original size:85 final size:85
Alignment explanation
Indices: 31456607--31457128 Score: 416
Period size: 87 Copynumber: 6.4 Consensus size: 85
31456597 TTTCTGTTTG
* *
31456607 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGAGGCACTCTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACTCTGAGGTATTTTCAATT
* * *
31456672 TTTATTTTTTAATTTATGTT
66 TCTATTTTTCAAATTATGTT
* * *
31456692 TCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGCCACATGTCGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACAC-TCT-GAGGTATTTTCAA
* * *
31456757 ATTCTGTTTTTCAAATTCTGTT
64 TTTCTATTTTTCAAATTATGTT
* * *
31456779 TCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAAGACA-TGTTGAGGTATTTTCAA-
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACT-CTGAGGTATTTTCAAT
*
31456842 TT-TATGTTTC--A--A----
65 TTCTATTTTTCAAATTATGTT
* * * *
31456854 --AA--ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACAC-TCT-GAGGTATTTTCAA
** *
31456915 AATCTATTTTTCAAATTCTGTT
64 TTTCTATTTTTCAAATTATGTT
* * * *
31456937 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGATGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACTCTGAGGTATTTTCAATT
*
31457002 TC------T---GTT-TG--
66 TCTATTTTTCAAATTATGTT
** * * * *
31457010 TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGTCATATATCGAGGTATTTTCAA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACA-CTCT-GAGGTATTTTCAA
*** * *
31457075 AAGCTACTTTTCAAATTAAGTT
64 TTTCTATTTTTCAAATTATGTT
*
31457097 TCAAAAAGACCAACTCATATTGCGAGA-GTGAG
1 TC-AAAA-ATCAACTCATATTGCGAGAGGTGAG
31457129 CTCAAGATCA
Statistics
Matches: 350, Mismatches: 51, Indels: 69
0.74 0.11 0.15
Matches are distributed among these distances:
71 35 0.10
72 1 0.00
73 58 0.17
74 2 0.01
75 22 0.06
76 2 0.01
77 1 0.00
79 1 0.00
81 2 0.01
83 6 0.02
84 4 0.01
85 75 0.21
86 4 0.01
87 111 0.32
88 8 0.02
89 18 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (85 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACTCTGAGGTATTTTCAATT
TCTATTTTTCAAATTATGTT
Found at i:31456769 original size:14 final size:14
Alignment explanation
Indices: 31456750--31456779 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31456740 TGTCGAGGTA
31456750 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
31456764 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
31456778 TT
1 TT
31456780 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:31456782 original size:12 final size:13
Alignment explanation
Indices: 31456750--31456783 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
31456740 TGTCGAGGTA
31456750 TTTTCAAATTCTG
1 TTTTCAAATTCTG
31456763 TTTTTCAAATTCTG
1 -TTTTCAAATTCTG
31456777 -TTTCAAA
1 TTTTCAAA
31456784 AATCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
14 13 0.65
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (13 bp):
TTTTCAAATTCTG
Found at i:31456880 original size:71 final size:71
Alignment explanation
Indices: 31456764--31457049 Score: 302
Period size: 73 Copynumber: 3.8 Consensus size: 71
31456754 CAAATTCTGT
* * * *
31456764 TTTTCAAATTCTGTTTCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAAGACATGTT
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACATGTT
31456829 GAGGTA
66 GAGGTA
**
31456835 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAG--ACATG
*
31456900 TCGAGGTA
64 TTGAGGTA
31456908 TTTTCAAAATCTATTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAG
1 TTTTC---A---A--TTT---A---TGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAG
* * *
31456973 CCTCAAGACACGCTGATGTA
52 CCTCAAGACATGTTGAGGTA
* *
31456993 TTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
1 TTTTCAATTTATG-TT-TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
31457050 GGGTCATATA
Statistics
Matches: 182, Mismatches: 15, Indels: 34
0.79 0.06 0.15
Matches are distributed among these distances:
71 54 0.30
72 2 0.01
73 56 0.31
76 1 0.01
77 3 0.02
79 2 0.01
81 3 0.02
82 1 0.01
84 1 0.01
85 14 0.08
87 45 0.25
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (71 bp):
TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACATGTT
GAGGTA
Found at i:31457100 original size:160 final size:158
Alignment explanation
Indices: 31456677--31457128 Score: 672
Period size: 158 Copynumber: 2.8 Consensus size: 158
31456667 CAATTTTTAT
* * * * *
31456677 TTTTTAATTTATGTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGCCACATG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG
* * * *
31456742 TCGAGGTATTTTCAAATTCTGTTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGAGAGAGGT
66 TCGAGGTATTTTCAAAATCTATTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGCGAGAAGT
* *
31456807 GAGTTGAGCCTCAAGACATGTTGAGGTA
131 GAGTTGAGCCTCAAGACACGCTGAGGTA
31456835 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG
31456900 TCGAGGTATTTTCAAAATCTATTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGCGAGAAGT
66 TCGAGGTATTTTCAAAATCTATTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGCGAGAAGT
*
31456965 GAGTTGAGCCTCAAGACACGCTGATGTA
131 GAGTTGAGCCTCAAGACACGCTGAGGTA
* * *
31456993 TTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGTCATA
1 TTTTCAATTTATG-TT-TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACA
* * * ** *
31457058 TATCGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAGACCAACTCATATTGCGAG
64 TGTCGAGGTATTTTCAAAATCTATTTTTCAAATTCTGTTTC-AAAA-ATCAACTCATATTGCGAG
31457123 -AGTGAG
127 AAGTGAG
31457129 CTCAAGATCA
Statistics
Matches: 269, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
158 158 0.59
159 2 0.01
160 82 0.30
161 10 0.04
162 17 0.06
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (158 bp):
TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATG
TCGAGGTATTTTCAAAATCTATTTTTCAAATTCTGTTTCAAAAATCAACTCATATTGCGAGAAGT
GAGTTGAGCCTCAAGACACGCTGAGGTA
Found at i:31457805 original size:15 final size:15
Alignment explanation
Indices: 31457785--31457814 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31457775 CCCTAATCAG
31457785 CCCCCACTTGCCTTC
1 CCCCCACTTGCCTTC
31457800 CCCCCACTTGCCTTC
1 CCCCCACTTGCCTTC
31457815 TGCCGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.60, G:0.07, T:0.27
Consensus pattern (15 bp):
CCCCCACTTGCCTTC
Found at i:31458569 original size:23 final size:22
Alignment explanation
Indices: 31458543--31458589 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
31458533 TCATGTTTTT
31458543 TATATAT-GTATATATCTTTAATG
1 TATATATAG-ATATATCTTT-ATG
*
31458566 TATATATAGGTATATCTTTATG
1 TATATATAGATATATCTTTATG
31458588 TA
1 TA
31458590 ACATTAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 16 0.73
24 1 0.05
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATAGATATATCTTTATG
Found at i:31463016 original size:46 final size:46
Alignment explanation
Indices: 31462941--31463122 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
31462931 TTATCTTTGA
* * * *
31462941 CATGATGCCATAGTATCTTTCAACTATGGTCTTACTCGTTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-ATTTCATGT
* *
31462987 CATGTTGCCATGGTATCATTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
31463033 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
31463079 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
31463123 TTCAGAGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 4 0.03
46 118 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:31463541 original size:23 final size:23
Alignment explanation
Indices: 31463509--31463623 Score: 90
Period size: 23 Copynumber: 4.9 Consensus size: 23
31463499 TTCAGAACCA
*
31463509 TATCGTGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * *
31463532 TATCGGGAAGCT-TCGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * *
31463554 ATATAACGGGAAGTTCAAG-CGAGCAC
1 -TAT--CGGGAAGCTCACGAAGAGC-C
* *
31463580 TATCGGGAGGCTCACAAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
*
31463603 TATTGGGAAGCTCACGAAGAG
1 TATCGGGAAGCTCACGAAGAG
31463624 TTGTATTTTG
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
22 7 0.10
23 42 0.61
24 4 0.06
25 14 0.20
26 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.17
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:31465755 original size:18 final size:18
Alignment explanation
Indices: 31465707--31465755 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
31465697 ATAATATAAT
31465707 TATTTAATTAATAAATATC
1 TATTTAA-TAATAAATATC
*
31465726 TTTTATAAAATAATAAATATC
1 TATT-T--AATAATAAATATC
31465747 TATTTAATA
1 TATTTAATA
31465756 TCTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 14 0.56
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAATAATAAATATC
Found at i:31465820 original size:24 final size:25
Alignment explanation
Indices: 31465793--31465839 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31465783 ATTTTTATCC
*
31465793 ATACACTTGTA-TATTTTATTTACT
1 ATACACTTGTACTAATTTATTTACT
*
31465817 ATACATTTGTACTAATTTATTTA
1 ATACACTTGTACTAATTTATTTA
31465840 TCATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (25 bp):
ATACACTTGTACTAATTTATTTACT
Found at i:31467373 original size:51 final size:51
Alignment explanation
Indices: 31467297--31467414 Score: 182
Period size: 51 Copynumber: 2.3 Consensus size: 51
31467287 ACACTGATCA
* *
31467297 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* *
31467348 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTAT
1 CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
* *
31467399 CACTTGTCACTGATCA
1 CATTTGTCACTTATCA
31467415 GAAGTACTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
CATTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:31481544 original size:26 final size:26
Alignment explanation
Indices: 31481511--31481564 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
31481501 CCCTGTGAAA
31481511 AGGAATGAGATTTGCCTGAGAAAGAG
1 AGGAATGAGATTTGCCTGAGAAAGAG
31481537 AGGAATGAGATTTGCCTGAGAAAGAG
1 AGGAATGAGATTTGCCTGAGAAAGAG
31481563 AG
1 AG
31481565 AAAGAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.35, T:0.19
Consensus pattern (26 bp):
AGGAATGAGATTTGCCTGAGAAAGAG
Found at i:31481659 original size:18 final size:18
Alignment explanation
Indices: 31481625--31481659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31481615 AGGTGATGGA
*
31481625 AAATGTAAAATATTTTCC
1 AAATGTAAAATACTTTCC
*
31481643 AAATGTAAAATGCTTTC
1 AAATGTAAAATACTTTC
31481660 AACCTTCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATGTAAAATACTTTCC
Found at i:31486222 original size:30 final size:31
Alignment explanation
Indices: 31486169--31486231 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
31486159 AAATAATCAT
* * *
31486169 TGAATTATTTAAAAATTTTTATTTAAGTCAC
1 TGAACTATTTAAAAATATTTATTTAAGGCAC
31486200 TGAACTATTTAAAAA-ATTTATTTAAGGCAC
1 TGAACTATTTAAAAATATTTATTTAAGGCAC
31486230 TG
1 TG
31486232 GTAGAGGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (31 bp):
TGAACTATTTAAAAATATTTATTTAAGGCAC
Found at i:31489858 original size:34 final size:34
Alignment explanation
Indices: 31489809--31489877 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
31489799 GTATTAAGAG
31489809 TCAGATTACAATTTACCCCATTTGCTTAAAAAAT
1 TCAGATTACAATTTACCCCATTTGCTTAAAAAAT
* *
31489843 TCAGATTGCATTTTACCCCATTTGCTTAAAAAAT
1 TCAGATTACAATTTACCCCATTTGCTTAAAAAAT
31489877 T
1 T
31489878 GGCAAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (34 bp):
TCAGATTACAATTTACCCCATTTGCTTAAAAAAT
Found at i:31492526 original size:6 final size:6
Alignment explanation
Indices: 31492515--31492541 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31492505 GGGGTTGAAT
31492515 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTA
31492542 TAACTATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:31495787 original size:27 final size:27
Alignment explanation
Indices: 31495757--31495809 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
31495747 TAGGTGTTAC
31495757 ATTTTAATGAAA-CTATAAGGTTTTTAA
1 ATTTTAATGAAATC-ATAAGGTTTTTAA
*
31495784 ATTTTAATGAAATCCTAAGGTTTTTA
1 ATTTTAATGAAATCATAAGGTTTTTA
31495810 TCGGATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (27 bp):
ATTTTAATGAAATCATAAGGTTTTTAA
Found at i:31499283 original size:16 final size:16
Alignment explanation
Indices: 31499262--31499292 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31499252 TCAAATTTAA
31499262 CTGAAATATGAGTCAT
1 CTGAAATATGAGTCAT
31499278 CTGAAATATGAGTCA
1 CTGAAATATGAGTCA
31499293 CACTCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
CTGAAATATGAGTCAT
Found at i:31501026 original size:23 final size:24
Alignment explanation
Indices: 31500992--31501040 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
31500982 GATAAAAACT
31500992 AAACCCTAAAAAACA-AAA-ATAAA
1 AAACCCT-AAAAACATAAACATAAA
*
31501015 AAACCCTCAAAACATAAACATAAA
1 AAACCCTAAAAACATAAACATAAA
31501039 AA
1 AA
31501041 TTCTCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 10 0.43
24 7 0.30
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.10
Consensus pattern (24 bp):
AAACCCTAAAAACATAAACATAAA
Found at i:31502241 original size:21 final size:21
Alignment explanation
Indices: 31502217--31502257 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31502207 CTGACCAACC
* *
31502217 CTTATGGGTTTCAGTTTAGCA
1 CTTATGGGCTTCAGTGTAGCA
*
31502238 CTTATGTGCTTCAGTGTAGC
1 CTTATGGGCTTCAGTGTAGC
31502258 CTTTAGGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (21 bp):
CTTATGGGCTTCAGTGTAGCA
Found at i:31504335 original size:32 final size:33
Alignment explanation
Indices: 31504256--31504340 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
31504246 TTCAAGTAAT
* *
31504256 ATTATGTTTATTTAAAAGATTTTACTTTAAATA
1 ATTATGTTTATTTAAAAGATATTACGTTAAATA
* * * * *
31504289 GTTATATTTATTTAAGATATATTA-GTTGAATA
1 ATTATGTTTATTTAAAAGATATTACGTTAAATA
31504321 ATTATGTTTATTTAAAAGAT
1 ATTATGTTTATTTAAAAGAT
31504341 GTAATTATTC
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 22 0.54
33 19 0.46
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (33 bp):
ATTATGTTTATTTAAAAGATATTACGTTAAATA
Found at i:31512083 original size:6 final size:6
Alignment explanation
Indices: 31512072--31512110 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
31512062 ATTTTCTCTC
31512072 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CAT
1 CATCTT CATCTT CATCTT CATCTT CATCTT CATCTT CAT
31512111 GTCGTGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (6 bp):
CATCTT
Found at i:31514183 original size:15 final size:15
Alignment explanation
Indices: 31514163--31514192 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
31514153 TAGAATCACG
31514163 TTTTTTTTTT-TGTT
1 TTTTTTTTTTATGTT
31514177 TTTTTTTTTTATGTT
1 TTTTTTTTTTATGTT
31514192 T
1 T
31514193 GAAATGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTATGTT
Found at i:31522896 original size:8 final size:8
Alignment explanation
Indices: 31522883--31522909 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31522873 GTCAAAATAT
31522883 TTATTTTA
1 TTATTTTA
31522891 TTATTTTA
1 TTATTTTA
31522899 TTATTTTA
1 TTATTTTA
31522907 TTA
1 TTA
31522910 AAGTTTAAGC
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:31523873 original size:25 final size:25
Alignment explanation
Indices: 31523845--31523895 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31523835 TGAGCGATAC
31523845 GAGGTAAGTTCGTATAATTAGAATT
1 GAGGTAAGTTCGTATAATTAGAATT
31523870 GAGGTAAGTTCGTATAATTAGAATT
1 GAGGTAAGTTCGTATAATTAGAATT
31523895 G
1 G
31523896 GACTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (25 bp):
GAGGTAAGTTCGTATAATTAGAATT
Found at i:31524131 original size:26 final size:24
Alignment explanation
Indices: 31524092--31524193 Score: 75
Period size: 23 Copynumber: 4.2 Consensus size: 24
31524082 GGACTCACCA
* *
31524092 CAGCTTGTATGAGCTTATCGATATAT
1 CAGCTCGTAAGAGCTTATCG-T-TAT
* *
31524118 CAGCTCGTAAGAGCTTACCGTTCT
1 CAGCTCGTAAGAGCTTATCGTTAT
* * *
31524142 CAGCTCGTAGGAGCTTATTGAT-T
1 CAGCTCGTAAGAGCTTATCGTTAT
* *
31524165 CAGCTTGTCAA-AGCTTACCGTT-T
1 CAGCTCGT-AAGAGCTTATCGTTAT
31524188 CAGCTC
1 CAGCTC
31524194 AATAGAGCTT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
23 22 0.36
24 21 0.34
25 1 0.02
26 17 0.28
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.33
Consensus pattern (24 bp):
CAGCTCGTAAGAGCTTATCGTTAT
Found at i:31524148 original size:24 final size:23
Alignment explanation
Indices: 31524117--31524193 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
31524107 TATCGATATA
31524117 TCAGCTCGTAAGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACCGTT
* ** *
31524140 CTCAGCTCGTAGGAGCTTATTGAT
1 -TCAGCTCGTAAGAGCTTACCGTT
*
31524164 TCAGCTTGTCAA-AGCTTACCGTT
1 TCAGCTCGT-AAGAGCTTACCGTT
31524187 TCAGCTC
1 TCAGCTC
31524194 AATAGAGCTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (23 bp):
TCAGCTCGTAAGAGCTTACCGTT
Found at i:31525733 original size:25 final size:24
Alignment explanation
Indices: 31525686--31525751 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
31525676 CGAAAGAGTG
*
31525686 TCCCGTTATTAGCTCTTATGAGCT
1 TCCCGTTATTAGCTCTTACGAGCT
* *
31525710 TCCCGTTATATAGTTCTTGCGAGCT
1 TCCCGTTAT-TAGCTCTTACGAGCT
** *
31525735 TCCTATTAATAGCTCTT
1 TCCCGTTATTAGCTCTT
31525752 CAAAGCATCC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.42
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTTACGAGCT
Found at i:31533598 original size:46 final size:46
Alignment explanation
Indices: 31533490--31533709 Score: 309
Period size: 46 Copynumber: 4.8 Consensus size: 46
31533480 GGCAACCTGA
*
31533490 GTGTAAGACCATGGTTGAAAGATACCATGGCAACTTGATAT-AAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAAT
*
31533535 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAAT
*
31533581 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAAT
*** *
31533627 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG-AAAT
* * * * *
31533673 GAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
31533710 TCAAAGATAA
Statistics
Matches: 160, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
45 41 0.26
46 119 0.74
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAAT
Found at i:31534284 original size:11 final size:11
Alignment explanation
Indices: 31534268--31534319 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
31534258 TATACTAAAT
31534268 AAATAATAATA
1 AAATAATAATA
*
31534279 AAATAAT-ATT
1 AAATAATAATA
* *
31534289 AAATATCTCATA
1 AAATA-ATAATA
*
31534301 AAATATTAATA
1 AAATAATAATA
31534312 AAATAATA
1 AAATAATA
31534320 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:31535867 original size:11 final size:11
Alignment explanation
Indices: 31535851--31535902 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
31535841 TATACTAAAT
31535851 AAATAATAATA
1 AAATAATAATA
*
31535862 AAATAAT-ATT
1 AAATAATAATA
* *
31535872 AAATATCTCATA
1 AAATA-ATAATA
*
31535884 AAATATTAATA
1 AAATAATAATA
31535895 AAATAATA
1 AAATAATA
31535903 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:31542001 original size:42 final size:42
Alignment explanation
Indices: 31541935--31542033 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
31541925 ACGGGCAGAG
* * * *
31541935 ACACGAGCGTGTGTCTTAGTTGTGTGTGTCACACGGCCTAGA
1 ACACGAGCATGTGTCTCAGCTGTGTGTGTCACACGACCTAGA
31541977 ACACGAGCATGTGTCTCAGCTGTGTGTGTCACACGACCTAGA
1 ACACGAGCATGTGTCTCAGCTGTGTGTGTCACACGACCTAGA
*
31542019 ACACGAGCATATGTC
1 ACACGAGCATGTGTC
31542034 CTGGCCGTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (42 bp):
ACACGAGCATGTGTCTCAGCTGTGTGTGTCACACGACCTAGA
Found at i:31544417 original size:14 final size:14
Alignment explanation
Indices: 31544398--31544448 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
31544388 TTATCTATTT
31544398 TTTATTTGTTTTTC
1 TTTATTTGTTTTTC
*
31544412 TTTA-TT-TCTTT-
1 TTTATTTGTTTTTC
*
31544423 ATTATTTGTTTTTC
1 TTTATTTGTTTTTC
31544437 TTTATTTGTTTT
1 TTTATTTGTTTT
31544449 ATAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 3 0.10
12 6 0.20
13 6 0.20
14 15 0.50
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTATTTGTTTTTC
Found at i:31544417 original size:21 final size:22
Alignment explanation
Indices: 31544393--31544443 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 22
31544383 GTTTTTTATC
31544393 TATTTT-TTATTTGTTTTTCTT
1 TATTTTATTATTTGTTTTTCTT
31544414 TATTTCTTTATTATTTGTTTTTCTT
1 TA--T-TTTATTATTTGTTTTTCTT
31544439 TATTT
1 TATTT
31544444 GTTTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 2 0.08
24 3 0.12
25 17 0.65
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (22 bp):
TATTTTATTATTTGTTTTTCTT
Found at i:31544819 original size:25 final size:25
Alignment explanation
Indices: 31544769--31544843 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
31544759 ACCTTTTGTC
* *
31544769 CTTTTTTTGCTTTTTTATTTGA-TTTT
1 CTTTATTTG-TTTATTATTT-ATTTTT
31544795 CTTTATTTGTTTATTATTTATTTTT
1 CTTTATTTGTTTATTATTTATTTTT
* *
31544820 CTTTATTTCTTTATTATTTGTTTT
1 CTTTATTTGTTTATTATTTATTTT
31544844 ATAATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 1 0.02
25 35 0.80
26 8 0.18
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (25 bp):
CTTTATTTGTTTATTATTTATTTTT
Found at i:31544869 original size:395 final size:391
Alignment explanation
Indices: 31544010--31545074 Score: 1471
Period size: 395 Copynumber: 2.7 Consensus size: 391
31544000 ATTTTTCTGT
* * *
31544010 TTTTTATTTGTTTTTCTTT-TTTATTATTATTTGTTTTATAATATTTTATGTATATTTTTCTGGT
1 TTTTTATTTATTTTTCTTTATTTTTTATTATTTGTTTTATAATATTTTATGTATATTTTTTTGGT
31544074 GGAGCCATTCTAAATGGTGCCACCAATACGTTCTTTTTTAATTTATTTTTTTATATTTAAAAATT
66 GGAGCCATTCTAAATGGTGCCACCAATACGTTCTTTTTTAA--TATTTTTTTATATTTAAAAATT
* *
31544139 TTAAAAAATAATATTTTATTTGGTGAAGCCATTCTATTTGGCGTGACCGAATTTATATATATAAG
129 TT-AAAAATAATATTTTATTTGGTG-AGCCATTCTATTTGGCATGACCAAATTTATATATATAAG
* *
31544204 ACTCTCAATGACACATGAATCTGAGTTGAAAGAAAAAAAATTACTTATACTTTGTTAGAGGATGA
192 CCTCTCAATGACACATGAATCTGAGTTAAAAG-AAAAAAATTACTTATACTTTGTTAGAGGATGA
31544269 ATGAGATGAAAAAATGGGGAGGGGGACTTTAAACAAATTTTCCTTTTTCTGGTGGAGCCAAATAA
256 ATGAGATGAAAAAATGGGGAGGGGGA-TTTAAACAAATTTTCCTTTTTCTGGTGGAGCCAAATAA
*
31544334 TTTGGCGCCACCAGATTCCAACGCCTCTGCTACCTTTTGTCCTTCTTCTGTTTTTTATCTATTTT
320 TTTGGCACCACCAGATTCCAACGCCTCTGCTACCTTTTGTCCTTCTTCTGTTTTTTATCTATTTT
31544399 TTATTTG
385 TTATTTG
* * *
31544406 TTTTTCTTTATTTCTT-TATTATTTGTTTTTCTTTATTTGTTTTATAATATTTTATGTATAATTT
1 TTTTTATTTATTT-TTCT-TTA--T-TTTTT-ATTATTTGTTTTATAATATTTTATGTATATTTT
* * *
31544470 TTTGGTGGAACCATTCTAAATGGTGCCACTAATAC-AT-TTTTTTAA-A-TTTTTTATATTTAAA
60 TTTGGTGGAGCCATTCTAAATGGTGCCACCAATACGTTCTTTTTTAATATTTTTTTATATTTAAA
* **
31544531 AATTTTAAAATATAATATTTTATTTGGTAGAGCCATTATATTTGGTTTGACCAAATTTATATATA
125 AATTTTAAAA-ATAATATTTTATTTGGT-GAGCCATTCTATTTGGCATGACCAAATTTATATATA
*
31544596 TAAGCCTATCAATGACACATGAATCTGAGTTAAAAGAAAAAAATTACTTATACTTTGTTAGAGGA
188 TAAGCCTCTCAATGACACATGAATCTGAGTTAAAAGAAAAAAATTACTTATACTTTGTTAGAGGA
* * *
31544661 TGAGTGGGATGAAAAAATGGGGGGAGGGGG-TTTAAACAAATTTT-CTTTTTTTGGTGGAGCCAA
253 TGAATGAGATGAAAAAAT--GGGGAGGGGGATTTAAACAAATTTTCCTTTTTCTGGTGGAGCCAA
* * *
31544724 ATAATTTGGCACCACCAGATTCCAACGCCTCTGCTACCTTTTGTCCTTTTTTTGCTTTTTTATTT
316 ATAATTTGGCACCACCAGATTCCAACGCCTCTGCTACCTTTTGTCCTTCTTCTG-TTTTTTATCT
31544789 GATTTTCTTTATTTG
380 -A-TTT-TTTATTTG
31544804 TTTATTATTTATTTTTCTTTATTTCTTTATTATTTGTTTTATAATATTTTATGTATATTTTTTTG
1 TTT-TTATTTATTTTTCTTTATTT-TTTATTATTTGTTTTATAATATTTTATGTATATTTTTTTG
* ** *
31544869 GTGGAGTCATTCTAAATGGCACCACCACCAATACGTTCTTTTTTAATTTATTTTTTTATAATTAA
64 GTGGAGCCATTCTAAATGG---TGCCACCAATACGTTCTTTTTTAA--TATTTTTTTATATTTAA
* * * * *
31544934 AATTTTTAAAAATAATATTTTATTTGGTGGAACCATTCTATTTGGCATGATCAAATTTGTATATG
124 AAATTTTAAAAATAATATTTTATTTGGT-GAGCCATTCTATTTGGCATGACCAAATTTATATATA
* * * *
31544999 CAAGCCTCTCATTGACACATGAATCTGAGTTGAAAGAAAAAAAAATTACTTATACTTTGTCAGAG
188 TAAGCCTCTCAATGACACATGAATCTGAGTT-AAA-AGAAAAAAATTACTTATACTTTGTTAGAG
31545064 GATGAATGAGA
251 GATGAATGAGA
31545075 GAGATATGAT
Statistics
Matches: 591, Mismatches: 49, Indels: 49
0.86 0.07 0.07
Matches are distributed among these distances:
394 69 0.12
395 126 0.21
396 119 0.20
397 19 0.03
398 25 0.04
399 11 0.02
400 17 0.03
401 5 0.01
402 63 0.11
403 75 0.13
404 26 0.04
405 36 0.06
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (391 bp):
TTTTTATTTATTTTTCTTTATTTTTTATTATTTGTTTTATAATATTTTATGTATATTTTTTTGGT
GGAGCCATTCTAAATGGTGCCACCAATACGTTCTTTTTTAATATTTTTTTATATTTAAAAATTTT
AAAAATAATATTTTATTTGGTGAGCCATTCTATTTGGCATGACCAAATTTATATATATAAGCCTC
TCAATGACACATGAATCTGAGTTAAAAGAAAAAAATTACTTATACTTTGTTAGAGGATGAATGAG
ATGAAAAAATGGGGAGGGGGATTTAAACAAATTTTCCTTTTTCTGGTGGAGCCAAATAATTTGGC
ACCACCAGATTCCAACGCCTCTGCTACCTTTTGTCCTTCTTCTGTTTTTTATCTATTTTTTATTT
G
Found at i:31548713 original size:15 final size:15
Alignment explanation
Indices: 31548693--31548723 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31548683 GTTGCAAGAG
31548693 AACATTAAAAATCAC
1 AACATTAAAAATCAC
31548708 AACATTAAAAATCAC
1 AACATTAAAAATCAC
31548723 A
1 A
31548724 TTCTTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (15 bp):
AACATTAAAAATCAC
Found at i:31553836 original size:186 final size:186
Alignment explanation
Indices: 31553522--31553893 Score: 726
Period size: 186 Copynumber: 2.0 Consensus size: 186
31553512 TTTTTTTTAA
31553522 TCGCAACTCTACTCTTTGCCGACCTTGAAATACACAACTAACATCACTTTCTACAATTTCACCAT
1 TCGCAACTCTACTCTTTGCCGACCTTGAAATACACAACTAACATCACTTTCTACAATTTCACCAT
31553587 AAAAAAGAATGTACACCAAAAACACCTCGTTATTCATCTTCAATAGAATTTTTGAACTCTCCTAC
66 AAAAAAGAATGTACACCAAAAACACCTCGTTATTCATCTTCAATAGAATTTTTGAACTCTCCTAC
*
31553652 TAAACACAATAATTTCACCATTCTATATATATTAGAAAACTAAGTGGTGGAGCCAT
131 TAAACACAACAATTTCACCATTCTATATATATTAGAAAACTAAGTGGTGGAGCCAT
*
31553708 TCGCAACTCTACTCTTTGCCGACCTTGATATACACAACTAACATCACTTTCTACAATTTCACCAT
1 TCGCAACTCTACTCTTTGCCGACCTTGAAATACACAACTAACATCACTTTCTACAATTTCACCAT
31553773 AAAAAAGAATGTACACCAAAAACACCTCGTTATTCATCTTCAATAGAATTTTTGAACTCTCCTAC
66 AAAAAAGAATGTACACCAAAAACACCTCGTTATTCATCTTCAATAGAATTTTTGAACTCTCCTAC
31553838 TAAACACAACAATTTCACCATTCTATATATATTAGAAAACTAAGTGGTGGAGCCAT
131 TAAACACAACAATTTCACCATTCTATATATATTAGAAAACTAAGTGGTGGAGCCAT
31553894 AAAGAATGGC
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 184 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (186 bp):
TCGCAACTCTACTCTTTGCCGACCTTGAAATACACAACTAACATCACTTTCTACAATTTCACCAT
AAAAAAGAATGTACACCAAAAACACCTCGTTATTCATCTTCAATAGAATTTTTGAACTCTCCTAC
TAAACACAACAATTTCACCATTCTATATATATTAGAAAACTAAGTGGTGGAGCCAT
Found at i:31554167 original size:10 final size:10
Alignment explanation
Indices: 31554135--31554168 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31554125 TTGAATAAAC
31554135 AAATATTATA
1 AAATATTATA
*
31554145 AAACATT-TA
1 AAATATTATA
31554154 AAATATTATA
1 AAATATTATA
31554164 AAATA
1 AAATA
31554169 AATTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATATTATA
Found at i:31554222 original size:68 final size:68
Alignment explanation
Indices: 31554031--31554326 Score: 321
Period size: 66 Copynumber: 4.2 Consensus size: 68
31554021 ATTATTTTTT
*
31554031 AAAAATT-TAAATATAATTAAAAAAATGTTTGAATAAACAAATATTATAAAACATTTAAAA-ATT
1 AAAAATTATAAATA-AATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATT
31554094 A-AA
65 ATAA
* *
31554097 AAAAATAATAAACAAATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTA
1 AAAAATTATAAATAAATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTA
31554162 TAA
66 TAA
* * *
31554165 AATAAATTATAAATAAATT-AAAAAACGTTTTAATAGACAAATATTACAAAACATTTAAAATATT
1 AA-AAATTATAAATAAATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATA-T
31554229 ATAAAGCAAATAA
64 -T-------ATAA
** * *
31554242 TAAACAATTTTATAAATAAATTTTAAAAATGTTTGAATAAATAAATATTATAAAACATTTAAAAT
1 -AAA-AA--TTATAAATAAATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAAT
31554307 ATTATAA
62 ATTATAA
*
31554314 AACAAATAATAAA
1 AA-AAATTATAAA
31554327 CAATTTTAAA
Statistics
Matches: 196, Mismatches: 15, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
66 51 0.26
67 9 0.05
68 44 0.22
69 21 0.11
70 1 0.01
71 4 0.02
72 5 0.03
77 5 0.03
78 4 0.02
79 1 0.01
80 14 0.07
81 37 0.19
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (68 bp):
AAAAATTATAAATAAATTAAAAAAACGTTTGAATAAACAAATATTATAAAACATTTAAAATATTA
TAA
Found at i:31554307 original size:27 final size:25
Alignment explanation
Indices: 31554253--31554307 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
31554243 AAACAATTTT
**
31554253 ATAAATAAATTTTAAAAATGTTTGA
1 ATAAATAAATTTTAAAAATGTTAAA
31554278 ATAAATAAATATTATAAAACAT-TTAAA
1 ATAAATAAAT-TT-TAAAA-ATGTTAAA
31554305 ATA
1 ATA
31554308 TTATAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 11 0.44
28 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
ATAAATAAATTTTAAAAATGTTAAA
Found at i:31554353 original size:16 final size:17
Alignment explanation
Indices: 31554316--31554355 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
31554306 TATTATAAAA
*
31554316 CAAATAATAAACAATTT
1 CAAAAAATAAACAATTT
*
31554333 TAAAAAATAAA-AATTT
1 CAAAAAATAAACAATTT
31554349 CAAAAAA
1 CAAAAAA
31554356 AAGTTTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (17 bp):
CAAAAAATAAACAATTT
Found at i:31554389 original size:86 final size:84
Alignment explanation
Indices: 31554173--31554427 Score: 356
Period size: 81 Copynumber: 3.0 Consensus size: 84
31554163 AAAATAAATT
* * * * * *
31554173 ATAAATAAATTAAAAAACGTTTTAATAGACAAATATTACAAAACATTTAAAATATTATAAAGCAA
1 ATAAA-AATTTAAAAAAAGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAA
*
31554238 ATAATAAACAATTTT-ATAA
65 ATAATAAACAATTTTAAAAA
* * *
31554257 AT--AAATTTTAAAAATGTTTGAATAAATAAATATTATAAAACATTTAAAATATTATAAAACAAA
1 ATAAAAATTTAAAAAAAGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAA
31554320 TAATAAACAATTTTAAAAA
66 TAATAAACAATTTTAAAAA
*
31554339 ATAAAAATTTCAAAAAAAAGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAATA
1 ATAAAAATTT--AAAAAAAGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAACA
31554404 AATAATAAACAA-TTTAAAAA
64 AATAATAAACAATTTTAAAAA
31554424 ATAA
1 ATAA
31554428 TAATAAACAA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
81 66 0.43
82 6 0.04
84 8 0.05
85 12 0.08
86 61 0.40
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (84 bp):
ATAAAAATTTAAAAAAAGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAA
TAATAAACAATTTTAAAAA
Found at i:31554402 original size:10 final size:10
Alignment explanation
Indices: 31554370--31554403 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31554360 TTGAATAAAC
31554370 AAATATTATA
1 AAATATTATA
*
31554380 AAACATT-TA
1 AAATATTATA
31554389 AAATATTATA
1 AAATATTATA
31554399 AAATA
1 AAATA
31554404 AATAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATATTATA
Found at i:31554440 original size:33 final size:33
Alignment explanation
Indices: 31554363--31554441 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
31554353 AAAAAGTTTG
* *
31554363 AATAAACAAATATTATAAAACATTTAAAATATTAT
1 AATAAACAAATA--ATAAAACATTTAAAAAATAAT
*
31554398 -A-AAATAAATAAT-AAACAATTTAAAAAATAAT
1 AATAAACAAATAATAAAAC-ATTTAAAAAATAAT
31554429 AATAAACAAATAA
1 AATAAACAAATAA
31554442 AGAAAAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 4 0.11
31 14 0.38
32 1 0.03
33 17 0.46
34 1 0.03
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (33 bp):
AATAAACAAATAATAAAACATTTAAAAAATAAT
Found at i:31554447 original size:23 final size:23
Alignment explanation
Indices: 31554398--31554447 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
31554388 AAAATATTAT
* *
31554398 AAAATAAATAATAAACAATTTAA
1 AAAATAAATAATAAACAAATAAA
31554421 AAAAT-AATAATAAACAAATAAA
1 AAAATAAATAATAAACAAATAAA
31554443 GAAAA
1 -AAAA
31554448 ACAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAATAAATAATAAACAAATAAA
Found at i:31558735 original size:53 final size:53
Alignment explanation
Indices: 31558655--31558763 Score: 191
Period size: 53 Copynumber: 2.1 Consensus size: 53
31558645 CATAATATCA
* *
31558655 TAGACAAAAGACACCAATAAGGAGATGATGTCGGTGGTCCATTAATTATTATT
1 TAGACAAAAGACACCAATAAGAAGATGATGTCGGTGGTCCACTAATTATTATT
*
31558708 TAGACAAAAGACACCAATAAGAAGATGATGTCGGTGGTGCACTAATTATTATT
1 TAGACAAAAGACACCAATAAGAAGATGATGTCGGTGGTCCACTAATTATTATT
31558761 TAG
1 TAG
31558764 TCATTGTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (53 bp):
TAGACAAAAGACACCAATAAGAAGATGATGTCGGTGGTCCACTAATTATTATT
Found at i:31559233 original size:11 final size:11
Alignment explanation
Indices: 31559217--31559241 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31559207 GATTTTAATA
31559217 TTAAATTATTT
1 TTAAATTATTT
31559228 TTAAATTATTT
1 TTAAATTATTT
31559239 TTA
1 TTA
31559242 TTTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAAATTATTT
Found at i:31559496 original size:25 final size:24
Alignment explanation
Indices: 31559463--31559521 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
31559453 TTTGTTTTAA
*
31559463 TATTTATTT-TTATGTTTTTAAATG
1 TATTTATTTATTAT-ATTTTAAATG
*
31559487 TATTTGATTTATTATATTTTAAATT
1 TATTT-ATTTATTATATTTTAAATG
*
31559512 TTTTTATTTA
1 TATTTATTTA
31559522 ATAAAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 16 0.53
26 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (24 bp):
TATTTATTTATTATATTTTAAATG
Found at i:31571495 original size:12 final size:12
Alignment explanation
Indices: 31571476--31571508 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
31571466 AGCTACGCCC
31571476 AAAA-AAAAAAA
1 AAAAGAAAAAAA
31571487 AAAAGAAAAAAA
1 AAAAGAAAAAAA
31571499 AAAAGAAAAA
1 AAAAGAAAAA
31571509 GTAAAGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:31575989 original size:6 final size:6
Alignment explanation
Indices: 31575980--31576005 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31575970 CTCCCTCTCC
31575980 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
31576006 ATTTTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:31577346 original size:2 final size:2
Alignment explanation
Indices: 31577339--31577363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31577329 CCTTGGAATC
31577339 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31577364 TGTGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31583592 original size:27 final size:27
Alignment explanation
Indices: 31583550--31583650 Score: 141
Period size: 27 Copynumber: 3.8 Consensus size: 27
31583540 TATTTTTTTG
**
31583550 AAATTTTACCTAGGGTAAAATTGTTAA
1 AAATTTTACCGGGGGTAAAATTGTTAA
31583577 AAATTTTACCGGGGGTAAAATTGTTAA
1 AAATTTTACCGGGGGTAAAATTGTTAA
* *
31583604 AAATTTTACTGGGGGTAAAATTG-TCA
1 AAATTTTACCGGGGGTAAAATTGTTAA
* *
31583630 AAATTTTACTGGGAGTAAAAT
1 AAATTTTACCGGGGGTAAAAT
31583651 AGGGGTGAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 22 0.32
27 47 0.68
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.35
Consensus pattern (27 bp):
AAATTTTACCGGGGGTAAAATTGTTAA
Found at i:31585598 original size:27 final size:28
Alignment explanation
Indices: 31585558--31585675 Score: 91
Period size: 27 Copynumber: 4.3 Consensus size: 28
31585548 AACATGTCAA
*
31585558 GAAA-GAAAAGCCTTTGTGGCGAATCAT
1 GAAATGAAAACCCTTTGTGGCGAATCAT
*
31585585 GAAATGAAAA-CCTTTGTGGCGAATCTT
1 GAAATGAAAACCCTTTGTGGCGAATCAT
* * * * * *
31585612 GAAAAGAATA-GCTTGCGTGGTGAATTAT
1 GAAATGAAAACCCTT-TGTGGCGAATCAT
* * *
31585640 GAAAGGAAATACCCTTTGTGGCGGATTAT
1 GAAATGAAA-ACCCTTTGTGGCGAATCAT
31585669 G-AATGAA
1 GAAATGAA
31585676 CAGCCTCTAT
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
27 31 0.43
28 26 0.36
29 12 0.17
30 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (28 bp):
GAAATGAAAACCCTTTGTGGCGAATCAT
Found at i:31587325 original size:17 final size:18
Alignment explanation
Indices: 31587283--31587331 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
31587273 AGTTGAAAAG
31587283 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
31587302 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
31587319 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
31587332 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:31588214 original size:40 final size:40
Alignment explanation
Indices: 31588148--31588314 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
31588138 AAATTGAATG
* * *
31588148 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
31588187 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
31588227 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
31588267 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
31588307 ATATCCGG
1 ATATCCGG
31588315 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:31595330 original size:17 final size:18
Alignment explanation
Indices: 31595288--31595336 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
31595278 AGTTGAAAAG
31595288 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
31595307 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
31595324 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
31595337 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:31596218 original size:40 final size:40
Alignment explanation
Indices: 31596152--31596302 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
31596142 AAATTGAATG
* * *
31596152 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
31596191 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
31596231 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
31596271 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
31596303 ACTTGATTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:31596316 original size:40 final size:40
Alignment explanation
Indices: 31596188--31596318 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
31596178 TATGCTGGAA
* * * *
31596188 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
** * *
31596228 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
31596268 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
31596308 ATTATATCCGG
1 ATTATATCCGG
31596319 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 3 0.04
40 70 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:31599976 original size:42 final size:42
Alignment explanation
Indices: 31599918--31600038 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
31599908 TAGGGTTACT
* * * *
31599918 GAGATTACGTGTAAGACCACATCTGGGATATAGCATCGATAT
1 GAGATTACATGTAAGACCATATCTGGGATATGGCATCGATAC
* * *
31599960 GAGACTTTC-TGTAAGACCATAGCTGGGCTATTGGCATCGATAC
1 GAGA-TTACATGTAAGACCATATCTGGGATA-TGGCATCGATAC
31600003 GAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 GAGATTACATGTAAGACCATATCTGGGATATGGCAT
31600039 TAGTACGGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 31 0.46
43 36 0.54
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (42 bp):
GAGATTACATGTAAGACCATATCTGGGATATGGCATCGATAC
Found at i:31604242 original size:20 final size:21
Alignment explanation
Indices: 31604217--31604264 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
31604207 GAAAAACTTT
31604217 TATTTGAACACT-TTTGAAAA
1 TATTTGAACACTATTTGAAAA
* * *
31604237 TATTTGGACATTATTTGATAA
1 TATTTGAACACTATTTGAAAA
31604258 T-TTTGAA
1 TATTTGAA
31604265 ATGTTTAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (21 bp):
TATTTGAACACTATTTGAAAA
Found at i:31604668 original size:21 final size:21
Alignment explanation
Indices: 31604630--31604669 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31604620 ATTTTTTAAA
*
31604630 ATAATACAAATGTGTTAATAT
1 ATAATACAAATATGTTAATAT
31604651 ATAATTACAAATAT-TTAAT
1 ATAA-TACAAATATGTTAAT
31604670 GGGTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAATACAAATATGTTAATAT
Found at i:31612576 original size:40 final size:41
Alignment explanation
Indices: 31612532--31612615 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
31612522 TGTGCATGAT
*
31612532 GTTCTTTGCATTTAT-TATCTGCTTCATGCTTGACTAAATA
1 GTTCTTTACATTTATATATCTGCTTCATGCTTGACTAAATA
31612572 GTTCTTTACATTTATATATCTGCTTCATGCTTGACTAAATA
1 GTTCTTTACATTTATATATCTGCTTCATGCTTGACTAAATA
31612613 GTT
1 GTT
31612616 TATGCTGTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 14 0.33
41 28 0.67
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.48
Consensus pattern (41 bp):
GTTCTTTACATTTATATATCTGCTTCATGCTTGACTAAATA
Found at i:31614292 original size:20 final size:19
Alignment explanation
Indices: 31614255--31614294 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
31614245 TTTTTTTTTT
31614255 TTTGGGGGGGGGGTGGTGG
1 TTTGGGGGGGGGGTGGTGG
31614274 TTTGGGGGTGGGTGG-GGTGG
1 TTTGGGGG-GGG-GGTGGTGG
31614294 T
1 T
31614295 CTCTGCATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.00, C:0.00, G:0.70, T:0.30
Consensus pattern (19 bp):
TTTGGGGGGGGGGTGGTGG
Found at i:31614459 original size:16 final size:16
Alignment explanation
Indices: 31614440--31614485 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
31614430 AATTTGGATC
* *
31614440 ACTGTAATAGAATAAG
1 ACTGTAATTGAATAAA
31614456 ACTGTAATTGAATAAA
1 ACTGTAATTGAATAAA
*
31614472 ATTGTAATTGAATA
1 ACTGTAATTGAATA
31614486 GAGTTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (16 bp):
ACTGTAATTGAATAAA
Found at i:31614492 original size:16 final size:16
Alignment explanation
Indices: 31614458--31614511 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
31614448 AGAATAAGAC
* *
31614458 TGTAATTGAATAAAAT
1 TGTAATTGAATAGAGT
31614474 TGTAATTGAATAGAGT
1 TGTAATTGAATAGAGT
*
31614490 TGTAA-TGTAATAGAGC
1 TGTAATTG-AATAGAGT
31614506 TGTAAT
1 TGTAAT
31614512 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 2 0.06
16 31 0.94
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (16 bp):
TGTAATTGAATAGAGT
Found at i:31614768 original size:58 final size:58
Alignment explanation
Indices: 31614676--31614814 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
31614666 TATTGTTATT
* *
31614676 AAATT-TTAATAAGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACT-
1 AAATTATTAACAAAATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAA-TA
* * * *
31614734 ATATT-TTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTATTAACAAAATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATA
*
31614791 AAATTATTAATAAAATTATTATTA
1 AAATTATTAACAAAATTATTATTA
31614815 TATGAATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 1 0.01
57 22 0.31
58 47 0.67
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (58 bp):
AAATTATTAACAAAATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAATA
Found at i:31614800 original size:12 final size:12
Alignment explanation
Indices: 31614785--31614811 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31614775 AATATATAAT
31614785 TTAATAAAATTA
1 TTAATAAAATTA
31614797 TTAATAAAATTA
1 TTAATAAAATTA
31614809 TTA
1 TTA
31614812 TTATATGAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATAAAATTA
Found at i:31615032 original size:23 final size:25
Alignment explanation
Indices: 31614988--31615042 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
31614978 TATGAAACAT
31614988 TTTAATTTACCTTTTCAAAATTCGATC
1 TTTAATTTACCTTTT--AAATTCGATC
*
31615015 TTTAATTTACC-TTT-AATTTGATC
1 TTTAATTTACCTTTTAAATTCGATC
31615038 TTTAA
1 TTTAA
31615043 AAGTTGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 13 0.48
26 3 0.11
27 11 0.41
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTAATTTACCTTTTAAATTCGATC
Found at i:31616181 original size:16 final size:16
Alignment explanation
Indices: 31616156--31616188 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31616146 AATATTTTAT
*
31616156 ATCAAGTGTATGCCTC
1 ATCAAATGTATGCCTC
31616172 ATCAAATGTATGCCTC
1 ATCAAATGTATGCCTC
31616188 A
1 A
31616189 CTAGCTTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (16 bp):
ATCAAATGTATGCCTC
Found at i:31618187 original size:29 final size:29
Alignment explanation
Indices: 31618145--31618202 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31618135 TCAAAGGTTC
31618145 TAACAAACCCAATTTACAGAAGCTGCAAA
1 TAACAAACCCAATTTACAGAAGCTGCAAA
31618174 TAACAAACCCAATTTACAGAAGCTGCAAA
1 TAACAAACCCAATTTACAGAAGCTGCAAA
31618203 ACATGATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.10, T:0.17
Consensus pattern (29 bp):
TAACAAACCCAATTTACAGAAGCTGCAAA
Found at i:31619445 original size:3 final size:3
Alignment explanation
Indices: 31619437--31619483 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
31619427 TATTCTTACG
31619437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31619484 TATGACCTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31621293 original size:53 final size:54
Alignment explanation
Indices: 31621163--31621412 Score: 248
Period size: 55 Copynumber: 4.7 Consensus size: 54
31621153 ATGCGGGTAC
* * * *
31621163 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
31621212 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
31621265 CTCACCAATGCCATGCCTTGGCACGGTCTTACATGAG-A-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTATCC-TTGCCTTAT-GAAA
* * * *
31621320 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
31621373 CCTTACCAATTGTCATGCCTTGAGATGGTCTTACATGGTA
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA
31621413 CCATTAAACC
Statistics
Matches: 166, Mismatches: 22, Indels: 20
0.80 0.11 0.10
Matches are distributed among these distances:
49 38 0.23
50 1 0.01
52 2 0.01
53 47 0.28
54 11 0.07
55 65 0.39
56 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:31621354 original size:108 final size:110
Alignment explanation
Indices: 31621210--31621409 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
31621200 ATCCTTTTGA
* *
31621210 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
31621273 -TGCCATGCCTTG-GCACGGTCTTACATGAGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGAG-ACGGTCTTACATGAGACCTTTGCCTTATAGT
* * *
31621318 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
* *
31621383 TGTCATGCCTTGAGATGGTCTTACATG
66 TGCCATGCCTTGAGACGGTCTTACATG
31621410 GTACCATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
107 1 0.01
108 49 0.60
109 7 0.09
110 23 0.28
111 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGAGACGGTCTTACATGAGACCTTTGCCTTATAGT
Done.