Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 31 of 284
Found at i:10797035 original size:15 final size:15
Alignment explanation
Indices: 10797015--10797050 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
10797005 CATAATTTAG
10797015 TTCAATTTTATTCAA
1 TTCAATTTTATTCAA
10797030 TTCAATTTTATTCAA
1 TTCAATTTTATTCAA
10797045 TTCAAT
1 TTCAAT
10797051 ATCAATACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCAATTTTATTCAA
Found at i:10797960 original size:17 final size:16
Alignment explanation
Indices: 10797938--10797969 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
10797928 TGTCATTATA
10797938 TTAATATAATATAATTT
1 TTAATATAATA-AATTT
10797955 TTAATATAATAAATT
1 TTAATATAATAAATT
10797970 AATAATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATATAATAAATTT
Found at i:10797985 original size:19 final size:18
Alignment explanation
Indices: 10797961--10797996 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10797951 ATTTTTAATA
*
10797961 TAATAAATTAATAATTTAG
1 TAATAAAATAAT-ATTTAG
10797980 TAATAAAATAATATTTA
1 TAATAAAATAATATTTA
10797997 CTTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATAAAATAATATTTAG
Found at i:10800777 original size:22 final size:22
Alignment explanation
Indices: 10800736--10800789 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
10800726 ACGGCTCAAT
* * *
10800736 GCCATAGATAGGACAGCACATA
1 GCCATAAACAGGACAACACATA
*
10800758 GCCGTAAACAGGACAACACATA
1 GCCATAAACAGGACAACACATA
10800780 GCCATAAACA
1 GCCATAAACA
10800790 TTGCAGCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (22 bp):
GCCATAAACAGGACAACACATA
Found at i:10801020 original size:22 final size:22
Alignment explanation
Indices: 10800992--10801056 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
10800982 GCAAATACGT
*
10800992 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
10801014 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
10801036 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
10801057 AATAATTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:10801256 original size:41 final size:41
Alignment explanation
Indices: 10801199--10801280 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
10801189 AAAAGCCACC
* *
10801199 GGTGGATCCACGGTCGTCAAGCAACTATGCGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
*
10801240 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTTAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
10801281 TCTTCCTCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTCAATT
Found at i:10801597 original size:27 final size:27
Alignment explanation
Indices: 10801539--10801616 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
10801529 GGTAAATCTA
* *
10801539 CAAACCAAGGGTATTTCTGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTC
*
10801566 TAAATC-AGGCGTATTTCTGTAATTTTC
1 CAAATCAAGG-GTATTTCTGTAATTTTC
* *
10801593 CAAATCAAGGTTATTTCGGTAATT
1 CAAATCAAGGGTATTTCTGTAATT
10801617 CTACCCTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTC
Found at i:10803056 original size:20 final size:20
Alignment explanation
Indices: 10803025--10803080 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
10803015 AGACGATGAA
10803025 CCATTCCATTTACTTACTTT
1 CCATTCCATTTACTTACTTT
*
10803045 CTACTT-CATTTACTTACTTT
1 CCA-TTCCATTTACTTACTTT
10803065 CCATTCCATTTACTTA
1 CCATTCCATTTACTTA
10803081 GCATAAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (20 bp):
CCATTCCATTTACTTACTTT
Found at i:10803149 original size:21 final size:21
Alignment explanation
Indices: 10803125--10803165 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10803115 TAGTGTGTTT
*
10803125 ATTCATAACATAGGTAAATTC
1 ATTCATAACATAAGTAAATTC
*
10803146 ATTCATAGCATAAGTAAATT
1 ATTCATAACATAAGTAAATT
10803166 TCTCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
ATTCATAACATAAGTAAATTC
Found at i:10809644 original size:40 final size:40
Alignment explanation
Indices: 10809548--10809767 Score: 194
Period size: 40 Copynumber: 5.5 Consensus size: 40
10809538 ACCCAAGTTT
* * * * * *
10809548 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGC
1 CTTCGGGACTTAGCCCGGATAAAAGCACTAGCACAAATGC
* * * * * * *
10809587 CTTCAGGTCTTAACCCGGGT-ATAGCAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATAAAAGC-ACTAGCACAAATGC
* * ** *
10809627 CTTCGGGCCTTAGCCCGGAT-ATAGCAACCCGTACAAATGC
1 CTTCGGGACTTAGCCCGGATAAAAGC-ACTAGCACAAATGC
* * *
10809667 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATAAAAGCACTAGCACAAATGC
* *
10809707 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATAAAAGCACTAGCACAAATGC
10809747 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
10809768 TCATTCAAAT
Statistics
Matches: 150, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 10 0.07
40 137 0.91
41 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATAAAAGCACTAGCACAAATGC
Found at i:10812103 original size:9 final size:9
Alignment explanation
Indices: 10812089--10812113 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10812079 ACAAGTTTTG
10812089 CAATTTATT
1 CAATTTATT
10812098 CAATTTATT
1 CAATTTATT
10812107 CAATTTA
1 CAATTTA
10812114 GTCCCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CAATTTATT
Found at i:10816327 original size:26 final size:26
Alignment explanation
Indices: 10816298--10816357 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
10816288 TCCCTTTGAA
* * *
10816298 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
10816324 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
10816352 CCATTC
1 TCATTC
10816358 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:10816343 original size:28 final size:28
Alignment explanation
Indices: 10816312--10816383 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
10816302 TCGATATTTT
*
10816312 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
10816340 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
10816368 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
10816384 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:10818166 original size:45 final size:45
Alignment explanation
Indices: 10818103--10818193 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
10818093 GAATTATGTA
* *
10818103 ATCTGAACTCAATGAGTTGTGGTTTGAGTTCATGATATATGTGAC
1 ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
*
10818148 ATCTGAACTCATTAAGTTGTGGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
10818193 A
1 A
10818194 CATGTTTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCAATAAGTTGTGGTCTGAGTTCATGATATATGTGAC
Found at i:10829004 original size:40 final size:40
Alignment explanation
Indices: 10828949--10829030 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
10828939 TTGCCATAGA
10828949 AGGGAAAAAAATTCAGCGTGTCATAGAACATAAGAAAAAT
1 AGGGAAAAAAATTCAGCGTGTCATAGAACATAAGAAAAAT
10828989 AGGGAAAAAAATTCAGCGTGTCATAGAACATAAGAAAAAT
1 AGGGAAAAAAATTCAGCGTGTCATAGAACATAAGAAAAAT
10829029 AG
1 AG
10829031 ATAAATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (40 bp):
AGGGAAAAAAATTCAGCGTGTCATAGAACATAAGAAAAAT
Found at i:10829709 original size:44 final size:44
Alignment explanation
Indices: 10829644--10829730 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
10829634 ATGATATCTC
* *
10829644 AAAGTCCATGGTTGTACCATGGCAATTAAGGAAGAATGGACGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATGGACGGA
* * * *
10829688 AAAGTCCAT-GTTCATAACATGGCATTTGAGGAGGAATTGACGG
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATGGACGG
10829731 TTAAGGATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 3 0.08
44 33 0.92
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATGGACGGA
Found at i:10831417 original size:47 final size:47
Alignment explanation
Indices: 10831359--10831580 Score: 232
Period size: 47 Copynumber: 4.6 Consensus size: 47
10831349 ACATTGGCAC
*
10831359 TAAGACAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
10831406 TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * * *** *
10831453 TAAGATAAGAATATCATGTAAGACCATGCCAAGG--CATGGGATTGGTGAG
1 TAAGACAAGGATACCATGTAAGACCATG-TTTGGAACATGGCATT--TG-G
* *
10831502 TTCATAAGGCAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGG
1 ----TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * *
10831553 TAAGATAAGAATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
10831581 CCAAGGCATG
Statistics
Matches: 142, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
46 8 0.06
47 93 0.65
48 4 0.03
49 1 0.01
51 1 0.01
52 4 0.03
53 23 0.16
54 8 0.06
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:10831526 original size:100 final size:100
Alignment explanation
Indices: 10831406--10831634 Score: 422
Period size: 100 Copynumber: 2.3 Consensus size: 100
10831396 TGGCATTTGG
* *
10831406 TAAGACAAGGATAACATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGAATATCATG
1 TAAGGCAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGAATATCATG
*
10831471 TAAGACCATGCCAAGGCATGGGATTGGTGAGTTCA
66 TAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
*
10831506 TAAGGCAAGGATACCATGTAAGACTATGTTTGGAACATGGCATTTGGTAAGATAAGAATATCATG
1 TAAGGCAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGAATATCATG
10831571 TAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
66 TAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
10831606 TAAGGCAAGGATACCATGTAAGACCATGT
1 TAAGGCAAGGATACCATGTAAGACCATGT
10831635 CAAGACATGG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 124 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (100 bp):
TAAGGCAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGAATATCATG
TAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
Found at i:10831629 original size:53 final size:53
Alignment explanation
Indices: 10831467--10831648 Score: 193
Period size: 53 Copynumber: 3.5 Consensus size: 53
10831457 ATAAGAATAT
*
10831467 CATGTAAGACCATGCCAAGGCATGGGATTGGTGAGTTCATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC
* *** * *
10831520 CATGTAAGACTATG-TTTGGAACATGGCATTTGGTAAG---ATAA-G--A--ATAT
1 CATGTAAGACCATGCCAAGG--CATGGCA-TTGGTGAGTTCATAAGGCAAGGATAC
10831567 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC
* *
10831620 CATGTAAGACCATGTCAAGACATGGCATT
1 CATGTAAGACCATGCCAAGGCATGGCATT
10831649 ATAATGACCC
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
45 7 0.07
46 7 0.07
47 16 0.16
48 6 0.06
49 2 0.02
51 2 0.02
52 6 0.06
53 43 0.42
54 6 0.06
55 7 0.07
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (53 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC
Found at i:10832065 original size:22 final size:24
Alignment explanation
Indices: 10832033--10832085 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
10832023 AGTTAATAAA
10832033 AGAAATAGAATAAAGAAAAGA-AAC
1 AGAAA-AGAATAAAGAAAAGAGAAC
*
10832057 A-AAAAGAATAGAGAAAAGAGAAC
1 AGAAAAGAATAAAGAAAAGAGAAC
10832080 AGAAAA
1 AGAAAA
10832086 CATTCGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.54
23 7 0.27
24 5 0.19
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (24 bp):
AGAAAAGAATAAAGAAAAGAGAAC
Found at i:10832074 original size:27 final size:30
Alignment explanation
Indices: 10832030--10832084 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 30
10832020 TAAAGTTAAT
10832030 AAAAGAAATAGAATAAAGA-AA-AGAAACA
1 AAAAGAAATAGAATAAAGAGAACAGAAACA
10832058 AAAAG-AATAGAGA-AAAGAGAACAGAAA
1 AAAAGAAATAGA-ATAAAGAGAACAGAAA
10832085 ACATTCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (30 bp):
AAAAGAAATAGAATAAAGAGAACAGAAACA
Found at i:10833570 original size:23 final size:21
Alignment explanation
Indices: 10833544--10833593 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
10833534 AGGCACTTTA
10833544 TGTGTCATATTTCAGGCACCTCG
1 TGTGTCATA--TCAGGCACCTCG
*
10833567 TGTGTCGTATCAGGCACCTCG
1 TGTGTCATATCAGGCACCTCG
10833588 TGTGTC
1 TGTGTC
10833594 GTTTTAGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 18 0.69
23 8 0.31
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (21 bp):
TGTGTCATATCAGGCACCTCG
Found at i:10833579 original size:21 final size:21
Alignment explanation
Indices: 10833555--10833618 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
10833545 GTGTCATATT
10833555 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
*
10833576 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* * **
10833597 TTAGGCACTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
10833618 T
1 T
10833619 ACTAATCAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:10834811 original size:53 final size:53
Alignment explanation
Indices: 10834712--10834840 Score: 161
Period size: 53 Copynumber: 2.4 Consensus size: 53
10834702 TAGGGGGTGT
* * *
10834712 GACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAA
1 GACATGGCATTGGTGAGTT-C-ATAAGGCAAAGGTACCACGTAAGACCATGCCAA
* *
10834767 GGCATGGCATTGGTGAGTTCATAAGGC-AAGGATACCACGTAAGACCATGTCAA
1 GACATGGCATTGGTGAGTTCATAAGGCAAAGG-TACCACGTAAGACCATGCCAA
* *
10834820 GACATGGCAATGGTAAGTTCA
1 GACATGGCATTGGTGAGTTCA
10834841 AAAAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
52 4 0.06
53 43 0.66
54 1 0.02
55 17 0.26
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (53 bp):
GACATGGCATTGGTGAGTTCATAAGGCAAAGGTACCACGTAAGACCATGCCAA
Found at i:10834975 original size:17 final size:16
Alignment explanation
Indices: 10834942--10834975 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10834932 CTTATTTAAT
*
10834942 ATTGAGATTCTAAGTA
1 ATTGAGATTATAAGTA
10834958 ATTGAGATTATCAAGTA
1 ATTGAGATTAT-AAGTA
10834975 A
1 A
10834976 GTGATGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (16 bp):
ATTGAGATTATAAGTA
Found at i:10851818 original size:40 final size:40
Alignment explanation
Indices: 10851713--10851889 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
10851703 CGGATGATAA
* *
10851713 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
10851753 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
10851792 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
10851832 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
10851872 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10851890 TACTTGGTTT
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
39 51 0.40
40 75 0.60
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:10851878 original size:79 final size:79
Alignment explanation
Indices: 10851713--10851889 Score: 243
Period size: 79 Copynumber: 2.2 Consensus size: 79
10851703 CGGATGATAA
* * *
10851713 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
*
10851778 GCGAGTTACTATAT
66 GCAAGTTACTATAT
*
10851792 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTT
10851856 GAGCAAG-TAGCTATAT
64 GAGCAAGTTA-CTATAT
* *
10851872 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10851890 TACTTGGTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 2 0.02
79 60 0.68
80 26 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
GCAAGTTACTATAT
Found at i:10853720 original size:22 final size:22
Alignment explanation
Indices: 10853695--10853739 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
10853685 TTGCAATTTG
10853695 ATCCACACAGTTTTGGAGACTT
1 ATCCACACAGTTTTGGAGACTT
10853717 ATCCACACAGTTTTGGAGACTT
1 ATCCACACAGTTTTGGAGACTT
10853739 A
1 A
10853740 CACGACTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
ATCCACACAGTTTTGGAGACTT
Found at i:10855971 original size:19 final size:20
Alignment explanation
Indices: 10855933--10855972 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10855923 GATTATATTC
* *
10855933 CTTTTATTTTTTTTTGATAT
1 CTTTTATTTTTCTTTAATAT
10855953 CTTTTA-TTTTCTTTAATAT
1 CTTTTATTTTTCTTTAATAT
10855972 C
1 C
10855973 ACATATCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (20 bp):
CTTTTATTTTTCTTTAATAT
Found at i:10870539 original size:59 final size:59
Alignment explanation
Indices: 10870461--10870594 Score: 205
Period size: 59 Copynumber: 2.3 Consensus size: 59
10870451 GTATAGTAAT
* * * *
10870461 GCACTTGGAGAATATTATTATGTGGTGAACTATTAATTATGTTGTTTAGTACTAAATAC
1 GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
* *
10870520 GTACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAT
1 GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
*
10870579 GCACTTGGGCAATATT
1 GCACTTGGACAATATT
10870595 GTAGTCATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (59 bp):
GCACTTGGACAATATTATTATGTGATGAACTATTAATTATGTGGTGTAGTACTAAATAC
Found at i:10870697 original size:3 final size:3
Alignment explanation
Indices: 10870689--10870768 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
10870679 AGCTAATTTT
*
10870689 TTG TTG TTG TTG TTG TTG TT- TCTG TTG TTG TTG TTG TTG TTG CTG
1 TTG TTG TTG TTG TTG TTG TTG T-TG TTG TTG TTG TTG TTG TTG TTG
10870734 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
10870769 ATTATTATTA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 1 0.01
3 71 0.97
4 1 0.01
ACGTcount: A:0.00, C:0.03, G:0.31, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:10870773 original size:3 final size:3
Alignment explanation
Indices: 10870767--10870792 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10870757 GTTGTTGTTG
10870767 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
10870793 CAATCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10877369 original size:65 final size:65
Alignment explanation
Indices: 10877283--10877434 Score: 214
Period size: 65 Copynumber: 2.3 Consensus size: 65
10877273 TGCGGACTAC
* * *
10877283 CGCAGTTCTTTGTAAGCGTCCTATTATATGATTGGTTGTGATCCTACATATATTGCGGACACAAA
1 CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
* * * * *
10877348 CGTAGCTCTTTGTAAGCGTCCTATTTTATGATCGGTTGTGATCCTGCATATGTTGTAGACACAAA
1 CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
* *
10877413 CGCATCTCTTTGTTAGCGTCCT
1 CGCAGCTCTTTGTAAGCGTCCT
10877435 GATATGGCTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (65 bp):
CGCAGCTCTTTGTAAGCGTCCTATTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
Found at i:10877521 original size:26 final size:27
Alignment explanation
Indices: 10877474--10877539 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
10877464 TGGCTATCCA
*
10877474 GAGC-TCCTGATTAAAGGCTCTTCG-T
1 GAGCTTCCTGATTAAAAGCTCTTCGTT
* *
10877499 GAGCTTCCTGATTAAAAGTTCTTTGTT
1 GAGCTTCCTGATTAAAAGCTCTTCGTT
* *
10877526 GAACTTCTTGATTA
1 GAGCTTCCTGATTA
10877540 TGACTCTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 4 0.12
26 17 0.50
27 13 0.38
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (27 bp):
GAGCTTCCTGATTAAAAGCTCTTCGTT
Found at i:10886048 original size:3 final size:3
Alignment explanation
Indices: 10886034--10886064 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
10886024 AATTCAAAGC
*
10886034 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10886065 AATTCTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:10895504 original size:31 final size:31
Alignment explanation
Indices: 10895466--10895529 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
10895456 CCTTTTCATA
10895466 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** * *
10895497 TTTCATATTTCATATTATTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
10895528 TT
1 TT
10895530 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:10908939 original size:11 final size:11
Alignment explanation
Indices: 10908923--10908949 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10908913 TGAACCCAGG
10908923 GTCCTCCTAGC
1 GTCCTCCTAGC
10908934 GTCCTCCTAGC
1 GTCCTCCTAGC
10908945 GTCCT
1 GTCCT
10908950 TAGCCACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.44, G:0.19, T:0.30
Consensus pattern (11 bp):
GTCCTCCTAGC
Found at i:10909262 original size:22 final size:20
Alignment explanation
Indices: 10909217--10909262 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
10909207 ATACTTACAG
10909217 TAATATTTTTCTAATAATAA
1 TAATATTTTTCTAATAATAA
* *
10909237 TAATAATTTTATCTCATAATAC
1 TAAT-ATTTT-TCTAATAATAA
10909259 TAAT
1 TAAT
10909263 TAAAATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 5 0.23
22 13 0.59
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTTTCTAATAATAA
Found at i:10910742 original size:22 final size:22
Alignment explanation
Indices: 10910717--10910762 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
10910707 GCTTATTCAA
10910717 CTGTGGATAATCGATGCACATT
1 CTGTGGATAATCGATGCACATT
10910739 CTGTGGATAATCGATGCACATT
1 CTGTGGATAATCGATGCACATT
10910761 CT
1 CT
10910763 CATAGTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (22 bp):
CTGTGGATAATCGATGCACATT
Found at i:10916397 original size:5 final size:5
Alignment explanation
Indices: 10916387--10916426 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
10916377 GATAAAAACC
10916387 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
10916427 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:10922831 original size:47 final size:47
Alignment explanation
Indices: 10922740--10922831 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
10922730 GTAAGGTGCC
* *
10922740 GATGCCATATCCCAGACACGATCTTACACTAGCTCATATTTCATATT
1 GATGCCATATCCCAGACACGATCTTACACTAACTCATATCTCATATT
*
10922787 GATGCCATGTCCCAGACATCG-TCTTACACTAACT-ATCATCTCATA
1 GATGCCATATCCCAGACA-CGATCTTACACTAACTCAT-ATCTCATA
10922832 GCCAATGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 2 0.05
47 36 0.90
48 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.30
Consensus pattern (47 bp):
GATGCCATATCCCAGACACGATCTTACACTAACTCATATCTCATATT
Found at i:10922892 original size:47 final size:46
Alignment explanation
Indices: 10922790--10922961 Score: 136
Period size: 47 Copynumber: 3.7 Consensus size: 46
10922780 TCATATTGAT
* ** *
10922790 GCCATGTCCCAGACATCGTCTTACACTAACTATCATCTCATA-GCC-AA
1 GCCATGTCCTAGACAT-GTCTTACACTGGCT-TCGTCTCA-AGGCCGAA
* *
10922837 TG-CTTGTCCTAGACATGTCTTACACTGGCTTACGTGTCAAAGGCCGAA
1 -GCCATGTCCTAGACATGTCTTACACTGGCTT-CGTCTC-AAGGCCGAA
* * * * *
10922885 G-CATGTCCTAGACATGTCTTACACTAGCACTCGTCTCGATGCCGAT
1 GCCATGTCCTAGACATGTCTTACACTGGC-TTCGTCTCAAGGCCGAA
*
10922931 GCCATGTCCCAGACATGGTCTTACACTGGCT
1 GCCATGTCCTAGACAT-GTCTTACACTGGCT
10922962 CTCATAATAT
Statistics
Matches: 101, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
45 1 0.01
46 24 0.24
47 60 0.59
48 16 0.16
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GCCATGTCCTAGACATGTCTTACACTGGCTTCGTCTCAAGGCCGAA
Found at i:10938364 original size:49 final size:48
Alignment explanation
Indices: 10938213--10938386 Score: 174
Period size: 49 Copynumber: 3.6 Consensus size: 48
10938203 AATAAGATGC
* **
10938213 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTAGCA-C-ATCAAAGT
1 CGATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCATCTATC-GGGT
* * *
10938261 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGG-
1 CGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCG-GGT
* * *
10938309 CTGATGCCGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTATTGGTGT
1 C-GATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGG-GT
* * *
10938359 CGATGCCACGTCGCAGATAGGTCTTACA
1 CGATGCCATGTCCCAGACAGGTCTTACA
10938387 TTGACACACA
Statistics
Matches: 105, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
47 16 0.15
48 21 0.20
49 67 0.64
50 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGGGT
Found at i:10938469 original size:48 final size:48
Alignment explanation
Indices: 10938409--10938577 Score: 182
Period size: 48 Copynumber: 3.6 Consensus size: 48
10938399 AAGCTGACAC
* * *
10938409 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCGAGGCCAATG
* * *
10938457 CATGTCCTAGACATGTCTTTCACTAGCTTGCATCTCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCGAGGCCAATG
* ** * * * *
10938505 TATGTCCCAGACATGTCTTACACCGGCTCT-CGTA-AT-GTGGACAATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TGCATATCTCGAGGCCAATG
*
10938551 CATGTCCCAGACATGTCTTACAATAGC
1 CATGTCCCAGACATGTCTTACACTAGC
10938578 ACACATATCA
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
46 31 0.31
47 1 0.01
48 67 0.67
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGCATATCTCGAGGCCAATG
Found at i:10950418 original size:20 final size:20
Alignment explanation
Indices: 10950393--10950454 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
10950383 ATTATGTCAT
10950393 ATTTTTATGTTTGAGATGTG
1 ATTTTTATGTTTGAGATGTG
*
10950413 ATTTTTA---TT--GATAT-
1 ATTTTTATGTTTGAGATGTG
10950427 ATTTTTATGTTTGAGATGTG
1 ATTTTTATGTTTGAGATGTG
10950447 ATTTTTAT
1 ATTTTTAT
10950455 TGACTTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
17 4 0.12
19 4 0.12
20 15 0.44
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.60
Consensus pattern (20 bp):
ATTTTTATGTTTGAGATGTG
Found at i:10950429 original size:34 final size:34
Alignment explanation
Indices: 10950391--10950457 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
10950381 TCATTATGTC
10950391 ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
1 ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
10950425 ATATTTTTATGTTTGAGATGTGATTTTTATTGA
1 ATATTTTTATGTTTGAGATGTGATTTTTATTGA
10950458 CTTGTTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (34 bp):
ATATTTTTATGTTTGAGATGTGATTTTTATTGAT
Found at i:10950457 original size:17 final size:17
Alignment explanation
Indices: 10950403--10950457 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
10950393 ATTTTTATGT
10950403 TTGAGATGTGATTTTTA
1 TTGAGATGTGATTTTTA
*
10950420 TT--GATAT-ATTTTTA
1 TTGAGATGTGATTTTTA
10950434 TGTTTGAGATGTGATTTTTA
1 ---TTGAGATGTGATTTTTA
10950454 TTGA
1 TTGA
10950458 CTTGTTAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 8 0.27
19 4 0.13
20 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (17 bp):
TTGAGATGTGATTTTTA
Found at i:10953543 original size:24 final size:25
Alignment explanation
Indices: 10953490--10953536 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
10953480 CACATTATAT
10953490 TATTATAATTATAATTATAAAAAAG
1 TATTATAATTATAATTATAAAAAAG
10953515 TATTATAA-TATAATTATAAAAA
1 TATTATAATTATAATTATAAAAA
10953537 TATATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTATAATTATAATTATAAAAAAG
Found at i:10958477 original size:84 final size:84
Alignment explanation
Indices: 10958336--10958492 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 84
10958326 GTCTTATAAG
* * * * * * *
10958336 GACTATCTTTTGTGGAAAGTCTGCCCAGGACTATCTTATGTGGAAAGTCCACCAAGGACTATCTT
1 GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
10958401 ATGTGGAAATTCCTCCAAC
66 ATGTGGAAATTCCTCCAAC
* * *
10958420 GACTATCTTATGTGGAAAATCCGCCAATGAATATCTTAGGTGGAATGTCTACCAAGGACTACCTT
1 GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
10958485 ATGTGGAA
66 ATGTGGAA
10958493 TTTTTCCAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (84 bp):
GACTATCTTATGTGGAAAATCCGCCAAGGAATATCTTAGGTGGAAAGTCCACCAAGGACTACCTT
ATGTGGAAATTCCTCCAAC
Found at i:10958493 original size:28 final size:28
Alignment explanation
Indices: 10958333--10958492 Score: 178
Period size: 28 Copynumber: 5.7 Consensus size: 28
10958323 GAAGTCTTAT
* *
10958333 AAGGACTATCTTTTGTGGAAAGTCTGCC
1 AAGGACTATCTTATGTGGAAAGTCTACC
* *
10958361 CAGGACTATCTTATGTGGAAAGTCCACC
1 AAGGACTATCTTATGTGGAAAGTCTACC
*
10958389 AAGGACTATCTTATGTGGAAATTCCT-CC
1 AAGGACTATCTTATGTGGAAAGT-CTACC
* * **
10958417 AACGACTATCTTATGTGGAAAATCCGCC
1 AAGGACTATCTTATGTGGAAAGTCTACC
* * * *
10958445 AATGAATATCTTAGGTGGAATGTCTACC
1 AAGGACTATCTTATGTGGAAAGTCTACC
*
10958473 AAGGACTACCTTATGTGGAA
1 AAGGACTATCTTATGTGGAA
10958493 TTTTTCCAGT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
27 1 0.01
28 107 0.98
29 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (28 bp):
AAGGACTATCTTATGTGGAAAGTCTACC
Found at i:10961175 original size:29 final size:29
Alignment explanation
Indices: 10961142--10961215 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
10961132 GTTGTGAGAT
* *
10961142 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
10961171 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
10961200 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
10961216 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:10977724 original size:44 final size:46
Alignment explanation
Indices: 10977652--10977773 Score: 115
Period size: 46 Copynumber: 2.7 Consensus size: 46
10977642 GGATAAGATA
* **
10977652 CCGATGCCAAGTCCC-GGACATGGTCTTACACTAACTTA-A-CTCGTAG
1 CCGATG-CATGTCCCAGG-CAT-GTCTTACACTAACTTACATCTCAAAG
**
10977698 CCGATGCATGTCCCAGGCATGTCTTACACTGGCTTACATCTCAAAG
1 CCGATGCATGTCCCAGGCATGTCTTACACTAACTTACATCTCAAAG
** * *
10977744 CTAATGCATGTCCCAGACGTGTCTTACACT
1 CCGATGCATGTCCCAGGCATGTCTTACACT
10977774 GGCTCTCGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
44 14 0.22
45 11 0.17
46 39 0.61
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (46 bp):
CCGATGCATGTCCCAGGCATGTCTTACACTAACTTACATCTCAAAG
Found at i:10983847 original size:34 final size:34
Alignment explanation
Indices: 10983804--10983871 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
10983794 AGACATTTCA
*
10983804 GAGTTTGTATCAAAATTTTTAGTGTGCCAACAAG
1 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
10983838 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
1 GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
10983872 TGAAGGCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (34 bp):
GAGTTTGTATCAAAATGTTTAGTGTGCCAACAAG
Found at i:10985873 original size:30 final size:30
Alignment explanation
Indices: 10985839--10985895 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
10985829 TCAAAATTTC
* *
10985839 AAGCCTAGGGGTAAAATGGTCATTTTGTGA
1 AAGCCGAGGGGCAAAATGGTCATTTTGTGA
*
10985869 AAGCCGGGGGGCAAAATGGTCATTTTG
1 AAGCCGAGGGGCAAAATGGTCATTTTG
10985896 CCCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.33, T:0.26
Consensus pattern (30 bp):
AAGCCGAGGGGCAAAATGGTCATTTTGTGA
Found at i:10989952 original size:29 final size:29
Alignment explanation
Indices: 10989889--10989956 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
10989879 TAATCAACCG
*
10989889 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
10989918 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
10989947 CGCACACTTA
1 CGCACACTTA
10989957 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:10990069 original size:174 final size:174
Alignment explanation
Indices: 10989778--10990105 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
10989768 AACTCAAGGT
* * *
10989778 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
*
10989843 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
10989908 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
10989952 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
10990017 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
10990082 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
10990106 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:10990097 original size:29 final size:30
Alignment explanation
Indices: 10990058--10990136 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
10990048 CTTAATAATC
10990058 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
10990088 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
10990117 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
10990137 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:10996611 original size:6 final size:5
Alignment explanation
Indices: 10996538--10996618 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
10996528 TTATTCTGCA
* ** ** * *
10996538 AAAAT AAAAT AAAAT -AAAT AAAAAT AAAAC AAGCT TGAAC AAAAA AAAACT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
10996589 AAAAT AAAAT AAAAT AAAGAT AAAGAT AAA
1 AAAAT AAAAT AAAAT AAA-AT AAA-AT AAA
10996619 TTCAATAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
4 4 0.07
5 36 0.61
6 19 0.32
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:10998683 original size:27 final size:27
Alignment explanation
Indices: 10998653--10998830 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10998643 ATATTGAGTC
* * * *
10998653 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
10998680 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10998707 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
10998735 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
10998762 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
10998789 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10998816 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10998831 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:10998792 original size:82 final size:81
Alignment explanation
Indices: 10998674--10998829 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10998664 TGCTATATAA
* *
10998674 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
10998739 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
10998756 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
10998820 CACTTAGTGC
65 CACTTAGTGC
10998830 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:11009426 original size:17 final size:17
Alignment explanation
Indices: 11009406--11009457 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
11009396 AACACATCAT
11009406 TCATATGCTACCATCTA
1 TCATATGCTACCATCTA
* *
11009423 TCATA--C-ACAAAC-A
1 TCATATGCTACCATCTA
11009436 TCATATGCTACCATCTA
1 TCATATGCTACCATCTA
11009453 TCATA
1 TCATA
11009458 CACAAACATC
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 2 0.07
16 4 0.15
17 11 0.41
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (17 bp):
TCATATGCTACCATCTA
Found at i:11009431 original size:30 final size:29
Alignment explanation
Indices: 11009393--11009468 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
11009383 CAACCAAGAC
*
11009393 ATCA-ACACATCATTCATATGCTACCATCT
1 ATCATACACAACA-TCATATGCTACCATCT
11009422 ATCATACACAAACATCATATGCTACCATCT
1 ATCATACAC-AACATCATATGCTACCATCT
11009452 ATCATACACAAACATCA
1 ATCATACAC-AACATCA
11009469 CATACTTATC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 4 0.09
30 37 0.84
31 3 0.07
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.26
Consensus pattern (29 bp):
ATCATACACAACATCATATGCTACCATCT
Found at i:11010178 original size:41 final size:41
Alignment explanation
Indices: 11010133--11010233 Score: 202
Period size: 41 Copynumber: 2.5 Consensus size: 41
11010123 ATTCACGGGC
11010133 CTGCTCACACAAGCTGTCAATCAGGACGTAGCTACACAGTG
1 CTGCTCACACAAGCTGTCAATCAGGACGTAGCTACACAGTG
11010174 CTGCTCACACAAGCTGTCAATCAGGACGTAGCTACACAGTG
1 CTGCTCACACAAGCTGTCAATCAGGACGTAGCTACACAGTG
11010215 CTGCTCACACAAGCTGTCA
1 CTGCTCACACAAGCTGTCA
11010234 GGTATCCACA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.20
Consensus pattern (41 bp):
CTGCTCACACAAGCTGTCAATCAGGACGTAGCTACACAGTG
Found at i:11013645 original size:20 final size:20
Alignment explanation
Indices: 11013620--11013666 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
11013610 CCAAATGGGC
11013620 GTGTGCTGATGCACACGGCT
1 GTGTGCTGATGCACACGGCT
*
11013640 GTGTGCTGATGTACACGGCT
1 GTGTGCTGATGCACACGGCT
11013660 GTGTGCT
1 GTGTGCT
11013667 TTTGGGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.21, G:0.36, T:0.30
Consensus pattern (20 bp):
GTGTGCTGATGCACACGGCT
Found at i:11015702 original size:42 final size:42
Alignment explanation
Indices: 11015583--11015702 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
11015573 CCGTACCAAC
* * *
11015583 GCCATATCCCAGGTATGGTCTTACATGTAATCTCGTATCGAT
1 GCCATATCCCAGATATGGTCTTACACGTAATCTCATATCGAT
* * * *
11015625 GCAAATAGCCCAGTTGTGGTCTTACACG-AAGTCTCATATCGAT
1 GC-CATATCCCAGATATGGTCTTACACGTAA-TCTCATATCGAT
*
11015668 GCCATATCCCAGATATGGTCTTGCACGTAATCTCA
1 GCCATATCCCAGATATGGTCTTACACGTAATCTCA
11015703 GTAACCCTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGTAATCTCATATCGAT
Found at i:11017084 original size:21 final size:21
Alignment explanation
Indices: 11017023--11017084 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
11017013 TGGGCATGTG
* *
11017023 TTTTGGACACACGGTCATGTC
1 TTTTGGACACACGGTCGTGTA
** *
11017044 TGATGGGCACACGGGT-GTGTA
1 TTTTGGACACAC-GGTCGTGTA
11017065 TTTTGGACACACGGTCGTGT
1 TTTTGGACACACGGTCGTGT
11017085 CTGGTGGGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 3 0.10
21 25 0.81
22 3 0.10
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (21 bp):
TTTTGGACACACGGTCGTGTA
Found at i:11027931 original size:28 final size:28
Alignment explanation
Indices: 11027865--11028018 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
11027855 ATATTAAGTC
* *
11027865 CGCACACTCAGTGCTATATAAT-AAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
11027892 CGCACACGTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
11027920 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
11027948 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
11027976 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
11028004 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11028019 GTACAATTTA
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 20 0.17
28 100 0.83
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:11027960 original size:56 final size:56
Alignment explanation
Indices: 11027865--11028043 Score: 261
Period size: 56 Copynumber: 3.2 Consensus size: 56
11027855 ATATTAAGTC
* * *
11027865 CGCACACTCAGTGCTATATAAT-AAACTCGCACACGTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* *
11027920 CGCACACTTAGTGCTACATAATCAAATTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* * * *
11027976 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAA-TCAAACT
11028033 CGCACACTTAG
1 CGCACACTTAG
11028044 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
55 20 0.18
56 75 0.68
57 16 0.14
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
Found at i:11031036 original size:3 final size:3
Alignment explanation
Indices: 11031021--11031064 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
11031011 ATTATAGTAC
* * * *
11031021 AAT AAT GAT AAT AAT AAT ATT AAT AGT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11031065 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11031472 original size:3 final size:3
Alignment explanation
Indices: 11031466--11031629 Score: 102
Period size: 3 Copynumber: 53.3 Consensus size: 3
11031456 GTAAAATAAG
* * *
11031466 ATA ATA ATA ATA ATA ATA AT- ATA TTG ATA ATA AGTA AAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * * * *
11031510 AGGA ATA AAA ATA ATA GTA ATA ATA AGA ATA TTTA ATA ATA GTA ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
11031557 ATA ACA ATA AT- ATAA ATA ATA ATA TATA CATGA AAA ATA ATA ATA ACA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A ATA ATA ATA ATA ATA
* *
11031605 ATA AAA ATA ATA GA-A AAA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA A
11031630 AATTAACTAA
Statistics
Matches: 123, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
2 7 0.06
3 99 0.80
4 16 0.13
5 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:11033122 original size:88 final size:88
Alignment explanation
Indices: 11032982--11033720 Score: 668
Period size: 88 Copynumber: 8.7 Consensus size: 88
11032972 CCATGCAACT
* * * *** *
11032982 TTAGGGAGATAAAATCTG-AATTTCCAGCCTGTTACCCTACTGCTTAATAGGTTAAGGCCCTTCG
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
*
11033046 TCTCCGATCTGCTCCACTACTGC
66 TCTTCGATCTGCTCCACTACTGC
* * * * *
11033069 TTAGGGAGACAAGATTTGTAATTTTCAGCCTGTTACCCTACTGTTTAGGAGGTTAAGGCCCTTCA
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
*
11033134 TCTTCGATCTGCTCCACTATTGC
66 TCTTCGATCTGCTCCACTACTGC
* *
11033157 TTAGGG-GAACAAGATCTGAAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTC
1 TTAGGGAG-ACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTC
* *
11033221 GTCTTCGATCTGCTCTACTTCTGC
65 GTCTTCGATCTGCTCCACTACTGC
* * **
11033245 TTAGGGAGACAAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCTCACCG
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
*
11033310 TCTTCGATCTACTCCACTACTGC
66 TCTTCGATCTGCTCCACTACTGC
* * * **
11033333 TTAGGGAGAAAAGATCTGTAATTTTTAGCCTAG-TACCCTACTGCTTAGGGGGTCAAGGCTCACC
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCT-GTTACCCTACTGCTTAGGGGGTCAAGGCCCTTC
* * **
11033397 GTCCTCGATCTACTCTGCTACTGC
65 GTCTTCGATCTGCTCCACTACTGC
* * * * * *
11033421 TTAGAGAGAAAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG-CC--CA
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
*
11033483 T-AT-G-T-T--TCC-CTACTGC
66 TCTTCGATCTGCTCCACTACTGC
* * * * * * * *
11033499 TTAGGGTGATAAGATCTGTAA-ATTCATCCTGTTACCCTACTACTTAGGGGTTTAAGG-CC--CA
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
11033560 T-TT-G-T-T--TCC-CTACTGC
66 TCTTCGATCTGCTCCACTACTGC
* * * * * * * *
11033576 TTAGGGTGATAAGATCTGTAA-ATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCA
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
* * * *
11033640 CCTTCGATCTGTTTCC-CTGCTGT
66 TCTTCGATCTG-CTCCACTACTGC
* * ** * * *
11033663 TTGGGGGGTTAGGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGC
11033721 TTCTGAATTT
Statistics
Matches: 572, Mismatches: 64, Indels: 32
0.86 0.10 0.05
Matches are distributed among these distances:
77 106 0.19
78 26 0.05
79 2 0.00
80 2 0.00
81 3 0.01
82 2 0.00
83 2 0.00
84 2 0.00
85 2 0.00
87 75 0.13
88 348 0.61
89 2 0.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (88 bp):
TTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTCAAGGCCCTTCG
TCTTCGATCTGCTCCACTACTGC
Found at i:11033548 original size:77 final size:77
Alignment explanation
Indices: 11033414--11033720 Score: 380
Period size: 77 Copynumber: 3.8 Consensus size: 77
11033404 ATCTACTCTG
* * * *
11033414 CTACTGCTTAGAGAGAAAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 CTACTGCTTAGGGTGATAAGATCTGTAAATT-CAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG
11033479 CCCATATGTTTCC
65 CCCATATGTTTCC
* *
11033492 CTACTGCTTAGGGTGATAAGATCTGTAAATTCATCCTGTTACCCTACTACTTAGGGGTTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
*
11033557 CCATTTGTTTCC
66 CCATATGTTTCC
11033569 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
11033634 TCATCACCTTCGATCTGTTTCC
66 -C--CA---T--A--TGTTTCC
* * * * * * * *
11033656 CTGCTGTTTGGGGGGTTAGGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
11033721 TTCTGAATTT
Statistics
Matches: 201, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
77 106 0.53
78 28 0.14
80 2 0.01
83 1 0.00
87 64 0.32
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (77 bp):
CTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGC
CCATATGTTTCC
Found at i:11033713 original size:43 final size:43
Alignment explanation
Indices: 11033562--11033716 Score: 132
Period size: 43 Copynumber: 3.6 Consensus size: 43
11033552 AAGGCCCATT
* * * * *
11033562 TGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTCAGCC
1 TGTTACCCTACTGCTTAGGGGGTTAGGATCTGTAAATTTAGCC
* * * * ** * *
11033605 TGTTACCCTACTGCTTAGGGGTTTAAGGCTC-ATCACCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTT-AGGATCTGTAAATTTAG-CC
* * * *
11033649 TGTTTCCCTGCTGTTTGGGGGGTTAGGATCTGTAAATTTAGCC
1 TGTTACCCTACTGCTTAGGGGGTTAGGATCTGTAAATTTAGCC
11033692 TGTTACCCTACTGCTTAGGGGGTTA
1 TGTTACCCTACTGCTTAGGGGGTTA
11033717 AGGCTTCTGA
Statistics
Matches: 80, Mismatches: 29, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
43 51 0.64
44 29 0.36
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGGGTTAGGATCTGTAAATTTAGCC
Found at i:11042864 original size:39 final size:40
Alignment explanation
Indices: 11042819--11042986 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
11042809 CGGGGTTTAG
* * *
11042819 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
11042858 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
11042898 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
11042938 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
11042979 CCGGATAT
1 CCGGATAT
11042987 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:11042969 original size:41 final size:40
Alignment explanation
Indices: 11042842--11042986 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
11042832 CTCGCACAAG
* * * * *
11042842 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
11042882 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
11042922 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
11042963 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
11042987 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:11053397 original size:199 final size:199
Alignment explanation
Indices: 11052947--11053409 Score: 698
Period size: 199 Copynumber: 2.3 Consensus size: 199
11052937 GCTACTCGTT
* * * * *
11052947 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGA
11053012 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTT
65 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTT
11053077 CGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAAC
130 CGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAAC
11053142 TCGCA
195 TCGCA
* * *
11053147 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCAG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCC-G
* *
11053211 AA-TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCT
64 AATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCT
* * *
11053275 TCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAACCCGGATTTAGTAA
129 TCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAA
11053340 CTCGCA
194 CTCGCA
* ** * *
11053346 CCAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
11053410 GACATCATTC
Statistics
Matches: 239, Mismatches: 19, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
198 3 0.01
199 173 0.72
200 60 0.25
201 3 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (199 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGAA
TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTC
GGGACTTAACCCGAATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAATTTAGTAACT
CGCA
Found at i:11053411 original size:40 final size:40
Alignment explanation
Indices: 11052947--11053411 Score: 695
Period size: 40 Copynumber: 11.7 Consensus size: 40
11052937 GCTACTCGTT
* *
11052947 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
11052987 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11053027 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11053067 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11053107 CAAATGCCTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
11053147 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
11053187 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
11053226 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11053266 CCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11053306 CCAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
11053346 CCAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
11053387 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
11053412 CATCATTCGA
Statistics
Matches: 399, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
39 38 0.10
40 349 0.87
41 12 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:11054686 original size:38 final size:38
Alignment explanation
Indices: 11054644--11054719 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
11054634 CAAGAACTCC
*
11054644 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
11054682 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
11054720 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTGTCGGCCAAAAGAAATGAA
Found at i:11060468 original size:68 final size:67
Alignment explanation
Indices: 11060396--11060545 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
11060386 CATCATGTGT
* * * *
11060396 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
11060458 ATGTAG
62 ATGTAG
** * *
11060464 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
11060529 AG
66 AG
11060531 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
11060546 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:11060501 original size:64 final size:64
Alignment explanation
Indices: 11060420--11060603 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
11060410 AGACATTATG
* *
11060420 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
11060484 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
11060549 AA
63 AA
* * * *
11060551 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
11060604 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:11063419 original size:22 final size:22
Alignment explanation
Indices: 11063375--11063419 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11063365 TGCAGCGCTA
* *
11063375 TTTTAAGTTCTTCTATCTTCTC
1 TTTTAAGTTCTTCAATCTACTC
11063397 TTTTAA-TTCTTCAATTCTACTC
1 TTTTAAGTTCTTCAA-TCTACTC
11063419 T
1 T
11063420 GACTAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAGTTCTTCAATCTACTC
Found at i:11063526 original size:18 final size:18
Alignment explanation
Indices: 11063503--11063544 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
11063493 AATCTTTAAT
11063503 CCTTCTTTCTCATTTTGG
1 CCTTCTTTCTCATTTTGG
11063521 CCTTCTTTCTCATTTTGG
1 CCTTCTTTCTCATTTTGG
*
11063539 CTTTCT
1 CCTTCT
11063545 ACCAAACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.29, G:0.10, T:0.57
Consensus pattern (18 bp):
CCTTCTTTCTCATTTTGG
Found at i:11080056 original size:131 final size:131
Alignment explanation
Indices: 11079822--11080117 Score: 358
Period size: 131 Copynumber: 2.3 Consensus size: 131
11079812 ACTGATTGGA
** * * ** * *
11079822 AAATTAGCTAAAACAAATGAGATTGCTCATGATATTCTATCGAATGAACTTATGTTGCAATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
* * *** **
11079887 AATTAGCCAACATTAACAATATCAGCTGTGATATTAAATCAACGGGCTATTTGGAGTAACGATAT
66 AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACGATAT
11079952 T
131 T
*
11079953 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACGATCTTA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
* * * * * **
11080018 AATCAGAGAACCTTTACAATATCAGCTACAATATTAAATCAGCAAGCTGTTTGGAGTAGTGATAT
66 AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACGATAT
11080083 T
131 T
* * *
11080084 AAATAAGCTAACTCAGATAAGACTGTTCATGATA
1 AAATTAGCTAACTCAAATAAGATTGTTCATGATA
11080118 AATAAAGTAA
Statistics
Matches: 139, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
131 139 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (131 bp):
AAATTAGCTAACTCAAATAAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTACAATCTTA
AATCAGACAACATTAACAATATCAGCTACAATATTAAATCAACAAGCTATTTGGAGTAACGATAT
T
Found at i:11083721 original size:36 final size:36
Alignment explanation
Indices: 11083674--11083746 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
11083664 TTATGGAGTG
11083674 TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
1 TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
11083710 TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
1 TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
11083746 T
1 T
11083747 AACATTTCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.45
Consensus pattern (36 bp):
TTAATAAGATAGTATTAAAGTTTTGTTAGGAAATTT
Found at i:11090072 original size:14 final size:14
Alignment explanation
Indices: 11090053--11090080 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11090043 CTGTACCTTG
11090053 GAAAATTTTTGAAA
1 GAAAATTTTTGAAA
11090067 GAAAATTTTTGAAA
1 GAAAATTTTTGAAA
11090081 TATAGCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
GAAAATTTTTGAAA
Found at i:11092890 original size:21 final size:19
Alignment explanation
Indices: 11092861--11092901 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11092851 ACTCCCTTGA
11092861 CCCCAAAACATTTTTATTTCT
1 CCCCAAAAC--TTTTATTTCT
*
11092882 CCCCTAAACTTTTATTTCT
1 CCCCAAAACTTTTATTTCT
11092901 C
1 C
11092902 ACATTTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (19 bp):
CCCCAAAACTTTTATTTCT
Found at i:11102412 original size:10 final size:10
Alignment explanation
Indices: 11102396--11102451 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
11102386 TAAACACCTA
11102396 AAAAATAAAT
1 AAAAATAAAT
*
11102406 CAAAATAAAT
1 AAAAATAAAT
*
11102416 AAAGAATAAAG
1 AAA-AATAAAT
*
11102427 AATTGAATAAAT
1 AA--AAATAAAT
11102439 AAAAATAAAT
1 AAAAATAAAT
11102449 AAA
1 AAA
11102452 CCAAATTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 21 0.57
11 8 0.22
12 8 0.22
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:11106550 original size:26 final size:26
Alignment explanation
Indices: 11106514--11106565 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11106504 TTCTTTTTGG
11106514 AATGAGTGAACCTCTTATTAATAAAT
1 AATGAGTGAACCTCTTATTAATAAAT
11106540 AATGAGTGAACCTCTTATTAATAAAT
1 AATGAGTGAACCTCTTATTAATAAAT
11106566 CCAAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (26 bp):
AATGAGTGAACCTCTTATTAATAAAT
Found at i:11108629 original size:27 final size:28
Alignment explanation
Indices: 11108599--11108652 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
11108589 TAATCCAATT
* *
11108599 ATAAAAAAA-ATATTTTAAGCATTCAAA
1 ATAAAAAAATACAATTTAAGCATTCAAA
11108626 ATAAAAAAATTACAATTTAAGCATTCA
1 ATAAAAAAA-TACAATTTAAGCATTCA
11108653 TGTTACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
29 14 0.61
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (28 bp):
ATAAAAAAATACAATTTAAGCATTCAAA
Found at i:11109030 original size:195 final size:194
Alignment explanation
Indices: 11108688--11109074 Score: 587
Period size: 195 Copynumber: 2.0 Consensus size: 194
11108678 CACTCCCATT
* * *
11108688 AAAATTACAAACGACAAGTTGATGTGGTAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
1 AAAAATACAAACGACAAGATGATGTGGCAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
* *
11108753 AATATTTACATATTATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
66 AATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
* *
11108818 TTCTCAATTTGATCCTAATTCTAAAAAAATTCAAAGAAATATATAAAAATACATAAATATTTTCA
131 TTCTCAATTTAATCCTAATT-TAAAAAAATTCAAAGAAATATATAAAAAAACATAAATATTTTCA
* * * * *
11108883 AAAAATACAAACGTCAAGATGATGTGGCAGTTAAAAATATATGTATAATAATAAATTTAGCCC-T
1 AAAAATACAAACGACAAGATGATGTGGCAATTAAAAA-ATAGGTATAATAACAAATTTAGCCCGC
* *
11108947 CAATTTTTAAATATCATATCGATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAAT
65 CAATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAAT
* * * *
11109012 GTTCTCAATTTAATCCTAATTTTAAAAAGTTCAAAGAAATATATAAAAAAACATACATATTTT
130 ATTCTCAATTTAATCCTAATTTAAAAAAATTCAAAGAAATATATAAAAAAACATAAATATTTT
11109075 TTAAAATTTT
Statistics
Matches: 173, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
194 38 0.22
195 112 0.65
196 23 0.13
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (194 bp):
AAAAATACAAACGACAAGATGATGTGGCAATTAAAAAATAGGTATAATAACAAATTTAGCCCGCC
AATATTTAAATATCATATCAATTTAGTCATAATTTTAAAAAATTAACCCTCATAATTTACAAATA
TTCTCAATTTAATCCTAATTTAAAAAAATTCAAAGAAATATATAAAAAAACATAAATATTTTCA
Found at i:11111252 original size:49 final size:49
Alignment explanation
Indices: 11111049--11111268 Score: 179
Period size: 49 Copynumber: 4.6 Consensus size: 49
11111039 ATGTGTGTGT
* * * *
11111049 TAGTGTAAGACCTGTCTGGGACACGGCATCGATATAGATAAGTG-AGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCA-AGC
* * * * * *
11111098 CAGTGTAAGACCTATCTGGGACATGGTATTGGCCTCAAGAT-A-TGCAAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCA-TCGACACAA-ATAAGTGCAAGC
* * * * * * *
11111147 TAGTGTAAAACCTGTCTGGGACATGGCATCG--GC--TTGAG-GTATGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCAAGC
*
11111191 TAGTGTAAGACCTGTCTAGGACATGGCATCGACACAAATAAGTG-AGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCA-AGC
11111240 TAGTGTAAGACCTGTCTGGGACATGGCAT
1 TAGTGTAAGACCTGTCTGGGACATGGCAT
11111269 TAACTTAGAT
Statistics
Matches: 132, Mismatches: 28, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
43 1 0.01
44 33 0.25
46 2 0.02
48 6 0.05
49 83 0.63
50 5 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAAATAAGTGCAAGC
Found at i:11118884 original size:49 final size:49
Alignment explanation
Indices: 11118810--11118940 Score: 217
Period size: 49 Copynumber: 2.7 Consensus size: 49
11118800 ATGTGTGTGT
*
11118810 TAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCATGATATGCAAAC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
* *
11118859 TAGTGTAAGACCTGTCTGGGGCATGGCATCAGCCTCATGATATGCAAGC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
* *
11118908 TAGTGTAAGACTTGTCTAGGGCATGGCATCGGC
1 TAGTGTAAGACCTGTCTGGGGCATGGCATCGGC
11118941 TTGAGGTGTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGGCATGGCATCGGCCTCATGATATGCAAAC
Found at i:11119092 original size:142 final size:142
Alignment explanation
Indices: 11118803--11119092 Score: 306
Period size: 142 Copynumber: 2.0 Consensus size: 142
11118793 TTGGGTGATG
* * ** *
11118803 TGTGTGTTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCATGATATGCAAACTAGTGTAAG
1 TGTGTGTTAGTGTAAGACCTGTCTAGGACATGGCATCGACCAAATGATATGCAAACCAGTGTAAG
* * * *
11118868 ACCTGTCTGGGGCATGGCATCAGCCTCATGATATGCAAGCTAGTGTAAGACTTGTCTAGGGCATG
66 ACCTGTCTAGGACATGGAATCAGCCTCATGATATGCAAGCTAGTGTAAGACCTGTCTAGGGCATG
* * *
11118933 GCATCGGCTTGA
131 GCAACGACTTAA
* * *
11118945 GGTGTGTTAGTGTAAGACCTGTCTAGGATATGGCATCGACACAAAT-A-AGTG-AGAGCCAGTGT
1 TGTGTGTTAGTGTAAGACCTGTCTAGGACATGGCATCGAC-CAAATGATA-TGCA-AACCAGTGT
* * *
11119007 AAGACTTGTCTAGGACATGGAATCA-CCTCGATG-TATGTAAG-TCAGTGTAAGACCTGTC-GGG
63 AAGACCTGTCTAGGACATGGAATCAGCCTC-ATGATATGCAAGCT-AGTGTAAGACCTGTCTAGG
11119068 GACATGGCAACGACTTAAA
126 G-CATGGCAACGACTT-AA
11119087 TGTGTG
1 TGTGTG
11119093 AGCCAATGTA
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
140 4 0.03
141 39 0.32
142 76 0.62
143 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (142 bp):
TGTGTGTTAGTGTAAGACCTGTCTAGGACATGGCATCGACCAAATGATATGCAAACCAGTGTAAG
ACCTGTCTAGGACATGGAATCAGCCTCATGATATGCAAGCTAGTGTAAGACCTGTCTAGGGCATG
GCAACGACTTAA
Found at i:11123896 original size:220 final size:220
Alignment explanation
Indices: 11123508--11123951 Score: 606
Period size: 220 Copynumber: 2.0 Consensus size: 220
11123498 CAATAGATTT
* * * * *
11123508 TTTTATTCATGGGTAAACTCAGTCTTTCAGTGAGTAAGTCAACTAAGAATATCAAGACTGTTAAT
1 TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
* * *
11123573 TCCAAAGACGTCCTAACAATGGGAGTAGCATAAGTAGTTAAGCTACAAATCAGTCAATGGAAAGG
66 TCCAAAGACGTCCTAACAATGCGAGTAGCACAAGGAGTTAAGCTACAAATCAGTCAATGGAAAGG
* * * * **
11123638 TAAGGAAGAATTCGAGGTAATCCACTTGGATGATTACGATTTTTTTCTTGGCTTGAATTTTTTTT
131 AAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTCTTGGCTT-AAATTTCATT
11123703 GACAAGATTAATGCTCTTTTGGTTCC
195 GACAAGATTAATGCTCTTTTGGTTCC
* *
11123729 TTTTA-TCATGGGTAAACTCAATCTCTCAATAAGTGAGTCAACTAAGAAGATTAAGACTGTTAAT
1 TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
* * * * * *
11123793 TCCAAAGAGGT-CTCGACTATGCGAGTAGCACAAGGAGTTGAGCTATAGATC-GATCAATGGAAA
66 TCCAAAGACGTCCT-AACAATGCGAGTAGCACAAGGAGTTAAGCTACAAATCAG-TCAATGGAAA
* * *
11123856 GGAAAGGAAGACTTTGAGGTAATCCACTTTGATAATTACGATTTTATTCTTGGCTTAAATTTCAT
129 GGAAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTCTTGGCTTAAATTTCAT
*
11123921 TGACAAGATTAATGCTCTTTTGGTTCT
194 TGACAAGATTAATGCTCTTTTGGTTCC
11123948 TTTT
1 TTTT
11123952 TCCAACTATA
Statistics
Matches: 195, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
219 39 0.20
220 151 0.77
221 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (220 bp):
TTTTATTCATGGGTAAACTCAATCTCTCAATAAGTAAGTCAACTAAGAAGATCAAGACTGTTAAT
TCCAAAGACGTCCTAACAATGCGAGTAGCACAAGGAGTTAAGCTACAAATCAGTCAATGGAAAGG
AAAGGAAGAATTCGAGGTAATCCACTTGGATAATTACGATTTTATTCTTGGCTTAAATTTCATTG
ACAAGATTAATGCTCTTTTGGTTCC
Found at i:11125816 original size:22 final size:22
Alignment explanation
Indices: 11125745--11125821 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
11125735 GAAAATTATA
*
11125745 CGAACTCTATGTGTTATTCATG
1 CGAACCCTATGTGTTATTCATG
* * * *
11125767 CAAACCCTTCATG-ATTATTTATA
1 CGAACCC-T-ATGTGTTATTCATG
11125790 CGAACCCTATGTGTTATTCATG
1 CGAACCCTATGTGTTATTCATG
*
11125812 TGAACCCTAT
1 CGAACCCTAT
11125822 ATATTTGTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
21 3 0.07
22 22 0.52
23 14 0.33
24 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (22 bp):
CGAACCCTATGTGTTATTCATG
Found at i:11125818 original size:45 final size:44
Alignment explanation
Indices: 11125721--11125820 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 44
11125711 TATATATCCT
*
11125721 TGTGAACCCTACATGAAAATTATACGAACTCTATGTGTTATTCA
1 TGTGAACCCTACATGAAAATTATACGAACCCTATGTGTTATTCA
** * * *
11125765 TGCAAACCCTTCATGATTATTTATACGAACCCTATGTGTTATTCA
1 TGTGAACCCTACATGA-AAATTATACGAACCCTATGTGTTATTCA
11125810 TGTGAACCCTA
1 TGTGAACCCTA
11125821 TATATTTGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 13 0.28
45 33 0.72
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (44 bp):
TGTGAACCCTACATGAAAATTATACGAACCCTATGTGTTATTCA
Found at i:11131156 original size:40 final size:41
Alignment explanation
Indices: 11131109--11131210 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
11131099 ATGAATCGAT
*
11131109 TATATATGGCACTTAGTGTGCAA-ATCGGA-ATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCAAGA-CGGAGATAGCTTCAGC
* * *
11131149 TATATATGGCAGTTAATGTGCAAGACTGAGATAGCTTCAGC
1 TATATATGGCACTTAGTGTGCAAGACGGAGATAGCTTCAGC
*
11131190 TATGA-AAGGCACTTAGTGTGC
1 TAT-ATATGGCACTTAGTGTGC
11131211 TAGATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 24 0.46
41 27 0.52
42 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (41 bp):
TATATATGGCACTTAGTGTGCAAGACGGAGATAGCTTCAGC
Found at i:11140581 original size:40 final size:40
Alignment explanation
Indices: 11140534--11140719 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
11140524 ATGAATCGAT
**
11140534 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
* *
11140574 TATATATGGCACTTAGTGTGTGAATCGGAATAGCTTCAGC
1 TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
* * * *
11140614 TATATATGGCACTTAGTGTGC-AAGACTAAAATAGTTTCGGC
1 TATATATGGCACTTAGTGTGCGAA-TC-GAAATAGCTTCAGC
* * *
11140655 TATGA-AAGGCACTTAGTGTACGAGAT-TATAATAGCTTCAGC
1 TAT-ATATGGCACTTAGTGTGCGA-ATCGA-AATAGCTTCAGC
* *
11140696 TATGCTTTGGCACTTAGTGTGCGA
1 TAT-ATATGGCACTTAGTGTGCGA
11140720 GATATTGAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.02
40 58 0.49
41 41 0.34
42 17 0.14
43 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGAATCGAAATAGCTTCAGC
Found at i:11144934 original size:28 final size:27
Alignment explanation
Indices: 11144877--11145028 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
11144867 TAAATTGTGC
*
11144877 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
11144904 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
11144932 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
11144959 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
11144987 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
11145014 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
11145029 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:11144942 original size:55 final size:55
Alignment explanation
Indices: 11144877--11145028 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
11144867 TAAATTGTGC
*
11144877 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
11144932 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
11144987 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
11145029 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:11147861 original size:24 final size:24
Alignment explanation
Indices: 11147829--11147875 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11147819 CAAACACTTG
11147829 GTGTACACTCTCTTTCTATGTCTA
1 GTGTACACTCTCTTTCTATGTCTA
*
11147853 GTGTACACTCTCTTTCTGTGTCT
1 GTGTACACTCTCTTTCTATGTCT
11147876 TTCTTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (24 bp):
GTGTACACTCTCTTTCTATGTCTA
Found at i:11150469 original size:27 final size:26
Alignment explanation
Indices: 11150409--11150470 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
11150399 ATAAGATTCC
11150409 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
11150435 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
11150463 ATTTTATT
1 ATTTTATT
11150471 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:11150505 original size:20 final size:19
Alignment explanation
Indices: 11150465--11150508 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
11150455 ATTTTAGGAT
*
11150465 TTTATTTTAATTATCTTTA
1 TTTATTTTAATTATCTGTA
11150484 TTTATATTTAATTAAT-TGTA
1 TTTAT-TTTAATT-ATCTGTA
11150504 TTTAT
1 TTTAT
11150509 CTTTTTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 15 0.68
21 2 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTATTTTAATTATCTGTA
Found at i:11156654 original size:16 final size:16
Alignment explanation
Indices: 11156633--11156665 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11156623 AATTGAGTTG
11156633 AGAAATTTATTTAATT
1 AGAAATTTATTTAATT
11156649 AGAAATTTATTTAATT
1 AGAAATTTATTTAATT
11156665 A
1 A
11156666 AATTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AGAAATTTATTTAATT
Found at i:11159756 original size:40 final size:40
Alignment explanation
Indices: 11159674--11159825 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
11159664 GAATATGCCC
* * * * * *
11159674 CTGGCTTGAAGGCCCTTCGAAACTGAGTTCGGTCATGA-CA
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTAT-ATCA
* *
11159714 CTGG-TTCGAAAGTCCTTCGGAACTAAGTCCGGTTATATCA
1 CTGGCTT-AAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
*
11159754 CTGGCTTAAAAGCCCTTCAGAACTAAGTCCGGTTATATCA
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
11159794 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGG
1 CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGG
11159826 ATTTTAAATC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 94 0.95
41 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CTGGCTTAAAAGCCCTTCGGAACTAAGTCCGGTTATATCA
Found at i:11163319 original size:20 final size:19
Alignment explanation
Indices: 11163296--11163348 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
11163286 ATGATAAAAA
*
11163296 TTATAAAAAATATTTAAATT
1 TTATAAAAAAT-TATAAATT
*
11163316 TTATTAAAAATTATAAA-T
1 TTATAAAAAATTATAAATT
**
11163334 TTATTTAAAATTATA
1 TTATAAAAAATTATA
11163349 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 15 0.50
19 5 0.17
20 10 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATAAAAAATTATAAATT
Found at i:11163324 original size:30 final size:30
Alignment explanation
Indices: 11163290--11163392 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 30
11163280 CAGAAAATGA
*
11163290 TAAAAATTATAAAAAATATTTAAATTTTAT
1 TAAAAATTATAAAAATTATTTAAATTTTAT
* *
11163320 TAAAAATTAT-AAATTTATTTAAAATTATAT
1 TAAAAATTATAAAAATTATTT-AAATTTTAT
* * * *
11163350 AAAAAATTATTAAAATTATATAAAATTTAT
1 TAAAAATTATAAAAATTATTTAAATTTTAT
11163380 TATAAAA-TATAAA
1 TA-AAAATTATAAA
11163393 TATAAAGAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.13
30 40 0.67
31 12 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAAAATTATAAAAATTATTTAAATTTTAT
Found at i:11163325 original size:21 final size:20
Alignment explanation
Indices: 11163289--11163390 Score: 100
Period size: 20 Copynumber: 5.0 Consensus size: 20
11163279 GCAGAAAATG
* *
11163289 ATAAAAATTATAAAAAATAT
1 ATAAAATTTATTAAAAATAT
* *
11163309 TTAAATTTTATTAAAAAT-T
1 ATAAAATTTATTAAAAATAT
*
11163328 AT-AAATTTATTTAAAATTAT
1 ATAAAATTTA-TTAAAAATAT
* *
11163348 ATAAAAAATTATTAAAATTAT
1 AT-AAAATTTATTAAAAATAT
11163369 ATAAAATTTATTATAAAATAT
1 ATAAAATTTATTA-AAAATAT
11163390 A
1 A
11163391 AATATAAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
18 6 0.09
19 9 0.13
20 27 0.40
21 19 0.28
22 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAATTTATTAAAAATAT
Found at i:11163385 original size:12 final size:11
Alignment explanation
Indices: 11163325--11163387 Score: 62
Period size: 10 Copynumber: 5.9 Consensus size: 11
11163315 TTTATTAAAA
*
11163325 ATTATAAATTT
1 ATTATAAAATT
11163336 ATT-TAAAATT
1 ATTATAAAATT
*
11163346 A-TATAAAA-A
1 ATTATAAAATT
11163355 ATTATTAAAATT
1 ATTA-TAAAATT
11163367 A-TATAAAATTT
1 ATTATAAAA-TT
11163378 ATTATAAAAT
1 ATTATAAAAT
11163388 ATAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 2 0.05
10 19 0.44
11 14 0.33
12 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTATAAAATT
Found at i:11164837 original size:34 final size:34
Alignment explanation
Indices: 11164794--11164869 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
11164784 GATTTCAGAG
*
11164794 TGTGATGAATCAGTTGCTTGGTATGGGTGTCAAA
1 TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
11164828 TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
1 TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
*
11164862 TTTGATGA
1 TGTGATGA
11164870 CGAGATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.37
Consensus pattern (34 bp):
TGTGATGAATCAGTTACTTGGTATGGGTGTCAAA
Found at i:11169795 original size:131 final size:132
Alignment explanation
Indices: 11169493--11169961 Score: 353
Period size: 133 Copynumber: 3.5 Consensus size: 132
11169483 TTCCAAAGAA
* * * * * * * *
11169493 ATATCCGATTGTTTTGAACAAACGAGAGATTGCAA-CCAAGTACGACAGGGCACGA-TTCTCGAA
1 ATATTCGATTATTTTGAGCAAAC-AGAAATTACAACCCAA-CACGATAGGGCACGATTTCGCGAA
* * * * * ** * **
11169556 TTGCCAAACATCGAACATAGCCTTTGTTTTAAAGGGTTTTCTTAAGAA-ACATGAGTGAAA-ACC
64 TGGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTT-TTAA-AAGACATGAATGAAAGTTC
* *
11169619 TAAAGGA
127 -GAAGGG
* * * * * *
11169626 ATATTCGATCATTTTGAACAAACAAGAAATCACAACCCAGCACGATAGGGCATGATTTC-TGAAT
1 ATATTCGATTATTTTGAGCAAAC-AGAAATTACAACCCAACACGATAGGGCACGATTTCGCGAAT
* * ** * * * * * *
11169690 TGTCAAACA-CCGAGTATTGCCTTCGTTTTAGAGGA-TTTTTAGAAGACCTGAATGGAA-TCTCG
65 GGCCAAACATCAAACT-TTGCCTTCGTTTTAAAGAATTTTTTAAAAGACATGAATGAAAGT-TCG
11169752 AAGGG
128 AAGGG
*
11169757 ATATTTGATTATTTTGAGCAAACGAGAAATTACAACCCAACAC-ATTAGGGCACGATTTCGCGAA
1 ATATTCGATTATTTTGAGCAAAC-AGAAATTACAACCCAACACGA-TAGGGCACGATTTCGCGAA
* * * *
11169821 TGGCCAAATATCAAACTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAGTTTGA
64 TGGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGACATGAATGAAAGTTCGA
11169886 AGGG
129 AGGG
* * * * *
11169890 ATATTCGATTATTTCGAGCAAACACGAAATTGCAACCCAACACGTTAGGGCACTATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACA-GAAATTACAACCCAACACGATAGGGCACGATTTCGCGAAT
*
11169955 TGCCAAA
65 GGCCAAA
11169962 TATCGAATCT
Statistics
Matches: 266, Mismatches: 58, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
130 3 0.01
131 66 0.25
132 34 0.13
133 156 0.59
134 7 0.03
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (132 bp):
ATATTCGATTATTTTGAGCAAACAGAAATTACAACCCAACACGATAGGGCACGATTTCGCGAATG
GCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGACATGAATGAAAGTTCGAAG
GG
Found at i:11169984 original size:133 final size:132
Alignment explanation
Indices: 11169751--11169994 Score: 348
Period size: 133 Copynumber: 1.8 Consensus size: 132
11169741 ATGGAATCTC
* * *
11169751 GAAGGGATATTTGATTATTTTGAGCAAACGAGAAATTACAACCCAACACATTAGGGCACGATTTC
1 GAAGGGATATTCGATTATTTCGAGCAAACGAGAAATTACAACCCAACACATTAGGGCACGATTCC
*
11169816 GCGAATGGCCAAATATCAAACTTTGCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAG
66 GCGAATGGCCAAATATCAAACTAT-CCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAG
11169881 TTT
130 TTT
* * *
11169884 GAAGGGATATTCGATTATTTCGAGCAAAC-ACGAAATTGCAACCCAACACGTTAGGGCACTATTC
1 GAAGGGATATTCGATTATTTCGAGCAAACGA-GAAATTACAACCCAACACATTAGGGCACGATTC
* * *
11169948 CGCGAATTGCCAAATATCGAATCTCAT-CTTCTTTTTAAAGAATTTTT
65 CGCGAATGGCCAAATATC-AAACT-ATCCTTCGTTTTAAAGAATTTTT
11169995 AAATGAATAC
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
132 1 0.01
133 92 0.94
134 4 0.04
135 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (132 bp):
GAAGGGATATTCGATTATTTCGAGCAAACGAGAAATTACAACCCAACACATTAGGGCACGATTCC
GCGAATGGCCAAATATCAAACTATCCTTCGTTTTAAAGAATTTTTTAAAAGGCATGAGTGAAAGT
TT
Found at i:11173571 original size:20 final size:19
Alignment explanation
Indices: 11173534--11173585 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
11173524 TTCTATACTT
*
11173534 TTATATTTTATAACAATTT-
1 TTATATTTT-TAAAAATTTA
11173553 TATATATTTTTAATAAATTTA
1 T-TATATTTTTAA-AAATTTA
11173574 TTATAATTTTTA
1 TTAT-ATTTTTA
11173586 TATTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTTTTAAAAATTTA
Found at i:11173654 original size:46 final size:46
Alignment explanation
Indices: 11173532--11173673 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 46
11173522 TATTCTATAC
* *
11173532 TTTTATATTTTATAACAATTTTATATATTTTTAAT-AAATTTATTATAAT
1 TTTTATATTTTAT-A-AATTTTATATATTTTT-ATCTAATTT-TTATATT
* * *
11173581 TTTTATA--TTAAAATATTTTAAATATTTTTCTCTAATTTTTATATT
1 TTTTATATTTTATAA-ATTTTATATATTTTTATCTAATTTTTATATT
*
11173626 TGTTTATATTTTATAAATTTTATA-ATTTTTTTCT--TTTTTATCATT
1 T-TTTATATTTTATAAATTTTATATATTTTTATCTAATTTTTAT-ATT
11173671 TTT
1 TTT
11173674 CCATTATGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
44 9 0.11
45 13 0.16
46 35 0.44
47 10 0.13
48 5 0.06
49 7 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (46 bp):
TTTTATATTTTATAAATTTTATATATTTTTATCTAATTTTTATATT
Found at i:11173673 original size:27 final size:26
Alignment explanation
Indices: 11173613--11173673 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
11173603 TATTTTTCTC
11173613 TAATTTTTATATTTGTTTATATTTTA
1 TAATTTTTATATTTGTTTATATTTTA
* * * *
11173639 TAAATTTTATAATTTTTTTCTTTTTTA
1 TAATTTTTAT-ATTTGTTTATATTTTA
*
11173666 TCATTTTT
1 TAATTTTT
11173674 CCATTATGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (26 bp):
TAATTTTTATATTTGTTTATATTTTA
Found at i:11174020 original size:23 final size:24
Alignment explanation
Indices: 11173985--11174036 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
11173975 TTAAATTCAA
**
11173985 ATTT-AATATATAATTTAAATATT
1 ATTTAAATATATAAGGTAAATATT
*
11174008 ATTTAAATA-ATAAGGTAATTATT
1 ATTTAAATATATAAGGTAAATATT
11174031 ATTTAA
1 ATTTAA
11174037 CTTTATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTTAAATATATAAGGTAAATATT
Found at i:11174436 original size:19 final size:21
Alignment explanation
Indices: 11174412--11174455 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
11174402 ATTTTTATCT
11174412 TAAAAAAATT-AAATTCA-AA
1 TAAAAAAATTAAAATTCAGAA
**
11174431 TAAAAATCTTAAAATTCAGAA
1 TAAAAAAATTAAAATTCAGAA
11174452 TAAA
1 TAAA
11174456 GATATTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAAATTAAAATTCAGAA
Found at i:11174630 original size:34 final size:35
Alignment explanation
Indices: 11174592--11174658 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11174582 CAGTAAAATA
*
11174592 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
11174626 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
11174659 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:11174632 original size:20 final size:20
Alignment explanation
Indices: 11174607--11174646 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11174597 CGTAAAATGA
*
11174607 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
11174627 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
11174647 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:11174662 original size:14 final size:15
Alignment explanation
Indices: 11174586--11174662 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11174576 GATTGCCAGT
* *
11174586 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
11174600 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
11174614 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
11174634 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
11174649 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
11174663 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Done.