Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 128 of 333
Found at i:41290724 original size:12 final size:13
Alignment explanation
Indices: 41290687--41290721 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
41290677 TTGTAGATTC
*
41290687 AAAAAAAAAATCG
1 AAAAAAAAAATTG
41290700 AAAAAAAAAATTG
1 AAAAAAAAAATTG
41290713 AAAAAAAAA
1 AAAAAAAAA
41290722 TTGCATACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:41301574 original size:20 final size:20
Alignment explanation
Indices: 41301549--41301603 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
41301539 TGTGGTTCAA
*
41301549 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
41301569 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
41301589 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
41301604 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:41319032 original size:39 final size:41
Alignment explanation
Indices: 41318937--41319120 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
41318927 TTGAATGCTG
*
41318937 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
41318976 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
41319016 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
41319055 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
41319095 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41319121 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:41319072 original size:79 final size:81
Alignment explanation
Indices: 41318937--41319120 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
41318927 TTGAATGCTG
41318937 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
41319000 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
41319015 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
41319076 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
41319095 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41319121 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:41319142 original size:79 final size:79
Alignment explanation
Indices: 41318989--41319153 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
41318979 GGACTAAGAT
* ** *
41318989 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
41319054 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
41319068 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
41319130 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
41319147 CCGAAGG
1 CCGAAGG
41319154 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:41333540 original size:13 final size:13
Alignment explanation
Indices: 41333522--41333546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41333512 CAATTTAGGG
41333522 TCACACGCCCGTA
1 TCACACGCCCGTA
41333535 TCACACGCCCGT
1 TCACACGCCCGT
41333547 GTGACCAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (13 bp):
TCACACGCCCGTA
Found at i:41333949 original size:24 final size:24
Alignment explanation
Indices: 41333921--41333977 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
41333911 TGGCACTTTC
41333921 ACACATTCATAATGTCGTTCTATT
1 ACACATTCATAATGTCGTTCTATT
41333945 ACACATTCATAATGTCGTTCTATT
1 ACACATTCATAATGTCGTTCTATT
41333969 ACACATTCA
1 ACACATTCA
41333978 ATTAGTCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (24 bp):
ACACATTCATAATGTCGTTCTATT
Found at i:41334747 original size:15 final size:15
Alignment explanation
Indices: 41334727--41334756 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41334717 CATTGCATTA
41334727 CCCGTTGAACACTTG
1 CCCGTTGAACACTTG
41334742 CCCGTTGAACACTTG
1 CCCGTTGAACACTTG
41334757 GAATACTATT
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:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (15 bp):
CCCGTTGAACACTTG
Found at i:41338682 original size:24 final size:24
Alignment explanation
Indices: 41338631--41338676 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41338621 AATAATATAG
*
41338631 AATAATATATAATATGTATATAAA
1 AATAATATATAATATATATATAAA
* *
41338655 AATAATGTATAGTATATATATA
1 AATAATATATAATATATATATA
41338677 TCAATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
AATAATATATAATATATATATAAA
Found at i:41338735 original size:30 final size:30
Alignment explanation
Indices: 41338701--41338761 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41338691 AAGCACAAAT
*
41338701 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
41338731 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
41338761 A
1 A
41338762 CGTAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:41338738 original size:16 final size:16
Alignment explanation
Indices: 41338717--41338752 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41338707 ACCATATATA
*
41338717 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
41338733 AATAATAATATAAAAT
1 AATAATAATATAAAAT
41338749 AATA
1 AATA
41338753 TATTTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:41338839 original size:13 final size:14
Alignment explanation
Indices: 41338807--41338853 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
41338797 TAAGTGATAA
*
41338807 AATATAGTATAAAT
1 AATATAGGATAAAT
41338821 ATATATAGGA-AAAT
1 A-ATATAGGATAAAT
*
41338835 AATATACGATAAA-
1 AATATAGGATAAAT
41338848 AATATA
1 AATATA
41338854 AGTAGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 13 0.45
14 9 0.31
15 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
AATATAGGATAAAT
Found at i:41347690 original size:15 final size:15
Alignment explanation
Indices: 41347648--41347697 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41347638 ATAACTTTGC
* *
41347648 ATGCAAACG-ATGTG
1 ATGCAAATGCATGAG
41347662 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
41347677 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
41347691 ATGCAAA
1 ATGCAAA
41347698 AAGGATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:41347696 original size:14 final size:16
Alignment explanation
Indices: 41347661--41347697 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
41347651 CAAACGATGT
41347661 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
41347676 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
41347691 -ATGCAAA
1 GATGCAAA
41347698 AAGGATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:41351639 original size:24 final size:24
Alignment explanation
Indices: 41351588--41351633 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41351578 AATAATATAG
*
41351588 AATAATATATAATATGTATATAAA
1 AATAATATATAATATATATATAAA
* *
41351612 AATAATGTATAGTATATATATA
1 AATAATATATAATATATATATA
41351634 TCAATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
AATAATATATAATATATATATAAA
Found at i:41351692 original size:30 final size:30
Alignment explanation
Indices: 41351658--41351718 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41351648 AAGCACAAAT
*
41351658 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
41351688 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
41351718 A
1 A
41351719 CGTAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:41351695 original size:16 final size:16
Alignment explanation
Indices: 41351674--41351709 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41351664 ACCATATATA
*
41351674 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
41351690 AATAATAATATAAAAT
1 AATAATAATATAAAAT
41351706 AATA
1 AATA
41351710 TATTTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:41361958 original size:40 final size:40
Alignment explanation
Indices: 41361864--41362073 Score: 291
Period size: 40 Copynumber: 5.3 Consensus size: 40
41361854 ACCCAATTAT
* *** *
41361864 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
* * * ** *
41361902 CGTCGGGTCTTAGCCCGGATATGGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
41361942 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
41361982 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
41362022 CTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGC
41362062 CTTCGGGACTTA
1 CTTCGGGACTTA
41362074 ACCCCGTTAG
Statistics
Matches: 154, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 10 0.06
39 16 0.10
40 128 0.83
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
Found at i:41367017 original size:21 final size:21
Alignment explanation
Indices: 41366991--41367030 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41366981 ACACAATAGA
* *
41366991 CCTAGGGTAGGTATGTCATTT
1 CCTAGGATAAGTATGTCATTT
41367012 CCTAGGATAAGTATGTCAT
1 CCTAGGATAAGTATGTCAT
41367031 CTACATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
CCTAGGATAAGTATGTCATTT
Found at i:41371018 original size:48 final size:48
Alignment explanation
Indices: 41370947--41371052 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
41370937 CAAGATAAAT
* * *
41370947 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
41370995 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
41371043 ATGTGTATAT
1 ATATGTATAT
41371053 ATTGTGGCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:41371236 original size:37 final size:37
Alignment explanation
Indices: 41371186--41371257 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
41371176 GAAATATATT
*
41371186 CCAGGTAAGACCCGATGGCTACGTGTGGAGATTATGC
1 CCAGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
41371223 CCAGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCAGGTAAGACCCGATGACTACGTGTGGAGATTAT
41371258 TCGAGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (37 bp):
CCAGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Found at i:41380164 original size:40 final size:40
Alignment explanation
Indices: 41380127--41380312 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
41380117 GCTACTCGTT
* *
41380127 CAAATGCCTTCGGGACATACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41380167 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41380207 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
41380247 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41380288 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41380313 CATCATTCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 114 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41382138 original size:39 final size:39
Alignment explanation
Indices: 41382080--41382279 Score: 303
Period size: 39 Copynumber: 5.1 Consensus size: 39
41382070 TACGGGACTT
*
41382080 TATAACACCAGCA-GAAATGCCTTCGGGGCTTAGCCCGGA
1 TATAACACCAGCACG-AATGCCTTCGGGACTTAGCCCGGA
*
41382119 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGTA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
* * * * *
41382158 TATAACACCAACACGAATGCCTTTGGTACTTAGCTCAGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
*
41382197 TATAACACCAGCACGAATGCCTTTGGGACTTAGCCCGGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
*
41382236 TATAACACCAGCACGAATGCCTTCGGAACTTAGCCCGGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
41382275 TATAA
1 TATAA
41382280 TTCTCCATTA
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 145 0.99
40 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (39 bp):
TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
Found at i:41383600 original size:39 final size:39
Alignment explanation
Indices: 41383546--41383623 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
41383536 CTCTCCCTAA
41383546 ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
41383585 ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
41383624 CAACGTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (39 bp):
ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
Found at i:41389605 original size:25 final size:27
Alignment explanation
Indices: 41389577--41389639 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
41389567 AGTTATAAAT
41389577 ATTTTAATTTTGA-ATG-TAAAAATTC
1 ATTTTAATTTTGATATGATAAAAATTC
* * *
41389602 ATTTTACTTTT-ATATGATTACAATTC
1 ATTTTAATTTTGATATGATAAAAATTC
*
41389628 AATTTAATTTTG
1 ATTTTAATTTTG
41389640 TCTTACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 1 0.03
25 13 0.43
26 16 0.53
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (27 bp):
ATTTTAATTTTGATATGATAAAAATTC
Found at i:41389797 original size:24 final size:24
Alignment explanation
Indices: 41389770--41389823 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
41389760 TATTGTTCAC
41389770 TATTATATTATATTGATAATTAAA
1 TATTATATTATATTGATAATTAAA
* * * *
41389794 TATTTTTTTATATTTATTATTAAA
1 TATTATATTATATTGATAATTAAA
41389818 T-TTATA
1 TATTATA
41389824 AAACCTAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTATATTATATTGATAATTAAA
Found at i:41392136 original size:40 final size:40
Alignment explanation
Indices: 41392081--41392222 Score: 225
Period size: 40 Copynumber: 3.6 Consensus size: 40
41392071 TATTCGAATG
*
41392081 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
41392121 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
41392161 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
41392201 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41392223 TACTTGGGTT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.15
40 80 0.83
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:41393619 original size:5 final size:5
Alignment explanation
Indices: 41393609--41393649 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
41393599 AAACATTATA
*
41393609 ATATT ATATT ATATT ATATT AT-TT AT-TT -TATT ATAAT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
41393650 AATTAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 8 0.25
5 23 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:41393977 original size:17 final size:16
Alignment explanation
Indices: 41393947--41393980 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
41393937 AGCCGTACAC
41393947 TATATATTACTTATTA
1 TATATATTACTTATTA
*
41393963 TATATCATTATTTATTA
1 TATAT-ATTACTTATTA
41393980 T
1 T
41393981 TATGCTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATATTACTTATTA
Found at i:41395868 original size:5 final size:5
Alignment explanation
Indices: 41395855--41395887 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
41395845 TTGTGTGTTC
*
41395855 TTTAT TTTAC TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41395888 TTAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:41396129 original size:28 final size:28
Alignment explanation
Indices: 41396089--41396200 Score: 215
Period size: 28 Copynumber: 4.0 Consensus size: 28
41396079 AGATGAAGAG
*
41396089 AAGAAGCGTAAGGATCGGAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41396117 AAGAAGCGTAAGGATCGAAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41396145 AAGAAGCGTAAGGATCGAAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41396173 AAGAAGCGTAAGGATCGAAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41396201 CACAATTACA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 83 1.00
ACGTcount: A:0.42, C:0.11, G:0.33, T:0.14
Consensus pattern (28 bp):
AAGAAGCGTAAGGATCGAAAGGCGTTAA
Found at i:41402758 original size:36 final size:36
Alignment explanation
Indices: 41402711--41402785 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
41402701 GCCCAAAGTT
* *
41402711 AATCACACAAATTCTTAACATGTTTTCTAGGAATTG
1 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
41402747 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
1 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
41402783 AAT
1 AAT
41402786 AACTCTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
Found at i:41410303 original size:52 final size:48
Alignment explanation
Indices: 41410120--41410326 Score: 168
Period size: 47 Copynumber: 4.2 Consensus size: 48
41410110 TGCACATAGT
* ** * *
41410120 CACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACAT-CCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* * * * * * * *
41410168 CACGTATCACA-CTGATGCCATATCTCAGAAATGGTCTTATACAGTAG
1 CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
41410215 CACATATCACA-CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
41410262 CACATATCACATTTCTCCGAAGCCATAGCCCAGTTATGGTCTTATACGGAAAT
1 CACATATCACA----TCCGAAGCCATAGCCCAGATATGGTCTTATACGG-AAG
*
41410315 CACATTTCACAT
1 CACATATCACAT
41410327 GCTGCCATGG
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
46 25 0.19
47 52 0.40
48 10 0.08
49 1 0.01
52 29 0.22
53 12 0.09
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (48 bp):
CACATATCACATCCGAAGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:41412702 original size:30 final size:30
Alignment explanation
Indices: 41412650--41412746 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
41412640 TTATGGAGCA
41412650 AAGATAAGAAGAAAACC-GAATAAAGAAATCC
1 AAGAT-AG-AGAAAACCAGAATAAAGAAATCC
*
41412681 AAGATAGAGAAACCCAGAATAAAGAAATCC
1 AAGATAGAGAAAACCAGAATAAAGAAATCC
* * * * *
41412711 -AGAATAAAGAGATCCAGGATAAAGAAACCC
1 AAG-ATAGAGAAAACCAGAATAAAGAAATCC
41412741 AAGATA
1 AAGATA
41412747 CGATACTATG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 9 0.16
30 41 0.72
31 7 0.12
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGATAGAGAAAACCAGAATAAAGAAATCC
Found at i:41412706 original size:15 final size:15
Alignment explanation
Indices: 41412658--41412737 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
41412648 CAAAGATAAG
*
41412658 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
41412672 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
41412687 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
41412702 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
41412717 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
41412732 AAGAAA
1 AAGAAA
41412738 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:41412746 original size:15 final size:15
Alignment explanation
Indices: 41412669--41412746 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
41412659 AGAAAACCGA
41412669 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
41412684 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
41412698 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
41412713 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
41412729 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
41412744 ATA
1 ATA
41412747 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:41416463 original size:52 final size:48
Alignment explanation
Indices: 41416280--41416486 Score: 177
Period size: 47 Copynumber: 4.2 Consensus size: 48
41416270 TGCACATAGT
* * ** * *
41416280 CACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACAT-CCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * * * * *
41416328 CACGTATCACA-CTGATGCCATATCCCAGAAATGGTCTTATACAGTAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* *
41416375 CACATATCACA-CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
41416422 CACATATCACATTTCTCCGAAGCCATAGCCCAGTTATGGTCTTATACGGAAAT
1 CACATATCACA----TCCGAAGCCATATCCCAGATATGGTCTTATACGG-AAG
*
41416475 CACATTTCACAT
1 CACATATCACAT
41416487 GCTGCCATGG
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
46 26 0.20
47 53 0.40
48 10 0.08
49 1 0.01
52 29 0.22
53 12 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (48 bp):
CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
Found at i:41418876 original size:13 final size:13
Alignment explanation
Indices: 41418854--41418884 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41418844 TAGCAGAAAA
*
41418854 TGAGCTGACTTAG
1 TGAGCCGACTTAG
41418867 TGAGCCGACTTAG
1 TGAGCCGACTTAG
41418880 TGAGC
1 TGAGC
41418885 TGATCCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (13 bp):
TGAGCCGACTTAG
Found at i:41422502 original size:40 final size:40
Alignment explanation
Indices: 41422457--41422648 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
41422447 ATAACCACAA
* *
41422457 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
41422497 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
41422537 GCACAAATGCCTTCGGGTCTTAGA-CCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTA-ACCCGGAT-ATAGCAACTC
* * * * * *
41422577 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATAGCAACTC
* * *
41422617 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT
41422649 CATTCAAATG
Statistics
Matches: 138, Mismatches: 11, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 133 0.96
41 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:41422541 original size:80 final size:80
Alignment explanation
Indices: 41422428--41422647 Score: 232
Period size: 80 Copynumber: 2.8 Consensus size: 80
41422418 ACCCAAGTTT
* * * * * * * *
41422428 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATAAAAG
*
41422491 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
41422507 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGA-CCGGATAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTA-ACCCGGATAAA
* *
41422570 ATCACTAGCATAAATGC
64 AGCACTAGCACAAATGC
* * *
41422587 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATA
41422648 TCATTCAAAT
Statistics
Matches: 115, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
79 12 0.10
80 95 0.83
81 8 0.07
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATAAAAG
CACTAGCACAAATGC
Found at i:41426776 original size:16 final size:16
Alignment explanation
Indices: 41426755--41426786 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41426745 TCACAAAAAC
41426755 ACAAAAATTTCAAGAA
1 ACAAAAATTTCAAGAA
41426771 ACAAAAATTTCAAGAA
1 ACAAAAATTTCAAGAA
41426787 TTAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
ACAAAAATTTCAAGAA
Found at i:41428494 original size:12 final size:12
Alignment explanation
Indices: 41428462--41428500 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41428452 TAAAATTAAA
41428462 AAATTAA-AAC-
1 AAATTAAGAACT
41428472 AAATT-AGAACT
1 AAATTAAGAACT
41428483 AAATTAAGAACT
1 AAATTAAGAACT
41428495 AAATTA
1 AAATTA
41428501 TATTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 8 0.31
11 5 0.19
12 12 0.46
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (12 bp):
AAATTAAGAACT
Found at i:41428569 original size:15 final size:15
Alignment explanation
Indices: 41428549--41428578 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41428539 AAAAACAACA
41428549 AAAAAAAAGTAAAGT
1 AAAAAAAAGTAAAGT
*
41428564 AAAAAAAATTAAAGT
1 AAAAAAAAGTAAAGT
41428579 TACTTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (15 bp):
AAAAAAAAGTAAAGT
Found at i:41432725 original size:18 final size:18
Alignment explanation
Indices: 41432691--41432725 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41432681 AAATAGTTCG
*
41432691 AGTTATTTGAGTTAATTA
1 AGTTATTTGAGTCAATTA
*
41432709 AGTTATTTGGGTCAATT
1 AGTTATTTGAGTCAATT
41432726 CGAATAAAAA
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:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (18 bp):
AGTTATTTGAGTCAATTA
Found at i:41433310 original size:11 final size:11
Alignment explanation
Indices: 41433276--41433315 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41433266 CAATAATAAC
*
41433276 AAAATAGTAGC
1 AAAATAGTAGT
* *
41433287 AACATAATAGT
1 AAAATAGTAGT
41433298 AAAATAGTAGT
1 AAAATAGTAGT
41433309 AAAATAG
1 AAAATAG
41433316 GGAGAAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (11 bp):
AAAATAGTAGT
Found at i:41439971 original size:17 final size:17
Alignment explanation
Indices: 41439949--41439983 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41439939 ATGCTGTGAT
41439949 ATACCATACCCGGATCC
1 ATACCATACCCGGATCC
*
41439966 ATACCATACTCGGATCC
1 ATACCATACCCGGATCC
41439983 A
1 A
41439984 ATTATTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.37, G:0.11, T:0.20
Consensus pattern (17 bp):
ATACCATACCCGGATCC
Found at i:41442836 original size:37 final size:37
Alignment explanation
Indices: 41442776--41442853 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
41442766 TATTACGAAG
* * *
41442776 TCTTACCCGGACATAATCTCCACACGAAGTTATCGGA
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
* *
41442813 TCTTACCCGGACAAAATCCCCACACGTAGTCATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
41442850 TCTT
1 TCTT
41442854 TAGAGCTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGA
Found at i:41443050 original size:47 final size:47
Alignment explanation
Indices: 41442972--41443340 Score: 596
Period size: 47 Copynumber: 7.8 Consensus size: 47
41442962 CCCTTCGGGA
* * * * * *
41442972 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41443019 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41443066 CTTATCACATGTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41443113 CTTATCACATGTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41443160 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41443207 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41443256 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTA-GC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41443304 CTTATCACATATATACACTTTCACATTCATCACATCG
1 CTTATCACATATATACACTTTCACATTCATCACATCG
41443341 AATCCTAAAT
Statistics
Matches: 307, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
46 29 0.09
47 184 0.60
48 10 0.03
49 84 0.27
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41446312 original size:21 final size:21
Alignment explanation
Indices: 41446288--41446330 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41446278 TAAACAGTAA
41446288 GCTCTTCTGAGCTGAATAATG
1 GCTCTTCTGAGCTGAATAATG
41446309 GCTCTTCTGAGCTGAATAATG
1 GCTCTTCTGAGCTGAATAATG
41446330 G
1 G
41446331 GAAGCTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GCTCTTCTGAGCTGAATAATG
Found at i:41446337 original size:25 final size:25
Alignment explanation
Indices: 41446317--41446422 Score: 176
Period size: 25 Copynumber: 4.2 Consensus size: 25
41446307 TGGCTCTTCT
41446317 GAGCTGAATAATGGGAAGCTCATGC
1 GAGCTGAATAATGGGAAGCTCATGC
*
41446342 GAGTTGAATAATGGGAAGCTCATGC
1 GAGCTGAATAATGGGAAGCTCATGC
*
41446367 AAGCTGAATAATGGGAAGCTCATGC
1 GAGCTGAATAATGGGAAGCTCATGC
* *
41446392 GAGCTGAATAATGGGAAGCTGATAC
1 GAGCTGAATAATGGGAAGCTCATGC
41446417 GAGCTG
1 GAGCTG
41446423 TGGTGTGTCC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (25 bp):
GAGCTGAATAATGGGAAGCTCATGC
Found at i:41451490 original size:54 final size:54
Alignment explanation
Indices: 41451427--41451534 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
41451417 TTGAGTAAGT
41451427 GAAGTATTTTTTTTGGCTAAGTAGAGTATTTTGTAGGATTCGTTATTTGAAAAA
1 GAAGTATTTTTTTTGGCTAAGTAGAGTATTTTGTAGGATTCGTTATTTGAAAAA
41451481 GAAGTATTTTTTTTGGCTAAGTAGAGTATTTTGTAGGATTCGTTATTTGAAAAA
1 GAAGTATTTTTTTTGGCTAAGTAGAGTATTTTGTAGGATTCGTTATTTGAAAAA
41451535 TTCTTAGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (54 bp):
GAAGTATTTTTTTTGGCTAAGTAGAGTATTTTGTAGGATTCGTTATTTGAAAAA
Found at i:41454055 original size:17 final size:18
Alignment explanation
Indices: 41454033--41454066 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41454023 TAAATGAGTT
41454033 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
41454050 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
41454067 AAAACAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:41457673 original size:24 final size:26
Alignment explanation
Indices: 41457644--41457691 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
41457634 CATTCAGATT
*
41457644 TTCCAAATGAC-TCACCAC-AAGGGC
1 TTCCAAATAACTTCACCACTAAGGGC
41457668 TTCCAAATAACTTCACCACTAAGG
1 TTCCAAATAACTTCACCACTAAGG
41457692 CTTTCTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.21
Consensus pattern (26 bp):
TTCCAAATAACTTCACCACTAAGGGC
Found at i:41462649 original size:24 final size:24
Alignment explanation
Indices: 41462622--41462675 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
41462612 TGTTCTAGGG
*
41462622 ATAGTTAGTGTTCCTTCTTAATAT
1 ATAGTTAGTGTTCCTTCTCAATAT
41462646 ATAGTTAGTGTTCCTTCTCAATAT
1 ATAGTTAGTGTTCCTTCTCAATAT
41462670 ATAGTT
1 ATAGTT
41462676 GATAAGGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (24 bp):
ATAGTTAGTGTTCCTTCTCAATAT
Found at i:41466870 original size:17 final size:17
Alignment explanation
Indices: 41466844--41466878 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41466834 AATTTAGTCC
*
41466844 TATATTTATTATATTAT
1 TATATATATTATATTAT
*
41466861 TATATATATTGTATTAT
1 TATATATATTATATTAT
41466878 T
1 T
41466879 TGTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TATATATATTATATTAT
Found at i:41466959 original size:20 final size:22
Alignment explanation
Indices: 41466934--41466984 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
41466924 TTATTATGAG
41466934 TATTATTTTTAATTA-TATAT-
1 TATTATTTTTAATTATTATATA
* *
41466954 TATTATTATTACTTATTATATA
1 TATTATTTTTAATTATTATATA
41466976 TATTATTTT
1 TATTATTTT
41466985 CCTTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 13 0.50
21 5 0.19
22 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTTTTAATTATTATATA
Found at i:41466994 original size:23 final size:24
Alignment explanation
Indices: 41466934--41466999 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
41466924 TTATTATGAG
*
41466934 TATTATT-TTTAATTATATATTAT
1 TATTATTACTTAATTATATATTAT
41466957 TATTATTACTT-ATTATATA-TAT
1 TATTATTACTTAATTATATATTAT
*
41466979 TATT-TTCCTTAAATTAT-TATT
1 TATTATTACTT-AATTATATATT
41467000 TTACATCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 5 0.14
22 9 0.24
23 21 0.57
24 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATTACTTAATTATATATTAT
Found at i:41469287 original size:48 final size:48
Alignment explanation
Indices: 41469225--41469581 Score: 615
Period size: 48 Copynumber: 7.4 Consensus size: 48
41469215 TATATATGTG
41469225 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
41469273 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
41469321 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
41469369 TGTGGTAAAGCTGAATGGCTAATGTGAAATAAGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* * *
41469417 CGTGGTAAAGCCGAATGGATAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
41469465 CGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* **
41469513 GGTGGTAAAGCCGAATGGCTAATGCAAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
41469561 TGTGGTAAAGCCGAATGGCTA
1 TGTGGTAAAGCCGAATGGCTA
41469582 GTGATTCGGC
Statistics
Matches: 294, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 294 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:41469804 original size:37 final size:37
Alignment explanation
Indices: 41469754--41469856 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
41469744 GGAAATATAT
41469754 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
* *
41469791 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
* * *
41469828 TTCGAGTAAGACCCGATAACTACCTGTGG
1 TCCGGGTAAGACCCGATAACTACGTGTGG
41469857 GGACTATTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTATG
Found at i:41480551 original size:39 final size:40
Alignment explanation
Indices: 41480459--41480551 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
41480449 NNNNNNNNNN
* * *
41480459 CTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGG
1 CTAAATCCCGAAGGCATTTGAGCAAGTTACTATAACCGGG
* * *
41480499 CTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTGTATCC-GG
1 CTAAATCCCGAAGGCATTTGAGCAAGTTA-CTATAACCGGG
*
41480538 CTAAATTCCGAAGG
1 CTAAATCCCGAAGG
41480552 TACTTGGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 16 0.35
40 30 0.65
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CTAAATCCCGAAGGCATTTGAGCAAGTTACTATAACCGGG
Found at i:41483603 original size:37 final size:37
Alignment explanation
Indices: 41483550--41483653 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
41483540 TGAATAGTCC
*
41483550 CCACACGTAGTT-ATCGGGTCTTACCTGGAAAAAATCT
1 CCACACGTA-TTCATCGGGTCTTACCCGGAAAAAATCT
* *
41483587 CCACACGTATTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTATTCATCGGGTCTTACCCGGAAAAAATCT
*
41483624 CCACACGTAGTCATCGGGTCTTACCCGGAA
1 CCACACGTATTCATCGGGTCTTACCCGGAA
41483654 TATATTTCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 2 0.03
37 59 0.97
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
CCACACGTATTCATCGGGTCTTACCCGGAAAAAATCT
Found at i:41483851 original size:48 final size:48
Alignment explanation
Indices: 41483793--41487676 Score: 5151
Period size: 48 Copynumber: 80.9 Consensus size: 48
41483783 ATATACACAC
* * *
41483793 ATCTCCTACATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41483841 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41483889 ATCTCATACATATTTCACATTAGCCATTCGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41483937 ATCTCATACATATTTCACATTAGCTATTCGGCTTTACAACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41483985 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACAACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41484033 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41484081 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41484129 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484177 ATCTCATACATATTTCACATCAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484225 ATCTCATACATATTTCCCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41484273 ATCTCATAAATATTTCGCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41484321 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
**
41484369 ATCTCATACATATTTCACATTAGTTATTCGGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTC-GGCTTTACCACATATACAT
**
41484418 ATCTCATACATATTTCACATTAGTTATTCGGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTC-GGCTTTACCACATATACAT
41484467 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484515 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACTTATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484563 ATCTCAAACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41484611 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484659 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
41484707 ATCTCATATATATTTCACATAAGCCATTCGGCTTTACCTTTACCACATATAAAT
1 ATCTCATACATATTTCACATTAGCCATTCGG------CTTTACCACATATACAT
* *
41484761 ATCTCATACATATTTCACATTAGCCATTTGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41484809 ATCTCATACATATTTCACATTAGCCATTCGGCTTCACCACAT-TACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * * ** * ** *
41484856 ATTTTCACCTA-ACT-TTCCACATT-GACAAAACGCACAATA--ATCATAGAACAGTCTT
1 A-TCTCA--TACA-TATTTCACATTAG-CCATTCG-GCTTTACCA-CATA-TACA----T
* * * * * *
41484911 ATTGCTTTACTCACATATGCATCACATAATGACCTT-GTGATTTAGTCCA-A-AT-CA-
1 A-T-C-TCA-T-ACATAT--TTCACATTA-GCCATTCG-GCTTTA--CCACATATACAT
* * * * * * * * * * **
41484965 AGCTTAAATATAATCTCAAAATA--CATAC--C-TGACCAGCTTA-ACGC
1 ATCTCATACAT-ATTTCACATTAGCCATTCGGCTTTACCA-CATATACAT
* * * * *** *
41485009 AT-TGA-ACGTATTT---ATTA-CCAATT-GTTACTGTGAAGTCGTAT--A-
1 ATCTCATACATATTTCACATTAGCC-ATTCG--GCT-TTACCACATATACAT
* *** * * * ** * * *
41485051 ATCTTATGTTTTACTTGA-ATCTTCAGCGAAAC--CTTTAGCTCGA-ATA-GT
1 ATCTCAT-ACATATTTCACA--TT-AGCCATTCGGCTTTACCAC-ATATACAT
* * * * * * * *
41485099 -CCCCACACGTAGTTATCGGGTC-TTA-CC--T-GGAAAAAATCT-CCACACGTATTCAT
1 ATCTCATACATA-TT-TC---ACATTAGCCATTCGG-----CTTTACCACA--TATACAT
* * * * * * *
41485152 CGGGTCTTACCTGGACATAATCTCCACACGTAGTCA-TCGGGTCTTACC-CGGA-ATATAT
1 ---ATC-T-CAT--ACAT-AT-TTCACA-TTAGCCATTCGGCT-TTACCAC--ATATACAT
* ** * * *
41485210 TTC-CA-AGTTTCATGT-ACATTTA---A-TC-ACATGTTACAACAT-TCACAT
1 ATCTCATA-CAT-ATTTCACA-TTAGCCATTCGGC-T-TTACCACATAT-ACAT
* * * * * *
41485255 CGA-CT-GT-CATATTTGTA-ATT---CATTC-GCCTCATCAAATAT-C-T
1 --ATCTCATACATATTT-CACATTAGCCATTCGGCTTTACCACATATACAT
* * * * * * * * * *
41485296 A-ATAATACACACCTTTCACATTTGGTCATTCGGC--CACAATATACACAC
1 ATCTCATACATA--TTTCACA-TTAGCCATTCGGCTTTACCACATATACAT
* *
41485344 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41485392 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485440 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41485488 ATCTCATACATATTTCACATTAGCCATTCGGC-TT--CAC-CATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41485532 ATCTCA-ACATA--TC-CATTAG-CA----GCTTTACAACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41485571 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACAACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485619 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485667 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485715 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41485763 ATCTCATACATATTTCACATTAGCCATTAGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485811 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT-CAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485858 AT-TCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485905 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41485953 ATCTCATACATATTTCACATTAGCCATTCGGC-TTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486000 ATCTCA-ACATATTTCACATTAGCCATTCGGCTTTACAACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486047 ATCTCATACATATTTCACATTAGCCATTCGGCTTTA-CACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486094 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486142 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486190 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486238 ATCTCATACATATTTCACATTAGCCATTAGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486286 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATCCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486334 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486382 ATCTCATAAATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486430 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486478 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486526 ATCTCATACATATTTCCCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486574 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486622 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486670 ATCTCATACATATTTCCCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486718 ATCTCATACATATTTCGCATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486766 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* **
41486814 ATCTCATAAATATTTCACATTAGTTATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41486862 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486910 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACTTATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41486958 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACTTATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487006 ATCTCATACATATTTCACATTAGCCTTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41487054 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487102 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487150 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGG------CTTTACCACATATACAT
* *
41487204 ATCTCATACATATTTCACATTAGCCATTTGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487252 ATCTCATACATATTTCACATTAGCCATTCGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41487300 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487348 ATCTCATACATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487396 ATCTCATACATATTTCACATTAGCCATTCGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487444 ATCTCATACATATTTCACATTAGCCATTCGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487492 ATCTCATACATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41487540 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487588 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41487636 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
41487677 CACATATATA
Statistics
Matches: 3460, Mismatches: 225, Indels: 302
0.87 0.06 0.08
Matches are distributed among these distances:
35 2 0.00
36 2 0.00
38 5 0.00
39 17 0.00
40 17 0.00
41 9 0.00
42 10 0.00
43 27 0.01
44 29 0.01
45 28 0.01
46 93 0.03
47 125 0.04
48 2797 0.81
49 126 0.04
50 14 0.00
51 9 0.00
52 4 0.00
53 1 0.00
54 91 0.03
55 6 0.00
56 2 0.00
57 5 0.00
58 8 0.00
59 5 0.00
60 12 0.00
61 8 0.00
62 5 0.00
63 2 0.00
64 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:41485154 original size:37 final size:37
Alignment explanation
Indices: 41485101--41485204 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
41485091 CGAATAGTCC
41485101 CCACACGTAGTT-ATCGGGTCTTACCTGGAAAAAATCT
1 CCACACGTA-TTCATCGGGTCTTACCTGGAAAAAATCT
* *
41485138 CCACACGTATTCATCGGGTCTTACCTGGACATAATCT
1 CCACACGTATTCATCGGGTCTTACCTGGAAAAAATCT
* *
41485175 CCACACGTAGTCATCGGGTCTTACCCGGAA
1 CCACACGTATTCATCGGGTCTTACCTGGAA
41485205 TATATTTCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 2 0.03
37 59 0.97
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (37 bp):
CCACACGTATTCATCGGGTCTTACCTGGAAAAAATCT
Found at i:41488884 original size:148 final size:148
Alignment explanation
Indices: 41488672--41488967 Score: 574
Period size: 148 Copynumber: 2.0 Consensus size: 148
41488662 CAAATAATTT
41488672 ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATGTATTTATAA
1 ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATGTATTTATAA
41488737 TATTGGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
66 TATTGGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
41488802 ATCCTTTATGCCCTAAGC
131 ATCCTTTATGCCCTAAGC
*
41488820 ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATTTATTTATAA
1 ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATGTATTTATAA
*
41488885 TATTTGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
66 TATTGGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
41488950 ATCCTTTATGCCCTAAGC
131 ATCCTTTATGCCCTAAGC
41488968 CGAATACACT
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 146 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (148 bp):
ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATGTATTTATAA
TATTGGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
ATCCTTTATGCCCTAAGC
Found at i:41490290 original size:11 final size:11
Alignment explanation
Indices: 41490276--41490307 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
41490266 GCATTTCAAA
41490276 CACATATTAAG
1 CACATATTAAG
41490287 CACATATTAAG
1 CACATATTAAG
41490298 CACATATTAA
1 CACATATTAA
41490308 CCTGTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (11 bp):
CACATATTAAG
Found at i:41491174 original size:40 final size:40
Alignment explanation
Indices: 41491129--41491447 Score: 548
Period size: 40 Copynumber: 8.0 Consensus size: 40
41491119 GAATGCACAT
* * * * *
41491129 CACCAGCATGATTGCTCTTTGGGACCTAGCCCAGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
41491169 CACCAGCATGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
41491209 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
41491249 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
41491289 CACCAGCACGAATGCTTTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
41491329 CATCAGCACGAATGCTCTTCGGGACTTAGCCCGGACATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
41491369 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
41491409 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGCTATA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
41491448 TAACTCTCAA
Statistics
Matches: 267, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 267 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:41494139 original size:29 final size:28
Alignment explanation
Indices: 41494103--41494180 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
41494093 TCATGAGATT
41494103 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
41494133 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
41494160 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
41494181 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:41502116 original size:29 final size:28
Alignment explanation
Indices: 41502080--41502157 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
41502070 TCATGAGATT
41502080 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
41502110 -GCACTAAGTGTGTGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
41502137 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
41502158 GATTATTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.80
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:41503918 original size:37 final size:37
Alignment explanation
Indices: 41503860--41503967 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
41503850 TAGCTCGAAT
* *
41503860 AATCCCCACACGTAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
41503897 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
41503934 AATCTTCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
41503968 ATATATTTCC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAA
Found at i:41504166 original size:48 final size:48
Alignment explanation
Indices: 41504108--41504484 Score: 655
Period size: 48 Copynumber: 7.9 Consensus size: 48
41504098 ATATACACGC
* *
41504108 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41504156 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41504204 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
41504252 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41504300 ATCTCATACACATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* **
41504348 TTCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAGGCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
41504396 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATTCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
41504444 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
41504485 CACATATATA
Statistics
Matches: 314, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 314 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:41505749 original size:148 final size:148
Alignment explanation
Indices: 41505481--41505776 Score: 565
Period size: 148 Copynumber: 2.0 Consensus size: 148
41505471 CAAATAATTT
41505481 ACCTTGGCCGATCATGTATAATGTTTTGTAACTTAATAAATTTAACATACATTATGTATTAATAA
1 ACCTTGGCCGATCATGTATAATGTTTTGTAACTTAATAAATTTAACATACATTATGTATTAATAA
*
41505546 TATTTGTGCAGCCAATTATCCATGGTCATACACATACAATCAAAAATAAATACCAAATTTTTCAT
66 TATTTGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
41505611 ATCCTTTATGCCCTAAGC
131 ATCCTTTATGCCCTAAGC
* *
41505629 ACCTTGGCCGATCATGTATAATGTTTTGTAGCTTAATAAATTTAACATACATTATGTATTTATAA
1 ACCTTGGCCGATCATGTATAATGTTTTGTAACTTAATAAATTTAACATACATTATGTATTAATAA
41505694 TATTTGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
66 TATTTGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
41505759 ATCCTTTATGCCCTAAGC
131 ATCCTTTATGCCCTAAGC
41505777 CGAATACACT
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 145 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (148 bp):
ACCTTGGCCGATCATGTATAATGTTTTGTAACTTAATAAATTTAACATACATTATGTATTAATAA
TATTTGTGCAGCCAATTATCCATGGTCATACACACACAATCAAAAATAAATACCAAATTTTTCAT
ATCCTTTATGCCCTAAGC
Found at i:41508762 original size:55 final size:54
Alignment explanation
Indices: 41508607--41508813 Score: 193
Period size: 53 Copynumber: 3.8 Consensus size: 54
41508597 TTCCTTTTTA
* * * *
41508607 AACTTACCATTTCCATGTCTTGACATGGTCTTACGT-AGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGA-TATCCTTGCCTTATAG
** * * ** *
41508660 AACTCGCCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAG
** * * * * *
41508714 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAG
* * *
41508769 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
41508814 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 31, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
53 42 0.35
54 38 0.32
55 40 0.33
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAG
Found at i:41513227 original size:58 final size:58
Alignment explanation
Indices: 41513153--41513264 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 58
41513143 TATTTTAGTA
* * *
41513153 TTGTCAGCTCAGAAATGTGTCCAGAAAGGTTACGAGGCATATTTGGCTTACATCAGCT
1 TTGTCAGCTCAAAAATGTGTCCAAAAAGGTTACAAGGCATATTTGGCTTACATCAGCT
*
41513211 TTGTCAGCTCAAAAATGTGTCTAAAAAGGTTACAAGGCATATTTGGCTTACATC
1 TTGTCAGCTCAAAAATGTGTCCAAAAAGGTTACAAGGCATATTTGGCTTACATC
41513265 TTAGATACCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (58 bp):
TTGTCAGCTCAAAAATGTGTCCAAAAAGGTTACAAGGCATATTTGGCTTACATCAGCT
Found at i:41519883 original size:34 final size:34
Alignment explanation
Indices: 41519840--41519910 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
41519830 TGGGTGGAGA
41519840 AAACATTCCAGATACCGACATAAAAAACTTGCAT
1 AAACATTCCAGATACCGACATAAAAAACTTGCAT
41519874 AAACATTCCAGATACCGACATAAAAAACTTGCAT
1 AAACATTCCAGATACCGACATAAAAAACTTGCAT
41519908 AAA
1 AAA
41519911 TACCAATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.20
Consensus pattern (34 bp):
AAACATTCCAGATACCGACATAAAAAACTTGCAT
Found at i:41534172 original size:40 final size:40
Alignment explanation
Indices: 41534105--41534199 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
41534095 TCAATGTCTT
* * *
41534105 GCACACTAAGTGACGTACATAGCCGAAGCTATCTTAAATC
1 GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATC
* * * *
41534145 GCACACTAAGTGCCATATATAGTCGAAGCTATGTCGAATC
1 GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATC
*
41534185 GTACACTAAGTGCCA
1 GCACACTAAGTGCCA
41534200 CAAATAACCG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (40 bp):
GCACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATC
Found at i:41535534 original size:33 final size:33
Alignment explanation
Indices: 41535484--41535552 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
41535474 GACATTGTAG
41535484 AGGCCACTATATGGAAAATGGCTGAAGAACATA
1 AGGCCACTATATGGAAAATGGCTGAAGAACATA
* *
41535517 AGGCCACTGTGAT-GAAAATGGCTGAAGAATATA
1 AGGCCACTAT-ATGGAAAATGGCTGAAGAACATA
41535550 AGG
1 AGG
41535553 TTGCGATTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.19
Consensus pattern (33 bp):
AGGCCACTATATGGAAAATGGCTGAAGAACATA
Found at i:41536389 original size:103 final size:103
Alignment explanation
Indices: 41536205--41536509 Score: 305
Period size: 103 Copynumber: 3.0 Consensus size: 103
41536195 TTAAGTTGCT
* * * * * * *
41536205 AGCTTAACTTAACTAACCTTTAAACATC-AGTAGGGAATGTAGGTCCGC-AGGCTATTTCAGAGT
1 AGCTTAACTCAGCTAACCTTTAAACATCAACTA-GGAACGTAAGTCCACGA-GCCATTTCAGAGT
* * * *
41536268 TGTGAGCTTAACTTAGCTAACTCAAATAATTTTA-G-TAGCG
64 TGCGAGCTTAACTAAGCTAACTCAAATAA-CTTAGGTTA-CA
* * **
41536308 AGTTTAACTCAGCTAACCTTTAAACATCAACTAGGAAGGTAAGTCCACGAGCCATTTTGGAGTTG
1 AGCTTAACTCAGCTAACCTTTAAACATCAACTAGGAACGTAAGTCCACGAGCCATTTCAGAGTTG
*
41536373 CGATCTTAACTAAGCTAACTCAAATAACTTAGGTTACA
66 CGAGCTTAACTAAGCTAACTCAAATAACTTAGGTTACA
* * * * * ** *
41536411 AGCTTAACTCAGCTGACCTTTAAACCTTAGCTAGGAACGTAGGTCTGCGAGCTATTTCAGAGTTG
1 AGCTTAACTCAGCTAACCTTTAAACATCAACTAGGAACGTAAGTCCACGAGCCATTTCAGAGTTG
*
41536476 CAAGCTTAACTCAA-CTAACTCAAATAACTTAGGT
66 CGAGCTTAACT-AAGCTAACTCAAATAACTTAGGT
41536510 ACAGATTTCT
Statistics
Matches: 168, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
102 3 0.02
103 157 0.93
104 8 0.05
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (103 bp):
AGCTTAACTCAGCTAACCTTTAAACATCAACTAGGAACGTAAGTCCACGAGCCATTTCAGAGTTG
CGAGCTTAACTAAGCTAACTCAAATAACTTAGGTTACA
Found at i:41542083 original size:53 final size:53
Alignment explanation
Indices: 41542004--41542108 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
41541994 TTCCTTTTTA
* * * * *
41542004 AACTTACCATTTTCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTCACCATTTCCATGCCTTAACATGGTCTTACATGGGATCCTTGCCTTATG
* *
41542057 AACTCACCATTTCCATGCCTTAACATGGTCTTACATGGGATCTTTGTCTTAT
1 AACTCACCATTTCCATGCCTTAACATGGTCTTACATGGGATCCTTGCCTTAT
41542109 CGTAGTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (53 bp):
AACTCACCATTTCCATGCCTTAACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:41543368 original size:25 final size:25
Alignment explanation
Indices: 41543340--41543391 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
41543330 ACTAGGTAAA
41543340 TTATAAAAATTAATCCGAATATACT
1 TTATAAAAATTAATCCGAATATACT
*
41543365 TTATAAAAATTAATCGGAATATACT
1 TTATAAAAATTAATCCGAATATACT
41543390 TT
1 TT
41543392 TCTATCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (25 bp):
TTATAAAAATTAATCCGAATATACT
Found at i:41549502 original size:53 final size:54
Alignment explanation
Indices: 41549433--41549639 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 54
41549423 TTTCCTTTTT
* * * **
41549433 AACTTCCCATTGCCATGTCTTGACATGGTCTTATTTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * * *
41549486 AACTCACCATTGCCATGCCTTGGCATGGTCTTATATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * *
41549540 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
41549595 AACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
41549640 AAACCCTAAT
Statistics
Matches: 121, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 45 0.37
54 37 0.31
55 39 0.32
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:41549572 original size:55 final size:53
Alignment explanation
Indices: 41549443--41549627 Score: 163
Period size: 55 Copynumber: 3.4 Consensus size: 53
41549433 AACTTCCCAT
* * *
41549443 TGCCATGTCTTGACATGGTCTTATTTGGTATCCTTGCCTTATGAACTCACCAT
1 TGCCATGTCTTGACATGGTCTTATATGGGATCCTTGCCTTATGAACTCACCAA
* * * ** * *
41549496 TGCCATGCCTTGGCATGGTCTTATATGGGATCTTTGCCTTATCGTAGTTTATCAA
1 TGCCATGTCTTGACATGGTCTTATATGGGATCCTTGCCTTAT-G-AACTCACCAA
* *** * * *
41549551 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAA
1 TGCCATGTCTTGACATGGTCTTATATGGGATCCTTGCCTTAT-GAACTCACCAA
* * *
41549605 TGTCATGCCTTGGCATGGTCTTA
1 TGCCATGTCTTGACATGGTCTTA
41549628 CTTGGTATCC
Statistics
Matches: 104, Mismatches: 26, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 37 0.36
54 28 0.27
55 39 0.38
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (53 bp):
TGCCATGTCTTGACATGGTCTTATATGGGATCCTTGCCTTATGAACTCACCAA
Found at i:41552660 original size:17 final size:17
Alignment explanation
Indices: 41552638--41552674 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41552628 ATACATATGC
41552638 AATGAAGAGCATAGATA
1 AATGAAGAGCATAGATA
41552655 AATGAAGAGCATAGATA
1 AATGAAGAGCATAGATA
41552672 AAT
1 AAT
41552675 AAAAAGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (17 bp):
AATGAAGAGCATAGATA
Found at i:41570771 original size:5 final size:5
Alignment explanation
Indices: 41570761--41570787 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41570751 ACTGGTCAAG
41570761 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
41570788 ACTATTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:41572200 original size:16 final size:18
Alignment explanation
Indices: 41572174--41572206 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41572164 ATCAAACCAC
41572174 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
41572191 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
41572207 CTCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:41579614 original size:18 final size:17
Alignment explanation
Indices: 41579572--41579614 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41579562 AAAAATATAA
41579572 TAAAAAATAGAATTTAG
1 TAAAAAATAGAATTTAG
*
41579589 -ATAGAAATAGAATTTTAG
1 TA-AAAAATAGAA-TTTAG
41579607 TAAAAAAT
1 TAAAAAAT
41579615 TTTAAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.05
17 9 0.43
18 10 0.48
19 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (17 bp):
TAAAAAATAGAATTTAG
Found at i:41587884 original size:30 final size:32
Alignment explanation
Indices: 41587840--41587900 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
41587830 AATAATATTT
* *
41587840 AAATGATGCATGATATA-AAA-AAAATAAATC
1 AAATAATGCATGATATACAAATAAAAGAAATC
*
41587870 AAATAATGTATGATATACAAATAAAAGAAAT
1 AAATAATGCATGATATACAAATAAAAGAAAT
41587901 ATAGTGCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 3 0.12
32 8 0.31
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.25
Consensus pattern (32 bp):
AAATAATGCATGATATACAAATAAAAGAAATC
Found at i:41588336 original size:18 final size:19
Alignment explanation
Indices: 41588291--41588338 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
41588281 CATGATATAC
*
41588291 ATAACATATATATTAAAACA
1 ATAACATA-ATATGAAAACA
*
41588311 ATAA-ATAATATGAAAATA
1 ATAACATAATATGAAAACA
41588329 A-AACATAATA
1 ATAACATAATA
41588339 AAGATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAACATAATATGAAAACA
Found at i:41588537 original size:20 final size:20
Alignment explanation
Indices: 41588501--41588538 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41588491 GGAAAATAAT
*
41588501 ATATATAATAAGTAATAACA
1 ATATATAATAAGAAATAACA
41588521 ATATATAATTAA-AAATAA
1 ATATATAA-TAAGAAATAA
41588539 TACTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGAAATAACA
Found at i:41590291 original size:83 final size:83
Alignment explanation
Indices: 41590147--41590919 Score: 1050
Period size: 83 Copynumber: 9.2 Consensus size: 83
41590137 TTCGATTTGT
* * * *
41590147 AAGGATGTCAAATTATCTTGAGTCTGCTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
41590212 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
41590230 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
41590295 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
41590313 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
*
41590378 TTTGTTCCTTGTAAGTAC
66 TTTGTTCCTTGTAAGCAC
41590396 AAGGATGCCAAA-CATCTTGA-TCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGT-C-C--
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
41590455 -----T-CTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
41590467 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
41590532 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
41590550 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCCCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
41590615 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
41590633 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
* *
41590698 TTTGTTTCTTGTAAACAC
66 TTTGTTCCTTGTAAGCAC
* * * *
41590716 AAGAATGCCAAATCATCTTG-GATCTGAAGGTTAGATCTGCTATATTTGAGAACGTCTGAGAGTC
1 AAGGATGCCAAATCATCTTGAG-TCT----GTTTGA---G-AACATTTGAG-A-GTC----A-T-
* *
41590780 AAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCAC
49 --ATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
*
41590817 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTTGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
* * *
41590882 TTTGTTTCTTGTAAACAT
66 TTTGTTCCTTGTAAGCAC
* *
41590900 AAGAATACCAAATCATCTTG
1 AAGGATGCCAAATCATCTTG
41590920 GATCTGCTTC
Statistics
Matches: 623, Mismatches: 35, Indels: 64
0.86 0.05 0.09
Matches are distributed among these distances:
71 22 0.04
72 9 0.01
73 36 0.06
74 1 0.00
75 1 0.00
79 1 0.00
80 1 0.00
81 36 0.06
82 10 0.02
83 412 0.66
86 1 0.00
87 6 0.01
90 1 0.00
91 11 0.02
92 2 0.00
93 11 0.02
94 1 0.00
97 6 0.01
98 1 0.00
101 53 0.09
102 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:41590886 original size:184 final size:184
Alignment explanation
Indices: 41590576--41590925 Score: 628
Period size: 184 Copynumber: 1.9 Consensus size: 184
41590566 CTTGAGTCTG
* *
41590576 TTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCCCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCAACGTCCCCGATTTGTTCCTTGTAAGCACAAGGATGC
41590641 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTTC
66 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTTC
*
41590706 TTGTAAACACAAGAATGCCAAATCATCTTGGATCTGAAGGTTAGATCTGCTATA
131 TTGTAAACACAAGAATACCAAATCATCTTGGATCTGAAGGTTAGATCTGCTATA
* * *
41590760 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCAACGTCCCCGATTTGTTCCTTGTAAGCACAAGGATGC
*
41590825 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTTGATTTGTTTC
66 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTTC
*
41590890 TTGTAAACATAAGAATACCAAATCATCTTGGATCTG
131 TTGTAAACACAAGAATACCAAATCATCTTGGATCTG
41590926 CTTCAATATA
Statistics
Matches: 158, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
184 158 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (184 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCAACGTCCCCGATTTGTTCCTTGTAAGCACAAGGATGC
CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTTC
TTGTAAACACAAGAATACCAAATCATCTTGGATCTGAAGGTTAGATCTGCTATA
Found at i:41602283 original size:18 final size:19
Alignment explanation
Indices: 41602260--41602296 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41602250 TTGTACTAGG
41602260 TAGATA-AAA-AATGAATAC
1 TAGATATAAAGAAT-AATAC
41602278 TAGATATAAAGAATAATAC
1 TAGATATAAAGAATAATAC
41602297 ATAAAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (19 bp):
TAGATATAAAGAATAATAC
Found at i:41602481 original size:1 final size:1
Alignment explanation
Indices: 41602475--41602556 Score: 155
Period size: 1 Copynumber: 82.0 Consensus size: 1
41602465 TGATACATAC
41602475 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
41602540 AAAAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAA
41602557 TATGTAAAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.99, C:0.00, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:41602594 original size:27 final size:27
Alignment explanation
Indices: 41602545--41602601 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
41602535 AAAAAAAAAA
41602545 AAAAAATAAAAATATGTAAA-ATAATAT
1 AAAAAATAAAAATATGTAAATA-AATAT
41602572 AAAAAATAATAATATATGT-AATAAATAT
1 AAAAAATAA-AA-ATATGTAAATAAATAT
41602600 AA
1 AA
41602602 TGATAAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 9 0.33
28 11 0.41
29 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAATAAAAATATGTAAATAAATAT
Found at i:41602691 original size:1 final size:1
Alignment explanation
Indices: 41602685--41602804 Score: 150
Period size: 1 Copynumber: 120.0 Consensus size: 1
41602675 TAAATAATAT
* *
41602685 AAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * * *
41602750 AAAAATAATTATATAATATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41602805 TAATTAAATA
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 101 1.00
ACGTcount: A:0.92, C:0.01, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:41602814 original size:58 final size:56
Alignment explanation
Indices: 41602686--41602821 Score: 148
Period size: 48 Copynumber: 2.6 Consensus size: 56
41602676 AAATAATATA
*
41602686 AAAAAACAAAAA-AAAAAAAAAAAA-A-A-A-AA-A-AAAAAAAAAAAAAAAA-AA
1 AAAAAAAAAAAATAAAAAAAAAAAATATATATAATATAAAAAAAAAAAAAAAAAAA
* *
41602734 AAAAAAAATAAA-AAAAAAAAATAAT-TATATAATATAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAATAAAAAAAAAAAATATATATAATATAAAAAAAAAAAAAAAAAAA
* **
41602788 AAAAAAAAAAAATAAAATAATTAAATATATATAA
1 AAAAAAAAAAAATAAAAAAAAAAAATATATATAA
41602822 AAAATAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
48 21 0.30
49 1 0.01
50 1 0.01
51 2 0.03
52 1 0.01
53 16 0.23
54 13 0.18
55 9 0.13
56 7 0.10
ACGTcount: A:0.88, C:0.01, G:0.00, T:0.12
Consensus pattern (56 bp):
AAAAAAAAAAAATAAAAAAAAAAAATATATATAATATAAAAAAAAAAAAAAAAAAA
Found at i:41602814 original size:71 final size:70
Alignment explanation
Indices: 41602697--41602843 Score: 213
Period size: 71 Copynumber: 2.1 Consensus size: 70
41602687 AAAAACAAAA
*
41602697 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAATAATTAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAATAATAAT
41602762 ATAAT
66 ATAAT
* * ** * * *
41602767 ATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAATAATTAAATATATATAAAAAATAATAA
1 A-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAATAATAA
41602832 TATAAT
65 TATAAT
41602838 AAAAAA
1 AAAAAA
41602844 TAAACAAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 6 0.09
71 62 0.91
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (70 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAATAATAAT
ATAAT
Found at i:41602821 original size:19 final size:19
Alignment explanation
Indices: 41602799--41602905 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 19
41602789 AAAAAAAAAA
41602799 ATAAAATAATTAAATATAT
1 ATAAAATAATTAAATATAT
*
41602818 ATAAAA-AATAATAATATAAT
1 ATAAAATAATTA-AATAT-AT
* **
41602838 AAAAAATAAACAAATAAATAGT
1 ATAAAATAATTAAAT--ATA-T
*
41602860 ATATAAATAAATATATAATAAAT
1 ATA-AAAT-AAT-TA-AATATAT
*
41602883 AAAACAATAATTAAATA-AT
1 ATAA-AATAATTAAATATAT
41602902 ATAA
1 ATAA
41602906 TATTCCCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.06
19 16 0.24
20 14 0.21
21 6 0.09
22 9 0.13
23 10 0.15
24 4 0.06
25 1 0.01
26 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (19 bp):
ATAAAATAATTAAATATAT
Found at i:41602836 original size:15 final size:15
Alignment explanation
Indices: 41602762--41602908 Score: 65
Period size: 15 Copynumber: 10.5 Consensus size: 15
41602752 AAATAATTAT
41602762 ATAATATAAAAAA-A
1 ATAATATAAAAAATA
41602776 A-AA-A-AAAAAA-A
1 ATAATATAAAAAATA
*
41602787 A-AA-A-AAAAAAAA
1 ATAATATAAAAAATA
* *
41602799 ATAAAATAATTAAAT-
1 ATAATATAA-AAAATA
41602814 AT-ATATAAAAAATA
1 ATAATATAAAAAATA
41602828 ATAATATAATAAAA-A
1 ATAATATAA-AAAATA
*
41602843 ATAA-ACAAATAAATA
1 ATAATATAAA-AAATA
*
41602858 GT-ATATAAATAAATA
1 ATAATATAAA-AAATA
*
41602873 TATAATA-AATAAAACA
1 -ATAATATAA-AAAATA
*
41602889 ATAAT-TAAATAAT-
1 ATAATATAAAAAATA
41602902 ATAATAT
1 ATAATAT
41602909 TCCCAAAACG
Statistics
Matches: 106, Mismatches: 11, Indels: 32
0.71 0.07 0.21
Matches are distributed among these distances:
11 17 0.16
12 3 0.03
13 14 0.13
14 20 0.19
15 34 0.32
16 14 0.13
17 4 0.04
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (15 bp):
ATAATATAAAAAATA
Found at i:41602841 original size:17 final size:21
Alignment explanation
Indices: 41602801--41602905 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 21
41602791 AAAAAAAAAT
41602801 AAAATAATTAAATATATATAA
1 AAAATAATTAAATATATATAA
41602822 AAAATAA-T-AATATA-ATAA
1 AAAATAATTAAATATATATAA
** *
41602840 AAAATAAACAAATAAATAGTATA
1 AAAATAATTAAATATATA-TA-A
* * * *
41602863 TAAATAAATATATAATAAATAA
1 AAAATAATTAAAT-ATATATAA
41602885 AACAATAATTAAATA-ATATAA
1 AA-AATAATTAAATATATATAA
41602906 TATTCCCAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
18 11 0.17
19 6 0.09
20 6 0.09
21 13 0.20
22 5 0.08
23 22 0.33
24 3 0.05
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.29
Consensus pattern (21 bp):
AAAATAATTAAATATATATAA
Found at i:41602869 original size:4 final size:4
Alignment explanation
Indices: 41602739--41602905 Score: 66
Period size: 4 Copynumber: 42.5 Consensus size: 4
41602729 AAAAAAAAAA
* * * * * *
41602739 AAAT AAA- AAA- AAA- AAAT AATT ATAT AATAT AAAA AAAA AAAA AAAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* * * *
41602785 AAAA AAAA AAAA AAAT AAAAT AATT AAAT ATATAT AAA- AAAT -AAT -AAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT
* * * *
41602833 ATAAT AAA- AAAT AAAC AAAT AAAT -AGT ATAT AAAT AAAT ATAT -AAT
1 A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
41602879 AAAT AAA- ACAAT AATT AAAT AATAT AA
1 AAAT AAAT A-AAT AAAT AAAT AA-AT AA
41602906 TATTCCCAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 27
0.74 0.10 0.15
Matches are distributed among these distances:
3 26 0.20
4 83 0.63
5 19 0.15
6 3 0.02
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:41617885 original size:27 final size:27
Alignment explanation
Indices: 41617855--41618032 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
41617845 ATATTGAGTC
* *
41617855 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
41617882 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41617909 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
41617937 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41617964 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
41617991 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
41618018 CGC-CACCTTAGTGCT
1 CGCACA-CTTAGTGCT
41618033 GTAAAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.02
27 102 0.80
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41617994 original size:82 final size:81
Alignment explanation
Indices: 41617876--41618031 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
41617866 TGCTATATAA
* *
41617876 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCG-C
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCC
41617940 ACACTTAGTGCCGCATGG
65 AC-CTTAGTGCCGCATGG
* * **
41617958 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCC
41618022 ACCTTAGTGC
65 ACCTTAGTGC
41618032 TGTAAAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 12 0.18
82 54 0.82
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCCA
CCTTAGTGCCGCATGG
Found at i:41618015 original size:54 final size:54
Alignment explanation
Indices: 41617855--41618031 Score: 189
Period size: 54 Copynumber: 3.3 Consensus size: 54
41617845 ATATTGAGTC
* * * *
41617855 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
41617909 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
41617964 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
41618018 CGC-CACCTTAGTGC
1 CGCACA-CTTAGTGC
41618032 TGTAAAATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 54 0.52
55 45 0.44
56 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:41623417 original size:47 final size:47
Alignment explanation
Indices: 41623311--41623417 Score: 105
Period size: 47 Copynumber: 2.3 Consensus size: 47
41623301 AAGGCTGGTA
** * *
41623311 ATAAA-GT-GATAAGGCCTAAGGCCGATGTATGAATGTGAAGTGTAT
1 ATAAATGTGGATAAGGCCTAAGGCCGATGTAAAAATGTGAAATGAAT
* *
41623356 ATATATGTGAATAAGGCCTAAGGCCGATG-AAAAATGT-AAATGAAT
1 ATAAATGTGGATAAGGCCTAAGGCCGATGTAAAAATGTGAAATGAAT
*
41623401 GTGAAATCGTGGATAAG
1 AT-AAAT-GTGGATAAG
41623418 ATAATGTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
45 11 0.22
46 11 0.22
47 27 0.55
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.25
Consensus pattern (47 bp):
ATAAATGTGGATAAGGCCTAAGGCCGATGTAAAAATGTGAAATGAAT
Found at i:41623622 original size:1 final size:1
Alignment explanation
Indices: 41623618--41623645 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
41623608 TGATAAGGCC
41623618 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
41623646 TTATAGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41624578 original size:48 final size:48
Alignment explanation
Indices: 41624519--41624929 Score: 491
Period size: 48 Copynumber: 8.6 Consensus size: 48
41624509 AGGGGTGTTA
*
41624519 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* *
41624567 CAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* ** * *
41624615 CAAACATGGTCTTACACTAGCTCACATATCGAGGTCGATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * * * *
41624663 CAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATACTATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * ** * *
41624711 CAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATACCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * * *
41624759 CAGACATGGTCTTACACTAGCTCTCATTTAAATGCCGATACCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * ** *
41624807 CAAACATGGTCTTACACTGGCTCACATATCGAGGCC-ATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
** * * * *
41624854 CAGGCATGGTCTTATACAAGCTCTCATATAAATGCTGATGCCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* *
41624902 CAAACATGGTCTTACACTGGCTCACATA
1 CAAACATGGTCTTACACTAGCTCTCATA
41624930 CCCCTAGTAT
Statistics
Matches: 301, Mismatches: 61, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
47 35 0.12
48 266 0.88
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (48 bp):
CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
Found at i:41624683 original size:96 final size:96
Alignment explanation
Indices: 41624514--41624929 Score: 654
Period size: 96 Copynumber: 4.3 Consensus size: 96
41624504 GGGATAGGGG
* * * ** * *
41624514 TGTTACAAACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
*
41624579 TACACTAGCTCTCATATAAATGCCGATGCCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
* *
41624610 TGTTCCAAACATGGTCTTACACTAGCTCACATATCGAGGTCGATGCCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
* *
41624675 TACACTAGCTCTCATATAAATGTCGATACTA
66 TACACTAGCTCTCATATAAATGCCGATACCA
*
41624706 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATACCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
*
41624771 TACACTAGCTCTCATTTAAATGCCGATACCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
*
41624802 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCC-ATGCCATGTCCCAGGCATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
* * * *
41624866 TATACAAGCTCTCATATAAATGCTGATGCCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
41624897 TGTTCCAAACATGGTCTTACACTGGCTCACATA
1 TGTTCCAAACATGGTCTTACACTGGCTCACATA
41624930 CCCCTAGTAT
Statistics
Matches: 297, Mismatches: 23, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
95 80 0.27
96 217 0.73
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (96 bp):
TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
TACACTAGCTCTCATATAAATGCCGATACCA
Found at i:41642667 original size:27 final size:27
Alignment explanation
Indices: 41642637--41642814 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
41642627 ATATTGAGCC
* *
41642637 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
41642664 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41642691 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
41642719 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41642746 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
41642773 CTCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
41642800 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41642815 GTAGAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41642779 original size:82 final size:81
Alignment explanation
Indices: 41642658--41642813 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
41642648 TGCTATATAA
* *
41642658 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41642723 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
41642740 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCTCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41642804 CACTTAGTGC
65 CACTTAGTGC
41642814 TGTAGAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41650780 original size:27 final size:27
Alignment explanation
Indices: 41650750--41650927 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41650740 ATATTGAGCC
* * * *
41650750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41650777 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41650804 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41650832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41650859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41650886 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41650913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41650928 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:41650889 original size:82 final size:81
Alignment explanation
Indices: 41650771--41650926 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41650761 TGCTATATAA
* *
41650771 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41650836 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41650853 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41650917 CACTTAGTGC
65 CACTTAGTGC
41650927 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:41658822 original size:27 final size:27
Alignment explanation
Indices: 41658792--41658968 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
41658782 ATATTGAGTC
* *
41658792 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
41658819 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41658846 CGCACACTTAGTGC-ACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
41658873 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
41658900 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
41658927 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
41658954 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41658969 GTACATTTAA
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 6 0.05
27 113 0.90
28 7 0.06
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41658874 original size:54 final size:53
Alignment explanation
Indices: 41658792--41658967 Score: 199
Period size: 54 Copynumber: 3.3 Consensus size: 53
41658782 ATATTGAGTC
* * * * *
41658792 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
41658846 CGCACACTTAGTGCACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ***
41658900 CGCACACTTAGTGCATCATATTCGTTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
41658954 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41658968 TGTACATTTA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 6 0.06
54 91 0.88
55 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:41664362 original size:49 final size:49
Alignment explanation
Indices: 41664300--41664872 Score: 972
Period size: 49 Copynumber: 11.9 Consensus size: 49
41664290 TAGTATGGCG
*
41664300 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664349 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664398 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664445 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
41664494 TAATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
41664541 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664590 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664639 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664686 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
41664735 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
41664782 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
41664829 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
41664873 TCCCGAAGGG
Statistics
Matches: 504, Mismatches: 12, Indels: 18
0.94 0.02 0.03
Matches are distributed among these distances:
47 236 0.47
48 1 0.00
49 267 0.53
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:41664466 original size:96 final size:97
Alignment explanation
Indices: 41664300--41664872 Score: 966
Period size: 96 Copynumber: 6.0 Consensus size: 97
41664290 TAGTATGGCG
*
41664300 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41664365 GAATGTGAAAGTGTATATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
41664398 TAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
41664462 AATGTGAAAGTGTATATATATGTGATAAGGCC
66 AATGTGAAAGTGTATATATATGTGATAAGGCC
* *
41664494 TAATAGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
41664558 AATGTGAAAGTGTATATATATGTGATAAGGCC
66 AATGTGAAAGTGTATATATATGTGATAAGGCC
41664590 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41664655 GAATGTGAAAGTG--TATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
41664686 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41664751 GAATGTGAAAGTG--TATATATGTGATAAGGCC
65 GAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * * *
41664782 TAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
41664846 GATGTGAAAGTGTATA-A-ATGTGATAAG
66 AATGTGAAAGTGTATATATATGTGATAAG
41664873 TCCCGAAGGG
Statistics
Matches: 459, Mismatches: 12, Indels: 12
0.95 0.02 0.02
Matches are distributed among these distances:
94 50 0.11
95 1 0.00
96 334 0.73
98 74 0.16
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (97 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:41664576 original size:145 final size:145
Alignment explanation
Indices: 41664300--41664872 Score: 996
Period size: 145 Copynumber: 4.0 Consensus size: 145
41664290 TAGTATGGCG
*
41664300 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41664365 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
66 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
41664428 ATATATGTGATAAGGCC
129 ATATATGTGATAAGGCC
*
41664445 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41664510 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
66 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
41664575 ATATGTGATAAGGCC
131 ATATGTGATAAGGCC
41664590 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41664655 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
66 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
41664720 ATATGTGATAAGGCC
131 ATATGTGATAAGGCC
41664735 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * * * * * *
41664798 GAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-
66 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
41664862 A-ATGTGATAAG
131 ATATGTGATAAG
41664873 TCCCGAAGGG
Statistics
Matches: 414, Mismatches: 12, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
141 10 0.02
142 1 0.00
143 137 0.33
145 266 0.64
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (145 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATATGTGATAAGGCC
Found at i:41665848 original size:48 final size:48
Alignment explanation
Indices: 41665789--41666199 Score: 491
Period size: 48 Copynumber: 8.6 Consensus size: 48
41665779 AGGGGTGTTA
*
41665789 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* *
41665837 CAGACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* ** * *
41665885 CAAACATGGTCTTACACTAGCTCACATATCGAGGTCGATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * * * *
41665933 CAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATACTATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * ** * *
41665981 CAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATACCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * * *
41666029 CAGACATGGTCTTACACTAGCTCTCATTTAAATGCCGATACCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* * ** *
41666077 CAAACATGGTCTTACACTGGCTCACATATCGAGGCC-ATGCCATGTCC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
** * * * *
41666124 CAGGCATGGTCTTATACAAGCTCTCATATAAATGCTGATGCCATGTTC
1 CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
* *
41666172 CAAACATGGTCTTACACTGGCTCACATA
1 CAAACATGGTCTTACACTAGCTCTCATA
41666200 CCCCTAGTAT
Statistics
Matches: 301, Mismatches: 61, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
47 35 0.12
48 266 0.88
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (48 bp):
CAAACATGGTCTTACACTAGCTCTCATATAAATGCCGATGCCATGTCC
Found at i:41665953 original size:96 final size:96
Alignment explanation
Indices: 41665784--41666199 Score: 654
Period size: 96 Copynumber: 4.3 Consensus size: 96
41665774 GGGATAGGGG
* * * ** * *
41665784 TGTTACAAACATGGTCTTACACTAGCTCTCATATAAATGCCAATGCCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
*
41665849 TACACTAGCTCTCATATAAATGCCGATGCCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
* *
41665880 TGTTCCAAACATGGTCTTACACTAGCTCACATATCGAGGTCGATGCCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
* *
41665945 TACACTAGCTCTCATATAAATGTCGATACTA
66 TACACTAGCTCTCATATAAATGCCGATACCA
*
41665976 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATACCATGTCCCAGACATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
*
41666041 TACACTAGCTCTCATTTAAATGCCGATACCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
*
41666072 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCC-ATGCCATGTCCCAGGCATGGTCT
1 TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
* * * *
41666136 TATACAAGCTCTCATATAAATGCTGATGCCA
66 TACACTAGCTCTCATATAAATGCCGATACCA
41666167 TGTTCCAAACATGGTCTTACACTGGCTCACATA
1 TGTTCCAAACATGGTCTTACACTGGCTCACATA
41666200 CCCCTAGTAT
Statistics
Matches: 297, Mismatches: 23, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
95 80 0.27
96 217 0.73
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (96 bp):
TGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCT
TACACTAGCTCTCATATAAATGCCGATACCA
Found at i:41672554 original size:22 final size:22
Alignment explanation
Indices: 41672529--41672572 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41672519 TTGTGGGCCT
41672529 TAACATACCTTGAGTGCACATA
1 TAACATACCTTGAGTGCACATA
41672551 TAACATACCTTGAGTGCACATA
1 TAACATACCTTGAGTGCACATA
41672573 CTTTTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
TAACATACCTTGAGTGCACATA
Found at i:41690031 original size:43 final size:44
Alignment explanation
Indices: 41689984--41690070 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
41689974 CCAAAACATG
*
41689984 TGTCACATATATCATGAACTC-GACCACAACTCATGAGTTCAGA
1 TGTCACATATATCATGAACTCAGACAACAACTCATGAGTTCAGA
41690027 TGTCACATATATCATGAACTCAGACAACAACTCATGAGTTCAGA
1 TGTCACATATATCATGAACTCAGACAACAACTCATGAGTTCAGA
41690071 ACACATAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 21 0.50
44 21 0.50
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (44 bp):
TGTCACATATATCATGAACTCAGACAACAACTCATGAGTTCAGA
Done.