Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold157
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: 1658850
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 45522 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:1196888 original size:92 final size:92
Alignment explanation
Indices: 1196791--1196968 Score: 338
Period size: 92 Copynumber: 1.9 Consensus size: 92
1196781 TATAACCTTA
*
1196791 ATTGTGTCTTACTAGTAAGTTATCATTATATAAAACTTAAATGTTGAATAATAATATATACACGG
1 ATTGTGTCTTACTAGTAAGTTATCATTATATAAAACTTAAATGTTGAATAATAATATATACACGA
1196856 GATGATTATATTTTTAAAAGTTATATC
66 GATGATTATATTTTTAAAAGTTATATC
*
1196883 ATTGTGTCTTACTAGTAAGTTATCATTATTTAAAACTTAAATGTTGAATAATAATATATACACGA
1 ATTGTGTCTTACTAGTAAGTTATCATTATATAAAACTTAAATGTTGAATAATAATATATACACGA
1196948 GATGATTATATTTTTAAAAGT
66 GATGATTATATTTTTAAAAGT
1196969 ACCAGATATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (92 bp):
ATTGTGTCTTACTAGTAAGTTATCATTATATAAAACTTAAATGTTGAATAATAATATATACACGA
GATGATTATATTTTTAAAAGTTATATC
Found at i:1215678 original size:51 final size:51
Alignment explanation
Indices: 1215619--1215902 Score: 326
Period size: 51 Copynumber: 5.6 Consensus size: 51
1215609 TATCAATGAA
* *
1215619 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAACCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATGTTGGT
* * * * * *
1215670 CACATGTGTAGTCCTAAGTGAAGGCTACAATGTGTACCGAGAAGAT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAA-ATGTTGGT
* * * *
1215721 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATGTTGGT
* *
1215772 CACATGTGTAGTACTAAGTGAAGGCTACTATGT-ATACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGA-ACCGATAAATG--TTGGT
* * ** *
1215823 CACGTGTGTAGTACTATGTGAAGGCCACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATGTTGGT
1215873 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA
1215903 CGTGTATCGA
Statistics
Matches: 194, Mismatches: 31, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 39 0.20
51 151 0.78
52 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATGTTGGT
Found at i:1215795 original size:102 final size:102
Alignment explanation
Indices: 1215619--1215900 Score: 422
Period size: 102 Copynumber: 2.8 Consensus size: 102
1215609 TATCAATGAA
* *
1215619 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAACCGATAAATGATGGTCACATGTGTAGTCC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
* *
1215684 TAAGTGAAGGCTACAATGTGTACCGAGAAGATTTGGT
66 TAAGTGAAGGCTACAATGTATACCGAAAAGATTTGGT
*
1215721 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
* *
1215786 TAAGTGAAGGCTACTATGTATACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTATACCGAAAAGATTTGGT
* * *** * *
1215823 CACGTGTGTAGTACTATGTGAAGGCCACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
*
1215887 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
1215901 TACGTGTATC
Statistics
Matches: 164, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
101 33 0.20
102 131 0.80
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTATACCGAAAAGATTTGGT
Found at i:1220300 original size:24 final size:23
Alignment explanation
Indices: 1220273--1220343 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
1220263 CAAAATCCAT
1220273 CTCATTCCCTTACTCTTCTCTTTC
1 CTCA-TCCCTTACTCTTCTCTTTC
* *
1220297 CTCAT-CCTCACTATCTTCCCTTTC
1 CTCATCCCTTAC--TCTTCTCTTTC
* *
1220321 CTCACTCCCTTGCTCTTTTCTTT
1 CTCA-TCCCTTACTCTTCTCTTT
1220344 ATGCTCGGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
22 5 0.14
23 1 0.03
24 26 0.70
25 1 0.03
26 4 0.11
ACGTcount: A:0.08, C:0.42, G:0.01, T:0.48
Consensus pattern (23 bp):
CTCATCCCTTACTCTTCTCTTTC
Found at i:1223341 original size:45 final size:44
Alignment explanation
Indices: 1223291--1223425 Score: 135
Period size: 45 Copynumber: 3.2 Consensus size: 44
1223281 TTCATACAAA
*
1223291 ATATTAATTGTATATATTTTACCGAATTTATTAATATAAACAATT
1 ATATTAATTGTATATATTTTACTGAATTTATTAATATAAA-AATT
* *
1223336 ATATTACTTGT-TAGTA---TA-TGATTTTATTAATAT--AAA--
1 ATATTAATTGTATA-TATTTTACTGAATTTATTAATATAAAAATT
* *
1223372 ATATTAATTGTATATATTTTACTAAATTTATTAATATAAATAGTT
1 ATATTAATTGTATATATTTTACTGAATTTATTAATATAAA-AATT
1223417 ATATTAATT
1 ATATTAATT
1223426 AATTTCGGTC
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
36 12 0.17
37 2 0.03
38 2 0.03
39 3 0.04
40 13 0.18
41 13 0.18
42 3 0.04
43 1 0.01
44 2 0.03
45 21 0.29
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (44 bp):
ATATTAATTGTATATATTTTACTGAATTTATTAATATAAAAATT
Found at i:1223379 original size:81 final size:82
Alignment explanation
Indices: 1223264--1223422 Score: 248
Period size: 81 Copynumber: 2.0 Consensus size: 82
1223254 ATAGATATAA
* *
1223264 TTAGTATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATATA
1 TTAGTATATGAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
1223329 AACAATTATATTACTTG
66 AACAATTATATTACTTG
* * *
1223346 TTAGTATATG-ATTTTATTAATATAAAATATTAATTGTATATATTTTACTAAATTTATTAATATA
1 TTAGTATATGAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
* *
1223410 AATAGTTATATTA
66 AACAATTATATTA
1223423 ATTAATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 60 0.86
82 10 0.14
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (82 bp):
TTAGTATATGAATTTGATTAATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
AACAATTATATTACTTG
Found at i:1223411 original size:40 final size:40
Alignment explanation
Indices: 1223272--1223411 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
1223262 AATTAGTATA
* *
1223272 TGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC
1 TGAATTT-ATTAATATAAAATATTAATTGTATATATTTTAC
* * * * *
1223313 CGAATTTATTAATATAAACA-ATTATATTACT-TGTTAGTATA-
1 TGAATTTATTAATATAAA-ATATTA-ATT-GTAT-ATATTTTAC
*
1223354 TGATTTTATTAATATAAAATATTAATTGTATATATTTTAC
1 TGAATTTATTAATATAAAATATTAATTGTATATATTTTAC
*
1223394 TAAATTTATTAATATAAA
1 TGAATTTATTAATATAAA
1223412 TAGTTATATT
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
39 6 0.08
40 34 0.44
41 31 0.40
42 6 0.08
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (40 bp):
TGAATTTATTAATATAAAATATTAATTGTATATATTTTAC
Found at i:1223576 original size:75 final size:75
Alignment explanation
Indices: 1223459--1223605 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 75
1223449 ATGTAAATTA
* *
1223459 ATATTCTTTTAGAAAGAAGATAATTTCTTTTTTGAACTTTTCATTTGCCTTCTCTATTAATAAAG
1 ATATTCTTTTAGAAAGAAGATAATTTCTTTTTTGAACATTTCATTTGCCTTCACTATTAATAAAG
1223524 GAATAATTCT
66 GAATAATTCT
* * *
1223534 ATATTCTTTTGGAAAGAATATAA-TTCATTTTTTTAACATTTCATTTGCCTTCACTATTAATAAA
1 ATATTCTTTTAGAAAGAAGATAATTTC-TTTTTTGAACATTTCATTTGCCTTCACTATTAATAAA
*
1223598 GGGATAAT
65 GGAATAAT
1223606 CCTAGTTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 3 0.05
75 62 0.95
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTAGAAAGAAGATAATTTCTTTTTTGAACATTTCATTTGCCTTCACTATTAATAAAG
GAATAATTCT
Found at i:1225026 original size:12 final size:12
Alignment explanation
Indices: 1225009--1225033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1224999 CCCTACACGC
1225009 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1225021 CCGTGTGCTAGG
1 CCGTGTGCTAGG
1225033 C
1 C
1225034 AGCAAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.40, T:0.24
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:1230051 original size:18 final size:16
Alignment explanation
Indices: 1230028--1230067 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1230018 TTTCTAAAGA
*
1230028 ATTTTTACATTTTGTTTT
1 ATTTTT-CAATTT-TTTT
1230046 ATTTTTCAATTTTTTT
1 ATTTTTCAATTTTTTT
1230062 ATTTTT
1 ATTTTT
1230068 TTTGTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (16 bp):
ATTTTTCAATTTTTTT
Found at i:1237851 original size:21 final size:21
Alignment explanation
Indices: 1237825--1237867 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1237815 CACATGAAAG
*
1237825 AGAAGAGGAAGGAAAGGATGA
1 AGAAGAAGAAGGAAAGGATGA
* *
1237846 AGAAGAAGAAGGAGATGATGA
1 AGAAGAAGAAGGAAAGGATGA
1237867 A
1 A
1237868 ATGGATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.40, T:0.07
Consensus pattern (21 bp):
AGAAGAAGAAGGAAAGGATGA
Found at i:1245086 original size:20 final size:19
Alignment explanation
Indices: 1245045--1245089 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1245035 AAATTGTGAA
*
1245045 AAATTTGAAATTAAGGGGT
1 AAATTTGAAAATAAGGGGT
1245064 AAATTTGAAAAT-AGGGAGCT
1 AAATTTGAAAATAAGGG-G-T
1245084 AAATTT
1 AAATTT
1245090 AGCTTAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.31
Consensus pattern (19 bp):
AAATTTGAAAATAAGGGGT
Found at i:1245917 original size:19 final size:19
Alignment explanation
Indices: 1245883--1245974 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
1245873 AATAGAAAAT
*
1245883 ATGAGAAATG-AATATGAT
1 ATGAGAAATGAAATATGAA
1245901 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
* * *
1245920 ATGATGAAATGAGATGTAAA
1 ATGA-GAAATGAAATATGAA
* *
1245940 ACT-TGAAATG-AATATGAG
1 A-TGAGAAATGAAATATGAA
1245958 ATGAGAAATGAAATATG
1 ATGAGAAATGAAATATG
1245975 GTGTTTTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
17 1 0.02
18 21 0.36
19 23 0.39
20 13 0.22
21 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.23, T:0.25
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:1246267 original size:54 final size:54
Alignment explanation
Indices: 1246181--1246294 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
1246171 ACAAGCTGAC
* * *
1246181 ACACGGGCTACGACATGGCCATGTGACCCAAGTTAGTGAGTTACACGAGCAAAGG
1 ACACGGGCTACGACACGACCATGTGACCCAAGTCAGTGAGTTACACGAGC-AAGG
* * *
1246236 -CACGGGCTGA-GACACGACCATGTGTCTCAAGTCAGTGAGTTACACGGGCAAGG
1 ACACGGGCT-ACGACACGACCATGTGACCCAAGTCAGTGAGTTACACGAGCAAGG
1246289 ACACGG
1 ACACGG
1246295 TCGTGTGTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
53 4 0.08
54 46 0.90
55 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.16
Consensus pattern (54 bp):
ACACGGGCTACGACACGACCATGTGACCCAAGTCAGTGAGTTACACGAGCAAGG
Found at i:1249324 original size:50 final size:50
Alignment explanation
Indices: 1249223--1249409 Score: 257
Period size: 50 Copynumber: 3.6 Consensus size: 50
1249213 GAATGAGATT
*
1249223 CCATGTAAGACCATGCCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTC
1 CCATGTAAGACCATGCCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC
* *
1249279 CCATGTAAGACCATGCCTGGGACATAGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
*
1249329 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * *
1249379 CCATGTAAGACCACGTCTAGGACATGGCATT
1 CCATGTAAGACCATGCCTGGGACATGGCATT
1249410 TGGTAGTACA
Statistics
Matches: 123, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 86 0.70
53 3 0.02
55 1 0.01
56 33 0.27
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
CCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:1249431 original size:100 final size:102
Alignment explanation
Indices: 1249223--1249464 Score: 267
Period size: 100 Copynumber: 2.4 Consensus size: 102
1249213 GAATGAGATT
* *
1249223 CCATGTAAGACCATGCCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATGAGAGGTCCCATGTAAG
* * * * * **
1249288 ACCATGCCTGGGACATAGCGTTGGCACCGAGATGAGAGGTC
63 ACCACGCCTAGGACATAGCGTTGGCA-CGACAAGAAACATC
1249329 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C-CGAG-ATGAGAGGTCCCATGTAAGACC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCATGTAAGACC
* * * *
1249391 ACGTCTAGGACATGGCATTTGGTA-GTACAAGAAACATC
66 ACGCCTAGGACATAGC-GTTGGCACG-ACAAGAAACATC
* *
1249429 CCATGTAAGACCATGTCTAGGACATGGCTTTGGCAT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1249465 GTTATTATCA
Statistics
Matches: 118, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
99 1 0.01
100 74 0.63
101 5 0.04
103 3 0.03
105 1 0.01
106 34 0.29
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (102 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCATGTAAGACC
ACGCCTAGGACATAGCGTTGGCACGACAAGAAACATC
Found at i:1250182 original size:16 final size:16
Alignment explanation
Indices: 1250161--1250194 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1250151 GATAGTATAA
* *
1250161 AATGAATTATAGAGTT
1 AATGAAATATAGAATT
1250177 AATGAAATATAGAATT
1 AATGAAATATAGAATT
1250193 AA
1 AA
1250195 ATCTTATCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (16 bp):
AATGAAATATAGAATT
Found at i:1255152 original size:19 final size:20
Alignment explanation
Indices: 1255128--1255172 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1255118 AAATTGTAAA
* *
1255128 AAATTTGAAATTAAGG-GGT
1 AAATTTGAAAATAAGGAGCT
1255147 AAATTTGAAAATAAGGAGCT
1 AAATTTGAAAATAAGGAGCT
1255167 AAATTT
1 AAATTT
1255173 AGCTGAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (20 bp):
AAATTTGAAAATAAGGAGCT
Found at i:1259156 original size:12 final size:12
Alignment explanation
Indices: 1259139--1259164 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1259129 TGAGTTACAT
1259139 GGCCTAACACAC
1 GGCCTAACACAC
1259151 GGCCTAACACAC
1 GGCCTAACACAC
1259163 GG
1 GG
1259165 GTTTTGGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (12 bp):
GGCCTAACACAC
Found at i:1259532 original size:20 final size:20
Alignment explanation
Indices: 1259507--1259626 Score: 136
Period size: 20 Copynumber: 5.7 Consensus size: 20
1259497 ATATTGGCAG
1259507 GTTATGATTATAGGTATCGA
1 GTTATGATTATAGGTATCGA
*
1259527 GTTATGATTATAGG-ATTTGAACA
1 GTTATGATTATAGGTA-TCG---A
1259550 GTTATGATTATAGGTATCGA
1 GTTATGATTATAGGTATCGA
*
1259570 GTTATGATTATAGG-ATTTGAACA
1 GTTATGATTATAGGTA-TCG---A
1259593 GTTATGATTATAGGTATCGA
1 GTTATGATTATAGGTATCGA
1259613 GTTATGATTATAGG
1 GTTATGATTATAGG
1259627 ATTTGAACAG
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.02
20 48 0.56
23 34 0.40
24 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTATGATTATAGGTATCGA
Found at i:1259556 original size:23 final size:23
Alignment explanation
Indices: 1259526--1259638 Score: 134
Period size: 23 Copynumber: 5.2 Consensus size: 23
1259516 ATAGGTATCG
1259526 AGTTATGATTATAGGATTTGAAC
1 AGTTATGATTATAGGATTTGAAC
*
1259549 AGTTATGATTATAGG---T-ATC
1 AGTTATGATTATAGGATTTGAAC
1259568 GAGTTATGATTATAGGATTTGAAC
1 -AGTTATGATTATAGGATTTGAAC
*
1259592 AGTTATGATTATAGG---T-ATC
1 AGTTATGATTATAGGATTTGAAC
1259611 GAGTTATGATTATAGGATTTGAAC
1 -AGTTATGATTATAGGATTTGAAC
1259635 AGTT
1 AGTT
1259639 GACCTAAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.05
20 32 0.42
23 36 0.47
24 4 0.05
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (23 bp):
AGTTATGATTATAGGATTTGAAC
Found at i:1259568 original size:43 final size:43
Alignment explanation
Indices: 1259507--1259638 Score: 264
Period size: 43 Copynumber: 3.1 Consensus size: 43
1259497 ATATTGGCAG
1259507 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1259550 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1259593 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1 GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
1259636 GTT
1 GTT
1259639 GACCTAAATT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (43 bp):
GTTATGATTATAGGTATCGAGTTATGATTATAGGATTTGAACA
Found at i:1265825 original size:74 final size:75
Alignment explanation
Indices: 1265585--1265870 Score: 412
Period size: 74 Copynumber: 3.8 Consensus size: 75
1265575 TATCCGTTAT
* * *
1265585 CGGTGGATTCAGCACTTAGCAACCACCAGTGATTCTGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* * *
1265650 CTTCAAAAATA
66 ATT-TAAGATA
** * * * *
1265661 TAGTGGAATCAGCACTAAGCAAACACCAATGAATCGGGGAATCAGCACTTAGCAACACCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1265726 ATTTAAGATA
66 ATTTAAGATA
*
1265736 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAG-ACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1265800 ATTTAAGATA
66 ATTTAAGATA
* * *
1265810 CGGTGGAATCGGCACTTAGCAACCACCAATGATCCAGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
1265871 GGGGGAATCA
Statistics
Matches: 186, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
74 69 0.37
75 59 0.32
76 58 0.31
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATA
Found at i:1268100 original size:21 final size:22
Alignment explanation
Indices: 1268068--1268110 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1268058 AGTATATACC
*
1268068 CATATTAGTTCATTTC-GAACT
1 CATATTAGTTCATATCAGAACT
1268089 CATATT-GTTTCATATCAGAACT
1 CATATTAG-TTCATATCAGAACT
1268111 TTACCCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (22 bp):
CATATTAGTTCATATCAGAACT
Found at i:1270426 original size:23 final size:21
Alignment explanation
Indices: 1270384--1270430 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
1270374 AGTTTCGATT
1270384 AAAAAAATTTTCAAATATATA
1 AAAAAAATTTTCAAATATATA
1270405 AAAAAAAGTTTGTGCAAA-ATATA
1 AAAAAAA-TTT-T-CAAATATATA
1270428 AAA
1 AAA
1270431 TTTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 9 0.39
24 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (21 bp):
AAAAAAATTTTCAAATATATA
Found at i:1273707 original size:27 final size:27
Alignment explanation
Indices: 1273687--1274048 Score: 465
Period size: 27 Copynumber: 13.4 Consensus size: 27
1273677 GGGTATAACA
*
1273687 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
1273714 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
1273741 GCCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
1273768 GTCATTTTACCCTAAT-AGGGTATTTCG
1 GTCATTTTACCCT-ATGGGGGTATTTCG
* *
1273795 ATCATTTTACCCTATGGGGGTATATCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
1273822 GTCATTTTACCCTATGGGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
1273849 ATCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
1273876 GTCATTCTACCCTATGGGAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
1273903 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** *
1273930 GTCATTTTATCCTATAAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
1273957 GTCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
1273984 ATCATTTTACTCTATGGAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
1274011 GTCATCTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
1274038 GTTATTTTACC
1 GTCATTTTACC
1274049 TATTTTAGGG
Statistics
Matches: 289, Mismatches: 44, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 2 0.01
27 285 0.99
28 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:1278120 original size:21 final size:22
Alignment explanation
Indices: 1278088--1278130 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1278078 AGTATATACC
*
1278088 CATATTAGTTCATTTC-GAACT
1 CATATTAGTTCATATCAGAACT
1278109 CATATT-GTTTCATATCAGAACT
1 CATATTAG-TTCATATCAGAACT
1278131 TTACCCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (22 bp):
CATATTAGTTCATATCAGAACT
Found at i:1285960 original size:13 final size:13
Alignment explanation
Indices: 1285942--1286012 Score: 83
Period size: 13 Copynumber: 5.5 Consensus size: 13
1285932 AATGCTTTTA
1285942 AAAAGTGTTGTGG
1 AAAAGTGTTGTGG
*
1285955 AAAAGTGCTT-TTG
1 AAAAGTG-TTGTGG
1285968 AAAAGTGTTGTGG
1 AAAAGTGTTGTGG
*
1285981 AAAAGTGCTT-TTG
1 AAAAGTG-TTGTGG
*
1285994 AAAAGTGCTGTGG
1 AAAAGTGTTGTGG
1286007 AAAAGT
1 AAAAGT
1286013 TTAGTTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
12 3 0.06
13 42 0.86
14 4 0.08
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (13 bp):
AAAAGTGTTGTGG
Found at i:1285971 original size:26 final size:26
Alignment explanation
Indices: 1285934--1286012 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
1285924 AGTATGGCAA
*
1285934 TGCTTTTAAAAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGTTGTGGAAAAG
1285960 TGCTTTTGAAAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGTTGTGGAAAAG
*
1285986 TGCTTTTGAAAAGTGCTGTGGAAAAG
1 TGCTTTTGAAAAGTGTTGTGGAAAAG
1286012 T
1 T
1286013 TTAGTTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGTTGTGGAAAAG
Found at i:1287545 original size:20 final size:19
Alignment explanation
Indices: 1287482--1287603 Score: 59
Period size: 20 Copynumber: 5.9 Consensus size: 19
1287472 TAAAATTTGT
*
1287482 AATTTTTTAACTTTCTTTATA
1 AATTTTTTAA-TTT-TTTAAA
* **
1287503 TATTTTTTAGATTTTTTTGA
1 AATTTTTTA-ATTTTTTAAA
1287523 AATTTTTATAATTTTTTAAA
1 AATTTTT-TAATTTTTTAAA
1287543 AATATATTTTGGAATTTTTATAAA
1 AAT-T-TTTT--AATTTTT-TAAA
* **
1287567 CA--TTTTAAAATTTTAAA
1 AATTTTTTAATTTTTTAAA
1287584 AATTATTTTGAATTATTTTA
1 AATT-TTTT-AATT-TTTTA
1287604 TATTTTTTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
17 5 0.06
18 5 0.06
20 29 0.38
21 17 0.22
22 9 0.12
23 7 0.09
24 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTTTTAATTTTTTAAA
Found at i:1287702 original size:9 final size:9
Alignment explanation
Indices: 1287680--1287721 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1287670 AAGCTAATAT
*
1287680 GTTATTCGA
1 GTTATTTGA
*
1287689 ATTATTTGA
1 GTTATTTGA
1287698 GTTATTTGA
1 GTTATTTGA
*
1287707 ATTATTTGA
1 GTTATTTGA
1287716 GTTATT
1 GTTATT
1287722 CATTTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (9 bp):
GTTATTTGA
Found at i:1287703 original size:18 final size:18
Alignment explanation
Indices: 1287680--1287722 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1287670 AAGCTAATAT
1287680 GTTATTCGAATTATTTGA
1 GTTATTCGAATTATTTGA
*
1287698 GTTATTTGAATTATTTGA
1 GTTATTCGAATTATTTGA
1287716 GTTATTC
1 GTTATTC
1287723 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (18 bp):
GTTATTCGAATTATTTGA
Found at i:1287861 original size:189 final size:190
Alignment explanation
Indices: 1287533--1287911 Score: 751
Period size: 189 Copynumber: 2.0 Consensus size: 190
1287523 AATTTTTATA
1287533 ATTTTTTAAAAATATATTTTGGAATTTTTATAAACATTTTAAAATTTTAAAAATTATTTTGAATT
1 ATTTTTTAAAAATATATTTTGGAATTTTTATAAACATTTTAAAATTTTAAAAATTATTTTGAATT
1287598 ATTTTATATTTTTTGTTGAGGCAAAAACCAATTTGTTTATTTTCAAACTTAACAATGACCAAAAG
66 ATTTTATATTTTTTGTTGAGGCAAAAACCAATTTGTTTATTTTCAAACTTAACAATGACCAAAAG
1287663 AGTATTTAAGCTAATATGTTATTCGAATTATTTGAGTTATTTGAATTATTTGAGTTATTC
131 AGTATTTAAGCTAATATGTTATTCGAATTATTTGAGTTATTTGAATTATTTGAGTTATTC
1287723 ATTTTTT-AAAATATATTTTGGAATTTTTATAAACATTTTAAAATTTTAAAAATTATTTTGAATT
1 ATTTTTTAAAAATATATTTTGGAATTTTTATAAACATTTTAAAATTTTAAAAATTATTTTGAATT
1287787 ATTTTATATTTTTTGTTGAGGCAAAAACCAATTTGTTTATTTTCAAACTTAACAATGACCAAAAG
66 ATTTTATATTTTTTGTTGAGGCAAAAACCAATTTGTTTATTTTCAAACTTAACAATGACCAAAAG
1287852 AGTATTTAAGCTAATATGTTATTCGAATTATTTGAGTTATTTGAATTATTTGAGTTATTC
131 AGTATTTAAGCTAATATGTTATTCGAATTATTTGAGTTATTTGAATTATTTGAGTTATTC
1287912 GAATCATAAA
Statistics
Matches: 189, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 182 0.96
190 7 0.04
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.47
Consensus pattern (190 bp):
ATTTTTTAAAAATATATTTTGGAATTTTTATAAACATTTTAAAATTTTAAAAATTATTTTGAATT
ATTTTATATTTTTTGTTGAGGCAAAAACCAATTTGTTTATTTTCAAACTTAACAATGACCAAAAG
AGTATTTAAGCTAATATGTTATTCGAATTATTTGAGTTATTTGAATTATTTGAGTTATTC
Found at i:1287891 original size:9 final size:9
Alignment explanation
Indices: 1287869--1287910 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1287859 AAGCTAATAT
*
1287869 GTTATTCGA
1 GTTATTTGA
*
1287878 ATTATTTGA
1 GTTATTTGA
1287887 GTTATTTGA
1 GTTATTTGA
*
1287896 ATTATTTGA
1 GTTATTTGA
1287905 GTTATT
1 GTTATT
1287911 CGAATCATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (9 bp):
GTTATTTGA
Found at i:1287892 original size:18 final size:18
Alignment explanation
Indices: 1287869--1287915 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1287859 AAGCTAATAT
1287869 GTTATTCGAATTATTTGA
1 GTTATTCGAATTATTTGA
*
1287887 GTTATTTGAATTATTTGA
1 GTTATTCGAATTATTTGA
1287905 GTTATTCGAAT
1 GTTATTCGAAT
1287916 CATAAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (18 bp):
GTTATTCGAATTATTTGA
Found at i:1288443 original size:12 final size:10
Alignment explanation
Indices: 1288414--1288506 Score: 69
Period size: 11 Copynumber: 8.5 Consensus size: 10
1288404 AACTAAATCC
1288414 TTTCTCTCAA
1 TTTCTCTCAA
*
1288424 TTTGTCTCTAA
1 TTTCTCTC-AA
1288435 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
1288447 TTCCTCTCAA
1 TTTCTCTCAA
*
1288457 TTTTCTTTCAAA
1 -TTTCTCTC-AA
*
1288469 TTCCTCTCAA
1 TTTCTCTCAA
1288479 TTTCCTCTCAAA
1 TTT-CTCTC-AA
*
1288491 TTCCTCTCAAA
1 TTTCTCTC-AA
1288502 TTTCT
1 TTTCT
1288507 ATTTAAAAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
10 13 0.20
11 38 0.58
12 15 0.23
ACGTcount: A:0.23, C:0.29, G:0.01, T:0.47
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:1288455 original size:11 final size:11
Alignment explanation
Indices: 1288439--1288503 Score: 94
Period size: 11 Copynumber: 5.9 Consensus size: 11
1288429 CTCTAATATT
1288439 CTCTCAAATTC
1 CTCTCAAATTC
* *
1288450 CTCTCAATTTT
1 CTCTCAAATTC
*
1288461 CTTTCAAATTC
1 CTCTCAAATTC
*
1288472 CTCTCAATTTC
1 CTCTCAAATTC
1288483 CTCTCAAATTC
1 CTCTCAAATTC
1288494 CTCTCAAATT
1 CTCTCAAATT
1288504 TCTATTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:1288459 original size:33 final size:33
Alignment explanation
Indices: 1288417--1288503 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
1288407 TAAATCCTTT
1288417 CTCTCAATTTGTCTCT-AATATT-CTCTCAAATTC
1 CTCTCAATTT-TCTCTCAA-ATTCCTCTCAAATTC
* *
1288450 CTCTCAATTTTCTTTCAAATTCCTCTCAATTTC
1 CTCTCAATTTTCTCTCAAATTCCTCTCAAATTC
* *
1288483 CTCTCAAATTCCTCTCAAATT
1 CTCTCAATTTTCTCTCAAATT
1288504 TCTATTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.15
33 40 0.85
ACGTcount: A:0.24, C:0.30, G:0.01, T:0.45
Consensus pattern (33 bp):
CTCTCAATTTTCTCTCAAATTCCTCTCAAATTC
Found at i:1288462 original size:22 final size:22
Alignment explanation
Indices: 1288414--1288506 Score: 116
Period size: 22 Copynumber: 4.2 Consensus size: 22
1288404 AACTAAATCC
**
1288414 TTTCTCTC-AATTTGTCTCTAAT
1 TTTCTCTCAAATTCCTCTC-AAT
*
1288436 ATTCTCTCAAATTCCTCTCAAT
1 TTTCTCTCAAATTCCTCTCAAT
*
1288458 TTTCTTTCAAATTCCTCTCAAT
1 TTTCTCTCAAATTCCTCTCAAT
* *
1288480 TTCCTCTCAAATTCCTCTCAAA
1 TTTCTCTCAAATTCCTCTCAAT
1288502 TTTCT
1 TTTCT
1288507 ATTTAAAAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 53 0.87
23 8 0.13
ACGTcount: A:0.23, C:0.29, G:0.01, T:0.47
Consensus pattern (22 bp):
TTTCTCTCAAATTCCTCTCAAT
Found at i:1288570 original size:14 final size:13
Alignment explanation
Indices: 1288547--1288579 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1288537 TTTAAAAAAG
1288547 TTTT-AAATTTTAT
1 TTTTAAAATTTT-T
1288560 TTTTAAAATTTTT
1 TTTTAAAATTTTT
1288573 TTTTAAA
1 TTTTAAA
1288580 TCGTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAAATTTTT
Found at i:1294218 original size:126 final size:125
Alignment explanation
Indices: 1293988--1294278 Score: 422
Period size: 126 Copynumber: 2.3 Consensus size: 125
1293978 CCAAACATGC
* *
1293988 GCTACTGTAGCAAAAGCGCGTCCACGTGAGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATTCT
1 GCTACTGTAGCAAAAGCGCGTCCACTTG-GAGCTTCTTTCAATACTTCTGCTGACAAAGCATTCT
* * * *
1294053 GTTTAAAGCGTTTTTTACACTATTTGCTCAGAAATGTCTACTCGAAATTATTTTTTAAGGA
65 GCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTAAGGA
* *
1294114 GTTACTGTAGCAAAAACGCGTCCACATTGGAGCTTCTTTCAATACTTCTGCTGACAAAGCA-TCT
1 GCTACTGTAGCAAAAGCGCGTCCAC-TTGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATTC-
*
1294178 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
64 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTAAGGA
* * * *
1294240 GCTACTGTAGTAAAAGTGAGTCCACGTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCAC-TTGGAGCTTCTTT
1294279 AAATTAACAA
Statistics
Matches: 147, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
125 2 0.01
126 143 0.97
127 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (125 bp):
GCTACTGTAGCAAAAGCGCGTCCACTTGGAGCTTCTTTCAATACTTCTGCTGACAAAGCATTCTG
CTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTAAGGA
Found at i:1294459 original size:96 final size:97
Alignment explanation
Indices: 1294318--1294581 Score: 271
Period size: 96 Copynumber: 2.8 Consensus size: 97
1294308 CCAAACCTCA
* *
1294318 AACCCTAATTTATTTAAGTTTTTACTTAAAAACTCTAAACACTAAACCCTAATCTAATTTTATAA
1 AACCCTAATTTATTTAAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTT-TAA
*
1294383 A-AATTTATAATTAATTTACTCAAGTAACCCTG
65 ATAATTTATAATTAAATTACTCAAGTAACCCTG
* * * * * *
1294415 AACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTTAACTCTAAACCATTATCTGATTTTTAAA
1 AACCCTAATTTATTTAAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTAAA
*
1294479 TAATTTTTAATTAAATTACTCAAGTAACCCT-
66 TAATTTATAATTAAATTACTCAAGTAACCCTG
* * * ** * * *
1294510 AA---T--TTTA-TTGATTTTTTTCTTAAAAAACAATAAACACGAAACC-TAATCCAATTTTGAA
1 AACCCTAATTTATTTAAGTTTTTACTT-AAAAACCCTAAACACTAAACCATAATCTAATTTTTAA
1294568 A-AATTTATAATTAA
65 ATAATTTATAATTAA
1294582 TTTAATTGGC
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
89 16 0.11
90 24 0.17
91 16 0.11
92 1 0.01
95 6 0.04
96 64 0.45
97 16 0.11
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (97 bp):
AACCCTAATTTATTTAAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTAAA
TAATTTATAATTAAATTACTCAAGTAACCCTG
Found at i:1294668 original size:6 final size:6
Alignment explanation
Indices: 1294659--1294689 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1294649 AAAACACCAA
1294659 AACCCT AACCCT -ACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AA
1294690 TACCCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:1294676 original size:11 final size:12
Alignment explanation
Indices: 1294659--1294689 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1294649 AAAACACCAA
1294659 AACCCTAACCCT
1 AACCCTAACCCT
1294671 -ACCCTAACCCT
1 AACCCTAACCCT
1294682 AACCCTAA
1 AACCCTAA
1294690 TACCCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.16
Consensus pattern (12 bp):
AACCCTAACCCT
Found at i:1300686 original size:121 final size:125
Alignment explanation
Indices: 1300355--1300677 Score: 420
Period size: 121 Copynumber: 2.6 Consensus size: 125
1300345 ATAAAATAGC
* * * * * * *
1300355 ATAAAATCACTTCTAGCATGATGGTATTTGAGAAGAATTTACGAAATCGCGCCTTCATGGACGCG
1 ATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGAACGCG
* * *
1300420 TTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGT
66 TTTTTGCTACAGTAGGTCATGTAAGAAATAA-TATTTTTTTGACGTTTCTGAGCAAATAAT
* * * * * * *
1300481 ATAAAATCGCTTCTAGGAGGATGCTATTTGAGAAGAA--TGTGAAATCGCGGCCTAGTCAGCGCG
1 ATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGAACGCG
1300544 TTTTTGCTACAGTAGGTCATGTAAGAAAT-A-ATTTTTTTGACGTTTCTGAGCAAATAAT
66 TTTTTGCTACAGTAGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAAT
* *
1300602 ATAAAATCGTTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCGCACCCTCGTGAACGCG
1 ATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGAACGCG
* *
1300667 CTTTTACTACA
66 TTTTTGCTACA
1300678 ATAGCATGTT
Statistics
Matches: 168, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
121 61 0.36
123 30 0.18
124 44 0.26
126 33 0.20
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (125 bp):
ATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGAACGCG
TTTTTGCTACAGTAGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAAT
Found at i:1301518 original size:12 final size:12
Alignment explanation
Indices: 1301501--1301526 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1301491 GGCTTATTTT
1301501 CTGAACCGGAGC
1 CTGAACCGGAGC
1301513 CTGAACCGGAGC
1 CTGAACCGGAGC
1301525 CT
1 CT
1301527 ATTCCAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.31, T:0.12
Consensus pattern (12 bp):
CTGAACCGGAGC
Found at i:1304046 original size:23 final size:23
Alignment explanation
Indices: 1304046--1304235 Score: 134
Period size: 29 Copynumber: 7.5 Consensus size: 23
1304036 AGGTTAGGGT
* *
1304046 TTAGGATTTTTAAGTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
1304069 TTAGGGTTTTTAAGTT-AA--GGG
1 TTAGGGTTTTTAA-TTAAATTAGG
*
1304090 TTTAGGATTTTTAATTAAATTAGGTTAGGG
1 -TTAGGGTTTTTAATT-AA--A--TTA-GG
1304120 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT-AA--A--TTA-GG
1304149 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT-AA--A--TTA-GG
1304178 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
*
1304201 CTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
1304224 TTAGGGTTTTTA
1 TTAGGGTTTTTA
1304236 TTACATCAAA
Statistics
Matches: 148, Mismatches: 8, Indels: 22
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.03
22 12 0.08
23 50 0.34
24 4 0.03
25 1 0.01
26 1 0.01
28 2 0.01
29 72 0.49
30 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:1304078 original size:75 final size:74
Alignment explanation
Indices: 1303986--1304150 Score: 276
Period size: 75 Copynumber: 2.2 Consensus size: 74
1303976 TAAAATTATC
* *
1303986 AAATTAGGTTAGAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAATTAAATTAGGTTAGGGTTTAGG
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGATTTTAAATTAAATTAGGTTAGGG-TTAGG
1304051 ATTTTTAAGT
65 ATTTTTAAGT
* *
1304061 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTAGGG
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGATTTTAAATTAAATTAGGTTAGGGTTAGGA
*
1304126 TTTTTAATT
66 TTTTTAAGT
1304135 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
1304151 AGGGTTTTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 29 0.34
75 56 0.66
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (74 bp):
AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGATTTTAAATTAAATTAGGTTAGGGTTAGGA
TTTTTAAGT
Found at i:1304094 original size:22 final size:22
Alignment explanation
Indices: 1304041--1304107 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1304031 AAATTAGGTT
*
1304041 AGGGTTTAGGATTTTTAAGTAA
1 AGGGTTTAGGATTTTTAAGTTA
* *
1304063 ATTAGG-TTAGGGTTTTTAAGTTA
1 A--GGGTTTAGGATTTTTAAGTTA
1304086 AGGGTTTAGGATTTTTAA-TTA
1 AGGGTTTAGGATTTTTAAGTTA
1304107 A
1 A
1304108 ATTAGGTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 6 0.16
22 13 0.35
23 16 0.43
24 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (22 bp):
AGGGTTTAGGATTTTTAAGTTA
Found at i:1304156 original size:35 final size:29
Alignment explanation
Indices: 1304086--1304231 Score: 223
Period size: 29 Copynumber: 5.2 Consensus size: 29
1304076 TTTTAAGTTA
*
1304086 AGGGTTTAGGATTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
1304116 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1304145 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1304174 AGGGTTAGGGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
1304198 A-GGCTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1304226 AGGGTT
1 AGGGTT
1304232 TTTATTACAT
Statistics
Matches: 107, Mismatches: 3, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
23 16 0.15
24 5 0.05
26 2 0.02
28 5 0.05
29 75 0.70
30 4 0.04
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:1304159 original size:58 final size:53
Alignment explanation
Indices: 1304067--1304231 Score: 214
Period size: 58 Copynumber: 3.1 Consensus size: 53
1304057 AAGTAAATTA
*
1304067 GGTTAGGGTTTTTAAGTT--A--AGGGTTTAGGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAA-TTAAATTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAG
1304118 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATT-AA--A--TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
*
1304176 GGTTAGGGTTTTTAATTAAATTA-GGCTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
1304228 GGTT
1 GGTT
1304232 TTTATTACAT
Statistics
Matches: 103, Mismatches: 2, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
50 2 0.02
51 15 0.15
52 32 0.31
53 3 0.03
55 2 0.02
57 2 0.02
58 43 0.42
59 4 0.04
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (53 bp):
GGTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:1304179 original size:52 final size:49
Alignment explanation
Indices: 1304118--1304238 Score: 145
Period size: 52 Copynumber: 2.3 Consensus size: 49
1304108 ATTAGGTTAG
** *
1304118 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTT-ATT-AATTAAATTA-GGCTAGGGTTTTTAATTAAATTA
1304170 GGTTAGGGTTAGGGTTT-TTAATTAAATTAGGCTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTT----TTTATTAATTAAATTAGGCTAGGGTTTTTAATTAAATTA
1304222 GGTTAGGGTTTTTATTA
1 GGTTAGGGTTTTTATTA
1304239 CATCAAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
48 3 0.05
49 3 0.05
52 42 0.69
53 8 0.13
54 2 0.03
56 3 0.05
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (49 bp):
GGTTAGGGTTTTTATTAATTAAATTAGGCTAGGGTTTTTAATTAAATTA
Found at i:1304223 original size:18 final size:19
Alignment explanation
Indices: 1304178--1304220 Score: 50
Period size: 23 Copynumber: 2.1 Consensus size: 19
1304168 TAGGTTAGGG
1304178 TTAGGGTTTTTAATTAAAT
1 TTAGGGTTTTTAATTAAAT
1304197 TAGGCTAGGGTTTTTAATTAAAT
1 T----TAGGGTTTTTAATTAAAT
1304220 T
1 T
1304221 AGGTTAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.05
23 19 0.95
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (19 bp):
TTAGGGTTTTTAATTAAAT
Found at i:1306600 original size:51 final size:51
Alignment explanation
Indices: 1306544--1306664 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
1306534 TTTAAAAAAA
* * * *
1306544 GAAATTGAGAGCAAATTGAAATTAAATATGGGTTTGA-GAGATTTTTGGAAT
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGGAAG
* *
1306595 GAAATTGAGAGGAGATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
1306646 GAAATTGAGAGAAAATTGA
1 GAAATTGAGAGAAAATTGA
1306665 GAGGAAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.31
Consensus pattern (51 bp):
GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
Found at i:1306663 original size:11 final size:11
Alignment explanation
Indices: 1306644--1306689 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
1306634 GAATTTTGGA
1306644 AGGAAATTGAG
1 AGGAAATTGAG
*
1306655 AGAAAATTGAG
1 AGGAAATTGAG
1306666 AGGAAATTGAG
1 AGGAAATTGAG
1306677 AGGAAATATGAG
1 AGGAAAT-TGAG
1306689 A
1 A
1306690 TAGGATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:1307232 original size:51 final size:53
Alignment explanation
Indices: 1307135--1307257 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 53
1307125 TTAAAAAAAG
*
1307135 AAATTGAGAGGAAATTGAAATATTCAAAATATGGATTTGAGAGAATTTTTGAAGA
1 AAATTGAGAGGAAATTG-AATATT-AAAATATGGATTTGAGAGAATTTTGGAAGA
*
1307190 AAATTGAGAGGAAATTGAA-ATT-AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATTGAGAGGAAATTGAATATTAAAATATGGATTTGAGAGAATTTTGGAAGA
1307241 AAATTGAGAGG-AATTGA
1 AAATTGAGAGGAAATTGA
1307258 GAGGAAATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
50 6 0.09
51 38 0.58
53 3 0.05
54 2 0.03
55 17 0.26
ACGTcount: A:0.45, C:0.01, G:0.25, T:0.29
Consensus pattern (53 bp):
AAATTGAGAGGAAATTGAATATTAAAATATGGATTTGAGAGAATTTTGGAAGA
Found at i:1307272 original size:12 final size:11
Alignment explanation
Indices: 1307238--1307272 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
1307228 GAATTTTGGA
1307238 AGGAAATTGAG
1 AGGAAATTGAG
1307249 AGG-AATTGAG
1 AGGAAATTGAG
1307259 AGGAAATATGAG
1 AGGAAAT-TGAG
1307271 AG
1 AG
1307273 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:1309229 original size:23 final size:23
Alignment explanation
Indices: 1309187--1309248 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1309177 AATGTTCACA
**
1309187 AACATGTTCATGTAAC-TTAATTG
1 AACATGTTCATG-AACATTAAACG
*
1309210 AACATGTTCACGAACATTAAACG
1 AACATGTTCATGAACATTAAACG
*
1309233 AATATGTTCATGAACA
1 AACATGTTCATGAACA
1309249 ATGTTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAACATTAAACG
Found at i:1309274 original size:15 final size:15
Alignment explanation
Indices: 1309254--1309287 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1309244 GAACAATGTT
*
1309254 AATAAATGATAAACA
1 AATAAATAATAAACA
*
1309269 AATAAATAATAAATA
1 AATAAATAATAAACA
1309284 AATA
1 AATA
1309288 CAAACACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAAATAATAAACA
Found at i:1310513 original size:16 final size:16
Alignment explanation
Indices: 1310494--1310536 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1310484 TAAATTTATC
1310494 ATTATATTTTTAAAAT
1 ATTATATTTTTAAAAT
* *
1310510 ATTATATATTTTTATAT
1 ATTATAT-TTTTAAAAT
1310527 ATTA-ATTTTT
1 ATTATATTTTT
1310537 TTATAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATATTTTTAAAAT
Found at i:1310514 original size:22 final size:22
Alignment explanation
Indices: 1310473--1310514 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1310463 CTTGACATTT
*
1310473 TTATATTTATTTAAATTTATCA
1 TTATATTTATTAAAATTTATCA
1310495 TTATATTT-TTAAAATATTAT
1 TTATATTTATTAAAAT-TTAT
1310515 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATTTATTAAAATTTATCA
Found at i:1317361 original size:9 final size:9
Alignment explanation
Indices: 1317347--1317374 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1317337 TGAGTTTTTG
1317347 AATTCGAAT
1 AATTCGAAT
1317356 AATTCGAAT
1 AATTCGAAT
1317365 AATTCGAAT
1 AATTCGAAT
1317374 A
1 A
1317375 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1319046 original size:21 final size:20
Alignment explanation
Indices: 1318999--1319038 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1318989 CCAAACACGG
*
1318999 TCGTGTGGCTATCCACACAC
1 TCGTGTGACTATCCACACAC
*
1319019 TTGTGTGACTATTCCACACA
1 TCGTGTGACTA-TCCACACA
1319039 TCCGTGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (20 bp):
TCGTGTGACTATCCACACAC
Found at i:1335590 original size:179 final size:179
Alignment explanation
Indices: 1335290--1335644 Score: 638
Period size: 179 Copynumber: 2.0 Consensus size: 179
1335280 TCGGTCTAGT
*
1335290 AATTTTATTAAATTGATAGTTAATTAAAGTATAAGGATTAAATCATAAAAATGGTAAAAGTTTAA
1 AATTTTATTAAATTGATAGTTAATTAAAGTATAAGGATTAAATCATAAAAATGATAAAAGTTTAA
* *
1335355 TCGATATAGATTTTTAATTAGCTAATAGAACAAAAGAGCAATTGTTAGTAGTGGATAGTGGAATT
66 TCGATATAGATTTTTAATTAGCTAATAGAACAAAAGAGCAATTATTAATAGTGGATAGTGGAATT
*
1335420 TCATGATGGAATCCACGTTGTTTGATTAGTAGATAAATAAGATTAAAGC
131 TCATGATGGAATCCAAGTTGTTTGATTAGTAGATAAATAAGATTAAAGC
*
1335469 AATTTTATTAAATTGATAGTTAATTAAAGTATAAGGATTAAATCGTAAAAATGATAAAAGTTTAA
1 AATTTTATTAAATTGATAGTTAATTAAAGTATAAGGATTAAATCATAAAAATGATAAAAGTTTAA
*
1335534 TCGCTATAGATTTTTAATTAGCTAATAGAACAAAAGAGCAATTATTAATAGTGGATAGTGGAATT
66 TCGATATAGATTTTTAATTAGCTAATAGAACAAAAGAGCAATTATTAATAGTGGATAGTGGAATT
* *
1335599 TCATGATGGAATCCAATTTGTTTGATTTGTAGATAAATAAGATTAA
131 TCATGATGGAATCCAAGTTGTTTGATTAGTAGATAAATAAGATTAA
1335645 GTAAATTGTG
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 168 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (179 bp):
AATTTTATTAAATTGATAGTTAATTAAAGTATAAGGATTAAATCATAAAAATGATAAAAGTTTAA
TCGATATAGATTTTTAATTAGCTAATAGAACAAAAGAGCAATTATTAATAGTGGATAGTGGAATT
TCATGATGGAATCCAAGTTGTTTGATTAGTAGATAAATAAGATTAAAGC
Found at i:1337713 original size:25 final size:25
Alignment explanation
Indices: 1337678--1337805 Score: 104
Period size: 25 Copynumber: 5.2 Consensus size: 25
1337668 ATACAGGTAT
*
1337678 GCTCATGCGAGCATGTAATCGGGAA
1 GCTCATTCGAGCATGTAATCGGGAA
* * *
1337703 GCTCTTTCGAGCCATATAAT-GAGAA
1 GCTCATTCGAG-CATGTAATCGGGAA
1337728 GCTCATGT-GAGCCATGTAAT-GGGAA
1 GCTCAT-TCGAG-CATGTAATCGGGAA
** *
1337753 GCTCATAAGAGC-CGTAATCGGGAA
1 GCTCATTCGAGCATGTAATCGGGAA
* *
1337777 GCTCATGCGAGC-TAGTTATCGGGAA
1 GCTCATTCGAGCAT-GTAATCGGGAA
1337802 GCTC
1 GCTC
1337806 GTGAGAGCCA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.06
24 16 0.19
25 56 0.66
26 8 0.09
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (25 bp):
GCTCATTCGAGCATGTAATCGGGAA
Found at i:1337824 original size:25 final size:25
Alignment explanation
Indices: 1337697--1337880 Score: 111
Period size: 25 Copynumber: 7.4 Consensus size: 25
1337687 AGCATGTAAT
* ** *
1337697 CGGGAAGCTCTTTCGAGCCATATAA
1 CGGGAAGCTCATGAGAGCCAAATAA
* * * **
1337722 TGAGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATGAGAGCCAAATAA
* * *
1337747 TGGGAAGCTCATAAGAGCC--GTAA
1 CGGGAAGCTCATGAGAGCCAAATAA
* * ** *
1337770 TCGGGAAGCTCATGCGAGCTAGTTAT
1 -CGGGAAGCTCATGAGAGCCAAATAA
*
1337796 CGGGAAGCTCGTGAGAGCCAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAA
* * *
1337821 CGGGAAGCTCAAGAGAGCCATATAT
1 CGGGAAGCTCATGAGAGCCAAATAA
* * *
1337846 CGGGATGCTCATAAGAGCTAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAA
* *
1337871 CAGGACGCTC
1 CGGGAAGCTC
1337881 TTGCGAGATG
Statistics
Matches: 123, Mismatches: 33, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
23 4 0.03
24 15 0.12
25 102 0.83
26 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAA
Found at i:1337856 original size:99 final size:99
Alignment explanation
Indices: 1337678--1337863 Score: 241
Period size: 99 Copynumber: 1.9 Consensus size: 99
1337668 ATACAGGTAT
* ** * * * *
1337678 GCTCATGCGAGCATGTAATCGGGAAGCTCTTTCGAGCCATATAATGAGAAGCTCATGTGAGCCAT
1 GCTCATGCGAGCATGTAATCGGGAAGCTCGTGAGAGCCAAATAACGAGAAGCTCAAGAGAGCCAT
*
1337743 GTAATGGGAAGCTCATAAGAGCCGTAATCGGGAA
66 ATAATGGGAAGCTCATAAGAGCCGTAATCGGGAA
* *
1337777 GCTCATGCGAGC-TAGTTATCGGGAAGCTCGTGAGAGCCAAATAACGGGAAGCTCAAGAGAGCCA
1 GCTCATGCGAGCAT-GTAATCGGGAAGCTCGTGAGAGCCAAATAACGAGAAGCTCAAGAGAGCCA
*
1337841 TAT-ATCGGGATGCTCATAAGAGC
65 TATAAT-GGGAAGCTCATAAGAGC
1337864 TAAATAACAG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
98 3 0.04
99 71 0.96
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (99 bp):
GCTCATGCGAGCATGTAATCGGGAAGCTCGTGAGAGCCAAATAACGAGAAGCTCAAGAGAGCCAT
ATAATGGGAAGCTCATAAGAGCCGTAATCGGGAA
Found at i:1337869 original size:50 final size:49
Alignment explanation
Indices: 1337725--1337880 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 49
1337715 CATATAATGA
*
1337725 GAAGCTCATGTGAGCCATGTAAT-GGGAAGCTCATAAGAGCCGT-AAT--CGG
1 GAAGCTCATGAGAGCCAT-T-ATCGGGAAGCTCATAAGAG-C-TAAATAACGG
* * * * *
1337774 GAAGCTCATGCGAGCTAGTTATCGGGAAGCTCGTGAGAGCCAAATAACGG
1 GAAGCTCATGAGAGCCA-TTATCGGGAAGCTCATAAGAGCTAAATAACGG
* * *
1337824 GAAGCTCAAGAGAGCCATATATCGGGATGCTCATAAGAGCTAAATAACAG
1 GAAGCTCATGAGAGCCAT-TATCGGGAAGCTCATAAGAGCTAAATAACGG
*
1337874 GACGCTC
1 GAAGCTC
1337881 TTGCGAGATG
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
48 6 0.07
49 31 0.36
50 50 0.57
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.19
Consensus pattern (49 bp):
GAAGCTCATGAGAGCCATTATCGGGAAGCTCATAAGAGCTAAATAACGG
Found at i:1342791 original size:50 final size:50
Alignment explanation
Indices: 1342733--1342968 Score: 237
Period size: 50 Copynumber: 4.7 Consensus size: 50
1342723 CGTTAAGATT
* * *
1342733 ATGAGAGGTCCTATGCAAGACCATGTCTGAGACATGGAGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGCACCGAG
* *
1342783 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGAAGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGCACCGAG
* ** * *
1342833 ATGAGGGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-AGTTGGCACCGAG
** * * *
1342883 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCA-TTGGCA--GTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG-AGTTGGCACCG-AG
* * ** *
1342932 AAGAAACATCCCATGTAAGACCATGTCTAGGACATGG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
1342969 CTTTGGCATG
Statistics
Matches: 157, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
48 1 0.01
49 32 0.20
50 123 0.78
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGAGTTGGCACCGAG
Found at i:1353776 original size:45 final size:45
Alignment explanation
Indices: 1353712--1353802 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1353702 TAAAAGTGTG
1353712 TAAAGCTATTTGATTGTTTTCATTGATATAAGTGGACCTTTTCCA
1 TAAAGCTATTTGATTGTTTTCATTGATATAAGTGGACCTTTTCCA
1353757 TAAAGCTATTTGATTGTTTTCATTGATATAAGTGGACCTTTTCCA
1 TAAAGCTATTTGATTGTTTTCATTGATATAAGTGGACCTTTTCCA
1353802 T
1 T
1353803 CGAGAAGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (45 bp):
TAAAGCTATTTGATTGTTTTCATTGATATAAGTGGACCTTTTCCA
Found at i:1357112 original size:23 final size:23
Alignment explanation
Indices: 1357082--1357148 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1357072 GCCTTATCGA
*
1357082 TCAGGCACTTTATGTGTCATATC
1 TCAGGCACTTTATGTGTCGTATC
1357105 TCAGGCACTTTATGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATC
* *
1357126 TCAGGCACCTCATGTGTCGTATC
1 TCAGGCACTTTATGTGTCGTATC
1357149 AGACACTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 19 0.49
23 20 0.51
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATC
Found at i:1357131 original size:21 final size:21
Alignment explanation
Indices: 1357081--1357168 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
1357071 GGCCTTATCG
* *
1357081 ATCAGGCACTTTATGTGTCAT
1 ATCAGGCACTTCATGTGTCGT
*
1357102 ATCTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTCATGTGTCGT
*
1357125 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACTTCATGTGTCGT
* *
1357146 ATCAGACACTTCGTGTGTCGT
1 ATCAGGCACTTCATGTGTCGT
1357167 AT
1 AT
1357169 ACTGATCAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
21 39 0.66
23 20 0.34
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (21 bp):
ATCAGGCACTTCATGTGTCGT
Found at i:1358054 original size:12 final size:11
Alignment explanation
Indices: 1358037--1358065 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1358027 TGTCGAAATT
1358037 AAAAAAAAAAC
1 AAAAAAAAAAC
1358048 AAAAAAAAAAC
1 AAAAAAAAAAC
1358059 AAAAAAA
1 AAAAAAA
1358066 TGAAGCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1370313 original size:18 final size:18
Alignment explanation
Indices: 1370290--1370325 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1370280 TTTAAATTTT
1370290 TTTTAAAAAATT-TAAAAA
1 TTTT-AAAAATTATAAAAA
1370308 TTTTAAAAATTATAAAAA
1 TTTTAAAAATTATAAAAA
1370326 ACTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTAAAAATTATAAAAA
Found at i:1370988 original size:40 final size:39
Alignment explanation
Indices: 1370911--1371023 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
1370901 AGCGGCACAT
** * *
1370911 TTAGCGGCGTTTGGAACAAAAGGGCCACTCAAAATCGAGCA
1 TTAGCGGCGTTT-TTACAAAAGCGCCGCT-AAAATCGAGCA
1370952 TTAGCGGCGTTTTTACAAAAGCGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTTTTACAAAAGCGCCGCTAAA-ATCGAGCA
* * * *
1370992 TCAGCGGCGTATTTCCAAAATCGCCGCTAAAA
1 TTAGCGGCGTTTTTACAAAAGCGCCGCTAAAA
1371024 ATAGGAATCA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.06
40 47 0.75
41 12 0.19
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (39 bp):
TTAGCGGCGTTTTTACAAAAGCGCCGCTAAAATCGAGCA
Found at i:1371165 original size:41 final size:41
Alignment explanation
Indices: 1371091--1371288 Score: 140
Period size: 41 Copynumber: 4.9 Consensus size: 41
1371081 CGTTTTTCGA
* * **
1371091 GCCTTTAGCGGCGTTTTTG-CGGATGCGAAGCTAATG-ATCG
1 GCCTTTAGCGGCGTTTTTGTC-TAAGCGCCGCTAATGAATCG
*
1371131 GACCTTTAGCGGCGTTTTTAGT-TAAGCGCCGCTAATG-CTCAG
1 G-CCTTTAGCGGCGTTTTT-GTCTAAGCGCCGCTAATGAATC-G
* * * * * *
1371173 GCCTTTAGTGGCGTTTATGTCTATGCGCTGCTACTGCA-CG
1 GCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGAATCG
* * *
1371213 GGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAAT-G
1 GCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGAATCG
* * *
1371253 TAG-CTTTAGCGGCGTTTTTGACGAAGTGCCGCTAAT
1 --GCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
1371289 AGTAACAAAA
Statistics
Matches: 126, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
40 36 0.29
41 86 0.68
42 4 0.03
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (41 bp):
GCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGAATCG
Found at i:1371424 original size:40 final size:40
Alignment explanation
Indices: 1371369--1371486 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 40
1371359 GCGTTTGGAA
* * * *
1371369 CAAAAGCGCCACTAAAAATCGAGCATTAGCGGCGTTTTTG
1 CAAAAGCGCCGCTAAAAATAGAGCATCAGCGGCGTTTTTC
* * *
1371409 CAAAAGCGCCGCTAAAGATTGAGCATCAGCGGCGTATTTC
1 CAAAAGCGCCGCTAAAAATAGAGCATCAGCGGCGTTTTTC
* * *
1371449 CAAAATCGTCGCTAAAAATAG-GAATCAGCGGCGTTTTT
1 CAAAAGCGCCGCTAAAAATAGAGCATCAGCGGCGTTTTT
1371487 TATAAAGCGC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 15 0.23
40 51 0.77
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAAAGCGCCGCTAAAAATAGAGCATCAGCGGCGTTTTTC
Found at i:1371606 original size:41 final size:41
Alignment explanation
Indices: 1371534--1371730 Score: 168
Period size: 41 Copynumber: 4.8 Consensus size: 41
1371524 GTTTTTCGAG
* * *
1371534 CCTTTAGCGGCGTTTTTG-CGGATGCGACGCTAATGATCGGA
1 CCTTTAGCGGCGTTTTTGTC-TAAGCGCCGCTAATGATCGGA
* * *
1371575 CCTTTAACGGCGTTTTTAGT-TAAGCGCCGCTAATGCTCGGG
1 CCTTTAGCGGCGTTTTT-GTCTAAGCGCCGCTAATGATCGGA
* * * * * *
1371616 CCTTTAGTGGCATTTCTGTCTATGCGCCGCTACTGCTCGG-
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGATCGGA
* * * *
1371656 GCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAAT-GTA
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATG-ATCGGA
* * *
1371697 GCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
1371731 AGTAACAAAA
Statistics
Matches: 127, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
40 32 0.25
41 94 0.74
42 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGATCGGA
Found at i:1371676 original size:40 final size:41
Alignment explanation
Indices: 1371595--1371690 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 41
1371585 CGTTTTTAGT
1371595 TAAGCGCCGCTAATGCTCGGGCCTTTAGTGGCATTTCTGTC
1 TAAGCGCCGCTAATGCTCGGGCCTTTAGTGGCATTTCTGTC
* * *
1371636 TATGCGCCGCTACTGCTCGGG-CTTTAGTGGCGCTTT-TGTC
1 TAAGCGCCGCTAATGCTCGGGCCTTTAGTGGC-ATTTCTGTC
1371676 TAAGCGCCGCTAATG
1 TAAGCGCCGCTAATG
1371691 AATGTAGCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 27 0.55
41 22 0.45
ACGTcount: A:0.14, C:0.27, G:0.28, T:0.31
Consensus pattern (41 bp):
TAAGCGCCGCTAATGCTCGGGCCTTTAGTGGCATTTCTGTC
Found at i:1371707 original size:442 final size:442
Alignment explanation
Indices: 1370883--1371764 Score: 1620
Period size: 442 Copynumber: 2.0 Consensus size: 442
1370873 TAGAAACACT
* *
1370883 ACACCAGAATGGGCTTTTAGCGGCACATTTAGCGGCGTTTGGAACAAAAGGGCCACTCAAAATCG
1 ACACCAGAATGGGCTTTTAGCGGCACATTTAGCGGCGTTTGGAACAAAAGCGCCACTAAAAATCG
1370948 AGCATTAGCGGCGTTTTTACAAAAGCGCCGCTAAAGATCGAGCATCAGCGGCGTATTTCCAAAAT
66 AGCATTAGCGGCGTTTTTACAAAAGCGCCGCTAAAGATCGAGCATCAGCGGCGTATTTCCAAAAT
*
1371013 CGCCGCTAAAAATAGGAATCAGTGGCGTTTTTTATAAAGCGCCACAAAAGACCTAAGACCAACGA
131 CGCCGCTAAAAATAGGAATCAGCGGCGTTTTTTATAAAGCGCCACAAAAGACCTAAGACCAACGA
* * *
1371078 TGTCGTTTTTCGAGCCTTTAGCGGCGTTTTTGCGGATGCGAAGCTAATGATCGGACCTTTAGCGG
196 CGTAGTTTTTCGAGCCTTTAGCGGCGTTTTTGCGGATGCGAAGCTAATGATCGGACCTTTAACGG
* *
1371143 CGTTTTTAGTTAAGCGCCGCTAATGCTCAGGCCTTTAGTGGCGTTTATGTCTATGCGCTGCTACT
261 CGTTTTTAGTTAAGCGCCGCTAATGCTCAGGCCTTTAGTGGCATTTATGTCTATGCGCCGCTACT
1371208 GCACGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAATGTAGCTTTAGCGGCGTTTTTG
326 GCACGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAATGTAGCTTTAGCGGCGTTTTTG
*
1371273 ACGAAGTGCCGCTAATAGTAACAAAAAATCTTATAAGTTGAAATAATTAACC
391 ACGAAGCGCCGCTAATAGTAACAAAAAATCTTATAAGTTGAAATAATTAACC
1371325 ACACCAGAATGGGCTTTTAGCGGCACATTTAGCGGCGTTTGGAACAAAAGCGCCACTAAAAATCG
1 ACACCAGAATGGGCTTTTAGCGGCACATTTAGCGGCGTTTGGAACAAAAGCGCCACTAAAAATCG
* *
1371390 AGCATTAGCGGCGTTTTTGCAAAAGCGCCGCTAAAGATTGAGCATCAGCGGCGTATTTCCAAAAT
66 AGCATTAGCGGCGTTTTTACAAAAGCGCCGCTAAAGATCGAGCATCAGCGGCGTATTTCCAAAAT
*
1371455 CGTCGCTAAAAATAGGAATCAGCGGCGTTTTTTATAAAGCGCCACAAAAGACCTAAGACCAACGA
131 CGCCGCTAAAAATAGGAATCAGCGGCGTTTTTTATAAAGCGCCACAAAAGACCTAAGACCAACGA
*
1371520 CGTAGTTTTTCGAGCCTTTAGCGGCGTTTTTGCGGATGCGACGCTAATGATCGGACCTTTAACGG
196 CGTAGTTTTTCGAGCCTTTAGCGGCGTTTTTGCGGATGCGAAGCTAATGATCGGACCTTTAACGG
* *
1371585 CGTTTTTAGTTAAGCGCCGCTAATGCTCGGGCCTTTAGTGGCATTTCTGTCTATGCGCCGCTACT
261 CGTTTTTAGTTAAGCGCCGCTAATGCTCAGGCCTTTAGTGGCATTTATGTCTATGCGCCGCTACT
*
1371650 GCTCGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAATGTAGCTTTAGCGGCGTTTTTG
326 GCACGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAATGTAGCTTTAGCGGCGTTTTTG
1371715 ACGAAGCGCCGCTAATAGTAACAAAAAATCTTATAAGTTGAAATAATTAA
391 ACGAAGCGCCGCTAATAGTAACAAAAAATCTTATAAGTTGAAATAATTAA
1371765 TATTTTGTTC
Statistics
Matches: 424, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
442 424 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (442 bp):
ACACCAGAATGGGCTTTTAGCGGCACATTTAGCGGCGTTTGGAACAAAAGCGCCACTAAAAATCG
AGCATTAGCGGCGTTTTTACAAAAGCGCCGCTAAAGATCGAGCATCAGCGGCGTATTTCCAAAAT
CGCCGCTAAAAATAGGAATCAGCGGCGTTTTTTATAAAGCGCCACAAAAGACCTAAGACCAACGA
CGTAGTTTTTCGAGCCTTTAGCGGCGTTTTTGCGGATGCGAAGCTAATGATCGGACCTTTAACGG
CGTTTTTAGTTAAGCGCCGCTAATGCTCAGGCCTTTAGTGGCATTTATGTCTATGCGCCGCTACT
GCACGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCGCTAATGAATGTAGCTTTAGCGGCGTTTTTG
ACGAAGCGCCGCTAATAGTAACAAAAAATCTTATAAGTTGAAATAATTAACC
Found at i:1372432 original size:150 final size:149
Alignment explanation
Indices: 1372237--1372513 Score: 502
Period size: 150 Copynumber: 1.8 Consensus size: 149
1372227 TAAGGTTTGG
1372237 GATTTAAGGTTAATTTAAGGGTTAGAGGTCTAGGGGTTTGGGATTTAGGGTTTCAACGGTCATGT
1 GATTTAAGGTTAATTTAAGGGTTAGAGGTCTAGGGGTTTGGGATTTAGGGTTTCAACGGTCATGT
*
1372302 TAGG-TAAACATATAAATAGACATTTGATATTTTTGATATATATGGATATATATATATAGTTACA
66 TAGGATAAACATATAAAGAGACATTTGATATTTTTGATATATAT-G-TATATATATATAGTTACA
1372366 TTTTAAGGAGTACGGGGTATA
129 TTTTAAGGAGTACGGGGTATA
*
1372387 GATTTAAGGTTAATTTAGGGGTTAGAGGTCTAGGGGTTTGGGATTTAGGGTTTCAACGGTCATGT
1 GATTTAAGGTTAATTTAAGGGTTAGAGGTCTAGGGGTTTGGGATTTAGGGTTTCAACGGTCATGT
1372452 TAGGTATAAACATATAAAGAGACATTTGATATTTTTGATATATATGTATATATATATAGTTA
66 TAGG-ATAAACATATAAAGAGACATTTGATATTTTTGATATATATGTATATATATATAGTTA
1372514 TTAATTATTT
Statistics
Matches: 123, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
150 84 0.68
151 1 0.01
152 38 0.31
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.39
Consensus pattern (149 bp):
GATTTAAGGTTAATTTAAGGGTTAGAGGTCTAGGGGTTTGGGATTTAGGGTTTCAACGGTCATGT
TAGGATAAACATATAAAGAGACATTTGATATTTTTGATATATATGTATATATATATAGTTACATT
TTAAGGAGTACGGGGTATA
Found at i:1372612 original size:27 final size:26
Alignment explanation
Indices: 1372574--1372624 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1372564 AATAAACAAA
* *
1372574 TAAATAAGTAGGTAATTATTTATTTGT
1 TAAATAAATAGGT-ATTAATTATTTGT
1372601 TAAATAAATAGGTATTAATTATTT
1 TAAATAAATAGGTATTAATTATTT
1372625 AAATGTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (26 bp):
TAAATAAATAGGTATTAATTATTTGT
Found at i:1372781 original size:62 final size:62
Alignment explanation
Indices: 1372684--1372805 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
1372674 AAAAACGCCG
1372684 TAAAAGTTAGCATTTACCGACGTTTTAGTCAAAAACGCCACAAATGTTGCAATATACGACGT
1 TAAAAGTTAGCATTTACCGACGTTTTAGTCAAAAACGCCACAAATGTTGCAATATACGACGT
* **
1372746 TAAAAGTTAGCCTTTACCGGTGTTTTAGTCAAAAACGCCACAAATGTTGCAATATACGAC
1 TAAAAGTTAGCATTTACCGACGTTTTAGTCAAAAACGCCACAAATGTTGCAATATACGAC
1372806 ATCGTTACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (62 bp):
TAAAAGTTAGCATTTACCGACGTTTTAGTCAAAAACGCCACAAATGTTGCAATATACGACGT
Found at i:1373339 original size:273 final size:272
Alignment explanation
Indices: 1372852--1373396 Score: 955
Period size: 273 Copynumber: 2.0 Consensus size: 272
1372842 GTTTTATTGG
* * *
1372852 GAAACGCCGCAAATATTCATGAAACTTTGTCAAAACGGCGTCATTTCAGTTGAATGATGTACTCT
1 GAAACGCCACAAATATTCATGAAACTTTGTCAAAACGACGTCATTTCACTTGAATGATGTACTCT
** *
1372917 GCTAGTGGCGTTTTTTGCGAAAACGCCACAACTATGTCTACAATTTTGTGAAAACGGCACCGTTT
66 GCTAGTGGCGTTTTCCGCGAAAACGCCACAACTATGTCTACAATTTTGTGAAAACAGCACCGTTT
1372982 CTTTTGTGTAATTGAAATTTTAGTGGCATTTATTTCCTTAGCGCCGCAAAAGGGCATGCAATAGC
131 CTTTTGTGTAATTGAAATTTTAGTGGCATTTATTTCCTTAGCGCCGCAAAAGGGCATGCAATAGC
*
1373047 GGCATTTTACGCAAAAACGCCGCAAATGTGACTTAAAAAACGGCGTCGTTTCTTTAAAGGCCATT
196 GGCATTTTACGCAAAAACGCCGCAAATGTGACTTAAAAAACGGCGCCG-TTCTTTAAAGGCCATT
1373112 TAACCCGTGTCCT
260 TAACCCGTGTCCT
* *
1373125 GAAACGCCACAAATATTCATGAAACTTTGTCAAAATGACGTCGTTTCACTTGAATGATGTACTCT
1 GAAACGCCACAAATATTCATGAAACTTTGTCAAAACGACGTCATTTCACTTGAATGATGTACTCT
* *
1373190 GTTAGTGGCGTTTTCCGCGAAAACGCCGCAACTATGTCTACAATTTTGTGAAAACAGCACCGTTT
66 GCTAGTGGCGTTTTCCGCGAAAACGCCACAACTATGTCTACAATTTTGTGAAAACAGCACCGTTT
* *
1373255 CTTTTGTGTAATTGAAATTTTAGTGGCGTTTATTTCCTTAGCGCCGCAAAAGGGCATGCAATAGT
131 CTTTTGTGTAATTGAAATTTTAGTGGCATTTATTTCCTTAGCGCCGCAAAAGGGCATGCAATAGC
*
1373320 GGCGTTTTACGCAAAAACGCCGCAAATGTGACTTAAAAAACGGCGCCGTTCTTTAAAGGCCATTT
196 GGCATTTTACGCAAAAACGCCGCAAATGTGACTTAAAAAACGGCGCCGTTCTTTAAAGGCCATTT
1373385 AACCCGTGTCCT
261 AACCCGTGTCCT
1373397 CATCCTTTAC
Statistics
Matches: 258, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
272 29 0.11
273 229 0.89
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (272 bp):
GAAACGCCACAAATATTCATGAAACTTTGTCAAAACGACGTCATTTCACTTGAATGATGTACTCT
GCTAGTGGCGTTTTCCGCGAAAACGCCACAACTATGTCTACAATTTTGTGAAAACAGCACCGTTT
CTTTTGTGTAATTGAAATTTTAGTGGCATTTATTTCCTTAGCGCCGCAAAAGGGCATGCAATAGC
GGCATTTTACGCAAAAACGCCGCAAATGTGACTTAAAAAACGGCGCCGTTCTTTAAAGGCCATTT
AACCCGTGTCCT
Found at i:1373528 original size:58 final size:59
Alignment explanation
Indices: 1373432--1373550 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 59
1373422 ATAAAAAAAA
1373432 TGCATTTTCTATACCAACTTTTATAAAAAAAATTTGTTTTTTATATAAAGAGACAAAATT
1 TGCATTTTCTATACCAACTTTTAT-AAAAAAATTTGTTTTTTATATAAAGAGACAAAATT
1373492 TGCATTTTCTATACCAACTTTTAT-AAAAAATTTGTTTTTTATATAAAGAGACAAAATT
1 TGCATTTTCTATACCAACTTTTATAAAAAAATTTGTTTTTTATATAAAGAGACAAAATT
1373550 T
1 T
1373551 ATTGTACCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 35 0.59
60 24 0.41
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (59 bp):
TGCATTTTCTATACCAACTTTTATAAAAAAATTTGTTTTTTATATAAAGAGACAAAATT
Found at i:1373994 original size:22 final size:22
Alignment explanation
Indices: 1373940--1373994 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1373930 GTTTGGCTGG
*
1373940 GGTTTAGG-GTTTGGTATATAT
1 GGTTTAGGAGTTTGGTATATAA
* *
1373961 GGATTTA-AAGTTTGGTATTTAA
1 GG-TTTAGGAGTTTGGTATATAA
1373983 GGTTTAGGAGTT
1 GGTTTAGGAGTT
1373995 AGGGGTCGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (22 bp):
GGTTTAGGAGTTTGGTATATAA
Found at i:1374061 original size:167 final size:166
Alignment explanation
Indices: 1373785--1374117 Score: 585
Period size: 167 Copynumber: 2.0 Consensus size: 166
1373775 GTACGAGCCG
*
1373785 GGTATATATGGATTTAAGGTTTGGTATTTAAGGTTTAGGAGTTAGGGGTCGGGTTATGCCTTAAG
1 GGTATATATGGATTTAAAGTTTGGTATTTAAGGTTTAGGAGTTAGGGGTCGGGTTATGCCTTAAG
* *
1373850 GGTTACACACGTGGATTTAGGGGTTAGGGCTAAGGTTAATTAGGGGTTTAGGGGGATTTAAGGTT
66 GGTTACACACGTGGATTTAGGGGTTAGGGCCAAGGTTAATTA-GGGTTTAAGGGGATTTAAGGTT
**
1373915 AGAGAGGTTTTAGGGGTTTGGCTGGGGTTTAGGGTTT
130 AGAGAGGTTTTAGGGGTTTGGCCCGGGTTTAGGGTTT
*
1373952 GGTATATATGGATTTAAAGTTTGGTATTTAAGGTTTAGGAGTTAGGGGTCGGGTTATGCCTTAGG
1 GGTATATATGGATTTAAAGTTTGGTATTTAAGGTTTAGGAGTTAGGGGTCGGGTTATGCCTTAAG
* *
1374017 GGTTACACACGTGGATTTAGGGGTTATGGCCAGGGTTAATTAGGGTTTAAGGGGATTTAAGGTTA
66 GGTTACACACGTGGATTTAGGGGTTAGGGCCAAGGTTAATTAGGGTTTAAGGGGATTTAAGGTTA
1374082 GAGAGGTTTTAGGGGTTTGGCCCGGGTTTAGGGTTT
131 GAGAGGTTTTAGGGGTTTGGCCCGGGTTTAGGGTTT
1374118 CAACGGTCAT
Statistics
Matches: 158, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
166 56 0.35
167 102 0.65
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.36
Consensus pattern (166 bp):
GGTATATATGGATTTAAAGTTTGGTATTTAAGGTTTAGGAGTTAGGGGTCGGGTTATGCCTTAAG
GGTTACACACGTGGATTTAGGGGTTAGGGCCAAGGTTAATTAGGGTTTAAGGGGATTTAAGGTTA
GAGAGGTTTTAGGGGTTTGGCCCGGGTTTAGGGTTT
Found at i:1374536 original size:27 final size:27
Alignment explanation
Indices: 1374506--1374557 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1374496 AATAAACAAA
*
1374506 TAAATAAGTAGGTAA-TAATTTATTTGT
1 TAAATAAATAGGTAATTAA-TTATTTGT
1374533 TAAATAAATAGGTAATTAATTATTT
1 TAAATAAATAGGTAATTAATTATTT
1374558 AAATGTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (27 bp):
TAAATAAATAGGTAATTAATTATTTGT
Found at i:1375891 original size:18 final size:18
Alignment explanation
Indices: 1375868--1375902 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1375858 TGATGAAGCT
1375868 GATGATGACTCCG-ATGAA
1 GATGATGA-TCCGTATGAA
1375886 GATGATGATCCGTATGA
1 GATGATGATCCGTATGA
1375903 GGCGGGCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (18 bp):
GATGATGATCCGTATGAA
Found at i:1381060 original size:43 final size:42
Alignment explanation
Indices: 1380945--1381077 Score: 196
Period size: 42 Copynumber: 3.1 Consensus size: 42
1380935 TAAAGAACAT
* *
1380945 GCGGCGCTTA-ATAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGA-AAAAAACGCCGCTAAAGAACATGATCTTTA
* *
1380987 GCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATCATCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTA
*
1381029 GTGGCGCTTAGAAAAAAAGCGCCGCTAAAGAACATGATCTTTA
1 GCGGCGCTTAGAAAAAAA-CGCCGCTAAAGAACATGATCTTTA
1381072 GCGGCG
1 GCGGCG
1381078 TTTTTGTTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
42 53 0.65
43 28 0.35
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTA
Found at i:1382127 original size:19 final size:20
Alignment explanation
Indices: 1382098--1382137 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1382088 ATAAATGGAC
**
1382098 TATTGTATTTGGTTTTTATT
1 TATTGTATTTGAATTTTATT
1382118 TATT-TATTTGAATTTTATT
1 TATTGTATTTGAATTTTATT
1382137 T
1 T
1382138 GTCTTGGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (20 bp):
TATTGTATTTGAATTTTATT
Found at i:1383323 original size:84 final size:85
Alignment explanation
Indices: 1383223--1383392 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 85
1383213 ATTTAATAAC
1383223 AAAATAATTCTATAAAGAATATTTGAAAAAAAATCCAAAAGTCTTATTAAATTGAAATTTTAAGT
1 AAAATAATTCTATAAAGAATATTTGAAAAAAAATCCAAAAGTCTTATTAAATTGAAATTTTAAGT
1383288 TTTAATTGATTTATATATAT
66 TTTAATTGATTTATATATAT
1383308 AAAATAATTCT-TAAAGAATATTTGAAAAAAAATCCAAAAGTCTTATTAAATTGAAATTTTAAGT
1 AAAATAATTCTATAAAGAATATTTGAAAAAAAATCCAAAAGTCTTATTAAATTGAAATTTTAAGT
1383372 TTTAATTGATTTATATATAT
66 TTTAATTGATTTATATATAT
1383392 A
1 A
1383393 TAGTTAAAGC
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 74 0.87
85 11 0.13
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (85 bp):
AAAATAATTCTATAAAGAATATTTGAAAAAAAATCCAAAAGTCTTATTAAATTGAAATTTTAAGT
TTTAATTGATTTATATATAT
Found at i:1390735 original size:34 final size:34
Alignment explanation
Indices: 1390697--1390761 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1390687 CTTAAAGTTT
*
1390697 TAGTATGTGAACCCCCATATTATATAGTATGACA
1 TAGTATGCGAACCCCCATATTATATAGTATGACA
*
1390731 TAGTATGCGAACCCCCATGTTATATAGTATG
1 TAGTATGCGAACCCCCATATTATATAGTATG
1390762 TGATTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (34 bp):
TAGTATGCGAACCCCCATATTATATAGTATGACA
Found at i:1390814 original size:15 final size:15
Alignment explanation
Indices: 1390785--1390878 Score: 66
Period size: 15 Copynumber: 6.4 Consensus size: 15
1390775 GCGAACCTTG
* *
1390785 TATGTGTGGATCCTA
1 TATGTGTGAACCCTA
*
1390800 TATGTGGGAACCCTA
1 TATGTGTGAACCCTA
** *
1390815 TACATGTGAACTCTA
1 TATGTGTGAACCCTA
* * *
1390830 GATGCGTGAACCTTA
1 TATGTGTGAACCCTA
* *
1390845 GATGTG-CAA-CCTA
1 TATGTGTGAACCCTA
1390858 TATGTGTGAACCCTA
1 TATGTGTGAACCCTA
*
1390873 CATGTG
1 TATGTG
1390879 AACATGTCAT
Statistics
Matches: 58, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
13 8 0.14
14 4 0.07
15 46 0.79
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (15 bp):
TATGTGTGAACCCTA
Found at i:1390850 original size:28 final size:27
Alignment explanation
Indices: 1390815--1390881 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
1390805 GGGAACCCTA
*
1390815 TACATGTGAACTCTAGATGCGTGAACCT
1 TACATGTGAAC-CTAGATGCGTGAACCC
* * *
1390843 TAGATGTGCAACCTATATGTGTGAACCC
1 TACATGTG-AACCTAGATGCGTGAACCC
1390871 TACATGTGAAC
1 TACATGTGAAC
1390882 ATGTCATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 3 0.09
28 27 0.82
29 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (27 bp):
TACATGTGAACCTAGATGCGTGAACCC
Found at i:1392562 original size:151 final size:147
Alignment explanation
Indices: 1392318--1392589 Score: 318
Period size: 151 Copynumber: 1.8 Consensus size: 147
1392308 TCCATTTATT
* *
1392318 TATTTAACTTCAATTTTAATCAAATTTACATTAGTTTCTATTTATTTATTTACTTAATATCTTCT
1 TATTTAACTTCAATTTTAATCAAATTTACATTAGTTTATATTTATTTATCTACTTAATATCTTCT
* * * *
1392383 AAATTGATTTGTTCATTTTAATTTTTACCCTT-ATTAATGTCATTTTTATTTCATTACCTATTTA
66 AAATTGATTTGTT-ATTATAATTCTTA-CCTTCATTAAAGTCATTTTTACTTCATTACCTATTTA
1392447 TTTATTATTTTTTTCTGAA
129 TTTATTATTTTTTTCTGAA
* * * *
1392466 TATTTAACTTCAATTTTTAATCAAATTTATATTAGTTTTTATATTTGTTTATCTACTTAGTATTT
1 TATTTAACTTCAA-TTTTAATCAAATTTACATTAG--TTTATATTTATTTATCTACTTAATATCT
** *
1392531 TCT-TTTTAGTATACTTGTT-TTAT-ATTCTTACCTTCATTAAAGTCATTTTTGCTTCATTA
63 TCTAAATT-G-AT--TTGTTATTATAATTCTTACCTTCATTAAAGTCATTTTTACTTCATTA
1392590 TTTACTTATT
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
148 13 0.13
149 20 0.19
150 6 0.06
151 54 0.52
152 5 0.05
154 5 0.05
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.57
Consensus pattern (147 bp):
TATTTAACTTCAATTTTAATCAAATTTACATTAGTTTATATTTATTTATCTACTTAATATCTTCT
AAATTGATTTGTTATTATAATTCTTACCTTCATTAAAGTCATTTTTACTTCATTACCTATTTATT
TATTATTTTTTTCTGAA
Found at i:1392656 original size:21 final size:21
Alignment explanation
Indices: 1392632--1392678 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1392622 AAAAATTTAG
1392632 ATTATTATAATGGTTATTATC
1 ATTATTATAATGGTTATTATC
* * * *
1392653 ATTACTGTTATGGTTATTTTC
1 ATTATTATAATGGTTATTATC
1392674 ATTAT
1 ATTAT
1392679 CAATATTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (21 bp):
ATTATTATAATGGTTATTATC
Found at i:1398710 original size:89 final size:88
Alignment explanation
Indices: 1398559--1399014 Score: 538
Period size: 89 Copynumber: 5.1 Consensus size: 88
1398549 AGTAGATTGA
* * * * *
1398559 TTATCTCCCTGAGAAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTCTTCTTGTATTGGCAGC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
*
1398624 GAAGTAGATCGAAGATATAAAGCC
66 GAAGTAGATCGAAGA-ACAAAGCC
*
1398648 TTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
* **
1398713 GAAGTAGATCGAAGACCCCAGCC
66 GAAGTAGATCGAAGAACAAAGCC
* * * *
1398736 TTATCTCCCTG-GACAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAG
1 TTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAG
*
1398800 CGAAGTAGATCGAAGATAGTAAA-CC
65 CGAAGTAGATCGAAGA-A-CAAAGCC
* * *
1398825 TTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTTCTATATTGGCAGC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
* **
1398890 GAAGTAGATCGAAGACCCCAGCC
66 GAAGTAGATCGAAGAACAAAGCC
* * * ** * ** *
1398913 TTATCTCCCTGAGCGGCAGTAGAGCAGACTGAAAACAGCAGATCTTACCTTCCTGTATTGGCAGC
1 TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
* * *
1398978 GAAGGAAATCGAAGAACACCAGCC
66 GAAGTAGATCGAAGAACA-AAGCC
**
1399002 TTGCCTCCCTGAG
1 TTATCTCCCTGAG
1399015 TTTGCAGTGG
Statistics
Matches: 313, Mismatches: 48, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
87 2 0.01
88 146 0.47
89 164 0.52
90 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (88 bp):
TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGC
GAAGTAGATCGAAGAACAAAGCC
Found at i:1398862 original size:177 final size:177
Alignment explanation
Indices: 1398559--1398925 Score: 639
Period size: 177 Copynumber: 2.1 Consensus size: 177
1398549 AGTAGATTGA
* * *
1398559 TTATCTCCCTGAGAAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTCTTCTTGTATTGGCAGC
1 TTATCTCCCTGAGAAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAGC
* * *
1398624 GAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAG
66 GAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCAG
1398689 ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
131 ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
1398736 TTATCTCCCTG-GACAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAG
1 TTATCTCCCTGAGA-AACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAG
1398800 CGAAGTAGATCGAAGATAGTAAA-CCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGC
65 CGAAGTAGATCGAAGATA-TAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGC
*
1398864 AGATCTTGTCTTTCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
129 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
1398913 TTATCTCCCTGAG
1 TTATCTCCCTGAG
1398926 CGGCAGTAGA
Statistics
Matches: 180, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
176 2 0.01
177 173 0.96
178 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (177 bp):
TTATCTCCCTGAGAAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAGC
GAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCAG
ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
Found at i:1398957 original size:177 final size:177
Alignment explanation
Indices: 1398559--1398992 Score: 613
Period size: 177 Copynumber: 2.5 Consensus size: 177
1398549 AGTAGATTGA
* * ** *
1398559 TTATCTCCCTGAGA-AACAGTGGAGTAGGTTGAAAATAACAGATCTTGTCTTCTTGTATTGGCAG
1 TTATCTCCCTG-GACAACAGTAGAGCAGACTGAAAATAACAGATCTTGTCTTCCTGTATTGGCAG
* * *
1398623 CGAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCA
65 CGAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCA
1398688 GATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
130 GATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
* * ** * *
1398736 TTATCTCCCTGGACAACAGTGGAGTAGGTTGAAAATAACAGATCTTGTATTCCTCTATTGGCAGC
1 TTATCTCCCTGGACAACAGTAGAGCAGACTGAAAATAACAGATCTTGTCTTCCTGTATTGGCAGC
1398801 GAAGTAGATCGAAGATAGTAAA-CCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCA
66 GAAGTAGATCGAAGATA-TAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCA
*
1398865 GATCTTGTCTTTCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
130 GATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
** * * **
1398913 TTATCTCCCT-GAGCGGCAGTAGAGCAGACTGAAAACAGCAGATCTTACCTTCCTGTATTGGCAG
1 TTATCTCCCTGGA-CAACAGTAGAGCAGACTGAAAATAACAGATCTTGTCTTCCTGTATTGGCAG
* *
1398977 CGAAGGAAATCGAAGA
65 CGAAGTAGATCGAAGA
1398993 ACACCAGCCT
Statistics
Matches: 233, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
176 4 0.02
177 225 0.97
178 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (177 bp):
TTATCTCCCTGGACAACAGTAGAGCAGACTGAAAATAACAGATCTTGTCTTCCTGTATTGGCAGC
GAAGTAGATCGAAGATATAAAGCCTTATCTCCCTGAACAGCAGTGGAGTAGGTTAAAAATAGCAG
ATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACCCCAGCC
Found at i:1399046 original size:90 final size:90
Alignment explanation
Indices: 1398590--1399115 Score: 289
Period size: 89 Copynumber: 5.9 Consensus size: 90
1398580 GAGTAGGTTG
* ** * * * * **
1398590 AAAATAACAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATATA-AAGCCTTATCT
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGA-ACACCAGCCTTGCCT
** * * ** *
1398654 CCCTGAG-CAGTAGTGGAGTAGGTTG
65 CCCTGAGTTTGCAGTGGAGCAGACTA
* * ** * * * **
1398679 AAAATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAG-ACCCCAGCCTTATCTC
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTC
**** * ** *
1398743 CCTG-GACAACAGTGGAGTAGGTTG
66 CCTGAGTTTGCAGTGGAGCAGACTA
* *** * * * * **
1398767 AAAATAACAGATCTTGTATTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGTA--AACCTTATC
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGA-A-CACCAGCCTTGCC
*** * **
1398830 TCCCTGA-ACAGCAGTGGAGTAGGTTA
64 TCCCTGAGTTTGCAGTGGAGCAGACTA
* * ** * * * * **
1398856 AAAATAGCAGATCTTGTCTTTCTATATTGGCAGCGAAGTAGATCGAAG-ACCCCAGCCTTATCTC
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTC
** * *
1398920 CCTGAG-CGGCAGTAGAGCAGACTG
66 CCTGAGTTTGCAGTGGAGCAGACTA
* * *
1398944 AAAACAGCAGATCTTACCTTCCTGTATTGGCAGCGAAGGAAATCGAAGAACACCAGCCTTGCCTC
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTC
1399009 CCTGAGTTTGCAGTGGAGCAGACTA
66 CCTGAGTTTGCAGTGGAGCAGACTA
* * * * * * *
1399034 AAAACAACAGATCTTATCTTTCTGTACTGGCAGCGAAACAGATCG-ACAACACTAGTCTTGCCTC
1 AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTC
*
1399098 TCTGAGTTTGCAGTGGAG
66 CCTGAGTTTGCAGTGGAG
1399116 TAGGTTGAAG
Statistics
Matches: 372, Mismatches: 54, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
87 3 0.01
88 144 0.39
89 172 0.46
90 53 0.14
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (90 bp):
AAAACAACAGATCTTACCTTCCTGTATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTC
CCTGAGTTTGCAGTGGAGCAGACTA
Found at i:1399185 original size:44 final size:44
Alignment explanation
Indices: 1399137--1399449 Score: 156
Period size: 44 Copynumber: 7.1 Consensus size: 44
1399127 TTGTAGATCC
1399137 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
* * **** *
1399181 TATCTTCCC-AAGGTAGTAG-GGAAGCAGATTTAAG-CCACCAATCC
1 TATC-TCCCTAA-GCAGTAGTGG-AGCAGATTAAAGACGGTGAATCT
* * * * ** *
1399225 TATCTCCCTGAA-CAGCAGTGGAGTAGGTTGAAGATTGT-AGATCC
1 TATCTCCCT-AAGCAGTAGTGGAGCAGATTAAAGACGGTGA-ATCT
* *
1399269 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGATGAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
* * **** *
1399313 TATCTTCCC-AAGGTAGTAG-GGAAGCAGATTTAAG-CCACCAATCC
1 TATC-TCCCTAA-GCAGTAGTGG-AGCAGATTAAAGACGGTGAATCT
* * * * * * ** *
1399357 TATTTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
*** * * *
1399401 CGGCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGGTGAATTT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
1399445 TATCT
1 TATCT
1399450 TTCCAAGGTA
Statistics
Matches: 192, Mismatches: 61, Indels: 32
0.67 0.21 0.11
Matches are distributed among these distances:
43 38 0.20
44 110 0.57
45 44 0.23
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGGTGAATCT
Found at i:1399606 original size:132 final size:132
Alignment explanation
Indices: 1399107--1399582 Score: 758
Period size: 132 Copynumber: 3.6 Consensus size: 132
1399097 CTCTGAGTTT
*
1399107 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
1399172 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAA
66 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAG
1399237 CA
131 CA
1399239 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
1399304 GATGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATTTCCCTGAG
66 GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAG
1399369 CA
131 CA
* * ** *
1399371 GCAGTGGAGTAGGTTGAAGAATGTAAAT-CTCGGCTCCCTAAGCAGTAGTGGAGTAGATCAAAGA
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
* * * *
1399435 CGGTGAATTTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAACCACCAATCCTATCTCTCTGA
65 CGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGA
1399500 GCA
130 GCA
* * * * *
1399503 GCAGTGGAGTAGGTTGAAGATTGTAGATCATGTCTCGCTAAGCAGTAGTGAAGCAGATCAAAGAT
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
1399568 AGTGAATCTTA-CTTC
66 GGTGAATCTTATCTTC
1399583 TCTGACGTTG
Statistics
Matches: 316, Mismatches: 26, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
131 5 0.02
132 310 0.98
133 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
GGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAG
CA
Found at i:1399623 original size:50 final size:49
Alignment explanation
Indices: 1399568--1399732 Score: 258
Period size: 50 Copynumber: 3.3 Consensus size: 49
1399558 GATCAAAGAT
1399568 AGTGAATCTTACTTCTCTGACGTTGCAGTAAAACAGATTGAAGCTACAAC
1 AGTGAATCTTACTTCTC-GACGTTGCAGTAAAACAGATTGAAGCTACAAC
*
1399618 AGTGAATCTTACTTCTCCGACATTGCAGTAAAACAGATTGAAGCTACAAC
1 AGTGAATCTTACTTCT-CGACGTTGCAGTAAAACAGATTGAAGCTACAAC
* * *
1399668 AGCGAATCTTACTTCTACGACGTTGTAGTAAAATAGATTGAAGCTACAAC
1 AGTGAATCTTACTTCT-CGACGTTGCAGTAAAACAGATTGAAGCTACAAC
*
1399718 AGGGAATCTTACTTC
1 AGTGAATCTTACTTC
1399733 CCCTAAAGTT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 106 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (49 bp):
AGTGAATCTTACTTCTCGACGTTGCAGTAAAACAGATTGAAGCTACAAC
Found at i:1400230 original size:19 final size:19
Alignment explanation
Indices: 1400206--1400247 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1400196 TATTCATAAA
*
1400206 AAAGGGAGG-AAATTAGTGT
1 AAAGGG-GGAAAATCAGTGT
1400225 AAAGGGGGAAAATCAGTGT
1 AAAGGGGGAAAATCAGTGT
1400244 AAAG
1 AAAG
1400248 AGAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.45, C:0.02, G:0.36, T:0.17
Consensus pattern (19 bp):
AAAGGGGGAAAATCAGTGT
Found at i:1400258 original size:20 final size:21
Alignment explanation
Indices: 1400233--1400281 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1400223 GTAAAGGGGG
*
1400233 AAAATCAGTGTAAA-GAGAAA
1 AAAATCAGTGCAAAGGAGAAA
*
1400253 AAAATCATTGCAAAGGGAGAAA
1 AAAATCAGTGCAAA-GGAGAAA
1400275 AAAATCA
1 AAAATCA
1400282 AAAAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.14
Consensus pattern (21 bp):
AAAATCAGTGCAAAGGAGAAA
Found at i:1401098 original size:24 final size:24
Alignment explanation
Indices: 1401071--1401185 Score: 96
Period size: 23 Copynumber: 4.9 Consensus size: 24
1401061 TTATTGTATA
*
1401071 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* *
1401095 TTATTATTTGT-AATTTATCA-ATA
1 TTATTATTT-TAAATTTATCATGTT
*
1401118 TTATTATTTTAAATTCATC--GTT
1 TTATTATTTTAAATTTATCATGTT
**
1401140 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
1401164 ATATTTATTTCAAATTTATCAT
1 TTA-TTATTTTAAATTTATCAT
1401186 TAATATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 35 0.47
24 35 0.47
25 2 0.03
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:1401158 original size:46 final size:46
Alignment explanation
Indices: 1401097--1401217 Score: 124
Period size: 47 Copynumber: 2.6 Consensus size: 46
1401087 ATCATGTTTT
* *
1401097 ATTATTTGT-AATTTATCAATATTATTATTTTAAATTCATCGTTAAC
1 ATTATTT-TAAATTTATCAATATTATTATTTCAAATTCATCATTAAC
* * *
1401143 ATTATTTTAAATTTATC-ATGTATATTTATTTCAAATTTATCATTAAT
1 ATTATTTTAAATTTATCAATAT-TA-TTATTTCAAATTCATCATTAAC
*
1401190 A-T-TTTTAAATTTATTATATATTATTATT
1 ATTATTTTAAATTTATCA-ATATTATTATT
1401218 AATTATTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
45 21 0.33
46 20 0.32
47 22 0.35
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (46 bp):
ATTATTTTAAATTTATCAATATTATTATTTCAAATTCATCATTAAC
Found at i:1401191 original size:24 final size:23
Alignment explanation
Indices: 1401033--1401217 Score: 128
Period size: 24 Copynumber: 8.0 Consensus size: 23
1401023 CTTATTATCA
*
1401033 TTAAATTAATCATTAATATTA-T
1 TTAAATTTATCATTAATATTATT
* * ** *
1401055 CTAAGTTTATTGTATATTATTATT
1 TTAAATTTATCAT-TAATATTATT
* **
1401079 TTAGATTTATCATGTTTTATTATT
1 TTAAATTTATCAT-TAATATTATT
* *
1401103 TGT-AATTTATCAATATTATTATT
1 T-TAAATTTATCATTAATATTATT
* * *
1401126 TTAAATTCATCGTTAACATTATT
1 TTAAATTTATCATTAATATTATT
1401149 TTAAATTTATCATGT-ATATTTATT
1 TTAAATTTATCAT-TAATA-TTATT
*
1401173 TCAAATTTATCATTAATA-T-TT
1 TTAAATTTATCATTAATATTATT
* *
1401194 TTAAATTTATTATATATTATTATT
1 TTAAATTTATCAT-TAATATTATT
1401218 AATTATTTTT
Statistics
Matches: 125, Mismatches: 28, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
21 13 0.10
22 14 0.11
23 47 0.38
24 50 0.40
25 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (23 bp):
TTAAATTTATCATTAATATTATT
Found at i:1403832 original size:23 final size:23
Alignment explanation
Indices: 1403806--1403852 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1403796 CAGCATCATA
1403806 TTTCATTACAAAAACCAATCAAT
1 TTTCATTACAAAAACCAATCAAT
* *
1403829 TTTCATTACAAAGACCAGTCAAT
1 TTTCATTACAAAAACCAATCAAT
1403852 T
1 T
1403853 CATACAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (23 bp):
TTTCATTACAAAAACCAATCAAT
Found at i:1405064 original size:36 final size:36
Alignment explanation
Indices: 1405017--1405124 Score: 157
Period size: 36 Copynumber: 3.0 Consensus size: 36
1405007 TGTCAGTGTC
*
1405017 TGATTACTACACCAAGATATCTCGTGCAAGTTTATA
1 TGATTACTACACCAAGATATCTCGTACAAGTTTATA
1405053 TGATTACTACACCAAGATATCTCGTACAAGTTTATA
1 TGATTACTACACCAAGATATCTCGTACAAGTTTATA
** *
1405089 T--TTTGTCACACCAAGATATCTCATACAAGTTTATA
1 TGATTACT-ACACCAAGATATCTCGTACAAGTTTATA
1405124 T
1 T
1405125 TTTATCTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 3 0.04
35 28 0.42
36 36 0.54
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
TGATTACTACACCAAGATATCTCGTACAAGTTTATA
Found at i:1405107 original size:35 final size:35
Alignment explanation
Indices: 1405020--1405128 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
1405010 CAGTGTCTGA
* *
1405020 TTACTACACCAAGATATCTCGTGCAAGTTTATATGA
1 TTACTACACCAAGATATCTCGTACAAGTTTATAT-T
1405056 TTACTACACCAAGATATCTCGTACAAGTTTATATT
1 TTACTACACCAAGATATCTCGTACAAGTTTATATT
* *
1405091 TT-GTCACACCAAGATATCTCATACAAGTTTATATT
1 TTACT-ACACCAAGATATCTCGTACAAGTTTATATT
1405126 TTA
1 TTA
1405129 TCTAAACATG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
34 1 0.01
35 33 0.49
36 33 0.49
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (35 bp):
TTACTACACCAAGATATCTCGTACAAGTTTATATT
Found at i:1417654 original size:32 final size:32
Alignment explanation
Indices: 1417599--1417708 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 32
1417589 GAATGGCTAC
* *
1417599 AAGCCATAAGTA-CAGTAATATGATTGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
* *
1417630 AAGCCATTAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCGGCACA
* * *
1417662 CAA-CCATCAGTAACGGTAATATGATCGGGACA
1 -AAGCCATCAGTAGCAGTAATATGATCGGCACA
1417694 AAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
1417709 TCACAGCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
31 13 0.20
32 51 0.77
33 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATCGGCACA
Found at i:1417786 original size:26 final size:27
Alignment explanation
Indices: 1417728--1417780 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1417718 AGTTTCCAAT
1417728 AACAGTATATGTGGCCAAACCACCAGA
1 AACAGTATATGTGGCCAAACCACCAGA
1417755 AACAGTGAT-TGTGG-CAAAGCCACCAG
1 AACAGT-ATATGTGGCCAAA-CCACCAG
1417781 TACAGTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 18 0.75
28 2 0.08
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (27 bp):
AACAGTATATGTGGCCAAACCACCAGA
Found at i:1417963 original size:27 final size:27
Alignment explanation
Indices: 1417933--1418107 Score: 219
Period size: 27 Copynumber: 6.6 Consensus size: 27
1417923 GGTATATTGA
* *
1417933 TCATTTTACCCTACAAGGGTATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
1417960 TCATTTTACTCTATAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
1417987 TCATTTTACTCTACAGGGG-ATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * * *
1418013 TCATTTTATCCTA-AGGGGTATTATGA
1 TCATTTTACCCTACAGGGGCATTACGG
* *
1418039 TCATTTTACCTTACAGGGGCATTACAG
1 TCATTTTACCCTACAGGGGCATTACGG
1418066 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
1418093 TTATTTTAACCTACA
1 TCATTTTACCCTACA
1418108 TAGGCTGTAA
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
25 5 0.04
26 34 0.27
27 88 0.69
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGG
Found at i:1417968 original size:53 final size:52
Alignment explanation
Indices: 1417906--1418075 Score: 182
Period size: 53 Copynumber: 3.2 Consensus size: 52
1417896 GGGCAAAATA
* *
1417906 GTCATTTTACCTTTGGAGGTA-TATTGATCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCTTAGG-GGTATTA-TGATCATTTTACCCTACAAGGGCATTACG
* * * * *
1417959 GTCATTTTACTCTATAGGGGCATTACGGTCATTTTACTCTAC-AGGGGATTACG
1 GTCATTTTAC-CT-TAGGGGTATTATGATCATTTTACCCTACAAGGGCATTACG
* * * *
1418012 GTCATTTTATCCTAAGGGGTATTATGATCATTTTACCTTACAGGGGCATTACA
1 GTCATTTTA-CCTTAGGGGTATTATGATCATTTTACCCTACAAGGGCATTACG
1418065 GTCATTTTACC
1 GTCATTTTACC
1418076 CTACAGGGGC
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
52 24 0.25
53 48 0.49
54 20 0.21
55 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (52 bp):
GTCATTTTACCTTAGGGGTATTATGATCATTTTACCCTACAAGGGCATTACG
Found at i:1418060 original size:79 final size:81
Alignment explanation
Indices: 1417933--1418107 Score: 239
Period size: 79 Copynumber: 2.2 Consensus size: 81
1417923 GGTATATTGA
* * * * *
1417933 TCATTTTACCCTACAAGGGTATTACGGTCATTTTACTCTATAGGGGCATTACGGTCATTTTACTC
1 TCATTTTAACCTACAAGGGTATTACGATCATTTTACTCTACAGGGGCATTACAGTCATTTTACCC
1417998 TACAGGGG-ATTACGG
66 TACAGGGGCATTACGG
* * *
1418013 TCATTTTATCCTA-AGGGGTATTATGATCATTTTAC-CTTACAGGGGCATTACAGTCATTTTACC
1 TCATTTTAACCTACAAGGGTATTACGATCATTTTACTC-TACAGGGGCATTACAGTCATTTTACC
1418076 CTACAGGGGCATTACGG
65 CTACAGGGGCATTACGG
*
1418093 TTATTTTAACCTACA
1 TCATTTTAACCTACA
1418108 TAGGCTGTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 51 0.61
80 30 0.36
81 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (81 bp):
TCATTTTAACCTACAAGGGTATTACGATCATTTTACTCTACAGGGGCATTACAGTCATTTTACCC
TACAGGGGCATTACGG
Found at i:1420046 original size:18 final size:17
Alignment explanation
Indices: 1420013--1420051 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1420003 TTTTATAAAT
1420013 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1420031 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1420048 TGTG
1 TGTG
1420052 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1420296 original size:23 final size:23
Alignment explanation
Indices: 1420269--1420390 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
1420259 AGTGTTATTG
1420269 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
1420292 TTCAGTGGTAGCTACCGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1420315 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * * *
1420338 TTTAATGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1420361 ATCAGTCGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1420384 ATCAGTG
1 ATCAGTG
1420391 TGGCACTTAT
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1420322 original size:46 final size:46
Alignment explanation
Indices: 1420269--1420390 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
1420259 AGTGTTATTG
1420269 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACCGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACCGCTACAT
* * * *
1420315 ATCAGTGGTAGCTTCGGCTACATTTTAATGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACCGCTACAT
* *
1420361 ATCAGTCGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
1420391 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACCGCTACAT
Done.