Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 135 of 182
Found at i:42276675 original size:28 final size:28
Alignment explanation
Indices: 42276644--42276702 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
42276634 TTGATTCTTT
* *
42276644 GAAAAGAGGT-CGTTTATTGGTCTTTCAA
1 GAAAAG-GGTCCGTATATTGATCTTTCAA
*
42276672 GAAAAGGGTCCGTATATTGATTTTTCAA
1 GAAAAGGGTCCGTATATTGATCTTTCAA
42276700 GAA
1 GAA
42276703 CTCGATTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (28 bp):
GAAAAGGGTCCGTATATTGATCTTTCAA
Found at i:42277081 original size:6 final size:6
Alignment explanation
Indices: 42277062--42277139 Score: 67
Period size: 6 Copynumber: 13.7 Consensus size: 6
42277052 ACTTTGGACA
* * *
42277062 TAAATT TAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT T-TATG
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT
* *
42277108 TAAATT TAAATT CAAA-A TAAATT T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
42277140 AATAAACTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 39 0.70
7 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:42277085 original size:18 final size:17
Alignment explanation
Indices: 42277062--42277137 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
42277052 ACTTTGGACA
*
42277062 TAAATTTAATTTTAAATT
1 TAAATTT-ATTATAAATT
*
42277080 TAAATTTATAATAAATT
1 TAAATTTATTATAAATT
*
42277097 TAAATTT-TATGTAAATT
1 TAAATTTAT-TATAAATT
* **
42277114 TAAATTCAAAATAAATT
1 TAAATTTATTATAAATT
42277131 T-AATTTA
1 TAAATTTA
42277138 AAAATAAACT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
16 6 0.13
17 34 0.72
18 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
TAAATTTATTATAAATT
Found at i:42277096 original size:17 final size:17
Alignment explanation
Indices: 42277074--42277137 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
42277064 AATTTAATTT
42277074 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
42277091 TAAATTTAAATTT-TATG
1 TAAATTTAAATTTATA-A
* *
42277108 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTATAA
42277125 TAAATTT-AATTTA
1 TAAATTTAAATTTA
42277138 AAAATAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.17
17 32 0.80
18 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:42277141 original size:17 final size:17
Alignment explanation
Indices: 42277074--42277145 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
42277064 AATTTAATTT
* *
42277074 TAAATTTAAATTTATAA
1 TAAATTTAAATTAAAAA
** **
42277091 TAAATTTAAATTTTATG
1 TAAATTTAAATTAAAAA
*
42277108 TAAATTTAAATTCAAAA
1 TAAATTTAAATTAAAAA
*
42277125 TAAATTTAATTTAAAAA
1 TAAATTTAAATTAAAAA
42277142 TAAA
1 TAAA
42277146 CTTATATCCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTAAAAA
Found at i:42277946 original size:194 final size:196
Alignment explanation
Indices: 42277650--42278131 Score: 603
Period size: 194 Copynumber: 2.4 Consensus size: 196
42277640 ATCTCTTCAG
* * * * * *
42277650 GAAGCTAACCGTTTTATTACTTTGACCCGCTTCTCAATGTCTCATCAGGAAGTTGGGTTCAAAGA
1 GAAGCTAACC-ATTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGTTCGAAGA
* * *
42277715 TTTGCTCGTATCGAGCGTTGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGACCG
65 TTTGCTCGTATTGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGACCG
42277780 CATCACTTGTTTTAATTCGCTTCTCTAAATCTCCTCAAG-AAGACGAATTCGGTCCA-A-TC-AT
130 CATCACTTGTTTTAATTCGCTTCTCTAAATCTCCTC-AGTAAGACGAATTCGGTCCACAGTCTAT
42277841 CAA
194 CAA
*
42277844 GAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGATTCGAAGA
1 GAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGG-TTCGAAGA
* * * * *
42277909 TTTACTCGCATTGAGCCTGGGTTTGTTTTGGTCTTCTTCTTAGTGTCTCATCAGGAAGATGACCG
65 TTTGCTCGTATTGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGACCG
* ** * *
42277974 CATCTCTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGTTAGACGAATTTGGTCCACTTCTCAGT
130 CATCACTTGTTTTAATTCGCTTCTCTAAATCTCCTCAGTAAGACGAATTCGGTCCA-----CA--
42278039 GTCTTATCAA
188 GTC-TATCAA
* *
42278049 GAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGGTTCGAAG
1 GAAGCTAACCA-TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAG-TTGGGTTCGAAG
*
42278114 GTTTGCTCGTATTTGAGC
64 ATTTGCTCGTA-TTGAGC
42278132 GTTGAGTTAG
Statistics
Matches: 246, Mismatches: 26, Indels: 19
0.85 0.09 0.07
Matches are distributed among these distances:
193 42 0.17
194 122 0.50
200 1 0.00
203 2 0.01
205 16 0.07
206 53 0.22
207 10 0.04
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (196 bp):
GAAGCTAACCATTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGTTCGAAGAT
TTGCTCGTATTGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGACCGC
ATCACTTGTTTTAATTCGCTTCTCTAAATCTCCTCAGTAAGACGAATTCGGTCCACAGTCTATCA
A
Found at i:42278336 original size:39 final size:39
Alignment explanation
Indices: 42278291--42278419 Score: 109
Period size: 39 Copynumber: 3.3 Consensus size: 39
42278281 TCGAATTTTG
*
42278291 GGGGTAAGAGATTGGTTGACGACGATCTGCCCTAGGCTC
1 GGGGTAAAAGATTGGTTGACGACGATCTGCCCTAGGCTC
**** * *
42278330 GGGGTAAAAGATCAAATGGCTG-CAATCTGCCCT-GGCTC
1 GGGGTAAAAGATTGGTTGAC-GACGATCTGCCCTAGGCTC
* * * * * * *
42278368 GTGGTAAGATATTGGTTGATGATGATTTGCCCCAGGCTC
1 GGGGTAAAAGATTGGTTGACGACGATCTGCCCTAGGCTC
42278407 GGGGTAAAAGATT
1 GGGGTAAAAGATT
42278420 AAATGGCTTC
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
37 1 0.02
38 23 0.36
39 39 0.61
40 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (39 bp):
GGGGTAAAAGATTGGTTGACGACGATCTGCCCTAGGCTC
Found at i:42278399 original size:77 final size:79
Alignment explanation
Indices: 42278293--42278459 Score: 239
Period size: 77 Copynumber: 2.1 Consensus size: 79
42278283 GAATTTTGGG
*
42278293 GGTAAGAGATTGGTTGACGACGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTGCAATCT
1 GGTAAGAGATTGGTTGACGACGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGCAATCT
42278358 G-CCC-TGGCTCGT
66 GCCCCTTGGCTCGT
* * * * * *
42278370 GGTAAGATATTGGTTGATGATGATTTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCTTCAATCT
1 GGTAAGAGATTGGTTGACGACGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGCAATCT
*
42278435 GCCCCTTGGCTCGG
66 GCCCCTTGGCTCGT
*
42278449 GGCAAGAGATT
1 GGTAAGAGATT
42278460 AGAATCTCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 59 0.76
78 3 0.04
79 16 0.21
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (79 bp):
GGTAAGAGATTGGTTGACGACGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTGCAATCT
GCCCCTTGGCTCGT
Found at i:42278438 original size:39 final size:39
Alignment explanation
Indices: 42278315--42278460 Score: 104
Period size: 39 Copynumber: 3.7 Consensus size: 39
42278305 GTTGACGACG
* * *
42278315 ATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTGCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCTTCA
* * * * *
42278354 ATCTG-CCCTGGCTCGTGGT--AAGA-T-ATTGGTTGATGA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCT--TCA
*
42278390 TGATTTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCTTCA
1 --ATCTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCTTCA
* * *
42278431 ATCTGCCCCTTGGCTCGGGGCAAGAGATTA
1 ATCTGCCCC-AGGCTCGGGGTAAAAGATTA
42278461 GAATCTCTAT
Statistics
Matches: 79, Mismatches: 18, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
34 5 0.06
36 5 0.06
38 15 0.19
39 25 0.32
40 17 0.22
41 6 0.08
42 1 0.01
43 5 0.06
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAAAGATTAAATGGCTTCA
Found at i:42290956 original size:30 final size:29
Alignment explanation
Indices: 42290873--42291091 Score: 174
Period size: 30 Copynumber: 7.3 Consensus size: 29
42290863 TAATTTCGAG
* *
42290873 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
1 AGTTTAGGGG-CAAAAATGTAATTTTTGGA
** ***
42290903 AG-TTAGGGGTTGAAAACAAAATTTTTTGGA
1 AGTTTAGGGG-CAAAAATGTAA-TTTTTGGA
*
42290933 AGTTTAGGGGCAAAAATTTAATTTTTGGA
1 AGTTTAGGGGCAAAAATGTAATTTTTGGA
* * *
42290962 AGTTTCGTGGTCAAAAAATAG-AAGTTTTGGA
1 AGTTTAG-GGGC-AAAAAT-GTAATTTTTGGA
* **
42290993 AGTTTAGGGGTAAAAATGTAATTTTTCAA
1 AGTTTAGGGGCAAAAATGTAATTTTTGGA
* *
42291022 AGTTTTAGGGTCAAAAATGTAATTTTAGAGA
1 AG-TTTAGGGGCAAAAATGTAATTTTTG-GA
*
42291053 AGTTCAGGGGTC-AAAATGTAATTTTTGGA
1 AGTTTAGGGG-CAAAAATGTAATTTTTGGA
42291082 TAGTTTAGGG
1 -AGTTTAGGG
42291092 ACCTATAGAG
Statistics
Matches: 149, Mismatches: 30, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.01
29 44 0.30
30 72 0.48
31 32 0.21
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
AGTTTAGGGGCAAAAATGTAATTTTTGGA
Found at i:42291087 original size:90 final size:89
Alignment explanation
Indices: 42290873--42291091 Score: 232
Period size: 90 Copynumber: 2.4 Consensus size: 89
42290863 TAATTTCGAG
* **
42290873 AGTTTCGGGGTCAAAAATGGAATTTTTGGAAG-TTAGGGGTTGAAAACAAAATTTTTTGGAAGTT
1 AGTTTCGGGGTCAAAAAT-GAATTTTTGGAAGTTTAGGGGTTAAAAACAAAATTTTTTCAAAGTT
* *
42290937 TAGGGGCAAAAATTTAATTTTTGGA
65 TAGGGGCAAAAATGTAATTTTAGGA
* * ***
42290962 AGTTTCGTGGTCAAAAAATAGAAGTTTTGGAAGTTTAGGGG-TAAAAATGTAA-TTTTTCAAAGT
1 AGTTTCGGGGTC-AAAAAT-GAATTTTTGGAAGTTTAGGGGTTAAAAACAAAATTTTTTCAAAG-
*
42291025 TTTAGGGTCAAAAATGTAATTTTAGAGA
63 TTTAGGGGCAAAAATGTAATTTTAG-GA
42291053 AG-TTCAGGGGTC-AAAATGTAATTTTTGGATAGTTTAGGG
1 AGTTTC-GGGGTCAAAAATG-AATTTTTGGA-AGTTTAGGG
42291092 ACCTATAGAG
Statistics
Matches: 109, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
88 1 0.01
89 33 0.30
90 59 0.54
91 16 0.15
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (89 bp):
AGTTTCGGGGTCAAAAATGAATTTTTGGAAGTTTAGGGGTTAAAAACAAAATTTTTTCAAAGTTT
AGGGGCAAAAATGTAATTTTAGGA
Found at i:42292645 original size:26 final size:28
Alignment explanation
Indices: 42292615--42292685 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
42292605 TCTGCTTTTG
42292615 TATTGATTC-TT-AGAAAAGAGGT-CGTA
1 TATTGATTCTTTAAGAAAAG-GGTCCGTA
*
42292641 TATTG-GTCTTTCAAGAAAAGGGTCCGTA
1 TATTGATTCTTT-AAGAAAAGGGTCCGTA
42292669 TATTGATT-TTTCAAGAA
1 TATTGATTCTTT-AAGAA
42292686 CTCGGGTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 7 0.18
27 3 0.08
28 25 0.66
29 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (28 bp):
TATTGATTCTTTAAGAAAAGGGTCCGTA
Found at i:42292657 original size:28 final size:28
Alignment explanation
Indices: 42292626--42292685 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
42292616 ATTGATTCTT
*
42292626 AGAAAAGAGGT-CGTATATTGGTCTTTCA
1 AGAAAAG-GGTCCGTATATTGATCTTTCA
*
42292654 AGAAAAGGGTCCGTATATTGATTTTTCA
1 AGAAAAGGGTCCGTATATTGATCTTTCA
42292682 AGAA
1 AGAA
42292686 CTCGGGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (28 bp):
AGAAAAGGGTCCGTATATTGATCTTTCA
Found at i:42293075 original size:6 final size:6
Alignment explanation
Indices: 42293058--42293109 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
42293048 TTTGGACATT
* *
42293058 AATTTA ATTTTA AATTTA AATTT- -ATTTA AATTTA AA-ATA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
42293102 AATTTA AA
1 AATTTA AA
42293110 AATAAACTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 9 0.24
6 25 0.66
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:42293084 original size:22 final size:22
Alignment explanation
Indices: 42293056--42293109 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42293046 ACTTTGGACA
* *
42293056 TTAATTTAATTTTAAATTTAAAT
1 TTAATTTAAATTTAAA-ATAAAT
42293079 TT-ATTTAAATTTAAAATAAAT
1 TTAATTTAAATTTAAAATAAAT
42293100 TTAATTTAAA
1 TTAATTTAAA
42293110 AATAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 19 0.68
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTTAAATTTAAAATAAAT
Found at i:42293111 original size:17 final size:17
Alignment explanation
Indices: 42293066--42293115 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
42293056 TTAATTTAAT
**
42293066 TTTAAATTT-AAATTTA
1 TTTAAATTTAAAATAAA
42293082 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
42293099 TTT-AATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
42293116 CTTATATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:42296210 original size:19 final size:19
Alignment explanation
Indices: 42296185--42296222 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42296175 GCCCCGTAAG
42296185 ATTTTTTT-TATAATTTAT
1 ATTTTTTTCTATAATTTAT
*
42296203 ATTTTTTTCTATATTTTAT
1 ATTTTTTTCTATAATTTAT
42296222 A
1 A
42296223 CATATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTTCTATAATTTAT
Found at i:42303539 original size:17 final size:17
Alignment explanation
Indices: 42303513--42303546 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42303503 TAAATTGCCC
42303513 TTTTAATTTTAATTTAA
1 TTTTAATTTTAATTTAA
* *
42303530 TTTTACTTTTTATTTAA
1 TTTTAATTTTAATTTAA
42303547 AATTTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTAATTTAA
Found at i:42304175 original size:16 final size:16
Alignment explanation
Indices: 42304154--42304190 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
42304144 TGTGACTAAC
42304154 TGGACTGATAATACAA
1 TGGACTGATAATACAA
* *
42304170 TGGACTGATAGTACAT
1 TGGACTGATAATACAA
42304186 TGGAC
1 TGGAC
42304191 AAGACCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (16 bp):
TGGACTGATAATACAA
Found at i:42305154 original size:17 final size:18
Alignment explanation
Indices: 42305132--42305167 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
42305122 TAAAATCGGG
42305132 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
42305149 TTGAGAAAATTAATTTAA
1 TTGAGAAAATTAATTTAA
42305167 T
1 T
42305168 AAATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:42315376 original size:17 final size:18
Alignment explanation
Indices: 42315349--42315390 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
42315339 ATTTTTATTT
42315349 ATATATTTTAAATATATAA
1 ATAT-TTTTAAATATATAA
* *
42315368 A-ATTTTTAATTTTATAA
1 ATATTTTTAAATATATAA
42315385 ATATTT
1 ATATTT
42315391 GGATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 13 0.65
18 6 0.30
19 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTAAATATATAA
Found at i:42321458 original size:44 final size:44
Alignment explanation
Indices: 42321409--42321523 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 44
42321399 CCGCAAAAAA
*
42321409 TAGCGGCG-TTTATGCAAAAAAGCGCCGTTGAAAGCCATGTTCTT
1 TAGCGGCGCTTTAT-CAAAAAAGCGCCGCTGAAAGCCATGTTCTT
* * * *
42321453 TAGCGGCGCTTTCTC-CACAAGCGCCGCTGAAGGCCATGTTCTT
1 TAGCGGCGCTTTATCAAAAAAGCGCCGCTGAAAGCCATGTTCTT
* *
42321496 TACCGGCGCTTTATC-CAAAAGCGCCGCT
1 TAGCGGCGCTTTATCAAAAAAGCGCCGCT
42321524 AATATAACAG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 49 0.79
44 9 0.15
45 4 0.06
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (44 bp):
TAGCGGCGCTTTATCAAAAAAGCGCCGCTGAAAGCCATGTTCTT
Found at i:42321478 original size:43 final size:43
Alignment explanation
Indices: 42321426--42321523 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
42321416 GTTTATGCAA
* * *
42321426 AAAAGCGCCGTTGAAAGCCATGTTCTTTAGCGGCGCTTTCTCC
1 AAAAGCGCCGCTGAAAGCCATGTTCTTTACCGGCGCTTTATCC
* *
42321469 ACAAGCGCCGCTGAAGGCCATGTTCTTTACCGGCGCTTTATCC
1 AAAAGCGCCGCTGAAAGCCATGTTCTTTACCGGCGCTTTATCC
42321512 AAAAGCGCCGCT
1 AAAAGCGCCGCT
42321524 AATATAACAG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.24
Consensus pattern (43 bp):
AAAAGCGCCGCTGAAAGCCATGTTCTTTACCGGCGCTTTATCC
Found at i:42321871 original size:24 final size:21
Alignment explanation
Indices: 42321824--42321876 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
42321814 CTTGTAGCCT
* *
42321824 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
*
42321845 CTGCTGCCTCCGCTTGCCTTG
1 CTGCTGCCTCCGCTTGCCTCG
42321866 CTGCTGCCTCC
1 CTGCTGCCTCC
42321877 ACTTTAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.21, T:0.34
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Found at i:42321978 original size:66 final size:66
Alignment explanation
Indices: 42321878--42322019 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 66
42321868 GCTGCCTCCA
*
42321878 CTTTAAGTTGTATGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAACCTCC
1 CTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAACCT-C
42321943 TT
65 TT
* * ** *
42321945 -TTTAAGTTTTA-GATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGTTGCAGCCTC
1 CTTTAAGTTGTATG-TGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAACCTC
42322008 TT
65 TT
42322010 CTTTAAGTTG
1 CTTTAAGTTG
42322020 AGCAATTTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 4 0.06
66 62 0.94
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (66 bp):
CTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGCAACCTCT
T
Found at i:42323583 original size:49 final size:49
Alignment explanation
Indices: 42323405--42323651 Score: 435
Period size: 49 Copynumber: 5.1 Consensus size: 49
42323395 ATTAAAAATT
* * * *
42323405 TTAATATAATTATTTACCTTAATATAATTAAATAATTAAGT-ATTTAAT
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
42323453 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
*
42323502 TTAATATAA-TATTTACTTTAATAAAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
42323550 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
42323599 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
42323648 TTAA
1 TTAA
42323652 ATATTTAATT
Statistics
Matches: 191, Mismatches: 6, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
48 86 0.45
49 105 0.55
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (49 bp):
TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
Found at i:42323663 original size:26 final size:24
Alignment explanation
Indices: 42323484--42323655 Score: 85
Period size: 26 Copynumber: 7.1 Consensus size: 24
42323474 ATATAATTAA
42323484 ATAATTAAATCTTTTAACTT-AAT
1 ATAATTAAATCTTTTAACTTAAAT
** *
42323507 ATAA-TATTTAC-TTTAA-TAAAATT
1 ATAATTAAAT-CTTTTAACTTAAA-T
42323530 AAATAATTAAATCTTTTAACTT-AAT
1 --ATAATTAAATCTTTTAACTTAAAT
** *
42323555 ATAATTATTTAC-TTTAA-TATAATTAA
1 ATAATTAAAT-CTTTTAACT-TAA--AT
42323581 ATAATTAAATCTTTTAACTT-AAT
1 ATAATTAAATCTTTTAACTTAAAT
** *
42323604 ATAATTATTTAC-TTTAA-TATAATTAA
1 ATAATTAAAT-CTTTTAACT-TAA--AT
42323630 ATAATTAAATCTTTTAACTTAAAT
1 ATAATTAAATCTTTTAACTTAAAT
42323654 AT
1 AT
42323656 TTAATTAATC
Statistics
Matches: 109, Mismatches: 18, Indels: 43
0.64 0.11 0.25
Matches are distributed among these distances:
21 1 0.01
22 12 0.11
23 35 0.32
24 7 0.06
25 9 0.08
26 42 0.39
27 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAATTAAATCTTTTAACTTAAAT
Found at i:42326289 original size:15 final size:15
Alignment explanation
Indices: 42326269--42326299 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42326259 TTTGATAGTT
42326269 CAAATTCAGTATTTA
1 CAAATTCAGTATTTA
42326284 CAAATTCAGTATTTA
1 CAAATTCAGTATTTA
42326299 C
1 C
42326300 TCCTATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (15 bp):
CAAATTCAGTATTTA
Found at i:42326576 original size:35 final size:35
Alignment explanation
Indices: 42326530--42326599 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
42326520 TGGTAGAAGG
42326530 TAATACCGATAGGGTTTGCGGCTGTCGGATCGGGA
1 TAATACCGATAGGGTTTGCGGCTGTCGGATCGGGA
*
42326565 TAATATCGATAGGGTTTGCGGCTGTCGGATCGGGA
1 TAATACCGATAGGGTTTGCGGCTGTCGGATCGGGA
42326600 CGAGCAGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (35 bp):
TAATACCGATAGGGTTTGCGGCTGTCGGATCGGGA
Found at i:42326711 original size:22 final size:22
Alignment explanation
Indices: 42326683--42326740 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
42326673 AAGACAACTC
42326683 TGCTTACAGTTTTCCTTCTTGT
1 TGCTTACAGTTTTCCTTCTTGT
*
42326705 TGCTTACAATTTTCCTTCTTGT
1 TGCTTACAGTTTTCCTTCTTGT
42326727 TGCTTACAGTTTTC
1 TGCTTACAGTTTTC
42326741 AAACCCGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (22 bp):
TGCTTACAGTTTTCCTTCTTGT
Found at i:42327028 original size:25 final size:25
Alignment explanation
Indices: 42326999--42327071 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
42326989 TATAATAAAG
42326999 TTTAATTAAATATTATGTTTAATTT
1 TTTAATTAAATATTATGTTTAATTT
* * *
42327024 TTTAAATAATTATTAATG-AT-ATTT
1 TTTAATTAAATATT-ATGTTTAATTT
*
42327048 TATTAAATTAAA-ATAATGTTTAAT
1 T-TT-AATTAAATATTATGTTTAAT
42327072 AAACAGAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
24 8 0.22
25 18 0.50
26 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTAATTAAATATTATGTTTAATTT
Found at i:42327851 original size:17 final size:17
Alignment explanation
Indices: 42327829--42327866 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
42327819 AAATTAACGG
42327829 CGCTTATGGGAAAGCGC
1 CGCTTATGGGAAAGCGC
42327846 CGCTTATGGGAAAGCGC
1 CGCTTATGGGAAAGCGC
42327863 CGCT
1 CGCT
42327867 AATGCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.18
Consensus pattern (17 bp):
CGCTTATGGGAAAGCGC
Found at i:42327962 original size:41 final size:40
Alignment explanation
Indices: 42327853--42328218 Score: 291
Period size: 41 Copynumber: 9.0 Consensus size: 40
42327843 CGCCGCTTAT
*
42327853 GGGAAAGCGCCGCTAATG-CAC-ACCTTTAGCGACGCTTATTA
1 GGGAAAGCGCCGCTAATGAC-CTACCTTTAGCGGCGC-T-TTA
* *
42327894 -GAAAAGCGCCGCTAAATGATCCTACCTTTAGTGGCGCTTTA
1 GGGAAAGCGCCGCT-AATGA-CCTACCTTTAGCGGCGCTTTA
* *
42327935 GGGAAAGCGCCGCTAATGATCATACCTTTAGCGGCGCTTGA
1 GGGAAAGCGCCGCTAATGA-CCTACCTTTAGCGGCGCTTTA
* * * *
42327976 GTGAAAGCACCGCTAATTACCCTACCTTTAGCGGCGATTTA
1 GGGAAAGCGCCGCTAATGA-CCTACCTTTAGCGGCGCTTTA
* * * *
42328017 GAGAAAGCGCCGTTAATGACTTGAACTTTAGCGGCGCTTTA
1 GGGAAAGCGCCGCTAATGACCT-ACCTTTAGCGGCGCTTTA
** * *
42328058 -TCACAAGCGCCGCTAATGACCTGACCTTTAGCTGCACTTGT-
1 GGGA-AAGCGCCGCTAATGACCT-ACCTTTAGCGGCGCTT-TA
42328099 GGGTAAAGCGCCGCTAATGACCCTACCTTTAGCGGCGC-TT-
1 GGG-AAAGCGCCGCTAATGA-CCTACCTTTAGCGGCGCTTTA
** * * *
42328139 GTGTTAAGCGCCGCTAATG-CTTTACCTTTTGCGGCGCATTA
1 G-GGAAAGCGCCGCTAATGAC-CTACCTTTAGCGGCGCTTTA
* * * *
42328180 AGAAAAGCGCCGCTAATG-CTTTACCTTTTGCGGCGCTTT
1 GGGAAAGCGCCGCTAATGAC-CTACCTTTAGCGGCGCTTT
42328219 GTTTCTAAAC
Statistics
Matches: 270, Mismatches: 40, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.00
39 14 0.05
40 68 0.25
41 128 0.47
42 42 0.16
43 17 0.06
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
GGGAAAGCGCCGCTAATGACCTACCTTTAGCGGCGCTTTA
Found at i:42328000 original size:82 final size:81
Alignment explanation
Indices: 42327853--42328217 Score: 332
Period size: 82 Copynumber: 4.5 Consensus size: 81
42327843 CGCCGCTTAT
* * * *
42327853 GGGAAAGCGCCGCTAATG-CACACCTTTAGCGACGCTT-ATTAGAAAAGCGCCGCTAAATGATCC
1 GGGAAAGCGCCGCTAATGACATACCTTTAGCGGCGCTTGAGT-G-AAAGCGCCGCT-AATGACCC
*
42327916 TACCTTTAGTGGCGCTTTA
63 TACCTTTAGCGGCGCTTTA
* *
42327935 GGGAAAGCGCCGCTAATGATCATACCTTTAGCGGCGCTTGAGTGAAAGCACCGCTAATTACCCTA
1 GGGAAAGCGCCGCTAATGA-CATACCTTTAGCGGCGCTTGAGTGAAAGCGCCGCTAATGACCCTA
*
42328000 CCTTTAGCGGCGATTTA
65 CCTTTAGCGGCGCTTTA
* * * * * *
42328017 GAGAAAGCGCCGTTAATGACTTGAACTTTAGCGGCGCTTTA-TCACAAGCGCCGCTAATGA-CCT
1 GGGAAAGCGCCGCTAATGACAT-ACCTTTAGCGGCGCTTGAGTGA-AAGCGCCGCTAATGACCCT
* *
42328080 GACCTTTAGCTGCACTTGT-
64 -ACCTTTAGCGGCGCTT-TA
* * * **
42328099 GGGTAAAGCGCCGCTAATGACCCTACCTTTAGCGGCGCTTGTGT-TAAGCGCCGCTAATG-CTTT
1 GGG-AAAGCGCCGCTAATGA-CATACCTTTAGCGGCGCTTGAGTGAAAGCGCCGCTAATGACCCT
* *
42328162 ACCTTTTGCGGCGCATTA
64 ACCTTTAGCGGCGCTTTA
* * * *
42328180 AGAAAAGCGCCGCTAATG-CTTTACCTTTTGCGGCGCTT
1 GGGAAAGCGCCGCTAATGAC-ATACCTTTAGCGGCGCTT
42328218 TGTTTCTAAA
Statistics
Matches: 234, Mismatches: 36, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
78 1 0.00
79 16 0.07
80 16 0.07
81 20 0.09
82 117 0.50
83 41 0.18
84 21 0.09
85 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (81 bp):
GGGAAAGCGCCGCTAATGACATACCTTTAGCGGCGCTTGAGTGAAAGCGCCGCTAATGACCCTAC
CTTTAGCGGCGCTTTA
Found at i:42334327 original size:16 final size:16
Alignment explanation
Indices: 42334306--42334343 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42334296 CTTTCTATTT
42334306 TTTTCTATCGCTTC-AA
1 TTTTCTATC-CTTCTAA
*
42334322 TTTTCTATCTTTCTAA
1 TTTTCTATCCTTCTAA
42334338 TTTTCT
1 TTTTCT
42334344 TTTCAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTCTATCCTTCTAA
Found at i:42334666 original size:31 final size:32
Alignment explanation
Indices: 42334631--42334699 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
42334621 ATTTTTTTTA
* *
42334631 TCAATTTGGCTCTCAACTTTTT-AAAAAGAGT
1 TCAATTTGACTATCAACTTTTTCAAAAAGAGT
*
42334662 TCAATTTGACTATCAATTTTTTCAAAAAGAGT
1 TCAATTTGACTATCAACTTTTTCAAAAAGAGT
*
42334694 TGAATT
1 TCAATT
42334700 ATTATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (32 bp):
TCAATTTGACTATCAACTTTTTCAAAAAGAGT
Found at i:42334819 original size:16 final size:17
Alignment explanation
Indices: 42334798--42334845 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
42334788 TTTTTTATAT
*
42334798 ATTTTTTGAAATTT-GA
1 ATTTTTTAAAATTTAGA
42334814 A-TTTTTAAAATTTAGA
1 ATTTTTTAAAATTTAGA
42334830 ATATTTTTATAAATTT
1 AT-TTTTTA-AAATTT
42334846 TAAATTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.41
16 4 0.15
18 6 0.22
19 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTTTAAAATTTAGA
Found at i:42337745 original size:12 final size:13
Alignment explanation
Indices: 42337715--42337744 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42337705 CCTAGATCCG
42337715 TTTTTATTGTTCT
1 TTTTTATTGTTCT
*
42337728 TTTTTATTTTTCT
1 TTTTTATTGTTCT
42337741 TTTT
1 TTTT
42337745 AAAAAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTTATTGTTCT
Found at i:42338630 original size:32 final size:32
Alignment explanation
Indices: 42338572--42338632 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
42338562 AAAAATAAAA
42338572 TTTTATTTTATTATTATTATTATTTATTTGAG
1 TTTTATTTTATTATTATTATTATTTATTTGAG
42338604 TTTTA-TTTATTATATATATATT-TTTATTT
1 TTTTATTTTATTAT-TAT-TATTATTTATTT
42338633 TATTTTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 8 0.30
32 15 0.56
33 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (32 bp):
TTTTATTTTATTATTATTATTATTTATTTGAG
Found at i:42339369 original size:96 final size:96
Alignment explanation
Indices: 42339182--42339398 Score: 305
Period size: 96 Copynumber: 2.3 Consensus size: 96
42339172 TACTAAATTT
* *
42339182 GCCGTTGCGACTTAAAT-TTTTCCTTTCATGTCTCTGAGGTACAAGGTTCACTGTTGCGACTTAA
1 GCCGTTGCGACTTAAATCTTTTCCTTTCACGTCTCTGAAGTACAAGGTTCACTGTTGCGACTTAA
* *
42339246 CCTTTTCCTTTGTATTTGTGGTACTGGATTC
66 CCTTTCCCTTTGTATCTGTGGTACTGGATTC
* * **
42339277 GCCGTTACGGCTTAAATCTTTTCCTTT-ACG-CTTCTGAAGTACAAGGTTCGTTGTTGCGACTTA
1 GCCGTTGCGACTTAAATCTTTTCCTTTCACGTC-TCTGAAGTACAAGGTTCACTGTTGCGACTT-
42339340 AACCTTTCCCTTTGTATCTGTGGTACTGGATTC
64 AACCTTTCCCTTTGTATCTGTGGTACTGGATTC
* *
42339373 ACCGTTGCGACTTAAATCTTTCCCTT
1 GCCGTTGCGACTTAAATCTTTTCCTT
42339399 CATATCTTCG
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
94 1 0.01
95 44 0.41
96 62 0.58
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (96 bp):
GCCGTTGCGACTTAAATCTTTTCCTTTCACGTCTCTGAAGTACAAGGTTCACTGTTGCGACTTAA
CCTTTCCCTTTGTATCTGTGGTACTGGATTC
Found at i:42339436 original size:49 final size:49
Alignment explanation
Indices: 42339121--42339462 Score: 204
Period size: 49 Copynumber: 7.1 Consensus size: 49
42339111 ATGTTTTTGC
* * * * * * *
42339121 GGTACTAGATTCGCCGTTGCGGCTTCAAT-TTCCCCTTTCGTGTCTTCAT
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCC-TTCATATCTTCGT
** * * * * *
42339170 GGTACTAAATTTGCCGTTGCGACTTAAATTTTTCCTTTCATGTC-TCTGA
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTC-GT
* * * * * **
42339219 GGTACAAGG-TTCACTGTTGCGACTT-AACCTTTTCCTTTGTAT-TT-GT
1 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * *
42339265 GGTACTGGATTCGCCGTTACGGCTTAAATCTTTTCCTT--TACGCTTC-T
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATA-TCTTCGT
* ** * **
42339312 GAAGTACAAGG-TTCGTTGTTGCGACTTAAACCTTTCCCTTTGTATC-T-GT
1 G--GTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
*
42339361 GGTACTGGATTCACCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * * *
42339410 GGTACTGGATTCGTCGTTGTGGCTTAAATCTTTCCTTTCATATCTTCAT
1 GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
42339459 GGTA
1 GGTA
42339463 ATGAAACCTG
Statistics
Matches: 224, Mismatches: 51, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
45 4 0.02
46 20 0.09
47 48 0.21
48 14 0.06
49 129 0.58
50 7 0.03
51 2 0.01
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (49 bp):
GGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
Found at i:42350225 original size:30 final size:30
Alignment explanation
Indices: 42350171--42350228 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
42350161 TAAAAAACAT
*
42350171 AAAAAAAATTCATTTTTCAATCCATTTTAAA
1 AAAAAAAATTCAATTTTC-ATCCATTTTAAA
42350202 AAAAAAACATTCAATTTTC-TCCATTTT
1 AAAAAAA-ATTCAATTTTCATCCATTTT
42350229 TCTCTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 7 0.28
32 10 0.40
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAAAAAATTCAATTTTCATCCATTTTAAA
Found at i:42351283 original size:14 final size:15
Alignment explanation
Indices: 42351266--42351296 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
42351256 TAATTTTGGA
42351266 TTTGTAAATGGA-TT
1 TTTGTAAATGGACTT
42351280 TTTGTAAATGGACTT
1 TTTGTAAATGGACTT
42351295 TT
1 TT
42351297 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (15 bp):
TTTGTAAATGGACTT
Found at i:42351345 original size:26 final size:25
Alignment explanation
Indices: 42351311--42351372 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
42351301 ATAAAATTTT
42351311 ATTTTATTTTTATTATTT-TTATTTGG
1 ATTTTATTTTTA-TATTTCTT-TTTGG
*
42351337 ATTTTATTTATTATATTTCTTTTTTG
1 ATTTTATTT-TTATATTTCTTTTTGG
42351363 ATTTTATTTT
1 ATTTTATTTT
42351373 CTGGGGTCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 1 0.03
26 27 0.82
27 5 0.15
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (25 bp):
ATTTTATTTTTATATTTCTTTTTGG
Found at i:42352342 original size:29 final size:32
Alignment explanation
Indices: 42352277--42352342 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
42352267 AAATGCAACT
**
42352277 ATATGTCTTATTTATTTATTTATTATTGATATT
1 ATATGTCTTATTTATTTATTTATTATT-ATAAA
42352310 ATATGTCTTATTTATTTA-TTATT-TT-TAAA
1 ATATGTCTTATTTATTTATTTATTATTATAAA
42352339 ATAT
1 ATAT
42352343 CAATTAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.19
31 2 0.06
32 5 0.16
33 18 0.58
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (32 bp):
ATATGTCTTATTTATTTATTTATTATTATAAA
Found at i:42361456 original size:30 final size:30
Alignment explanation
Indices: 42361420--42361541 Score: 172
Period size: 30 Copynumber: 4.1 Consensus size: 30
42361410 AACAGGTTCA
42361420 CACTTTGGCTTACTATCTTTAACAAGCTCG
1 CACTTTGGCTTACTATCTTTAACAAGCTCG
* * *
42361450 CACTTTGGCTTACTGTCTTTGACAGGCTCG
1 CACTTTGGCTTACTATCTTTAACAAGCTCG
* * *
42361480 TACTTTGGCTTACTGTCTTTAACAAGCTTG
1 CACTTTGGCTTACTATCTTTAACAAGCTCG
* *
42361510 CACTTTGGCTTACTATCTTTGACAGGCTCG
1 CACTTTGGCTTACTATCTTTAACAAGCTCG
42361540 CA
1 CA
42361542 TTCTTTTTGC
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (30 bp):
CACTTTGGCTTACTATCTTTAACAAGCTCG
Found at i:42361485 original size:60 final size:60
Alignment explanation
Indices: 42361421--42361539 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
42361411 ACAGGTTCAC
*
42361421 ACTTTGGCTTACTATCTTTAACAAGCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCGT
1 ACTTTGGCTTACTATCTTTAACAAGCTCGCACTTTGGCTTACTATCTTTGACAGGCTCGT
* *
42361481 ACTTTGGCTTACTGTCTTTAACAAGCTTGCACTTTGGCTTACTATCTTTGACAGGCTCG
1 ACTTTGGCTTACTATCTTTAACAAGCTCGCACTTTGGCTTACTATCTTTGACAGGCTCG
42361540 CATTCTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (60 bp):
ACTTTGGCTTACTATCTTTAACAAGCTCGCACTTTGGCTTACTATCTTTGACAGGCTCGT
Found at i:42361529 original size:90 final size:89
Alignment explanation
Indices: 42361377--42361541 Score: 242
Period size: 90 Copynumber: 1.8 Consensus size: 89
42361367 CAGGCTCACA
* *
42361377 CTTTGACAGACTCGTACTTTGCTTGCTGTCTTCAACAGGTTCACACTTTGGCTTACTATCTTTAA
1 CTTTGACAGACTCGTACTTTGCTTACTGTCTTCAACAGCTTCACACTTTGGCTTACTATCTTTAA
42361442 CAAGCTCGCACTTTGGCTTACTGT
66 CAAGCTCGCACTTTGGCTTACTGT
* * *
42361466 CTTTGACAGGCTCGTACTTTGGCTTACTGTCTTTAACAAGCTT-GCACTTTGGCTTACTATCTTT
1 CTTTGACAGACTCGTACTTT-GCTTACTGTCTTCAAC-AGCTTCACACTTTGGCTTACTATCTTT
* *
42361530 GACAGGCTCGCA
64 AACAAGCTCGCA
42361542 TTCTTTTTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
89 19 0.28
90 44 0.66
91 4 0.06
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (89 bp):
CTTTGACAGACTCGTACTTTGCTTACTGTCTTCAACAGCTTCACACTTTGGCTTACTATCTTTAA
CAAGCTCGCACTTTGGCTTACTGT
Found at i:42363073 original size:10 final size:10
Alignment explanation
Indices: 42363058--42363083 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42363048 CTTGTAGGTT
42363058 TAGCAGTTGA
1 TAGCAGTTGA
42363068 TAGCAGTTGA
1 TAGCAGTTGA
42363078 TAGCAG
1 TAGCAG
42363084 AACTTGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (10 bp):
TAGCAGTTGA
Found at i:42365856 original size:37 final size:37
Alignment explanation
Indices: 42365800--42365873 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
42365790 ACCCCTTAAC
*
42365800 TTTTACATATTATACCAATTTAATCATAATTTTAAAA
1 TTTTACAAATTATACCAATTTAATCATAATTTTAAAA
*
42365837 TTTTACAAATTAT-CTCAATTTAATCTTAATTTTAAAA
1 TTTTACAAATTATAC-CAATTTAATCATAATTTTAAAA
42365874 AATTCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 33 0.97
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (37 bp):
TTTTACAAATTATACCAATTTAATCATAATTTTAAAA
Found at i:42373457 original size:14 final size:14
Alignment explanation
Indices: 42373438--42373467 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42373428 TTTTGACGTA
42373438 GTCAAACATCTTTT
1 GTCAAACATCTTTT
42373452 GTCAAACATCTTTT
1 GTCAAACATCTTTT
42373466 GT
1 GT
42373468 AACTAGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (14 bp):
GTCAAACATCTTTT
Found at i:42380432 original size:29 final size:29
Alignment explanation
Indices: 42380392--42380450 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
42380382 TCGTGGAAGA
* * *
42380392 GGTGGAGAACTTGTTCGTTGAGAGTTCGT
1 GGTGAAGAACTTGTTCATTGAGAATTCGT
42380421 GGTGAAGAACTTGTTCATTGAGAATTCGT
1 GGTGAAGAACTTGTTCATTGAGAATTCGT
42380450 G
1 G
42380451 TCAACGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTGAGAATTCGT
Found at i:42380562 original size:5 final size:5
Alignment explanation
Indices: 42380552--42380580 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42380542 ACTACACTTC
42380552 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
42380581 GATTAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:42383138 original size:19 final size:21
Alignment explanation
Indices: 42383093--42383138 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
42383083 TTTTTATAAT
42383093 TTTTTAAAAATATAAATTTTGA
1 TTTTTAAAAATAT-AATTTTGA
*
42383115 ATTTTAAAAAT-T-ATTTTGA
1 TTTTTAAAAATATAATTTTGA
42383134 TTTTT
1 TTTTT
42383139 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTAAAAATATAATTTTGA
Found at i:42383230 original size:9 final size:9
Alignment explanation
Indices: 42383216--42383245 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42383206 AAACCAATCT
42383216 ATTATTCGA
1 ATTATTCGA
42383225 ATTATTCGA
1 ATTATTCGA
*
42383234 GTTATTCGA
1 ATTATTCGA
42383243 ATT
1 ATT
42383246 GTGAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
ATTATTCGA
Found at i:42392434 original size:21 final size:20
Alignment explanation
Indices: 42392387--42392440 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
42392377 ATACTAGTTC
42392387 TACTACCGATACAAGTATTA
1 TACTACCGATACAAGTATTA
*
42392407 TTTCTACCGATACAAGTCATGTA
1 -TACTACCGATACAAGT-AT-TA
42392430 -ACTACCGATAC
1 TACTACCGATAC
42392441 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.86
22 2 0.07
23 2 0.07
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (20 bp):
TACTACCGATACAAGTATTA
Found at i:42396230 original size:27 final size:27
Alignment explanation
Indices: 42396169--42396326 Score: 156
Period size: 27 Copynumber: 5.9 Consensus size: 27
42396159 ACTTCATAAG
*
42396169 TCGTCACAAAGGTTATTCTTTCTGAGT
1 TCGTCACAAAGGTTATTCTTTCAGAGT
* * * *
42396196 TC-TCCACAAGGGTTAGTCTCTCAAAGT
1 TCGT-CACAAAGGTTATTCTTTCAGAGT
* * *
42396223 TCGTCACAAAGGCTATTCTTTCATATT
1 TCGTCACAAAGGTTATTCTTTCAGAGT
* * *
42396250 TCGTCACAAAGGCTACTCTTTTAGAGT
1 TCGTCACAAAGGTTATTCTTTCAGAGT
* * *
42396277 TCGTCAAAAAAGTTATTCTCTCAGAGT
1 TCGTCACAAAGGTTATTCTTTCAGAGT
* *
42396304 TCGTCACAAAGGCTATTTTTTCA
1 TCGTCACAAAGGTTATTCTTTCA
42396327 TGACATGTTT
Statistics
Matches: 103, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 1 0.01
27 101 0.98
28 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (27 bp):
TCGTCACAAAGGTTATTCTTTCAGAGT
Found at i:42398211 original size:80 final size:80
Alignment explanation
Indices: 42398075--42398232 Score: 212
Period size: 80 Copynumber: 2.0 Consensus size: 80
42398065 AAAAACATGA
* * * ** *
42398075 GCTTAATTGCTTTTTTTTAAATAGTTTGAAGGCCTTTTTTATGCATTTTAGCAGTTCAAGTATCC
1 GCTTAAATGCTTTTTTTAAAATAGTTTGAAGGCCTTTTTAATGCATTTTAAAAGTTCAAATA-CC
*
42398140 AATTTAGTGCAAAATG
65 AATTGAGTGCAAAATG
*
42398156 GCTTAAATGCTTTTTTTGAAAAT-GTTT-AAGGGCTTTTTAATGCATTTTAAAAGTTCAAATACC
1 GCTTAAATGCTTTTTTT-AAAATAGTTTGAAGGCCTTTTTAATGCATTTTAAAAGTTCAAATACC
42398219 AATTGAGTGCAAAA
65 AATTGAGTGCAAAA
42398233 AAAAAAAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 15 0.22
80 29 0.43
81 20 0.29
82 4 0.06
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (80 bp):
GCTTAAATGCTTTTTTTAAAATAGTTTGAAGGCCTTTTTAATGCATTTTAAAAGTTCAAATACCA
ATTGAGTGCAAAATG
Found at i:42402197 original size:24 final size:24
Alignment explanation
Indices: 42402169--42402223 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
42402159 TCTTTCTAAA
*
42402169 ATATTTAGTATTTATTAATATAAT
1 ATATTTAGCATTTATTAATATAAT
*
42402193 ATATTTAGCATTTATTAGTATAAT
1 ATATTTAGCATTTATTAATATAAT
*
42402217 TTATTTA
1 ATATTTA
42402224 ACGTACGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (24 bp):
ATATTTAGCATTTATTAATATAAT
Found at i:42404782 original size:18 final size:18
Alignment explanation
Indices: 42404761--42404829 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
42404751 TAATGCTATT
42404761 ACGAGCCAGTATGCTTAA
1 ACGAGCCAGTATGCTTAA
* * *
42404779 ACGAGCTAGTACGCTCAA
1 ACGAGCCAGTATGCTTAA
*
42404797 ACGAGCTAGTATGCTTAA
1 ACGAGCCAGTATGCTTAA
42404815 ACGAGCCAGTATGCT
1 ACGAGCCAGTATGCT
42404830 ATTTCTTCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (18 bp):
ACGAGCCAGTATGCTTAA
Found at i:42406804 original size:36 final size:36
Alignment explanation
Indices: 42406760--42407023 Score: 327
Period size: 36 Copynumber: 7.4 Consensus size: 36
42406750 TGATGATTGT
*
42406760 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
* * *
42406796 TGAGACAGTAAATATGT-AGGTATGTTATTCAAGTCA
1 TGTGACAGTAAATATGTGA-GTATGTTATTCATGCCA
* * *
42406832 TGTGACAGTAAATGTGT-AGTATGTTACTCATGACA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
42406867 TGTGACAGTAAATATGTG-GTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
* * * *
42406902 TGTGACAGTAAATGTGTGGGAATTTTATTCATGCCA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
* * *
42406938 TGAGATAGTAAATATGTAAGTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
* * *
42406974 TGTGACAATAAATATGTGGGCATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
*
42407010 TGTGATAGTGAAAT
1 TGTGACAGT-AAAT
42407024 GTTGTGCTAA
Statistics
Matches: 194, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
35 63 0.32
36 127 0.65
37 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (36 bp):
TGTGACAGTAAATATGTGAGTATGTTATTCATGCCA
Found at i:42407018 original size:72 final size:72
Alignment explanation
Indices: 42406760--42407011 Score: 364
Period size: 72 Copynumber: 3.5 Consensus size: 72
42406750 TGATGATTGT
42406760 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATT
1 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATT
* *
42406825 CAAGTCA
66 CATGCCA
* * *
42406832 TGTGACAGTAAATGTGT-AGTATGTTACTCATGACATGTGACAGTAAATATGT-GGTATGTTATT
1 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATT
42406895 CATGCCA
66 CATGCCA
* * * * *
42406902 TGTGACAGTAAATGTGTGGGAATTTTATTCATGCCATGAGATAGTAAATATGTAAGTATGTTATT
1 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATT
42406967 CATGCCA
66 CATGCCA
* * * *
42406974 TGTGACAATAAATATGTGGGCATGTTATTCATGCCATG
1 TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATG
42407012 TGATAGTGAA
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
70 33 0.20
71 60 0.37
72 68 0.42
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (72 bp):
TGTGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATT
CATGCCA
Found at i:42407059 original size:142 final size:141
Alignment explanation
Indices: 42406762--42407023 Score: 335
Period size: 142 Copynumber: 1.8 Consensus size: 141
42406752 ATGATTGTTG
* * * *
42406762 TGACAGTAAATGTGTGAGTATGTTATTCATGCCATGAGACAGTAAATATGTAGGTATGTTATTCA
1 TGACAGTAAATGTGTGGGAATTTTATTCATGCCATGAGACAGTAAATATGTAAGTATGTTATTCA
* * * * *
42406827 AGTCATGTGACAGTAAATGTGTAGTATGTTACTCATGACATGTGACAGTAAATATGTGGTATGTT
66 AGCCATGTGACAATAAATATGTAGCATGTTACTCATGACATGTGACAGTAAATATGT-GTATGCT
* * *
42406892 ATTCATGCCATG
130 AATCATGCAATA
*
42406904 TGACAGTAAATGTGTGGGAATTTTATTCATGCCATGAGATAGTAAATATGTAAGTATGTTATTCA
1 TGACAGTAAATGTGTGGGAATTTTATTCATGCCATGAGACAGTAAATATGTAAGTATGTTATTCA
* * * * *
42406969 TGCCATGTGACAATAAATATGTGGGCATGTTATTCATGCCATGTGATAGTGAAAT
66 AGCCATGTGACAATAAATATGT-AGCATGTTACTCATGACATGTGACAGT-AAAT
42407024 GTTGTGCTAA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
142 78 0.75
143 22 0.21
144 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (141 bp):
TGACAGTAAATGTGTGGGAATTTTATTCATGCCATGAGACAGTAAATATGTAAGTATGTTATTCA
AGCCATGTGACAATAAATATGTAGCATGTTACTCATGACATGTGACAGTAAATATGTGTATGCTA
ATCATGCAATA
Found at i:42408681 original size:19 final size:19
Alignment explanation
Indices: 42408627--42408681 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
42408617 TATAAAAGTC
* *
42408627 TACAAGAAAATATGGATAAA
1 TACAAGAATATAT-GAAAAA
*
42408647 TA-AAGCATATAGTGAAAAA
1 TACAAGAATATA-TGAAAAA
42408666 TACAAGAATATATGAA
1 TACAAGAATATATGAA
42408682 TTTTGTAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (19 bp):
TACAAGAATATATGAAAAA
Found at i:42409149 original size:28 final size:28
Alignment explanation
Indices: 42409109--42409190 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
42409099 TTACGTGCAT
*
42409109 TTAGCACTTTGTGTGTTCTCTGTTCTGA
1 TTAGCACTTTGTGTGCTCTCTGTTCTGA
*
42409137 TTAGCACTTTGTGTGCTCTCTGTTCCGA
1 TTAGCACTTTGTGTGCTCTCTGTTCTGA
42409165 TTAGCACTTTGTGTGCTCTCTGTTCT
1 TTAGCACTTTGTGTGCTCTCTGTTCT
42409191 ATAATAGCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.48
Consensus pattern (28 bp):
TTAGCACTTTGTGTGCTCTCTGTTCTGA
Found at i:42409209 original size:28 final size:27
Alignment explanation
Indices: 42409109--42409202 Score: 134
Period size: 28 Copynumber: 3.3 Consensus size: 27
42409099 TTACGTGCAT
*
42409109 TTAGCACTTTGTGTGTTCTCTGTTCTGA
1 TTAGCACTTTGTGTGCTCTCTGTTCT-A
*
42409137 TTAGCACTTTGTGTGCTCTCTGTTCCGA
1 TTAGCACTTTGTGTGCTCTCTGTT-CTA
42409165 TTAGCACTTTGTGTGCTCTCTGTTCTA
1 TTAGCACTTTGTGTGCTCTCTGTTCTA
42409192 TAATAGCACTT
1 T--TAGCACTT
42409203 CGGTGCTTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
27 3 0.05
28 48 0.80
29 9 0.15
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (27 bp):
TTAGCACTTTGTGTGCTCTCTGTTCTA
Found at i:42410814 original size:23 final size:23
Alignment explanation
Indices: 42410419--42410807 Score: 460
Period size: 23 Copynumber: 17.0 Consensus size: 23
42410409 ATTAAATGTG
*
42410419 TTAAATATTAATGTGATTTATAC
1 TTAAATATTAATGTGATTTATGC
* *
42410442 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
42410465 TTAAA-AGTTAATATGATTTATGT
1 TTAAATA-TTAATGTGATTTATGC
* **
42410488 TTAAATATTAATGTGATTTGTAA
1 TTAAATATTAATGTGATTTATGC
*
42410511 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
** *
42410534 TTAAATATTAATAAGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
42410557 TTAAATATTGATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* **
42410580 TTAAATATTAATGTGGTTTATTA
1 TTAAATATTAATGTGATTTATGC
*
42410603 TTAAATA-TAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
42410625 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
42410648 TTAAATATTAATGTGACTTATGC
1 TTAAATATTAATGTGATTTATGC
* * *
42410671 TTAAATGTTAATATGACTTATGC
1 TTAAATATTAATGTGATTTATGC
42410694 TTAAA-AGTTAATGTGATTTATGC
1 TTAAATA-TTAATGTGATTTATGC
* **
42410717 TTAAATATTAATGTGATTTGTAT
1 TTAAATATTAATGTGATTTATGC
* * *
42410740 TTAACTGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
42410763 TTAAATATTAATGTAATCTATGC
1 TTAAATATTAATGTGATTTATGC
*
42410786 TTAAATATTAATATGATTTATG
1 TTAAATATTAATGTGATTTATG
42410808 TGTAAATGGA
Statistics
Matches: 312, Mismatches: 49, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.06
23 292 0.94
24 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:42415282 original size:14 final size:14
Alignment explanation
Indices: 42415263--42415293 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42415253 GAAAATAATT
42415263 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
42415277 TTTAATTAATTAAA
1 TTTAATTAAATAAA
42415291 TTT
1 TTT
42415294 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:42415287 original size:9 final size:9
Alignment explanation
Indices: 42415264--42415306 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
42415254 AAAATAATTT
42415264 TTAATTAAA
1 TTAATTAAA
* *
42415273 TAAATTTAA
1 TTAATTAAA
42415282 TTAATTAAA
1 TTAATTAAA
**
42415291 TTTTTTAAA
1 TTAATTAAA
42415300 TTAATTA
1 TTAATTA
42415307 CAACTAAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTAATTAAA
Found at i:42416599 original size:21 final size:23
Alignment explanation
Indices: 42416575--42416626 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
42416565 AAACTCCATT
*
42416575 AAAAGAAATGGAGAAG-AG-AGA
1 AAAAGAAAGGGAGAAGCAGAAGA
* *
42416596 AAAATAGAGGGAGAAGCAGAAGA
1 AAAAGAAAGGGAGAAGCAGAAGA
*
42416619 GAAAGAAA
1 AAAAGAAA
42416627 AAAAAAGAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 13 0.57
22 2 0.09
23 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.33, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGGGAGAAGCAGAAGA
Found at i:42417063 original size:34 final size:34
Alignment explanation
Indices: 42417010--42417112 Score: 136
Period size: 34 Copynumber: 3.0 Consensus size: 34
42417000 GGATGTTCAA
*
42417010 CCTTTCATCTTTTAACCTTCCATTTTCCTTAACTT
1 CCTTTGATC-TTTAACCTTCCATTTTCCTTAACTT
* *
42417045 CCTTTGATCTTTAACCTTCCATCTTCCTTAACCT
1 CCTTTGATCTTTAACCTTCCATTTTCCTTAACTT
* *
42417079 CCCTTGATCTTTAACCTTTCATCTTT-CTTAACTT
1 CCTTTGATCTTTAACCTTCCAT-TTTCCTTAACTT
42417113 TTCATAGTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 50 0.83
35 10 0.17
ACGTcount: A:0.17, C:0.32, G:0.02, T:0.49
Consensus pattern (34 bp):
CCTTTGATCTTTAACCTTCCATTTTCCTTAACTT
Found at i:42417075 original size:17 final size:17
Alignment explanation
Indices: 42417008--42417110 Score: 61
Period size: 17 Copynumber: 6.2 Consensus size: 17
42416998 ATGGATGTTC
*
42417008 AACCTTTCATCTT--TT
1 AACCTTCCATCTTCCTT
*
42417023 AACCTTCCATTTTCCTT
1 AACCTTCCATCTTCCTT
* *
42417040 AA-CTTCC-TTTGATCTTT
1 AACCTTCCATCT--TCCTT
42417057 AACCTTCCATCTTCCTT
1 AACCTTCCATCTTCCTT
* * ** *
42417074 AACCTCCCTTGATCTTT
1 AACCTTCCATCTTCCTT
* *
42417091 AACCTTTCATCTTTCTT
1 AACCTTCCATCTTCCTT
42417108 AAC
1 AAC
42417111 TTTTCATAGT
Statistics
Matches: 65, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
15 14 0.22
16 5 0.08
17 39 0.60
18 5 0.08
19 2 0.03
ACGTcount: A:0.19, C:0.32, G:0.02, T:0.47
Consensus pattern (17 bp):
AACCTTCCATCTTCCTT
Found at i:42418365 original size:24 final size:24
Alignment explanation
Indices: 42418327--42418374 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42418317 CACACTAGTA
* *
42418327 GTCGTGGTCGAGGACATGGGCGTG
1 GTCGTGATCGAGGACATGGACGTG
* *
42418351 GTCGTGATCGTGGACGTGGACGTG
1 GTCGTGATCGAGGACATGGACGTG
42418375 AACGAGGTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.48, T:0.23
Consensus pattern (24 bp):
GTCGTGATCGAGGACATGGACGTG
Found at i:42423143 original size:19 final size:20
Alignment explanation
Indices: 42423119--42423161 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
42423109 AAACCCAAAT
*
42423119 AAAAAAAGAAG-AACAAAAC
1 AAAAAAAGAAGAAAAAAAAC
42423138 AAAAAAAGAAGAAAAAAAAC
1 AAAAAAAGAAGAAAAAAAAC
42423158 AAAA
1 AAAA
42423162 CAAAAAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAGAAAAAAAAC
Found at i:42425724 original size:95 final size:95
Alignment explanation
Indices: 42425528--42425846 Score: 456
Period size: 95 Copynumber: 3.4 Consensus size: 95
42425518 AAGGGAAAAG
* * *
42425528 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATAAAGCTTT-AAATGTC-ATTTTTTTTATCC
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAA-TTTTCAAATGTCAATTTTTTTTATCC
42425591 TCTTGAAGTTAT-GTTAAA-ATTGGATAATGAA
65 TCTTGAAGTTATAG-TAAAGA-TGGATAATGAA
*
42425622 TCTTCATCTCTCTTAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTTTTTTTATCCT
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTTTTTTTATCCT
42425687 CTTGAAGTTATAGTAAAGATGGATAATGAA
66 CTTGAAGTTATAGTAAAGATGGATAATGAA
*
42425717 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTTAA---TTTTTATCCT
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTTTTTTTATCCT
* *
42425779 CTTGAAGTTATAGTAAAGATGGATAAAGAG
66 CTTGAAGTTATAGTAAAGATGGATAATGAA
* * *
42425809 TCTTTATCTCTCTGAAATTGA-AGTAAGAGTAAGATGAA
1 TCTTCATCTCTCTGAAGTT-ATAGTAAGAGCAAGATGAA
42425847 GCACCAACAT
Statistics
Matches: 209, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
92 71 0.34
93 4 0.02
94 42 0.20
95 90 0.43
96 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (95 bp):
TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTTTTTTTATCCT
CTTGAAGTTATAGTAAAGATGGATAATGAA
Found at i:42425869 original size:92 final size:92
Alignment explanation
Indices: 42425773--42426987 Score: 1720
Period size: 92 Copynumber: 13.2 Consensus size: 92
42425763 TGTTAATTTT
* * * * * *
42425773 TATCCTCTTGAAGTT-ATAGTAAAGATGGATAA-AGAGTCTTTATCTCTCTGAAATTGAAGTAAG
1 TATCCTCTTGAAATTGA-AGTAGAGCTGGATAACA-AGCCTTTGTCCCTCTGAAATTGAAGTAAG
*
42425836 AG-TAAGATGAAGCACCAACATCATTTTCC
64 AGCT-AGATAAAGCACCAACATCATTTTCC
* *
42425865 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
42425930 CTAGATAAAGCACCAACATCATTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42425957 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
* * *
42426022 CAAGATGAAGCACCGACATC-TTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
*
42426048 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
42426113 CTAGATAAAGCACCAACATCATTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* * * *
42426140 TATCCTGTTGAAATTGAAGTAGAGTTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
*
42426205 CTAGATAAAGCACCAACATCATTTTTC
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42426232 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
* * *
42426297 CAAGATGAAGCACCGACATC-TTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42426323 TATCCTCTTGAAATTGAAGTAGAGCTAGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
42426388 CTAGATAAAGCACCAACATCATTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* * *
42426415 TAT-CTCTTTAAATTGAAGTAGAGCTGGATATCAAGACTTTGTCCCTCTGAAATTGAAG--AGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
42426477 CTAGATAAAGCACCAACATCATTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42426504 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
42426569 CTAGATAAAGCACCAACAT--TTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42426594 TATCCTCTTGAAATTGAAGTACAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
* * **
42426659 CAAGATGAAGCACTGACATC-TTTTCC
66 CTAGATAAAGCACCAACATCATTTTCC
* * *
42426685 TATCCTCTTGAAATTGAATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGAAATTGAA
1 TATCCTCTTG--A---AATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCC--TCTGAAATTGAA
*
42426750 GTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
59 GTAAGAGCTAGATAAAGCA-CCAACATCATTTTCC
* *
42426785 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
* * * *
42426850 CAAGATGAAGCACCGACATC-TTTTCT
66 CTAGATAAAGCACCAACATCATTTTCC
* *
42426876 TATTCTCTTGAAATTGATTGAGGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
1 TATCCTCTTGAAATTGA---A-GTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTA
* * *
42426941 AGAGCAAGATGAAGCACCGACATC-TTTTCC
62 AGAGCTAGATAAAGCACCAACATCATTTTCC
42426971 TATCCTC-TGAAATTGAA
1 TATCCTCTTGAAATTGAA
42426988 TAAGAGCAAG
Statistics
Matches: 1027, Mismatches: 74, Indels: 45
0.90 0.06 0.04
Matches are distributed among these distances:
89 34 0.03
90 136 0.13
91 258 0.25
92 364 0.35
93 32 0.03
94 10 0.01
95 110 0.11
96 32 0.03
98 29 0.03
99 6 0.01
100 16 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (92 bp):
TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
CTAGATAAAGCACCAACATCATTTTCC
Found at i:42426110 original size:183 final size:183
Alignment explanation
Indices: 42425773--42426987 Score: 1714
Period size: 183 Copynumber: 6.6 Consensus size: 183
42425763 TGTTAATTTT
* * * * * *
42425773 TATCCTCTTGAAGTT-ATAGTAAAGATGGATAA-AGAGTCTTTATCTCTCTGAAATTGAAGTAAG
1 TATCCTCTTGAAATTGA-AGTAGAGCTGGATAACA-AGACTTTGTCCCTCTGAAATTGAAGTAAG
* *
42425836 AG-TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAA
64 AGCT-AGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAA
*
42425900 GACTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCC
128 GACTTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATC-TTTTCC
* * *
42425957 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* * *
42426022 CAAGATGAAGCACCGACATC-TTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
66 CTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
*
42426086 TTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCC
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATC-TTTTCC
* * *
42426140 TATCCTGTTGAAATTGAAGTAGAGTTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* * *
42426205 CTAGATAAAGCACCAACATCATTTTTCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCC
66 CTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
* * *
42426270 TTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGCACCGACATCTTTTCC
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATCTTTTCC
*
42426323 TATCCTCTTGAAATTGAAGTAGAGCTAGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* *
42426388 CTAGATAAAGCACCAACATCATTTTCCTAT-CTCTTTAAATTGAAGTAGAGCTGGATATCAAGAC
66 CTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
*
42426452 TTTGTCCCTCTGAAATTGAAG--AGAGCTAGATAAAGCACCAACATCATTTTCC
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATC-TTTTCC
*
42426504 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* *
42426569 CTAGATAAAGCACCAACAT--TTTTCCTATCCTCTTGAAATTGAAGTACAGCTGGATAACAAGCC
66 CTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
* * **
42426632 TTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGCACTGACATCTTTTCC
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATCTTTTCC
* * * *
42426685 TATCCTCTTGAAATTGAATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGAAATTGAA
1 TATCCTCTTG--A---AATTGAAGTAGAGCTGGATAACAAGACTTTGTCCC--TCTGAAATTGAA
* *
42426750 GTAAGAGCTAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT
59 GTAAGAGCTAGATAAAGCA-CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGAT
* * * * *
42426815 AACAAGCCTTTTTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGCACCGACATCTTTTCT
123 AACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATCTTTTCC
* * *
42426876 TATTCTCTTGAAATTGATTGAGGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
1 TATCCTCTTGAAATTGA---A-GTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTA
* * *
42426941 AGAGCAAGATGAAGCACCGACATC-TTTTCCTATCCTC-TGAAATTGAA
62 AGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAA
42426988 TAAGAGCAAG
Statistics
Matches: 940, Mismatches: 69, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
179 9 0.01
180 71 0.08
181 104 0.11
182 70 0.07
183 270 0.29
184 156 0.17
185 12 0.01
186 50 0.05
187 6 0.01
188 58 0.06
189 8 0.01
190 25 0.03
191 101 0.11
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (183 bp):
TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
CTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGAC
TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATAAAGCACCAACATCTTTTCC
Found at i:42426130 original size:275 final size:275
Alignment explanation
Indices: 42425773--42426987 Score: 1865
Period size: 275 Copynumber: 4.4 Consensus size: 275
42425763 TGTTAATTTT
* * * * * *
42425773 TATCCTCTTGAAGTT-ATAGTAAAGATGGATAA-AGAGTCTTTATCTCTCTGAAATTGAAGTAAG
1 TATCCTCTTGAAATTGA-AGTAGAGCTGGATAACA-AGACTTTGTCCCTCTGAAATTGAAGTAAG
42425836 AG-TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAA
64 AGCT-AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAA
42425900 GACTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCT
128 GACTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCT
42425965 TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGA
193 TGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGA
42426030 AGCACCGACATCTTTTCC
258 AGCACCGACATCTTTTCC
42426048 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* * *
42426113 CTAGATAAAGCACCAACATCATTTTCCTATCCTGTTGAAATTGAAGTAGAGTTGGATATCAAGAC
66 CTAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
*
42426178 TTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTTCTATCCTCTTGA
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGA
42426243 AATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGC
196 AATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGC
42426308 ACCGACATCTTTTCC
261 ACCGACATCTTTTCC
*
42426323 TATCCTCTTGAAATTGAAGTAGAGCTAGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* *
42426388 CTAGATAAAGCACCAACATCATTTTCCTAT-CTCTTTAAATTGAAGTAGAGCTGGATATCAAGAC
66 CTAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
42426452 TTTGTCCCTCTGAAATTGAAG--AGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGA
131 TTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGA
* * * * * *
42426515 AATTGAAGTAGAGCTGGATATCAAGACTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGC
196 AATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGC
*
42426580 ACCAACAT-TTTTCC
261 ACCGACATCTTTTCC
* * *
42426594 TATCCTCTTGAAATTGAAGTACAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
* ** * *
42426659 CAAGATGAAGCACTGACATC-TTTTCCTATCCTCTTGAAATTGAATTGAAGTAAAGCTGGATAAC
66 CTAGATGAAGCACCAACATCATTTTCCTATCCTCTTG--A---AATTGAAGTAGAGCTGGATATC
* * * *
42426723 AAGCCTTTTTCCCTTTTTGAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCCTAT
126 AAGACTTTGTCCC--TCTGAAATTGAAGTAAGAGCTAGATAAAGCA-CCAACATCATTTTCCTAT
**
42426788 CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTCTGAAATTGAAGTAAGAGCAA
188 CCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAA
*
42426853 GATGAAGCACCGACATCTTTTCT
253 GATGAAGCACCGACATCTTTTCC
* * *
42426876 TATTCTCTTGAAATTGATTGAGGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTA
1 TATCCTCTTGAAATTGA---A-GTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTA
* *
42426941 AGAGCAAGATGAAGCACCGACATC-TTTTCCTATCCTC-TGAAATTGAA
62 AGAGCTAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAA
42426988 TAAGAGCAAG
Statistics
Matches: 871, Mismatches: 50, Indels: 33
0.91 0.05 0.03
Matches are distributed among these distances:
270 9 0.01
271 88 0.10
272 107 0.12
273 1 0.00
274 52 0.06
275 353 0.41
276 34 0.04
278 12 0.01
280 23 0.03
281 91 0.10
282 21 0.02
283 1 0.00
285 3 0.00
286 76 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (275 bp):
TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGACTTTGTCCCTCTGAAATTGAAGTAAGAG
CTAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
TTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGCACCAACATCATTTTCCTATCCTCTTGA
AATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGC
ACCGACATCTTTTCC
Found at i:42426747 original size:42 final size:42
Alignment explanation
Indices: 42426701--42426846 Score: 127
Period size: 53 Copynumber: 3.3 Consensus size: 42
42426691 CTTGAAATTG
42426701 AATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGA
1 AATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGA
* * *
42426743 AATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTT-CCTATCCTCTTGA
1 AATTGAAGTAA-AGCTGGAT--A--A-CAAGC--CTTTTTCCCT-T--T-TTGA
*
42426796 AATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCC--TCTGA
1 AATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGA
42426836 AATTGAAGTAA
1 AATTGAAGTAA
42426847 GAGCAAGATG
Statistics
Matches: 84, Mismatches: 7, Indels: 28
0.71 0.06 0.24
Matches are distributed among these distances:
40 14 0.17
41 1 0.01
42 11 0.13
43 7 0.08
45 6 0.07
46 2 0.02
47 5 0.06
48 5 0.06
49 3 0.04
50 7 0.08
52 8 0.10
53 15 0.18
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (42 bp):
AATTGAAGTAAAGCTGGATAACAAGCCTTTTTCCCTTTTTGA
Found at i:42427604 original size:11 final size:11
Alignment explanation
Indices: 42427590--42427698 Score: 52
Period size: 11 Copynumber: 10.1 Consensus size: 11
42427580 AACCAAACCC
42427590 ATTTTAAATTT
1 ATTTTAAATTT
*
42427601 ATTTTAAGATTA
1 ATTTTAA-ATTT
* **
42427613 AATTT-GTTTT
1 ATTTTAAATTT
* *
42427623 AAATTTAAGTTT
1 -ATTTTAAATTT
42427635 ATTTTAAATTT
1 ATTTTAAATTT
42427646 A----A-ATTT
1 ATTTTAAATTT
42427652 ATTTTAAATTT
1 ATTTTAAATTT
*
42427663 AAATTT-AATTT
1 -ATTTTAAATTT
*
42427674 GAGTTTAAATTT
1 -ATTTTAAATTT
42427686 ATTTTCAAATTT
1 ATTTT-AAATTT
42427698 A
1 A
42427699 AAATAATTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
6 5 0.07
7 1 0.01
10 3 0.04
11 39 0.53
12 26 0.35
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:42427615 original size:17 final size:17
Alignment explanation
Indices: 42427592--42427716 Score: 153
Period size: 17 Copynumber: 7.3 Consensus size: 17
42427582 CCAAACCCAT
42427592 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
42427610 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
42427626 TTTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
42427643 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
42427660 TTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAA
42427677 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
42427695 TTTAAAATAATTATAAA
1 TTTAAATTTATTTTAAA
42427712 TTTAA
1 TTTAA
42427717 TTAAAATGTC
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
16 1 0.01
17 79 0.86
18 12 0.13
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:42427629 original size:6 final size:6
Alignment explanation
Indices: 42427620--42427700 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
42427610 TTAAATTTGT
* * *
42427620 TTTAAA TTTAAG TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
42427666 TTT-AA TTTGAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
42427701 ATAATTATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
5 17 0.28
6 39 0.65
7 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:42427646 original size:23 final size:22
Alignment explanation
Indices: 42427620--42427686 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
42427610 TTAAATTTGT
*
42427620 TTTAAATTTAAGTTTATTTTAAA
1 TTTAAATTT-AGTTTAATTTAAA
*
42427643 TTTAAATTTATTTTAAATTTAAA
1 TTTAAATTTAGTTT-AATTTAAA
42427666 TTT-AATTTGAGTTTAAATTTA
1 TTTAAATTT-AGTTT-AATTTA
42427687 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 9 0.23
23 30 0.77
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTAAATTTAGTTTAATTTAAA
Found at i:42427739 original size:14 final size:15
Alignment explanation
Indices: 42427715--42427751 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42427705 TTATAAATTT
*
42427715 AATTA-AAATGTC-C
1 AATTACAAATGTCTA
42427728 AATTACAAATGTCTA
1 AATTACAAATGTCTA
42427743 AATTACAAA
1 AATTACAAA
42427752 GGCCAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (15 bp):
AATTACAAATGTCTA
Found at i:42429675 original size:29 final size:30
Alignment explanation
Indices: 42429627--42429843 Score: 122
Period size: 29 Copynumber: 7.5 Consensus size: 30
42429617 CTAAACTTTT
* *
42429627 CAAAATT-CTATTTTAACCT-AATTTCACC
1 CAAAATTACCATTTTACCCTAAATTTCACC
*
42429655 CAAAATTACCATTTTACCCTAAACTTT---T
1 CAAAATTACCATTTTACCCTAAA-TTTCACC
* *
42429683 CAAAATT-CTATTTTAACCC-CAATTTCACC
1 CAAAATTACCATTTT-ACCCTAAATTTCACC
*
42429712 CAAAATTACCATTTTACCCTCAAACTT--CC
1 CAAAATTACCATTTTACCCT-AAATTTCACC
* * * **
42429741 CTAAA-TCCCATTTTTAACCTCGATTTCACC
1 CAAAATTACCA-TTTTACCCTAAATTTCACC
*
42429771 CAAAATTACCATTTTACCCCCAAATCTT---C
1 CAAAATTACCATTTTA-CCCTAAAT-TTCACC
* ** *
42429800 CAAAATT-CCATTTTTAACCTCGATTTCA-T
1 CAAAATTACCA-TTTTACCCTAAATTTCACC
42429829 CAAAATTACCATTTT
1 CAAAATTACCATTTT
42429844 GTCCCCCCCC
Statistics
Matches: 143, Mismatches: 26, Indels: 39
0.69 0.12 0.19
Matches are distributed among these distances:
26 3 0.02
27 10 0.07
28 32 0.22
29 59 0.41
30 22 0.15
31 15 0.10
32 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.01, T:0.36
Consensus pattern (30 bp):
CAAAATTACCATTTTACCCTAAATTTCACC
Found at i:42429701 original size:28 final size:28
Alignment explanation
Indices: 42429595--42429701 Score: 105
Period size: 28 Copynumber: 3.8 Consensus size: 28
42429585 CCCAAAACTT
* * *
42429595 TTTTTAAAATTATATTTTGACCCTAAAC
1 TTTTCAAAATTCTATTTTAACCCTAAAC
42429623 TTTTCAAAATTCTATTTTAA-CCT-AA-
1 TTTTCAAAATTCTATTTTAACCCTAAAC
* *
42429648 TTTCACCCAAAATTACCATTTT-ACCCTAAAC
1 TTT---TCAAAATT-CTATTTTAACCCTAAAC
42429679 TTTTCAAAATTCTATTTTAACCC
1 TTTTCAAAATTCTATTTTAACCC
42429702 CAATTTCACC
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.05
26 2 0.03
27 9 0.14
28 36 0.56
29 9 0.14
30 2 0.03
31 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTTCAAAATTCTATTTTAACCCTAAAC
Found at i:42429783 original size:59 final size:58
Alignment explanation
Indices: 42429600--42429843 Score: 286
Period size: 59 Copynumber: 4.2 Consensus size: 58
42429590 AACTTTTTTT
* * *
42429600 AAAATTA-TATTTTGACCCT-AAACTTTTCAAAATTCTA-TTTTAACCT-AATTTCACCC
1 AAAATTACCATTTT-ACCCTCAAAC-TTCCAAAATTCCATTTTTAACCTCAATTTCACCC
* * *
42429656 AAAATTACCATTTTACCCT-AAACTTTTCAAAATTCTA-TTTTAACCCCAATTTCACCC
1 AAAATTACCATTTTACCCTCAAAC-TTCCAAAATTCCATTTTTAACCTCAATTTCACCC
* * *
42429713 AAAATTACCATTTTACCCTCAAACTTCCCTAAATCCCATTTTTAACCTCGATTTCACCC
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAATTCCATTTTTAACCTCAATTTCACCC
* * *
42429772 AAAATTACCATTTTACCCCCAAATCTTCCAAAATTCCATTTTTAACCTCGATTTCA-TC
1 AAAATTACCATTTTACCCTCAAA-CTTCCAAAATTCCATTTTTAACCTCAATTTCACCC
42429830 AAAATTACCATTTT
1 AAAATTACCATTTT
42429844 GTCCCCCCCC
Statistics
Matches: 170, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
56 38 0.22
57 36 0.21
58 26 0.15
59 67 0.39
60 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATTTTTAACCTCAATTTCACCC
Found at i:42437129 original size:37 final size:37
Alignment explanation
Indices: 42437076--42437260 Score: 194
Period size: 37 Copynumber: 5.0 Consensus size: 37
42437066 GCATCTAAGA
42437076 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCTGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCTGGTGT
* * *
42437113 ATTCGGGCTATATGCCTAGCAGGCTTCGTG-TCGGTGG
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCT-GGTGT
* * * *
42437150 ATTTGAGCTATGTGCTTAGCAGGCTTTGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCTGGTGT
* * *
42437187 GTTCAGGCTATGTGCCTAGCAGGCTTCGTG-TCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCT-GGTGT
* * * * *
42437224 GTTCGGGCTTTGTGCTTAGCAGACCTTTGTGCCGGTG
1 ATTCGGGCTATGTGCCTAGCAG-GCTTTGTGCTGGTG
42437261 ATCAAAAAAT
Statistics
Matches: 120, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
36 1 0.01
37 109 0.91
38 10 0.08
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (37 bp):
ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCTGGTGT
Found at i:42437193 original size:21 final size:21
Alignment explanation
Indices: 42437169--42437238 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
42437159 ATGTGCTTAG
42437169 CAGGCTTTGTGCCGGTGTGTT
1 CAGGCTTTGTGCCGGTGTGTT
* *
42437190 CAGGCTATGTGCC--T-AG--
1 CAGGCTTTGTGCCGGTGTGTT
* *
42437206 CAGGCTTCGTGTCGGTGTGTT
1 CAGGCTTTGTGCCGGTGTGTT
*
42437227 CGGGCTTTGTGC
1 CAGGCTTTGTGC
42437239 TTAGCAGACC
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
16 10 0.29
18 2 0.06
19 2 0.06
21 21 0.60
ACGTcount: A:0.07, C:0.21, G:0.37, T:0.34
Consensus pattern (21 bp):
CAGGCTTTGTGCCGGTGTGTT
Found at i:42437203 original size:74 final size:74
Alignment explanation
Indices: 42437077--42437260 Score: 253
Period size: 74 Copynumber: 2.5 Consensus size: 74
42437067 CATCTAAGAA
* * * *
42437077 TTCGGGCTATGTGCCTAGCAGGCTTTGTGCTGGTGTATTCGGGCTATATGCCTAGCAGGCTTCGT
1 TTCGAGCTATGTGCTTAGCAGGCTTTGTGCCGGTGTATTCAGGCTATATGCCTAGCAGGCTTCGT
42437142 GTCGGTG-G
66 GTCGGTGTG
* * *
42437150 ATTTGAGCTATGTGCTTAGCAGGCTTTGTGCCGGTGTGTTCAGGCTATGTGCCTAGCAGGCTTCG
1 -TTCGAGCTATGTGCTTAGCAGGCTTTGTGCCGGTGTATTCAGGCTATATGCCTAGCAGGCTTCG
42437215 TGTCGGTGTG
65 TGTCGGTGTG
* * *
42437225 TTCGGGCTTTGTGCTTAGCAGACCTTTGTGCCGGTG
1 TTCGAGCTATGTGCTTAGCAG-GCTTTGTGCCGGTG
42437261 ATCAAAAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
74 83 0.86
75 14 0.14
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (74 bp):
TTCGAGCTATGTGCTTAGCAGGCTTTGTGCCGGTGTATTCAGGCTATATGCCTAGCAGGCTTCGT
GTCGGTGTG
Found at i:42438206 original size:19 final size:19
Alignment explanation
Indices: 42438184--42438220 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42438174 TTCATTTATT
*
42438184 CTTTCCAACTTCTTTTAAG
1 CTTTCAAACTTCTTTTAAG
*
42438203 CTTTCAAACTTGTTTTAA
1 CTTTCAAACTTCTTTTAA
42438221 ATCTGTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (19 bp):
CTTTCAAACTTCTTTTAAG
Found at i:42446170 original size:45 final size:45
Alignment explanation
Indices: 42446106--42446197 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
42446096 TTATTGAAAA
42446106 TTCTCTTAGATCTAACATCAGTTTCGTCTACTTGTCTTGAGTGCC
1 TTCTCTTAGATCTAACATCAGTTTCGTCTACTTGTCTTGAGTGCC
42446151 TTCTCTTAGATCTAACATCAGTTTCGTCTACTTGTCTTGAGTGCC
1 TTCTCTTAGATCTAACATCAGTTTCGTCTACTTGTCTTGAGTGCC
42446196 TT
1 TT
42446198 TCCTTTTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (45 bp):
TTCTCTTAGATCTAACATCAGTTTCGTCTACTTGTCTTGAGTGCC
Found at i:42461138 original size:13 final size:15
Alignment explanation
Indices: 42461109--42461141 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
42461099 AAATTAATGT
42461109 AATTTGAATATTAAA
1 AATTTGAATATTAAA
42461124 AATTTG-ATA-TAAA
1 AATTTGAATATTAAA
42461137 AATTT
1 AATTT
42461142 ATTCAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
AATTTGAATATTAAA
Found at i:42463354 original size:5 final size:5
Alignment explanation
Indices: 42463346--42463374 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42463336 ATATAATATA
42463346 ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
42463375 ATAACAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
ATAGT
Found at i:42464898 original size:16 final size:16
Alignment explanation
Indices: 42464877--42464932 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
42464867 CAACTTTGGC
* *
42464877 TTAGAATAATTGTTGT
1 TTAGAATAACTATTGT
*
42464893 TTAGAACAACTATTGT
1 TTAGAATAACTATTGT
*
42464909 TTGAGAATAGCTA-TGT
1 TT-AGAATAACTATTGT
*
42464925 TCAGAATA
1 TTAGAATA
42464933 GGGCTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.18
16 19 0.58
17 8 0.24
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (16 bp):
TTAGAATAACTATTGT
Found at i:42472459 original size:20 final size:21
Alignment explanation
Indices: 42472434--42472473 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
42472424 CAACGAAGCA
42472434 AAAAGAAGAATT-AAAGAATT
1 AAAAGAAGAATTAAAAGAATT
42472454 AAAAGAAGAATTAAAAGAAT
1 AAAAGAAGAATTAAAAGAAT
42472474 AAAGAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAAGAAGAATTAAAAGAATT
Found at i:42472464 original size:12 final size:12
Alignment explanation
Indices: 42472447--42472472 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42472437 AGAAGAATTA
42472447 AAGAATTAAAAG
1 AAGAATTAAAAG
42472459 AAGAATTAAAAG
1 AAGAATTAAAAG
42472471 AA
1 AA
42472473 TAAAGAAATG
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAGAATTAAAAG
Found at i:42473396 original size:33 final size:33
Alignment explanation
Indices: 42473359--42473423 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
42473349 GAGAAAGAAA
42473359 AGTTAGCTCTGTAAGCAATGATCCATCATTAAT
1 AGTTAGCTCTGTAAGCAATGATCCATCATTAAT
* *
42473392 AGTTAGCTTTGTCAGCAATGATCCATCATTAA
1 AGTTAGCTCTGTAAGCAATGATCCATCATTAA
42473424 CCCTAGTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
AGTTAGCTCTGTAAGCAATGATCCATCATTAAT
Found at i:42480225 original size:25 final size:24
Alignment explanation
Indices: 42480164--42480227 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
42480154 GGAACGTATG
42480164 CAATGGATGAAAAAGAAACATCTT
1 CAATGGATGAAAAAGAAACATCTT
**
42480188 CAATGGATGAAAAAGAAATGTCTT
1 CAATGGATGAAAAAGAAACATCTT
42480212 CAATGGCA-GAAAAAGA
1 CAATGG-ATGAAAAAGA
42480228 GGATTCATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.19
Consensus pattern (24 bp):
CAATGGATGAAAAAGAAACATCTT
Found at i:42481367 original size:42 final size:43
Alignment explanation
Indices: 42481247--42481417 Score: 179
Period size: 43 Copynumber: 4.0 Consensus size: 43
42481237 ATGCCATTAT
* *
42481247 AGAACATGGTCTTTAGTGG-CTCTTTTCCCACAAACACCGCTAA
1 AGAACATGTTCTTTAGCGGCCT-TTTTCCCACAAACACCGCTAA
* *
42481290 AGAACATGTTCTATAGCGGCGC-TTTTCCCAAAAACACCG-TAAA
1 AGAACATGTTCTTTAGCGGC-CTTTTTCCCACAAACACCGCT-AA
* * *
42481333 AGAACATGTT-TTTAGCGACCTTTTTCCCACAAACACTGCTAT
1 AGAACATGTTCTTTAGCGGCCTTTTTCCCACAAACACCGCTAA
* * * **
42481375 AGAACATGTTCTTTAGTGGCGTTTTTCTCACAAATGCCGCTAA
1 AGAACATGTTCTTTAGCGGCCTTTTTCCCACAAACACCGCTAA
42481418 CATTAGCAGA
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 34 0.32
43 69 0.66
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (43 bp):
AGAACATGTTCTTTAGCGGCCTTTTTCCCACAAACACCGCTAA
Found at i:42489893 original size:30 final size:29
Alignment explanation
Indices: 42489855--42489943 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 29
42489845 TCTGCTAATC
*
42489855 TAAAAAAAAATCATAATTTAATAATTATTATT
1 TAAAAAAAAAT-A-ATTTTAATAATT-TTATT
42489887 TAAAAAAAAATAATTTTAATAATTTTATAT
1 TAAAAAAAAATAATTTTAATAATTTTAT-T
****
42489917 TTTTTAAAAATAATTTTAATAATTTTA
1 TAAAAAAAAATAATTTTAATAATTTTA
42489944 AAATCATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 4 0.08
30 35 0.69
31 1 0.02
32 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAAAAAAATAATTTTAATAATTTTATT
Found at i:42489942 original size:21 final size:21
Alignment explanation
Indices: 42489904--42489946 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
42489894 AAATAATTTT
*
42489904 AATAATTTTATATTTTTTAAA
1 AATAATTTTATATATTTTAAA
42489925 AATAATTTTA-ATAATTTTAAA
1 AATAATTTTATAT-ATTTTAAA
42489946 A
1 A
42489947 TCATTTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATTTTATATATTTTAAA
Found at i:42490715 original size:41 final size:39
Alignment explanation
Indices: 42490582--42490726 Score: 139
Period size: 41 Copynumber: 3.5 Consensus size: 39
42490572 GGGAAAATGC
42490582 CGCTATTGCTTAACCTTTAGCGGCGTTTTTCCCATAAACG
1 CGCTATTGCTTAACCTTTAGCGGC-TTTTTCCCATAAACG
* * *
42490622 CCGCTAATT-CTCTAACTTTCCTTTTGCGGCGTTTTCCCATAAACAC
1 -CGCT-ATTGCT-TAA----CCTTTAGCGGCTTTTTCCCATAAAC-G
*
42490668 CGCTATTGCTTAACCTTTAGCGGCATTTTTTCCATAAACG
1 CGCTATTGCTTAACCTTTAGCGGC-TTTTTCCCATAAACG
*
42490708 CGACTATTGCTTTACCTTT
1 CG-CTATTGCTTAACCTTT
42490727 TACGACGTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
40 12 0.14
41 33 0.38
42 6 0.07
44 6 0.07
45 19 0.22
46 10 0.12
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (39 bp):
CGCTATTGCTTAACCTTTAGCGGCTTTTTCCCATAAACG
Found at i:42491575 original size:92 final size:92
Alignment explanation
Indices: 42491418--42491601 Score: 309
Period size: 92 Copynumber: 2.0 Consensus size: 92
42491408 GGTGGGTATG
*
42491418 TATGAAAGGTCATAAAGAAATAAGATTCTAGTTTGATTGTTTGTAATATTTTATTAATTATTTTT
1 TATGAAAGGTCATAAAGAAATAAGATTCTAATTTGATTGTTTGTAATATTTTATTAATTATTTTT
*
42491483 TTGAGGATTTTGGAATATAATTAGAGT
66 TTGAGGATTTCGGAATATAATTAGAGT
*
42491510 TATGAAAGGTCATAAAGAAATAAGATTTTAATTTGATTGTTTGTAAT-TATTTATT-ATTATTTT
1 TATGAAAGGTCATAAAGAAATAAGATTCTAATTTGATTGTTTGTAATAT-TTTATTAATTATTTT
*
42491573 TTTGAGGATTTCGGGATATAATTAGAGT
65 TTTGAGGATTTCGGAATATAATTAGAGT
42491601 T
1 T
42491602 GATGCAAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
91 36 0.41
92 51 0.59
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.46
Consensus pattern (92 bp):
TATGAAAGGTCATAAAGAAATAAGATTCTAATTTGATTGTTTGTAATATTTTATTAATTATTTTT
TTGAGGATTTCGGAATATAATTAGAGT
Found at i:42492478 original size:40 final size:40
Alignment explanation
Indices: 42492434--42492627 Score: 162
Period size: 42 Copynumber: 4.8 Consensus size: 40
42492424 ATCCATAAAT
* *
42492434 GCCGCTATTGATTTACATTTTGCGGCATTTATGGTAAAAC
1 GCCGCTATTGATTTACCTTTTGCGGCGTTTATGGTAAAAC
* * *
42492474 GCCGCTA-TAATTTTACCTTTTGCGGCGTTT-T-TTCATAAAT
1 GCCGCTATTGA-TTTACCTTTTGCGGCGTTTATGGT-A-AAAC
* * *
42492514 GCCGCTATT-ACTCTTTACCTTTTTCTGCGTTTATGATAAAAC
1 GCCGCTATTGA---TTTACCTTTTGCGGCGTTTATGGTAAAAC
* * *
42492556 GCCGCTATTGCTGTTTACCTTTTGCGGCGTTTATTGAAAAAC
1 GCCGCTATTG--ATTTACCTTTTGCGGCGTTTATGGTAAAAC
* * *
42492598 GCCGCTATTGTTTTACTTTTTGCAGCGTTT
1 GCCGCTATTGATTTACCTTTTGCGGCGTTT
42492628 TTTGTTCAAA
Statistics
Matches: 124, Mismatches: 19, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 52 0.42
41 1 0.01
42 63 0.51
43 2 0.02
44 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.42
Consensus pattern (40 bp):
GCCGCTATTGATTTACCTTTTGCGGCGTTTATGGTAAAAC
Found at i:42492544 original size:42 final size:40
Alignment explanation
Indices: 42492404--42492631 Score: 181
Period size: 40 Copynumber: 5.6 Consensus size: 40
42492394 ACTAATGCTC
* ** * **
42492404 TTTACTTTTTGCGGCGTTTTATCCATAAATGCCGCTATTGA
1 TTTACCTTTTGCGGCGTTTT-TTGATAAACGCCGCTATTCT
* * * * **
42492445 TTTACATTTTGCGGC-ATTTATGGTAAAACGCCGCTATAAT
1 TTTACCTTTTGCGGCGTTTTTTGAT-AAACGCCGCTATTCT
* *
42492485 TTTACCTTTTGCGGCGTTTTTTCATAAATGCCGCTATTACT
1 TTTACCTTTTGCGGCGTTTTTTGATAAACGCCGCTATT-CT
* * *
42492526 CTTTACCTTTTTCTGCG-TTTATGATAAAACGCCGCTATTGCT
1 -TTTACCTTTTGCGGCGTTTTTTGAT-AAACGCCGCTATT-CT
* * *
42492568 GTTTACCTTTTGCGGCGTTTATTGAAAAACGCCGCTATTGT
1 -TTTACCTTTTGCGGCGTTTTTTGATAAACGCCGCTATTCT
* *
42492609 TTTACTTTTTGCAGCGTTTTTTG
1 TTTACCTTTTGCGGCGTTTTTTG
42492632 TTCAAATGCC
Statistics
Matches: 147, Mismatches: 34, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
39 1 0.01
40 59 0.40
41 27 0.18
42 55 0.37
43 5 0.03
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (40 bp):
TTTACCTTTTGCGGCGTTTTTTGATAAACGCCGCTATTCT
Found at i:42500313 original size:17 final size:17
Alignment explanation
Indices: 42500291--42500353 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
42500281 ATTTTAATTG
42500291 TTTAATATTAAATTAAA
1 TTTAATATTAAATTAAA
* *
42500308 TTTAATATTAAAATGATTA
1 TTTAATATT-AAATTA-AA
*
42500327 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATTAAA
*
42500345 TCTAATATT
1 TTTAATATT
42500354 TATCTTGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 16 0.43
18 7 0.19
19 6 0.16
20 8 0.22
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:42502742 original size:13 final size:13
Alignment explanation
Indices: 42502724--42502754 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
42502714 GTGTGACTAT
42502724 TCCATGACTTGTG
1 TCCATGACTTGTG
42502737 TCCATGACTTGTG
1 TCCATGACTTGTG
42502750 TCCAT
1 TCCAT
42502755 TCTAGATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (13 bp):
TCCATGACTTGTG
Found at i:42503327 original size:123 final size:123
Alignment explanation
Indices: 42503179--42503791 Score: 822
Period size: 123 Copynumber: 5.0 Consensus size: 123
42503169 AAGGATTTCG
42503179 TTAAATATT-AAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAA-AAAGCCTT
1 TTAAATATTAAAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAATAAA-CCTT
* * * * *
42503242 TCATATATTTCTATAAGGGAATAATTCCGTTTTAATTTGAGATATTAAATAAAAGGAAA
65 CCATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
*
42503301 TTAAATATTAAAAACATGGAAGTTAATATCCTTTTT-GAAAGGATATAATGTTTTAACAAACCTT
1 TTAAATATTAAAAACATGGAAGTTAATAT-CTTTTTAGAAAGGATATAATGTTTTAATAAACCTT
* * *
42503365 CCATATATTTCTATAAAAGAA-ATTT-CGTTTTAACATGAGATATTAAATAAAAGGAAA
65 CCATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
* * * *
42503422 TTAAATATTAAGAACATGAAAGTCAATATCTTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAATAAACCTTC
* * ** * *
42503487 CATATATTTCTCTAAGGGAATGTTTTTGTTTTGATATGAAATATTAAATAAAAGGAAA
66 CATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
* * * * * * * * *
42503545 CTGAATAATAAAAATATGGAAGTTAATATCCTCTTGGAAATGATATAATATTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAATAAACCTTC
* ** * *
42503610 CATATATTTCTCTAAAAGAATATTTCTATTTTAATATCAGATATTAAATAAAAGTAAA
66 CATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
* * * *
42503668 TTGAATATTAAAAACATGTAAGTTAATATCCTTTTAAAAAGGATATAATGTTTTAATAAACCTTC
1 TTAAATATTAAAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAATAAACCTTC
* *
42503733 CATATATTTCTCTAAAGGAATATTTCCATTTTAATATTAGATATTAAATAAAAGGAAA
66 CATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
42503791 T
1 T
42503792 ATAGCAGAAT
Statistics
Matches: 434, Mismatches: 51, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
120 6 0.01
121 101 0.23
122 15 0.03
123 303 0.70
124 9 0.02
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (123 bp):
TTAAATATTAAAAACATGGAAGTTAATATCTTTTTAGAAAGGATATAATGTTTTAATAAACCTTC
CATATATTTCTCTAAAGGAATATTTCCGTTTTAATATGAGATATTAAATAAAAGGAAA
Found at i:42503688 original size:22 final size:21
Alignment explanation
Indices: 42503650--42503696 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
42503640 TTAATATCAG
42503650 ATATTAAATAAAAGTAAATTGA
1 ATATTAAATAAAAGTAAATT-A
* *
42503672 ATATTAAA-AACATGTAAGTTA
1 ATATTAAATAA-AAGTAAATTA
42503693 ATAT
1 ATAT
42503697 CCTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (21 bp):
ATATTAAATAAAAGTAAATTA
Found at i:42508501 original size:16 final size:17
Alignment explanation
Indices: 42508457--42508539 Score: 69
Period size: 17 Copynumber: 4.7 Consensus size: 17
42508447 TCAAGAACAT
*
42508457 AGTTCAAAATTCACTTA
1 AGTTCAAAATTTACTTA
*
42508474 ATTTCAAAATTTACTTA
1 AGTTCAAAATTTACTTA
*
42508491 AGTTCAAATTTTTA-TTA
1 AGTTCAAA-ATTTACTTA
* **
42508508 AGTCTTCAAAATATGTTTAA
1 AG--TTCAAAATTTACTT-A
42508528 AGTTCAAAATTT
1 AGTTCAAAATTT
42508540 GCTAAGGTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
17 27 0.51
18 15 0.28
19 8 0.15
20 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
AGTTCAAAATTTACTTA
Found at i:42513039 original size:19 final size:20
Alignment explanation
Indices: 42513015--42513053 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42513005 TGCATTTTTA
*
42513015 GCATTT-TAACTTAGTGATT
1 GCATTTCTAACTCAGTGATT
42513034 GCATTTGCTAACTCAGTGAT
1 GCATTT-CTAACTCAGTGAT
42513054 GCTTGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (20 bp):
GCATTTCTAACTCAGTGATT
Found at i:42536742 original size:17 final size:15
Alignment explanation
Indices: 42536704--42536746 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
42536694 AAAGCTTAGG
42536704 GAAGAAGAA-GCATA
1 GAAGAAGAAGGCATA
42536718 GCAAGAAGAAGGCCATGA
1 G-AAGAAGAAGG-CAT-A
42536736 GAAGAAGAAGG
1 GAAGAAGAAGG
42536747 AAGGAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 8 0.32
16 1 0.04
17 13 0.52
18 2 0.08
ACGTcount: A:0.51, C:0.09, G:0.35, T:0.05
Consensus pattern (15 bp):
GAAGAAGAAGGCATA
Found at i:42537102 original size:21 final size:20
Alignment explanation
Indices: 42537062--42537110 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
42537052 TGATTCGAAG
* *
42537062 GATAAGAACAAAAAGTGCAAA
1 GATAAGAAGAAAAAGCGC-AA
*
42537083 GATAAGAAGAAGAAGCGCAA
1 GATAAGAAGAAAAAGCGCAA
42537103 -ATAAGAAG
1 GATAAGAAG
42537111 GCGAGCACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 15 0.60
ACGTcount: A:0.59, C:0.08, G:0.24, T:0.08
Consensus pattern (20 bp):
GATAAGAAGAAAAAGCGCAA
Found at i:42537838 original size:10 final size:11
Alignment explanation
Indices: 42537825--42537870 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
42537815 AAAAATTCAC
42537825 AAAAAG-AAAG
1 AAAAAGAAAAG
42537835 AAAAAG-AAAG
1 AAAAAGAAAAG
*
42537845 AAGAAGAAAAG
1 AAAAAGAAAAG
42537856 AAAAAAGAAAAG
1 -AAAAAGAAAAG
42537868 AAA
1 AAA
42537871 TATATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:42537856 original size:15 final size:15
Alignment explanation
Indices: 42537825--42537864 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
42537815 AAAAATTCAC
42537825 AAAAAGAAAGAAAAAGA
1 AAAAAG-AAG-AAAAGA
*
42537842 AAGAAGAAGAAAAGA
1 AAAAAGAAGAAAAGA
42537857 AAAAAGAA
1 AAAAAGAA
42537865 AAGAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 3 0.14
17 5 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAGA
Found at i:42537964 original size:39 final size:39
Alignment explanation
Indices: 42537920--42538036 Score: 225
Period size: 39 Copynumber: 3.0 Consensus size: 39
42537910 AGATTCAAAG
42537920 CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
1 CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
42537959 CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
1 CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
*
42537998 CATGTTACTAACATTGGTGAAGTTGCAATTTTAATTATT
1 CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
42538037 TGTTTGTGAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (39 bp):
CATGTTACTAACATTGGTGAAGTTGCAGTTTTAATTATT
Found at i:42538408 original size:29 final size:29
Alignment explanation
Indices: 42538366--42538423 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42538356 ATGCAGCCAC
*
42538366 AAGTTAGCTTGGAATTGCGGCCAGAGATG
1 AAGTTAGCTTGGAATTACGGCCAGAGATG
42538395 AAGTTAGCTTGGAATTACGGCCAGAGATG
1 AAGTTAGCTTGGAATTACGGCCAGAGATG
42538424 TCAATGCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (29 bp):
AAGTTAGCTTGGAATTACGGCCAGAGATG
Found at i:42545228 original size:15 final size:17
Alignment explanation
Indices: 42545193--42545228 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42545183 AAAATAATCC
42545193 AAAATTACAAGTCTCCA
1 AAAATTACAAGTCTCCA
42545210 AAAATTA-AAGTCT-CA
1 AAAATTACAAGTCTCCA
42545225 AAAA
1 AAAA
42545229 CACTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAATTACAAGTCTCCA
Found at i:42545228 original size:16 final size:17
Alignment explanation
Indices: 42545193--42545228 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
42545183 AAAATAATCC
*
42545193 AAAATTACAAGTCTCCA
1 AAAATTACAAGTCTCAA
42545210 AAAATTA-AAGTCTCAA
1 AAAATTACAAGTCTCAA
42545226 AAA
1 AAA
42545229 CACTTTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAATTACAAGTCTCAA
Done.