Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 138 of 207
Found at i:42374781 original size:30 final size:31
Alignment explanation
Indices: 42374723--42374785 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
42374713 TAAGATAGTT
*
42374723 ATTAAATTATTTAAAAATTTTAATTTAAGTC
1 ATTAAATTAATTAAAAATTTTAATTTAAGTC
* *
42374754 ATTAAATTAATTGAAAGTTTT-ATTTAAGTC
1 ATTAAATTAATTAAAAATTTTAATTTAAGTC
42374784 AT
1 AT
42374786 CGTATTGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (31 bp):
ATTAAATTAATTAAAAATTTTAATTTAAGTC
Found at i:42380907 original size:43 final size:43
Alignment explanation
Indices: 42380838--42380923 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
42380828 ATGGTGATTT
42380838 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC
1 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC
* * *
42380881 TTCAAAGTTAACCTACTGTTGTTGTCCAAAACTGTTTTAGTGC
1 TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC
42380924 AAGATGTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (43 bp):
TTCAAAGCTAACCTACTGCTGCTGTCCAAAACTGTTTTAGTGC
Found at i:42385657 original size:48 final size:50
Alignment explanation
Indices: 42385596--42385750 Score: 127
Period size: 48 Copynumber: 3.3 Consensus size: 50
42385586 TGTATGAACT
42385596 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA
1 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA
* * * * *
42385646 TGATT-TA-ATTTGCTTACTAACTTG---TAA-CATATT-TGCA--AGA-ACT
1 TGATTGTATATTTG-TTA--AACATGAATTAATAATATTGTACATGAAACACA
* * *
42385689 TGATTGTATATTTGTTGAACATTAATTAATAATATTGCACATGAAACACA
1 TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA
42385739 TGATT-TA-ATTTG
1 TGATTGTATATTTG
42385751 CTTACTAACT
Statistics
Matches: 79, Mismatches: 13, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
42 4 0.05
43 7 0.09
44 6 0.08
45 8 0.10
46 8 0.10
47 7 0.09
48 13 0.16
49 9 0.11
50 12 0.15
51 5 0.06
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (50 bp):
TGATTGTATATTTGTTAAACATGAATTAATAATATTGTACATGAAACACA
Found at i:42385691 original size:93 final size:93
Alignment explanation
Indices: 42385569--42385788 Score: 370
Period size: 93 Copynumber: 2.4 Consensus size: 93
42385559 TTATTAACTG
* * *
42385569 CTAAATTGTAACATATTTGTATGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGT
1 CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC
42385634 ACATGAAACACATGATTTAATTTGCTTA
66 ACATGAAACACATGATTTAATTTGCTTA
* * *
42385662 CTAACTTGTAACATATTTGCAAGAACTTGATTGTATATTTGTTGAACATTAATTAATAATATTGC
1 CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC
42385727 ACATGAAACACATGATTTAATTTGCTTA
66 ACATGAAACACATGATTTAATTTGCTTA
42385755 CTAACTTGTAACATATTTGTATA-AACTTGATTGT
1 CTAACTTGTAACATATTTGTA-AGAACTTGATTGT
42385789 CACATATATT
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 118 0.99
94 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (93 bp):
CTAACTTGTAACATATTTGTAAGAACTTGATTGTATATTTGTTAAACATGAATTAATAATATTGC
ACATGAAACACATGATTTAATTTGCTTA
Found at i:42388243 original size:95 final size:92
Alignment explanation
Indices: 42388080--42388249 Score: 238
Period size: 95 Copynumber: 1.8 Consensus size: 92
42388070 ATTTTAACAC
* *
42388080 AAATCTAATTATTCAAACAAACATATAATGTTCAATGTTATATCTTAAAATATACAAATTATTCT
1 AAATCTAATTATTCAAACAAACATATAATGATCAATGTTACATCTTAAAATATACAAATTATTCT
*
42388145 TACAATATAATGATCAATTTTAAATCT
66 TACAAAATAATGATCAATTTTAAATCT
42388172 AAATCTAATTATTCAACACAAATCTAATATAATGATCAATG-TACA-CTTAAAACTATACAAATT
1 AAATCTAATTATTCAA-ACAAA-C--ATATAATGATCAATGTTACATCTTAAAA-TATACAAATT
42388235 A-TCATTACAAAATAA
61 ATTC-TTACAAAATAA
42388250 AATAAACTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
92 16 0.23
93 5 0.07
94 10 0.14
95 24 0.35
96 14 0.20
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (92 bp):
AAATCTAATTATTCAAACAAACATATAATGATCAATGTTACATCTTAAAATATACAAATTATTCT
TACAAAATAATGATCAATTTTAAATCT
Found at i:42398296 original size:23 final size:23
Alignment explanation
Indices: 42398266--42398310 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
42398256 ATATGAATTA
*
42398266 TGTAATATTCCAAAAATTACTAT
1 TGTAATATCCCAAAAATTACTAT
42398289 TGTAATATCCCAAAAATTACTA
1 TGTAATATCCCAAAAATTACTA
42398311 CAGTAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (23 bp):
TGTAATATCCCAAAAATTACTAT
Found at i:42398316 original size:23 final size:23
Alignment explanation
Indices: 42398267--42398316 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
42398257 TATGAATTAT
* **
42398267 GTAATATTCCAAAAATTACTATT
1 GTAATATCCCAAAAATTACTACA
42398290 GTAATATCCCAAAAATTACTACA
1 GTAATATCCCAAAAATTACTACA
42398313 GTAA
1 GTAA
42398317 GAAAGTAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (23 bp):
GTAATATCCCAAAAATTACTACA
Found at i:42401206 original size:14 final size:14
Alignment explanation
Indices: 42401177--42401224 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
42401167 TTTACATACT
42401177 TATACATATATGTATA
1 TATACATATA--TATA
* *
42401193 TTTTCATATATATA
1 TATACATATATATA
*
42401207 TATACATATACATA
1 TATACATATATATA
42401221 TATA
1 TATA
42401225 TATTTACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 19 0.70
16 8 0.30
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (14 bp):
TATACATATATATA
Found at i:42407484 original size:17 final size:17
Alignment explanation
Indices: 42407462--42407510 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
42407452 TCTAGCCCGG
*
42407462 CGCCGCCACCATTCTGT
1 CGCCGCCACCGTTCTGT
42407479 CGCCGCCACCGTTCTGT
1 CGCCGCCACCGTTCTGT
42407496 CGCCGCCACCGTTCT
1 CGCCGCCACCGTTCT
42407511 AACACCGCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.08, C:0.49, G:0.20, T:0.22
Consensus pattern (17 bp):
CGCCGCCACCGTTCTGT
Found at i:42409221 original size:111 final size:110
Alignment explanation
Indices: 42409028--42409349 Score: 547
Period size: 111 Copynumber: 2.9 Consensus size: 110
42409018 AAGGAAAATT
*
42409028 TTTCAAAATAAGGTAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
42409093 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA
66 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA
42409138 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
1 TTTCAAAATAAGGCAATGTTTTGCCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
* *
42409203 GTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
65 GTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA
* * *
42409249 TTTTAAAATAAGGCAATGTTTTG-CTTTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTG
1 TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* * *
42409313 TCGATTTTTCTCATTTAACCAAATAGCCAAATATCCT
66 TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
42409350 CTTGAATTTC
Statistics
Matches: 200, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
109 67 0.34
110 32 0.16
111 101 0.50
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (110 bp):
TTTCAAAATAAGGCAATGTTTTGCCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
TCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAA
Found at i:42410609 original size:107 final size:107
Alignment explanation
Indices: 42410420--42410629 Score: 287
Period size: 107 Copynumber: 2.0 Consensus size: 107
42410410 AAATGGGTTT
* * *
42410420 TTCACTGTACAAAAAATTAGGTTGTAACTCTATTTCATCAATACAAATCACGTGAGAGGGATTAG
1 TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG
* * *
42410485 AAAGATAATGACGTAACATCAATACATGGAACACATTAGCTC
66 AAAAATAACGACATAACATCAATACATGGAACACATTAGCTC
* * * ** *
42410527 TTCACTGTACGAAAAATCGGGTTGCAACTCTATTTCTTCTGTACAAATCACGTGAGAGGGA-CCG
1 TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG
*
42410591 AAACAATAACGACATAACATCGATACATGGAACACATTA
66 AAA-AATAACGACATAACATCAATACATGGAACACATTA
42410630 TGAATCTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 4 0.04
107 85 0.96
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (107 bp):
TTCACTGTACAAAAAATCAGGTTGCAACTCTATTTCATCAATACAAATCACGTGAGAGGGATCAG
AAAAATAACGACATAACATCAATACATGGAACACATTAGCTC
Found at i:42411898 original size:42 final size:42
Alignment explanation
Indices: 42411824--42411997 Score: 165
Period size: 42 Copynumber: 4.1 Consensus size: 42
42411814 ACGCCTCTAA
* * * ** *
42411824 ATTTAGCGGCGTTTATGTGAAAAACGCCGCTAAAGGTCATGAC
1 ATTTAGCGGCGCTT-TGTCACAAACGCCGCTAAAGAACATAAC
*
42411867 ATTTAGCGGCGCTTTGTCACAAACGTCGCTAAAGAACATAAC
1 ATTTAGCGGCGCTTTGTCACAAACGCCGCTAAAGAACATAAC
* * * *
42411909 CTTTAGCAGCGCTTTTATCACAAACGCCACTAAAGAACA-AAC
1 ATTTAGCGGCGC-TTTGTCACAAACGCCGCTAAAGAACATAAC
* *
42411951 ATTTAGCGGAGCTTT-TAGCAAAAACGCCGCTAAA-AACATAAC
1 ATTTAGCGGCGCTTTGT--CACAAACGCCGCTAAAGAACATAAC
*
42411993 CTTTA
1 ATTTA
42411998 AAAAAAATTA
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 7 0.06
42 65 0.60
43 36 0.33
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (42 bp):
ATTTAGCGGCGCTTTGTCACAAACGCCGCTAAAGAACATAAC
Found at i:42412403 original size:43 final size:43
Alignment explanation
Indices: 42412337--42412427 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
42412327 CACATTGCAA
* * *
42412337 GGTAATAAAAAATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
* *
42412380 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
42412423 -GTAAT
1 GGTAAT
42412428 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAAATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:42414880 original size:29 final size:29
Alignment explanation
Indices: 42414778--42414880 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
42414768 AAAAAAAATT
*
42414778 AAAACCAAAATAAAGAGGAAAAATACTGG
1 AAAAACAAAATAAAGAGGAAAAATACTGG
** *
42414807 AAAAACAAAATAAA-ATCTCAAAGAA-AAT-G
1 AAAAACAAAATAAAGA--GGAAA-AATACTGG
* *
42414836 AAGCGAAGAAAATAAAGAGGAAAAATACTGG
1 AA--AAACAAAATAAAGAGGAAAAATACTGG
*
42414867 AAAAATAAAATAAA
1 AAAAACAAAATAAA
42414881 ATCAAGGGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
28 1 0.02
29 28 0.51
30 10 0.18
31 15 0.27
32 1 0.02
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.12
Consensus pattern (29 bp):
AAAAACAAAATAAAGAGGAAAAATACTGG
Found at i:42415206 original size:23 final size:23
Alignment explanation
Indices: 42415175--42415218 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
42415165 AAAGATGTCG
*
42415175 TTTTAATCTGTTAAAAATTATTTA
1 TTTTAATCTGCT-AAAATTATTTA
42415199 TTTT-ATCTGCTAAAATTATT
1 TTTTAATCTGCTAAAATTATT
42415219 AGTTAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTAATCTGCTAAAATTATTTA
Found at i:42416188 original size:22 final size:21
Alignment explanation
Indices: 42416139--42416188 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
42416129 AAACCCCAAC
*
42416139 CCTTAAACCATAATCCATAAT
1 CCTTAAACCATAATCCATAAA
* *
42416160 CCATAAACACATAATCCCTAAA
1 CCTTAAAC-CATAATCCATAAA
42416182 CCTTAAA
1 CCTTAAA
42416189 ATAGTAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAATCCATAAA
Found at i:42416398 original size:41 final size:39
Alignment explanation
Indices: 42416301--42416411 Score: 150
Period size: 40 Copynumber: 2.7 Consensus size: 39
42416291 GCTAAAAATA
* * *
42416301 GAGCATTAGCGGCGCTTCTTTAAAAACACCGCTAAAGCCT
1 GAGCATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGCCC
*
42416341 GAGCATTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTTT-CAAAAACGCCGCTAAAG-CCC
42416382 GAGCATTAGCGGCGCTTTTTCAAAAACGCC
1 GAGCATTAGCGGCGC-TTTTCAAAAACGCC
42416412 AAAAACGTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.03
40 31 0.49
41 26 0.41
42 4 0.06
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (39 bp):
GAGCATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCC
Found at i:42416569 original size:40 final size:40
Alignment explanation
Indices: 42416472--42416642 Score: 157
Period size: 40 Copynumber: 4.3 Consensus size: 40
42416462 TAGGTTTTTC
* *** * *
42416472 GCGGCGCTTTTTGGAAAATGCCGCTAATGCT-AATTTTTA
1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA
* ****
42416511 ACGGCGTTTTCCAAAAAGCACCGCTAATGCTCGATCTTTA
1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA
*
42416551 GCGGCGTTTTTTGGAAAGCGCCGCTAATGCTCGATCTTTA
1 GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA
* * * * *
42416591 GAGGCATTTTTTGGAAAG-AGCCGCTAATTCTTGATTTTTA
1 GCGGCGTTTTTTGGAAAGCA-CCGCTAATGCTCGATCTTTA
*
42416631 GCGGCATTTTTT
1 GCGGCGTTTTTT
42416643 TATCCAAACG
Statistics
Matches: 106, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 22 0.21
40 84 0.79
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
GCGGCGTTTTTTGGAAAGCACCGCTAATGCTCGATCTTTA
Found at i:42419427 original size:29 final size:28
Alignment explanation
Indices: 42419387--42419483 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 28
42419377 ATAATATATG
* *
42419387 TAAATTAAAATATTTAAATAAGTTTAAA
1 TAAATTAAAATATTAAAATAAGTTGAAA
42419415 TAAATTAACAATATTAAAATAAGTTGAAA
1 TAAATTAA-AATATTAAAATAAGTTGAAA
* * *
42419444 TGAATTAAAGATGTTAAAAT-ATTTGAAA
1 TAAATTAAA-ATATTAAAATAAGTTGAAA
*
42419472 GAAA-TAAAATAT
1 TAAATTAAAATAT
42419484 CTATATAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.05
27 4 0.07
28 18 0.31
29 34 0.58
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (28 bp):
TAAATTAAAATATTAAAATAAGTTGAAA
Found at i:42421033 original size:16 final size:16
Alignment explanation
Indices: 42421012--42421051 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
42421002 TTTATTTGCA
42421012 TATGGGCTGGGCAAAT
1 TATGGGCTGGGCAAAT
42421028 TATGGGCTGGGCAAAT
1 TATGGGCTGGGCAAAT
*
42421044 TTTGGGCT
1 TATGGGCT
42421052 TGTACAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (16 bp):
TATGGGCTGGGCAAAT
Found at i:42421488 original size:44 final size:44
Alignment explanation
Indices: 42421421--42421591 Score: 127
Period size: 44 Copynumber: 3.9 Consensus size: 44
42421411 GATGCGATCT
* * *
42421421 GCTCTACTATAACTTC-AGAGAGATAAGATCT-CTGGTTTTAATCC
1 GCTCCACTACAACTTCAAG-GAGATAAGAT-TACTGGCTTTAATCC
* * * *
42421465 G-TACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCT
1 GCT-CCACTACAACTTCAAGGAGATAAGATTACTGGCTTTAATCC
* * *
42421509 GCTCCGCTACAACTTCAGGGAGATAAGATT-C-GCCATCTTCAATCC
1 GCTCCACTACAACTTCAAGGAGATAAGATTACTGGC-T-TT-AATCC
* * * *
42421554 GCTCCACTGCAACTTCAGGGAGATATGATTATTGGCTT
1 GCTCCACTACAACTTCAAGGAGATAAGATTACTGGCTT
42421592 CAATATGCTT
Statistics
Matches: 99, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 56 0.57
45 35 0.35
46 1 0.01
47 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
GCTCCACTACAACTTCAAGGAGATAAGATTACTGGCTTTAATCC
Found at i:42421577 original size:89 final size:89
Alignment explanation
Indices: 42421460--42421633 Score: 242
Period size: 89 Copynumber: 2.0 Consensus size: 89
42421450 CTCTGGTTTT
* *
42421460 AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCTCCGCTACAACTTC
1 AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTTC
*
42421525 AGGGAGATAAGATTCGCCATCTTC
66 AGGGAGATAAGATCCGCCATCTTC
* * * **
42421549 AATCCGCT-CCACTGCAACTTCAGGGAGATATGATTATTGGCTTCAATATGCTTCGCTGTAACTT
1 AATCCG-TACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTT
* *
42421613 TAGGGAGATGAGATCCGCCAT
65 CAGGGAGATAAGATCCGCCAT
42421634 AATTTTTAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 73 0.99
90 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (89 bp):
AATCCGTACCACTGCAACTTCAAGGAGATAGGATTATTGGCTTCAATATGCTCCGCTACAACTTC
AGGGAGATAAGATCCGCCATCTTC
Found at i:42421612 original size:44 final size:44
Alignment explanation
Indices: 42421471--42421626 Score: 150
Period size: 44 Copynumber: 3.5 Consensus size: 44
42421461 ATCCGTACCA
* * *
42421471 CTGCAACTTCAAGGAGATAGGATTATTGGCTTTAATCTGCTCCG
1 CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG
* ***** * *
42421515 CTACAACTTCAGGGAGATAAGATTCGCCATCTTCAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-ATTGGCTTCAATCTGCTCCG
* * *
42421560 CTGCAACTTCAGGGAGATATGATTATTGGCTTCAATATGCTTCG
1 CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG
* * *
42421604 CTGTAACTTTAGGGAGATGAGAT
1 CTGCAACTTCAGGGAGATAAGAT
42421627 CCGCCATAAT
Statistics
Matches: 85, Mismatches: 26, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
44 51 0.60
45 34 0.40
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATTATTGGCTTCAATCTGCTCCG
Found at i:42434056 original size:29 final size:29
Alignment explanation
Indices: 42434024--42434089 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
42434014 AATTAAAATT
*
42434024 TTAAAATAAGTTTAAATAAATGAACA-ATA
1 TTAAAATAAGTTGAAATAAATGAA-AGATA
* *
42434053 TTAAAATAAGTTGAAATGAATTAAAGATA
1 TTAAAATAAGTTGAAATAAATGAAAGATA
42434082 TTAAAATA
1 TTAAAATA
42434090 TTTGAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (29 bp):
TTAAAATAAGTTGAAATAAATGAAAGATA
Found at i:42434431 original size:3 final size:3
Alignment explanation
Indices: 42434419--42434485 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
42434409 ATAATAGCAG
* * * *
42434419 TAA TAG TAA TAA TAT TAA TAA TAA TGAA -AG TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *
42434464 TTA TAA TAA CAA CAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
42434486 CCTAATATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.02
3 49 0.94
4 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42440119 original size:18 final size:18
Alignment explanation
Indices: 42440082--42440119 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
42440072 TAAATGATGA
42440082 ATTTGAAGTATTAGTTGTT
1 ATTTGAAGTATTA-TTGTT
42440101 ATTTGTAAGTATT-TTGTT
1 ATTTG-AAGTATTATTGTT
42440119 A
1 A
42440120 AGTGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (18 bp):
ATTTGAAGTATTATTGTT
Found at i:42441553 original size:20 final size:20
Alignment explanation
Indices: 42441528--42441582 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
42441518 AAGCTTATGC
42441528 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
42441548 TAAGTAAAT-GAAGTGGAAAG
1 TAAGTAAATGGAA-TGGAAAG
42441568 TAAGTAAATGGAATG
1 TAAGTAAATGGAATG
42441583 ATTCATCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:42444576 original size:20 final size:20
Alignment explanation
Indices: 42444551--42444622 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
42444541 TATAAGCCAC
*
42444551 TCCATTTACTTACTTACCAT
1 TCCATTTACTTACTTTCCAT
42444571 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
*
42444591 TTCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
42444611 TCCATTTACTTA
1 TCCATTTACTTA
42444623 GCATAAGCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (20 bp):
TCCATTTACTTACTTTCCAT
Found at i:42444611 original size:15 final size:16
Alignment explanation
Indices: 42444560--42444592 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42444550 CTCCATTTAC
42444560 TTACTTACCATTCCAT
1 TTACTTACCATTCCAT
*
42444576 TTACTTA-CTTTCCAT
1 TTACTTACCATTCCAT
42444591 TT
1 TT
42444593 CATTTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACTTACCATTCCAT
Found at i:42448918 original size:24 final size:25
Alignment explanation
Indices: 42448898--42448957 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
42448888 AAATTTATCG
42448898 ATATTT-T-TAAAAAAT-ATTTTAT
1 ATATTTATATAAAAAATAATTTTAT
*
42448920 ATATTTATATAAAAAATAATTTTAA
1 ATATTTATATAAAAAATAATTTTAT
*
42448945 ATA-TTAAATAAAA
1 ATATTTATATAAAA
42448958 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 17 0.52
25 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTATATAAAAAATAATTTTAT
Found at i:42448975 original size:18 final size:18
Alignment explanation
Indices: 42448929--42448977 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
42448919 TATATTTATA
42448929 TAAAAAATAATTTTAAATAT
1 TAAAAAA-AA-TTTAAATAT
* *
42448949 TAAATAAAATTTAAATTT
1 TAAAAAAAATTTAAATAT
42448967 ATAAAAAAAAT
1 -TAAAAAAAAT
42448978 GCACAATGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAAAAAATTTAAATAT
Found at i:42459280 original size:16 final size:16
Alignment explanation
Indices: 42459259--42459289 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42459249 TTCACTATTA
*
42459259 TGTCTTTTTTATTTTC
1 TGTCTTTTATATTTTC
42459275 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
42459290 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:42459793 original size:28 final size:30
Alignment explanation
Indices: 42459754--42459810 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 30
42459744 CCTCTTTACT
42459754 TTCCCTCCAAAACTTTTACT-CCCTCCCAC
1 TTCCCTCCAAAACTTTTACTCCCCTCCCAC
42459783 TTCCC-CCAAAACTTTTACTCCCCTCCCA
1 TTCCCTCCAAAACTTTTACTCCCCTCCCA
42459811 TCCCCCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (30 bp):
TTCCCTCCAAAACTTTTACTCCCCTCCCAC
Found at i:42461526 original size:39 final size:39
Alignment explanation
Indices: 42461434--42461531 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
42461424 CCCAGCCCAA
* **
42461434 ACCCAATTACCCAACCCAGTAAAACTAAAACTAAAATTT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAAACT
*
42461473 ATCCAATTACCCAACCCAATAAAACTAAAACTAAAAGACT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAA-ACT
42461513 ACCCAATTA-CCAACCCAAT
1 ACCCAATTACCCAACCCAAT
42461532 TTACTAAAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 44 0.83
40 9 0.17
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAACTAAAACTAAAAACT
Found at i:42461607 original size:11 final size:11
Alignment explanation
Indices: 42461593--42461631 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
42461583 GCTGCCATTT
*
42461593 TTTTTCCCTAA
1 TTTTTCTCTAA
*
42461604 TTTTTCTCT-T
1 TTTTTCTCTAA
42461614 TTTTTCTCTAA
1 TTTTTCTCTAA
42461625 TTTTTCT
1 TTTTTCT
42461632 TGTTCTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTCTCTAA
Found at i:42461617 original size:21 final size:21
Alignment explanation
Indices: 42461591--42461631 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42461581 CGGCTGCCAT
42461591 TTTTTTTCCCTAATTTTTCTC
1 TTTTTTTCCCTAATTTTTCTC
*
42461612 TTTTTTTCTCTAATTTTTCT
1 TTTTTTTCCCTAATTTTTCT
42461632 TGTTCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTTCCCTAATTTTTCTC
Found at i:42462236 original size:31 final size:31
Alignment explanation
Indices: 42462201--42462260 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
42462191 TGTTTGCAAT
*
42462201 TTCTTATCCACTTTCATATGCAATTTCTTAA
1 TTCTTATCCACTTTCATAAGCAATTTCTTAA
42462232 TTCTTATCCACTTTCATAAGCAATTTCTT
1 TTCTTATCCACTTTCATAAGCAATTTCTT
42462261 CCTGCTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.48
Consensus pattern (31 bp):
TTCTTATCCACTTTCATAAGCAATTTCTTAA
Found at i:42462677 original size:18 final size:18
Alignment explanation
Indices: 42462645--42462696 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
42462635 GGTATTTTTC
42462645 GGTAATTCG-GTTAATTCA-
1 GGTAATTCGAG-TAATT-AG
*
42462663 GGTAATTTGAGTAATTAG
1 GGTAATTCGAGTAATTAG
*
42462681 GGTACTTCGAGTAATT
1 GGTAATTCGAGTAATT
42462697 TTTAACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (18 bp):
GGTAATTCGAGTAATTAG
Found at i:42469574 original size:22 final size:21
Alignment explanation
Indices: 42469546--42469608 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
42469536 TCGAAATACT
* *
42469546 AACAGAGGCATCGTAGTGCAA
1 AACAGAGGCACCGAAGTGCAA
*
42469567 ATACAGAGGCACCAAAGTGC-A
1 A-ACAGAGGCACCGAAGTGCAA
42469588 AACAGAGGCACCGAAGTGCAA
1 AACAGAGGCACCGAAGTGCAA
42469609 TATCATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.47
21 4 0.11
22 15 0.42
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.10
Consensus pattern (21 bp):
AACAGAGGCACCGAAGTGCAA
Found at i:42471198 original size:7 final size:7
Alignment explanation
Indices: 42471176--42471230 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
42471166 TTCTTTTCAG
*
42471176 CTCAATA
1 CTCAATC
*
42471183 CTTAATC
1 CTCAATC
42471190 CTCAATC
1 CTCAATC
42471197 CTCAATC
1 CTCAATC
*
42471204 ATCAATC
1 CTCAATC
*
42471211 ATCAATC
1 CTCAATC
* *
42471218 ATCAATT
1 CTCAATC
42471225 CTCAAT
1 CTCAAT
42471231 TCATAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (7 bp):
CTCAATC
Found at i:42478191 original size:2 final size:2
Alignment explanation
Indices: 42478180--42478216 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
42478170 CTAGGGTTTA
42478180 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42478217 TAATCTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:42480676 original size:19 final size:18
Alignment explanation
Indices: 42480652--42480699 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
42480642 TTGTATTTTT
* *
42480652 AAAAATATTAATTACTATA
1 AAAAATATCAA-TACGATA
42480671 AAAAATTATCAATACGATA
1 AAAAA-TATCAATACGATA
42480690 AAATAATATC
1 AAA-AATATC
42480700 TAAACGAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAATATCAATACGATA
Found at i:42481705 original size:30 final size:31
Alignment explanation
Indices: 42481660--42481732 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
42481650 ATTTTTAAAA
*
42481660 AAAAATTGAAGGGGTTAAATTATAAATATTC
1 AAAAATTGAAGGGGTTAAATTAAAAATATTC
* *
42481691 AAAAGTTG-AGGGGTTAAATTAAAAATA-TA
1 AAAAATTGAAGGGGTTAAATTAAAAATATTC
42481720 AAAAATTTGAAGG
1 AAAAA-TTGAAGG
42481733 ACTAAAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.14
30 21 0.58
31 10 0.28
ACGTcount: A:0.51, C:0.01, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAAATTGAAGGGGTTAAATTAAAAATATTC
Found at i:42489223 original size:16 final size:15
Alignment explanation
Indices: 42489202--42489236 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42489192 TGAATATAAA
*
42489202 TATATAATTATTATTT
1 TATATAATTAAT-TTT
42489218 TATATAATTAATTTT
1 TATATAATTAATTTT
42489233 TATA
1 TATA
42489237 ATATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATAATTAATTTT
Found at i:42489236 original size:13 final size:14
Alignment explanation
Indices: 42489202--42489243 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
42489192 TGAATATAAA
42489202 TATATAATTATTATTT
1 TATATAATTA--ATTT
42489218 TATATAATTAATTT
1 TATATAATTAATTT
42489232 T-TATAATATAAT
1 TATATAAT-TAAT
42489244 ATACTTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 9 0.36
16 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATAATTAATTT
Found at i:42491030 original size:109 final size:109
Alignment explanation
Indices: 42490855--42491072 Score: 373
Period size: 109 Copynumber: 2.0 Consensus size: 109
42490845 TCCTAACAGC
*
42490855 ATTTGCCCGCAACTGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC
1 ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC
*
42490920 GTTGACTGGTCGTACCTGCAGCAAAAAGCAGAAACAAACAGCAA
66 GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA
* * *
42490964 ATTTGCCCGTAGCCGCCGCACATCCTAACAGCAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC
1 ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC
* *
42491029 GTTGACTGGTCGTACCTGCAGCAACAAGCAAAAAGAAACAGCAA
66 GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA
42491073 CGAAATAATA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.28, C:0.36, G:0.20, T:0.16
Consensus pattern (109 bp):
ATTTGCCCGCAACCGCCGCACATCCTAACAACAGCCCCGCACATGTCGCGCACGTTCGCCTCCAC
GTTGACTGGTCGTACCTGCAGCAAAAAGCAAAAACAAACAGCAA
Found at i:42491807 original size:16 final size:15
Alignment explanation
Indices: 42491757--42491821 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
42491747 CCCTGTTCTA
*
42491757 TTTTAATTTCATTTTT
1 TTTTAATTT-GTTTTT
* *
42491773 TGGTTATTTTGTTTTT
1 T-TTTAATTTGTTTTT
*
42491789 TTTCAATTTGTTTTT
1 TTTTAATTTGTTTTT
*
42491804 TTTTAAATTGTTATTT
1 TTTTAATTTGTT-TTT
42491820 TT
1 TT
42491822 AAAATTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 21 0.54
16 12 0.31
17 6 0.15
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (15 bp):
TTTTAATTTGTTTTT
Found at i:42491826 original size:15 final size:15
Alignment explanation
Indices: 42491781--42491827 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
42491771 TTTGGTTATT
* *
42491781 TTGTTTTTTTTCAAT
1 TTGTTTTTTTTAAAA
*
42491796 TTGTTTTTTTTTAAA
1 TTGTTTTTTTTAAAA
*
42491811 TTGTTATTTTTAAAA
1 TTGTTTTTTTTAAAA
42491826 TT
1 TT
42491828 ATTACTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (15 bp):
TTGTTTTTTTTAAAA
Found at i:42492006 original size:11 final size:10
Alignment explanation
Indices: 42491990--42492023 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
42491980 TTTTAACCTT
42491990 TATATACTTTA
1 TATATA-TTTA
42492001 TATATATTATA
1 TATATATT-TA
42492012 TATATATTTA
1 TATATATTTA
42492022 TA
1 TA
42492024 CATTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATATTTA
Found at i:42492101 original size:21 final size:21
Alignment explanation
Indices: 42492063--42492102 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42492053 ATATACATAC
* **
42492063 TTTTATTTTTATTTTTCTTTA
1 TTTTATTTTCATAATTCTTTA
42492084 TTTTATTTTCATAATTCTT
1 TTTTATTTTCATAATTCTT
42492103 ACATATACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTATTTTCATAATTCTTTA
Found at i:42496937 original size:13 final size:13
Alignment explanation
Indices: 42496915--42496966 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
42496905 TCGTAAAAAT
42496915 AATG-AAATGAAA
1 AATGAAAATGAAA
*
42496927 AGTGAAAATGAAA
1 AATGAAAATGAAA
42496940 AATGAAAAATGGAAA
1 AATG-AAAAT-GAAA
42496955 AA-GAAAA-GAAA
1 AATGAAAATGAAA
42496966 A
1 A
42496967 GGAGAGGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 5 0.14
12 3 0.09
13 15 0.43
14 6 0.17
15 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (13 bp):
AATGAAAATGAAA
Found at i:42496954 original size:8 final size:7
Alignment explanation
Indices: 42496919--42496961 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
42496909 AAAAATAATG
42496919 AAATGAA
1 AAATGAA
*
42496926 AAGTG-A
1 AAATGAA
42496932 AAATGAA
1 AAATGAA
42496939 AAATGAA
1 AAATGAA
42496946 AAATGGAA
1 AAAT-GAA
42496954 AAA-GAA
1 AAATGAA
42496960 AA
1 AA
42496962 GAAAAGGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 10 0.31
7 16 0.50
8 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:42498383 original size:44 final size:44
Alignment explanation
Indices: 42498254--42499149 Score: 693
Period size: 44 Copynumber: 20.3 Consensus size: 44
42498244 AAAAGCAGCA
* * * ***
42498254 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
*** * ***
42498298 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAATG
1 GATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAATG
* * * * *
42498343 GATCTTGGCTTCATATATTAACATGAAGTAGATCAGAGATAGTA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
* * *
42498387 GATCTTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGTA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
* *
42498431 GATCTTATCTTCATGTATTGACATGAAGTAGATC-GAAGATGATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG
* *
42498475 GATATTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGCA-G
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA--ATG
* * **
42498520 G-TATTGCCTTCATGTATTGACATGAAGTAGATCAGAGATAACA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
* * * *
42498563 TATCTTATTTTCATGTATTGACATGAAGTAGATC-GAAGGTAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG
***
42498607 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
*** * ** *
42498651 GATCTTGTCTTCCCATACTGGTAGTGAAGTAGATC-GAAGGTAATG
1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAG-AGATAATG
***
42498696 GATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGA-AGTAGATCAGAGATAATG
42498740 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT-A-G
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
*
42498782 GATATCTTATCTTCATGTATTGACATGAAGTAGATC-GAAGATAATG
1 G--ATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG
***
42498828 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
* *
42498872 GATCTTGTCTTCATGTACT-AGCGTGAAGTAGATC-GAAGA-AA-G
1 GATCTTGTCTTCATGTATTGA-CATGAAGTAGATCAG-AGATAATG
* * * * **
42498914 CAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAAAACA
1 --GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
* * *
42498960 GATATTGTCTTCATGTACTGACGTGAAGTAGATC-GAAGA-AA-G
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG
* * * * * **
42499002 CAAATCTTGTCTTCCTGTACT-AGCAGTGAAGTATATCAAAGATAACA
1 --GATCTTGTCTTCATGTATTGA-CA-TGAAGTAGATCAGAGATAATG
*** * ** *
42499049 GATCTTGTCTTCCCATACTGGTAGCGAAGTAGATC-GAAGA-AA-G
1 GATCTTGTCTTCATGTATTGACA-TGAAGTAGATCAG-AGATAATG
* * * *
42499092 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGTA
1 --GATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAATG
42499138 GATCTTGTCTTC
1 GATCTTGTCTTC
42499150 CCATACTGGT
Statistics
Matches: 692, Mismatches: 116, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
42 2 0.00
43 10 0.01
44 538 0.78
45 137 0.20
46 5 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (44 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAATG
Found at i:42498456 original size:88 final size:88
Alignment explanation
Indices: 42498253--42499149 Score: 857
Period size: 88 Copynumber: 10.1 Consensus size: 88
42498243 AAAAAGCAGC
* * * *** *
42498253 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTA-TT
***
42498318 GTGGTGAAGTAGATC-GAAGATAAT
65 GACATGAAGTAGATCAG-AGATAAT
* * * * *
42498342 GGATCTTGGCTTCATATATTAACATGAAGTAGATC-AGAGATAGTAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT
* *
42498406 GACATGGAGTAGATCAGAGATAGT
65 GACATGAAGTAGATCAGAGATAAT
* *
42498430 AGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGAT-G-ATGGATATTGTCTTCATGTAT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCA--GATCTTGTCTTCATGTAT
* **
42498493 TGACATGGAGTAGATCAGAGATAGC
64 TGACATGAAGTAGATCAGAGATAAT
* * * * * * *
42498518 AGGTATTGCCTTCATGTATTGACATGAAGTAGATC-AGAGATAACATATCTTATTTTCATGTATT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT
*
42498582 GACATGAAGTAGATC-GAAGGTAAT
65 GACATGAAGTAGATCAG-AGATAAT
* *** *
42498606 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTATT
** *
42498670 GGTAGTGAAGTAGATC-GAAGGTAAT
65 GACA-TGAAGTAGATCAG-AGATAAT
*
42498695 GGATCTTGTCTTCATGTATTGACAT-AGAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTAT
1 AGATCTTGTCTTCATGTATTGACATGA-AGTAGATCGA-AGATAGCAGATCTTGTCTTCATGTAT
**
42498758 TGACATGAAGTAGATCAGAGATAGG
64 TGACATGAAGTAGATCAGAGATAAT
* * ***
42498783 ATATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
**
42498848 ACATGAAGTAGATCAGAGATAGC
66 ACATGAAGTAGATCAGAGATAAT
* * * *
42498871 AGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT
* * * *
42498935 GGCATGAAGTAGATCAAAGAAAAC
65 GACATGAAGTAGATCAGAGATAAT
* * * * * * *
42498959 AGATATTGTCTTCATGTACTGACGTGAAGTAGATCGAAGAAAGCAAATCTTGTCTTCCTGTACT-
1 AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
* * *
42499023 AGCAGTGAAGTATATCAAAGATAAC
66 A-CA-TGAAGTAGATCAGAGATAAT
*** * ** * *
42499048 AGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATT
* * *
42499113 GGCGTGAAGTAGATC-GAAGATAGT
65 GACATGAAGTAGATCAG-AGATAAT
42499137 AGATCTTGTCTTC
1 AGATCTTGTCTTC
42499150 CCATACTGGT
Statistics
Matches: 685, Mismatches: 102, Indels: 42
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.00
87 4 0.01
88 443 0.65
89 199 0.29
90 38 0.06
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (88 bp):
AGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTG
ACATGAAGTAGATCAGAGATAAT
Found at i:42498901 original size:353 final size:353
Alignment explanation
Indices: 42498252--42499149 Score: 1207
Period size: 353 Copynumber: 2.5 Consensus size: 353
42498242 TAAAAAGCAG
* *
42498252 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT
* * *
42498317 GGTGGTGAAGTAGATCGAAGATAATGGATCTTGGCTTCATATATTAACATGAAGTAGATCAGAGA
66 GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGAAGTAGATCAGAGA
* *
42498382 TAGTAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAGAGATAGTAGATCTTATCTTCATGT
131 TAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATGT
* *
42498447 ATTGACATGAAGTAGATCGAAGATGATGGATATTGTCTTCATGTATTGACATGGAGTAGATCAGA
196 ATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAGA
* * * *
42498512 GATAGCAGGTATTGCCTTCATGTATTGACATGAAGTAGATC-AGAGATAA-CATATCTTATTTTC
261 GATAGCAGATATTGCCTTCATGTATAGACATGAAGTAGATCGA-AGA-AAGCAGATCTTATCTTC
* * **
42498575 ATGTATTGACATGAAGTAGATCGAAGGTAA
324 ATGTACTGACATGAAGTAGATCAAAGAAAA
** *
42498605 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT
* *
42498670 GGTAGTGAAGTAGATCGAAGGTAATGGATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAGAG
66 GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGA-AGTAGATCAGAG
* *
42498734 ATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGGATATCTTATCTTCATG
130 ATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATG
*
42498799 TATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG
195 TATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAG
* * * *
42498864 AGATAGCAGATCTTGTCTTCATGTACTAG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
260 AGATAGCAGATATTGCCTTCATGTA-TAGACATGAAGTAGATCGAAGAAAGCAGATCTTATCTTC
*
42498928 ATGTACTGGCATGAAGTAGATCAAAGAAAA
324 ATGTACTGACATGAAGTAGATCAAAGAAAA
* * * * **
42498958 CAGATATTGTCTTCATGTACTGACGTGAAGTAGATC-GAAGAAAGCAAATCTTGTCTTCCTGTAC
1 CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAG-AGATAGCAGATCTTGTCTTCCCATAC
* * * * ** ** * ** *
42499022 TAGCAGTGAAGTATATCAAAGATAACAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATC-GA
65 TGGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACA-TGAAGTAGATCAG-
* * * *
42499086 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAGTAGATCTTGTCTTC
128 AGATAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGTAGATCTTATCTTC
42499150 CCATACTGGT
Statistics
Matches: 477, Mismatches: 59, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
352 4 0.01
353 405 0.85
354 67 0.14
355 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (353 bp):
CAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAGAGATAGCAGATCTTGTCTTCCCATACT
GGTAGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATATATTGACATGAAGTAGATCAGAGA
TAGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTATCTTCATGT
ATTGACATGAAGTAGATCGAAGATAATGGATATTGTCTTCATGTATTGACATGAAGTAGATCAGA
GATAGCAGATATTGCCTTCATGTATAGACATGAAGTAGATCGAAGAAAGCAGATCTTATCTTCAT
GTACTGACATGAAGTAGATCAAAGAAAA
Found at i:42499221 original size:89 final size:89
Alignment explanation
Indices: 42498808--42499221 Score: 227
Period size: 88 Copynumber: 4.7 Consensus size: 89
42498798 GTATTGACAT
** * * * * * * *
42498808 GAAGTAGATCGAAGATAA-TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGC
1 GAAGTAGATCGAAGA-AACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGAT-AGAAGATAGT
*** * * *
42498871 AGATCTTGTCTTCATGTACTAG-CGT
64 AGATCTTGTCTTCCCATACTGGTAGC
* * * * * * * * **
42498896 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCA-AAGAAAACA
1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGAT-AGAAGATAGTA
* *** *
42498960 GATATTGTCTTCATGTACT-G-ACGT
65 GATCTTGTCTTCCCATACTGGTA-GC
* * * * * * * * *
42498984 GAAGTAGATCGAAGAAAGCAAATCTTGTCTTCC-TGTACTAGCAGTGAAGTATATCA-AAGATAA
1 GAAGTAGATCGAAGAAACCAGATCTTATC-TCCATGAATTGGC-GTGAAGCAGAT-AGAAGATAG
*
42499047 CAGATCTTGTCTTCCCATACTGGTAGC
63 TAGATCTTGTCTTCCCATACTGGTAGC
* * * * * *
42499074 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAG
1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGATAGAAGATAGTAG
*
42499139 ATCTTGTCTTCCCATACTGGTGGC
66 ATCTTGTCTTCCCATACTGGTAGC
* * *
42499163 GAAGTAGATCGAAGATACCAG-TCTTATCTCCCTGAAGTT-GCAGTGGAGCAGATAGAAGA
1 GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAA-TTGGC-GTGAAGCAGATAGAAGA
42499222 AACCAATCCT
Statistics
Matches: 278, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
87 3 0.01
88 123 0.44
89 114 0.41
90 37 0.13
91 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAACCAGATCTTATCTCCATGAATTGGCGTGAAGCAGATAGAAGATAGTAG
ATCTTGTCTTCCCATACTGGTAGC
Found at i:42499237 original size:44 final size:44
Alignment explanation
Indices: 42499168--42499259 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
42499158 GTGGCGAAGT
* * * * *
42499168 AGATCGAAGATACCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC
* *
42499212 AGATAGAAGAAACCAATCCTATCTCCTTGAAGTTGCAATGGAGT
1 AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC
42499256 AGAT
1 AGAT
42499260 TAAAACCACA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
AGATAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAATGGAGC
Found at i:42499681 original size:20 final size:20
Alignment explanation
Indices: 42499652--42499692 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
42499642 CAATAAACAG
42499652 ACCCAATTAA-TAGCCCAAA
1 ACCCAATTAACTAGCCCAAA
42499671 ACCCAAATTAACCTAGCCCAAA
1 ACCC-AATTAA-CTAGCCCAAA
42499693 CATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
22 9 0.47
ACGTcount: A:0.46, C:0.34, G:0.05, T:0.15
Consensus pattern (20 bp):
ACCCAATTAACTAGCCCAAA
Found at i:42501339 original size:29 final size:29
Alignment explanation
Indices: 42501284--42501340 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
42501274 TCTATATTGG
*
42501284 ATAAATATAATTATATGTATATGCAATAT
1 ATAAATATAATAATATGTATATGCAATAT
42501313 ATAAATATAA-AATGATGCTATAT-CAATA
1 ATAAATATAATAAT-ATG-TATATGCAATA
42501341 ATTGTGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 18 0.72
30 5 0.20
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (29 bp):
ATAAATATAATAATATGTATATGCAATAT
Found at i:42504158 original size:9 final size:9
Alignment explanation
Indices: 42504144--42504180 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42504134 TATAGTTTGA
42504144 TATTCGAAT
1 TATTCGAAT
42504153 TATTCGAAT
1 TATTCGAAT
*
42504162 TATTCGAGT
1 TATTCGAAT
42504171 TATTCGAAT
1 TATTCGAAT
42504180 T
1 T
42504181 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42504726 original size:20 final size:20
Alignment explanation
Indices: 42504703--42504746 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42504693 AGTTTTATAC
42504703 TTTTTAATAATTT-AAATAA
1 TTTTTAATAATTTAAAATAA
*
42504722 TTTTTAA-ATTTTAAAAATAA
1 TTTTTAATAATTT-AAAATAA
42504742 TTTTT
1 TTTTT
42504747 TTATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTAATAATTTAAAATAA
Found at i:42506957 original size:25 final size:25
Alignment explanation
Indices: 42506925--42507058 Score: 178
Period size: 25 Copynumber: 5.4 Consensus size: 25
42506915 ATACAATACA
* *
42506925 CCACAAAGACTTTTTAGATAATTCG
1 CCACAAAGGCTTTTCAGATAATTCG
* * * *
42506950 CCATAAAGGCTTTACAGATAACTCA
1 CCACAAAGGCTTTTCAGATAATTCG
42506975 CCACAAAGGCTTTTCAGATAATTCG
1 CCACAAAGGCTTTTCAGATAATTCG
* * * *
42507000 CCATAAAGGCTTTACAGATAACTCA
1 CCACAAAGGCTTTTCAGATAATTCG
42507025 CCACAAAGGCTTTTCAGATAATTCG
1 CCACAAAGGCTTTTCAGATAATTCG
42507050 CCACAAAGG
1 CCACAAAGG
42507059 TTTGCCACCA
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 91 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (25 bp):
CCACAAAGGCTTTTCAGATAATTCG
Found at i:42506977 original size:50 final size:50
Alignment explanation
Indices: 42506923--42507058 Score: 245
Period size: 50 Copynumber: 2.7 Consensus size: 50
42506913 TCATACAATA
* *
42506923 CACCACAAAGACTTTTTAGATAATTCGCCATAAAGGCTTTACAGATAACT
1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT
42506973 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT
1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT
*
42507023 CACCACAAAGGCTTTTCAGATAATTCGCCACAAAGG
1 CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGG
42507059 TTTGCCACCA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (50 bp):
CACCACAAAGGCTTTTCAGATAATTCGCCATAAAGGCTTTACAGATAACT
Found at i:42510138 original size:20 final size:21
Alignment explanation
Indices: 42510101--42510156 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
42510091 TTCTCTTATA
42510101 TATAT-ATTATATTAAACTTG-
1 TATATGATTAT-TTAAACTTGC
*
42510121 TATATGATTATTTTAACTTGC
1 TATATGATTATTTAAACTTGC
*
42510142 TTTATAGATTATTTA
1 TATAT-GATTATTTA
42510157 CATTAAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
21 9 0.30
22 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (21 bp):
TATATGATTATTTAAACTTGC
Found at i:42510153 original size:22 final size:22
Alignment explanation
Indices: 42510121--42510183 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 22
42510111 ATTAAACTTG
42510121 TATATGATTATTTTAACTTGCTT
1 TATA-GATTATTTTAACTTGCTT
*
42510144 TATAGATTATTTACATTAAGTTGCTT
1 TATAGATTA-TT---TTAACTTGCTT
*
42510170 TATATATTATTTTA
1 TATAGATTATTTTA
42510184 TTTTAAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 8 0.24
23 6 0.18
25 2 0.06
26 18 0.53
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (22 bp):
TATAGATTATTTTAACTTGCTT
Found at i:42510191 original size:27 final size:26
Alignment explanation
Indices: 42510128--42510215 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
42510118 TTGTATATGA
* *
42510128 TTATTTTAACTTGCTTTATAGATTAT
1 TTATTTTAAGTTGCTTTATATATTAT
**
42510154 TTACATTAAGTTGCTTTATATATTATT
1 TTATTTTAAGTTGCTTTATATATTA-T
** *
42510181 TTATTTTAAGTTATTTTATATATTAC
1 TTATTTTAAGTTGCTTTATATATTAT
42510207 TTATTTTAA
1 TTATTTTAA
42510216 AATTAACTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 30 0.58
27 22 0.42
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59
Consensus pattern (26 bp):
TTATTTTAAGTTGCTTTATATATTAT
Found at i:42510224 original size:16 final size:17
Alignment explanation
Indices: 42510186--42510226 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
42510176 TTATTTTATT
* *
42510186 TTAAGTTATTTTATATA
1 TTAACTTATTTTATAAA
42510203 TT-ACTTATTTTA-AAA
1 TTAACTTATTTTATAAA
42510218 TTAACTTAT
1 TTAACTTAT
42510227 ACTATTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAACTTATTTTATAAA
Found at i:42510226 original size:27 final size:27
Alignment explanation
Indices: 42510169--42510232 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
42510159 TTAAGTTGCT
* * **
42510169 TTATATATTATTTTATTTTAAGTTATT
1 TTATATATTATCTTATTTTAAATTAAC
42510196 TTATATATTA-CTTATTTTAAAATTAAC
1 TTATATATTATCTTATTTT-AAATTAAC
42510223 TTATACTATT
1 TTATA-TATT
42510233 TGCTTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 20 0.65
28 4 0.13
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (27 bp):
TTATATATTATCTTATTTTAAATTAAC
Found at i:42510388 original size:28 final size:30
Alignment explanation
Indices: 42510324--42510391 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
42510314 TCTGCGTGTC
*
42510324 TATT-TTTAAACTTTATTTTATTATATACT
1 TATTATTTAAACTTTATTTTATTATATAAT
*
42510353 TAGTTTATTTCAACTTT-TTTTA-TATATAAT
1 TA--TTATTTAAACTTTATTTTATTATATAAT
42510383 TATTATTTA
1 TATTATTTA
42510392 TATTAAGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 6 0.18
29 2 0.06
30 9 0.27
31 7 0.21
32 9 0.27
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (30 bp):
TATTATTTAAACTTTATTTTATTATATAAT
Found at i:42516079 original size:10 final size:10
Alignment explanation
Indices: 42516066--42516135 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
42516056 AAATTCAAAG
42516066 AAATATATAA
1 AAATATATAA
*
42516076 AAATATGTAA
1 AAATATATAA
** * *
42516086 CTATTTTTAA
1 AAATATATAA
*
42516096 AAATAAATAA
1 AAATATATAA
*
42516106 TAAA-ATTTAA
1 -AAATATATAA
42516116 AAATATATAA
1 AAATATATAA
*
42516126 AAATAAATAA
1 AAATATATAA
42516136 TTTCAAAAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
9 3 0.07
10 38 0.86
11 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AAATATATAA
Found at i:42516130 original size:26 final size:26
Alignment explanation
Indices: 42516100--42516150 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42516090 TTTTAAAAAT
*
42516100 AAATAATAAAATTT-AAAAATATATAA
1 AAATAA-AAAATTTCAAAAAAATATAA
*
42516126 AAATAAATAATTTCAAAAAAATATA
1 AAATAAAAAATTTCAAAAAAATATA
42516151 GTAAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATAAAAAATTTCAAAAAAATATAA
Found at i:42516552 original size:31 final size:29
Alignment explanation
Indices: 42516482--42516555 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
42516472 GGCTCAAGTT
* *
42516482 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
42516511 ACGTTTTAGTCACTTATGTTATCATGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
42516542 ACATTTTAGTCACT
1 ACATTTTAGTCACT
42516556 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:42517399 original size:6 final size:6
Alignment explanation
Indices: 42517390--42517438 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
42517380 TCTTTTAAAT
* *
42517390 TTAATA TTAATA TTAATA TTAATA TATAA-A TTAAAA TTATTA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA T-TAATA TTAATA TTAATA TTAATA
42517437 TT
1 TT
42517439 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
5 7 0.18
6 28 0.74
7 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:42517411 original size:18 final size:18
Alignment explanation
Indices: 42517384--42517438 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
42517374 GAGGGTTCTT
*
42517384 TTAAATTTAATATTAATA
1 TTAAAATTAATATTAATA
*
42517402 TTAATATTAATATATAA-A
1 TTAAAATTAATAT-TAATA
*
42517420 TTAAAATTATTATT-ATA
1 TTAAAATTAATATTAATA
42517437 TT
1 TT
42517439 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 4 0.13
18 23 0.74
19 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATTAATATTAATA
Found at i:42517446 original size:21 final size:22
Alignment explanation
Indices: 42517420--42517468 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
42517410 AATATATAAA
*
42517420 TTAAAATTA-TTAT-TATATTT
1 TTAAAAATATTTATGTATATTT
*
42517440 TTAAAAATATTTATGTATTTTT
1 TTAAAAATATTTATGTATATTT
42517462 TTAAAAA
1 TTAAAAA
42517469 AAATTTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAAAATATTTATGTATATTT
Found at i:42519951 original size:39 final size:39
Alignment explanation
Indices: 42519908--42520040 Score: 214
Period size: 39 Copynumber: 3.4 Consensus size: 39
42519898 AGTTTATCCA
42519908 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
* *
42519947 CCACCCAAGTCACCCAGCAAGCCGCCAAGTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
42519986 CCACCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
42520025 CCGA-CCAAGCCACCAA
1 CC-ACCCAAGTCACCAA
42520041 CTTACGCCCC
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 87 0.99
40 1 0.01
ACGTcount: A:0.28, C:0.47, G:0.14, T:0.11
Consensus pattern (39 bp):
CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
Found at i:42520041 original size:27 final size:27
Alignment explanation
Indices: 42520003--42520066 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
42519993 AGTCACCCAG
* *
42520003 CAAGCCGCCAACTTACGCTCCTCCGA-C
1 CAAGCCACCAACTTACGCCCCTCC-ACC
42520030 CAAGCCACCAACTTACGCCCCTCCACC
1 CAAGCCACCAACTTACGCCCCTCCACC
42520057 CAAGCCACCA
1 CAAGCCACCA
42520067 GTTTATCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.27, C:0.52, G:0.11, T:0.11
Consensus pattern (27 bp):
CAAGCCACCAACTTACGCCCCTCCACC
Found at i:42520503 original size:2 final size:2
Alignment explanation
Indices: 42520496--42520524 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42520486 ATTTGAGTTC
42520496 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
42520525 AATGGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42522310 original size:24 final size:24
Alignment explanation
Indices: 42522276--42522323 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42522266 TTCATTAAAT
*
42522276 ATTAATGGAAGATAGAAGTTTATA
1 ATTAATGGAAGATAGAAATTTATA
* *
42522300 ATTAATTGAAGATGGAAATTTATA
1 ATTAATGGAAGATAGAAATTTATA
42522324 GATTTCACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (24 bp):
ATTAATGGAAGATAGAAATTTATA
Found at i:42525107 original size:29 final size:29
Alignment explanation
Indices: 42525036--42525210 Score: 160
Period size: 29 Copynumber: 6.0 Consensus size: 29
42525026 TTTGATTTAT
* *
42525036 GTTTAGGGTTTTTGAGTTTGGGGATTTAGG
1 GTTTAGGGTTTTTGAATTTGGGGATTT-TG
* *
42525066 GTTTTA-AGTTGTTGAATTTGGGGATTTTG
1 G-TTTAGGGTTTTTGAATTTGGGGATTTTG
* *
42525095 GTTTATGGTTGTTGAATTTGGGGATTTT-
1 GTTTAGGGTTTTTGAATTTGGGGATTTTG
* *
42525123 TTGTTAGCGG-TTTT-AATTTTGGGGATTTTT
1 GT-TTAG-GGTTTTTGAA-TTTGGGGATTTTG
* *
42525153 GTTTAGGGTTTTTTAATATTGGGGATTTTT
1 GTTTAGGGTTTTTGAAT-TTGGGGATTTTG
* *
42525183 GTTTAGGGTTTTTAAATTTTGGGATTTT
1 GTTTAGGGTTTTTGAATTTGGGGATTTT
42525211 TTTGTTTTCG
Statistics
Matches: 125, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
28 9 0.07
29 60 0.48
30 52 0.42
31 4 0.03
ACGTcount: A:0.15, C:0.01, G:0.30, T:0.54
Consensus pattern (29 bp):
GTTTAGGGTTTTTGAATTTGGGGATTTTG
Found at i:42525182 original size:58 final size:60
Alignment explanation
Indices: 42525029--42525211 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 60
42525019 TTGTTATTTT
* * * *** * * *
42525029 GATTTATGTTTAGGGTTTTTGAGTTTGGGGATTTAGGGTTTTA-AGTTGTTGAA-TTTGGG
1 GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTG-TTTAGGGTTTTTAAATTTTGGG
* *
42525088 GATTTTGGTTTATGGTTGTTGAATTTGGGGATTTTTTG-TTAGCGG-TTTT-AATTTTGGG
1 GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTGTTTAG-GGTTTTTAAATTTTGGG
* *
42525146 GATTTTTGTTTAGGGTTTTTTAATATTGGGGA-TTTTTGTTTAGGGTTTTTAAATTTT-GG
1 GATTTTTGTTTAGGGTTGTTGAAT-TTGGGGATTTTTTGTTTAGGGTTTTTAAATTTTGGG
42525205 GATTTTT
1 GATTTTT
42525212 TTGTTTTCGA
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
57 5 0.05
58 37 0.36
59 55 0.53
60 6 0.06
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.54
Consensus pattern (60 bp):
GATTTTTGTTTAGGGTTGTTGAATTTGGGGATTTTTTGTTTAGGGTTTTTAAATTTTGGG
Found at i:42525682 original size:14 final size:15
Alignment explanation
Indices: 42525646--42525686 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
42525636 ATATTAATAT
*
42525646 TTTGTTTGTCTATAC
1 TTTGTTTGTCTACAC
*
42525661 TTTTTTTG-CTACAC
1 TTTGTTTGTCTACAC
42525675 TTTGTTTGTCTA
1 TTTGTTTGTCTA
42525687 TTATTATGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTGTTTGTCTACAC
Found at i:42526197 original size:48 final size:48
Alignment explanation
Indices: 42526130--42526245 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
42526120 GTTTTTGTGG
* * **
42526130 TGGTAATAAATGTGTTGAGGGTTTAAATGGGGAGGGTGTTAAGGTTGT
1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
* *
42526178 TGGTAGTAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTGAGGTTGT
1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
* * *
42526226 TGGCAATAAAAGTGGTGAGG
1 TGGTAATAAAGGTGATGAGG
42526246 TTGAGGGTGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.28, C:0.01, G:0.41, T:0.31
Consensus pattern (48 bp):
TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
Found at i:42526297 original size:81 final size:81
Alignment explanation
Indices: 42526197--42526346 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
42526187 AGGTGATGAG
*
42526197 GGTTTAAATAAGGAGGGTGTTGAGGTTGTTGGCAATAAA-AGTGGTGAGGTTGAGGGTGGTGAAG
1 GGTTTAAATAAGGAGGGTGTGGAGGTTGTTGGCAATAAAGA-TGGTGAGGTTGAGGGTGGTGAAG
42526261 ATGGTGAGAGTGTTGAA
65 ATGGTGAGAGTGTTGAA
* *
42526278 GGTTTAAAT-AGGTAGGGTGTGGAGGTTGTTGGCAGTTAAGATGGTGAGGTTGAGGGTGGTGAAG
1 GGTTTAAATAAGG-AGGGTGTGGAGGTTGTTGGCAATAAAGATGGTGAGGTTGAGGGTGGTGAAG
*
42526342 GTGGT
65 ATGGT
42526347 AAGGGTATTG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
80 3 0.05
81 59 0.94
82 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.45, T:0.29
Consensus pattern (81 bp):
GGTTTAAATAAGGAGGGTGTGGAGGTTGTTGGCAATAAAGATGGTGAGGTTGAGGGTGGTGAAGA
TGGTGAGAGTGTTGAA
Found at i:42528992 original size:158 final size:157
Alignment explanation
Indices: 42528736--42529047 Score: 435
Period size: 158 Copynumber: 2.0 Consensus size: 157
42528726 GGTGAGGGTC
* * * *
42528736 ACAACAGAAGATCATGCATTCAACCTAACACAACTGGATCACAAGTATATCGTAAACACTTTTTC
1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
* * * **
42528801 ATTGTCAAGTTCCAACATATTTAAATATAATTTGGGGTTTTGTATTTTATTCTCAATCTGATATG
66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTG-ATTTTATTCTCAATCTGATACA
*
42528866 AGTATAAGAACTAGAAGCCAAAAAAAGA
130 AGTACAAGAACTAGAAGCCAAAAAAAGA
* * *
42528894 ACAACAAAATATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCATAAACACTTTTTT
1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
* * * ** * *
42528959 ATTCTCAAGTTCCAAAATATTTAAATTTAATTTGGGGTTGTGATTTTTTTGTCTGTTTGGTACAA
66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTATTCTCAATCTGATACAA
42529024 GTACAAGAACTAGAAGCCAAAAAA
131 GTACAAGAACTAGAAGCCAAAAAA
42529048 GGAGGGTATA
Statistics
Matches: 134, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
157 38 0.28
158 96 0.72
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (157 bp):
ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTATTCTCAATCTGATACAA
GTACAAGAACTAGAAGCCAAAAAAAGA
Found at i:42530666 original size:28 final size:28
Alignment explanation
Indices: 42530603--42530667 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
42530593 CAAACCAGAT
* **
42530603 TGACCAAAAAAAACATTAGGTGGTAAAG
1 TGACCAAAAAAAACATAAGGTGCCAAAG
*
42530631 TGCTCCAAAAAAAACATAAAGG-GCCAAAG
1 TG-ACCAAAAAAAACAT-AAGGTGCCAAAG
42530660 TGACCAAA
1 TGACCAAA
42530668 CATCCAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 7 0.23
29 20 0.67
30 3 0.10
ACGTcount: A:0.51, C:0.17, G:0.18, T:0.14
Consensus pattern (28 bp):
TGACCAAAAAAAACATAAGGTGCCAAAG
Found at i:42532673 original size:16 final size:16
Alignment explanation
Indices: 42532648--42532682 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42532638 TAAAAGGAGC
42532648 TTTACAAAACA-AAGT
1 TTTACAAAACATAAGT
42532663 TTTATCAAAACATAAGT
1 TTTA-CAAAACATAAGT
42532680 TTT
1 TTT
42532683 TTATACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (16 bp):
TTTACAAAACATAAGT
Found at i:42535107 original size:5 final size:5
Alignment explanation
Indices: 42535097--42535159 Score: 110
Period size: 5 Copynumber: 12.8 Consensus size: 5
42535087 TCATCACGAA
*
42535097 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC TTATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
42535147 ATATC ATA-C ATAT
1 ATATC ATATC ATAT
42535160 TAGAAGCAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
4 4 0.07
5 51 0.93
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:42536726 original size:41 final size:41
Alignment explanation
Indices: 42536676--42536756 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
42536666 TTAAACAGAT
* *
42536676 TCACTGGCACTTAGCCTGCTAGGCTTAAAGCTTGATTCAGG
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGG
*
42536717 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAG
42536757 TTCTAGCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGG
Found at i:42542697 original size:25 final size:25
Alignment explanation
Indices: 42542669--42542731 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
42542659 TTATGTGTTT
*
42542669 TTAGTATAGT-CTATCTATAGTAGTC
1 TTAGTATA-TACTACCTATAGTAGTC
42542694 TTAGTATATACTACCTATAGTAGT-
1 TTAGTATATACTACCTATAGTAGTC
*
42542718 TTCAGGATATACTA
1 TT-AGTATATACTA
42542732 TCAAACACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (25 bp):
TTAGTATATACTACCTATAGTAGTC
Found at i:42555311 original size:40 final size:40
Alignment explanation
Indices: 42555108--42555311 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
42555098 CGGAATTTAA
** *
42555108 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
42555148 CCAGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42555188 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42555227 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42555267 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42555307 CCGGA
1 CCGGA
42555312 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 89 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42558640 original size:36 final size:36
Alignment explanation
Indices: 42558593--42558664 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
42558583 TCGGATCAAC
42558593 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT
1 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT
42558629 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT
1 TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT
42558665 GACTTCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (36 bp):
TACTCGTCAACTTTCGATTTCGCTCGATCTAAATCT
Found at i:42564443 original size:27 final size:27
Alignment explanation
Indices: 42564412--42564589 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
42564402 TAAATTGTAC
*
42564412 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
42564439 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42564465 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
42564493 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42564520 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
42564548 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
42564575 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42564590 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:42564475 original size:54 final size:55
Alignment explanation
Indices: 42564412--42564589 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
42564402 TAAATTGTAC
* **
42564412 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
42564467 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
42564520 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
42564575 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42564590 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:42567275 original size:75 final size:75
Alignment explanation
Indices: 42567099--42567371 Score: 390
Period size: 75 Copynumber: 3.6 Consensus size: 75
42567089 TGGATTTAGC
* * * * * *
42567099 ACTTAGTAACC-CCAGTGATTCGGGGAATCATCACTTAGCAACCCCTTTCACATTCAAAAATACG
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATT-TAAAATACG
* *
42567163 GTGGAATCAGC-
65 ATGGGATCA-CA
*
42567174 ACTTAGCAACCACCAGTGAA-TCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG
1 ACTTAGCAACCACCAAT-AATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG
42567238 ATGGGATCACA
65 ATGGGATCACA
*
42567249 ACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTTCAGATTTAAAATACGA
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA
42567314 TGGGATCACA
66 TGGGATCACA
* *
42567324 ACTTAGCAACCACCAATGATTCGAGGAATCAACACTTAGCAACCCCTT
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTT
42567372 GGGGGAATCA
Statistics
Matches: 182, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
74 3 0.02
75 140 0.77
76 38 0.21
77 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (75 bp):
ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA
TGGGATCACA
Found at i:42569404 original size:26 final size:26
Alignment explanation
Indices: 42569337--42569408 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
42569327 TCTCATCTCA
* * *
42569337 ATTTTA-CTTCAGTAAAATTTTGACT
1 ATTTTACCTTAAGTAAAATTTTAACG
*
42569362 ATTTTACCTTAACTAAAATTTTAACG
1 ATTTTACCTTAAGTAAAATTTTAACG
*
42569388 ATTTTACCCTT-GGTAAAATTT
1 ATTTTA-CCTTAAGTAAAATTT
42569409 CGAGAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
25 6 0.15
26 29 0.74
27 4 0.10
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (26 bp):
ATTTTACCTTAAGTAAAATTTTAACG
Found at i:42571011 original size:11 final size:11
Alignment explanation
Indices: 42570995--42571020 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42570985 TAGAAGAGAC
42570995 GAAACAGGGGA
1 GAAACAGGGGA
42571006 GAAACAGGGGA
1 GAAACAGGGGA
42571017 GAAA
1 GAAA
42571021 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:42578589 original size:138 final size:136
Alignment explanation
Indices: 42578287--42578705 Score: 635
Period size: 136 Copynumber: 3.1 Consensus size: 136
42578277 AAGAAAAAGG
*
42578287 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* *
42578352 TATAACTATTTATATTAATAAATTTGGTAATATATATA-ATTAATATTTTGTATGAATCAAATTC
66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTC
*
42578416 GTATATT
130 ATATATT
* * * * * *
42578423 AATTATATTATTTCCAAAAGAAAATTAATTTTCACGTATTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* **
42578488 TATAACTGTTTATATTAATAAAGTTGGTAAAATATTTACCATTAATATTTTAAATGAATCAAATT
66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATA-CATTAATATTTTGTATGAATCAAATT
42578553 CATATATT
129 CATATATT
*
42578561 AATTATATTCTTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* *
42578626 TATAATTG-TTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATT-GGTAAAATATATAC-ATTAATATTTTGTATGAATCAAATT
42578690 CATATATT
129 CATATATT
42578698 AATTATAT
1 AATTATAT
42578706 CTACGATTAA
Statistics
Matches: 253, Mismatches: 26, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
136 95 0.38
137 63 0.25
138 95 0.38
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTCA
TATATT
Found at i:42584817 original size:65 final size:63
Alignment explanation
Indices: 42584737--42584865 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 63
42584727 CGGTAAGCCC
42584737 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTAAGTTCGAA
1 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCT-A-TTCGAA
42584802 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA
1 AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA
42584865 A
1 A
42584866 CTTCAGCTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 7 0.11
64 1 0.02
65 56 0.88
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28
Consensus pattern (63 bp):
AAAGAGCGTCGTCTAAACCTAGGCTCCAATCCTTCCTACCCACATTTCACTTCTCTATTCGAA
Found at i:42588236 original size:23 final size:23
Alignment explanation
Indices: 42588210--42588256 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
42588200 CTGATATTAA
42588210 GCATGTATGATATATGCATTTTG
1 GCATGTATGATATATGCATTTTG
* * *
42588233 GCATTTGTTATATATGCATTTTG
1 GCATGTATGATATATGCATTTTG
42588256 G
1 G
42588257 ATGAGATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (23 bp):
GCATGTATGATATATGCATTTTG
Found at i:42588269 original size:23 final size:23
Alignment explanation
Indices: 42588219--42588270 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
42588209 AGCATGTATG
**
42588219 ATATATGCATTTTGGCATTTGTT
1 ATATATGCATTTTGGCATGAGTT
42588242 ATATATGCATTTTGG-ATGAGATT
1 ATATATGCATTTTGGCATGAG-TT
*
42588265 GTATAT
1 ATATAT
42588271 ATGGAGGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (23 bp):
ATATATGCATTTTGGCATGAGTT
Found at i:42596164 original size:38 final size:38
Alignment explanation
Indices: 42596101--42596313 Score: 255
Period size: 38 Copynumber: 5.6 Consensus size: 38
42596091 ACACTGGCAA
* * * *
42596101 TAAGCCTACTAGGCACTAAGCCTGAATAACACCAACAC
1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
* * * *
42596139 TAAGCCTACTAGGGACAAAGTCTGAATAACACCGACAC
1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
*
42596177 TAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC
1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
* * * *
42596215 TAAGCATGCTAGGAACAAAGCCTGAACAACATCGGCAC
1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
* * * *
42596253 TATGCCTGCTAGGCACAAAGCCTAAACTACACCGGCAC
1 TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
**
42596291 TGTGCCTGCTAGGCACAAAGCCT
1 TAAGCCTGCTAGGCACAAAGCCT
42596314 AAATAAGGGT
Statistics
Matches: 154, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 154 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (38 bp):
TAAGCCTGCTAGGCACAAAGCCTGAACAACACCGACAC
Found at i:42603309 original size:38 final size:38
Alignment explanation
Indices: 42603263--42603379 Score: 171
Period size: 38 Copynumber: 3.1 Consensus size: 38
42603253 AACTTTAATT
* * * *
42603263 ACACCGGCAATAAGCCTACTAGGCACTAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
*
42603301 ACATCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
* *
42603339 ACACCGACACTAAGCCTGCTAGGCACAAAACCTAAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
42603377 ACA
1 ACA
42603380 GTGTAACTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (38 bp):
ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
Found at i:42607606 original size:3 final size:3
Alignment explanation
Indices: 42607598--42607632 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
42607588 CACCCTTTTG
42607598 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
42607633 GCTTAGCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42607698 original size:14 final size:14
Alignment explanation
Indices: 42607676--42607711 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
42607666 AGTAATTGCT
*
42607676 AATCATAGTAAAGA
1 AATCCTAGTAAAGA
42607690 AATCCTAGTAAAGA
1 AATCCTAGTAAAGA
42607704 AATCCTAG
1 AATCCTAG
42607712 CAAAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (14 bp):
AATCCTAGTAAAGA
Found at i:42609313 original size:18 final size:19
Alignment explanation
Indices: 42609282--42609381 Score: 116
Period size: 18 Copynumber: 5.3 Consensus size: 19
42609272 AGAAATATAA
*
42609282 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAAAAATT
*
42609302 ATTTTTAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
*
42609321 ATTTT-AAATTTAAAAATT
1 ATTTTGAATTTTAAAAATT
42609339 ATTTTGAA-TTTAAAAATT
1 ATTTTGAATTTTAAAAATT
*
42609357 ATTTTGAATTTTTGAAAATT
1 ATTTTGAA-TTTTAAAAATT
42609377 ATTTT
1 ATTTT
42609382 ATTTTATTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
18 43 0.60
19 10 0.14
20 19 0.26
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:42610082 original size:32 final size:32
Alignment explanation
Indices: 42610016--42610082 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
42610006 TTAGGTTTTG
** *
42610016 ATTTCTAAATTTATTGCATTTCATTTGAATAT
1 ATTTCTAAATTTATTGCATTAAATTTGAAAAT
42610048 ATTTCTAAATTTATTTGCA-TAAATATT-AAAAT
1 ATTTCTAAATTTA-TTGCATTAAAT-TTGAAAAT
42610080 ATT
1 ATT
42610083 GTAATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.51
Consensus pattern (32 bp):
ATTTCTAAATTTATTGCATTAAATTTGAAAAT
Found at i:42611483 original size:10 final size:9
Alignment explanation
Indices: 42611462--42611573 Score: 62
Period size: 9 Copynumber: 11.7 Consensus size: 9
42611452 TTTCTATACA
42611462 TTTTATAAT
1 TTTTATAAT
*
42611471 TTTTATGAT
1 TTTTATAAT
42611480 TTTTATAATT
1 TTTTATAA-T
*
42611490 TTTTCTAAT
1 TTTTATAAT
*
42611499 TTTTAATAAA
1 TTTT-ATAAT
** *
42611509 AATTAAATAT
1 TTTTATA-AT
*
42611519 TTCTTATATT
1 TT-TTATAAT
*
42611529 TTTTATTAAAA
1 TTTTA-T-AAT
*
42611540 TTTAATAAT
1 TTTTATAAT
*
42611549 TTTTATAAC
1 TTTTATAAT
*
42611558 TTTTATTTAT
1 TTTTA-TAAT
42611568 TTTTAT
1 TTTTAT
42611574 TTTTATCATT
Statistics
Matches: 75, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
9 40 0.53
10 26 0.35
11 9 0.12
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:42611530 original size:29 final size:29
Alignment explanation
Indices: 42611497--42611555 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
42611487 ATTTTTTCTA
42611497 ATTTTTAATAAAAATTAAAT-ATTTCTTAT
1 ATTTTTAATAAAAATTAAATAATTT-TTAT
* * *
42611526 ATTTTTTATTAAAATTTAATAATTTTTAT
1 ATTTTTAATAAAAATTAAATAATTTTTAT
42611555 A
1 A
42611556 ACTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTTTAATAAAAATTAAATAATTTTTAT
Found at i:42613496 original size:13 final size:14
Alignment explanation
Indices: 42613480--42613509 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
42613470 CCATTTTTCA
42613480 TATTTTATTT-TTT
1 TATTTTATTTATTT
42613493 TATTTTATTTATTT
1 TATTTTATTTATTT
42613507 TAT
1 TAT
42613510 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:42613672 original size:6 final size:6
Alignment explanation
Indices: 42613631--42613665 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
42613621 GCTTTAGCCC
42613631 ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
42613666 TTGTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:42613672 original size:18 final size:18
Alignment explanation
Indices: 42613631--42613665 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
42613621 GCTTTAGCCC
42613631 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATTTTT
42613649 ATTTTTA-TTTTATTTTT
1 ATTTTTATTTTTATTTTT
42613666 TTGTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
ATTTTTATTTTTATTTTT
Found at i:42613792 original size:29 final size:29
Alignment explanation
Indices: 42613739--42613835 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 29
42613729 AATATATAAA
* * *
42613739 TTACATTTTGGCCTCTAAACTTTTTCAAAT
1 TTACATTTTGACCCCT-AACATTTTCAAAT
42613769 TTACATTTTGACCCCTAACATTTTCTAAAAT
1 TTACATTTTGACCCCTAACATTTTC--AAAT
* * * *
42613800 TT-CATCTTAACCCCTAATATTTTGTAAA-
1 TTACATTTTGACCCCTAACATTTT-CAAAT
42613828 TTACATTT
1 TTACATTT
42613836 GGGCCCTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
28 2 0.04
29 15 0.27
30 32 0.58
31 6 0.11
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (29 bp):
TTACATTTTGACCCCTAACATTTTCAAAT
Found at i:42613814 original size:30 final size:31
Alignment explanation
Indices: 42613765--42613827 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
42613755 AAACTTTTTC
* *
42613765 AAATTTACATTTTGACCCCTAACATTTTCTA
1 AAATTTACATCTTAACCCCTAACATTTTCTA
* *
42613796 AAATTT-CATCTTAACCCCTAATATTTTGTA
1 AAATTTACATCTTAACCCCTAACATTTTCTA
42613826 AA
1 AA
42613828 TTACATTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATTTACATCTTAACCCCTAACATTTTCTA
Found at i:42614443 original size:13 final size:13
Alignment explanation
Indices: 42614417--42614481 Score: 80
Period size: 13 Copynumber: 4.9 Consensus size: 13
42614407 GCCCCGAAGA
42614417 AGAAGAAGAAAAAG
1 AGAAGAA-AAAAAG
42614431 A-AAGGAAAAAAAG
1 AGAA-GAAAAAAAG
42614444 AGAAGAAAAAAGAG
1 AGAAGAAAAAA-AG
*
42614458 AGAAGAAAAAGAG
1 AGAAGAAAAAAAG
42614471 A-AAGAAAAAAA
1 AGAAGAAAAAAA
42614482 TATCTTACAC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
12 9 0.20
13 19 0.41
14 18 0.39
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAG
Found at i:42614465 original size:27 final size:26
Alignment explanation
Indices: 42614417--42614481 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
42614407 GCCCCGAAGA
42614417 AGAAGAAGAAAAAGAAAGGAAAAAAAG
1 AGAAGAA-AAAAAGAAAGGAAAAAAAG
*
42614444 AGAAG-AAAAAAGAGA-GAAGAAAAAG
1 AGAAGAAAAAAAGAAAGGAA-AAAAAG
42614469 AGAAAGAAAAAAA
1 AG-AAGAAAAAAA
42614482 TATCTTACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 3 0.09
25 16 0.47
26 4 0.12
27 11 0.32
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (26 bp):
AGAAGAAAAAAAGAAAGGAAAAAAAG
Found at i:42614837 original size:13 final size:12
Alignment explanation
Indices: 42614809--42614847 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
42614799 ACACCCAGCA
42614809 AAAAAAAAAAGAG
1 AAAAAAAAAAG-G
42614822 AAAGAAAAAAAGG
1 AAA-AAAAAAAGG
42614835 AAAAAAGAAAAGG
1 AAAAAA-AAAAGG
42614848 GCCCACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 13 0.54
14 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:42615335 original size:18 final size:19
Alignment explanation
Indices: 42615290--42615337 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
42615280 AAAATAAACA
42615290 ATCGTATTTCAAAAGTTTTC
1 ATCGT-TTTCAAAAGTTTTC
42615310 AT-GTTTTCAAAA-TTTTC
1 ATCGTTTTCAAAAGTTTTC
42615327 -TCGTGTTTCAA
1 ATCGT-TTTCAA
42615338 CAAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.27
18 14 0.54
19 2 0.08
20 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (19 bp):
ATCGTTTTCAAAAGTTTTC
Found at i:42615422 original size:15 final size:16
Alignment explanation
Indices: 42615398--42615430 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42615388 TTAAAAAAAC
42615398 AATTTCCGTG-TTTCA
1 AATTTCCGTGTTTTCA
*
42615413 AATTTTCGTGTTTTCA
1 AATTTCCGTGTTTTCA
42615429 AA
1 AA
42615431 AAATTCTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (16 bp):
AATTTCCGTGTTTTCA
Found at i:42615447 original size:18 final size:19
Alignment explanation
Indices: 42615412--42615450 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42615402 TCCGTGTTTC
*
42615412 AAATTTTCGTGTTTTCAAA
1 AAATTCTCGTGTTTTCAAA
42615431 AAATTCTCGTG-TTTCAAA
1 AAATTCTCGTGTTTTCAAA
42615449 AA
1 AA
42615451 TTTTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (19 bp):
AAATTCTCGTGTTTTCAAA
Done.