Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 192 of 444
Found at i:53631567 original size:30 final size:29
Alignment explanation
Indices: 53631473--53631574 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
53631463 TATAGTGAAT
* * *
53631473 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
53631502 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
53631530 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
53631560 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
53631575 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:53635025 original size:27 final size:27
Alignment explanation
Indices: 53634995--53635056 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
53634985 TAAAACAATC
*
53634995 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
53635022 ATTTTATACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
53635049 ATTTTACA
1 ATTTTACA
53635057 AAATGGGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:53635066 original size:27 final size:27
Alignment explanation
Indices: 53635005--53635085 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
53634995 ATTTTACCCT
* **
53635005 ACAAGGGTATTTCGGTAATTTTATACT
1 ACAAGGGTATTTCGGTAATTTTACAAA
53635032 ACAAGGGTATTTCGGTAATTTTACAAA
1 ACAAGGGTATTTCGGTAATTTTACAAA
*** **
53635059 ATGGGGGTATTTCGAAAATTTTACAAA
1 ACAAGGGTATTTCGGTAATTTTACAAA
53635086 TCGGGGTCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (27 bp):
ACAAGGGTATTTCGGTAATTTTACAAA
Found at i:53639762 original size:28 final size:28
Alignment explanation
Indices: 53639697--53639797 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
53639687 ATAGTGAATC
*
53639697 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
53639726 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53639754 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
53639784 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53639798 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53654665 original size:39 final size:38
Alignment explanation
Indices: 53654581--53654759 Score: 198
Period size: 39 Copynumber: 4.9 Consensus size: 38
53654571 TATGGTAACC
** * *
53654581 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAA-T
*
53654621 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAA-T
53654660 CGCACAATTGCCTTCGGGCTTAGCCCGG--AT-AT-AT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAAT
*
53654694 -GCAC-A----CTTCGGGCTTAGCCCGGATATCACAAT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAAT
*
53654726 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
53654760 CTCGAACATT
Statistics
Matches: 121, Mismatches: 8, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
28 17 0.14
30 2 0.02
31 1 0.01
32 3 0.02
33 8 0.07
34 2 0.02
35 1 0.01
36 2 0.02
37 2 0.02
38 23 0.19
39 45 0.37
40 15 0.12
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (38 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAAT
Found at i:53654749 original size:66 final size:67
Alignment explanation
Indices: 53654632--53654757 Score: 227
Period size: 66 Copynumber: 1.9 Consensus size: 67
53654622 GCACAATTGC
*
53654632 CTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATATGCA
1 CTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATATGCA
53654697 CA
66 CA
*
53654699 CTTCGGGCTTAGCCCGGATATCACAA-TTGCACAATTGCCTTCGGGCTTAGCCCGGATAT
1 CTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATAT
53654758 CACTCGAACA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 32 0.56
67 25 0.44
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (67 bp):
CTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATATGCA
CA
Found at i:53657435 original size:16 final size:16
Alignment explanation
Indices: 53657414--53657452 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
53657404 AAGCTGAAAT
*
53657414 GTCGAAATGCCAAAAA
1 GTCGAAATACCAAAAA
53657430 GTCGAAATACCAAAAA
1 GTCGAAATACCAAAAA
53657446 GTCGAAA
1 GTCGAAA
53657453 GTTTGGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (16 bp):
GTCGAAATACCAAAAA
Found at i:53657720 original size:29 final size:28
Alignment explanation
Indices: 53657663--53657777 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
53657653 GTGAGCGTGA
* * *
53657663 ATATGAATGTGACTAGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
53657691 ATATAAATGTGACTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* *
53657720 ATATTCAA-GTGATTGGGGACTAATGGGCC
1 ATA-TGAATGTGATT-GGGCCTAATGGGCC
* *
53657749 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
53657777 A
1 A
53657778 GATACAGGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 29 0.40
29 41 0.56
30 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:53661580 original size:47 final size:47
Alignment explanation
Indices: 53661505--53661615 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 47
53661495 CCCCTCGGGA
* * *
53661505 CTTATCACATT-TATACACTTTCATATTCATCGCATTGGCCATTCGGC
1 CTTATCAC-TTATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
53661552 CTTATCACTTATATACACTTTGACATTCATCACATCGGCCATTCGGC
1 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
53661599 CTTATCACATATATACA
1 CTTATCACTTATATACA
53661616 TCTCATACAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 2 0.03
47 56 0.97
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.36
Consensus pattern (47 bp):
CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:53661677 original size:46 final size:46
Alignment explanation
Indices: 53661619--53661754 Score: 254
Period size: 46 Copynumber: 3.0 Consensus size: 46
53661609 ATATACATCT
* *
53661619 CATACATGTTTCATACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
53661665 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
53661711 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATAT
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATAT
53661755 ATATTTAACT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (46 bp):
CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
Found at i:53664504 original size:40 final size:40
Alignment explanation
Indices: 53664446--53664559 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 40
53664436 GGATATAGCG
* * * *
53664446 ACTCGCTCGATTGTCTTCGGGACATAGCCCGG-TTATAGTG
1 ACTCGCACAATTGCCTTCGGGACATAGCCCGGATT-TAGTA
*
53664486 ATTCGCACAATTGCCTTCGGGA-ATTAGCCCGGATTTAGTA
1 ACTCGCACAATTGCCTTCGGGACA-TAGCCCGGATTTAGTA
** *
53664526 ACTCGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 ACTCGCACAATTGCCTTCGGGACATAGCCCGGAT
53664560 ACCATTCGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
39 1 0.02
40 59 0.95
41 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
ACTCGCACAATTGCCTTCGGGACATAGCCCGGATTTAGTA
Found at i:53665319 original size:40 final size:40
Alignment explanation
Indices: 53665219--53665524 Score: 474
Period size: 40 Copynumber: 7.7 Consensus size: 40
53665209 CCAGCATGAT
* *
53665219 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
53665259 TGCTC-TCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* * *
53665298 TGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
53665338 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
53665378 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
53665418 TGCTCTT-GGAACTTAGCCCGGATACGTCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
53665457 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
53665497 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGAACTTAGCCCGGATACATC
53665525 GTCGAGACCT
Statistics
Matches: 247, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 75 0.30
40 172 0.70
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:53665429 original size:119 final size:120
Alignment explanation
Indices: 53665203--53665524 Score: 542
Period size: 119 Copynumber: 2.7 Consensus size: 120
53665193 GCCCGAATAC
* * * *
53665203 ACGTCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAATGCTC-TCG
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
* *
53665267 GAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAT
66 GAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
*
53665322 ACGTCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
*
53665387 GAACTTAGCCCGGATATATCACTAGCACGAATGCTCTT-GGAACTTAGCCCGGAT
66 GAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
53665441 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
*
53665506 GGACTTAGCCCGGAT-CATC
66 GAACTTAGCCCGGATACATC
53665525 GTCGAGACCT
Statistics
Matches: 191, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
118 3 0.02
119 149 0.78
120 39 0.20
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCG
GAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
Found at i:53665512 original size:159 final size:159
Alignment explanation
Indices: 53665219--53665520 Score: 487
Period size: 159 Copynumber: 1.9 Consensus size: 159
53665209 CCAGCATGAT
* *
53665219 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAATGCTCTCGGAACTTAGTCCGGATAC
1 TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTCGGAACTTAGCCCGGATAC
* * *
53665284 ATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACGTCACTAGCATGAATGCTCTTCGGA
66 ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA
53665349 ACTTAGCCCGGATATATCACTAGCACGAA
131 ACTTAGCCCGGATATATCACTAGCACGAA
* * *
53665378 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAATGCTCTTGGAACTTAGCCCGGATAC
1 TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTCGGAACTTAGCCCGGATAC
* * * * *
53665443 GTCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGG
66 ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA
53665508 ACTTAGCCCGGAT
131 ACTTAGCCCGGAT
53665521 CATCGTCGAG
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
159 130 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (159 bp):
TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTCGGAACTTAGCCCGGATAC
ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA
ACTTAGCCCGGATATATCACTAGCACGAA
Found at i:53668154 original size:47 final size:47
Alignment explanation
Indices: 53668079--53668189 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
53668069 CCCCTCGGGA
* * *
53668079 CTTATCACATT-TATACACTTTCATATTCATCGCATTGGCCATTCGGC
1 CTTATCAC-TTATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
53668126 CTTATCACTTATATACACTTTGACATTCATCACATCGGCCATTCGGC
1 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
**
53668173 CTTATCAAATATATACA
1 CTTATCACTTATATACA
53668190 TCTCATACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 2 0.04
47 55 0.96
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (47 bp):
CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:53668245 original size:46 final size:46
Alignment explanation
Indices: 53668193--53668374 Score: 319
Period size: 46 Copynumber: 4.0 Consensus size: 46
53668183 ATATACATCT
* * *
53668193 CATACATGTTTCATACTAGCCATTTGGCTTTACCACACATATATCT
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
53668239 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
53668285 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
* *
53668331 CACACATATTTCACACTAACCATTTGGCTTTACCACACATATAT
1 CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATAT
53668375 ATATTTAACT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (46 bp):
CATACATATTTCACACTAGCCATTTGGCTTTACCACACATATATCA
Found at i:53678274 original size:27 final size:27
Alignment explanation
Indices: 53678243--53678298 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
53678233 GTCGTTAAGA
*
53678243 CCCTAATTTGTAAAATTATCGAAATAC
1 CCCTAATTTGTAAAATTACCGAAATAC
*
53678270 CCCTATTTTGTAAAATTACCGAAATAC
1 CCCTAATTTGTAAAATTACCGAAATAC
53678297 CC
1 CC
53678299 TTGTAGGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (27 bp):
CCCTAATTTGTAAAATTACCGAAATAC
Found at i:53678309 original size:27 final size:27
Alignment explanation
Indices: 53678252--53678312 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
53678242 ACCCTAATTT
* ***
53678252 GTAAAATTATCGAAATACCCCTATTTT
1 GTAAAATTACCGAAATACCCCTATAGG
* *
53678279 GTAAAATTACCGAAATACCCTTGTAGG
1 GTAAAATTACCGAAATACCCCTATAGG
53678306 GTAAAAT
1 GTAAAAT
53678313 GACTGTTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCCTATAGG
Found at i:53678719 original size:22 final size:22
Alignment explanation
Indices: 53678671--53678730 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
53678661 GTAATCTGAT
53678671 TATGGCTCTGTGCCAACCTAAA
1 TATGGCTCTGTGCCAACCTAAA
* * *
53678693 AATGGCTCTGTGCC-ATCTCGAA
1 TATGGCTCTGTGCCAACCT-AAA
*
53678715 TATGGCTTTGTGCCAA
1 TATGGCTCTGTGCCAA
53678731 ACGTATTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.87
23 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (22 bp):
TATGGCTCTGTGCCAACCTAAA
Found at i:53679700 original size:17 final size:19
Alignment explanation
Indices: 53679678--53679719 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
53679668 TTACTTTAGC
*
53679678 TTTCAAAT-AAGA-ATGGT
1 TTTCAAATGAAAACATGGT
53679695 TTTC-AATGAAAACATGGT
1 TTTCAAATGAAAACATGGT
53679713 TTTCAAA
1 TTTCAAA
53679720 AAACACTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 9 0.43
19 2 0.10
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
TTTCAAATGAAAACATGGT
Found at i:53679724 original size:16 final size:17
Alignment explanation
Indices: 53679690--53679724 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
53679680 TCAAATAAGA
53679690 ATGGTTTTCAATGAAAAC
1 ATGGTTTTCAA-GAAAAC
53679708 ATGGTTTTCAA-AAAAC
1 ATGGTTTTCAAGAAAAC
53679724 A
1 A
53679725 CTTCAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
ATGGTTTTCAAGAAAAC
Found at i:53682493 original size:27 final size:27
Alignment explanation
Indices: 53682463--53682595 Score: 105
Period size: 27 Copynumber: 4.9 Consensus size: 27
53682453 AACACCCCGA
*
53682463 TTTGTAAAATTATCGAAATAACCC-AGG
1 TTTGTAAAATTACCGAAATAACCCTA-G
*
53682490 TTTGTAAAATTACCGAAATACCCCTAG
1 TTTGTAAAATTACCGAAATAACCCTAG
* ** *
53682517 ATTGTAAAATTACTAAAAT-ACTCTCAG
1 TTTGTAAAATTACCGAAATAACCCT-AG
* *
53682544 TTTGTAAAATAACCAAAAT-ACCCTTA-
1 TTTGTAAAATTACCGAAATAACCC-TAG
*
53682570 TAGTT-TAAAATTACCGAAATACCCCT
1 T--TTGTAAAATTACCGAAATAACCCT
53682596 GTAGGGTAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.05
27 75 0.87
28 7 0.08
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
TTTGTAAAATTACCGAAATAACCCTAG
Found at i:53682590 original size:54 final size:53
Alignment explanation
Indices: 53682464--53682593 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 53
53682454 ACACCCCGAT
* * *
53682464 TTGTAAAATTATCGAAATAACCCAGGTTTGTAAAATTACCGAAATACCCCTAGA
1 TTGTAAAATTACCGAAAT-ACCCAGGTTTGTAAAATAACCAAAATACCCCTAGA
** * *
53682518 TTGTAAAATTACTAAAATACTCTCA-GTTTGTAAAATAACCAAAATACCCTTATA
1 TTGTAAAATTACCGAAATAC-C-CAGGTTTGTAAAATAACCAAAATACCCCTAGA
53682572 GTT-TAAAATTACCGAAATACCC
1 -TTGTAAAATTACCGAAATACCC
53682594 CTGTAGGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
52 1 0.02
53 3 0.05
54 56 0.88
55 4 0.06
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (53 bp):
TTGTAAAATTACCGAAATACCCAGGTTTGTAAAATAACCAAAATACCCCTAGA
Found at i:53682605 original size:27 final size:27
Alignment explanation
Indices: 53682492--53682607 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
53682482 AACCCAGGTT
* *
53682492 TGTAAAATTACCGAAATACCCCTAG-AT
1 TGTAAAATTACCAAAATACCCCT-GTAG
* * * *
53682519 TGTAAAATTACTAAAATACTCTCAGT-T
1 TGTAAAATTACCAAAATAC-CCCTGTAG
* * *
53682546 TGTAAAATAACCAAAATACCCTTATAG
1 TGTAAAATTACCAAAATACCCCTGTAG
* *
53682573 TTTAAAATTACCGAAATACCCCTGTAG
1 TGTAAAATTACCAAAATACCCCTGTAG
*
53682600 GGTAAAAT
1 TGTAAAAT
53682608 GACTATTTTG
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
26 2 0.03
27 64 0.94
28 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCCTGTAG
Found at i:53682925 original size:50 final size:49
Alignment explanation
Indices: 53682845--53682939 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 49
53682835 GAAGTACTGT
** * * *
53682845 TCTGATAAGGTCGTACGGGTCGCACGAGACGATTGTGGATCCAATATTGA
1 TCTGATAAGGTCACACGGGTCGCACAAGACGACTATGGA-CCAATATTGA
*
53682895 TCTGTTAAGGTCACACGGGTCGCACAAGACGACTATGGACCAATA
1 TCTGATAAGGTCACACGGGTCGCACAAGACGACTATGGACCAATA
53682940 GATGGCTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 6 0.15
50 33 0.85
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
TCTGATAAGGTCACACGGGTCGCACAAGACGACTATGGACCAATATTGA
Found at i:53684998 original size:28 final size:28
Alignment explanation
Indices: 53684903--53685000 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 28
53684893 GAACATGTGA
*
53684903 CCTAACGGGCCATATAAATGTGACTTGGG
1 CCTAATGGGCCATATAAATGTGA-TTGGG
*
53684932 CCTAATGGGCCATATTCAA-GTGATTGGGG
1 CCTAATGGGCCATA-TAAATGTGATT-GGG
* *
53684961 CCTAATGGGCCATATGAATATGATTGGG
1 CCTAATGGGCCATATAAATGTGATTGGG
*
53684989 CTTAATGGGCCA
1 CCTAATGGGCCA
53685001 GATACAGGCA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
28 19 0.31
29 39 0.64
30 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (28 bp):
CCTAATGGGCCATATAAATGTGATTGGG
Found at i:53688484 original size:2 final size:2
Alignment explanation
Indices: 53688477--53688503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53688467 CGTGATGCAC
53688477 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53688504 CATAAGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53689077 original size:59 final size:58
Alignment explanation
Indices: 53688978--53689112 Score: 225
Period size: 59 Copynumber: 2.3 Consensus size: 58
53688968 TTAAAAATTG
*
53688978 TACAGCACTATGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAACTGAAAATA
1 TACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAACTGAAAATA
* *
53689036 TACAGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATA
1 TACAGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAACTGAAAATA
*
53689095 TATAGCACTAAGTGTGCG
1 TACAGCACTAAGTGTGCG
53689113 GATTCACTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 25 0.35
59 47 0.65
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (58 bp):
TACAGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAACTGAAAATA
Found at i:53689124 original size:29 final size:29
Alignment explanation
Indices: 53688981--53689112 Score: 219
Period size: 29 Copynumber: 4.5 Consensus size: 29
53688971 AAAATTGTAC
* *
53688981 AGCACTATGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
* *
53689010 AGCACTAAGTGTGCGAACTGAAAATATAC
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
53689039 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
53689069 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
53689098 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53689113 GATTCACTAT
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 70 0.71
30 28 0.29
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:53692179 original size:29 final size:29
Alignment explanation
Indices: 53692147--53692219 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
53692137 CTTCGAGCTC
*
53692147 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53692176 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53692205 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
53692220 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53700142 original size:29 final size:29
Alignment explanation
Indices: 53700110--53700182 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
53700100 CTTCGAGCTC
*
53700110 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53700139 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53700168 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
53700183 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53707816 original size:28 final size:28
Alignment explanation
Indices: 53707747--53707847 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
53707737 GACAAGATTG
* * * *
53707747 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
53707777 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
53707805 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
53707834 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53707848 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:53715775 original size:28 final size:28
Alignment explanation
Indices: 53715706--53715806 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
53715696 GACAAGATTG
* * * *
53715706 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
53715736 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
53715764 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
53715793 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53715807 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:53723379 original size:40 final size:40
Alignment explanation
Indices: 53723271--53723480 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
53723261 CGGGATTTAA
* * * * *
53723271 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
53723311 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
53723351 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
53723391 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
53723431 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
53723471 CCGGATATAT
1 CCGGATATAT
53723481 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:53727917 original size:86 final size:85
Alignment explanation
Indices: 53727768--53727933 Score: 278
Period size: 86 Copynumber: 1.9 Consensus size: 85
53727758 ACAGAAGAAT
* **
53727768 AATTTGGTAAATTCCTTAATTATTAAAAAAATTACATATTAACTTACTGTTTATTGAAGCTCTTT
1 AATTCGGTAAATTCCTTAATTATTAAAAAAATTACATATTAACTTACCATTTATTGAAGCTCTTT
53727833 CACAGATGCCAAACATAGAC
66 CACAGATGCCAAACATAGAC
53727853 AATTCGGTAAATTCCTTAAATTATTAAAAAAATTACATATTAACTTACCATTTATTGAAGCTCTT
1 AATTCGGTAAATTCCTT-AATTATTAAAAAAATTACATATTAACTTACCATTTATTGAAGCTCTT
**
53727918 TCGTAGATGCCAAACA
65 TCACAGATGCCAAACA
53727934 CAGTCAAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 16 0.21
86 59 0.79
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (85 bp):
AATTCGGTAAATTCCTTAATTATTAAAAAAATTACATATTAACTTACCATTTATTGAAGCTCTTT
CACAGATGCCAAACATAGAC
Found at i:53735979 original size:27 final size:28
Alignment explanation
Indices: 53735922--53735991 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
53735912 AAATTTGTAC
**
53735922 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
53735950 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
53735977 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53735992 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:53736000 original size:27 final size:27
Alignment explanation
Indices: 53735922--53736003 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
53735912 AAATTTGTAC
* *
53735922 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
53735950 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
53735977 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
53736004 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:53743902 original size:27 final size:28
Alignment explanation
Indices: 53743845--53743914 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
53743835 AAATTTGTAC
**
53743845 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
53743873 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
53743900 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53743915 GACTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:53743923 original size:27 final size:27
Alignment explanation
Indices: 53743845--53743926 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
53743835 AAATTTGTAC
* *
53743845 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGGACTT-ATTATAT
* *
53743873 AGCACTATGTGTGC-GAGCTGATTATAT
1 AGCACTAAGTGTGCGGA-CTTATTATAT
53743900 AGCACTAAGTGTGCGGACTTATTATAT
1 AGCACTAAGTGTGCGGACTTATTATAT
53743927 GCTTTTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 30 0.65
28 16 0.35
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGACTTATTATAT
Found at i:53746719 original size:26 final size:25
Alignment explanation
Indices: 53746690--53746741 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
53746680 ACTTTAGTTA
53746690 AGGGACT-TTTGATGAAAATGTGAAAT
1 AGGGACTATTTG-TG-AAATGTGAAAT
53746716 AGGGACTAATTTGTGAAATGTGAAAT
1 AGGGACT-ATTTGTGAAATGTGAAAT
53746742 TTATCAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 18 0.75
27 2 0.08
28 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (25 bp):
AGGGACTATTTGTGAAATGTGAAAT
Found at i:53756409 original size:41 final size:42
Alignment explanation
Indices: 53756342--53756471 Score: 165
Period size: 43 Copynumber: 3.1 Consensus size: 42
53756332 GAGATGTTGC
*
53756342 CATCGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGG
1 CATCGATATGTGATTACGTGTAAGACCATGTTTGGGAC-TTGG
* * *
53756385 CATCG-TATTTGATT-CGTGTAAGACCCTATTTGGGACTATGG
1 CATCGATATGTGATTACGTGTAAGACCATGTTTGGGACT-TGG
* *
53756426 CATCGATATGTGATTACATGTAAGACCACGTTTGGGACGTTGG
1 CATCGATATGTGATTACGTGTAAGACCATGTTTGGGAC-TTGG
53756469 CAT
1 CAT
53756472 TGTTCGATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.36
42 16 0.22
43 29 0.39
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
CATCGATATGTGATTACGTGTAAGACCATGTTTGGGACTTGG
Found at i:53758091 original size:40 final size:39
Alignment explanation
Indices: 53758013--53758234 Score: 245
Period size: 40 Copynumber: 5.5 Consensus size: 39
53758003 ACCCAAGTAT
* *
53758013 CTTCGGGATTTAGCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCGGATATAGTC-ACTAGCACAAATGC
* **
53758052 CTTCGGGTCTTAGCCAGGATATAGTCACTAGCATTAATGC
1 CTTCGGGACTTAGCC-GGATATAGTCACTAGCACAAATGC
*
53758092 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAATGC
53758132 CTTCGGGACTTAGCCCGG-TATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAGTC-ACTA---GCACAAATGC
* * *
53758174 TTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAATGC
53758214 C-TCGGGACTTAGCTCGGATAT
1 CTTCGGGACTTAGC-CGGATAT
53758235 CATCCGAATA
Statistics
Matches: 159, Mismatches: 14, Indels: 20
0.82 0.07 0.10
Matches are distributed among these distances:
38 2 0.01
39 40 0.25
40 79 0.50
41 3 0.02
42 27 0.17
43 8 0.05
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAGTCACTAGCACAAATGC
Found at i:53758195 original size:82 final size:80
Alignment explanation
Indices: 53758013--53758234 Score: 258
Period size: 82 Copynumber: 2.8 Consensus size: 80
53758003 ACCCAAGTAT
* * *
53758013 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCAGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCAGGATATAG
**
53758076 TCACTAGCATTAATGC
65 TCACTAGCACAAATGC
* *
53758092 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCAGGATATAGT
53758155 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* * *
53758174 TTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCC-TCGGGACTTAGCTC-GGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC-CAGGATAT
53758235 CATCCGAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
78 1 0.01
79 21 0.17
80 38 0.31
81 15 0.12
82 49 0.40
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCAGGATATAGT
CACTAGCACAAATGC
Found at i:53767162 original size:27 final size:27
Alignment explanation
Indices: 53766535--53767381 Score: 965
Period size: 27 Copynumber: 31.0 Consensus size: 27
53766525 AAAGTACTCC
53766535 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53766562 TGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
53766589 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
53766616 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
53766643 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
53766670 CGATTTACAGAATTACCGTTTTACCTT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
53766697 C-AGTTTATAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
53766724 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
53766751 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53766778 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
53766805 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53766832 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
53766859 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53766886 C-AGTTTACAGAATTACCATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
53766913 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
53766940 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
53766967 CGATTTACAGAATTACCG-TTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* ** * **
53766993 CAATTTGTAAAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53767020 CGATTTACAGAATTACCCTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
53767047 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
53767074 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** ** * *
53767101 TAATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
53767128 CGATTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
53767155 CAGTTTACCCTCAGTTTACAGAATTACCATTTTACCCT
1 C-G---A---T--T--TACAGAATTACCGTTTTACCCT
*
53767193 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
53767220 C-AGTTTACAGAATTA-CTTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* **
53767246 CGATTTACAAAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
53767273 CGATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
53767300 CGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
53767327 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
53767354 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
53767381 C
1 C
53767382 AATTGTGAAA
Statistics
Matches: 700, Mismatches: 93, Indels: 54
0.83 0.11 0.06
Matches are distributed among these distances:
26 49 0.07
27 619 0.88
28 7 0.01
31 2 0.00
34 2 0.00
37 1 0.00
38 20 0.03
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:53767163 original size:11 final size:11
Alignment explanation
Indices: 53767147--53767173 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53767137 AAATTATCGT
53767147 TTTACCCTCAG
1 TTTACCCTCAG
53767158 TTTACCCTCAG
1 TTTACCCTCAG
53767169 TTTAC
1 TTTAC
53767174 AGAATTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.33, G:0.07, T:0.41
Consensus pattern (11 bp):
TTTACCCTCAG
Found at i:53767178 original size:119 final size:118
Alignment explanation
Indices: 53767039--53767273 Score: 373
Period size: 119 Copynumber: 2.0 Consensus size: 118
53767029 GAATTACCCT
* *
53767039 TTTACCCTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTTAA
1 TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAA
** *
53767104 TTTGTAAAATTACTGTTTTACCCTCGATTTACAAAATTA-TCGTTTTACCCTCAG
66 TTTACAAAATTACT-TTTTACCCTCGATTTACAAAATTACT-ATTTTACCCTCAG
* *
53767158 TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCAG
1 TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAA
*
53767223 TTTACAGAATTACTTTTTACCCTCGATTTACAAAATTACTATTTTACCCTC
66 TTTACAAAATTACTTTTTACCCTCGATTTACAAAATTACTATTTTACCCTC
53767274 GATTTGTAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
118 34 0.32
119 73 0.68
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (118 bp):
TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAA
TTTACAAAATTACTTTTTACCCTCGATTTACAAAATTACTATTTTACCCTCAG
Found at i:53767200 original size:38 final size:38
Alignment explanation
Indices: 53767120--53767193 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
53767110 AAATTACTGT
* *
53767120 TTTACCCTCGATTTACAAAATTATCGTTTTACCCTCAG
1 TTTACCCTCGATTTACAAAATTACCATTTTACCCTCAG
*
53767158 TTTACCCTC-AGTTTACAGAATTACCATTTTACCCTC
1 TTTACCCTCGA-TTTACAAAATTACCATTTTACCCTC
53767194 GATTTACAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (38 bp):
TTTACCCTCGATTTACAAAATTACCATTTTACCCTCAG
Found at i:53767299 original size:199 final size:199
Alignment explanation
Indices: 53766959--53767354 Score: 543
Period size: 199 Copynumber: 2.0 Consensus size: 199
53766949 GAATTACTAT
**
53766959 TTTACCCTCGATTTACAGAATTACCGTTTACCCTCAATTTGTAAAATTACTATTTTACCCTCGAT
1 TTTACCCTCGATTTACAGAATTACCGTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGAT
* *
53767024 TTACAGAATTACCCTTTTACCCTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAGAATTA
66 TTACAGAATTACCCTTTTACCCTCAGTTTACAAAATTACTATTTTACCCTCGATTTACAAAATTA
* * *
53767089 CCGTTTTACCCTTAATTTGTAAAATTACTGTTTTACCCTC-GATTTACAAAATTATCGTTTTACC
131 CCGTTTTACCCTCAATTTATAAAATTACTGGTTTACCCTCAG-TTTACAAAATTATCGTTTTACC
53767153 CTCAG
195 CTCAG
* * * *
53767158 TTTACCCTC-AGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTA-TCGTTTTACCCTC
1 TTTACCCTCGA-TTTACAGAATTACC-GTTTACCCTCAATTTACAAAATTACT-ATTTTACCCTC
* **
53767221 -AGTTTACAGAATTA-CTTTTTACCCTC-GATTTACAAAATTACTATTTTACCCTCGATTTGTAA
63 GA-TTTACAGAATTACCCTTTTACCCTCAG-TTTACAAAATTACTATTTTACCCTCGATTTACAA
* * *
53767283 AATTACTGTTTTACCCTCGATTTATAGAATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTT
126 AATTACCGTTTTACCCTCAATTTATAAAATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTT
53767348 TACCCTC
191 TACCCTC
53767355 GATTTACAGA
Statistics
Matches: 174, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
198 2 0.01
199 130 0.75
200 42 0.24
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (199 bp):
TTTACCCTCGATTTACAGAATTACCGTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGAT
TTACAGAATTACCCTTTTACCCTCAGTTTACAAAATTACTATTTTACCCTCGATTTACAAAATTA
CCGTTTTACCCTCAATTTATAAAATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCC
TCAG
Found at i:53767382 original size:226 final size:226
Alignment explanation
Indices: 53766689--53767354 Score: 348
Period size: 226 Copynumber: 3.0 Consensus size: 226
53766679 GAATTACCGT
* * * *
53766689 TTTACCTTCAGTTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGA
1 TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCG-TTTACCCTCAA
** ** * * * *
53766754 TTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTGTA-A-AA
65 TTTACAAAATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTT-TACAGAA
** * * * * *
53766817 TTACCGTTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTTA
128 TTACTATTTTACCCTCGATTTACAGAATTACCGGTTTACCCTCAATTTACAAAATTACTGTTTTA
* * *
53766882 CCCTC-AGTTTACAGAATTACCATTTTACCCTC-G
193 CCCTCGA-TTTACAAAATTATCGTTTTACCCTCAG
** *
53766915 ---------A-TTTACAGAATTACCATTTTACCCTC-AGTTTACAGAATTACTATTTTACCCTCG
1 TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGA-TTTACAGAATTAC-CGTTTACCCTCA
* ** * ** *
53766969 ATTTACAGAATTAC-CGTTTACCCTCAATTTGTAAAATTACTATTTTACCCTC-GATTTACAGAA
64 ATTTACAAAATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAG-TTTACAGAA
** *** * * *
53767032 TTACCCTTTTACCCTC-AGTTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTT
128 TTACTATTTTACCCTCGA-TTTACAGAATTACCGGTTTACCCTCAATTTACAAAATTACTGTTTT
** **
53767096 ACCCTTAATTTGTAAAATTA-CTGTTTTACCCTC-G
192 ACCCTCGATTTACAAAATTATC-GTTTTACCCTCAG
* ** ** * *
53767130 ATTTA--C-AAAATTATC-GTTTTACCCTCAGTTTACCCTC-AGTTTACAGAATTACCATTTTAC
1 -TTTACCCTCAGTTTA-CAGAATTA--C-CATTTTACCCTCGA-TTTACAGAATTACC-GTTTAC
* * * * *
53767190 CCTCGATTTACAGAATTA-TCGTTTTACCCTC-AGTTTACAGAATTA-CTTTTTACCCTC-GATT
59 CCTCAATTTACAAAATTACT-ATTTTACCCTCGA-TTTACAAAATTACCATTTTACCCTCAG-TT
* ** * * * * * *
53767251 TACAAAATTACTATTTTACCCTCGATTTGTAAAATTACTGTTTTACCCTCGATTTATAGAATTAC
121 TACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGGTTTACCCTCAATTTACAAAATTAC
*
53767316 TGGTTTACCCTC-AGTTTACAAAATTATCGTTTTACCCTC
186 TGTTTTACCCTCGA-TTTACAAAATTATCGTTTTACCCTC
53767355 GATTTACAGA
Statistics
Matches: 362, Mismatches: 51, Indels: 54
0.78 0.11 0.12
Matches are distributed among these distances:
213 2 0.01
214 5 0.01
215 115 0.32
216 58 0.16
217 1 0.00
222 1 0.00
223 7 0.02
224 1 0.00
225 2 0.01
226 150 0.41
227 20 0.06
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (226 bp):
TTTACCCTCAGTTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTACCCTCAAT
TTACAAAATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAGTTTACAGAATTA
CTATTTTACCCTCGATTTACAGAATTACCGGTTTACCCTCAATTTACAAAATTACTGTTTTACCC
TCGATTTACAAAATTATCGTTTTACCCTCAG
Found at i:53767393 original size:107 final size:107
Alignment explanation
Indices: 53767184--53767396 Score: 322
Period size: 107 Copynumber: 2.0 Consensus size: 107
53767174 AGAATTACCA
* * *
53767184 TTTTACCCTCGATTTACAGAATTATCGTTTTACCCTCAGTTTACAGAATTACTTTTTACCCTCGA
1 TTTTACCCTCGATTTACAGAATTATCGGTTTACCCTCAGTTTACAAAATTACGTTTTACCCTCGA
*
53767249 TTTACAAAATTACTATTTTACCCTCGATTTGTAAAATTACTG
66 TTTACAAAATTACTATTTTACCCTCGAATTGTAAAATTACTG
*
53767291 TTTTACCCTCGATTTATAGAATTA-CTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCCTC
1 TTTTACCCTCGATTTACAGAATTATC-GGTTTACCCTCAGTTTACAAAATTA-CGTTTTACCCTC
* * *
53767355 GATTTACAGAATTACTGTTTTACCCTC-AATTGTGAAATTACT
64 GATTTACAAAATTACTATTTTACCCTCGAATTGTAAAATTACT
53767397 AAAATACCCC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 1 0.01
107 59 0.61
108 36 0.38
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (107 bp):
TTTTACCCTCGATTTACAGAATTATCGGTTTACCCTCAGTTTACAAAATTACGTTTTACCCTCGA
TTTACAAAATTACTATTTTACCCTCGAATTGTAAAATTACTG
Found at i:53767558 original size:27 final size:27
Alignment explanation
Indices: 53767398--53767585 Score: 223
Period size: 27 Copynumber: 7.0 Consensus size: 27
53767388 GAAATTACTA
53767398 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* **
53767425 AAATACCCCTATAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
** * * *
53767452 AAATACCTTTATAGGGTAGAATTATCA
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
53767479 AAATACCCCCGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
53767506 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
53767533 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* ** * *
53767560 AGATACCTTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
53767586 ATTTTGCCCC
Statistics
Matches: 138, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:53767815 original size:27 final size:26
Alignment explanation
Indices: 53767784--53767866 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
53767774 CAAAGGAAGC
*
53767784 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
53767811 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* *
53767837 GTATCTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
53767864 GTT
1 GTT
53767867 GACCGATCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 10 0.19
27 42 0.81
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:53768199 original size:27 final size:27
Alignment explanation
Indices: 53768177--53768250 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
53768167 TAGGTGGGTT
*
53768177 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
53768204 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
53768231 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
53768251 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:53768377 original size:6 final size:6
Alignment explanation
Indices: 53768368--53768469 Score: 95
Period size: 6 Copynumber: 16.8 Consensus size: 6
53768358 TTGCATTCAC
* *
53768368 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
53768417 -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTA ATTCTG ATTCTG
1 ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
53768465 ATTCT
1 ATTCT
53768470 CATTTTGGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 6 0.08
6 66 0.84
7 5 0.06
8 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:53768490 original size:30 final size:30
Alignment explanation
Indices: 53768368--53768469 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
53768358 TTGCATTCAC
*
53768368 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATTCTG
53768399 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACTAAT-TCTG
53768429 ATTCTGATTCTGATTCTGTTACTAATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
53768459 ATTCTGATTCT
1 ATTCTGATTCT
53768470 CATTTTGGTT
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
29 1 0.01
30 46 0.68
31 21 0.31
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATTCTG
Found at i:53769741 original size:40 final size:40
Alignment explanation
Indices: 53769663--53769886 Score: 256
Period size: 40 Copynumber: 5.5 Consensus size: 40
53769653 ACCCAAGTAT
* * *
53769663 CTTCGGGATTTAG-CTGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
53769702 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53769742 CTTCGGGACTTAGCCCGGATATATTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53769782 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCACACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
53769825 CTTCGGGACTTAGCCCGGATATAATAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53769865 CCTCGGGACTTAGCTCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
53769887 CATCCGAATA
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 12 0.08
40 111 0.70
41 1 0.01
43 34 0.22
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53769859 original size:83 final size:80
Alignment explanation
Indices: 53769663--53769886 Score: 263
Period size: 83 Copynumber: 2.8 Consensus size: 80
53769653 ACCCAAGTAT
* * ** * *
53769663 CTTCGGGATTTAG-CTGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
* **
53769727 CACTAGCATGAATGC
66 CACTAACACAAATGC
* * *
53769742 CTTCGGGACTTAGCCCGGATATATTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
53769806 CAACTACTCACACAAATGC
66 C-ACTA---ACACAAATGC
* * *
53769825 CTTCGGGACTTAGCCCGGATATAATAACTTGCACAAATGCCCTCGGGACTTAGCTCGGATAT
1 CTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
53769887 CATCCGAATA
Statistics
Matches: 123, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 13 0.11
80 47 0.38
83 63 0.51
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAACACAAATGC
Found at i:53780818 original size:40 final size:40
Alignment explanation
Indices: 53780735--53780954 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
53780725 ACCCAAGTAT
** * *
53780735 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53780773 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
53780813 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
53780853 CTTTGGGTCTTAGCTCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
53780893 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53780933 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
53780955 CATTCGAATA
Statistics
Matches: 149, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.11
40 120 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53782819 original size:43 final size:43
Alignment explanation
Indices: 53782772--53782911 Score: 121
Period size: 43 Copynumber: 3.3 Consensus size: 43
53782762 GTTCTCATTG
53782772 AAGACCACGTCTGGGATGTTGGCATCGATATGTGATTAACTGT
1 AAGACCACGTCTGGGATGTTGGCATCGATATGTGATTAACTGT
* ** * ** *
53782815 AAGACCATGAATGAGACATTGGCATC-ATATTTGATT--CGTGT
1 AAGACCACGTCTGGGATGTTGGCATCGATATGTGATTAAC-TGT
*
53782856 AAGACC-CTGTTTGGGACTG-TGGCATCGATATGTGATTATA-TGT
1 AAGACCAC-GTCTGGGA-TGTTGGCATCGATATGTGATTA-ACTGT
*
53782899 CAGACCACGTCTG
1 AAGACCACGTCTG
53782912 ATACGTTGGC
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
40 1 0.01
41 21 0.29
42 18 0.25
43 32 0.44
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
AAGACCACGTCTGGGATGTTGGCATCGATATGTGATTAACTGT
Found at i:53788155 original size:40 final size:40
Alignment explanation
Indices: 53788072--53788291 Score: 250
Period size: 40 Copynumber: 5.5 Consensus size: 40
53788062 GCCCAAGTAT
** * *
53788072 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53788110 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
53788150 CTTCGGGACTTAGCCCGGATATAGTCGCCAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53788190 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
53788230 CTTCGGATCTTAGTCCGGATATAGTCATTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53788270 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
53788292 CATTCGAATA
Statistics
Matches: 153, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.10
40 124 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53796027 original size:40 final size:40
Alignment explanation
Indices: 53795944--53796161 Score: 241
Period size: 39 Copynumber: 5.5 Consensus size: 40
53795934 ACCCAAGTAT
** * *
53795944 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53795982 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
53796022 CTTCGGGACTTAGCCCGGATATAGTCGC-AGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53796061 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
53796101 CTTCGGAT-TTAGTCCGGATATAGTCATTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
53796140 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
53796162 CATTCGAATA
Statistics
Matches: 151, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
37 1 0.01
38 12 0.08
39 79 0.52
40 59 0.39
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:53796074 original size:79 final size:79
Alignment explanation
Indices: 53795980--53796161 Score: 242
Period size: 79 Copynumber: 2.3 Consensus size: 79
53795970 CTCGCACAAG
* *
53795980 GCCTTCGGGTCTTAGCCCGGATATGGTC-ACTAGCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTC-GGACTTAGCCCGGATAT
*
53796044 AGTC-GCAGCACAAAT
64 AGTCAGCAGCACAAAA
* * *
53796059 GCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATTTAGTCCGGATATAG
1 GCCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAG
** *
53796124 TCATTAGCATAAAA
66 TCAGCAGCACAAAA
*
53796138 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
53796162 CATTCGAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
78 20 0.22
79 71 0.78
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGACTTAGCCCGGATATAG
TCAGCAGCACAAAA
Found at i:53803053 original size:11 final size:11
Alignment explanation
Indices: 53803037--53803061 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53803027 ATTTGGAGTA
53803037 TTCAGAATGTT
1 TTCAGAATGTT
53803048 TTCAGAATGTT
1 TTCAGAATGTT
53803059 TTC
1 TTC
53803062 CTGAAAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (11 bp):
TTCAGAATGTT
Found at i:53811374 original size:93 final size:93
Alignment explanation
Indices: 53811262--53811433 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53811252 GCCCATAAGT
* *
53811262 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53811327 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
53811355 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53811420 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
53811434 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53811429 original size:46 final size:46
Alignment explanation
Indices: 53811254--53811429 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
53811244 TGTAACCCGC
* * *
53811254 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
53811300 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
53811350 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
53811393 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53811430 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:53813835 original size:15 final size:15
Alignment explanation
Indices: 53813806--53813855 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
53813796 CAAAGATAAC
*
53813806 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
53813820 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
53813835 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
53813850 AAGAAA
1 AAGAAA
53813856 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:53813864 original size:15 final size:15
Alignment explanation
Indices: 53813817--53813864 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
53813807 AGAAAACCGA
53813817 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
53813831 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
53813847 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
53813862 ATA
1 ATA
53813865 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:53816888 original size:93 final size:93
Alignment explanation
Indices: 53816776--53816947 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53816766 GCCCATAAGT
* *
53816776 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53816841 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
53816869 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53816934 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
53816948 CAAATATCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:53816943 original size:46 final size:46
Alignment explanation
Indices: 53816768--53816943 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
53816758 TGTAACCCGC
* * *
53816768 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
53816814 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
53816864 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
53816907 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53816944 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:53821011 original size:40 final size:39
Alignment explanation
Indices: 53820954--53821136 Score: 221
Period size: 40 Copynumber: 4.7 Consensus size: 39
53820944 TCGAATGATG
* *
53820954 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* *
53820994 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
53821033 TCCGGGCTAAG--CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
*
53821071 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* *
53821111 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53821137 CTTGTGAGTA
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
37 23 0.18
38 12 0.10
39 12 0.10
40 72 0.57
41 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:53821074 original size:77 final size:80
Alignment explanation
Indices: 53820954--53821134 Score: 219
Period size: 77 Copynumber: 2.3 Consensus size: 80
53820944 TCGAATGATG
* *
53820954 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAG-TCCCGAAGGCAT
53821017 TCGTGCGAGTTACTA-A
64 TCGTGCGAGTTACTATA
* * ** *
53821033 TCCGGGCTAAG-CCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGTCCCGAAGGCATTC
53821096 GTGCGAGTTACTATA
66 GTGCGAGTTACTATA
* *
53821111 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATT
53821135 TGCTTGTGAG
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
76 1 0.01
77 49 0.56
78 16 0.18
79 11 0.12
80 11 0.12
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGTCCCGAAGGCATTC
GTGCGAGTTACTATA
Found at i:53824253 original size:71 final size:71
Alignment explanation
Indices: 53824169--53824332 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
53824159 CGATTTGTCT
53824169 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53824234 CTTTCA
66 CTTTCA
53824240 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53824305 CTTTCA
66 CTTTCA
53824311 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
53824333 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:53824370 original size:71 final size:70
Alignment explanation
Indices: 53824169--53824366 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
53824159 CGATTTGTCT
* * * *
53824169 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53824234 CTTTCA
65 CTTTCA
* * * *
53824240 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53824305 CTTTCA
65 CTTTCA
* *
53824311 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
53824367 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:53831815 original size:71 final size:71
Alignment explanation
Indices: 53831731--53831894 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
53831721 CGATTTGTCT
53831731 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53831796 CTTTCA
66 CTTTCA
53831802 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
53831867 CTTTCA
66 CTTTCA
53831873 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
53831895 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:53831932 original size:71 final size:70
Alignment explanation
Indices: 53831731--53831928 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
53831721 CGATTTGTCT
* * * *
53831731 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53831796 CTTTCA
65 CTTTCA
* * * *
53831802 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
53831867 CTTTCA
65 CTTTCA
* *
53831873 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
53831929 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:53837745 original size:56 final size:56
Alignment explanation
Indices: 53837659--53837768 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
53837649 ATTCACTATC
*
53837659 TGTACGTATGTCTGTTTTAATTTAATATAAGTAAAGATGATTGCTAATGTATAATG
1 TGTACGTATGTCTGTATTAATTTAATATAAGTAAAGATGATTGCTAATGTATAATG
* *
53837715 TGTACGTATGTTTGTATTGATTTAATATAAGTAAAGATGATTGCTAATGTATAA
1 TGTACGTATGTCTGTATTAATTTAATATAAGTAAAGATGATTGCTAATGTATAA
53837769 CGTACCATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (56 bp):
TGTACGTATGTCTGTATTAATTTAATATAAGTAAAGATGATTGCTAATGTATAATG
Found at i:53840468 original size:12 final size:12
Alignment explanation
Indices: 53840448--53840480 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
53840438 TCACAAAAAT
*
53840448 CACACGGGCTAC
1 CACATGGGCTAC
53840460 CACATGGGCTAC
1 CACATGGGCTAC
53840472 CACATGGGC
1 CACATGGGC
53840481 GTGTCCCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.27, T:0.12
Consensus pattern (12 bp):
CACATGGGCTAC
Found at i:53841907 original size:54 final size:53
Alignment explanation
Indices: 53841804--53841926 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 53
53841794 TTAGTTTACC
* *
53841804 AAATTACTGAAATACCTCTAGTTGTAAAATTACCAAAGTACCCCCAGTTTAT-A
1 AAATTACTGAAATACCTCGAGTTGTAAAAGTACCAAAGTACCCCCAGTTT-TCA
* * *
53841857 AAATTACTCAAATATCCTCGATTTGTAAAAGTACCGAAA-TACCCTCAGTTTTCA
1 AAATTACTGAAATA-CCTCGAGTTGTAAAAGTACC-AAAGTACCCCCAGTTTTCA
53841911 AAATTACTGAAATACC
1 AAATTACTGAAATACC
53841927 CTTGACATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
53 16 0.26
54 42 0.69
55 3 0.05
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (53 bp):
AAATTACTGAAATACCTCGAGTTGTAAAAGTACCAAAGTACCCCCAGTTTTCA
Found at i:53841927 original size:27 final size:27
Alignment explanation
Indices: 53841804--53841928 Score: 107
Period size: 27 Copynumber: 4.7 Consensus size: 27
53841794 TTAGTTTACC
*
53841804 AAATTACTGAAATA-CCTCTAG-TTGTA
1 AAATTACTGAAATACCCTC-AGTTTATA
* *
53841830 AAATTAC-CAAAGTACCCCCAGTTTATA
1 AAATTACTGAAA-TACCCTCAGTTTATA
* * *
53841857 AAATTACTCAAATATCCTC-GATTTGTA
1 AAATTACTGAAATACCCTCAG-TTTATA
* *
53841884 AAAGTACCGAAATACCCTCAGTTT-TCA
1 AAATTACTGAAATACCCTCAGTTTAT-A
53841911 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
53841929 TGACATGTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
25 3 0.04
26 13 0.16
27 59 0.74
28 5 0.06
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCAGTTTATA
Found at i:53841956 original size:54 final size:53
Alignment explanation
Indices: 53841804--53841973 Score: 159
Period size: 54 Copynumber: 3.2 Consensus size: 53
53841794 TTAGTTTACC
* *
53841804 AAATTACTGAAATACCTCT-AGTTGTAAAATTACCAAAGTACCCCCAGTTTAT-A
1 AAATTACTGAAATACCT-TGACTTGTAAAATTACCAAAGTACCCTCAGTTT-TCA
* * * *
53841857 AAATTACTCAAATATCCTCGATTTGTAAAAGTACCGAAA-TACCCTCAGTTTTCA
1 AAATTACTGAAATA-CCTTGACTTGTAAAATTACC-AAAGTACCCTCAGTTTTCA
* * * * *
53841911 AAATTACTGAAATACCCTTGACATGTAAAATTATCAAAGTTCCCTC-GAATTACA
1 AAATTACTGAAATA-CCTTGACTTGTAAAATTACCAAAGTACCCTCAG-TTTTCA
53841965 AAATTACTG
1 AAATTACTG
53841974 CTTTACCCTC
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
53 18 0.19
54 75 0.78
55 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (53 bp):
AAATTACTGAAATACCTTGACTTGTAAAATTACCAAAGTACCCTCAGTTTTCA
Found at i:53841982 original size:27 final size:27
Alignment explanation
Indices: 53841952--53842085 Score: 178
Period size: 27 Copynumber: 5.0 Consensus size: 27
53841942 TATCAAAGTT
* * **
53841952 CCCTCGAATTACAAAATTACTGCTTTA
1 CCCTCGATTTACAGAATTACTATTTTA
53841979 CCCTCGATTTACAGAATTACTATTTTA
1 CCCTCGATTTACAGAATTACTATTTTA
53842006 CCCTCGATTTACAGAATTACTATTTTA
1 CCCTCGATTTACAGAATTACTATTTTA
**
53842033 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACTATTTTA
* * * *
53842060 ACCTCGATTTATAAAATTACCATTTT
1 CCCTCGATTTACAGAATTACTATTTT
53842086 GCCCCTATGG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 97 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACTATTTTA
Found at i:53841997 original size:54 final size:54
Alignment explanation
Indices: 53841939--53842052 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
53841929 TGACATGTAA
*
53841939 AATTATCAAAGTT-CCCTCGAATTACAAAATTACTGCTTTACCCTCGATTTACAG
1 AATTA-CAAAGTTACCCTCGAATTACAAAATTACTACTTTACCCTCGATTTACAG
* ** * * *
53841993 AATTACTATTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAG
1 AATTACAAAGTTACCCTCGAATTACAAAATTACTACTTTACCCTCGATTTACAG
53842047 AATTAC
1 AATTAC
53842053 CGTTTTAACC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
53 4 0.08
54 48 0.92
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (54 bp):
AATTACAAAGTTACCCTCGAATTACAAAATTACTACTTTACCCTCGATTTACAG
Found at i:53842534 original size:31 final size:31
Alignment explanation
Indices: 53842488--53842629 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
53842478 TTGCATTCAC
*
53842488 ATTCTGATTTTTGATTCTGTTACCTGATACTA
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
53842520 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53842551 ATTCTGATTTTGATTCTGTTACTTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
53842582 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53842613 ATTCTGATTCTGATTCT
1 ATTCTGATTTTGATTCT
53842630 AGTTCTGATA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 96 0.93
32 7 0.07
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:53842551 original size:6 final size:6
Alignment explanation
Indices: 53842488--53842638 Score: 96
Period size: 6 Copynumber: 24.3 Consensus size: 6
53842478 TTGCATTCAC
* * * *
53842488 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTA ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
53842538 -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG -TTACTTG ATACTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-C-TG ATTCTG ATTCTG
* *
53842588 ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
53842637 AT
1 AT
53842639 AATGTTTCTT
Statistics
Matches: 112, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
5 8 0.07
6 83 0.74
7 17 0.15
8 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:53842583 original size:19 final size:19
Alignment explanation
Indices: 53842530--53842587 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
53842520 ATTCTGATTT
*
53842530 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACTTGATAC
53842549 TGATTCTG--A-TT--T--
1 TGATTCTGTTACTTGATAC
53842561 TGATTCTGTTACTTGATAC
1 TGATTCTGTTACTTGATAC
53842580 TGATTCTG
1 TGATTCTG
53842588 ATTCTGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
12 8 0.26
14 2 0.06
15 2 0.06
16 1 0.03
17 2 0.06
19 16 0.52
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (19 bp):
TGATTCTGTTACTTGATAC
Found at i:53846158 original size:40 final size:40
Alignment explanation
Indices: 53846103--53846284 Score: 253
Period size: 40 Copynumber: 4.6 Consensus size: 40
53846093 TATTCGGATG
* *
53846103 ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGAAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
53846143 ATATCCGAGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
53846183 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
53846223 ATA-CCTGGGCTAAGACCTGAAGGCATTTGTGCGAGTTG-CT
1 ATATCC-GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
53846263 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
53846285 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.11
40 109 0.86
41 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:53851961 original size:40 final size:40
Alignment explanation
Indices: 53851917--53852039 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
53851907 GTGCTAAGTG
* *
53851917 ACTAAATCCGGAATAAGATCCGACGGCATACGTGCGAGTT
1 ACTAAATCCGGAATAAGATCCGAAGGCATTCGTGCGAGTT
* * * * *
53851957 ACTAAATCCAGACTAAGATCCGAAGGCTTTCGAGCGAGCT
1 ACTAAATCCGGAATAAGATCCGAAGGCATTCGTGCGAGTT
**
53851997 ACTAAATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTT
1 ACTAAATCCGGAATAAGAT-CCGAAGGCATTCGTGCGAGTT
53852037 ACT
1 ACT
53852040 GTAATCGGGC
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 68 0.99
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (40 bp):
ACTAAATCCGGAATAAGATCCGAAGGCATTCGTGCGAGTT
Found at i:53852057 original size:40 final size:40
Alignment explanation
Indices: 53851882--53852066 Score: 137
Period size: 40 Copynumber: 4.6 Consensus size: 40
53851872 TTCGAATGAT
* * *
53851882 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGAGC-GAGCT-ACTAA
** * * * *
53851922 ATCCGGAATAAGAT-CCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGAGCGAGCTACTAA
* * *
53851962 ATCCAGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGAGCGAGCTACTAA
* * * *
53852002 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGAGCGAGCTACT-AA
*
53852043 AT-CGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
53852067 TGAATGTGTA
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 107 0.91
41 10 0.08
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGAGCGAGCTACTAA
Found at i:53852060 original size:80 final size:80
Alignment explanation
Indices: 53851882--53852069 Score: 197
Period size: 80 Copynumber: 2.3 Consensus size: 80
53851872 TTCGAATGAT
* *
53851882 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAATAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
53851947 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* * * **
53851962 ATCCAGACTAAGAT-CCGAAGGCTTTCGAGC-GAGCT-ACTAAATCCGGGTTAAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGAATAAGAT-CCGAAGG
* *
53852023 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
53852043 AT-CGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
53852070 ATGTGTAGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
79 2 0.02
80 76 0.85
81 11 0.12
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGAATAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:53857226 original size:26 final size:26
Alignment explanation
Indices: 53857197--53857337 Score: 138
Period size: 27 Copynumber: 5.3 Consensus size: 26
53857187 ATCCCTATTT
* *
53857197 AAAATACTTTGGTTTACAAAATTACC
1 AAAATACCTTGGTTTATAAAATTACC
* * * *
53857223 AAAATACCCTGCTTTGTAAAATTACT
1 AAAATACCTTGGTTTATAAAATTACC
53857249 AAAATACCCTTGGTTTATAAAATTACC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * * *
53857276 AAAATACCCCTAGTTTGTAAAATTATC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * *
53857303 AAAATACCCCTAGTTTGTAAAATTACC
1 AAAATA-CCTTGGTTTATAAAATTACC
53857330 AAAATACC
1 AAAATACC
53857338 CCTAATTTGT
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 28 0.28
27 71 0.72
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (26 bp):
AAAATACCTTGGTTTATAAAATTACC
Found at i:53857279 original size:27 final size:27
Alignment explanation
Indices: 53857214--53857365 Score: 189
Period size: 27 Copynumber: 5.7 Consensus size: 27
53857204 TTTGGTTTAC
*
53857214 AAAATTACCAAAATA-CCCTGCTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
53857240 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
53857267 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
53857294 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
**
53857321 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
53857348 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
53857366 TCGACCTGTA
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 14 0.13
27 97 0.87
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:53857324 original size:54 final size:54
Alignment explanation
Indices: 53857208--53857365 Score: 214
Period size: 54 Copynumber: 2.9 Consensus size: 54
53857198 AAATACTTTG
* * *
53857208 GTTTACAAAATTACCAAAATA-CCCT-GCTTTGTAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACTAAAATACCCCTA
53857261 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACT-AAAATACCCCTA
* * * *
53857315 GTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCC
1 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCC
53857366 TCGACCTGTA
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
53 21 0.22
54 71 0.76
55 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (54 bp):
GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCCTA
Found at i:53857334 original size:81 final size:80
Alignment explanation
Indices: 53857214--53857437 Score: 227
Period size: 81 Copynumber: 2.8 Consensus size: 80
53857204 TTTGGTTTAC
* * * *
53857214 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
**
53857279 ATACCCCTAG-TTTGT
66 ATA-CCCTAGACCTGT
* * * * **
53857294 AAAATTATCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTG
1 AAAATTATCAAAATA-CCCTGA-TTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCA
*
53857358 AAATACCCTCGACCTGT
64 AAATACCCTAGACCTGT
** * * * *
53857375 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACC
53857438 GTTTTACCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
80 23 0.20
81 91 0.79
82 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
ATACCCTAGACCTGT
Found at i:53857376 original size:54 final size:54
Alignment explanation
Indices: 53857214--53857437 Score: 213
Period size: 54 Copynumber: 4.2 Consensus size: 54
53857204 TTTGGTTTAC
** * * *
53857214 AAAATTACCAAAATA-CCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
* *
53857267 AAAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACT-AAAATACCCTCGA-TTTGT
* * **
53857321 AAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
*** * * * * *
53857375 AAAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCCT-AATTTGTAAAATTACTAAAATACCCTCGATTTGT
*
53857429 AGAATTACC
1 AAAATTACC
53857438 GTTTTACCCT
Statistics
Matches: 138, Mismatches: 27, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
53 20 0.14
54 115 0.83
55 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
Found at i:53857379 original size:27 final size:27
Alignment explanation
Indices: 53857349--53857423 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
53857339 CTAATTTGTG
53857349 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
53857376 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
53857403 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
53857424 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:53857816 original size:27 final size:27
Alignment explanation
Indices: 53857415--53857814 Score: 507
Period size: 27 Copynumber: 14.8 Consensus size: 27
53857405 ATTACCAAAG
*
53857415 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
53857442 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
53857469 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
53857496 TACCCT-TAGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
53857523 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53857550 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* * *
53857577 TACCCCCGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
53857604 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
53857631 CACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
53857658 TACCCCCGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
53857685 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53857712 CACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53857739 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * **
53857766 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
53857793 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
53857815 TAAAATACCC
Statistics
Matches: 326, Mismatches: 43, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
26 2 0.01
27 322 0.99
28 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:53859084 original size:25 final size:25
Alignment explanation
Indices: 53859056--53859103 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53859046 TTATACCATG
* * *
53859056 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
53859081 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53859104 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53859206 original size:20 final size:20
Alignment explanation
Indices: 53859146--53859206 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
53859136 ATAAATATGG
*
53859146 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
* *
53859166 CATGTATGATAGGCACATGA
1 TATGTATGATATGCACATGA
53859186 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
53859206 T
1 T
53859207 GTAATCATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:53859283 original size:24 final size:24
Alignment explanation
Indices: 53859256--53859398 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
53859246 GAGGAAGTGA
53859256 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
53859280 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
53859304 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
53859327 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
53859351 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
53859375 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53859399 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:53859349 original size:47 final size:47
Alignment explanation
Indices: 53859256--53859398 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
53859246 GAGGAAGTGA
53859256 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
53859304 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
53859351 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
53859399 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:53859372 original size:71 final size:72
Alignment explanation
Indices: 53859256--53859399 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
53859246 GAGGAAGTGA
*
53859256 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
53859319 CCAGTTAT
65 CCAGTTAT
** * *
53859327 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
53859392 CAGTTAT
66 CAGTTAT
53859399 A
1 A
53859400 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:53859625 original size:31 final size:31
Alignment explanation
Indices: 53859590--53859653 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53859580 CGTTTACAGT
53859590 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
53859621 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53859652 AA
1 AA
53859654 TGATTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53861416 original size:40 final size:39
Alignment explanation
Indices: 53861368--53861502 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 39
53861358 ATGATATCTG
53861368 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
53861407 AGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA-CC
1 -GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
* * *
53861446 TGGGCTAAGACCTGAAGGCATTTGTGCGAGTTG-CTATATCC
1 --GGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCC
*
53861487 GGCTAATTCCCGAAGG
1 GGCTAAGTCCCGAAGG
53861503 TACTTGGGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
39 15 0.18
40 66 0.78
41 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
Found at i:53863052 original size:27 final size:27
Alignment explanation
Indices: 53862960--53863112 Score: 132
Period size: 27 Copynumber: 5.7 Consensus size: 27
53862950 TTAGTTTACC
* *
53862960 AAATTACTAAAATACCCTC-AGTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * *
53862986 AAATTACCAAAGTACGCC-CGGTTTATA
1 AAATTACCAAAATAC-CCTCGATTTGTA
* *
53863013 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
53863040 AAATTACCAAAATGCCCTC-AGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*** **
53863067 AAATTATTGAAATACCCTCGACATGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
53863094 AAATTATCAAAGTACCCTC
1 AAATTACCAAAATACCCTC
53863113 AAATTACAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
26 17 0.17
27 82 0.82
28 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:53863069 original size:54 final size:54
Alignment explanation
Indices: 53862960--53863127 Score: 160
Period size: 54 Copynumber: 3.1 Consensus size: 54
53862950 TTAGTTTACC
** * *
53862960 AAATTACTAAAATACCCTC-AGTTGTAAAATTACCAAAGTACGCC-CGGTTTATA
1 AAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAGTAC-CCTCAGTTTATA
* * * * *
53863013 AAATTACCCAAATATCCTCGATTTGTAAAATTACCAAAATGCCCTCAGTTTGTA
1 AAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCAGTTTATA
*** * * ** *
53863067 AAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTCAAATTACA
1 AAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCAGTTTATA
53863121 AAATTAC
1 AAATTAC
53863128 TGTTTTACCC
Statistics
Matches: 91, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
53 18 0.20
54 73 0.80
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (54 bp):
AAATTACCCAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCAGTTTATA
Found at i:53863136 original size:27 final size:27
Alignment explanation
Indices: 53863106--53863295 Score: 209
Period size: 27 Copynumber: 7.0 Consensus size: 27
53863096 ATTATCAAAG
* *
53863106 TACCCTCAAATTACAAAATTACTGTTT
1 TACCCTCAATTTACAAAATTACTATTT
* * *
53863133 TACCCTAAATTTACAGAATTACTGTTT
1 TACCCTCAATTTACAAAATTACTATTT
* * * *
53863160 TTCCCTCGATTGACAGAATTACTATTT
1 TACCCTCAATTTACAAAATTACTATTT
*
53863187 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCAATTTACAAAATTACTATTT
* *
53863214 TACCCTTAATTTACAAAATTAATATTT
1 TACCCTCAATTTACAAAATTACTATTT
* * **
53863241 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCAATTTACAAAATTACTATTT
* * *
53863268 TACCCTTAATTTATAAAATTACCATTT
1 TACCCTCAATTTACAAAATTACTATTT
53863295 T
1 T
53863296 GCCCCTAGGG
Statistics
Matches: 138, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (27 bp):
TACCCTCAATTTACAAAATTACTATTT
Found at i:53863191 original size:81 final size:81
Alignment explanation
Indices: 53863106--53863295 Score: 254
Period size: 81 Copynumber: 2.3 Consensus size: 81
53863096 ATTATCAAAG
* * * * * *
53863106 TACCCTCAAATTACAAAATTACTGTTTTACCCTAAATTTACAGAATTACTGTTTTTCCCTCGATT
1 TACCCTCAATTTACAAAATTACTATTTTACCCTAAATTTACAAAATTAATATTTTACCCTCGATT
*
53863171 GACAGAATTACTATTT
66 GACAGAATTACCATTT
* *
53863187 TACCCTCGATTTACAAAATTACTATTTTACCCTTAATTTACAAAATTAATATTTTACCCTCGATT
1 TACCCTCAATTTACAAAATTACTATTTTACCCTAAATTTACAAAATTAATATTTTACCCTCGATT
* *
53863252 TACAGAATTACCGTTT
66 GACAGAATTACCATTT
* * *
53863268 TACCCTTAATTTATAAAATTACCATTTT
1 TACCCTCAATTTACAAAATTACTATTTT
53863296 GCCCCTAGGG
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 94 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (81 bp):
TACCCTCAATTTACAAAATTACTATTTTACCCTAAATTTACAAAATTAATATTTTACCCTCGATT
GACAGAATTACCATTT
Found at i:53863731 original size:19 final size:19
Alignment explanation
Indices: 53863709--53863766 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
53863699 TTTTGATTTT
53863709 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
53863728 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
53863740 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
53863759 TGATTCTG
1 TGATTCTG
53863767 ATTCTGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:53863736 original size:6 final size:6
Alignment explanation
Indices: 53863721--53863817 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
53863711 ATTCTGTTAC
* * *
53863721 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * *
53863770 CTGATT CTG-TCAC CTAATT CTGATT CTGATT CTAATT CT-AGTT CTGAT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
53863818 AATGTTTCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
5 4 0.05
6 61 0.84
7 6 0.08
8 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (6 bp):
CTGATT
Found at i:53863801 original size:31 final size:31
Alignment explanation
Indices: 53863709--53863833 Score: 155
Period size: 31 Copynumber: 4.1 Consensus size: 31
53863699 TTTTGATTTT
*
53863709 TGATTCTGTTACCTGATACTGATTCTGATTT
1 TGATTCTGTTACCTGATACTGATTCTGATTC
53863740 TGATTCTGTTACCTGATACTGATTCTGATTC
1 TGATTCTGTTACCTGATACTGATTCTGATTC
* * *
53863771 TGATTCTGTCACCTAATTCTGATTCTGATTC
1 TGATTCTGTTACCTGATACTGATTCTGATTC
* * * *
53863802 TAATTCTAGTT--CTGATAATGTTTCTTATTC
1 TGATTCT-GTTACCTGATACTGATTCTGATTC
53863832 TG
1 TG
53863834 TAATGGGTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
30 15 0.19
31 64 0.79
32 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (31 bp):
TGATTCTGTTACCTGATACTGATTCTGATTC
Found at i:53864847 original size:20 final size:20
Alignment explanation
Indices: 53864819--53864859 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53864809 ATTCCTTTGT
*
53864819 TATTCTGTTCTGCTCTATTC
1 TATTATGTTCTGCTCTATTC
* *
53864839 TATTATGTTTTGTTCTATTC
1 TATTATGTTCTGCTCTATTC
53864859 T
1 T
53864860 GTTTTGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (20 bp):
TATTATGTTCTGCTCTATTC
Found at i:53864854 original size:15 final size:15
Alignment explanation
Indices: 53864836--53864867 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53864826 TTCTGCTCTA
53864836 TTCTATTATGTTTTG
1 TTCTATTATGTTTTG
*
53864851 TTCTATTCTGTTTTG
1 TTCTATTATGTTTTG
53864866 TT
1 TT
53864868 TTTGTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.69
Consensus pattern (15 bp):
TTCTATTATGTTTTG
Found at i:53864872 original size:21 final size:20
Alignment explanation
Indices: 53864832--53864886 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
53864822 TCTGTTCTGC
*
53864832 TCTATTCTATTATGTTTTGT
1 TCTATTCTGTTATGTTTTGT
*
53864852 TCTATTCTGTTTTGTTTTTGT
1 TCTATTCTGTTATG-TTTTGT
*
53864873 TCTATTATGTTATG
1 TCTATTCTGTTATG
53864887 CTACCATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.13, C:0.09, G:0.13, T:0.65
Consensus pattern (20 bp):
TCTATTCTGTTATGTTTTGT
Found at i:53867854 original size:27 final size:26
Alignment explanation
Indices: 53867805--53867855 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
53867795 CGAGGCTGCC
53867805 AGATATTGTGACGAAGTCACCAGAAT
1 AGATATTGTGACGAAGTCACCAGAAT
* * *
53867831 AGATATATGTGGCGAGGTCTCCAGA
1 AGATAT-TGTGACGAAGTCACCAGA
53867856 TTGCAACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (26 bp):
AGATATTGTGACGAAGTCACCAGAAT
Found at i:53868140 original size:19 final size:19
Alignment explanation
Indices: 53868116--53868162 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
53868106 TAGGCTCGTT
53868116 GGCCCATTAGCCCATTTTC
1 GGCCCATTAGCCCATTTTC
* *
53868135 GGCCCATTGGCCCGTTTTC
1 GGCCCATTAGCCCATTTTC
53868154 GGCCCATTA
1 GGCCCATTA
53868163 AGCCTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.36, G:0.21, T:0.30
Consensus pattern (19 bp):
GGCCCATTAGCCCATTTTC
Found at i:53868631 original size:27 final size:27
Alignment explanation
Indices: 53868583--53868886 Score: 333
Period size: 27 Copynumber: 11.3 Consensus size: 27
53868573 GGGGCAAAAT
* * * * *
53868583 GGTAATTTTACCCCATAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53868610 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53868637 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
53868664 AATAATTCTACCCTAC-GGAGGTATTTC
1 GGTAATTCTACCCTACAGG-GGTATTTC
*
53868691 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53868718 GGTAATTCTACCTTAC-GAGGGTATTTC
1 GGTAATTCTACCCTACAG-GGGTATTTC
*
53868745 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53868772 GGTAATTCTACCTTATAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53868799 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * **
53868826 GATAATTCAACCTTATGGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
53868853 GGTAATTCTACCTTATAGGGGTACTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
53868880 AGTAATT
1 GGTAATT
53868887 TGGTAAACTA
Statistics
Matches: 236, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 231 0.98
28 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:53868727 original size:81 final size:80
Alignment explanation
Indices: 53868601--53868886 Score: 374
Period size: 81 Copynumber: 3.5 Consensus size: 80
53868591 TACCCCATAA
* * *
53868601 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTAGTATTTCTACCCTACAAGGGTATTTCAA
1 GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAA
53868666 TAATTCTACCCTACG
66 TAATTCTACCCTACG
* * * *
53868681 GAGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACGAGGGTATTTCA
1 G-GGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCA
*
53868746 GTAATTCTACCCTACAG
65 ATAATTCTACCCTAC-G
* * * * *
53868763 GGGTATTTCGGTAATTCTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
1 GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAA
* * *
53868828 TAATTCAACCTTATGG
66 TAATTCTACCCTA-CG
* * *
53868844 GGGTATTTCGGTAATTCTACCTTATAGGGGTACTTCAGTAATT
1 GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATT
53868887 TGGTAAACTA
Statistics
Matches: 180, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 177 0.98
82 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (80 bp):
GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAA
TAATTCTACCCTACG
Found at i:53873484 original size:47 final size:44
Alignment explanation
Indices: 53873421--53873636 Score: 145
Period size: 47 Copynumber: 4.7 Consensus size: 44
53873411 ATTGTATGCT
*
53873421 AGTGTAAAACATGTCTGGGACATGCATCAGCTACATT-ATG-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G--ACATTGA-GAAGAGCC
*
53873467 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATTGAG--AAGAGCC
* * * * * *
53873515 AGTGTAAGACATGTCTGGGACATGCATTGGC-TATAAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACAT-TGAGAAGAGCC
* * *
53873559 AGTGTAAGAACATGCCTGGGACATGGCATCGAC-TTAATGGACA-AACC
1 AGTGTAAG-ACATGTCTGGGACAT-GCATCGACATTGA--GA-AGAGCC
*
53873606 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
53873637 GTATTATACC
Statistics
Matches: 139, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
44 11 0.08
45 24 0.17
46 26 0.19
47 59 0.42
48 19 0.14
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGAAGAGCC
Found at i:53875327 original size:26 final size:26
Alignment explanation
Indices: 53875290--53875341 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
53875280 ATGAAAATTT
*
53875290 CCCAGATGAGCATATTTTTAGGTAAG
1 CCCAGATAAGCATATTTTTAGGTAAG
53875316 CCCAGATAAGCATATTTTTAGGTAAG
1 CCCAGATAAGCATATTTTTAGGTAAG
53875342 TCGAATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (26 bp):
CCCAGATAAGCATATTTTTAGGTAAG
Found at i:53879344 original size:18 final size:19
Alignment explanation
Indices: 53879310--53879346 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53879300 AGAATTGGCC
53879310 AAATGGGCCAAGATGGGCT
1 AAATGGGCCAAGATGGGCT
*
53879329 AAATGGGCC-TGATGGGCT
1 AAATGGGCCAAGATGGGCT
53879347 GTTGGGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.16, G:0.38, T:0.19
Consensus pattern (19 bp):
AAATGGGCCAAGATGGGCT
Done.