Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 180 of 205
Found at i:53488449 original size:40 final size:40
Alignment explanation
Indices: 53488405--53488668 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
53488395 GCTCCTCGTT
* *
53488405 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53488445 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53488485 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
53488525 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
53488565 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
53488604 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
53488645 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53488669 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53496699 original size:40 final size:40
Alignment explanation
Indices: 53496655--53496916 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
53496645 GCTCCTCGTT
* *
53496655 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
53496695 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53496735 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53496774 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
53496813 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
53496852 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
53496893 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53496917 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:53509084 original size:124 final size:124
Alignment explanation
Indices: 53508864--53509111 Score: 496
Period size: 124 Copynumber: 2.0 Consensus size: 124
53508854 GAGATGAAAG
53508864 CTTGAAATCTCAAATTCAACTCTTCAAAAAAAAAATTGTATCTAATTTGCGCACGAAAACAAACC
1 CTTGAAATCTCAAATTCAACTCTTCAAAAAAAAAATTGTATCTAATTTGCGCACGAAAACAAACC
53508929 GTACGCTAAGTATACACCCAATGGTATTACTATAATTCAAATACTTAAGGTAAAAACAC
66 GTACGCTAAGTATACACCCAATGGTATTACTATAATTCAAATACTTAAGGTAAAAACAC
53508988 CTTGAAATCTCAAATTCAACTCTTCAAAAAAAAAATTGTATCTAATTTGCGCACGAAAACAAACC
1 CTTGAAATCTCAAATTCAACTCTTCAAAAAAAAAATTGTATCTAATTTGCGCACGAAAACAAACC
53509053 GTACGCTAAGTATACACCCAATGGTATTACTATAATTCAAATACTTAAGGTAAAAACAC
66 GTACGCTAAGTATACACCCAATGGTATTACTATAATTCAAATACTTAAGGTAAAAACAC
53509112 TATATATACA
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (124 bp):
CTTGAAATCTCAAATTCAACTCTTCAAAAAAAAAATTGTATCTAATTTGCGCACGAAAACAAACC
GTACGCTAAGTATACACCCAATGGTATTACTATAATTCAAATACTTAAGGTAAAAACAC
Found at i:53509608 original size:23 final size:23
Alignment explanation
Indices: 53509561--53509637 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
53509551 TACAACACCT
**
53509561 AAGTGCCTG-AA-ACGACACACG
1 AAGTGCCTGAAATACGACACATA
*
53509582 AAGTGCCTGAAATATGACACATA
1 AAGTGCCTGAAATACGACACATA
* *
53509605 AAGTGCTTGAAATGCGACACATA
1 AAGTGCCTGAAATACGACACATA
53509628 AAGTGCCTGA
1 AAGTGCCTGA
53509638 TCGGCAAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.19
22 2 0.04
23 36 0.77
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (23 bp):
AAGTGCCTGAAATACGACACATA
Found at i:53509986 original size:26 final size:25
Alignment explanation
Indices: 53509955--53510004 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53509945 TAGTTCAATA
53509955 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
53509981 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
53510005 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:53510392 original size:11 final size:11
Alignment explanation
Indices: 53510376--53510400 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53510366 TTAAATTTTC
53510376 CTATTCAATTT
1 CTATTCAATTT
53510387 CTATTCAATTT
1 CTATTCAATTT
53510398 CTA
1 CTA
53510401 CCTTAAATTC
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:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (11 bp):
CTATTCAATTT
Found at i:53510815 original size:11 final size:11
Alignment explanation
Indices: 53510795--53510829 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
53510785 AAAACCCTAG
53510795 TTTTTCCTTTTC
1 TTTTT-CTTTTC
53510807 TTTTTCTTTTC
1 TTTTTCTTTTC
53510818 TTCTTTCTTTTC
1 TT-TTTCTTTTC
53510830 CCCTGTTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:53514722 original size:22 final size:21
Alignment explanation
Indices: 53514689--53514743 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 21
53514679 CAAGTGCTCC
*
53514689 CACAACTAAATCAACAGTTAA
1 CACAACTAAATCAAAAGTTAA
53514710 CACAAGCTAAATCAAAAGTTAA
1 CACAA-CTAAATCAAAAGTTAA
53514732 CACAACCTAAAT
1 CACAA-CTAAAT
53514744 TAGTAACGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.53, C:0.24, G:0.05, T:0.18
Consensus pattern (21 bp):
CACAACTAAATCAAAAGTTAA
Found at i:53515287 original size:5 final size:5
Alignment explanation
Indices: 53515277--53515312 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
53515267 GGGGATTTAG
*
53515277 AAAAT AAAAT AAAAT AAAAT AAAAT -AATT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
53515313 TAAAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 25 0.89
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:53515297 original size:15 final size:14
Alignment explanation
Indices: 53515277--53515312 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
53515267 GGGGATTTAG
53515277 AAAATAAAATAAAAT
1 AAAATAAAAT-AAAT
*
53515292 AAAATAAAATAATT
1 AAAATAAAATAAAT
53515306 AAAATAA
1 AAAATAA
53515313 TAAAAGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:53537740 original size:21 final size:21
Alignment explanation
Indices: 53537691--53537741 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
53537681 GCTTTATATC
*
53537691 AACTGCTGCTACAAATCTTTG
1 AACTGCTTCTACAAATCTTTG
*
53537712 AACTGCTTCTCCAAATCTTTG
1 AACTGCTTCTACAAATCTTTG
53537733 AACTGCTTC
1 AACTGCTTC
53537742 GTTGGTCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (21 bp):
AACTGCTTCTACAAATCTTTG
Found at i:53539475 original size:28 final size:28
Alignment explanation
Indices: 53539443--53539501 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
53539433 AAAATTTAGG
*
53539443 ATTTAAGGTCCAAGATTCAAGTTAAAAA
1 ATTTAAGGTACAAGATTCAAGTTAAAAA
*
53539471 ATTTAGGGTACAAGATTCAAGTTAAAAA
1 ATTTAAGGTACAAGATTCAAGTTAAAAA
53539499 ATT
1 ATT
53539502 ACTAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (28 bp):
ATTTAAGGTACAAGATTCAAGTTAAAAA
Found at i:53539640 original size:54 final size:54
Alignment explanation
Indices: 53539554--53539657 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
53539544 CATTAAATAA
* *
53539554 TTAATAAAAGATATAAAATGATATAATATCTTTGTTTCATATAATTTTTTTTCC
1 TTAATAAAAGATATAAAATGACATAATATCTTTATTTCATATAATTTTTTTTCC
* * * *
53539608 TTAATAAGAGATATAAAATGACGTAATGTCTTTATTTCGTATAATTTTTT
1 TTAATAAAAGATATAAAATGACATAATATCTTTATTTCATATAATTTTTT
53539658 CCAGAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (54 bp):
TTAATAAAAGATATAAAATGACATAATATCTTTATTTCATATAATTTTTTTTCC
Found at i:53540040 original size:9 final size:9
Alignment explanation
Indices: 53540026--53540052 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53540016 ATAGATCGAA
53540026 TAATTTTAG
1 TAATTTTAG
53540035 TAATTTTAG
1 TAATTTTAG
53540044 TAATTTTAG
1 TAATTTTAG
53540053 ATGGACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (9 bp):
TAATTTTAG
Found at i:53540747 original size:29 final size:29
Alignment explanation
Indices: 53540714--53540796 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
53540704 TCCACATTGA
*
53540714 CACGAATTCTCAACGAACAAATTCTTTGT
1 CACGAACTCTCAACGAACAAATTCTTTGT
*
53540743 CACGAACTCTCAATGAACAAATTCTTTGT
1 CACGAACTCTCAACGAACAAATTCTTTGT
* *
53540772 CATGAACTCTCAACGAACAAGTTCT
1 CACGAACTCTCAACGAACAAATTCT
53540797 CTACCTCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAATTCTTTGT
Found at i:53549287 original size:16 final size:17
Alignment explanation
Indices: 53549266--53549306 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
53549256 TTTCTATTTC
*
53549266 TTTATTATGTTT-TCAT
1 TTTATTATCTTTATCAT
53549282 TTTATTATCTTTATCAT
1 TTTATTATCTTTATCAT
53549299 TATTATTA
1 T-TTATTA
53549307 AAGTTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 5 0.23
18 6 0.27
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTATTATCTTTATCAT
Found at i:53549629 original size:43 final size:43
Alignment explanation
Indices: 53549365--53549609 Score: 330
Period size: 43 Copynumber: 5.7 Consensus size: 43
53549355 AAAAAATGCT
* *
53549365 GCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
* * * * *
53549408 ACTAAAGACCATGACCTTTAGCAGCCCTTTTATCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
53549451 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
* * *
53549494 GCGAAAGATCAAGACCTTTAGCTGCGCTTTTACCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
* * * *
53549537 GCTAAAGAACAAGACTTTTAGCGTCGCTTTCT-CCAAAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTT-TACCACAAACGCC
* *
53549580 GCTAAAGAACAAGACCTTTAGCGGCACTTT
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTT
53549610 CTCCAAAAAC
Statistics
Matches: 178, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 177 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (43 bp):
GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
Found at i:53550520 original size:23 final size:23
Alignment explanation
Indices: 53550494--53551028 Score: 268
Period size: 23 Copynumber: 23.4 Consensus size: 23
53550484 ATAAAACATC
*
53550494 TCAATTTCCAGCAACTAAACACT
1 TCAATTTACAGCAACTAAACACT
*
53550517 TCAATTTGCAGC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
**
53550540 TCAATTTACAGCAGTTAAACACT
1 TCAATTTACAGCAACTAAACACT
* * **
53550563 TAAATTTGCAGCAGTTAAACA-T
1 TCAATTTACAGCAACTAAACACT
* * ** * *
53550585 ATCAATTAACAACATTTATACACC
1 -TCAATTTACAGCAACTAAACACT
* *
53550609 ACAA-TTACAGCGA-TAAA-ACAT
1 TCAATTTACAGCAACTAAACAC-T
*
53550630 CTCAATTTCCAGCAACTAAACACT
1 -TCAATTTACAGCAACTAAACACT
* *
53550654 TCAATTTGCATC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
* * ** * *
53550677 TCAATTAACAACATTTATACACC
1 TCAATTTACAGCAACTAAACACT
53550700 TCAA-TTACAG-AGA-TAAA-ACAT
1 TCAATTTACAGCA-ACTAAACAC-T
*
53550721 CTCAATTTCCAGCAACTAAACACT
1 -TCAATTTACAGCAACTAAACACT
* *
53550745 TCAATTTGCATC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
* * ** * *
53550768 TCAATTAACAACATTTATACACC
1 TCAATTTACAGCAACTAAACACT
**
53550791 TCAA-TTACAGTGA-TAAA-ACAT
1 TCAATTTACAGCAACTAAACAC-T
*
53550812 CTCAATTTCCAGCAACTAAACACT
1 -TCAATTTACAGCAACTAAACACT
**
53550836 TCAATTTGTAGC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
*
53550859 TCAATTTGCAGC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
53550882 TCAATTTACAGC-ACTTAAACA-T
1 TCAATTTACAGCAAC-TAAACACT
* * ** * *
53550904 ATCAATTAACAACATTTATACACC
1 -TCAATTTACAGCAACTAAACACT
*
53550928 TCAA-TTACAGCGA-TAAA-ACAT
1 TCAATTTACAGCAACTAAACAC-T
* *
53550949 CTCAATTTCCAGCAACTAAATACT
1 -TCAATTTACAGCAACTAAACACT
* *
53550973 TCAATTTGCAAC-ACTTAAACACT
1 TCAATTTACAGCAAC-TAAACACT
**
53550996 TCAATTTACAGCATTTAAACACT
1 TCAATTTACAGCAACTAAACACT
*
53551019 TAAATTTACA
1 TCAATTTACA
53551029 AATCCACCAT
Statistics
Matches: 393, Mismatches: 83, Indels: 72
0.72 0.15 0.13
Matches are distributed among these distances:
20 8 0.02
21 13 0.03
22 45 0.11
23 298 0.76
24 21 0.05
25 8 0.02
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (23 bp):
TCAATTTACAGCAACTAAACACT
Found at i:53550887 original size:91 final size:91
Alignment explanation
Indices: 53550540--53550864 Score: 535
Period size: 91 Copynumber: 3.6 Consensus size: 91
53550530 CTTAAACACT
* ** * *
53550540 TCAATTTACAGCAGTTAAACACTTAAATTTGCAGCAGTTAAACA-TATCAATTAACAACATTTAT
1 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACT-TCAATTAACAACATTTAT
* *
53550604 ACACCACAATTACAGCGATAAAACATC
65 ACACCTCAATTACAGAGATAAAACATC
*
53550631 TCAATTTCCAGCAACTAAACACTTCAATTTGCATCACTTAAACACTTCAATTAACAACATTTATA
1 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTAACAACATTTATA
53550696 CACCTCAATTACAGAGATAAAACATC
66 CACCTCAATTACAGAGATAAAACATC
*
53550722 TCAATTTCCAGCAACTAAACACTTCAATTTGCATCACTTAAACACTTCAATTAACAACATTTATA
1 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTAACAACATTTATA
*
53550787 CACCTCAATTACAGTGATAAAACATC
66 CACCTCAATTACAGAGATAAAACATC
*
53550813 TCAATTTCCAGCAACTAAACACTTCAATTTGTAGCACTTAAACACTTCAATT
1 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATT
53550865 TGCAGCACTT
Statistics
Matches: 222, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
91 221 1.00
92 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (91 bp):
TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTAACAACATTTATA
CACCTCAATTACAGAGATAAAACATC
Found at i:53550961 original size:137 final size:137
Alignment explanation
Indices: 53550722--53551028 Score: 492
Period size: 137 Copynumber: 2.2 Consensus size: 137
53550712 ATAAAACATC
* * *
53550722 TCAATTTCCAGCAAC-TAAACACTTCAATTTGCATCACTTAAACACTTCAATTAACAACATTTAT
1 TCAATTTACAGC-ACTTAAACACTTCAATTTACAGCACTTAAACACTTCAATTAACAACATTTAT
* * *
53550786 ACACCTCAATTACAGTGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGTAGCACT
65 ACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAACACT
53550851 TAAACACT
130 TAAACACT
*
53550859 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCACTTAAACA-TATCAATTAACAACATTTAT
1 TCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTAAACACT-TCAATTAACAACATTTAT
*
53550923 ACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGCAACACT
65 ACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAACACT
53550988 TAAACACT
130 TAAACACT
* *
53550996 TCAATTTACAGCATTTAAACACTTAAATTTACA
1 TCAATTTACAGCACTTAAACACTTCAATTTACA
53551029 AATCCACCAT
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
136 3 0.02
137 155 0.98
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.30
Consensus pattern (137 bp):
TCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTAAACACTTCAATTAACAACATTTATA
CACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAACACTT
AAACACT
Found at i:53552051 original size:14 final size:14
Alignment explanation
Indices: 53552032--53552058 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53552022 TAATGCATCC
53552032 CGACTAGCCACAGT
1 CGACTAGCCACAGT
53552046 CGACTAGCCACAG
1 CGACTAGCCACAG
53552059 CAGCATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.37, G:0.22, T:0.11
Consensus pattern (14 bp):
CGACTAGCCACAGT
Found at i:53554104 original size:40 final size:40
Alignment explanation
Indices: 53554054--53554190 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 40
53554044 TGGGCTTAGG
* * *
53554054 TTTTTTGCGGTGTTTTTCAAAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTTC-AAAAAGCGCCGCTAATGCTCGA
* * * * ***
53554094 TTTTTCGCGGTGCTTTCCTGGAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
* **
53554134 TTTTTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
53554174 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
53554191 TATCTAAACG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 16 0.20
40 65 0.80
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
Found at i:53554122 original size:39 final size:40
Alignment explanation
Indices: 53554079--53554185 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
53554069 TTCAAAAAAA
* * * *
53554079 CGCCGCTAATGCTC-ATTTTTCGCGGTGCTTT-CCTGGAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTACGT-AAAG
*
53554118 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTACGTAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTACGTAAAG
53554158 CGCCGCTAATGCTCGATTTTTAGCGGCG
1 CGCCGCTAATGCTCGATTTTTAGCGGCG
53554186 TTTTTTATCT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
39 14 0.23
40 45 0.74
41 2 0.03
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTACGTAAAG
Found at i:53557588 original size:19 final size:19
Alignment explanation
Indices: 53557564--53557601 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53557554 AAAGCAATGG
53557564 TAGTTT-TAATTATAGTTAT
1 TAGTTTCTAATTAT-GTTAT
*
53557583 TAGTTTCTAGTTATGTTAT
1 TAGTTTCTAATTATGTTAT
53557602 GATGTATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (19 bp):
TAGTTTCTAATTATGTTAT
Found at i:53561156 original size:19 final size:19
Alignment explanation
Indices: 53561132--53561171 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53561122 AACTAAGTCG
53561132 ATTTGTGATATTTATAACA
1 ATTTGTGATATTTATAACA
53561151 ATTTGTGATATTTATAACA
1 ATTTGTGATATTTATAACA
53561170 AT
1 AT
53561172 AAGTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (19 bp):
ATTTGTGATATTTATAACA
Found at i:53562783 original size:125 final size:125
Alignment explanation
Indices: 53562487--53562925 Score: 698
Period size: 125 Copynumber: 3.5 Consensus size: 125
53562477 GATAAAATCA
* * * *
53562487 AAGCAGGATGCTTTATCAGAAGAATTTCTGTAATAGCGCCCACGTGGACGCACTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
53562552 AGGTCCTGAAAAAATAATTTCGAGTTGATGTTTCTGAGAAAATAGTATAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTC
*
53562613 AAGCAGGATGCTTTATCAGAAGACTTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
53562678 AGGTCCTGAAAAAATAATTTCGAATTGACATTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * *
53562738 AAGCAGGATGCTTTATCAGAAAAATGTCTGAAATCCCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
53562803 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAAAACACTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
53562863 AAGCAGGATGCTTTATCAGAAGAATTTATGAAATCGTGCCCTCGTGGACACGCTTTTTCTACA
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACA
53562926 TTAGCATGTT
Statistics
Matches: 288, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
125 184 0.64
126 104 0.36
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:53565827 original size:19 final size:19
Alignment explanation
Indices: 53565803--53565853 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
53565793 ATCTAACATT
53565803 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
53565822 TTG-T--T-AATTGTATTAA
1 TTGTTAGTAAAAT-TATTAA
53565838 TTGTTAGTAAAATTAT
1 TTGTTAGTAAAATTAT
53565854 CAAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 1 0.04
18 1 0.04
19 7 0.28
20 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:53565945 original size:102 final size:102
Alignment explanation
Indices: 53565769--53565963 Score: 363
Period size: 102 Copynumber: 1.9 Consensus size: 102
53565759 ATATTTTTTT
53565769 GTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
1 GTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
53565834 TTAATTGTTAGTAAAATTATCAAATTATTAATTGTTA
66 TTAATTGTTAGTAAAATTATCAAATTATTAATTGTTA
* *
53565871 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
1 GTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
*
53565936 TTAATTGTTAGTAAATTTATCAAATTAT
66 TTAATTGTTAGTAAAATTATCAAATTAT
53565964 ATCATATTAG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (102 bp):
GTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
TTAATTGTTAGTAAAATTATCAAATTATTAATTGTTA
Found at i:53566065 original size:21 final size:21
Alignment explanation
Indices: 53566040--53566107 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
53566030 AAGGGTTACA
53566040 GTTAGGATTTTTAAGTTAAGG
1 GTTAGGATTTTTAAGTTAAGG
* *
53566061 GTTAGGGTTTTTAAGTTAATG
1 GTTAGGATTTTTAAGTTAAGG
*
53566082 GTTA-GAGTTTTAAGTTAAGG
1 GTTAGGATTTTTAAGTTAAGG
53566102 GTTAGG
1 GTTAGG
53566108 GTTAGGGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
GTTAGGATTTTTAAGTTAAGG
Found at i:53566071 original size:20 final size:20
Alignment explanation
Indices: 53566048--53566110 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
53566038 CAGTTAGGAT
53566048 TTTTAAGTTAAGGGTTAGGG
1 TTTTAAGTTAAGGGTTAGGG
* *
53566068 TTTTTAAGTTAATGGTTAGAG
1 -TTTTAAGTTAAGGGTTAGGG
53566089 TTTTAAGTTAAGGGTTAGGG
1 TTTTAAGTTAAGGGTTAGGG
53566109 TT
1 TT
53566111 AGGGTTAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.44
Consensus pattern (20 bp):
TTTTAAGTTAAGGGTTAGGG
Found at i:53566688 original size:18 final size:18
Alignment explanation
Indices: 53566662--53566704 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53566652 GACTCGAAAA
* * *
53566662 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
53566680 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
53566698 AGGATAC
1 AGGATAC
53566705 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:53567358 original size:7 final size:7
Alignment explanation
Indices: 53567346--53567377 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
53567336 TATTAGTTAT
53567346 ATACATA
1 ATACATA
53567353 ATACATA
1 ATACATA
53567360 ATACATA
1 ATACATA
53567367 ATACATA
1 ATACATA
53567374 ATAC
1 ATAC
53567378 TAAATACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:53567598 original size:21 final size:21
Alignment explanation
Indices: 53567558--53567598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53567548 CTATTATTTT
*
53567558 TAAAAATCTACATAATAATTG
1 TAAAAATCTACATAAAAATTG
53567579 TAAAAATCTA-ATATAAAATT
1 TAAAAATCTACATA-AAAATT
53567599 TACCTCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAATCTACATAAAAATTG
Found at i:53568597 original size:11 final size:11
Alignment explanation
Indices: 53568585--53568634 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
53568575 AAATATGGAT
53568585 TTGAGA-GAAA
1 TTGAGAGGAAA
53568595 TTTG-GAAGGAAA
1 -TTGAGA-GGAAA
53568607 TTGAGAGGAAA
1 TTGAGAGGAAA
53568618 TTGAGAGGAAA
1 TTGAGAGGAAA
53568629 TTGAGA
1 TTGAGA
53568635 AAATAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.06
11 28 0.78
12 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:53570956 original size:16 final size:18
Alignment explanation
Indices: 53570930--53570977 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
53570920 TATAATTAGA
53570930 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
53570947 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
*
53570964 CTAATTTTAATTTT
1 -TAA-ATTAATTTT
53570978 GTTAAAGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.27
17 9 0.35
18 3 0.12
20 7 0.27
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:53571367 original size:16 final size:16
Alignment explanation
Indices: 53571346--53571380 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
53571336 TTATACACTT
53571346 ATTTAGTCACGAAGTC
1 ATTTAGTCACGAAGTC
53571362 ATTTAGTCACGAAGTC
1 ATTTAGTCACGAAGTC
53571378 ATT
1 ATT
53571381 CCACTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (16 bp):
ATTTAGTCACGAAGTC
Found at i:53572436 original size:20 final size:20
Alignment explanation
Indices: 53572397--53572436 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53572387 TGTTAATTAG
* *
53572397 ATTAAAATAAGCTTAGTTTA
1 ATTAAAATAAGATTAATTTA
*
53572417 ATTAAAGTAAGATTAATTTA
1 ATTAAAATAAGATTAATTTA
53572437 CATAATTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (20 bp):
ATTAAAATAAGATTAATTTA
Found at i:53572855 original size:32 final size:32
Alignment explanation
Indices: 53572817--53572880 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
53572807 AATGTGAAAT
53572817 TGATTATAGAAATAAGAAATAATGTTTCCCTA
1 TGATTATAGAAATAAGAAATAATGTTTCCCTA
53572849 TGATTATAGAAATAAGAAATAATGTTTCCCTA
1 TGATTATAGAAATAAGAAATAATGTTTCCCTA
53572881 AAGGGTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (32 bp):
TGATTATAGAAATAAGAAATAATGTTTCCCTA
Found at i:53574267 original size:19 final size:20
Alignment explanation
Indices: 53574216--53574267 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
53574206 ACCACTAAAG
53574216 AAATATCAATACCTTTCACTA
1 AAATATCAATA-CTTTCACTA
* * * *
53574237 GAGTATCGATACTTT-AGTA
1 AAATATCAATACTTTCACTA
53574256 AAATATCAATAC
1 AAATATCAATAC
53574268 CAAAATGAGC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATATCAATACTTTCACTA
Found at i:53579348 original size:20 final size:20
Alignment explanation
Indices: 53579325--53579365 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53579315 CATAATATTG
*
53579325 GCAGCTTGTCTACAGTACTA
1 GCAGCTTATCTACAGTACTA
* *
53579345 GCAGTTTATCTACATTACTA
1 GCAGCTTATCTACAGTACTA
53579365 G
1 G
53579366 TGGCTCAACC
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:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (20 bp):
GCAGCTTATCTACAGTACTA
Found at i:53580300 original size:21 final size:20
Alignment explanation
Indices: 53580254--53580307 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
53580244 TGAAGCTAAA
* *
53580254 AATGGTATCAATA-CTTGAC
1 AATGGTATCGATACCTTAAC
*
53580273 AAAGGTATCGATACCTATAAC
1 AATGGTATCGATACCT-TAAC
53580294 AATGGTATCGATAC
1 AATGGTATCGATAC
53580308 TTCATGTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
AATGGTATCGATACCTTAAC
Found at i:53584888 original size:16 final size:16
Alignment explanation
Indices: 53584867--53584904 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
53584857 AAGATTAAAC
*
53584867 AATAAAAATAAGATTT
1 AATAAAAATAACATTT
53584883 AAT-AAAATAACATTT
1 AATAAAAATAACATTT
*
53584898 AACAAAA
1 AATAAAA
53584905 CATTCATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAAAAATAACATTT
Found at i:53585356 original size:17 final size:17
Alignment explanation
Indices: 53585334--53585372 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
53585324 CATTACAGAC
53585334 ATCTGTCAACTACGGAA
1 ATCTGTCAACTACGGAA
*
53585351 ATCTGTCAACTACGGCA
1 ATCTGTCAACTACGGAA
53585368 ATCTG
1 ATCTG
53585373 GACAGCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (17 bp):
ATCTGTCAACTACGGAA
Found at i:53589193 original size:44 final size:45
Alignment explanation
Indices: 53589144--53589232 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
53589134 AGATTAAAAT
53589144 GTTTTGTCTTTGAA-TTTTAGTGAAATTGAGTAAATAGGGCTAAA
1 GTTTTGTCTTTGAATTTTTAGTGAAATTGAGTAAATAGGGCTAAA
53589188 GTTTTGTCTTTGAATTTTTAGTGAAATTGAGTAAATAGGGCTAAA
1 GTTTTGTCTTTGAATTTTTAGTGAAATTGAGTAAATAGGGCTAAA
53589233 TTGTGAAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 14 0.32
45 30 0.68
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.42
Consensus pattern (45 bp):
GTTTTGTCTTTGAATTTTTAGTGAAATTGAGTAAATAGGGCTAAA
Found at i:53589248 original size:44 final size:45
Alignment explanation
Indices: 53589158--53589250 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
53589148 TGTCTTTGAA
* *** *
53589158 TTTTAGTGAAATTGAGTAAATAGGGCTAAAGTTTTGTCTTTGAAT
1 TTTTAGTGAAATTGAGTAAATAGGGCTAAAGTTGTGAAATTAAAT
53589203 TTTTAGTGAAATTGAGTAAATAGGGCTAAA-TTGTGAAATTAAAT
1 TTTTAGTGAAATTGAGTAAATAGGGCTAAAGTTGTGAAATTAAAT
53589247 TTTT
1 TTTT
53589251 GGGGGACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 13 0.30
45 30 0.70
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (45 bp):
TTTTAGTGAAATTGAGTAAATAGGGCTAAAGTTGTGAAATTAAAT
Found at i:53590423 original size:41 final size:41
Alignment explanation
Indices: 53590378--53590522 Score: 265
Period size: 41 Copynumber: 3.5 Consensus size: 41
53590368 GACTTTAAGT
53590378 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
53590419 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
53590460 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
53590501 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
53590523 ATATGTTAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
40 1 0.01
41 101 0.99
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:53600613 original size:12 final size:12
Alignment explanation
Indices: 53600577--53600618 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
53600567 TAAGTTAAAT
*
53600577 ATTAAAATAAG-
1 ATTAAAATATGA
53600588 ATTAAAAATGATGA
1 ATT-AAAAT-ATGA
53600602 ATTAAAATATGA
1 ATTAAAATATGA
53600614 ATTAA
1 ATTAA
53600619 TTTATCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
13 7 0.26
14 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (12 bp):
ATTAAAATATGA
Found at i:53602669 original size:142 final size:142
Alignment explanation
Indices: 53602404--53602916 Score: 758
Period size: 142 Copynumber: 3.6 Consensus size: 142
53602394 TTCGGTCTAT
* * * * * *
53602404 TCCACCGTAATCTCAGGGAAATAAGATTACTGGCTTCAATCTGTTCCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGA
* * * *
53602469 TAAGATTTCTAGCTTCAATCTGATGCGATCTACTCTACTATAACTTCAGAGAGGTAAGACCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
*
53602534 ATATTAATCCGC
131 ATTTTAATCCGC
* * *
53602546 TCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGATGTAATCTCAAGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGA
* *
53602611 TAAGATTTCTGGTTTCAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
53602676 ATTTTAATCCGC
131 ATTTTAATCCGC
*
53602688 TCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC-AGGAAG
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGG-AG
* * * * * *
53602752 ATAATATTTCTGACTTCAATCAGATGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCTTT
65 ATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
53602817 TATTTTAATCCGC
130 TATTTTAATCCGC
* * * * *
53602830 CCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCAATCTGCTCCGTTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGA
53602895 TAAGATTTCTGGCTTCAATCTG
66 TAAGATTTCTGGCTTCAATCTG
53602917 CTCCACTGTA
Statistics
Matches: 332, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
141 3 0.01
142 327 0.98
143 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGA
TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
ATTTTAATCCGC
Found at i:53602743 original size:44 final size:44
Alignment explanation
Indices: 53602681--53602968 Score: 172
Period size: 44 Copynumber: 6.3 Consensus size: 44
53602671 CCTTTATTTT
* * * *
53602681 AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
53602725 AATCTGCTCCGCTGTAATCTCAGGAAGATAATATTTCT-GACTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAG-CTTC
* * ** * *
53602769 AATCAGATGCGATCTACTCTGCTGTAA-CTTTAGAGAGATAAGATCTTTTA-TTTT
1 AATC---T--G--CT-C-C-GCTGTAATC-TCAGGGAGATAAGAT-TACTAGCTTC
* * * * * *
53602823 AATCCGCCCCACTGTAATCTCAAGGAGATAGGATTACTATCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
53602867 AATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
53602911 AATCTGCTCCACTGTAA-CATCAGGGAGATAAGATTTAC-CGTCTTC
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGA-TTACTAG-CTTC
*
53602956 GATCTGCTCCGCT
1 AATCTGCTCCGCT
53602969 ATTGCTTAGG
Statistics
Matches: 185, Mismatches: 40, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
43 5 0.03
44 123 0.66
45 20 0.11
46 1 0.01
47 2 0.01
49 2 0.01
51 2 0.01
52 1 0.01
53 2 0.01
54 24 0.13
55 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:53605650 original size:543 final size:543
Alignment explanation
Indices: 53604623--53605708 Score: 2172
Period size: 543 Copynumber: 2.0 Consensus size: 543
53604613 CTTCATCCAA
53604623 TTTCAATTCAGCTAATACCCGAAGAGAAGGAATCTCCACTTCAATGGGTAAAACGACTTCCATCC
1 TTTCAATTCAGCTAATACCCGAAGAGAAGGAATCTCCACTTCAATGGGTAAAACGACTTCCATCC
53604688 CATAAACTAGCGAAAAGGGTGTTGCCCCAGTAGAGGTCCTAACAGATGTTCGGTAAGCTAAGAGA
66 CATAAACTAGCGAAAAGGGTGTTGCCCCAGTAGAGGTCCTAACAGATGTTCGGTAAGCTAAGAGA
53604753 GCAAATGATAGCTTTTCATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAAT
131 GCAAATGATAGCTTTTCATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAAT
53604818 GTTCTTATTGGTCGCCTCCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGAC
196 GTTCTTATTGGTCGCCTCCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGAC
53604883 TGATCTTGAACTGACTACAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCAGAT
261 TGATCTTGAACTGACTACAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCAGAT
53604948 ATGATTCTTTCAGGCATTCCATATCGACAAATGATCTCCTTTTTCAAGAATTTACTAACTGCTAA
326 ATGATTCTTTCAGGCATTCCATATCGACAAATGATCTCCTTTTTCAAGAATTTACTAACTGCTAA
53605013 TTTCGTGACATTTGCATATGAAGTAGCTTCCACCCATTTGGTAAAGTAATCAATGACCACAAAGA
391 TTTCGTGACATTTGCATATGAAGTAGCTTCCACCCATTTGGTAAAGTAATCAATGACCACAAAGA
53605078 TGAAACGATGCCCATTCGAAGCTTTCGGTGATATTGGCCCAATAACATCCATGCCCCACAACGAG
456 TGAAACGATGCCCATTCGAAGCTTTCGGTGATATTGGCCCAATAACATCCATGCCCCACAACGAG
53605143 AACGGCCATGGAGCAGTCATAAT
521 AACGGCCATGGAGCAGTCATAAT
53605166 TTTCAATTCAGCTAATACCCGAAGAGAAGGAATCTCCACTTCAATGGGTAAAACGACTTCCATCC
1 TTTCAATTCAGCTAATACCCGAAGAGAAGGAATCTCCACTTCAATGGGTAAAACGACTTCCATCC
53605231 CATAAACTAGCGAAAAGGGTGTTGCCCCAGTAGAGGTCCTAACAGATGTTCGGTAAGCTAAGAGA
66 CATAAACTAGCGAAAAGGGTGTTGCCCCAGTAGAGGTCCTAACAGATGTTCGGTAAGCTAAGAGA
53605296 GCAAATGATAGCTTTTCATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAAT
131 GCAAATGATAGCTTTTCATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAAT
53605361 GTTCTTATTGGTCGCCTCCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGAC
196 GTTCTTATTGGTCGCCTCCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGAC
53605426 TGATCTTGAACTGACTACAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCAGAT
261 TGATCTTGAACTGACTACAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCAGAT
53605491 ATGATTCTTTCAGGCATTCCATATCGACAAATGATCTCCTTTTTCAAGAATTTACTAACTGCTAA
326 ATGATTCTTTCAGGCATTCCATATCGACAAATGATCTCCTTTTTCAAGAATTTACTAACTGCTAA
53605556 TTTCGTGACATTTGCATATGAAGTAGCTTCCACCCATTTGGTAAAGTAATCAATGACCACAAAGA
391 TTTCGTGACATTTGCATATGAAGTAGCTTCCACCCATTTGGTAAAGTAATCAATGACCACAAAGA
53605621 TGAAACGATGCCCATTCGAAGCTTTCGGTGATATTGGCCCAATAACATCCATGCCCCACAACGAG
456 TGAAACGATGCCCATTCGAAGCTTTCGGTGATATTGGCCCAATAACATCCATGCCCCACAACGAG
53605686 AACGGCCATGGAGCAGTCATAAT
521 AACGGCCATGGAGCAGTCATAAT
53605709 GTGCAGAGGT
Statistics
Matches: 543, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
543 543 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (543 bp):
TTTCAATTCAGCTAATACCCGAAGAGAAGGAATCTCCACTTCAATGGGTAAAACGACTTCCATCC
CATAAACTAGCGAAAAGGGTGTTGCCCCAGTAGAGGTCCTAACAGATGTTCGGTAAGCTAAGAGA
GCAAATGATAGCTTTTCATGCCAATCCTTGTAGGTTTCAGTCATTTTCCCCACAATTCTCTTAAT
GTTCTTATTGGTCGCCTCCACTGCACCATTCATTTTTGGGCGATATGGCGACGAGTTATGGTGAC
TGATCTTGAACTGACTACAAACTTCCGCTATTGTGCTATTGTTCAAATTCAACGCATTGTCAGAT
ATGATTCTTTCAGGCATTCCATATCGACAAATGATCTCCTTTTTCAAGAATTTACTAACTGCTAA
TTTCGTGACATTTGCATATGAAGTAGCTTCCACCCATTTGGTAAAGTAATCAATGACCACAAAGA
TGAAACGATGCCCATTCGAAGCTTTCGGTGATATTGGCCCAATAACATCCATGCCCCACAACGAG
AACGGCCATGGAGCAGTCATAAT
Found at i:53608132 original size:13 final size:13
Alignment explanation
Indices: 53608114--53608139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53608104 CTCCTTATGA
53608114 GGTAGGATTTATT
1 GGTAGGATTTATT
53608127 GGTAGGATTTATT
1 GGTAGGATTTATT
53608140 TATCCTCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
GGTAGGATTTATT
Found at i:53608865 original size:13 final size:14
Alignment explanation
Indices: 53608831--53608868 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
53608821 TTAAACGTAC
*
53608831 CCTTCTTCTCTCCTT
1 CCTT-TTCTCTACTT
53608846 CCTTTTCTCTACTT
1 CCTTTTCTCTACTT
53608860 -CTTTTCTCT
1 CCTTTTCTCT
53608869 TTTGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (14 bp):
CCTTTTCTCTACTT
Found at i:53612083 original size:19 final size:19
Alignment explanation
Indices: 53612057--53612104 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
53612047 TTAATAATTT
* *
53612057 TGAATGCATATG-ATGACA
1 TGAATGCAAATGCATGAAA
53612075 TGTAATGCAAATGCATGAAA
1 TG-AATGCAAATGCATGAAA
53612095 TGAATGCAAA
1 TGAATGCAAA
53612105 AAAGAGCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (19 bp):
TGAATGCAAATGCATGAAA
Found at i:53615855 original size:12 final size:12
Alignment explanation
Indices: 53615819--53615860 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
53615809 TAAGTTAAAT
*
53615819 ATTAAAATAAG-
1 ATTAAAATATGA
53615830 ATTAAAAATGATGA
1 ATT-AAAAT-ATGA
53615844 ATTAAAATATGA
1 ATTAAAATATGA
53615856 ATTAA
1 ATTAA
53615861 TTTATCTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
13 7 0.26
14 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (12 bp):
ATTAAAATATGA
Found at i:53618959 original size:19 final size:19
Alignment explanation
Indices: 53618935--53618974 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53618925 ACTAAGTTAG
* *
53618935 ATAAAACTAATAAAACAAA
1 ATAAAAATAACAAAACAAA
*
53618954 ATAAAAATAACAAAACCAA
1 ATAAAAATAACAAAACAAA
53618973 AT
1 AT
53618975 TTCACCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (19 bp):
ATAAAAATAACAAAACAAA
Found at i:53624671 original size:17 final size:17
Alignment explanation
Indices: 53624649--53624681 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53624639 TGAAAGAACA
*
53624649 GTGAAAACGAGAATGAT
1 GTGAAAACGAAAATGAT
53624666 GTGAAAACGAAAATGA
1 GTGAAAACGAAAATGA
53624682 AATAGATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.27, T:0.15
Consensus pattern (17 bp):
GTGAAAACGAAAATGAT
Found at i:53632578 original size:27 final size:26
Alignment explanation
Indices: 53632510--53632579 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
53632500 CCTTTACATA
**
53632510 TATGCTCACACGAGCTGTGGAAAGAG
1 TATGCTCACACGAGCTGTAAAAAGAG
*
53632536 TATGCTCACACGAGCTGTAAAAATGGG
1 TATGCTCACACGAGCTGTAAAAA-GAG
* *
53632563 TCTGCTCACACAAGCTG
1 TATGCTCACACGAGCTG
53632580 AAGGTCGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTAAAAAGAG
Found at i:53639122 original size:15 final size:15
Alignment explanation
Indices: 53639102--53639132 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53639092 CCATATTTCA
53639102 ACCACATCCAAACAT
1 ACCACATCCAAACAT
*
53639117 ACCACATTCAAACAT
1 ACCACATCCAAACAT
53639132 A
1 A
53639133 TAAAAACAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (15 bp):
ACCACATCCAAACAT
Found at i:53639724 original size:26 final size:26
Alignment explanation
Indices: 53639656--53639726 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
53639646 CCTTTACATA
* * *
53639656 TATGCTCACACAAGCTATGGAAAGAG
1 TATGCTCACACGAGCTGTGAAAAGAG
53639682 TATGCTCACACGAGCTGTGAAAATG-G
1 TATGCTCACACGAGCTGTGAAAA-GAG
*
53639708 TCTGCTCACACGAGCTGTG
1 TATGCTCACACGAGCTGTG
53639727 GGTTAAAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAAAGAG
Found at i:53641294 original size:13 final size:14
Alignment explanation
Indices: 53641262--53641300 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
53641252 TTTTTTTATG
53641262 TTTCTTCTTCCTACCA
1 TTTCTT-TT-CTACCA
53641278 TTTCTTTTCTACC-
1 TTTCTTTTCTACCA
53641291 TTTCTTTTCT
1 TTTCTTTTCT
53641301 TCTCTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.43
14 5 0.22
15 2 0.09
16 6 0.26
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTCTTTTCTACCA
Found at i:53641474 original size:19 final size:18
Alignment explanation
Indices: 53641410--53641474 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
53641400 AATAGCGTAA
53641410 GTTTTGTTATGAATTTTT
1 GTTTTGTTATGAATTTTT
* *
53641428 GTTAATGTTCAT--TTTTTT
1 GTT-TTGTT-ATGAATTTTT
53641446 AAGTTTTGTTATGAATTTTT
1 --GTTTTGTTATGAATTTTT
53641466 GTTTATGTT
1 GTTT-TGTT
53641475 TGTTTCTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
18 14 0.39
19 12 0.33
20 10 0.28
ACGTcount: A:0.18, C:0.02, G:0.15, T:0.65
Consensus pattern (18 bp):
GTTTTGTTATGAATTTTT
Found at i:53643950 original size:5 final size:5
Alignment explanation
Indices: 53643940--53644004 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
53643930 TTTATTAACA
53643940 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
53643990 ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT
53644005 TATACGGTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
ATGTT
Found at i:53644032 original size:13 final size:13
Alignment explanation
Indices: 53644016--53644042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53644006 ATACGGTAAG
53644016 TTTTATCCAACTA
1 TTTTATCCAACTA
53644029 TTTTATCCAACTA
1 TTTTATCCAACTA
53644042 T
1 T
53644043 CTTTCAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTATCCAACTA
Found at i:53649361 original size:6 final size:6
Alignment explanation
Indices: 53649350--53649374 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53649340 ATGCTCTTTG
53649350 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
53649375 GGAATTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:53649461 original size:19 final size:18
Alignment explanation
Indices: 53649419--53649458 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
53649409 GATATTTTTA
*
53649419 TTTTAATGTTTTTAGTAT
1 TTTTAATGTTTATAGTAT
53649437 TTTTAATGTATTATA-TAT
1 TTTTAATGT-TTATAGTAT
53649455 TTTT
1 TTTT
53649459 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTTAATGTTTATAGTAT
Found at i:53655272 original size:3 final size:3
Alignment explanation
Indices: 53655264--53655305 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53655254 CAAGAAAACT
53655264 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53655306 CAAATAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53658058 original size:29 final size:27
Alignment explanation
Indices: 53658024--53658088 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
53658014 GTTTTACGTG
* *
53658024 TATAATTGCATTAAATTAAAGTTCATGTA
1 TATAATTACATAAAATTAAAGTTCA--TA
53658053 TATAATTTTACATAAAATTAAAGTTCATA
1 TATAA--TTACATAAAATTAAAGTTCATA
53658082 TATAATT
1 TATAATT
53658089 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
29 12 0.38
31 18 0.56
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAATTACATAAAATTAAAGTTCATA
Found at i:53661742 original size:16 final size:17
Alignment explanation
Indices: 53661721--53661753 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53661711 ATGTTTTCTC
53661721 TCTTTT-CTCTCTTTTT
1 TCTTTTCCTCTCTTTTT
*
53661737 TCTTTTCCTTTCTTTTT
1 TCTTTTCCTCTCTTTTT
53661754 CTTGTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTTCCTCTCTTTTT
Found at i:53661763 original size:8 final size:8
Alignment explanation
Indices: 53661714--53661769 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 8
53661704 AAGTTTGATG
53661714 TTTTCTCTC
1 TTTTCT-TC
53661723 TTTTCTCTC
1 TTTTCT-TC
53661732 TTTT-TTC
1 TTTTCTTC
53661739 TTTTCCTTTC
1 TTTT-C-TTC
*
53661749 TTTTTCTTG
1 -TTTTCTTC
53661758 TTTTCTTC
1 TTTTCTTC
53661766 TTTT
1 TTTT
53661770 GTTTGATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.15
8 12 0.29
9 15 0.37
10 4 0.10
11 4 0.10
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTTCTTC
Found at i:53666403 original size:86 final size:83
Alignment explanation
Indices: 53666275--53666430 Score: 215
Period size: 86 Copynumber: 1.8 Consensus size: 83
53666265 ATTCGATGAA
* *
53666275 TTCATCAAGTCCGTCAATAGACCACCCAAAATTTGGGATATGAACTCATTAAGAGTAATAAAATC
1 TTCATCAAGTCCGTCAATAGACCACCCAAAATCTAGGATATGAACTCATTAAGAGTAAT-AAATC
53666340 AACCTTTCAAGTTGGTGAC
65 AACCTTTCAAGTTGGTGAC
* * * *
53666359 TTCATCAAGTCCGTCTCAATAGGACCA-CCAAACTCTAGGCTATGAATTCATTAAGAGTAATAAC
1 TTCATCAAGTCCG--TCAATA-GACCACCCAAAATCTAGGATATGAACTCATTAAGAGTAATAAA
53666423 TCAACCTT
63 TCAACCTT
53666431 ATGCATGCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
84 13 0.21
85 10 0.16
86 35 0.56
87 5 0.08
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
TTCATCAAGTCCGTCAATAGACCACCCAAAATCTAGGATATGAACTCATTAAGAGTAATAAATCA
ACCTTTCAAGTTGGTGAC
Found at i:53667653 original size:15 final size:15
Alignment explanation
Indices: 53667628--53667662 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53667618 GATTCTATTT
*
53667628 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
53667642 TAATTAATATTAAGA
1 TAATTAATATTAAGA
53667657 TAATTA
1 TAATTA
53667663 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:53671613 original size:4 final size:4
Alignment explanation
Indices: 53671604--53671682 Score: 67
Period size: 4 Copynumber: 19.5 Consensus size: 4
53671594 CCAATTTTTA
*
53671604 TATT TATT TATT TATT TATT TA-T TATTT TCTT TACTT TATT TA-T TACTT
1 TATT TATT TATT TATT TATT TATT TA-TT TATT TA-TT TATT TATT TA-TT
*
53671653 TATTT TATT T-TAT TATT TA-T TAAT TATT TA
1 TA-TT TATT TAT-T TATT TATT TATT TATT TA
53671683 GATATTAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
3 10 0.16
4 39 0.62
5 14 0.22
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:53671668 original size:21 final size:20
Alignment explanation
Indices: 53671607--53671673 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
53671597 ATTTTTATAT
53671607 TTATTTA-TTTATTTATTTA
1 TTATTTATTTTATTTATTTA
53671626 TTATTT-TCTTTACTTTATTTA
1 TTATTTAT-TTTA-TTTATTTA
53671647 TTACTTTATTTTA--T-TTTA
1 TTA-TTTATTTTATTTATTTA
53671665 TTATTTATT
1 TTATTTATT
53671674 AATTATTTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.14
18 7 0.16
19 7 0.16
20 4 0.09
21 11 0.26
22 7 0.16
23 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTTATTTTATTTATTTA
Found at i:53673006 original size:101 final size:100
Alignment explanation
Indices: 53672816--53673004 Score: 256
Period size: 101 Copynumber: 1.8 Consensus size: 100
53672806 AAGAACATGT
* *
53672816 TGGGCTGAGTAATCAGGGTGAGGTGCTTGGCTGTCATCTCTTTTCGCGTCAAAAGGTTCGATGTG
1 TGGGCTGAGTAATCAGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGATATG
*
53672881 TTCTTAAGAAAAAATTATAATAAATTAGGAGTCTGC
66 TTCTAAAGAAAAAA-TATAATAAATTAGGAGTCTGC
* *
53672917 TGGGCTGAGTAA-CTGGGGTGAGGTTCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTAT
1 TGGGCTGAGTAATC-AGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTC-G-AT
53672981 AT-TTCTAAAGCATAAAAAATATAA
63 ATGTTCTAAAG---AAAAAATATAA
53673005 ATAATAAATA
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
100 1 0.01
101 54 0.70
102 8 0.10
103 3 0.04
104 5 0.06
105 6 0.08
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (100 bp):
TGGGCTGAGTAATCAGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGATATG
TTCTAAAGAAAAAATATAATAAATTAGGAGTCTGC
Found at i:53673632 original size:15 final size:15
Alignment explanation
Indices: 53673607--53673641 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53673597 GACTATATTT
*
53673607 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
53673621 TAATTAATATTAAGA
1 TAATTAATATTAAGA
53673636 TAATTA
1 TAATTA
53673642 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:53673657 original size:18 final size:17
Alignment explanation
Indices: 53673645--53673677 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53673635 ATAATTATTA
53673645 AGGA-TTATTTAATTTT
1 AGGATTTATTTAATTTT
53673661 AGGATTTTATTTAATTT
1 AGGA-TTTATTTAATTT
53673678 ATCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
AGGATTTATTTAATTTT
Found at i:53684506 original size:6 final size:6
Alignment explanation
Indices: 53684495--53684521 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53684485 GTTATTCATT
53684495 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
53684522 TATAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:53690380 original size:20 final size:21
Alignment explanation
Indices: 53690345--53690392 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
53690335 ATTTTTTATT
53690345 ATTTTAAAAATATAATATAAA
1 ATTTTAAAAATATAATATAAA
* **
53690366 ATTTT-AAATTATAATATATT
1 ATTTTAAAAATATAATATAAA
53690386 ATTTTAA
1 ATTTTAA
53690393 TCATATAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTAAAAATATAATATAAA
Found at i:53691141 original size:19 final size:18
Alignment explanation
Indices: 53691112--53691158 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
53691102 AATCCATTAA
*
53691112 ATTTAAAATATATGAATT
1 ATTTAATATATATGAATT
*
53691130 ACTTTAATATATATTAATT
1 A-TTTAATATATATGAATT
*
53691149 ATTAAATATA
1 ATTTAATATA
53691159 ACAAATCTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTAATATATATGAATT
Found at i:53691774 original size:31 final size:31
Alignment explanation
Indices: 53691713--53691803 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
53691703 AAAAAAACTT
* * *
53691713 AATAGCTTAGTGACTTTTAATAAAAGCTTTCG
1 AATAGTTTAGTGAC-TTAAATAAAAACTTTCG
*
53691745 AATAGTTTAGTAACTTAAATAAAAACTTTCG
1 AATAGTTTAGTGACTTAAATAAAAACTTTCG
* * * *
53691776 AACAATTTAGTGA-TTAAATTATAACTTT
1 AATAGTTTAGTGACTTAAATAAAAACTTT
53691804 TTAGTTAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 13 0.26
31 25 0.50
32 12 0.24
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (31 bp):
AATAGTTTAGTGACTTAAATAAAAACTTTCG
Found at i:53692843 original size:13 final size:13
Alignment explanation
Indices: 53692825--53692849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53692815 TTTTTGTTAA
53692825 TTTTTAATTAATG
1 TTTTTAATTAATG
53692838 TTTTTAATTAAT
1 TTTTTAATTAAT
53692850 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:53694802 original size:13 final size:13
Alignment explanation
Indices: 53694784--53694820 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
53694774 CTTGAAGAGC
53694784 ACTTTTCTAAAAT
1 ACTTTTCTAAAAT
53694797 ACTTTT-TAAAAAT
1 ACTTTTCT-AAAAT
53694810 ACTTTTC-AAAA
1 ACTTTTCTAAAA
53694821 GCATTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (13 bp):
ACTTTTCTAAAAT
Found at i:53710794 original size:22 final size:22
Alignment explanation
Indices: 53710753--53710800 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
53710743 CTAAAATCTT
*
53710753 GAGACAATTTGCCATATGTCTC
1 GAGACAATTTGCCATATGTCTA
53710775 GAGACAATTT-CTCGAT-TGTCTA
1 GAGACAATTTGC-C-ATATGTCTA
53710797 GAGA
1 GAGA
53710801 TAGGGCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (22 bp):
GAGACAATTTGCCATATGTCTA
Found at i:53712950 original size:67 final size:67
Alignment explanation
Indices: 53712660--53712950 Score: 306
Period size: 67 Copynumber: 4.3 Consensus size: 67
53712650 AGGTTTAAGG
** *
53712660 TGTAAGACCATAAATCGACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
1 TGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTACTAGGACATTAAACATAGGGTTAAA
*
53712725 TG
66 TA
* * * *
53712727 TGTAAGATCATAGCTTGACTATGACAA-C-ATGTGTAGTCTA-TCAGGACATTAAACATGGGGTT
1 TGTAAGACCATAGCTCGACTATGACAACCAAT-AG-AGTCTACT-AGGACATTAAACATAGGGTT
*
53712789 ACATA
63 AAATA
** * *
53712794 TGTAAGACCATAAATCAACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
1 TGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTACTAGGACATTAAACATAGGGTTAAA
*
53712859 TG
66 TA
* * * *
53712861 TGTAAGATCATAGCTTGACTATGACAA-C-ATGTGTAGTCTA-TCAGGACATTAAACATGGGGTT
1 TGTAAGACCATAGCTCGACTATGACAACCAAT-AG-AGTCTACT-AGGACATTAAACATAGGGTT
*
53712923 ACATA
63 AAATA
*
53712928 TGTAAGACCATAGCTCGTCTATG
1 TGTAAGACCATAGCTCGACTATG
53712951 GCAATAAATA
Statistics
Matches: 183, Mismatches: 32, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
65 4 0.02
66 6 0.03
67 168 0.92
68 3 0.02
69 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (67 bp):
TGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTACTAGGACATTAAACATAGGGTTAAA
TA
Found at i:53712950 original size:134 final size:134
Alignment explanation
Indices: 53712660--53712939 Score: 551
Period size: 134 Copynumber: 2.1 Consensus size: 134
53712650 AGGTTTAAGG
53712660 TGTAAGACCATAAATCGACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
1 TGTAAGACCATAAATCGACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
53712725 TGTGTAAGATCATAGCTTGACTATGACAACATGTGTAGTCTATCAGGACATTAAACATGGGGTTA
66 TGTGTAAGATCATAGCTTGACTATGACAACATGTGTAGTCTATCAGGACATTAAACATGGGGTTA
53712790 CATA
131 CATA
*
53712794 TGTAAGACCATAAATCAACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
1 TGTAAGACCATAAATCGACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
53712859 TGTGTAAGATCATAGCTTGACTATGACAACATGTGTAGTCTATCAGGACATTAAACATGGGGTTA
66 TGTGTAAGATCATAGCTTGACTATGACAACATGTGTAGTCTATCAGGACATTAAACATGGGGTTA
53712924 CATA
131 CATA
53712928 TGTAAGACCATA
1 TGTAAGACCATA
53712940 GCTCGTCTAT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 145 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (134 bp):
TGTAAGACCATAAATCGACTATGACAACCAATAGAGTCTACTAGGACATTAAGCATAGGGTTAAA
TGTGTAAGATCATAGCTTGACTATGACAACATGTGTAGTCTATCAGGACATTAAACATGGGGTTA
CATA
Found at i:53715005 original size:17 final size:19
Alignment explanation
Indices: 53714975--53715011 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53714965 AAACATTTAT
53714975 TTTTTAATGATATT-TGCA
1 TTTTTAATGATATTATGCA
*
53714993 TTTTTATTG-TATTATGCA
1 TTTTTAATGATATTATGCA
53715011 T
1 T
53715012 ACTCTATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (19 bp):
TTTTTAATGATATTATGCA
Found at i:53715208 original size:123 final size:123
Alignment explanation
Indices: 53714985--53715232 Score: 442
Period size: 123 Copynumber: 2.0 Consensus size: 123
53714975 TTTTTAATGA
*
53714985 TATTTGCATTTTTATTGTATTATGCATACTCTATTACCTTCATCAATTGTATATCTATATACTTA
1 TATTTGCATTTTTATTGTATTATGCATACTCTATTACCTCCATCAATTGTATATCTATATACTTA
* *
53715050 CTATTATTTAAGTTATTGACTAAGGTGGTGTCACGAATTGACCAGGCACCAACTTGGT
66 CTATTATTTAAGTCATTGACTAAGGTGGTGCCACGAATTGACCAGGCACCAACTTGGT
* *
53715108 TATTTGCATTTTTATTGTATTATGCATACTCTATTATCTCCATCAATTGTATATCTATATAGTTA
1 TATTTGCATTTTTATTGTATTATGCATACTCTATTACCTCCATCAATTGTATATCTATATACTTA
*
53715173 CTATTATTTAAGTCATTGACTAAGGTGGTGCCACGAATTGACCAGGCACCAACTTTGT
66 CTATTATTTAAGTCATTGACTAAGGTGGTGCCACGAATTGACCAGGCACCAACTTGGT
53715231 TA
1 TA
53715233 GGGAAATTAT
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (123 bp):
TATTTGCATTTTTATTGTATTATGCATACTCTATTACCTCCATCAATTGTATATCTATATACTTA
CTATTATTTAAGTCATTGACTAAGGTGGTGCCACGAATTGACCAGGCACCAACTTGGT
Found at i:53719842 original size:131 final size:131
Alignment explanation
Indices: 53719541--53720065 Score: 804
Period size: 131 Copynumber: 4.0 Consensus size: 131
53719531 CTCCTGGGGA
*
53719541 AGATAAGATCCGCAATCTT-CAACCTA-TCCCACTGCTGACCAGGGACATAA-GACTTGTGGCTT
1 AGATAAGATCTGCAAT-TTCCAACCTACT-CCACTGCTGACCAGGGACA-AAGGACTTGTGGCTT
** * *
53719603 AAATCTGTTTCCCTACTCCTAAGGAAGATAAGATTCGCTGTCTTTTGATCTGCTCCACTATTGCT
63 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC-TTCGATCTGCTCCACTATTGCT
53719668 TAGGG
127 TAGGG
* *
53719673 AGATAAGATCTGAAATTTCCAACCTACTCCACTCCTGACCAGGGACAAAGGACTTGTGGCTTAAA
1 AGATAAGATCTGCAATTTCCAACCTACTCCACTGCTGACCAGGGACAAAGGACTTGTGGCTTAAA
* * * * *
53719738 TCTGTTTTCGTAGTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTATTGTTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
53719803 G
131 G
* * * *
53719804 AGATAAGATCTGCTATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAA
1 AGATAAGATCTGCAATTTCCAACCTACTCCACTGCTGACCAGGGACAAAGGACTTGTGGCTTAAA
*
53719869 TCTGTTTCCCTACTCCTGTGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
53719934 G
131 G
* * * *
53719935 AAATAAGATCTGCAATTTCTAACCTACTCCACTGCTGACCAGGGACATAGGACTTGTAGCTTAAA
1 AGATAAGATCTGCAATTTCCAACCTACTCCACTGCTGACCAGGGACAAAGGACTTGTGGCTTAAA
53720000 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
53720065 G
131 G
53720066 TTTAGGGTTT
Statistics
Matches: 359, Mismatches: 31, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
131 272 0.76
132 86 0.24
133 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (131 bp):
AGATAAGATCTGCAATTTCCAACCTACTCCACTGCTGACCAGGGACAAAGGACTTGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGG
G
Found at i:53733000 original size:124 final size:124
Alignment explanation
Indices: 53732774--53733123 Score: 574
Period size: 124 Copynumber: 2.8 Consensus size: 124
53732764 CACAAACATG
* * *
53732774 CTACTGTAGCAAAAGCGTGCCCATGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
53732839 TAGAAGCGATTTTATACTATTTGGTCAGAAAGGTCAAAAAAAAATATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAAAATATTTCTTACATGAC
* *
53732898 CTACTGTAGCAAAAGCGCGTCCACGAGGCTGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *
53732963 TAAAAGCGATTTTATACTATTTGCTCAGAAATTTCAAAAAAAATTATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAAAATATTTCTTACATGAC
* *
53733022 CTACTGTAGCAAAAGTGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTTAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
53733087 TAAAAGTGATTTTATACTATTTGCTCAGAAAGATCAA
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAGGTCAA
53733124 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 209 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAAAATATTTCTTACATGAC
Found at i:53737788 original size:533 final size:533
Alignment explanation
Indices: 53736777--53737839 Score: 1892
Period size: 533 Copynumber: 2.0 Consensus size: 533
53736767 ACTCCATTCT
* *
53736777 CAAAATATCTACTAGATAAAATGTGTTGTATTTAGCATATCGCAATATTTTCGAGCATCAAATAT
1 CAAAATATCTACTAGATAAAAGGTGTTGTATTTAGCATATCGCAATATTTTCAAGCATCAAATAT
*
53736842 CAAGCGAAGAGAAAGCAGCAGTTTTAAATATAAGGGTGAAATCCACTGCTATTACCTTTACAAAC
66 CAAGCGAAGAGAAAGCAGCAGTTTTAAATATAAGGGTGAAATCCACTACTATTACCTTTACAAAC
* *
53736907 TTTGGCATGCTTAATTCGGTCTGACCAAAAAAGAGAAGGAAATAGAAAATTTGAAGTTCAATAAC
131 TTTGGCATGCTCAATTCGGTCTGACCAAAAAAGAGAAAGAAATAGAAAATTTGAAGTTCAATAAC
53736972 TGCCCTACAAAACCGTGCTCTATATCAAGAACTTGCTAATGTAAAAACTCAACTATACTAGCCTT
196 TGCCCTACAAAACCGTGCTCTATATCAAGAACTTGCTAATGTAAAAACTCAACTATACTAGCCTT
* *
53737037 GGTCAACAAGGGAAAATGATTGTGTACACTGATATGGACTAAACACAATTGTAAAGCACATATTT
261 AGTCAACAAGGGAAAATGATTGTGTACACTAATATGGACTAAACACAATTGTAAAGCACATATTT
*
53737102 ACACATATGTTCCTATTACCCCAATTTTCTAAGCACCCAACTAGCATAAGAACACAATGTACTTA
326 ACACATATGTTCCTATTACCCCAATTTTCTAAGCACCCAACCAGCATAAGAACACAATGTACTTA
*
53737167 ACTGAAACATCAATGAAAACCCAGAATTCAGAAGAAAAAAGAAAATAAATTAGAGCAGATAACAA
391 ACTGAAACATCAATGAAAACCCAAAATTCAGAAGAAAAAAGAAAATAAATTAGAGCAGATAACAA
53737232 CATTGAAGAAAAACACAAAAATAAAAACCCAATAAGAAAATTAAAAACAAAGAAAGAAAGGAAGC
456 CATTGAAGAAAAACACAAAAATAAAAACCCAATAAGAAAATTAAAAACAAAGAAAGAAAGGAAGC
*
53737297 TGAACTGTCTGAC
521 AGAACTGTCTGAC
* *
53737310 CAAAGTATCTACTAGATAAAAGGTGTTGTATTTAGCATATTGCAATATTTTCAAGCATCAAATAT
1 CAAAATATCTACTAGATAAAAGGTGTTGTATTTAGCATATCGCAATATTTTCAAGCATCAAATAT
*
53737375 CAAGTGAAGAGAAAGCAGCAGTTTTAAATATAAGGGTGAAATCCACTACTATTACCTTTACAAAC
66 CAAGCGAAGAGAAAGCAGCAGTTTTAAATATAAGGGTGAAATCCACTACTATTACCTTTACAAAC
* *
53737440 TTTGGCATGCTCAATTTGGTCTGACCAAAAAAGAGAAAGAAATAGAAAATTTGAAGTTCAGTAAC
131 TTTGGCATGCTCAATTCGGTCTGACCAAAAAAGAGAAAGAAATAGAAAATTTGAAGTTCAATAAC
* ** * *
53737505 TGCCTTGTAAAATCGTGCTCTATATCAAGAACTTGCTGATGTAAAAACTCAACTATACTAGCCTT
196 TGCCCTACAAAACCGTGCTCTATATCAAGAACTTGCTAATGTAAAAACTCAACTATACTAGCCTT
*
53737570 AGTCAACAAGGGAAAATGATTGTGTACACTAATATGGACTAAACACCATTGTAAAGCACATATTT
261 AGTCAACAAGGGAAAATGATTGTGTACACTAATATGGACTAAACACAATTGTAAAGCACATATTT
*
53737635 ACACATATGTTCCTATTACCCGAATTTTCTAAGCACCCAACCAGCATAAGAACACAATGTACTTA
326 ACACATATGTTCCTATTACCCCAATTTTCTAAGCACCCAACCAGCATAAGAACACAATGTACTTA
* *
53737700 ACTGAAACATCAATGAAAACCCAAAATTTAGAAGAAAAAAGAAAATAAATTAGGGCAGATAACAA
391 ACTGAAACATCAATGAAAACCCAAAATTCAGAAGAAAAAAGAAAATAAATTAGAGCAGATAACAA
* *
53737765 GATTGAAGAAAAACACAAAAATAAAAACCCAATAAGAAAATTAAAAACAAAGAAAGAATGGAAGC
456 CATTGAAGAAAAACACAAAAATAAAAACCCAATAAGAAAATTAAAAACAAAGAAAGAAAGGAAGC
53737830 AGAACTGTCT
521 AGAACTGTCT
53737840 TACCTGAGAC
Statistics
Matches: 504, Mismatches: 26, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
533 504 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (533 bp):
CAAAATATCTACTAGATAAAAGGTGTTGTATTTAGCATATCGCAATATTTTCAAGCATCAAATAT
CAAGCGAAGAGAAAGCAGCAGTTTTAAATATAAGGGTGAAATCCACTACTATTACCTTTACAAAC
TTTGGCATGCTCAATTCGGTCTGACCAAAAAAGAGAAAGAAATAGAAAATTTGAAGTTCAATAAC
TGCCCTACAAAACCGTGCTCTATATCAAGAACTTGCTAATGTAAAAACTCAACTATACTAGCCTT
AGTCAACAAGGGAAAATGATTGTGTACACTAATATGGACTAAACACAATTGTAAAGCACATATTT
ACACATATGTTCCTATTACCCCAATTTTCTAAGCACCCAACCAGCATAAGAACACAATGTACTTA
ACTGAAACATCAATGAAAACCCAAAATTCAGAAGAAAAAAGAAAATAAATTAGAGCAGATAACAA
CATTGAAGAAAAACACAAAAATAAAAACCCAATAAGAAAATTAAAAACAAAGAAAGAAAGGAAGC
AGAACTGTCTGAC
Found at i:53739770 original size:70 final size:72
Alignment explanation
Indices: 53739639--53739793 Score: 226
Period size: 70 Copynumber: 2.2 Consensus size: 72
53739629 AATTTGGGGA
*
53739639 AAAAAGAAAGGGAATTGGGACAAAAGTTAAGGATTTCGGGGAGGGGGGAACTGATTTGGGGAAAA
1 AAAAAGAAAGGGAATTGGGACAAAAATTAAGGATTTCGGGGAGGGGGGAACTGATTTGGGGAAAA
53739704 ATT-GAG
66 ATTAGAG
* * *
53739710 AAAAAGAAAGGGAATTGGGA-AAAAATTAGGGATTTCGGGGA-GGGGGACCTTATTTGGGGGAAA
1 AAAAAGAAAGGGAATTGGGACAAAAATTAAGGATTTCGGGGAGGGGGGAACTGATTT-GGGGAAA
*
53739773 AATTAGGG
65 AATTAGAG
53739781 AAAAACGAAAGGG
1 AAAAA-GAAAGGG
53739794 TTCTAGGAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
69 12 0.16
70 30 0.39
71 27 0.36
72 7 0.09
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (72 bp):
AAAAAGAAAGGGAATTGGGACAAAAATTAAGGATTTCGGGGAGGGGGGAACTGATTTGGGGAAAA
ATTAGAG
Found at i:53743603 original size:111 final size:111
Alignment explanation
Indices: 53743464--53743675 Score: 388
Period size: 111 Copynumber: 1.9 Consensus size: 111
53743454 TCCTATGTCT
53743464 ATCAAAGCAAAATAAGGAGCAGTATGAATGAAGAACGTACCGACGATAACATCTACGGTGTCTCT
1 ATCAAAGCAAAATAAGGAGCAGTATGAATGAAGAACGTACCGACGATAACATCTACGGTGTCTCT
*
53743529 ATCCTCACGGCGTCTAGCCGCATAAACCAGTGTAGGCATATGATCA
66 ATCCTCACGGCGTCTAGCCGCATAAACAAGTGTAGGCATATGATCA
* *
53743575 ATCAAAGCAAAATAAGGAGCAGTATGAATGAAGAATGTACTGACGATAACATCTACGGTGTCTCT
1 ATCAAAGCAAAATAAGGAGCAGTATGAATGAAGAACGTACCGACGATAACATCTACGGTGTCTCT
*
53743640 ATCCTCACGGCGTCTAGTCGCATAAACAAGTGTAGG
66 ATCCTCACGGCGTCTAGCCGCATAAACAAGTGTAGG
53743676 GAGCCTTGTC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 97 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (111 bp):
ATCAAAGCAAAATAAGGAGCAGTATGAATGAAGAACGTACCGACGATAACATCTACGGTGTCTCT
ATCCTCACGGCGTCTAGCCGCATAAACAAGTGTAGGCATATGATCA
Found at i:53751324 original size:22 final size:22
Alignment explanation
Indices: 53751282--53751371 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
53751272 GAAGATGAAA
***
53751282 CTGGAAATTGTTGCAATTTGTT
1 CTGGAAATTGTTTTGATTTGTT
* *
53751304 -TTGATATTGTTATTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
53751326 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
53751348 GCTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
53751372 AGTCAGTACA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
21 13 0.24
22 12 0.22
23 21 0.38
24 5 0.09
25 4 0.07
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:53756415 original size:92 final size:91
Alignment explanation
Indices: 53756258--53756466 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 91
53756248 TTGATTTTAG
* * *
53756258 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
53756323 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
53756350 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
53756414 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
53756442 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
53756467 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:53756429 original size:24 final size:25
Alignment explanation
Indices: 53756394--53756441 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
53756384 TTATGAAATT
53756394 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
53756418 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
53756442 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:53756529 original size:54 final size:54
Alignment explanation
Indices: 53756471--53756664 Score: 147
Period size: 54 Copynumber: 3.4 Consensus size: 54
53756461 TTATTAGTTA
53756471 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * * * **
53756525 TAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTTAAA-TTT-TATTA-A--ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
53756590 T
54 T
* * ** * *
53756591 TAATTA-TTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAA
1 TAATTATTTTA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
*
53756645 TAATTATTTTAAATTATATT
1 TAATTATTTTAAATTTTATT
53756665 TTATAGTATT
Statistics
Matches: 108, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
54 30 0.28
55 10 0.09
56 5 0.05
57 3 0.03
59 11 0.10
60 7 0.06
61 10 0.09
63 4 0.04
64 5 0.05
65 10 0.09
66 13 0.12
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (54 bp):
TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
Found at i:53756614 original size:38 final size:37
Alignment explanation
Indices: 53756572--53756738 Score: 101
Period size: 38 Copynumber: 4.2 Consensus size: 37
53756562 ATGATTTGAG
53756572 TAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
1 TAAATT-ATATAAGAATATTAATTATTAAGAATTTTAT
* * *
53756610 TAAATTATATATTTTTGTTAA-ATTATATTTAATAATAATTATT-T
1 TAAATTATATA----AG--AATATTA-A-TTATTAAGAATT-TTAT
* * * *
53756654 TAAATTATATTTTATAGTATT-ATATATTATG-ATTTTAT
1 TAAATTATA--TAAGAATATTAAT-TATTAAGAATTTTAT
53756692 TAAATTCATATAAGAATATTTAA-TATTAAGAATTTTAT
1 TAAATT-ATATAAGAATA-TTAATTATTAAGAATTTTAT
53756730 TAAATTATA
1 TAAATTATA
53756739 ATATATTTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 37
0.66 0.09 0.25
Matches are distributed among these distances:
37 21 0.22
38 32 0.33
39 9 0.09
40 1 0.01
41 4 0.04
42 4 0.04
43 3 0.03
44 20 0.21
45 2 0.02
46 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
TAAATTATATAAGAATATTAATTATTAAGAATTTTAT
Found at i:53756619 original size:59 final size:58
Alignment explanation
Indices: 53756556--53756746 Score: 162
Period size: 59 Copynumber: 3.2 Consensus size: 58
53756546 TATAGTATCA
*
53756556 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTAT-ATTTGATTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * *
53756615 TATA-TATTTTTG-TTAAATT-ATATTTAATAATAATT-ATT-TTAAATTATATTTTA-TAGTAT
1 TATATTATATTTGATTAAATTCATA--TAAGAAT-ATTAATTATT-AA-GA-ATTTTATTA--AA
53756674 T
58 T
*
53756675 ATATATTATGATTTTATTAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
1 -TATATTAT-ATTTGATTAAATTCATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
*
53756735 TATAATATATTT
1 TATATTATATTT
53756747 AATAATAATT
Statistics
Matches: 104, Mismatches: 11, Indels: 35
0.69 0.07 0.23
Matches are distributed among these distances:
55 3 0.03
56 8 0.08
57 15 0.14
58 13 0.12
59 17 0.16
60 4 0.04
61 10 0.10
62 7 0.07
63 14 0.13
64 10 0.10
65 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (58 bp):
TATATTATATTTGATTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:53756620 original size:120 final size:120
Alignment explanation
Indices: 53756482--53756749 Score: 403
Period size: 120 Copynumber: 2.2 Consensus size: 120
53756472 AATTATTTTA
* * * *
53756482 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTTTCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
53756547 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA-TTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAA-TATTAAG
** * *
53756602 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
* * *
53756667 ATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAG
53756722 AATTTTATTAAATTATAATATATTTAAT
1 AATTTTATTAAATTAT-ATAT-TTTAAT
53756750 AATAATTATG
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
120 120 0.91
121 8 0.06
122 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTTAATATTAAG
Found at i:53756815 original size:120 final size:119
Alignment explanation
Indices: 53756482--53756816 Score: 294
Period size: 120 Copynumber: 2.8 Consensus size: 119
53756472 AATTATTTTA
* * * * *
53756482 AATTTTATTAAATCATATATTTTAATTAAAA-TATATTTAATATTAATTATTTCAAATTTTCTTT
1 AATTTTATTAAATTATATATTTTAA-TAAAATTATATTTAATAATAATGATTT-AAATTATATTT
* ** *
53756546 TATAGT-ATCATATATTATG-ATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TATAATAAT-ATATATTATGAAAAT-ATTAAATTCATATAAGAATATTAATTATTAAG
** * *
53756602 AATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATAAAATTATATTTAATAATAATGA-TTTAAATTATATTTT
* * ***
53756667 ATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAA-TATTAAG
65 ATAATAATATATATTATGAAAATATTAAATTCATATAAGAATA-TTAATTATTAAG
*
53756722 AATTTTATTAAATTATAATATATTTAATAATAATTATGTTT-A-AAT-ATGA-TTAAATTATTTA
1 AATTTTATTAAATTAT-ATAT-TTTAATAA-AATTATATTTAATAATAATGATTTAAATTA--TA
* *
53756783 TTATTGATAATAATA-ATCTTATTAAAAT-TTAAAT
61 TT-TT-ATAATAATATATATTATGAAAATATTAAAT
53756817 AACAATAACA
Statistics
Matches: 181, Mismatches: 22, Indels: 24
0.80 0.10 0.11
Matches are distributed among these distances:
118 8 0.04
119 4 0.02
120 119 0.66
121 28 0.15
122 13 0.07
123 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATAAAATTATATTTAATAATAATGATTTAAATTATATTTTA
TAATAATATATATTATGAAAATATTAAATTCATATAAGAATATTAATTATTAAG
Found at i:53756935 original size:39 final size:40
Alignment explanation
Indices: 53756892--53756996 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
53756882 TTCCATTATG
53756892 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
53756931 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
53756976 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
53756997 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:53756990 original size:45 final size:44
Alignment explanation
Indices: 53756890--53756999 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
53756880 TTTTCCATTA
53756890 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
53756929 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
53756974 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
53757000 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:53756999 original size:16 final size:16
Alignment explanation
Indices: 53756980--53757033 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
53756970 GATTTGCTAT
* *
53756980 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
53756996 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
53757012 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
53757028 TACACC
1 TACACC
53757034 AAACCAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:53758279 original size:22 final size:22
Alignment explanation
Indices: 53758248--53758376 Score: 107
Period size: 22 Copynumber: 5.5 Consensus size: 22
53758238 AAATATGGAT
53758248 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
53758270 TTAAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* * **
53758292 TTGAGAGGAA-ATTGAAATTAAA
1 TTGAGA-GAATTTTGGAAGGAAA
53758314 TTTGGATTTAAGAGAATTTTGGAAGGAAA
1 -TT-G-----AGAGAATTTTGGAAGGAAA
*
53758343 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAGGAAA
53758365 TTGAGAGGAATT
1 TTGAGA-GAATT
53758377 GAGAGGAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
22 56 0.67
23 10 0.12
24 1 0.01
27 1 0.01
28 5 0.06
29 11 0.13
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:53758290 original size:73 final size:73
Alignment explanation
Indices: 53758212--53758378 Score: 264
Period size: 73 Copynumber: 2.3 Consensus size: 73
53758202 TATTTTAAAA
* *
53758212 AAGGAAATTTAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
53758277 AATTTTAG
66 AATTTTAG
* * *
53758285 AAGGAAATTGAGAGGAAATTGAAATTAAATTTGGATTTAAGAGAATTTTGGAAGGAAATTGAGAG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
*
53758350 AATTTTGG
66 AATTTTAG
*
53758358 AAAGAAATTGAGAGG-AATTGA
1 AAGGAAATTGAGAGGAAATTGA
53758379 GAGGAAATAC
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 6 0.07
73 81 0.93
ACGTcount: A:0.45, C:0.01, G:0.26, T:0.28
Consensus pattern (73 bp):
AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTAAGAGAATTTTGGAAGGAAATTAAGAG
AATTTTAG
Found at i:53759670 original size:28 final size:28
Alignment explanation
Indices: 53759637--53759694 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
53759627 AAAAGGAAAT
*
53759637 AAATTGAAATGATAACACAAGGAACAAG
1 AAATTGAAATGACAACACAAGGAACAAG
53759665 AAATTGAAATGACAACACAAGGAACAAG
1 AAATTGAAATGACAACACAAGGAACAAG
53759693 AA
1 AA
53759695 GCCAAGAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.12
Consensus pattern (28 bp):
AAATTGAAATGACAACACAAGGAACAAG
Found at i:53760225 original size:20 final size:21
Alignment explanation
Indices: 53760200--53760239 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
53760190 TTAGCCTTTT
53760200 TATTTTTATTTTT-ATTTAAA
1 TATTTTTATTTTTAATTTAAA
*
53760220 TATTTTTGTTTTTAATTTAA
1 TATTTTTATTTTTAATTTAA
53760240 TTTTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TATTTTTATTTTTAATTTAAA
Found at i:53772047 original size:22 final size:23
Alignment explanation
Indices: 53772001--53772047 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
53771991 CAGTGTAAAA
*
53772001 AATGATTTATTATTGTTGGAAAT
1 AATGATTTATAATTGTTGGAAAT
*
53772024 AATGATTTGTAATTGTT-GAAAT
1 AATGATTTATAATTGTTGGAAAT
53772046 AA
1 AA
53772048 ATTTGCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (23 bp):
AATGATTTATAATTGTTGGAAAT
Found at i:53774384 original size:6 final size:7
Alignment explanation
Indices: 53774363--53774387 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53774353 GACAAACCGT
53774363 AAATAAA
1 AAATAAA
53774370 AAATAAA
1 AAATAAA
53774377 AAATAAA
1 AAATAAA
53774384 AAAT
1 AAAT
53774388 GAACTTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:53776902 original size:45 final size:45
Alignment explanation
Indices: 53776842--53776928 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
53776832 AGAGAGAATA
*
53776842 TTTTTATTCATCTTCTCTTTTAGACTTCGTTATCATCGAAGATAT
1 TTTTTATTCATCTTCTCTGTTAGACTTCGTTATCATCGAAGATAT
53776887 TTTTTATTCATCTTCTCTGTTAGACTTCGTTATCATCGAAGA
1 TTTTTATTCATCTTCTCTGTTAGACTTCGTTATCATCGAAGA
53776929 AACCATGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (45 bp):
TTTTTATTCATCTTCTCTGTTAGACTTCGTTATCATCGAAGATAT
Found at i:53786054 original size:101 final size:101
Alignment explanation
Indices: 53785927--53786112 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 101
53785917 AAAGTGATGG
* ** *
53785927 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGAAT-G-ATGGGTTGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGAAT-GGTCACATGTGCAGT
*
53785990 ACTATGTGCAGGCTACTATGTATACCGAATAGGTTCAA
64 ACTATGTGCAAGCTACTATGTATACCGAATAGGTTCAA
*
53786028 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATGGTCACATGTGCAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGG-AATGGTCACATGTGCAGTA
53786093 CTATGTGCAAGCTACTATGT
65 CTATGTGCAAGCTACTATGT
53786113 GAATCGGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 2 0.03
101 40 0.53
102 32 0.42
103 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAATGGTCACATGTGCAGTAC
TATGTGCAAGCTACTATGTATACCGAATAGGTTCAA
Found at i:53786093 original size:51 final size:50
Alignment explanation
Indices: 53785923--53786119 Score: 193
Period size: 51 Copynumber: 3.9 Consensus size: 50
53785913 AGTTAAAGTG
*
53785923 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGAAT-G-
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGA
** * * * *
53785972 ATGGGTTGCATGTGTAGTACTATGTGCAGGCTACTATGTATACCGAATAGG-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT-GGA
* ** *
53786023 TTCAATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGG-A
* * * *
53786075 ATGGTCACATGTGCAGTACTATGTGCAAGCTACTATGTGAATCGG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
53786120 GTACCATTGA
Statistics
Matches: 117, Mismatches: 26, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
49 4 0.03
50 38 0.32
51 74 0.63
52 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGA
Found at i:53797082 original size:28 final size:28
Alignment explanation
Indices: 53797016--53797337 Score: 484
Period size: 28 Copynumber: 11.5 Consensus size: 28
53797006 ATATTAAGTC
* *
53797016 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797043 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
53797071 CGCACACCTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797099 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797127 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797155 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797183 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
53797211 CGCACACTTAGGGCTACATAATGAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797239 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
53797267 CGCACACTTAGGGCTACATAATGAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
53797295 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
53797323 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53797338 GTACAATTTA
Statistics
Matches: 271, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
27 22 0.08
28 249 0.92
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:53807792 original size:9 final size:9
Alignment explanation
Indices: 53807765--53807804 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
53807755 AGTATAAAAC
53807765 TTAACCGAA
1 TTAACCGAA
**
53807774 TTAATAGAA
1 TTAACCGAA
53807783 TTAACCGAA
1 TTAACCGAA
53807792 TTAACCGAA
1 TTAACCGAA
53807801 TTAA
1 TTAA
53807805 AGTATTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (9 bp):
TTAACCGAA
Found at i:53810625 original size:26 final size:26
Alignment explanation
Indices: 53810595--53810655 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
53810585 ATAAGGTTAA
* *
53810595 TTATTTTAAGTT-CTTTATATATTATT
1 TTATTTTAAGTTACTTTACATATTA-C
* *
53810621 TTATTTAAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
53810647 TTATTTTAA
1 TTATTTTAA
53810656 AATTAACCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:53810654 original size:27 final size:25
Alignment explanation
Indices: 53810594--53810656 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
53810584 CATAAGGTTA
*
53810594 ATTATTTT-AAGTTCTTTATATATT
1 ATTATTTTAAAGTTCTTTACATATT
* *
53810618 ATTTTATTTAAAGTTATTTTACATATT
1 ATTAT-TTTAAAGTT-CTTTACATATT
53810645 ACTTATTTTAAA
1 A-TTATTTTAAA
53810657 ATTAACCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 5 0.16
27 16 0.52
28 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAGTTCTTTACATATT
Found at i:53815370 original size:20 final size:20
Alignment explanation
Indices: 53815341--53815385 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53815331 TGTTACTATG
*
53815341 TTTTATTTTTAGACTTTTAC
1 TTTTAGTTTTAGACTTTTAC
* *
53815361 TTTTAGTTTTAGATTTTTAT
1 TTTTAGTTTTAGACTTTTAC
53815381 TTTTA
1 TTTTA
53815386 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTAGTTTTAGACTTTTAC
Found at i:53819635 original size:29 final size:28
Alignment explanation
Indices: 53819602--53819712 Score: 98
Period size: 30 Copynumber: 3.8 Consensus size: 28
53819592 TGTAATTTTT
*
53819602 AGAAAATTTAGGATTAAAATGAAATTTA
1 AGAAAATTTAGGGTTAAAATGAAATTTA
* *
53819630 ATGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 A-GAAAATTTA-GGGT-TAAAATGAAATTT-A
* *
53819661 AGAAAGTTTAAGGGTCAAAATGAAATTTA
1 AGAAAATTT-AGGGTTAAAATGAAATTTA
*
53819690 AGAAAAGTTTAGGGGTCAAAATG
1 AGAAAA-TTTA-GGGTTAAAATG
53819713 CAGTTTTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
28 1 0.01
29 15 0.22
30 49 0.71
31 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.29
Consensus pattern (28 bp):
AGAAAATTTAGGGTTAAAATGAAATTTA
Found at i:53819657 original size:30 final size:29
Alignment explanation
Indices: 53819617--53819712 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 29
53819607 ATTTAGGATT
53819617 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAA-GAAAGTTTAGGGGTC
* * *
53819647 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTT-AAGAAAGTTTAGGGGTC
53819677 AAAATGAAATTTAAGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAG-AAAGTTTAGGGGTC
53819707 AAAATG
1 AAAATG
53819713 CAGTTTTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.05
30 53 0.91
31 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (29 bp):
AAAATGAAATTTAAGAAAGTTTAGGGGTC
Found at i:53819781 original size:48 final size:49
Alignment explanation
Indices: 53819716--53819814 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
53819706 CAAAATGCAG
53819716 TTTTTATTTTTTAAAATTTTTTTTTGAAATTTTGAAAATTAAACACAAA
1 TTTTTATTTTTTAAAATTTTTTTTTGAAATTTTGAAAATTAAACACAAA
*
53819765 TTTTTA-TTTTTAAAATTTTTTTTTGAAATTTTGAAAATTAAACACTAA
1 TTTTTATTTTTTAAAATTTTTTTTTGAAATTTTGAAAATTAAACACAAA
53819813 TT
1 TT
53819815 CTAGTCGGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 43 0.88
49 6 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (49 bp):
TTTTTATTTTTTAAAATTTTTTTTTGAAATTTTGAAAATTAAACACAAA
Done.