Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 15 of 213
Found at i:4103705 original size:15 final size:16
Alignment explanation
Indices: 4103685--4103715 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4103675 TAATAATTTT
4103685 ATATTTT-TATAAAAA
1 ATATTTTCTATAAAAA
4103700 ATATTTTCTATAAAAA
1 ATATTTTCTATAAAAA
4103716 TTAGCTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTTCTATAAAAA
Found at i:4104651 original size:17 final size:17
Alignment explanation
Indices: 4104629--4104662 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4104619 ATCCACTAAT
*
4104629 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4104646 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4104663 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4109290 original size:17 final size:17
Alignment explanation
Indices: 4109268--4109301 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4109258 ATCCACTAAT
*
4109268 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4109285 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4109302 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4116423 original size:13 final size:13
Alignment explanation
Indices: 4116407--4116432 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4116397 CTTTGCATAT
4116407 TGTCTTCAACAGG
1 TGTCTTCAACAGG
4116420 TGTCTTCAACAGG
1 TGTCTTCAACAGG
4116433 CTCGCACTTT
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:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:4117784 original size:17 final size:17
Alignment explanation
Indices: 4117762--4117795 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4117752 ATCCACTAAT
*
4117762 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4117779 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4117796 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4122423 original size:17 final size:17
Alignment explanation
Indices: 4122401--4122434 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4122391 ATCCACTAAT
*
4122401 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4122418 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4122435 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4131848 original size:36 final size:36
Alignment explanation
Indices: 4131801--4131872 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
4131791 AAAAAGAGTA
*
4131801 AGAAAAGTGTACCTCTAACGTTAACTCTAGCTGATT
1 AGAAAAGTGTACCTCTAACGTTAACTCCAGCTGATT
4131837 AGAAAAGTGTACCTCTAACGTTAACTCCAGCTGATT
1 AGAAAAGTGTACCTCTAACGTTAACTCCAGCTGATT
4131873 GTTGGCTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (36 bp):
AGAAAAGTGTACCTCTAACGTTAACTCCAGCTGATT
Found at i:4135479 original size:33 final size:33
Alignment explanation
Indices: 4135442--4135506 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
4135432 TATTTTTTAG
4135442 TATTTAAATAATTTTGCGTAAAAT-ATTTTTCTT
1 TATTTAAATAATTTTGC-TAAAATCATTTTTCTT
* ** *
4135475 TATTTGAATTTTTTTTCTAAAATCATTTTTCT
1 TATTTAAATAATTTTGCTAAAATCATTTTTCT
4135507 AAATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (33 bp):
TATTTAAATAATTTTGCTAAAATCATTTTTCTT
Found at i:4143119 original size:3 final size:3
Alignment explanation
Indices: 4143113--4143139 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4143103 CAACAACAAC
4143113 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4143140 TTTTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4145681 original size:24 final size:23
Alignment explanation
Indices: 4145649--4145696 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
4145639 CAGTACAAAT
*
4145649 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAG-AAAAATAAC
4145673 AACAAAAACAACAGAAAAATAAC
1 AACAAAAACAACAGAAAAATAAC
4145696 A
1 A
4145697 GCACCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.73, C:0.17, G:0.04, T:0.06
Consensus pattern (23 bp):
AACAAAAACAACAGAAAAATAAC
Found at i:4146343 original size:11 final size:11
Alignment explanation
Indices: 4146323--4146366 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
4146313 CTCAACACCA
4146323 AAATTGAGAGG
1 AAATTGAGAGG
*
4146334 AAATTTAGAGG
1 AAATTGAGAGG
*
4146345 AAATTGAGAAG
1 AAATTGAGAGG
4146356 AAATTTGAGAG
1 AAA-TTGAGAG
4146367 ATGATTAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:4146351 original size:22 final size:23
Alignment explanation
Indices: 4146323--4146366 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4146313 CTCAACACCA
*
4146323 AAATTGAGAGGAAATTT-AGAGG
1 AAATTGAGAAGAAATTTGAGAGG
4146345 AAATTGAGAAGAAATTTGAGAG
1 AAATTGAGAAGAAATTTGAGAG
4146367 ATGATTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (23 bp):
AAATTGAGAAGAAATTTGAGAGG
Found at i:4163439 original size:103 final size:104
Alignment explanation
Indices: 4163260--4163524 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
4163250 AACCGTTATT
* * * *
4163260 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
4163325 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
4163363 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
4163427 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
4163467 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
4163525 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:4163886 original size:30 final size:29
Alignment explanation
Indices: 4163852--4163916 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
4163842 TAATCCACCA
4163852 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
4163882 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
4163912 CCCAA
1 CCCAA
4163917 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:4163890 original size:31 final size:30
Alignment explanation
Indices: 4163859--4163916 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4163849 CCACCCAACT
4163859 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
4163889 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
4163917 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:4168495 original size:62 final size:64
Alignment explanation
Indices: 4168393--4168520 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 64
4168383 CTTCTGATCA
* *
4168393 GTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAG-AAC-AAGTGATAAGTG
1 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTAACAAAGTGATAAGTG
*
4168455 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTAACAAAGTGATAAGTG
4168519 GT
1 GT
4168521 AGCATTAGCT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 45 0.74
63 2 0.03
64 14 0.23
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (64 bp):
GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTAACAAAGTGATAAGTG
Found at i:4168520 original size:46 final size:46
Alignment explanation
Indices: 4168455--4169205 Score: 1256
Period size: 46 Copynumber: 16.4 Consensus size: 46
4168445 GTGATAAGTG
*
4168455 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
4168501 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* * *
4168547 GTGAGAAAGTGATAAGTGGTTGCCTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
4168593 GTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTAATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
4168639 GTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
4168685 GTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
4168731 GTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
4168777 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
4168823 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* * * *
4168869 GAGATAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATAAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
4168915 GTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* * *
4168961 GAGATAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
4169007 GAGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
4169053 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
**
4169099 GTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
4169145 GTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-A
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
4169189 GGGAC-AATTGATAAGTG
1 GTGACAAAGTGATAAGTG
4169206 ATCATAAGTA
Statistics
Matches: 673, Mismatches: 32, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
43 11 0.02
44 5 0.01
45 19 0.03
46 638 0.95
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
Found at i:4170238 original size:3 final size:3
Alignment explanation
Indices: 4170232--4170272 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4170222 GTCGTCGTCG
4170232 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
4170273 TTCTTCTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:4172232 original size:22 final size:22
Alignment explanation
Indices: 4172202--4172244 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4172192 ACAGCAAAAC
*
4172202 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
4172224 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
4172245 AGCGCCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:4172472 original size:85 final size:86
Alignment explanation
Indices: 4172340--4172545 Score: 211
Period size: 85 Copynumber: 2.4 Consensus size: 86
4172330 TGAAAAAAAA
* * ***
4172340 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTCTCCCACAAACGCCGCTG-AAGA-CTGAGACC
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTTAAAACAAACGCCGC-GAAAGACCT-AGACC
4172403 TTTAGCGGC-GCTTTAGGACAAG
64 TTTAGCGGCAGCTTTAGGACAAG
* * * * *
4172425 CGCCGCTAAAGACCCTGATCTTTAGCGGTGTTTTTAAAAGAAGCGCCGCGAAAGACCTCGATCTT
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTTAAAACAAACGCCGCGAAAGACCTAGACCTT
** *
4172490 TAGCGGCATTTTTAGGAGAAG
66 TAGCGGCAGCTTTAGGACAAG
* ** * *
4172511 CGCCGCTAAAGATCAGGGTCTTTAGCGGGGTTTTT
1 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTT
4172546 TTCTCAAACG
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
84 1 0.01
85 57 0.57
86 42 0.42
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (86 bp):
CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTTAAAACAAACGCCGCGAAAGACCTAGACCTT
TAGCGGCAGCTTTAGGACAAG
Found at i:4172666 original size:86 final size:86
Alignment explanation
Indices: 4172576--4172736 Score: 238
Period size: 86 Copynumber: 1.9 Consensus size: 86
4172566 ACCTGGTCTA
*
4172576 TAGCGGCGCTTTCCCCTA-AAACGCCGC-AATAGA-CCCTGATCTATAACGACGCTTCGACCAAA
1 TAGCGGCGCTTTCCCC-ACAAACGCCGCTAA-AGACCCCT-ATCTATAACGACGCGTCGACCAAA
4172638 AACGCCACTAAAGAACCTAATCTT
63 AACGCCACTAAAGAACCTAATCTT
* * *
4172662 TAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCCCTATCTGTAGCGGCGCGTCGACCAAAAAC
1 TAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCCCTATCTATAACGACGCGTCGACCAAAAAC
4172727 GCCACTAAAG
66 GCCACTAAAG
4172737 GGGCAACACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
85 1 0.01
86 61 0.90
87 6 0.09
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.17
Consensus pattern (86 bp):
TAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCCCTATCTATAACGACGCGTCGACCAAAAAC
GCCACTAAAGAACCTAATCTT
Found at i:4172692 original size:43 final size:43
Alignment explanation
Indices: 4172337--4172736 Score: 201
Period size: 43 Copynumber: 9.3 Consensus size: 43
4172327 TTTTGAAAAA
*
4172337 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTCTC-CCAC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTT-TCACCAC
* * **
4172380 AAACGCCGCTGAAG-A-CTGAGACCTTTAGCGGCGCTTT-AGGAC
1 AAACGCCGCTAAAGAACCT--GATCTTTAGCGGCGCTTTCACCAC
* * * * * ** *
4172422 AAGCGCCGCTAAAGACCCTGATCTTTAGCGGTGTTTTTAAAAG
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCACCAC
* * ** * ** *
4172465 AAGCGCCGCGAAAG-ACCTCGATCTTTAGCGGCATTTTTAGGAG
1 AAACGCCGCTAAAGAACCT-GATCTTTAGCGGCGCTTTCACCAC
* * ** * * * *** *
4172508 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGGGTTTTTTTCTC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCACCAC
* * *
4172551 AAACGCCGC-AATAGAACCTGGTCTATAGCGGCGCTTTCCCCTA-
1 AAACGCCGCTAA-AGAACCTGATCTTTAGCGGCGCTTTCACC-AC
* * * * *
4172594 AAACGCCGC-AATAGACCCTGATCTATAACGACGC-TTCGACCAA
1 AAACGCCGCTAA-AGAACCTGATCTTTAGCGGCGCTTTC-ACCAC
* * *
4172637 AAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCACCAC
* * * *
4172680 AAACGCCGCTAAAGACCCCT-ATCTGTAGCGGCGC-GTCGACCAA
1 AAACGCCGCTAAAGA-ACCTGATCTTTAGCGGCGCTTTC-ACCAC
*
4172723 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
4172737 GGGCAACACC
Statistics
Matches: 278, Mismatches: 63, Indels: 32
0.75 0.17 0.09
Matches are distributed among these distances:
41 2 0.01
42 41 0.15
43 224 0.81
44 11 0.04
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACCTGATCTTTAGCGGCGCTTTCACCAC
Found at i:4172772 original size:44 final size:44
Alignment explanation
Indices: 4172721--4172823 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
4172711 CGCGTCGACC
4172721 AAAAACGCCACTAAAGGGGCAACACCTTTAGTGGCGTTTTTTTT
1 AAAAACGCCACTAAAGGGGCAACACCTTTAGTGGCGTTTTTTTT
4172765 AAAAACGCCACTAAAGGGGCAACACCTTTAGTGGCGTTTTTTTT
1 AAAAACGCCACTAAAGGGGCAACACCTTTAGTGGCGTTTTTTTT
*
4172809 AAAAACGCTACTAAA
1 AAAAACGCCACTAAA
4172824 TTTGGCAGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (44 bp):
AAAAACGCCACTAAAGGGGCAACACCTTTAGTGGCGTTTTTTTT
Found at i:4173158 original size:21 final size:21
Alignment explanation
Indices: 4173132--4173223 Score: 112
Period size: 21 Copynumber: 4.4 Consensus size: 21
4173122 TTTGACGCTG
4173132 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
4173153 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
4173174 CTGTGCTTCCCTCACTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
4173195 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
4173216 ATCTGCTT
1 CTCTGCTT
4173224 TAAGTTGTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:4178728 original size:25 final size:25
Alignment explanation
Indices: 4178700--4180032 Score: 179
Period size: 27 Copynumber: 48.5 Consensus size: 25
4178690 TAAATTATGT
*
4178700 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* **
4178725 ATTATGTAAGTTGTGTACCATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* * *
4178750 ATTATGCTATG-TAAG--TTATGTAA
1 ATTATG-TAAGTTATGTATTATGAAA
* * * *
4178773 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGAAA
* *
4178798 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* * *
4178823 ATTAAGTAGGTTATGTAATTTACGAATA
1 ATTATGTAAGTTATGT-A-TTATGAA-A
* *
4178851 ATTAAAAAAATGTAAGTTATGTAAGT-TGTAA
1 ATT------ATGTAAGTTATGT-ATTATGAAA
* * *
4178882 GTTATGTAAGTTATGTATAAT-ATTA
1 ATTATGTAAGTTATGTATTATGA-AA
**
4178907 ATTAACTAAGTTATGTAATTTATGTATAA
1 ATTATGTAAGTTATGT-A-TTATG-A-AA
* * *
4178936 CATTAAAGTAAGTTATGTAATTTATGTAT
1 -ATT-ATGTAAGTTATGT-A-TTATGAAA
4178965 ATTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
4178994 TATTAATGTAAGTTATGTAATTTATGTATAA
1 -ATT-ATGTAAGTTATGT-A-TTATG-A-AA
** *
4179025 TATTAATGTACTTTATGTA-TAT--TA
1 -ATT-ATGTAAGTTATGTATTATGAAA
* *
4179049 TTTAAT-TAAGTTATGTAATTTATATATAA
1 ATT-ATGTAAGTTATGT-A-TTAT-GA-AA
*
4179078 TATTAATGTAAGTTATGTATAAT-ATAA
1 -ATT-ATGTAAGTTATGTATTATGA-AA
4179105 ATTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
4179134 TATTAATGTAAGTTATGTACTTTATGTATATAA
1 -ATT-ATGTAAGTTATGTA--TTATG---A-AA
*
4179167 ATTAAGTAAGTTATGTAATTTATGTATAAA
1 ATTATGTAAGTTATGT-A-TTATG---AAA
** * *
4179197 ATTAATGTACTTTACGTA-TAT--TA
1 ATT-ATGTAAGTTATGTATTATGAAA
*
4179220 TTTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
*
4179249 TATTAATGTAAGTTATGTATAAT-ATAA
1 -ATT-ATGTAAGTTATGTATTATGA-AA
4179276 ATTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
4179305 TATTAATGTAAGTTATGTACTTTATGTATATAA
1 -ATT-ATGTAAGTTATGTA--TTATG---A-AA
*
4179338 ATTAAGTAAGTTATGTAATTTATGTATAA
1 ATTATGTAAGTTATGT-A-TTATG-A-AA
** *
4179367 TATTAATGTACTTTATGTA-TAT--TA
1 -ATT-ATGTAAGTTATGTATTATGAAA
*
4179391 TTTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
** *
4179420 TATTAATGTACTTTATGTA-TAT--TA
1 -ATT-ATGTAAGTTATGTATTATGAAA
*
4179444 TTTAAT-TAAGTTATGTAATTTATGTATAA
1 ATT-ATGTAAGTTATGT-A-TTATG-A-AA
4179473 TATTAATGTAAGTTATGTACTTTATGTATATAA
1 -ATT-ATGTAAGTTATGTA--TTATG---A-AA
*
4179506 ATTAAGTAAGTTATGTAATTTATGTATAA
1 ATTATGTAAGTTATGT-A-TTATG-A-AA
4179535 TATTAATGTAAGTTATGTACTTTATGTATATTA
1 -ATT-ATGTAAGTTATGTA--TTATG-A-A--A
* **
4179568 ATTTATGTAAGTTATTTAATTTATTTAA
1 A-TTATGTAAGTTATGT-A-TTATGAAA
* * *
4179596 GTTATGTAAGTTATTTAATTTATGTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * **
4179623 GTTATGTAAGTTATTTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * *
4179650 GTTATGTAAGTTATTTAATTTATGTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * *
4179677 GTTATGTAAGTTATTTAATTTATGTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * *
4179704 GTTATGTAAGTTATTTAATTTATGTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179731 GTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * **
4179758 TTTATTTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179785 TTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179812 GTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179839 GTTATGTAAGTTATGTATGTTATTTAA
1 ATTATGTAAGTTATGTA--TTATGAAA
* **
4179866 TTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179893 TTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* **
4179920 TTTATGTAAGTTATGTAAGTTATTTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* * * *
4179947 GTTATGTAAATTATTTAATTTATGTAA
1 ATTATGTAAGTTATGT-A-TTATGAAA
* *
4179974 GTTATGTAAGTTATGTATTATGTTAA
1 ATTATGTAAGTTATGTATTATG-AAA
* * *
4180000 A-CATGT-A--TATGTATTAAGTAA
1 ATTATGTAAGTTATGTATTATGAAA
4180021 ATTATGTAAGTT
1 ATTATGTAAGTT
4180033 GTCTTATATA
Statistics
Matches: 1089, Mismatches: 117, Indels: 204
0.77 0.08 0.14
Matches are distributed among these distances:
21 4 0.00
22 48 0.04
23 37 0.03
24 5 0.00
25 140 0.13
26 24 0.02
27 410 0.38
28 23 0.02
29 33 0.03
30 63 0.06
31 237 0.22
32 32 0.03
33 20 0.02
34 13 0.01
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGAAA
Found at i:4178771 original size:9 final size:9
Alignment explanation
Indices: 4178757--4179021 Score: 117
Period size: 9 Copynumber: 29.7 Consensus size: 9
4178747 AAAATTATGC
4178757 TATGTAAGT
1 TATGTAAGT
4178766 TATGTAAGT
1 TATGTAAGT
* *
4178775 CATATAAGT
1 TATGTAAGT
4178784 TATGT-A-T
1 TATGTAAGT
4178791 TATGTAAGT
1 TATGTAAGT
4178800 TATGTAAGT
1 TATGTAAGT
*
4178809 TAT-TTA-T
1 TATGTAAGT
* *
4178816 TATGAAAAT
1 TATGTAAGT
* *
4178825 TAAGTAGGT
1 TATGTAAGT
*
4178834 TATGTAATT
1 TATGTAAGT
*
4178843 TACG-AA-T
1 TATGTAAGT
* **
4178850 AAT-TAAAAA
1 TATGT-AAGT
*
4178859 AATGTAAGT
1 TATGTAAGT
4178868 TATGTAAG-
1 TATGTAAGT
4178876 T-TGTAAGT
1 TATGTAAGT
4178884 TATGTAAGT
1 TATGTAAGT
*
4178893 TATGTATA-A
1 TATGTA-AGT
4178902 TAT-TAA-T
1 TATGTAAGT
**
4178909 TAACTAAGT
1 TATGTAAGT
*
4178918 TATGTAATT
1 TATGTAAGT
*
4178927 TATGTATAACAT
1 TATG--TAA-GT
*
4178939 TAAAGTAAGT
1 T-ATGTAAGT
*
4178949 TATGTAATT
1 TATGTAAGT
4178958 TATGTATA-T
1 TATGTA-AGT
4178967 TAAT-TAAGT
1 T-ATGTAAGT
*
4178976 TATGTAATT
1 TATGTAAGT
*
4178985 TATGTATAATAT
1 TATG--TAA-GT
4178997 TAATGTAAGT
1 T-ATGTAAGT
*
4179007 TATGTAATT
1 TATGTAAGT
4179016 TATGTA
1 TATGTA
4179022 TAATATTAAT
Statistics
Matches: 195, Mismatches: 36, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
7 21 0.11
8 19 0.10
9 125 0.64
10 9 0.05
11 12 0.06
12 4 0.02
13 5 0.03
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (9 bp):
TATGTAAGT
Found at i:4178800 original size:16 final size:16
Alignment explanation
Indices: 4178686--4178805 Score: 69
Period size: 16 Copynumber: 7.9 Consensus size: 16
4178676 ATAATTAAGC
*
4178686 TATGTAAATTATGTAT
1 TATGTAAGTTATGTAT
*
4178702 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
4178718 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
* *
4178727 TATGTAAGTTGTGTAC
1 TATGTAAGTTATGTAT
* * * *
4178743 CATGAAAATTATG--C
1 TATGTAAGTTATGTAT
4178757 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
4178775 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
4178791 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
4178806 AGTTATTTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 42 0.55
17 1 0.01
18 12 0.16
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:4178882 original size:16 final size:16
Alignment explanation
Indices: 4178861--4178893 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4178851 ATTAAAAAAA
4178861 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
4178877 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
4178893 T
1 T
4178894 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:4178898 original size:34 final size:33
Alignment explanation
Indices: 4178757--4178898 Score: 87
Period size: 34 Copynumber: 4.2 Consensus size: 33
4178747 AAAATTATGC
4178757 TATGTAAGTTATGTAAGTCATATAAGTTATGT--AT
1 TATGTAAGTTATGTAAGT--T-TAAGTTATGTAAAT
* *
4178791 TATGTAAGTTATGTAAGTTATTTA-TTATGAAAAT
1 TATGTAAGTTATGTAAG-T-TTAAGTTATGTAAAT
* * * * *
4178825 TAAGTAGGTTATGTAA-TTTACGAATAAT-TAAAAA
1 TATGTAAGTTATGTAAGTTTA--AGTTATGT-AAAT
* *
4178859 AATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTT-TAAGTTATGTAAAT
4178893 TATGTA
1 TATGTA
4178899 TAATATTAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
31 2 0.02
32 6 0.07
33 3 0.04
34 65 0.79
35 4 0.05
36 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (33 bp):
TATGTAAGTTATGTAAGTTTAAGTTATGTAAAT
Found at i:4178920 original size:84 final size:87
Alignment explanation
Indices: 4178779--4179017 Score: 242
Period size: 84 Copynumber: 2.7 Consensus size: 87
4178769 GTAAGTCATA
* * * * *
4178779 TAAGTTATGTATTATGTAAGTTATGTAAGTTATTTATTATGA-AAATTAAGTAGGTTATGTAATT
1 TAAGTTATGTAAT-TGTAAGTTATGTAAGTTATGTATAAT-ATTAATTAAGTAAGTTATGTAATT
4178843 TACGAAT-A-ATTAAA-AA-AATG
64 TACGAATAACATTAAAGAAGAATG
*
4178863 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTT
1 TAAGTTATGTAA-TTGTAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTT
* * *
4178928 ATGTATAACATTAAAGTAAGTTATG
65 ACGAATAACATTAAAG-AAG-AATG
* * *
4178953 TAATTTATGTATATTAATTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAAT
1 TAAGTTATGTA-ATT--GTAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAAT
4179015 TTA
63 TTA
4179018 TGTATAATAT
Statistics
Matches: 131, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
83 1 0.01
84 59 0.45
85 2 0.02
86 6 0.05
88 2 0.02
89 16 0.12
90 15 0.11
91 2 0.02
92 28 0.21
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (87 bp):
TAAGTTATGTAATTGTAAGTTATGTAAGTTATGTATAATATTAATTAAGTAAGTTATGTAATTTA
CGAATAACATTAAAGAAGAATG
Found at i:4178951 original size:31 final size:31
Alignment explanation
Indices: 4178877--4179972 Score: 868
Period size: 27 Copynumber: 38.7 Consensus size: 31
4178867 TTATGTAAGT
*
4178877 TGTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4178908 TTAACTAAGTTATGTAATTTATGTATAACATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
*
4178942 AGTAAGTTATGTAATTTATG--T-ATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4178970 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179000 TGTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
**
4179031 TGTACTTTATGT-A--TA--T-T-AT-TTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
4179054 T-TAAGTTATGTAATTTATATATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
4179084 TGTAAGTTATGT-A--TA-ATATAA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179110 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179140 TGTAAGTTATGTACTTTATGTATATAAATTAA
1 TGTAAGTTATGTAATTTATGTATA-ATATTAA
*
4179172 -GTAAGTTATGTAATTTATGTATAAAATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
** *
4179202 TGTACTTTACGT-A--TA--T-T-AT-TTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179225 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
4179255 TGTAAGTTATGT-A--TA-ATATAA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179281 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179311 TGTAAGTTATGTACTTTATGTATATAAATTAA
1 TGTAAGTTATGTAATTTATGTATA-ATATTAA
4179343 -GTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
**
4179373 TGTACTTTATGT-A--TA--T-T-AT-TTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179396 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
**
4179426 TGTACTTTATGT-A--TA--T-T-AT-TTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179449 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179479 TGTAAGTTATGTACTTTATGTATATAAATTAA
1 TGTAAGTTATGTAATTTATGTATA-ATATTAA
4179511 -GTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * *
4179541 TGTAAGTTATGTACTTTATGTATATTAATTTA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
* *
4179573 TGTAAGTTATTTAATTTAT-T-TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179600 TGTAAGTTATTTAATTTATG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * *
4179627 TGTAAGTTATTTAAGTTAT-T-TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179654 TGTAAGTTATTTAATTTATG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179681 TGTAAGTTATTTAATTTATG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179708 TGTAAGTTATTTAATTTATG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
4179735 TGTAAGTTATGTAAGTTAT-T-TAAT-TT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179762 TTTAAGTTATGTAAGTTAT-T-TAAT-TT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179789 TGTAAGTTATGTAAGTTAT-T-TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179816 TGTAAGTTATGTAAGTTAT-T-TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
4179843 TGTAAGTTATGT-ATGTTAT-T-TAAT-TT-A
1 TGTAAGTTATGTAAT-TTATGTATAATATTAA
*
4179870 TGTAAGTTATGTAAGTTAT-T-TAAT-TT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
4179897 TGTAAGTTATGTAAGTTAT-T-TAAT-TT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179924 TGTAAGTTATGTAAGTTAT-T-TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
4179951 TGTAAATTATTTAATTTATGTA
1 TGTAAGTTATGTAATTTATGTA
4179973 AGTTATGTAA
Statistics
Matches: 933, Mismatches: 58, Indels: 149
0.82 0.05 0.13
Matches are distributed among these distances:
22 31 0.03
23 24 0.03
24 7 0.01
25 32 0.03
26 19 0.02
27 381 0.41
28 30 0.03
29 20 0.02
30 67 0.07
31 255 0.27
32 40 0.04
34 27 0.03
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (31 bp):
TGTAAGTTATGTAATTTATGTATAATATTAA
Found at i:4179033 original size:22 final size:23
Alignment explanation
Indices: 4179008--4179065 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
4178998 AATGTAAGTT
4179008 ATGTAATTTATGTATAATA-TTA
1 ATGTAATTTATGTATAATATTTA
* *
4179030 ATGTACTTTATGTATATTATTTA
1 ATGTAATTTATGTATAATATTTA
*
4179053 AT-TAAGTTATGTA
1 ATGTAATTTATGTA
4179066 ATTTATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (23 bp):
ATGTAATTTATGTATAATATTTA
Found at i:4179059 original size:53 final size:53
Alignment explanation
Indices: 4178919--4179582 Score: 666
Period size: 53 Copynumber: 11.8 Consensus size: 53
4178909 TAACTAAGTT
* ** * * *
4178919 ATGTAATTTATGTATAACATTAAAGTAAGTTATGTAATTTATGTATATTAATTAA
1 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAAT-ATT-A
* *
4178974 GTTATGTAATTTATGTATAATA-TTAATGTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTACTTTATGTATATTATTTAAT-TAAGTTATGTAATTTATGTATAATATTA
*
4179030 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATATATAATATTA
1 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
** *
4179083 ATGTAAGTTATGTATAATATAAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAA
1 ATGTACTTTATGTAT-AT-T-ATTTAATTAAGTTATGTAATTTATGTAT-A-A-T-AT-T-A
* * * *
4179145 GTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAATTTATGTATAAAATTA
1 ---ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
*
4179201 ATGTACTTTACGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
** *
4179254 ATGTAAGTTATGTATAATATAAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAA
1 ATGTACTTTATGTAT-AT-T-ATTTAATTAAGTTATGTAATTTATGTAT-A-A-T-AT-T-A
* * *
4179316 GTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
4179372 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
4179425 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTAATGTAA
1 ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTAT-A-A-T-AT-T-A
* * *
4179484 GTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAATTTATGTATAATATTA
1 ---ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
** * * *
4179540 ATGTAAGTTATGTACT-TTATGTATATTAATTTATGTAAGTTAT
1 ATGTACTTTATGTA-TATTATTTA-ATTAAGTTATGTAATTTAT
4179583 TTAATTTATT
Statistics
Matches: 526, Mismatches: 43, Indels: 78
0.81 0.07 0.12
Matches are distributed among these distances:
53 229 0.44
54 27 0.05
55 3 0.01
56 58 0.11
57 13 0.02
58 50 0.10
59 5 0.01
60 7 0.01
61 5 0.01
62 99 0.19
64 4 0.01
65 26 0.05
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.49
Consensus pattern (53 bp):
ATGTACTTTATGTATATTATTTAATTAAGTTATGTAATTTATGTATAATATTA
Found at i:4179086 original size:22 final size:22
Alignment explanation
Indices: 4179061--4179111 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4179051 TAATTAAGTT
*
4179061 ATGTAATTTATATATAATATTA
1 ATGTAATTTATATATAATATAA
* *
4179083 ATGTAAGTTATGTATAATATAA
1 ATGTAATTTATATATAATATAA
4179105 AT-TAATT
1 ATGTAATT
4179112 AAGTTATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
ATGTAATTTATATATAATATAA
Found at i:4179142 original size:22 final size:22
Alignment explanation
Indices: 4179117--4179236 Score: 65
Period size: 22 Copynumber: 5.6 Consensus size: 22
4179107 TAATTAAGTT
4179117 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
* *
4179139 ATGTAAGTTATGTACT-TTATGT-
1 ATGTAATTTATGTA-TAATAT-TA
* * * *
4179161 ATATAAATTAAG--TAA-GTT-
1 ATGTAATTTATGTATAATATTA
*
4179179 ATGTAATTTATGTATAAAATTA
1 ATGTAATTTATGTATAATATTA
* * *
4179201 ATGTACTTTACGTATATTATTTA
1 ATGTAATTTATGTATAATA-TTA
*
4179224 AT-TAAGTTATGTA
1 ATGTAATTTATGTA
4179237 ATTTATGTAT
Statistics
Matches: 72, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
18 10 0.14
19 2 0.03
20 3 0.04
21 2 0.03
22 48 0.67
23 7 0.10
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:4179183 original size:171 final size:171
Alignment explanation
Indices: 4178879--4179603 Score: 1089
Period size: 171 Copynumber: 4.2 Consensus size: 171
4178869 ATGTAAGTTG
* * * *
4178879 TAAGTTATGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAACATTAAAG
1 TAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGT-A--TA-ATATAA-ATT-AAT
* *
4178944 TAAGTTATGTAATTTATG--T-ATATTAAT-TAAGTTATGTAATTTATGTATA-ATATTAATGTA
57 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAA-GTA
4179004 AGTTATGTAATTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
121 AGTTATGTAATTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
*
4179055 TAAGTTATGTAATTTATATATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
4179120 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
66 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
* *
4179185 TTTATGTATAAAATTAATGTACTTTACGTATATTATTTAAT
131 TTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
4179226 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
4179291 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
66 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
4179356 TTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
131 TTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
** *
4179397 TAAGTTATGTAATTTATGTATAATATTAATGTACTTTATGTAT-AT-T-ATTTAATTAAGTTATG
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
4179459 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
66 TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
** *
4179524 TTTATGTATAATATTAATGTAAGTTATGTACT-TTATGTATAT
131 TTTATGTATAATATTAATGTACTTTATGTA-TATTATTTA-AT
* * *
4179566 TAATTTATGTAAGTTAT-T-TAAT-TT-ATTTAAGTTATGTA
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTA
4179604 AGTTATTTAA
Statistics
Matches: 519, Mismatches: 23, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
165 11 0.02
166 2 0.00
167 24 0.05
168 118 0.23
169 25 0.05
170 12 0.02
171 282 0.54
172 7 0.01
173 10 0.02
175 1 0.00
176 27 0.05
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (171 bp):
TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAATATAAATTAATTAAGTTATG
TAATTTATGTATAATATTAATGTAAGTTATGTACTTTATGTATATAAATTAAGTAAGTTATGTAA
TTTATGTATAATATTAATGTACTTTATGTATATTATTTAAT
Found at i:4179257 original size:22 final size:22
Alignment explanation
Indices: 4179232--4179282 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4179222 TAATTAAGTT
*
4179232 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATAA
*
4179254 ATGTAAGTTATGTATAATATAA
1 ATGTAATTTATGTATAATATAA
4179276 AT-TAATT
1 ATGTAATT
4179283 AAGTTATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATAA
Found at i:4179415 original size:9 final size:9
Alignment explanation
Indices: 4178943--4179990 Score: 449
Period size: 9 Copynumber: 113.3 Consensus size: 9
4178933 TAACATTAAA
*
4178943 GTAAGTTAT
1 GTAATTTAT
4178952 GTAATTTAT
1 GTAATTTAT
*
4178961 GTATATTAAT
1 GTA-ATTTAT
*
4178971 -TAAGTTAT
1 GTAATTTAT
4178979 GTAATTTAT
1 GTAATTTAT
4178988 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179001 GTAAGTTAT
1 GTAATTTAT
4179010 GTAATTTAT
1 GTAATTTAT
4179019 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179032 GTACTTTAT
1 GTAATTTAT
4179041 GT-A--TAT
1 GTAATTTAT
4179047 -T-ATTTAAT
1 GTAATTT-AT
*
4179055 -TAAGTTAT
1 GTAATTTAT
4179063 GTAATTTATAT
1 GTAA-TT-TAT
*
4179074 ATAATATTAAT
1 GTAAT-TT-AT
*
4179085 GTAAGTTAT
1 GTAATTTAT
*
4179094 GT-ATAATAT
1 GTAAT-TTAT
* *
4179103 -AAATTAAT
1 GTAATTTAT
*
4179111 -TAAGTTAT
1 GTAATTTAT
4179119 GTAATTTAT
1 GTAATTTAT
4179128 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179141 GTAAGTTAT
1 GTAATTTAT
*
4179150 GTACTTTAT
1 GTAATTTAT
*
4179159 GTATATAAATTAA
1 GTA-AT---TTAT
*
4179172 GTAAGTTAT
1 GTAATTTAT
4179181 GTAATTTAT
1 GTAATTTAT
*
4179190 GTATAAAATTAAT
1 G--T--AATTTAT
* *
4179203 GTACTTTAC
1 GTAATTTAT
4179212 GT-A--TAT
1 GTAATTTAT
4179218 -T-ATTTAAT
1 GTAATTT-AT
*
4179226 -TAAGTTAT
1 GTAATTTAT
4179234 GTAATTTAT
1 GTAATTTAT
4179243 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179256 GTAAGTTAT
1 GTAATTTAT
*
4179265 GT-ATAATAT
1 GTAAT-TTAT
* *
4179274 -AAATTAAT
1 GTAATTTAT
*
4179282 -TAAGTTAT
1 GTAATTTAT
4179290 GTAATTTAT
1 GTAATTTAT
4179299 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179312 GTAAGTTAT
1 GTAATTTAT
*
4179321 GTACTTTAT
1 GTAATTTAT
*
4179330 GTATATAAATTAA
1 GTA-AT---TTAT
*
4179343 GTAAGTTAT
1 GTAATTTAT
4179352 GTAATTTAT
1 GTAATTTAT
4179361 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179374 GTACTTTAT
1 GTAATTTAT
4179383 GT-A--TAT
1 GTAATTTAT
4179389 -T-ATTTAAT
1 GTAATTT-AT
*
4179397 -TAAGTTAT
1 GTAATTTAT
4179405 GTAATTTAT
1 GTAATTTAT
4179414 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179427 GTACTTTAT
1 GTAATTTAT
4179436 GT-A--TAT
1 GTAATTTAT
4179442 -T-ATTTAAT
1 GTAATTT-AT
*
4179450 -TAAGTTAT
1 GTAATTTAT
4179458 GTAATTTAT
1 GTAATTTAT
4179467 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179480 GTAAGTTAT
1 GTAATTTAT
*
4179489 GTACTTTAT
1 GTAATTTAT
*
4179498 GTATATAAATTAA
1 GTA-AT---TTAT
*
4179511 GTAAGTTAT
1 GTAATTTAT
4179520 GTAATTTAT
1 GTAATTTAT
4179529 GTATAATATTAAT
1 G--TAAT-TT-AT
*
4179542 GTAAGTTAT
1 GTAATTTAT
*
4179551 GTACTTTAT
1 GTAATTTAT
4179560 GT-A--TAT
1 GTAATTTAT
4179566 -TAATTTAT
1 GTAATTTAT
*
4179574 GTAAGTTAT
1 GTAATTTAT
*
4179583 TTAATTTAT
1 GTAATTTAT
* *
4179592 TTAAGTTAT
1 GTAATTTAT
*
4179601 GTAAGTTAT
1 GTAATTTAT
*
4179610 TTAATTTAT
1 GTAATTTAT
*
4179619 GTAAGTTAT
1 GTAATTTAT
*
4179628 GTAAGTTAT
1 GTAATTTAT
* *
4179637 TTAAGTTAT
1 GTAATTTAT
* *
4179646 TTAAGTTAT
1 GTAATTTAT
*
4179655 GTAAGTTAT
1 GTAATTTAT
*
4179664 TTAATTTAT
1 GTAATTTAT
*
4179673 GTAAGTTAT
1 GTAATTTAT
*
4179682 GTAAGTTAT
1 GTAATTTAT
*
4179691 TTAATTTAT
1 GTAATTTAT
*
4179700 GTAAGTTAT
1 GTAATTTAT
*
4179709 GTAAGTTAT
1 GTAATTTAT
*
4179718 TTAATTTAT
1 GTAATTTAT
*
4179727 GTAAGTTAT
1 GTAATTTAT
*
4179736 GTAAGTTAT
1 GTAATTTAT
*
4179745 GTAAGTTAT
1 GTAATTTAT
*
4179754 TTAATTTAT
1 GTAATTTAT
* *
4179763 TTAAGTTAT
1 GTAATTTAT
*
4179772 GTAAGTTAT
1 GTAATTTAT
*
4179781 TTAATTTAT
1 GTAATTTAT
*
4179790 GTAAGTTAT
1 GTAATTTAT
*
4179799 GTAAGTTAT
1 GTAATTTAT
* *
4179808 TTAAGTTAT
1 GTAATTTAT
*
4179817 GTAAGTTAT
1 GTAATTTAT
*
4179826 GTAAGTTAT
1 GTAATTTAT
* *
4179835 TTAAGTTAT
1 GTAATTTAT
*
4179844 GTAAGTTAT
1 GTAATTTAT
4179853 GT-ATGTTAT
1 GTAAT-TTAT
*
4179862 TTAATTTAT
1 GTAATTTAT
*
4179871 GTAAGTTAT
1 GTAATTTAT
*
4179880 GTAAGTTAT
1 GTAATTTAT
*
4179889 TTAATTTAT
1 GTAATTTAT
*
4179898 GTAAGTTAT
1 GTAATTTAT
*
4179907 GTAAGTTAT
1 GTAATTTAT
*
4179916 TTAATTTAT
1 GTAATTTAT
*
4179925 GTAAGTTAT
1 GTAATTTAT
*
4179934 GTAAGTTAT
1 GTAATTTAT
* *
4179943 TTAAGTTAT
1 GTAATTTAT
*
4179952 GTAAATTAT
1 GTAATTTAT
*
4179961 TTAATTTAT
1 GTAATTTAT
*
4179970 GTAAGTTAT
1 GTAATTTAT
*
4179979 GTAAGTTAT
1 GTAATTTAT
4179988 GTA
1 GTA
4179991 TTATGTTAAA
Statistics
Matches: 818, Mismatches: 131, Indels: 180
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.01
6 15 0.02
7 4 0.00
8 44 0.05
9 563 0.69
10 33 0.04
11 77 0.09
12 21 0.03
13 52 0.06
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (9 bp):
GTAATTTAT
Found at i:4182330 original size:115 final size:115
Alignment explanation
Indices: 4182192--4182509 Score: 548
Period size: 115 Copynumber: 2.8 Consensus size: 115
4182182 AATAAACACC
4182192 TGCGGCGTTTTAACAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGTAAACACAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACAAA
* *
4182256 ATAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGTAACATATTT
66 ATAACA-TTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
* *
4182307 TGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACATA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACAAA
* * *
4182372 ATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTT
66 ATAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
*
4182422 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGGTAAACACAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACAAA
4182487 ATAACATTTTTGCGGCGTTTTAA
66 ATAACATTTTTGCGGCGTTTTAA
4182510 TAAAAACGCC
Statistics
Matches: 190, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
115 155 0.82
116 35 0.18
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (115 bp):
TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACAAA
ATAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
Found at i:4182335 original size:40 final size:40
Alignment explanation
Indices: 4182257--4182335 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
4182247 AAACACAAAA
* * * * * *
4182257 TAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
4182297 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
4182336 TACATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (40 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
Found at i:4182450 original size:40 final size:39
Alignment explanation
Indices: 4182373--4182450 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
4182363 AAACACATAA
* * *
4182373 TAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAG
1 TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
*
4182412 TAACATCTTTTGCGGCGTTTTAACAA-AAACGCCACTAAA
1 TAACAT-TTTTGCGGCATTTTAA-AAGAAACGCCACTAAA
4182451 TACATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.18
40 25 0.76
41 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (39 bp):
TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
Found at i:4182599 original size:74 final size:75
Alignment explanation
Indices: 4182412--4182583 Score: 301
Period size: 74 Copynumber: 2.3 Consensus size: 75
4182402 GCCGCTAAAG
4182412 TAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGG
1 TAACAT-TTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGG
4182477 TAAACACAAAA
65 TAAACACAAAA
* *
4182488 TAACATTTTTGCGGCGTTTTAATAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGT
1 TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGGT
4182552 AAACACAAAA
66 AAACACAAAA
*
4182562 TAACATTCTTGCGGCGTTTTAA
1 TAACATTTTTGCGGCGTTTTAA
4182584 GATAAGCGCC
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 51 0.55
75 36 0.39
76 6 0.06
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (75 bp):
TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGGT
AAACACAAAA
Found at i:4182625 original size:189 final size:191
Alignment explanation
Indices: 4182297--4182649 Score: 584
Period size: 189 Copynumber: 1.9 Consensus size: 191
4182287 GCCGCTAAAG
4182297 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * * *
4182362 TAAACACATAATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTTTGCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
*
4182427 CGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACATTTTGGTAAACACAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACATAAAAAAACGGTCACATTTTGGTAAACACAAAA
* *
4182488 TAACAT-TTTTGCGGCGTTTTAATAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * *
4182551 TAAACACAAAATAACATTCTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGCAAGATCTTTTCCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
4182616 CGTTTTAACAAAAACGCCACTAAAAACATAAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACATAAAAA
4182650 CGATTTCGTT
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
189 109 0.73
190 35 0.23
191 6 0.04
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (191 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
CGTTTTAACAAAAACGCCACTAAAAACATAAAAAAACGGTCACATTTTGGTAAACACAAAA
Found at i:4182923 original size:114 final size:114
Alignment explanation
Indices: 4182735--4182956 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
4182725 TTTCCAACGC
* * *
4182735 AGCGCCGCTAAAGGCTGACGTTTTCGGCGTTTTACAAAAAACGCCACTAATAAATCCTACACCAC
1 AGCGCCGCTAAAGGATGACGTTTTCGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACAAC
* *
4182800 GGCAGCG-TTTTATTAAAACAGAATCACATTTTGCGGCGTTTTTGACAT
66 GGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTTTGACAT
* * * *
4182848 AGCGCCGCTAAAGGATGATC-TTTTCCGGCGTTTTACCAAAAACGCCAGTAAGAAATCTTACAGA
1 AGCGCCGCTAAAGGATGA-CGTTTT-CGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACA
* *
4182912 ACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGGTGTTTT
64 ACGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTT
4182957 ACCCAAAACG
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
113 21 0.22
114 42 0.44
115 32 0.34
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (114 bp):
AGCGCCGCTAAAGGATGACGTTTTCGGCGTTTTACAAAAAACGCCACTAAGAAATCCTACACAAC
GGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTTTGACAT
Found at i:4183564 original size:21 final size:21
Alignment explanation
Indices: 4183540--4183611 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 21
4183530 CTAGACCCTG
4183540 AACCCCAACCCGTAAACCTTAA
1 AACCCCAACCCGTAAACCTT-A
4183562 ACCCCAACCCCAACCCGTAAACCTTA
1 A-----ACCCCAACCCGTAAACCTTA
*
4183588 AACCCCAACTCGTAAACCTTA
1 AACCCCAACCCGTAAACCTTA
4183609 AAC
1 AAC
4183612 TGTAAACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
21 22 0.50
22 1 0.02
26 2 0.05
27 19 0.43
ACGTcount: A:0.39, C:0.43, G:0.04, T:0.14
Consensus pattern (21 bp):
AACCCCAACCCGTAAACCTTA
Found at i:4183570 original size:27 final size:27
Alignment explanation
Indices: 4183540--4183596 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
4183530 CTAGACCCTG
4183540 AACCCCAACCCGTAAACCTTAAACCCC
1 AACCCCAACCCGTAAACCTTAAACCCC
4183567 AACCCCAACCCGTAAACCTTAAACCCC
1 AACCCCAACCCGTAAACCTTAAACCCC
4183594 AAC
1 AAC
4183597 TCGTAAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.47, G:0.04, T:0.11
Consensus pattern (27 bp):
AACCCCAACCCGTAAACCTTAAACCCC
Found at i:4184163 original size:73 final size:72
Alignment explanation
Indices: 4184066--4184203 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
4184056 AAAGACTCGA
4184066 AAACTAAGAAAACGATGTCATTGGGCTTAGGCTTTTTGCGGCG-CTTTTACAAAAACGCCACTAA
1 AAACTAAGAAAACGATGTCATTGGGCTTAGGCTTTTTGCGGCGACTTTTA-AAAAACGCCACTAA
4184130 AGCCTCCC
65 AGCCTCCC
* * * * * *
4184138 AAACTAAGAAAAACGATGTCGTTGGGCTTCGGTTTTTTGTGGCGATTTTTAAAAAACGCCGCTAA
1 AAACTAAG-AAAACGATGTCATTGGGCTTAGGCTTTTTGCGGCGACTTTTAAAAAACGCCACTAA
4184203 A
65 A
4184204 ACATTGAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 8 0.14
73 45 0.78
74 5 0.09
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (72 bp):
AAACTAAGAAAACGATGTCATTGGGCTTAGGCTTTTTGCGGCGACTTTTAAAAAACGCCACTAAA
GCCTCCC
Found at i:4184246 original size:114 final size:114
Alignment explanation
Indices: 4184103--4184429 Score: 417
Period size: 113 Copynumber: 2.9 Consensus size: 114
4184093 TAGGCTTTTT
** * ** *
4184103 GCGGCGCTTTTACAAAAACGCCACTAAAGCCTCCCAAACTAAGAAAAACGATGTCGTTGGGCTTC
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
* * * * *
4184168 GGTTTTTTGTGGCGATTTTTAAAAAACGCCGCTAAAACATTGAGCATTA
66 GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* *
4184217 GCGGCGCTTTCCCGAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAATGATGTCGTTGGGCTTA
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
* * * *
4184281 GGTCTTTTGCGGCGCTTTTTAAGAAACGCTGCTAAAGCCCTGAGAATTA
66 GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* * * *
4184330 -CTTGCGC-TTCTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTTGGTT
1 GC-GGCGCTTTC-CCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCT
*
4184393 TAGGTTTTTAGCGGCGCTTTTTAAGAAACGCCGCTAA
64 TAGGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAA
4184430 TGCTCATTAT
Statistics
Matches: 184, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
112 4 0.02
113 94 0.51
114 86 0.47
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
Found at i:4184501 original size:38 final size:37
Alignment explanation
Indices: 4184398--4184527 Score: 127
Period size: 38 Copynumber: 3.4 Consensus size: 37
4184388 TGGTTTAGGT
* *
4184398 TTTTAGCGGCGCTTTTTAAGAAACGCCGCTAATGCTCA
1 TTTTAGCGGCGTTTTTTAA-AAACGCCGCTAATGCTAA
* * * *
4184436 TTATTAGCGGC-TTTTTGTAAAAGCGCCGGTAATACTGA
1 TT-TTAGCGGCGTTTTT-TAAAAACGCCGCTAATGCTAA
* *
4184474 TATTTAGCGGCGTTTTTTTAAATCGCCGCTAATGCTTAA
1 T-TTTAGCGGCGTTTTTTAAAAACGCCGCTAATGC-TAA
4184513 TTTTTAGCGGCGTTT
1 -TTTTAGCGGCGTTT
4184528 GTTGTCCAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
38 43 0.57
39 32 0.42
40 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (37 bp):
TTTTAGCGGCGTTTTTTAAAAACGCCGCTAATGCTAA
Found at i:4184836 original size:19 final size:19
Alignment explanation
Indices: 4184812--4184850 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4184802 GGATGACCAA
4184812 ATTGCAAGCATTTCATTTT
1 ATTGCAAGCATTTCATTTT
4184831 ATTGCAAGCATTTCATTTT
1 ATTGCAAGCATTTCATTTT
4184850 A
1 A
4184851 GGTAGCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTGCAAGCATTTCATTTT
Found at i:4191575 original size:13 final size:14
Alignment explanation
Indices: 4191548--4191580 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4191538 GTTTCTAATT
*
4191548 AATTTTGATTTTTA
1 AATTTTGATTATTA
4191562 AATTTT-ATTATTA
1 AATTTTGATTATTA
4191575 AATTTT
1 AATTTT
4191581 CGCTATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
AATTTTGATTATTA
Found at i:4202870 original size:253 final size:254
Alignment explanation
Indices: 4202422--4202924 Score: 756
Period size: 253 Copynumber: 2.0 Consensus size: 254
4202412 ATATTGGGGT
* ** * * *
4202422 TGCAATTACTTCTTTATGTAAGAGTAGATTGGGCCTAAACTAATAGGTTATCCGGACGATTGTTG
1 TGCAATTACATCTTTATGTAAGAGTAGATTCAGCCTAAACTAATAGATGATCCAGACGATTGTTG
* * * *
4202487 AATAAAATCATTCACTTGGGGAGGCTCCGCAAATGTAGGATCATTGTGTCTAAACTACGTTATCA
66 AATAAAATCATTCACTAGGCGAGGCTCCACAAATGTAGGATCATTGTGTCTAAACTACGTTAACA
* *
4202552 AAGATCGGTTGTGTTAATTCTTTTCTACTCATATTTTTTTCGTTGCCCATTTTCGTTCTAACTTT
131 AAGACCGGTTGTGTCAATTCTTTTCTACTCATATTTTTTTCGTTGCCCATTTTCGTTCTAACTTT
* *
4202617 CACTACAACGAGCATT-AGCAAAGTTGATTTATCATGTCAGTAAACTAATTATTTATCA
196 CACTACAACGAGCATTAAGCAAAGTTGATTTATCATATCAGCAAACTAATTATTTATCA
* * * * *
4202675 TGCAATTACATCTTTGTGTAAGGGTATATTCAGCTTAAACTAATAGATGATCCAGATGATTGTTG
1 TGCAATTACATCTTTATGTAAGAGTAGATTCAGCCTAAACTAATAGATGATCCAGACGATTGTTG
* * * *
4202740 AATAAAATCATTCACTAGGCGAGGCTGCACAGATGTAGGATTATTGTGTCTGAACTACGTTAACA
66 AATAAAATCATTCACTAGGCGAGGCTCCACAAATGTAGGATCATTGTGTCTAAACTACGTTAACA
*
4202805 AAGACCGGTTGTGTCAATTCTTTTCTACTCTTATTTTTTTCGTTGCCCATTTTCGTTCTAACTTT
131 AAGACCGGTTGTGTCAATTCTTTTCTACTCATATTTTTTTCGTTGCCCATTTTCGTTCTAACTTT
* **
4202870 CACTACAATGAGCATTAAGCAAAGTTGATTTATCATATTGGCAAACTAATTATTT
196 CACTACAACGAGCATTAAGCAAAGTTGATTTATCATATCAGCAAACTAATTATTT
4202925 TTTCAATCTT
Statistics
Matches: 222, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
253 188 0.85
254 34 0.15
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (254 bp):
TGCAATTACATCTTTATGTAAGAGTAGATTCAGCCTAAACTAATAGATGATCCAGACGATTGTTG
AATAAAATCATTCACTAGGCGAGGCTCCACAAATGTAGGATCATTGTGTCTAAACTACGTTAACA
AAGACCGGTTGTGTCAATTCTTTTCTACTCATATTTTTTTCGTTGCCCATTTTCGTTCTAACTTT
CACTACAACGAGCATTAAGCAAAGTTGATTTATCATATCAGCAAACTAATTATTTATCA
Found at i:4203023 original size:27 final size:27
Alignment explanation
Indices: 4202984--4203035 Score: 88
Period size: 26 Copynumber: 1.9 Consensus size: 27
4202974 TGGACTAAAC
4202984 TACAAACAATTTAAACACAAAAAATATG
1 TACAAACAATTTAAA-ACAAAAAATATG
4203012 TACAAA-AATTTAAAACAAAAAATA
1 TACAAACAATTTAAAACAAAAAATA
4203036 GTTAGGGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 8 0.33
28 6 0.25
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (27 bp):
TACAAACAATTTAAAACAAAAAATATG
Found at i:4207132 original size:44 final size:44
Alignment explanation
Indices: 4207047--4207132 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
4207037 CATTTTCGAG
*** **
4207047 ATTTTACTTTTTATAATTTTTATATAGAATTTTTTTAAAATATA
1 ATTTTACTTTTTATAATTTTTATATAGAAAAATGGTAAAATATA
* *
4207091 ATTTTATTTTTTATAATTTTTATATAGAAAAATGGTCAAATA
1 ATTTTACTTTTTATAATTTTTATATAGAAAAATGGTAAAATA
4207133 GACAAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (44 bp):
ATTTTACTTTTTATAATTTTTATATAGAAAAATGGTAAAATATA
Found at i:4214341 original size:231 final size:231
Alignment explanation
Indices: 4213931--4214392 Score: 888
Period size: 231 Copynumber: 2.0 Consensus size: 231
4213921 TTTTAGTCAA
*
4213931 GGGTTTTTCAGCTTGTTCAATGTTCTACTTTAGCACTTGACACAAGGTAGGCAGTTTTATTATTA
1 GGGTTTGTCAGCTTGTTCAATGTTCTACTTTAGCACTTGACACAAGGTAGGCAGTTTTATTATTA
4213996 CTAGAAATTAACAAAAGAATGTGATTACCCTTTCGAATAGGACCTCTGCTATCCATCATGTTAGT
66 CTAGAAATTAACAAAAGAATGTGATTACCCTTTCGAATAGGACCTCTGCTATCCATCATGTTAGT
* *
4214061 AGCTGGATTTGTGAATAAATTAGGCTCATTTCTGGCATGGAAATTGTTTGCATGTTGGATGGTTG
131 AGCTGGATTTGTGAATAAATCAGGCTCATTTCTGGCATGGAAATTGTTTGCATGTTGGATGGTCG
4214126 ACCGTTTCAGTGATTGGTACTTGCTCCTCAATTGAT
196 ACCGTTTCAGTGATTGGTACTTGCTCCTCAATTGAT
4214162 GGGTTTGTCAGCTTGTTCAATGTTCTACTTTAGCACTTGACACAAGGTAGGCAGTTTTATTATTA
1 GGGTTTGTCAGCTTGTTCAATGTTCTACTTTAGCACTTGACACAAGGTAGGCAGTTTTATTATTA
*
4214227 CTAGAAGTTAACAAAAGAATGTGATTACCCTTTCGAATAGGACCTCTGCTATCCATCATGTTAGT
66 CTAGAAATTAACAAAAGAATGTGATTACCCTTTCGAATAGGACCTCTGCTATCCATCATGTTAGT
4214292 AGCTGGATTTGTGAATAAATCAGGCTCATTTCTGGCATGGAAATTGTTTGCATGTTGGATGGTCG
131 AGCTGGATTTGTGAATAAATCAGGCTCATTTCTGGCATGGAAATTGTTTGCATGTTGGATGGTCG
4214357 ACCGTTTCAGTGATTGGTACTTGCTCCTCAATTGAT
196 ACCGTTTCAGTGATTGGTACTTGCTCCTCAATTGAT
4214393 CATACATTTC
Statistics
Matches: 227, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 227 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (231 bp):
GGGTTTGTCAGCTTGTTCAATGTTCTACTTTAGCACTTGACACAAGGTAGGCAGTTTTATTATTA
CTAGAAATTAACAAAAGAATGTGATTACCCTTTCGAATAGGACCTCTGCTATCCATCATGTTAGT
AGCTGGATTTGTGAATAAATCAGGCTCATTTCTGGCATGGAAATTGTTTGCATGTTGGATGGTCG
ACCGTTTCAGTGATTGGTACTTGCTCCTCAATTGAT
Found at i:4235330 original size:30 final size:31
Alignment explanation
Indices: 4235294--4235359 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
4235284 AATAGTTTAT
* *
4235294 ATTTTTATAATTTTTAAAAGATTAAATTA-A
1 ATTTTTATAATTTCTAAAAGATTAAAGTATA
* * *
4235324 ATTTTTATTATTTCTAGAAGGTTAAAGTATA
1 ATTTTTATAATTTCTAAAAGATTAAAGTATA
4235355 ATTTT
1 ATTTT
4235360 ACCATTACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTCTAAAAGATTAAAGTATA
Found at i:4238652 original size:30 final size:30
Alignment explanation
Indices: 4238616--4238672 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
4238606 ACCAAAATGC
4238616 AACGATTATCATTTTCCTCACAATTTTGTA
1 AACGATTATCATTTTCCTCACAATTTTGTA
*
4238646 AACGATTATCATTTTTCTCACAATTTT
1 AACGATTATCATTTTCCTCACAATTTT
4238673 ATTTACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (30 bp):
AACGATTATCATTTTCCTCACAATTTTGTA
Found at i:4241603 original size:32 final size:32
Alignment explanation
Indices: 4241564--4241629 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
4241554 AATAACCTTG
**
4241564 TAAAAAAATGACATTGAAAATATTAATATAAA
1 TAAAAAAAACACATTGAAAATATTAATATAAA
* **
4241596 TAAAAAAAACTCATTTTAAATATTAATATAAA
1 TAAAAAAAACACATTGAAAATATTAATATAAA
4241628 TA
1 TA
4241630 TTATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (32 bp):
TAAAAAAAACACATTGAAAATATTAATATAAA
Found at i:4243920 original size:3 final size:3
Alignment explanation
Indices: 4243912--4243937 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4243902 ACAATATCTA
4243912 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4243938 CATAGTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4244256 original size:32 final size:32
Alignment explanation
Indices: 4244215--4244275 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4244205 AAACAGCAAA
* *
4244215 AACAGCAGCATTTTTTC-TTCTGCAAATTTAGG
1 AACAGCAGCAATTTATCTTTC-GCAAATTTAGG
4244247 AACAGCAGCAATTTATCTTTCGCAAATTT
1 AACAGCAGCAATTTATCTTTCGCAAATTT
4244276 GGGTTGAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (32 bp):
AACAGCAGCAATTTATCTTTCGCAAATTTAGG
Found at i:4245099 original size:17 final size:17
Alignment explanation
Indices: 4245077--4245110 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4245067 ATCCACTAAT
*
4245077 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4245094 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4245111 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4249737 original size:17 final size:17
Alignment explanation
Indices: 4249715--4249748 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4249705 ATCCACTAAT
*
4249715 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4249732 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4249749 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4250541 original size:10 final size:10
Alignment explanation
Indices: 4250526--4250551 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4250516 GTTGTTGTTG
4250526 CAAACCAGCT
1 CAAACCAGCT
4250536 CAAACCAGCT
1 CAAACCAGCT
4250546 CAAACC
1 CAAACC
4250552 GCAGCCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.42, G:0.08, T:0.08
Consensus pattern (10 bp):
CAAACCAGCT
Found at i:4253006 original size:17 final size:17
Alignment explanation
Indices: 4252984--4253017 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4252974 ATCCACTAAT
*
4252984 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4253001 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4253018 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4257645 original size:17 final size:17
Alignment explanation
Indices: 4257623--4257656 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4257613 ATCCACTAAT
*
4257623 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4257640 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4257657 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4260710 original size:42 final size:42
Alignment explanation
Indices: 4260638--4260717 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
4260628 GACCCCCCTA
* ** *
4260638 AAATGTAAAATTGCTATTTAGGCCCAAAAATTTTAAAATAGT
1 AAATGTAAAATTACTATTTACCCCCAAAAATTATAAAATAGT
*
4260680 AAATGTAAAATTAC-ACTTTACCCCCTAAAATTATAAAA
1 AAATGTAAAATTACTA-TTTACCCCCAAAAATTATAAAA
4260718 GTTTGATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.03
42 31 0.97
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
AAATGTAAAATTACTATTTACCCCCAAAAATTATAAAATAGT
Found at i:4273253 original size:37 final size:37
Alignment explanation
Indices: 4273188--4273370 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
4273178 TACGTATGAT
* *
4273188 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4273223 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4273260 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4273297 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
4273334 CATTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4273371 TAAAGCTATC
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 10 0.07
36 3 0.02
37 127 0.91
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:4273343 original size:111 final size:114
Alignment explanation
Indices: 4273188--4273417 Score: 326
Period size: 111 Copynumber: 2.0 Consensus size: 114
4273178 TACGTATGAT
*
4273188 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCTTGATCAGATAA
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAA
*
4273253 -GT-G-T-AGC-CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
66 GGTAGCTAAGCTCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
* * *
4273297 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCATTTATCACTTTGTCTCTTGATCAGAT
1 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGAT
4273362 AAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
64 AAG-GTAGCT-AAGC--TCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
4273417 C
1 C
4273418 GAAGCTATCA
Statistics
Matches: 105, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
109 10 0.10
110 3 0.03
111 48 0.46
113 2 0.02
114 1 0.01
115 1 0.01
117 3 0.03
120 37 0.35
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (114 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGATAA
GGTAGCTAAGCTCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
Found at i:4273404 original size:46 final size:46
Alignment explanation
Indices: 4273337--4273701 Score: 424
Period size: 46 Copynumber: 7.5 Consensus size: 46
4273327 GTGTAGCCAT
* **
4273337 TTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
* *
4273383 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
*
4273429 TTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCAC
1 TTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
* *
4273481 TTATCACTTTCCATTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCGC
1 TTATCA-----C--TTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
*
4273534 TTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
* *
4273580 TTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
* ** *
4273626 TTATCAGTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCA-----C-TTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
4273678 TTATCACTTTGTCACTTGATCAGA
1 TTATCACTTTGTCACTTGATCAGA
4273702 AGTACTCAAA
Statistics
Matches: 281, Mismatches: 21, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
46 153 0.54
47 1 0.00
48 1 0.00
49 1 0.00
51 1 0.00
52 80 0.28
53 41 0.15
56 2 0.01
57 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (46 bp):
TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCAC
Found at i:4273453 original size:52 final size:52
Alignment explanation
Indices: 4273377--4273695 Score: 383
Period size: 52 Copynumber: 6.3 Consensus size: 52
4273367 TAGCTAAAGC
* *
4273377 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* *
4273430 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * * * *
4273482 TATCACTTTCCATTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCGCT
1 TATCACTTTTCA-CTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
4273535 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
4273581 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * * ** *
4273627 TATCAGTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
4273679 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
4273696 ATCAGAAGTA
Statistics
Matches: 235, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
46 86 0.37
52 89 0.38
53 60 0.26
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:4273689 original size:98 final size:96
Alignment explanation
Indices: 4273340--4273701 Score: 462
Period size: 98 Copynumber: 3.7 Consensus size: 96
4273330 TAGCCATTTA
* * *
4273340 TCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCA
1 TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCA
4273405 GATAAGTATAGCCGAAGCTATCACTTATCACTTT
65 GATAAGTATAGCCGAAGCTATCACTTATCA--TT
* *
4273439 TCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACTTATCACTTTCCATTTTGTCACT
1 TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCA-----C--TTTGTCACT
* * *
4273504 TGATCAGATAAGTGTAGCTGAAGCTATCGCTTATCA--
59 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCATT
* * *
4273540 -C-TTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAG
1 TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
*
4273603 ATAAGTATAGCCGAAGCTATTACTTATCAGTT
66 ATAAGTATAGCCGAAGCTATCACTTATCA-TT
* *
4273635 TCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCA
1 T-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCA
4273700 GA
65 GA
4273702 AGTACTCAAA
Statistics
Matches: 230, Mismatches: 20, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
92 41 0.18
94 1 0.00
97 1 0.00
98 98 0.43
99 46 0.20
100 1 0.00
103 1 0.00
105 41 0.18
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (96 bp):
TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTTGATCAG
ATAAGTATAGCCGAAGCTATCACTTATCATT
Found at i:4292118 original size:15 final size:16
Alignment explanation
Indices: 4292098--4292128 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4292088 TTCTTTTGTC
4292098 TTTTTC-TTTCTGTTT
1 TTTTTCTTTTCTGTTT
4292113 TTTTTCTTTTCTGTTT
1 TTTTTCTTTTCTGTTT
4292129 GCTGCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTGTTT
Found at i:4299103 original size:38 final size:38
Alignment explanation
Indices: 4299054--4299126 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
4299044 GATAATTCAC
*
4299054 TATGTGAAATTCGAATGATTACAAGAGAAGTAGACTAT
1 TATGTGAAATTCGAATGATTACAAGAAAAGTAGACTAT
*
4299092 TATGTGGAATTCGAATGATTACAAGAAAAGTAGAC
1 TATGTGAAATTCGAATGATTACAAGAAAAGTAGAC
4299127 CATGTCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (38 bp):
TATGTGAAATTCGAATGATTACAAGAAAAGTAGACTAT
Found at i:4299557 original size:17 final size:17
Alignment explanation
Indices: 4299522--4299553 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4299512 TAATACATAA
4299522 AATATTATATTTAAAAT
1 AATATTATATTTAAAAT
4299539 AATA-TATATTTAAAA
1 AATATTATATTTAAAA
4299554 ATAAACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATATTTAAAAT
Found at i:4307006 original size:30 final size:30
Alignment explanation
Indices: 4306971--4307032 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
4306961 CATTTATGGG
* **
4306971 TATT-AATTAATTAAAATTTATTTATATTAA
1 TATTAAATT-ATTAAAATATATAAATATTAA
4307001 TATTAAATTATTAAAATATATAAATATTAA
1 TATTAAATTATTAAAATATATAAATATTAA
4307031 TA
1 TA
4307033 GAAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTAAATTATTAAAATATATAAATATTAA
Found at i:4308157 original size:15 final size:15
Alignment explanation
Indices: 4308137--4308170 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4308127 TAATAAAATC
4308137 AATATAAAAATTAAA
1 AATATAAAAATTAAA
* *
4308152 AATATATATATTAAA
1 AATATAAAAATTAAA
4308167 AATA
1 AATA
4308171 ATACTTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATATAAAAATTAAA
Found at i:4318427 original size:41 final size:41
Alignment explanation
Indices: 4318370--4318504 Score: 225
Period size: 41 Copynumber: 3.3 Consensus size: 41
4318360 AATTTAACAT
*
4318370 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
* * *
4318411 ATTCATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
4318452 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
*
4318493 ATTCAAATCACC
1 ATTCAGATCACC
4318505 AATTCCAAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTACTAGGTTTATAACCTG
Found at i:4318733 original size:41 final size:41
Alignment explanation
Indices: 4318676--4318771 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
4318666 TTTGTTCCTT
*
4318676 TGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCC
1 TGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACC
*
4318717 TGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACC
*
4318758 TGATTCAAATCACC
1 TGATTCAGATCACC
4318772 AATTTCAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
TGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACC
Found at i:4318989 original size:2 final size:2
Alignment explanation
Indices: 4318982--4319006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4318972 TTCGATCCAA
4318982 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4319007 TATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4320482 original size:510 final size:510
Alignment explanation
Indices: 4319523--4320542 Score: 1977
Period size: 510 Copynumber: 2.0 Consensus size: 510
4319513 AATTAAGTCC
4319523 AAAAATACATAAATGGAAAAATTACCATTTTGCCCCTAACATTTTACACTTTTTGCAATTTAGTC
1 AAAAATACATAAATGGAAAAATTACCATTTTGCCCCTAACATTTTACACTTTTTGCAATTTAGTC
*
4319588 CTTTTTGCACAAAACACAAAATACACAAAATTTGCCCACACTAAGCTAGGGCTGAATGTTCCTTG
66 CTTTTTGCACAAAACACAAAATACACAAAATTTGCCCACACTAAGCTAGGGCTGAATGCTCCTTG
4319653 TCTTCATAAAAGTCCACACATTTCATTTATTTCACATTTTAGTCTCTAAAAATATTATTTTTGCA
131 TCTTCATAAAAGTCCACACATTTCATTTATTTCACATTTTAGTCTCTAAAAATATTATTTTTGCA
4319718 ATTTAACCCTAATTACTCAATTTCACCAAAATTTCCAATACAAAACATATTAATCTAAAACATAT
196 ATTTAACCCTAATTACTCAATTTCACCAAAATTTCCAATACAAAACATATTAATCTAAAACATAT
4319783 CATTCATTATTCATTATCAAACATCACAAAACACAATTATTCATCAATGGCATAGCTCAAAATAT
261 CATTCATTATTCATTATCAAACATCACAAAACACAATTATTCATCAATGGCATAGCTCAAAATAT
4319848 TCATCAAAATAAAAAATTCAAGCATGGGTCGGATAGTACTCGAAGCAACGATCTCAAAAACATAA
326 TCATCAAAATAAAAAATTCAAGCATGGGTCGGATAGTACTCGAAGCAACGATCTCAAAAACATAA
*
4319913 AAATCATCAAAAACCGAACAAAATCCATACCTGAATCCAAGCTTGAAAGTGCCGAATGAAACAAA
391 AAATCATCAAAAACCGAACAAAATCCATACCTGAATCCAAGCTTGAAAGTGCAGAATGAAACAAA
4319978 GCTTTAAACCCTTTTATTTTCTTCCCAATTCGGCCAAAAAAAAGATGAAGAACAT
456 GCTTTAAACCCTTTTATTTTCTTCCCAATTCGGCCAAAAAAAAGATGAAGAACAT
* *
4320033 AAAAATACATAAATGGGAAAATTACCATTTTGCCCTTAACATTTTACACTTTTTGCAATTTAGTC
1 AAAAATACATAAATGGAAAAATTACCATTTTGCCCCTAACATTTTACACTTTTTGCAATTTAGTC
4320098 CTTTTTGCACAAAACACAAAATACACAAAATTTGCCCACACTAAGCTAGGGCTGAATGCTCCTTG
66 CTTTTTGCACAAAACACAAAATACACAAAATTTGCCCACACTAAGCTAGGGCTGAATGCTCCTTG
4320163 TCTTCATAAAAGTCCACACATTTCATTTATTTCACATTTTAGTCTCTAAAAATATTATTTTTGCA
131 TCTTCATAAAAGTCCACACATTTCATTTATTTCACATTTTAGTCTCTAAAAATATTATTTTTGCA
*
4320228 ATTTAACCCTAATTACTCAATTTCACCAAAATTTCCAATACAAAACATATTAATCTAAAGCATAT
196 ATTTAACCCTAATTACTCAATTTCACCAAAATTTCCAATACAAAACATATTAATCTAAAACATAT
4320293 CATTCATTATTCATTATCAAACATCACAAAACACAATTATTCATCAATGGCATAGCTCAAAATAT
261 CATTCATTATTCATTATCAAACATCACAAAACACAATTATTCATCAATGGCATAGCTCAAAATAT
*
4320358 TCATCAAAATCAAAAATTCAAGCATGGGTCGGATAGTACTCGAAGCAACGATCTCAAAAACATAA
326 TCATCAAAATAAAAAATTCAAGCATGGGTCGGATAGTACTCGAAGCAACGATCTCAAAAACATAA
*
4320423 AAATCATCAAAAACCGAACAAAATCCATACCTTAATCCAAGCTTGAAAGTGCAGAATGAAACAAA
391 AAATCATCAAAAACCGAACAAAATCCATACCTGAATCCAAGCTTGAAAGTGCAGAATGAAACAAA
4320488 GCTTTAAACCCTTTTATTTTCTTCCCAATTCGGCCAAAAAAAAGATGAAGAACAT
456 GCTTTAAACCCTTTTATTTTCTTCCCAATTCGGCCAAAAAAAAGATGAAGAACAT
4320543 GGCTTTTAAT
Statistics
Matches: 503, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
510 503 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (510 bp):
AAAAATACATAAATGGAAAAATTACCATTTTGCCCCTAACATTTTACACTTTTTGCAATTTAGTC
CTTTTTGCACAAAACACAAAATACACAAAATTTGCCCACACTAAGCTAGGGCTGAATGCTCCTTG
TCTTCATAAAAGTCCACACATTTCATTTATTTCACATTTTAGTCTCTAAAAATATTATTTTTGCA
ATTTAACCCTAATTACTCAATTTCACCAAAATTTCCAATACAAAACATATTAATCTAAAACATAT
CATTCATTATTCATTATCAAACATCACAAAACACAATTATTCATCAATGGCATAGCTCAAAATAT
TCATCAAAATAAAAAATTCAAGCATGGGTCGGATAGTACTCGAAGCAACGATCTCAAAAACATAA
AAATCATCAAAAACCGAACAAAATCCATACCTGAATCCAAGCTTGAAAGTGCAGAATGAAACAAA
GCTTTAAACCCTTTTATTTTCTTCCCAATTCGGCCAAAAAAAAGATGAAGAACAT
Found at i:4322831 original size:50 final size:50
Alignment explanation
Indices: 4322714--4322858 Score: 191
Period size: 50 Copynumber: 2.9 Consensus size: 50
4322704 TGATAATAAC
** * *
4322714 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * * * *
4322765 GTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
4322815 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
4322859 GTCTTGGTGC
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 47 0.59
51 33 0.41
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:4323237 original size:30 final size:30
Alignment explanation
Indices: 4323202--4323259 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4323192 CCTCGACTCT
*
4323202 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4323232 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4323260 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4326517 original size:16 final size:16
Alignment explanation
Indices: 4326492--4326527 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4326482 CGACTTGCAG
*
4326492 TTTGATAGGCTCACAC
1 TTTGACAGGCTCACAC
4326508 TTTGACAGGCTCACAC
1 TTTGACAGGCTCACAC
4326524 TTTG
1 TTTG
4326528 CTTGCTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (16 bp):
TTTGACAGGCTCACAC
Found at i:4328198 original size:175 final size:175
Alignment explanation
Indices: 4327903--4328774 Score: 1555
Period size: 175 Copynumber: 5.0 Consensus size: 175
4327893 CCTTTGGTGG
*
4327903 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGATC
1 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
* *
4327968 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCAC
66 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
4328033 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
131 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
* *
4328078 ACTACTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACGGCTTAGGGAGATAGGATC
1 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
* * *
4328143 TACCATCTTCGACCTGCTCCACTACTGCTTAGGAAGATAGGACTGGTGGCTTAAATCTGCTTCAC
66 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
* * *
4328208 TACTGCTTAGGAAGATAAGATTTGCCATCTTCAATCTGCTCCACT
131 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
*
4328253 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAAGATC
1 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
*
4328318 TACCATCTTCGACCTGATCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
66 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
4328383 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
131 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
*
4328428 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCTACTACTGCTTAGGGAGATAGGATC
1 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
* *
4328493 TACTATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
66 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
**
4328558 TACTGCTTAGGAAGATAAGATTTACCGTCTTCGATCTGCTCCACT
131 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
4328603 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
1 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
* *
4328668 TACCATCTTCGACCTGTTCTACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
66 TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
*
4328733 TACTGCTTAGGAAGATAAGATTCTCCGTCTTCGATCTGCTCC
131 TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCC
4328775 GCTAGTACTT
Statistics
Matches: 666, Mismatches: 31, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 666 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (175 bp):
ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGATC
TACCATCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCAC
TACTGCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
Found at i:4328772 original size:44 final size:44
Alignment explanation
Indices: 4327903--4328774 Score: 848
Period size: 44 Copynumber: 19.9 Consensus size: 44
4327893 CCTTTGGTGG
* * * *
4327903 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTACTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
*
4327947 ACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
***** ** *
4327991 ACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * * *
4328034 ACTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCT-ACCATCTTCGATCTGCTCCACT
* * * *
4328078 ACTACTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* *
4328122 ACGGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* ***** ** *
4328166 ACTGCTTAGGAAGATAGGA-CTGGTGGCTTAAATCTGCTTCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * * * *
4328209 ACTGCTTAGGAAGATAAGATTTGCCATCTTCAATCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * *
4328253 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * *
4328297 ACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTGATCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
*** ** *
4328341 ACTGCTTAGGGAGATAGGA-CTAGTGGT-TTAAATCTGCTTCACT
1 ACTGCTTAGGGAGATAGGATCTA-CCATCTTCGATCTGCTCCACT
* * * *
4328384 ACTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCT-ACCATCTTCGATCTGCTCCACT
* * * *
4328428 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCTACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * *
4328472 ACTGCTTAGGGAGATAGGATCTACTATCTTCGACCTACTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
*** ** *
4328516 ACTGCTTAGGGAGATAGGA-CTAGTGGT-TTAAATCTGCTTCACT
1 ACTGCTTAGGGAGATAGGATCTA-CCATCTTCGATCTGCTCCACT
* * * *
4328559 ACTGCTTAGGAAGATAAGATTTACCGTCTTCGATCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * *
4328603 ACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTGCTCCACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
* * *
4328647 ACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGTTCTACT
1 ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
*** ** *
4328691 ACTGCTTAGGGAGATAGGA-CTAGTGGT-TTAAATCTGCTTCACT
1 ACTGCTTAGGGAGATAGGATCTA-CCATCTTCGATCTGCTCCACT
* * *
4328734 ACTGCTTAGGAAGATAAGATTCT-CCGTCTTCGATCTGCTCC
1 ACTGCTTAGGGAGATAGGA-TCTACCATCTTCGATCTGCTCC
4328775 GCTAGTACTT
Statistics
Matches: 676, Mismatches: 136, Indels: 32
0.80 0.16 0.04
Matches are distributed among these distances:
43 165 0.24
44 507 0.75
45 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
ACTGCTTAGGGAGATAGGATCTACCATCTTCGATCTGCTCCACT
Found at i:4328892 original size:87 final size:87
Alignment explanation
Indices: 4328762--4329421 Score: 864
Period size: 87 Copynumber: 7.5 Consensus size: 87
4328752 ATTCTCCGTC
* * * * * *
4328762 TTCGATCTGCTCCGCTAG-T-ACTTAAGAAGGCAAGATTTACTATCTTTAACCAGCTCTACTGCA
1 TTCGATCTGCTTCGCT-GTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCA
*
4328825 ACCGATGAAGGCAAGGCTTTGTT
65 ACCGATGGAGGCAAGGCTTTGTT
* * *
4328848 TTCGGTCTGCTTCGCTGTTAACGCAGGAAGGCAAGGTCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* *
4328913 CTGGTGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
4328935 TTCGATCTACTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTGAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
4329000 TCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
4329022 TTCGATCTGCTTCGCTGGGCTTCGCTGTTAACATAGGAAGGCAAGATCTGCTATCTTTAACCAGC
1 TTCGA------T--CT--GCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGC
4329087 TCCACTGCAACCGATGGA-GCTAAGGCTTTGTTT
56 TCCACTGCAACCGATGGAGGC-AAGGCTTTG-TT
* *
4329120 TTGCG-TCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGTTATCTTTAACTAGCTCCACTGCA
1 TT-CGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCA
4329184 ACCGATGGAGGCAAGGCTTTGTT
65 ACCGATGGAGGCAAGGCTTTGTT
** * * *
4329207 TTTTATCTGCTTCGTTGTTAACGCAGGAAGACAAGATCTGCT-TCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* *
4329271 CCGATAGAGGTAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
4329293 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATTTGCT-TCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
4329357 CCGATGGAGGCAAGACTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
4329379 TTTGATCTGCTTCGCTATTAATGTAGAAAGGCAAGATCTGCTA
1 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTA
4329422 CTTCATTGAT
Statistics
Matches: 506, Mismatches: 50, Indels: 35
0.86 0.08 0.06
Matches are distributed among these distances:
85 1 0.00
86 170 0.34
87 178 0.35
88 71 0.14
89 2 0.00
90 2 0.00
92 1 0.00
93 1 0.00
95 2 0.00
96 2 0.00
97 70 0.14
98 4 0.01
99 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:4330656 original size:7 final size:7
Alignment explanation
Indices: 4330644--4330694 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
4330634 TTAGCCTCTC
4330644 CATTTTT
1 CATTTTT
*
4330651 CATTTTC
1 CATTTTT
4330658 CA-TTTT
1 CATTTTT
4330664 CATTTTT
1 CATTTTT
4330671 CATTTTTCAT
1 CA-TTTT--T
4330681 CATTTTT
1 CATTTTT
4330688 CATTTTT
1 CATTTTT
4330695 TTTGAAATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.13
7 22 0.58
8 4 0.11
9 4 0.11
10 3 0.08
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (7 bp):
CATTTTT
Found at i:4330661 original size:14 final size:14
Alignment explanation
Indices: 4330642--4330680 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
4330632 CCTTAGCCTC
4330642 TCCATTTTTCATTT
1 TCCATTTTTCATTT
4330656 TCCA-TTTTCATTT
1 TCCATTTTTCATTT
*
4330669 TTCATTTTTCAT
1 TCCATTTTTCAT
4330681 CATTTTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
TCCATTTTTCATTT
Found at i:4331136 original size:6 final size:6
Alignment explanation
Indices: 4331119--4331215 Score: 69
Period size: 6 Copynumber: 16.8 Consensus size: 6
4331109 CTTTTTTCTC
* * * * * *
4331119 ATTTTC ATTTTG ATTTTG ATCTTG ATTTTG ATTTTT TTTCTTC TTTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG ATTTTG
* * *
4331168 -TTTT- -TTTTG ATTTT- -TTTTC ATTTTC ATTTTG ACTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
4331211 ATTTT
1 ATTTT
4331216 TCTTTTTCTT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
4 8 0.11
5 4 0.05
6 59 0.78
7 5 0.07
ACGTcount: A:0.12, C:0.07, G:0.09, T:0.71
Consensus pattern (6 bp):
ATTTTG
Found at i:4331184 original size:19 final size:20
Alignment explanation
Indices: 4331144--4331191 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4331134 TTGATCTTGA
4331144 TTTTGATTTTTTTTC-TTCT
1 TTTTGATTTTTTTTCATTCT
* *
4331163 TTTTG-TTTTTTTTGATTTT
1 TTTTGATTTTTTTTCATTCT
*
4331182 TTTTCATTTT
1 TTTTGATTTT
4331192 CATTTTGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTGATTTTTTTTCATTCT
Found at i:4331221 original size:12 final size:10
Alignment explanation
Indices: 4331144--4331216 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
4331134 TTGATCTTGA
4331144 TTTTGATTTT
1 TTTTGATTTT
* *
4331154 TTTT-CTTCT
1 TTTTGATTTT
4331163 TTTTG-TTTT
1 TTTTGATTTT
4331172 TTTTGATTTT
1 TTTTGATTTT
*
4331182 TTTTCATTTT
1 TTTTGATTTT
*
4331192 CATTTTGACTTTGA
1 --TTTTGA-TTT-T
4331206 TTTTGATTTT
1 TTTTGATTTT
4331216 T
1 T
4331217 CTTTTTCTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
9 15 0.30
10 18 0.36
11 3 0.06
12 11 0.22
13 3 0.06
ACGTcount: A:0.10, C:0.07, G:0.08, T:0.75
Consensus pattern (10 bp):
TTTTGATTTT
Found at i:4335889 original size:3 final size:3
Alignment explanation
Indices: 4335881--4335967 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
4335871 AAAATAAAAC
* *
4335881 TAA TAA TAA TTAA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4335927 TAA TAAA TGA TAA TACA TTAA -AA TAA TTAA CAA -AA TAA TAA
1 TAA T-AA TAA TAA TA-A -TAA TAA TAA -TAA TAA TAA TAA TAA
4335968 GATTGCTAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.06
3 53 0.76
4 11 0.16
5 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4345049 original size:31 final size:29
Alignment explanation
Indices: 4344985--4345053 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
4344975 ACGATAACGT
** *
4344985 AAGTGACTAAAATGTAATATTTCAAACAT
1 AAGTGACTAAAATGTAATATGACAAACAA
*
4345014 AAGTGACTAAAATGTAATCTGAGACAAACAA
1 AAGTGACTAAAATGTAATAT--GACAAACAA
4345045 AAGTGACTA
1 AAGTGACTA
4345054 TTTTTGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAATATGACAAACAA
Found at i:4362091 original size:4 final size:4
Alignment explanation
Indices: 4362082--4362115 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
4362072 AAGTTTTATT
4362082 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
4362116 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4362123 original size:22 final size:22
Alignment explanation
Indices: 4362065--4362124 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
4362055 AAGTGGCCCA
*
4362065 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
4362089 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
4362110 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
4362125 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:4364425 original size:18 final size:19
Alignment explanation
Indices: 4364402--4364437 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4364392 AACAAGTGAG
4364402 GAAAAAGA-AAAAAAGAAT
1 GAAAAAGAGAAAAAAGAAT
*
4364420 GAAAAAGAGCAAAAAGAA
1 GAAAAAGAGAAAAAAGAA
4364438 ATTGAGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (19 bp):
GAAAAAGAGAAAAAAGAAT
Found at i:4364468 original size:18 final size:18
Alignment explanation
Indices: 4364447--4364485 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4364437 AATTGAGAGT
* *
4364447 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
4364465 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
4364483 GAA
1 GAA
4364486 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:4365894 original size:4 final size:4
Alignment explanation
Indices: 4365885--4365918 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
4365875 AAGTTTTATT
4365885 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
4365919 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4365926 original size:22 final size:22
Alignment explanation
Indices: 4365868--4365927 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
4365858 AAGTGGCCCA
*
4365868 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
4365892 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
4365913 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
4365928 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:4371706 original size:19 final size:20
Alignment explanation
Indices: 4371670--4371710 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4371660 TTTTAATTCT
*
4371670 TATAATTTTTTTCAATTTTTA
1 TATAATATTTTT-AATTTTTA
*
4371691 TATAATATTTTTATTTTTTA
1 TATAATATTTTTAATTTTTA
4371711 ATTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TATAATATTTTTAATTTTTA
Found at i:4374219 original size:18 final size:19
Alignment explanation
Indices: 4374188--4374225 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4374178 TGTTCAAATT
4374188 TCAATTGAAATCGAATTAA
1 TCAATTGAAATCGAATTAA
*
4374207 TCAATTG-AATCGATTTAA
1 TCAATTGAAATCGAATTAA
4374225 T
1 T
4374226 TCGGTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
TCAATTGAAATCGAATTAA
Found at i:4375354 original size:23 final size:21
Alignment explanation
Indices: 4375317--4375362 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
4375307 ATATTTGGAA
*
4375317 TTTAGTTTTTTTTTTTTACAT
1 TTTAGTTTTTTTTTTTTAAAT
4375338 TTTAGTCTTTTTGTTTTTTAAAT
1 TTTAGT-TTTTT-TTTTTTAAAT
4375361 TT
1 TT
4375363 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 11 0.50
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTAGTTTTTTTTTTTTAAAT
Found at i:4382270 original size:34 final size:34
Alignment explanation
Indices: 4382227--4382296 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
4382217 GAATTGAAGA
4382227 AAATTATATAGAAGTTTGCAAGCAAAGATGGCAT
1 AAATTATATAGAAGTTTGCAAGCAAAGATGGCAT
4382261 AAATTATATAGAAGTTTGCAAGCAAAGATGGCAT
1 AAATTATATAGAAGTTTGCAAGCAAAGATGGCAT
4382295 AA
1 AA
4382297 GTATAGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (34 bp):
AAATTATATAGAAGTTTGCAAGCAAAGATGGCAT
Found at i:4385522 original size:71 final size:71
Alignment explanation
Indices: 4385406--4385539 Score: 268
Period size: 71 Copynumber: 1.9 Consensus size: 71
4385396 CGGCTGTTGA
4385406 AAAAAGGTAATAAGCATAATTAGCTTGTAAACAATTTCGGGATGAGCATGAAATTAAGACCATAA
1 AAAAAGGTAATAAGCATAATTAGCTTGTAAACAATTTCGGGATGAGCATGAAATTAAGACCATAA
4385471 ACCAAT
66 ACCAAT
4385477 AAAAAGGTAATAAGCATAATTAGCTTGTAAACAATTTCGGGATGAGCATGAAATTAAGACCAT
1 AAAAAGGTAATAAGCATAATTAGCTTGTAAACAATTTCGGGATGAGCATGAAATTAAGACCAT
4385540 GAATCCATTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (71 bp):
AAAAAGGTAATAAGCATAATTAGCTTGTAAACAATTTCGGGATGAGCATGAAATTAAGACCATAA
ACCAAT
Found at i:4386738 original size:11 final size:11
Alignment explanation
Indices: 4386722--4386752 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4386712 AAGTATGGGT
4386722 AGGTATGGGAA
1 AGGTATGGGAA
*
4386733 AGGTATGGGCA
1 AGGTATGGGAA
4386744 AGGTATGGG
1 AGGTATGGG
4386753 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:4390852 original size:36 final size:36
Alignment explanation
Indices: 4390800--4390886 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
4390790 CCCAACTACT
*
4390800 GTATACGTGAACAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
4390836 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
4390872 GTATACGTGAATAGT
1 GTATACGTGAATAGT
4390887 GCCGTAAACG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
Found at i:4390887 original size:18 final size:18
Alignment explanation
Indices: 4390800--4390892 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
4390790 CCCAACTACT
* * *
4390800 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTGCC
4390818 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
* *
4390836 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTGCC
4390854 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
4390872 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
4390890 GTA
1 GTA
4390893 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:4391452 original size:11 final size:11
Alignment explanation
Indices: 4391436--4391466 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4391426 AAGTATGGGT
4391436 AGGTATGGGAA
1 AGGTATGGGAA
*
4391447 AGGTATGGGCA
1 AGGTATGGGAA
4391458 AGGTATGGG
1 AGGTATGGG
4391467 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:4411523 original size:19 final size:18
Alignment explanation
Indices: 4411501--4411554 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
4411491 ATTACAAAAT
*
4411501 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
*
4411520 AATTTAAAATATTTATAAA
1 AATTCAAAATATTTAT-AA
*
4411539 AATTCTAAAT-TTTATA
1 AATTCAAAATATTTATA
4411555 TTTTATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 19 0.63
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:4411538 original size:18 final size:19
Alignment explanation
Indices: 4411501--4411539 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4411491 ATTACAAAAT
*
4411501 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
4411520 AATTTAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
4411538 AA
1 AA
4411540 ATTCTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:4413162 original size:38 final size:39
Alignment explanation
Indices: 4413112--4413212 Score: 132
Period size: 38 Copynumber: 2.6 Consensus size: 39
4413102 TCATTTCTTT
*
4413112 TCATTTTAATAATTTTTTACAATATTTTACAATTTCTAA
1 TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
* *
4413151 -CATTTTTATAATTTTTTACAATATTTTATAGTTTCTAA
1 TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
* * *
4413189 TTACTTTTATATTTTTATTACAAT
1 TCATTTTTATAATTTT-TTACAAT
4413213 TTTAAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 35 0.65
39 12 0.22
40 7 0.13
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (39 bp):
TCATTTTTATAATTTTTTACAATATTTTACAATTTCTAA
Found at i:4413215 original size:19 final size:19
Alignment explanation
Indices: 4413154--4413216 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
4413144 TTTCTAACAT
*
4413154 TTTTATAATTTT-TTACAATA
1 TTTTATATTTTTATTAC-A-A
*
4413174 TTTTATAGTTTCTAATTAC--
1 TTTTATA-TTT-TTATTACAA
4413193 TTTTATATTTTTATTACAA
1 TTTTATATTTTTATTACAA
4413212 TTTTA
1 TTTTA
4413217 AAAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
17 6 0.17
18 3 0.09
19 12 0.34
20 7 0.20
21 2 0.06
22 1 0.03
23 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATATTTTTATTACAA
Found at i:4422061 original size:14 final size:14
Alignment explanation
Indices: 4422042--4422071 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4422032 TAAAATTGAG
*
4422042 AAAAATAACAATAA
1 AAAAATAACAACAA
4422056 AAAAATAACAACAA
1 AAAAATAACAACAA
4422070 AA
1 AA
4422072 CCAAATATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAATAACAACAA
Found at i:4435015 original size:21 final size:23
Alignment explanation
Indices: 4434968--4435025 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
4434958 TTCTCTAAAT
4434968 TGTATTT-GTATTTTCGTTGTTA
1 TGTATTTAGTATTTTCGTTGTTA
*
4434990 -ATATTTAGTATTTTC-TT-TTA
1 TGTATTTAGTATTTTCGTTGTTA
*
4435010 TGTATTATATTATTTT
1 TGTATT-TAGTATTTT
4435026 AAACTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 11 0.37
22 16 0.53
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (23 bp):
TGTATTTAGTATTTTCGTTGTTA
Found at i:4435118 original size:15 final size:15
Alignment explanation
Indices: 4435098--4435146 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4435088 AGCATTTATT
4435098 ATTTATTTGAGACTC
1 ATTTATTTGAGACTC
* *
4435113 ATTTA-TT-ATA-TT
1 ATTTATTTGAGACTC
4435125 ATTTATTTGAGACTC
1 ATTTATTTGAGACTC
4435140 ATTTATT
1 ATTTATT
4435147 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 4 0.15
15 13 0.48
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (15 bp):
ATTTATTTGAGACTC
Found at i:4435118 original size:22 final size:22
Alignment explanation
Indices: 4435090--4435153 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 22
4435080 CATATGAAAG
4435090 CATTTATTATTTATTTGAGACT
1 CATTTATTATTTATTTGAGACT
4435112 CATTTATTATATTATTTATTTGAGACT
1 C----ATT-TATTATTTATTTGAGACT
4435139 CATTTATTA-TTATTT
1 CATTTATTATTTATTT
4435154 TAAGTTTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
21 6 0.16
22 6 0.16
23 3 0.08
26 3 0.08
27 19 0.51
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (22 bp):
CATTTATTATTTATTTGAGACT
Found at i:4435129 original size:27 final size:27
Alignment explanation
Indices: 4435094--4435148 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4435084 TGAAAGCATT
4435094 TATTATTTATTTGAGACTCATTTATTA
1 TATTATTTATTTGAGACTCATTTATTA
4435121 TATTATTTATTTGAGACTCATTTATTA
1 TATTATTTATTTGAGACTCATTTATTA
4435148 T
1 T
4435149 TATTTTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (27 bp):
TATTATTTATTTGAGACTCATTTATTA
Found at i:4439684 original size:3 final size:3
Alignment explanation
Indices: 4439676--4439714 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4439666 TTTTCATACT
4439676 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4439715 AACTCAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4441630 original size:38 final size:38
Alignment explanation
Indices: 4441579--4441668 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
4441569 CCCTTCTAGC
*
4441579 TTCTGCTGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
1 TTCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
4441617 TTCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
1 TTCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
4441655 TTCTGCCGATTTGC
1 TTCTGCCGATTTGC
4441669 CAGTTTCTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.03, C:0.28, G:0.12, T:0.57
Consensus pattern (38 bp):
TTCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
Found at i:4441751 original size:25 final size:25
Alignment explanation
Indices: 4441723--4441772 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4441713 CAACATTACG
*
4441723 CTTGGCCTTCTCAACTAGTCAACCT
1 CTTGGCCTTCTCAACCAGTCAACCT
4441748 CTTGGCCTTCTCAACCAGTCAACCT
1 CTTGGCCTTCTCAACCAGTCAACCT
4441773 TTTCTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.38, G:0.12, T:0.30
Consensus pattern (25 bp):
CTTGGCCTTCTCAACCAGTCAACCT
Done.