Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 9 of 93
Found at i:4734430 original size:46 final size:46
Alignment explanation
Indices: 4734338--4734430 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
4734328 TAATATTACA
* * * * *
4734338 ACTGCCAAATGAACTTCACTGTTGCAAACATTAAACATAAAGAAAG
1 ACTGCCAAATGAAATTCAATGTTACAAACAATAAACATAAACAAAG
4734384 ACTGCCAAATGAAATTCAATGTTACAAACAATAAACA-AAGACAAAG
1 ACTGCCAAATGAAATTCAATGTTACAAACAATAAACATAA-ACAAAG
4734430 A
1 A
4734431 AAAGGAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
45 2 0.05
46 39 0.95
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (46 bp):
ACTGCCAAATGAAATTCAATGTTACAAACAATAAACATAAACAAAG
Found at i:4736573 original size:7 final size:7
Alignment explanation
Indices: 4736561--4736590 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4736551 ACCTACCACA
4736561 GCCATGG
1 GCCATGG
4736568 GCCATGG
1 GCCATGG
4736575 GCCATGG
1 GCCATGG
*
4736582 GCCACGG
1 GCCATGG
4736589 GC
1 GC
4736591 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.43, T:0.10
Consensus pattern (7 bp):
GCCATGG
Found at i:4739840 original size:39 final size:39
Alignment explanation
Indices: 4739792--4739872 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
4739782 AGAAGTTTAA
4739792 TTAAAGTCAGTTTTATTTATCACATTTAAGTTAGTGGGG
1 TTAAAGTCAGTTTTATTTATCACATTTAAGTTAGTGGGG
* *
4739831 TTAAGGTCAGTTTTATTTATCACGTTTAAGTTAGTGGGG
1 TTAAAGTCAGTTTTATTTATCACATTTAAGTTAGTGGGG
4739870 TTA
1 TTA
4739873 GGTTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (39 bp):
TTAAAGTCAGTTTTATTTATCACATTTAAGTTAGTGGGG
Found at i:4753895 original size:16 final size:15
Alignment explanation
Indices: 4753874--4753906 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
4753864 ACCTCTCTCC
4753874 TTTTTTCATTCTTTCA
1 TTTTTTCATT-TTTCA
4753890 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
4753905 TT
1 TT
4753907 ATTATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:4754022 original size:18 final size:18
Alignment explanation
Indices: 4753966--4754022 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
4753956 TGTCTACAGA
4753966 TATCCACTTTTGGTGGGT
1 TATCCACTTTTGGTGGGT
* * * * *
4753984 GACCCACATATGATGGGT
1 TATCCACTTTTGGTGGGT
*
4754002 TATCCACTTTTGGTGGAT
1 TATCCACTTTTGGTGGGT
4754020 TAT
1 TAT
4754023 AGGCATCCAT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (18 bp):
TATCCACTTTTGGTGGGT
Found at i:4754060 original size:25 final size:26
Alignment explanation
Indices: 4754031--4754130 Score: 80
Period size: 26 Copynumber: 3.9 Consensus size: 26
4754021 ATAGGCATCC
4754031 ATCCA-TTTTGATGGTAAAATTATCT
1 ATCCACTTTTGATGGTAAAATTATCT
4754056 ATCCACTTTT-AGTGGTAAAATTAT-T
1 ATCCACTTTTGA-TGGTAAAATTATCT
* ** * ** * *
4754081 TTTAAATTCAGATGATAAAATTATCC
1 ATCCACTTTTGATGGTAAAATTATCT
* *
4754107 ATCCACTTATGGTGGTAAAATTAT
1 ATCCACTTTTGATGGTAAAATTAT
4754131 AATTAAAATA
Statistics
Matches: 55, Mismatches: 16, Indels: 7
0.71 0.21 0.09
Matches are distributed among these distances:
25 22 0.40
26 33 0.60
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (26 bp):
ATCCACTTTTGATGGTAAAATTATCT
Found at i:4754137 original size:51 final size:51
Alignment explanation
Indices: 4754040--4754137 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
4754030 CATCCATTTT
* * * **
4754040 GATGGTAAAATTATCTATCCACTTTTAGTGGTAAAATTATTTTTAAATTCA
1 GATGATAAAATTATCCATCCACTTATAGTGGTAAAATTATAATTAAATTCA
*
4754091 GATGATAAAATTATCCATCCACTTATGGTGGTAAAATTATAATTAAA
1 GATGATAAAATTATCCATCCACTTATAGTGGTAAAATTATAATTAAA
4754138 ATAGTGATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (51 bp):
GATGATAAAATTATCCATCCACTTATAGTGGTAAAATTATAATTAAATTCA
Found at i:4754367 original size:53 final size:54
Alignment explanation
Indices: 4754238--4754397 Score: 169
Period size: 53 Copynumber: 2.9 Consensus size: 54
4754228 TATTAAATGA
* ** *
4754238 TGTCACATTCACTTCAGGAAATGTATGGATTTATAATTTTTCCATTAGTAGCTCGTT
1 TGTCACATTCACTTCAGGGAATG-A-ACATTCATAATTTTT-CATTAGTAGCTCGTT
* * * *
4754295 TGTCGCATTTACTTTAGGGAATGAACATTCATAATTTTT-ATTAGTAGCTTGTT
1 TGTCACATTCACTTCAGGGAATGAACATTCATAATTTTTCATTAGTAGCTCGTT
* * ** *
4754348 TGTCACATTCACTTCAGGGAATGGATATTCATGGTTTTTCATTAATAGCT
1 TGTCACATTCACTTCAGGGAATGAACATTCATAATTTTTCATTAGTAGCT
4754398 ATATAATAGC
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
53 45 0.52
54 9 0.10
55 12 0.14
56 1 0.01
57 19 0.22
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (54 bp):
TGTCACATTCACTTCAGGGAATGAACATTCATAATTTTTCATTAGTAGCTCGTT
Found at i:4756798 original size:2 final size:2
Alignment explanation
Indices: 4756787--4756817 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4756777 ACACACATAC
*
4756787 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4756818 GGAACTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4763653 original size:2 final size:2
Alignment explanation
Indices: 4763646--4763691 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
4763636 ATTTAAAGAT
*
4763646 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4763688 TA TA
1 TA TA
4763692 ATGACATGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4766069 original size:8 final size:8
Alignment explanation
Indices: 4766058--4766087 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4766048 CCAACATATG
4766058 AACAAAGA
1 AACAAAGA
4766066 AACAAAGA
1 AACAAAGA
4766074 AACAAAGA
1 AACAAAGA
4766082 AACAAA
1 AACAAA
4766088 CCCCATCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (8 bp):
AACAAAGA
Found at i:4779416 original size:59 final size:59
Alignment explanation
Indices: 4779314--4779437 Score: 221
Period size: 59 Copynumber: 2.1 Consensus size: 59
4779304 AATATGTTTA
* *
4779314 CTAAATCAACAATAGTTTCTCAAGAGTAAGATGAGCATATAATAAATTACTGAATTTGT
1 CTAATTCAACAATAGTTTCTCAACAGTAAGATGAGCATATAATAAATTACTGAATTTGT
*
4779373 CTAATTCAACAATAGTTTCTCAACAGTAAGATGAGCATGTAATAAATTACTGAATTTGT
1 CTAATTCAACAATAGTTTCTCAACAGTAAGATGAGCATATAATAAATTACTGAATTTGT
4779432 CTAATT
1 CTAATT
4779438 GATCCATCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (59 bp):
CTAATTCAACAATAGTTTCTCAACAGTAAGATGAGCATATAATAAATTACTGAATTTGT
Found at i:4782113 original size:55 final size:54
Alignment explanation
Indices: 4782014--4782123 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 54
4782004 GAATATCATT
* * *
4782014 ATTTTATTATATTTTTAAATTTTTAAATATTAAGATTACAAATTTATAATTAAA
1 ATTTTATTAAATTTTTAAATTTTTAAATATTAAGATTACAAATTTAAAACTAAA
* *
4782068 ATTTTATTTAAATTTTTAAA-TTTTAAATATTAACTGTTTA-TAATTTAAAACTAAA
1 ATTTTA-TTAAATTTTTAAATTTTTAAATATTAA--GATTACAAATTTAAAACTAAA
4782123 A
1 A
4782124 ACTAAACCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
54 19 0.40
55 25 0.52
56 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (54 bp):
ATTTTATTAAATTTTTAAATTTTTAAATATTAAGATTACAAATTTAAAACTAAA
Found at i:4790457 original size:16 final size:16
Alignment explanation
Indices: 4790436--4790467 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4790426 ATTAATATTT
*
4790436 TATATTTTAATTATAA
1 TATATTTAAATTATAA
4790452 TATATTTAAATTATAA
1 TATATTTAAATTATAA
4790468 ATAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTTAAATTATAA
Found at i:4796850 original size:20 final size:20
Alignment explanation
Indices: 4796813--4796851 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4796803 GTTAACTGTC
* *
4796813 ATATCAATTTTCATATAATT
1 ATATCAATTATCACATAATT
*
4796833 ATATCAGTTATCACATAAT
1 ATATCAATTATCACATAAT
4796852 CATGTTATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATCAATTATCACATAATT
Found at i:4800000 original size:24 final size:24
Alignment explanation
Indices: 4799973--4800019 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4799963 ATCGGCGACA
4799973 CCAACCCCATCTCCAACTCCTTCC
1 CCAACCCCATCTCCAACTCCTTCC
*
4799997 CCAACCCCATCTCCAGCTCCTTC
1 CCAACCCCATCTCCAACTCCTTC
4800020 AACAGCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.57, G:0.02, T:0.21
Consensus pattern (24 bp):
CCAACCCCATCTCCAACTCCTTCC
Found at i:4801302 original size:36 final size:35
Alignment explanation
Indices: 4801252--4801332 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
4801242 TGTTATGGAT
* * *
4801252 ATAATTAATATGGCTTTTCATCAACA-CTAAAAATGGA
1 ATAATTAGTTTGGCTTTTCAGCAA-AGCTAAAAA--GA
4801289 AT-ATTAGTTTGGCTTTTCAGCAAAGCTAAAAAGA
1 ATAATTAGTTTGGCTTTTCAGCAAAGCTAAAAAGA
4801323 ATAATTAGTT
1 ATAATTAGTT
4801333 AAAATTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
34 4 0.10
35 8 0.21
36 25 0.64
37 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (35 bp):
ATAATTAGTTTGGCTTTTCAGCAAAGCTAAAAAGA
Found at i:4809279 original size:22 final size:22
Alignment explanation
Indices: 4809254--4809306 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
4809244 CAATTAGTTA
*
4809254 TTAGGTATTACATTACTGGTTT
1 TTAGGTATTACATCACTGGTTT
** ** *
4809276 TTAGACATTGTATCATTGGTTT
1 TTAGGTATTACATCACTGGTTT
4809298 TTAGGTATT
1 TTAGGTATT
4809307 GTGAGATTGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.51
Consensus pattern (22 bp):
TTAGGTATTACATCACTGGTTT
Found at i:4809307 original size:22 final size:22
Alignment explanation
Indices: 4809270--4809329 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
4809260 ATTACATTAC
**
4809270 TGGTTTTTAGACATTGT-ATCAT
1 TGGTTTTTAGGTATTGTGA-CAT
*
4809292 TGGTTTTTAGGTATTGTGAGAT
1 TGGTTTTTAGGTATTGTGACAT
*
4809314 TGATTTTTAGGTATTG
1 TGGTTTTTAGGTATTG
4809330 CGTGACTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.52
Consensus pattern (22 bp):
TGGTTTTTAGGTATTGTGACAT
Found at i:4809533 original size:22 final size:22
Alignment explanation
Indices: 4809505--4809591 Score: 104
Period size: 22 Copynumber: 4.0 Consensus size: 22
4809495 TCATTTTAAC
*
4809505 TAGTCACGCAATACTTAAAAAT
1 TAGTCACACAATACTTAAAAAT
* *
4809527 CAGTCACATAATA-TCTAAAAAT
1 TAGTCACACAATACT-TAAAAAT
*
4809549 TAGTCACACAATGCTTAAAAAT
1 TAGTCACACAATACTTAAAAAT
**
4809571 TAGTCACGTAATACTTAAAAA
1 TAGTCACACAATACTTAAAAA
4809592 CTTGTTACTC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.02
22 52 0.96
23 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (22 bp):
TAGTCACACAATACTTAAAAAT
Found at i:4809605 original size:44 final size:44
Alignment explanation
Indices: 4809505--4809613 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
4809495 TCATTTTAAC
* *
4809505 TAGTCACGCAATACTTAAAAATCAGTCACATAATATCTAAAAAT
1 TAGTCACACAATGCTTAAAAATCAGTCACATAATATCTAAAAAT
* *
4809549 TAGTCACACAATGCTTAAAAATTAGTCACGTAATA-CTTAAAAACT
1 TAGTCACACAATGCTTAAAAATCAGTCACATAATATC-TAAAAA-T
* * *
4809594 T-GTTACTCAATGCTAAAAAA
1 TAGTCACACAATGCTTAAAAA
4809614 CCGATTACGT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 53 0.95
45 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.28
Consensus pattern (44 bp):
TAGTCACACAATGCTTAAAAATCAGTCACATAATATCTAAAAAT
Found at i:4809634 original size:22 final size:22
Alignment explanation
Indices: 4809562--4809634 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
4809552 TCACACAATG
* * *
4809562 CTTAAAAATTAGTCACGTAATA
1 CTTAAAAACTCGTTACGTAATA
* *
4809584 CTTAAAAACTTGTTAC-TCAATG
1 CTTAAAAACTCGTTACGT-AATA
*
4809606 CTAAAAAAC-CGATTACGTAATA
1 CTTAAAAACTCG-TTACGTAATA
4809628 CTTAAAA
1 CTTAAAA
4809635 TCCACCAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.05
22 37 0.93
23 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.30
Consensus pattern (22 bp):
CTTAAAAACTCGTTACGTAATA
Found at i:4818108 original size:12 final size:12
Alignment explanation
Indices: 4818093--4818157 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
4818083 TTTCTACACC
4818093 TCTTTCTCTTTT
1 TCTTTCTCTTTT
*
4818105 TCTTTTTCTTTT
1 TCTTTCTCTTTT
4818117 TCTCTTCTCTTTTGT
1 TCT-TTCTC-TTT-T
* *
4818132 GTCTTTTTATTTT
1 -TCTTTCTCTTTT
*
4818145 TATTTCTCTTTT
1 TCTTTCTCTTTT
4818157 T
1 T
4818158 TTTGTAACTC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 24 0.57
13 5 0.12
14 6 0.14
15 4 0.10
16 3 0.07
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (12 bp):
TCTTTCTCTTTT
Found at i:4818243 original size:75 final size:75
Alignment explanation
Indices: 4818142--4818294 Score: 290
Period size: 75 Copynumber: 2.0 Consensus size: 75
4818132 GTCTTTTTAT
4818142 TTTTATTTCTCTTTTTTTTGTAACTCACCATTCAAACACACTTTATTCTTCAAAAGAGATTTATG
1 TTTTATTTCTCTTTTTTTTGTAACTCACCATTCAAACACACTTTATTCTTCAAAAGAGATTTATG
4818207 AGCTTGTAAG
66 AGCTTGTAAG
4818217 TTTNTATTTCTC-TTTTTTTGTAACTCACCATTCAAACACACTTTATTCTTCAAAAGAGATTTAT
1 TTT-TATTTCTCTTTTTTTTGTAACTCACCATTCAAACACACTTTATTCTTCAAAAGAGATTTAT
4818281 GAGCTTGTAAG
65 GAGCTTGTAAG
4818292 TTT
1 TTT
4818295 GGACAAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 69 0.90
76 8 0.10
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.46
Consensus pattern (75 bp):
TTTTATTTCTCTTTTTTTTGTAACTCACCATTCAAACACACTTTATTCTTCAAAAGAGATTTATG
AGCTTGTAAG
Found at i:4822869 original size:22 final size:22
Alignment explanation
Indices: 4822842--4822941 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
4822832 TTTTTGTGGA
*
4822842 TTTTAGGCATTACATAACTAGT
1 TTTTAGGCATTACATAACTAAT
* * *
4822864 TTTTAGACATTACGTAACTAGT
1 TTTTAGGCATTACATAACTAAT
* * * *
4822886 TTTTATGCATTGCCTTACTAAT
1 TTTTAGGCATTACATAACTAAT
* *
4822908 TTTTAAGTATTACATAACTAAT
1 TTTTAGGCATTACATAACTAAT
*
4822930 TTTTAGGTATTA
1 TTTTAGGCATTA
4822942 TGTGACTAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (22 bp):
TTTTAGGCATTACATAACTAAT
Found at i:4823008 original size:22 final size:22
Alignment explanation
Indices: 4822858--4823008 Score: 63
Period size: 22 Copynumber: 6.8 Consensus size: 22
4822848 GCATTACATA
* *
4822858 ACTAGTTTTTAGACATTACGTA
1 ACTAGTTTTTAGATATTACGTG
* * * *
4822880 ACTAGTTTTTATG-CATTGCCTT
1 ACTAGTTTTTA-GATATTACGTG
* * *
4822902 ACTAATTTTTA-AGTATTACATA
1 ACTAGTTTTTAGA-TATTACGTG
* * *
4822924 ACTAATTTTTAGGTATTATGTG
1 ACTAGTTTTTAGATATTACGTG
* ** * * *
4822946 ACTAATTGATATGGTATTGCATG
1 ACTAGTTTTTA-GATATTACGTG
* * *
4822969 ACTGGTTAGTAAGATATTACGTG
1 ACTAGTT-TTTAGATATTACGTG
4822992 ACTAGTTTTTAGATATT
1 ACTAGTTTTTAGATATT
4823009 GTGTGACTTA
Statistics
Matches: 96, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
22 66 0.69
23 28 0.29
24 2 0.02
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (22 bp):
ACTAGTTTTTAGATATTACGTG
Found at i:4823102 original size:22 final size:21
Alignment explanation
Indices: 4823059--4823098 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4823049 TTTAAAAATT
4823059 AGTCACACAATACCTAAAACC
1 AGTCACACAATACCTAAAACC
4823080 AGTCACACAATACCTAAAA
1 AGTCACACAATACCTAAAA
4823099 ACCAAAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.30, G:0.05, T:0.15
Consensus pattern (21 bp):
AGTCACACAATACCTAAAACC
Found at i:4825594 original size:36 final size:36
Alignment explanation
Indices: 4825548--4825617 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
4825538 ACAAATAATT
4825548 AGTTTTAATAG-TTCCAGATATTATTACAAAAAAAAA
1 AGTTTTAATAGATT-CAGATATTATTACAAAAAAAAA
* * *
4825584 AGTTTTAATAGATTTAGGTATTATTTCAAAAAAA
1 AGTTTTAATAGATTCAGATATTATTACAAAAAAA
4825618 TATATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (36 bp):
AGTTTTAATAGATTCAGATATTATTACAAAAAAAAA
Found at i:4825652 original size:36 final size:36
Alignment explanation
Indices: 4825567--4825655 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
4825557 AGTTCCAGAT
* *
4825567 ATTATTACAAAAAAAAAAGTTTTAATAGATTTAGGT
1 ATTATTACAAAAAAAAAAGTTATAATAGATTTAGGC
* * * *
4825603 ATTATTTCAAAAAAATATA-TTCATAATAGTTTTATGC
1 ATTATTACAAAAAAA-AAAGTT-ATAATAGATTTAGGC
4825640 ATTATTACAAAAAAAA
1 ATTATTACAAAAAAAA
4825656 TAGTAACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 17 0.39
37 27 0.61
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.37
Consensus pattern (36 bp):
ATTATTACAAAAAAAAAAGTTATAATAGATTTAGGC
Found at i:4830863 original size:28 final size:28
Alignment explanation
Indices: 4830832--4830887 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4830822 AATGATCAAG
* *
4830832 TATTAATATTTTAAATA-AAAATATAAAT
1 TATTAATATTTAAAACATAAAAT-TAAAT
4830860 TATTAATATTTAAAACATAAAATTAAAT
1 TATTAATATTTAAAACATAAAATTAAAT
4830888 AAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TATTAATATTTAAAACATAAAATTAAAT
Found at i:4831014 original size:28 final size:28
Alignment explanation
Indices: 4830983--4831180 Score: 112
Period size: 28 Copynumber: 7.2 Consensus size: 28
4830973 ATTATTATTT
*
4830983 AAATGATAAATTATTAATA-TTATAAATA
1 AAAT-ATAAATTATTAATATTTAAAAATA
4831011 AAATATAAATTATTAATATTTAAAAATA
1 AAATATAAATTATTAATATTTAAAAATA
*
4831039 AAAAATAAA--A-TAATCA--TAAAAATCA
1 AAATATAAATTATTAAT-ATTTAAAAAT-A
* * * * *
4831064 TAATA-ACATT-TTATTA-TTATAAATT
1 AAATATAAATTATTAATATTTAAAAATA
* * * *
4831089 AAATATTATTATTTTTAATA-TTAATGATTA
1 AAATA-TA-AATTATTAATATTTAA-AAATA
* * *
4831119 AATTATAAATAAATTTAATATTT-TAAATA
1 AAATATAAAT-TA-TTAATATTTAAAAATA
*
4831148 AATTATAAATTATTAATATTTAAAAATA
1 AAATATAAATTATTAATATTTAAAAATA
4831176 AAATA
1 AAATA
4831181 ATTTAAAAAT
Statistics
Matches: 129, Mismatches: 25, Indels: 32
0.69 0.13 0.17
Matches are distributed among these distances:
24 9 0.07
25 13 0.10
26 11 0.09
27 24 0.19
28 35 0.27
29 23 0.18
30 12 0.09
31 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATATAAATTATTAATATTTAAAAATA
Found at i:4831032 original size:161 final size:159
Alignment explanation
Indices: 4830736--4831180 Score: 499
Period size: 161 Copynumber: 2.7 Consensus size: 159
4830726 AATAATATTT
* * * *
4830736 TAATCATAATAATATTTAAATTTTAAATAACATATTCATATTTTAAAATTTTAATGATTAAATGA
1 TAATCATAATAACATTTAAATTATAAATAA-ATATTAATATTTTAAAA-TTTAATGATTAATTGA
* * * *
4830801 TAAAT-AAAATATTAATATTTAAATGATCAAGTATTAATATTTTAAATAAAAATATAAATTATTA
64 TAAATAAAAATATTATTATTTAAATGATAAATTATTAATATTATAAAT-AAAATATAAATTATTA
*
4830865 ATATTTAAAACAT-AAAATTAAATAAAAATAAA
128 ATATTTAAAA-ATAAAAATAAAATAAAAATAAA
* *
4830897 TAATCACAATAACATTTAAATTATAAATACAATATTAATATTTTAGGAATTTAAT-AGTTAATTG
1 TAATCATAATAACATTTAAATTATAAATA-AATATTAATATTTTA-AAATTTAATGA-TTAATTG
*
4830961 ATAAGTAAAAATATTATTATTTAAATGATAAATTATTAATATTATAAATAAAATATAAATTATTA
63 ATAAATAAAAATATTATTATTTAAATGATAAATTATTAATATTATAAATAAAATATAAATTATTA
**
4831026 ATATTTAAAAATAAAAAATAAAATAATCATAAA
128 ATATTTAAAAAT-AAAAATAAAATAAAAATAAA
* * *
4831059 -AATCATAATAACATTTTATTATTATAAATTAAATATTATTATTTT-TAATATTAATGATTAAAT
1 TAATCATAATAACA-TTTA-AATTATAAA-TAAATATTAATATTTTAAAAT-TTAATGATT-AAT
** * *
4831122 T-ATAAATAAATTTAATATT-TTAAATAAATTATAAATTATTAATATTTAAAAATAAAATA
61 TGATAAATAAA---AATATTATTATTTAAATGATAAATTATTAATA-TTATAAATAAAATA
4831181 ATTTAAAAAT
Statistics
Matches: 245, Mismatches: 23, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
160 3 0.01
161 97 0.40
162 76 0.31
163 26 0.11
164 24 0.10
165 19 0.08
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (159 bp):
TAATCATAATAACATTTAAATTATAAATAAATATTAATATTTTAAAATTTAATGATTAATTGATA
AATAAAAATATTATTATTTAAATGATAAATTATTAATATTATAAATAAAATATAAATTATTAATA
TTTAAAAATAAAAATAAAATAAAAATAAA
Found at i:4831157 original size:36 final size:40
Alignment explanation
Indices: 4831079--4831165 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 40
4831069 ACATTTTATT
* *
4831079 ATTATAAATTAAATATTATTATTTTTAATATTAATGATTAA
1 ATTATAAA-TAAATATTAATATTTTTAATATAAATGATTAA
*
4831120 ATTATAAATAAAT-TTAATA-TTTTAA-ATAAATTA-TAA
1 ATTATAAATAAATATTAATATTTTTAATATAAATGATTAA
*
4831156 ATTATTAATA
1 ATTATAAATA
4831166 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 12 0.29
37 6 0.14
38 6 0.14
39 5 0.12
40 5 0.12
41 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (40 bp):
ATTATAAATAAATATTAATATTTTTAATATAAATGATTAA
Found at i:4831164 original size:137 final size:137
Alignment explanation
Indices: 4830988--4831291 Score: 395
Period size: 137 Copynumber: 2.2 Consensus size: 137
4830978 TATTTAAATG
* *
4830988 ATAAATTATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAATAAAA-AA-TAAAATA
1 ATAAAATATTAATATTTTAAATAAAATATAAATTATTAATATTTAAAAATAAAATAATTAAAA-A
** * *
4831051 ATCATAAAAATCATAAT-AACATTTTATTATTATAAATTAAATATTATTATTTT-TAATATTAAT
65 AT-A-AAAAATCATAATAAACA--TTAAAAGTATAAA-TAAATATTACTATTTTATAATATTAAT
*
4831114 GATTAAATTATAA
125 AATTAAATTATAA
* *
4831127 AT-AAAT-TTAATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAATAATTTAAAAA
1 ATAAAATATTAATATTTTAAATAAAATATAAATTATTAATATTTAAAAATAAAATAATTAAAAAA
* *
4831190 TAAATAATCATAATAAACATTAAAAGTATAAATAAATATTACTATTTTATAATATTAATAATTAG
66 TAAAAAATCATAATAAACATTAAAAGTATAAATAAATATTACTATTTTATAATATTAATAATTAA
4831255 ATTATAA
131 ATTATAA
4831262 ATAAAATATTAATATTTTAAAAATAAAATA
1 ATAAAATATTAATATTTT--AAATAAAATA
4831292 AATAAATATA
Statistics
Matches: 145, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
134 15 0.10
135 33 0.23
136 15 0.10
137 59 0.41
138 8 0.06
139 15 0.10
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (137 bp):
ATAAAATATTAATATTTTAAATAAAATATAAATTATTAATATTTAAAAATAAAATAATTAAAAAA
TAAAAAATCATAATAAACATTAAAAGTATAAATAAATATTACTATTTTATAATATTAATAATTAA
ATTATAA
Found at i:4831165 original size:18 final size:17
Alignment explanation
Indices: 4831116--4831165 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
4831106 ATATTAATGA
*
4831116 TTAAATTATAAATAAAT
1 TTAAATTATTAATAAAT
4831133 TTAATATT-TTAAATAAAT
1 TTAA-ATTATT-AATAAAT
4831151 TATAAATTATTAATA
1 T-TAAATTATTAATA
4831166 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.18
18 18 0.64
19 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTATTAATAAAT
Found at i:4831179 original size:29 final size:29
Alignment explanation
Indices: 4831117--4831177 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
4831107 TATTAATGAT
*
4831117 TAAATTATAAATAAATTTAATATTTTAAA
1 TAAATTATAAATAAATTTAATATTTAAAA
*
4831146 TAAATTATAAAT-TA-TTAATATTTAAAAA
1 TAAATTATAAATAAATTTAATATTT-AAAA
4831174 TAAA
1 TAAA
4831178 ATAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.31
28 8 0.28
29 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAATTATAAATAAATTTAATATTTAAAA
Found at i:4831180 original size:15 final size:16
Alignment explanation
Indices: 4831165--4831197 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4831155 AATTATTAAT
4831165 ATTTAAAAATAAAATA
1 ATTTAAAAATAAAATA
4831181 ATTTAAAAAT-AAATA
1 ATTTAAAAATAAAATA
4831196 AT
1 AT
4831198 CATAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTTAAAAATAAAATA
Found at i:4831282 original size:20 final size:20
Alignment explanation
Indices: 4831218--4831282 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
4831208 ATTAAAAGTA
*
4831218 TAAAT-AAATATTACTATTT
1 TAAATAAAATATTAATATTT
* * *
4831237 TATAATATTAATAATT-AGATTA
1 TA-AATA-AAAT-ATTAATATTT
4831259 TAAATAAAATATTAATATTT
1 TAAATAAAATATTAATATTT
4831279 TAAA
1 TAAA
4831283 AATAAAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 9
0.68 0.14 0.18
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 4 0.12
22 8 0.24
23 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAATAAAATATTAATATTT
Found at i:4831292 original size:42 final size:43
Alignment explanation
Indices: 4831216--4831316 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 43
4831206 ACATTAAAAG
* * * * *
4831216 TATAAAT-AAATATTACTATTTTATAATATTAATAATTAGAT-
1 TATAAATAAAATATTAATATTTTAAAATATAAATAAATAAATA
4831257 TATAAATAAAATATTAATATTTTAAAA-ATAAAATAAATAAATA
1 TATAAATAAAATATTAATATTTTAAAATAT-AAATAAATAAATA
4831300 TATATAATAAAAATATT
1 TATA-AAT-AAAATATT
4831317 TTTATTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 9 0.18
42 26 0.52
43 4 0.08
44 3 0.06
45 8 0.16
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
TATAAATAAAATATTAATATTTTAAAATATAAATAAATAAATA
Found at i:4833885 original size:335 final size:338
Alignment explanation
Indices: 4833257--4833887 Score: 730
Period size: 335 Copynumber: 1.9 Consensus size: 338
4833247 TATCAATAAT
* * ** *
4833257 ATTTGAAGTAACCAATACCAAACACTTGCAAAATAAAAAGTGATGTTGATAAGGATTAGAAAAGT
1 ATTTGAACTAACCAATACCAAACACTTGCAAAATAAAAAGTGATATTGATAAAAATTACAAAAGT
* * * * * * ** * *
4833322 GTAAATATAGTAAGTATCATGGAATTAAAATATGTTCATTGTATTGCAATTTACAGAATATTTCT
66 GCAAATATAATAAGTATCACGAAATTAAAATATATTAATTACATTGCAATTTACAGAACATTTAT
*
4833387 AAAAATTCATAATATTAGAAAAATAAATGGTATTGATAAAGATGTACAAGTATCTTTGTTAGGTA
131 AAAAATTCATAATATTAGAAAAATAAATGGTATTGATAAAGA-GTACAAGTATCTTTGTTAAGTA
** * * *
4833452 TTTTGAAATCTTGAATATGTTTAATTACACATTACATTTTACGAAGAATTTTTGTACTTCCATGA
195 CCTTGAAATCTTGAATATATTTAATCACACATTACATTTTACGAAGAACTTTTGTACTTCCATGA
*
4833517 ATATTAAACTTTAGTATGTTCTTAAAGTAAATATTTGATCAATTAATTAAATTTACGTGTCCTTA
260 ATATTAAACTTTAGTATGTTCTTAAAATAAATATTTGATCAATTAATTAAATTTACGTGTCCTTA
4833582 TTAGCCCTGGTAAG
325 TTAGCCCTGGTAAG
* *
4833596 ATTTGAACTAACCAATA-CTAGCACTTGC-AAATAAAAA-TGATATTGATAAAAATTACAAAAGT
1 ATTTGAACTAACCAATACCAAACACTTGCAAAATAAAAAGTGATATTGATAAAAATTACAAAAGT
* * * *
4833658 GCAAGTATAATAAGTATC-CGAAATTCAAATATATTAATTACATTGCATTTTATAGAACATTTAT
66 GCAAATATAATAAGTATCACGAAATTAAAATATATTAATTACATTGCAATTTACAGAACATTTAT
* * * * *
4833722 -TAACTTCTATGATATTAGTAAAATAAATGGTATTGATAAAGA-TACCAAGTATTTTTAG-TAAG
131 AAAAATTC-ATAATATTAGAAAAATAAATGGTATTGATAAAGAGTA-CAAGTATCTTT-GTTAAG
* * *
4833784 TACCTT-ATAATTTTGAATATATTTAGTCATACATTACATTTT--GTAGAGAACTTTTGTACTT-
193 TACCTTGA-AATCTTGAATATATTTAATCACACATTACATTTTACG-A-AGAACTTTTGTACTTC
* *
4833845 TATGAATATATATTAAACTTTA-T-TGTTGTTAAAATAAATATTT
255 CATG---A-ATATTAAACTTTAGTATGTTCTTAAAATAAATATTT
4833888 TTTTTCTTAT
Statistics
Matches: 244, Mismatches: 38, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
332 1 0.00
333 7 0.03
334 65 0.27
335 86 0.35
336 38 0.16
337 22 0.09
338 9 0.04
339 16 0.07
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (338 bp):
ATTTGAACTAACCAATACCAAACACTTGCAAAATAAAAAGTGATATTGATAAAAATTACAAAAGT
GCAAATATAATAAGTATCACGAAATTAAAATATATTAATTACATTGCAATTTACAGAACATTTAT
AAAAATTCATAATATTAGAAAAATAAATGGTATTGATAAAGAGTACAAGTATCTTTGTTAAGTAC
CTTGAAATCTTGAATATATTTAATCACACATTACATTTTACGAAGAACTTTTGTACTTCCATGAA
TATTAAACTTTAGTATGTTCTTAAAATAAATATTTGATCAATTAATTAAATTTACGTGTCCTTAT
TAGCCCTGGTAAG
Found at i:4845127 original size:51 final size:51
Alignment explanation
Indices: 4845072--4845172 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
4845062 AAACAAAAAA
**
4845072 AAAAAAGGTTCTAGAATAGAGCAAAGAAGGAAATAAACGAAGAAGACAAAG
1 AAAAAAGGTTCTAGAATAGAGCAAAGAAACAAATAAACGAAGAAGACAAAG
* *
4845123 AAAAAAGGTTCTAGAATAGAGCAAAGAAACAAATAAACTAAGCAGACAAA
1 AAAAAAGGTTCTAGAATAGAGCAAAGAAACAAATAAACGAAGAAGACAAA
4845173 AAGGAGGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.11
Consensus pattern (51 bp):
AAAAAAGGTTCTAGAATAGAGCAAAGAAACAAATAAACGAAGAAGACAAAG
Found at i:4845149 original size:26 final size:26
Alignment explanation
Indices: 4845072--4845151 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
4845062 AAACAAAAAA
4845072 AAAAAAGGTTCTAGAATAGAGCAAAG
1 AAAAAAGGTTCTAGAATAGAGCAAAG
* ** *
4845098 AAGGAAA---TAAACGAAGA-AGACAAAG
1 AA-AAAAGGTTCTA-GAATAGAG-CAAAG
4845123 AAAAAAGGTTCTAGAATAGAGCAAAG
1 AAAAAAGGTTCTAGAATAGAGCAAAG
4845149 AAA
1 AAA
4845152 CAAATAAACT
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
24 7 0.18
25 11 0.28
26 14 0.36
27 7 0.18
ACGTcount: A:0.59, C:0.07, G:0.23, T:0.11
Consensus pattern (26 bp):
AAAAAAGGTTCTAGAATAGAGCAAAG
Found at i:4881521 original size:2 final size:2
Alignment explanation
Indices: 4881514--4881541 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4881504 GACTTGGAAG
4881514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4881542 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4882685 original size:19 final size:20
Alignment explanation
Indices: 4882656--4882695 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4882646 GAGCTCAATG
*
4882656 AGCATAGCTCATTAAACCCA
1 AGCATAGCTCAATAAACCCA
*
4882676 AGCA-AGCTCAATAAAGCCA
1 AGCATAGCTCAATAAACCCA
4882695 A
1 A
4882696 ATTCAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.28, G:0.12, T:0.15
Consensus pattern (20 bp):
AGCATAGCTCAATAAACCCA
Found at i:4883044 original size:20 final size:20
Alignment explanation
Indices: 4883006--4883044 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4882996 TCATAATTGA
*
4883006 ATTCATCATGATAACTCAAT
1 ATTCATCATGATAAATCAAT
4883026 ATTCAATCATGA-AAATCAA
1 ATTC-ATCATGATAAATCAA
4883045 GAACAAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTCATCATGATAAATCAAT
Found at i:4891791 original size:10 final size:10
Alignment explanation
Indices: 4891776--4891801 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4891766 AATAAGAGAA
4891776 TCTCTCTGTC
1 TCTCTCTGTC
4891786 TCTCTCTGTC
1 TCTCTCTGTC
4891796 TCTCTC
1 TCTCTC
4891802 CTTAGCCTTC
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:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (10 bp):
TCTCTCTGTC
Found at i:4896617 original size:2 final size:2
Alignment explanation
Indices: 4896610--4896649 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
4896600 GCACAATAAT
* *
4896610 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4896650 CACAGACGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4897891 original size:29 final size:30
Alignment explanation
Indices: 4897859--4897922 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
4897849 TCGAATAAAA
4897859 AATTATAAAAAATA-ATTTT-TTATAAGTTT
1 AATTAT-AAAAATACATTTTATTATAAGTTT
* *
4897888 AATT-TAAAAATACTTTTTATTATAATTTT
1 AATTATAAAAATACATTTTATTATAAGTTT
4897917 AATTAT
1 AATTAT
4897923 TTTTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.23
28 5 0.17
29 17 0.57
30 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
AATTATAAAAATACATTTTATTATAAGTTT
Found at i:4897935 original size:11 final size:11
Alignment explanation
Indices: 4897913--4897947 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4897903 TTTATTATAA
4897913 TTTTAATT-AT
1 TTTTAATTAAT
4897923 TTTTAATTAAT
1 TTTTAATTAAT
4897934 TTTTAATATAAT
1 TTTTAAT-TAAT
4897946 TT
1 TT
4897948 AACAACAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 9 0.39
12 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:4898476 original size:23 final size:23
Alignment explanation
Indices: 4898443--4898487 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4898433 ATAATGTCCA
*
4898443 AGTCACACAATGCCTTGCTTACC
1 AGTCACACAATGCCTTACTTACC
* *
4898466 AGTCACGCAATGTCTTACTTAC
1 AGTCACACAATGCCTTACTTAC
4898488 TAATCACGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (23 bp):
AGTCACACAATGCCTTACTTACC
Found at i:4898494 original size:23 final size:23
Alignment explanation
Indices: 4898440--4898495 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
4898430 TAGATAATGT
* *
4898440 CCAAGTCACACAATGCCTTGCTTA
1 CCAA-TCACGCAATGCCTTACTTA
* *
4898464 CCAGTCACGCAATGTCTTACTTA
1 CCAATCACGCAATGCCTTACTTA
*
4898487 CTAATCACG
1 CCAATCACG
4898496 TAATACCATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (23 bp):
CCAATCACGCAATGCCTTACTTA
Found at i:4898550 original size:22 final size:22
Alignment explanation
Indices: 4898519--4898576 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4898509 ACCAGTCACG
* *
4898519 TAATGGCTAAAAATTAGTAACA
1 TAATGTCTAAAAACTAGTAACA
* *
4898541 TAATGTCTAAAAACTAGTCACG
1 TAATGTCTAAAAACTAGTAACA
*
4898563 TAATGTCAAAAAAC
1 TAATGTCTAAAAAC
4898577 AAATTACACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (22 bp):
TAATGTCTAAAAACTAGTAACA
Found at i:4898769 original size:19 final size:21
Alignment explanation
Indices: 4898726--4898769 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
4898716 TTCATATATA
* *
4898726 AAAAATCACTCCAAAATGCTT
1 AAAAATCACTCCAAAACGCTC
4898747 AAAAAT-ACT-CAAAACGCTC
1 AAAAATCACTCCAAAACGCTC
4898766 AAAA
1 AAAA
4898770 GTTTTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 3 0.14
21 6 0.29
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAATCACTCCAAAACGCTC
Found at i:4920826 original size:2 final size:2
Alignment explanation
Indices: 4920819--4920844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4920809 TGATTTTATG
4920819 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4920845 GAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4938805 original size:2 final size:2
Alignment explanation
Indices: 4938800--4938847 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
4938790 AGAAAAGATC
*
4938800 GA GA GA GA GA GA GA GA GA GA G- GA G- GA G- GA G- GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
4938838 GA GG GA GA GA
1 GA GA GA GA GA
4938848 AGGGTGGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4941375 original size:4 final size:4
Alignment explanation
Indices: 4941366--4941392 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4941356 TGAGTGTGTT
4941366 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
4941393 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:4945783 original size:2 final size:2
Alignment explanation
Indices: 4945778--4945802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4945768 ATATATATAT
4945778 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4945803 ATAGGAAATA
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:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4949451 original size:2 final size:2
Alignment explanation
Indices: 4949432--4949492 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
4949422 GGGTCCATAA
* * *
4949432 AT AT AA AT AT AA AT AT AT AT AT AA AT AGT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
4949475 AT AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT
4949493 TTTTTTCCTC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:4950687 original size:2 final size:2
Alignment explanation
Indices: 4950682--4950708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4950672 GTATATAGAG
4950682 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4950709 ATTCCATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4955834 original size:2 final size:2
Alignment explanation
Indices: 4955827--4955861 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4955817 ACATACATAC
4955827 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4955862 CTGTAGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4956678 original size:3 final size:3
Alignment explanation
Indices: 4956670--4956697 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4956660 AATTGCCATT
4956670 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
4956698 CAGTTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:4971348 original size:2 final size:2
Alignment explanation
Indices: 4971341--4971369 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4971331 TAGGGGCCAC
4971341 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
4971370 CATACAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:4979523 original size:4 final size:4
Alignment explanation
Indices: 4979516--4979541 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4979506 TGTGATAGAT
4979516 AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
4979542 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:4982860 original size:12 final size:11
Alignment explanation
Indices: 4982820--4982875 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
4982810 AATAATCCAA
4982820 AAAAAAAAAAG
1 AAAAAAAAAAG
* **
4982831 AAAAAGAAATT
1 AAAAAAAAAAG
*
4982842 ATAAAAAAAAG
1 AAAAAAAAAAG
*
4982853 AAACAAAAAAG
1 AAAAAAAAAAG
4982864 AAAAAGAAAAAG
1 AAAAA-AAAAAG
4982876 GAATATTACA
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
11 28 0.82
12 6 0.18
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:4988696 original size:24 final size:24
Alignment explanation
Indices: 4988669--4988716 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4988659 GTGTATCGAC
*
4988669 ATGTGTGCAGACGCTGGTTTGCTA
1 ATGTGTACAGACGCTGGTTTGCTA
* * *
4988693 ATGTTTACGGATGCTGGTTTGCTA
1 ATGTGTACAGACGCTGGTTTGCTA
4988717 CTTCGTTAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.38
Consensus pattern (24 bp):
ATGTGTACAGACGCTGGTTTGCTA
Found at i:5015279 original size:2 final size:2
Alignment explanation
Indices: 5015272--5015303 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5015262 TTTATACTGT
5015272 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5015304 TCATCTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5015368 original size:2 final size:2
Alignment explanation
Indices: 5015361--5015390 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5015351 TTTACGTAGT
5015361 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5015391 TCATCTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5025925 original size:31 final size:32
Alignment explanation
Indices: 5025889--5025958 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
5025879 ATCATGTTAA
* *
5025889 ACGTGTTGA-ACGTGTTATTAATCGTGT-CGTGT
1 ACGTGTT-ATACGTG-TATTAAACGTATACGTGT
5025921 -CGTGTTATACGTGTATTAAACGTATACGTGT
1 ACGTGTTATACGTGTATTAAACGTATACGTGT
5025952 ACGTGTT
1 ACGTGTT
5025959 TTAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 11 0.33
31 16 0.48
32 6 0.18
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (32 bp):
ACGTGTTATACGTGTATTAAACGTATACGTGT
Found at i:5026704 original size:40 final size:40
Alignment explanation
Indices: 5026620--5026696 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
5026610 TAAAATTTAC
* *
5026620 TATCACGTGACATTAATTTTACATGTAAATATAATAAACA
1 TATCACGTGACATGAATTTTACATGTAAAAATAATAAACA
* *
5026660 TATCATGTGACATGAATTTTGCATGTAAAAATAATAA
1 TATCACGTGACATGAATTTTACATGTAAAAATAATAA
5026697 TCTTATCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (40 bp):
TATCACGTGACATGAATTTTACATGTAAAAATAATAAACA
Found at i:5032656 original size:33 final size:33
Alignment explanation
Indices: 5032602--5032699 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
5032592 GCAGATGGGA
* * *
5032602 CAGATGAAAAGGTC-GAGGAAGTAGCTTCAGAGG
1 CAGATGAAAAGATCTCA-GAAGTGGCTTCAGAGG
* *
5032635 CAGATGGAAAGATTTCAGAAGTGGCTTCAGAGG
1 CAGATGAAAAGATCTCAGAAGTGGCTTCAGAGG
* *
5032668 CTGATGAAAAGATCTCAGAAGTGGCTTTAGAG
1 CAGATGAAAAGATCTCAGAAGTGGCTTCAGAG
5032700 ACCAATTTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (33 bp):
CAGATGAAAAGATCTCAGAAGTGGCTTCAGAGG
Found at i:5037636 original size:98 final size:99
Alignment explanation
Indices: 5037467--5037665 Score: 337
Period size: 98 Copynumber: 2.0 Consensus size: 99
5037457 TGACGCCACT
*
5037467 GCTCCAAGATTTTGATCCCTCCAAGGCTGATTTTGATTTTGATCTTTACCAAGTCATGGTAAGGC
1 GCTCCAAGATTTTGATCCCTCCAAGGCTCATTTTGATTTTGATCTTTACCAAGTCATGGTAAGGC
*
5037532 ATCCCAGACGGCCAGA-CCCAGATCCGACCACCC
66 ATCCCAGACGGCCAGACCCCAGAACCGACCACCC
** *
5037565 GCTCCAAGATTTTGATCTTTCCAAGGCTCATTTTGATTTTGATCTTTACCAAGTCATGGTCAGGC
1 GCTCCAAGATTTTGATCCCTCCAAGGCTCATTTTGATTTTGATCTTTACCAAGTCATGGTAAGGC
*
5037630 ATCCCAGACGGCCTGACCCCAGAACCGACCACCC
66 ATCCCAGACGGCCAGACCCCAGAACCGACCACCC
5037664 GC
1 GC
5037666 ACCCTTAACG
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 76 0.81
99 18 0.19
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (99 bp):
GCTCCAAGATTTTGATCCCTCCAAGGCTCATTTTGATTTTGATCTTTACCAAGTCATGGTAAGGC
ATCCCAGACGGCCAGACCCCAGAACCGACCACCC
Found at i:5039328 original size:2 final size:2
Alignment explanation
Indices: 5039321--5039346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5039311 CTTTCACATA
5039321 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5039347 TGGATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5040283 original size:9 final size:9
Alignment explanation
Indices: 5040269--5040302 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5040259 TTAACCATTG
5040269 TTTATTTAT
1 TTTATTTAT
5040278 TTTATTTAT
1 TTTATTTAT
*
5040287 TATTTTTTAT
1 T-TTATTTAT
5040297 TTTATT
1 TTTATT
5040303 AACAACTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:5041995 original size:19 final size:20
Alignment explanation
Indices: 5041958--5041996 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5041948 TAAATATGAA
* *
5041958 TTTTTATTTAATAATTATTG
1 TTTTTATTTAAAAAATATTG
5041978 TTTTTA-TTAAAAAATATTG
1 TTTTTATTTAAAAAATATTG
5041997 CGCTACTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTATTTAAAAAATATTG
Found at i:5043461 original size:44 final size:44
Alignment explanation
Indices: 5043394--5043477 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
5043384 TAGCGGTAAC
*
5043394 AGATATATTCAGGGTTATGACTTTTTGAGATAGAAATTTAGAAT
1 AGATATATTCAGGGTTATAACTTTTTGAGATAGAAATTTAGAAT
*
5043438 AGATATATTCAGGGTTCTAACTTTTTGAGATAGAAATTTA
1 AGATATATTCAGGGTTATAACTTTTTGAGATAGAAATTTA
5043478 AAAGTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (44 bp):
AGATATATTCAGGGTTATAACTTTTTGAGATAGAAATTTAGAAT
Found at i:5043803 original size:20 final size:19
Alignment explanation
Indices: 5043690--5043873 Score: 67
Period size: 21 Copynumber: 9.4 Consensus size: 19
5043680 TTTTTATTAT
*
5043690 ATATATTATTTAT-TTTTA
1 ATATATTATTTATAATTTA
* *
5043708 TTTTATT-TTTA-AATATTA
1 ATATATTATTTATAAT-TTA
* *
5043726 AT-TTTTATTTATAATCTA
1 ATATATTATTTATAATTTA
** *
5043744 ATATTAACATTATAAAATATTA
1 ATA-TATTATT-TATAAT-TTA
5043766 ATATATTATTTATAATTTA
1 ATATATTATTTATAATTTA
* *
5043785 A-ATATTATTATGATTATTTT
1 ATATATTATT-T-ATAATTTA
* * *
5043805 TTATTTTATTTTTTAATATTA
1 ATATATTA-TTTATAAT-TTA
**
5043826 ATA-ATTTATAAATAATTTA
1 ATATA-TTATTTATAATTTA
*
5043845 AAATATTAATTTGGATAATTTA
1 ATATATT-ATTT--ATAATTTA
5043867 A-ATATTA
1 ATATATTA
5043874 GTATTTTATT
Statistics
Matches: 119, Mismatches: 29, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
17 8 0.07
18 25 0.21
19 15 0.13
20 27 0.23
21 28 0.24
22 16 0.13
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATATTATTTATAATTTA
Found at i:5044209 original size:13 final size:14
Alignment explanation
Indices: 5044191--5044238 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5044181 ATTTTTTTAT
5044191 TTTTTAACTT-ATA
1 TTTTTAACTTAATA
5044204 TTTTT-ACTTAATA
1 TTTTTAACTTAATA
* *
5044217 GTTTTAAAATTAATA
1 -TTTTTAACTTAATA
5044232 TTTTTAA
1 TTTTTAA
5044239 AAGATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 4 0.14
13 8 0.28
14 10 0.34
15 7 0.24
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTTAACTTAATA
Found at i:5044231 original size:15 final size:15
Alignment explanation
Indices: 5044211--5044253 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
5044201 ATATTTTTAC
5044211 TTAATAGTTTTAAA-A
1 TTAATA-TTTTAAAGA
5044226 TTAATATTTTTAAAAGA
1 TTAATA-TTTT-AAAGA
5044243 TTAATATTTTA
1 TTAATATTTTA
5044254 TTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 7 0.28
17 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAATATTTTAAAGA
Found at i:5044247 original size:17 final size:15
Alignment explanation
Indices: 5044211--5044252 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
5044201 ATATTTTTAC
*
5044211 TTAATAGTTTTAAAA
1 TTAATATTTTTAAAA
5044226 TTAATATTTTTAAAAGA
1 TTAATATTTTT-AAA-A
5044243 TTAATATTTT
1 TTAATATTTT
5044253 ATTTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 3 0.12
17 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
TTAATATTTTTAAAA
Found at i:5044268 original size:20 final size:20
Alignment explanation
Indices: 5044245--5044307 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
5044235 TTAAAAGATT
5044245 AATATTTTATTTATAATTTA
1 AATATTTTATTTATAATTTA
5044265 AATA--TTA-TTATAATTTA
1 AATATTTTATTTATAATTTA
5044282 AATATTATT-TTT-TAATTTAA
1 AATATT-TTATTTATAATTT-A
5044302 AATATT
1 AATATT
5044308 AATTTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 14 0.37
18 3 0.08
19 6 0.16
20 15 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTATTTATAATTTA
Found at i:5044308 original size:20 final size:19
Alignment explanation
Indices: 5044245--5044313 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 19
5044235 TTAAAAGATT
5044245 AATATT-TTATTTATAATTTA
1 AATATTATT-TTT-TAATTTA
*
5044265 AATATTA--TTATAATTTA
1 AATATTATTTTTTAATTTA
5044282 AATATTATTTTTTAATTTAA
1 AATATTATTTTTTAATTT-A
5044302 AATATTAATTTT
1 AATATT-ATTTT
5044314 ATAAGTTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 14 0.33
18 2 0.05
19 8 0.19
20 13 0.31
21 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTTTAATTTA
Found at i:5048546 original size:25 final size:25
Alignment explanation
Indices: 5048518--5048568 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5048508 TAATTACATG
5048518 TCTTTTACTTT-GTCGTTATTTAGTT
1 TCTTTTA-TTTAGTCGTTATTTAGTT
* *
5048543 TCTTTTATTTAGTGGTTATTTGGTT
1 TCTTTTATTTAGTCGTTATTTAGTT
5048568 T
1 T
5048569 TAATGTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.65
Consensus pattern (25 bp):
TCTTTTATTTAGTCGTTATTTAGTT
Found at i:5048714 original size:17 final size:17
Alignment explanation
Indices: 5048692--5048725 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5048682 ATTGAGACAT
5048692 GGAATAAAGATTCTGTA
1 GGAATAAAGATTCTGTA
5048709 GGAATAAAGATTCTGTA
1 GGAATAAAGATTCTGTA
5048726 AAATCAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (17 bp):
GGAATAAAGATTCTGTA
Found at i:5049217 original size:14 final size:15
Alignment explanation
Indices: 5049198--5049226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5049188 ATCGGCCCAT
5049198 GAAAAA-GAAAAAAA
1 GAAAAAGGAAAAAAA
5049212 GAAAAAGGAAAAAAA
1 GAAAAAGGAAAAAAA
5049227 ATAGAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAGGAAAAAAA
Found at i:5051311 original size:25 final size:25
Alignment explanation
Indices: 5051272--5051319 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5051262 TTACATGTCT
*
5051272 TTTATTTTGTCGTTATTTAGTTTCC
1 TTTATTTGGTCGTTATTTAGTTTCC
*
5051297 TTTATTTGGTGGTTATTTAGTTT
1 TTTATTTGGTCGTTATTTAGTTT
5051320 TTCATGTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.17, T:0.65
Consensus pattern (25 bp):
TTTATTTGGTCGTTATTTAGTTTCC
Found at i:5052243 original size:16 final size:15
Alignment explanation
Indices: 5052208--5052259 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
5052198 GCTAACATGA
* *
5052208 AAATCAAATAACTACC
1 AAATAAAATAAC-ACT
5052224 AAATAAAATAACCACT
1 AAATAAAATAA-CACT
*
5052240 AAATAAAAGAA-ACT
1 AAATAAAATAACACT
5052254 AAATAA
1 AAATAA
5052260 CCACAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.28
16 22 0.69
17 1 0.03
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.17
Consensus pattern (15 bp):
AAATAAAATAACACT
Found at i:5056780 original size:7 final size:7
Alignment explanation
Indices: 5056768--5056805 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5056758 TTTTGGTTAT
5056768 TTATTTA
1 TTATTTA
5056775 TTATTTA
1 TTATTTA
5056782 TTA-TTA
1 TTATTTA
5056788 TTTATTTA
1 -TTATTTA
5056796 TTATTT-
1 TTATTTA
5056802 TTAT
1 TTAT
5056806 ATATACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 7 0.24
7 19 0.66
8 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:5056790 original size:21 final size:20
Alignment explanation
Indices: 5056764--5056805 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
5056754 AAAATTTTGG
5056764 TTATTTATTTATTATTTATTA
1 TTATTTATTTATTATTT-TTA
5056785 TTATTTATTTATTATTTTTA
1 TTATTTATTTATTATTTTTA
5056805 T
1 T
5056806 ATATACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTATTTATTATTTTTA
Found at i:5057165 original size:17 final size:18
Alignment explanation
Indices: 5057137--5057182 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
5057127 TTTTCTTCCA
5057137 ATTATATTATTTATTATT
1 ATTATATTATTTATTATT
*
5057155 ATTAT-TTATTTATTTTT
1 ATTATATTATTTATTATT
*
5057172 ATTTTATTATT
1 ATTATATTATT
5057183 ATCTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTATATTATTTATTATT
Found at i:5057173 original size:14 final size:14
Alignment explanation
Indices: 5057143--5057224 Score: 53
Period size: 15 Copynumber: 5.6 Consensus size: 14
5057133 TCCAATTATA
*
5057143 TTATTTA-TTATTA
1 TTATTTATTTATTT
5057156 TTATTTATTTATTT
1 TTATTTATTTATTT
5057170 TTATTTTATTATTATCTT
1 TTA-TTTA-T-TTAT-TT
*
5057188 TTAATTT-TCATATTT
1 TT-ATTTAT-TTATTT
*
5057203 TATATTTTTTTATTT
1 T-TATTTATTTATTT
5057218 TT-TTTAT
1 TTATTTAT
5057225 CTTAATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
13 11 0.20
14 9 0.16
15 17 0.30
16 7 0.12
17 4 0.07
18 7 0.12
19 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTTATTT
Found at i:5057184 original size:17 final size:17
Alignment explanation
Indices: 5057141--5057224 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 17
5057131 CTTCCAATTA
5057141 TATTATTTATTATTATTATT
1 TATTATTT-TTATT-TTA-T
5057161 TATTTATTTTTATTTTAT
1 TA-TTATTTTTATTTTAT
*
5057179 TATTATCTTTTAATTT-T
1 TATTAT-TTTTATTTTAT
* *
5057196 CA-TATTTTATATTTTTT
1 TATTATTTT-TATTTTAT
*
5057213 TATTTTTTTTAT
1 TATTATTTTTAT
5057225 CTTAATATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
15 3 0.06
16 8 0.15
17 11 0.20
18 16 0.30
19 3 0.06
20 7 0.13
21 6 0.11
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTATTTTTATTTTAT
Found at i:5057235 original size:5 final size:5
Alignment explanation
Indices: 5057227--5057259 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
5057217 TTTTTTATCT
5057227 TAATA TAATA TAATA TAATA TAATA TATATA TA
1 TAATA TAATA TAATA TAATA TAATA TA-ATA TA
5057260 TTTGCATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:5057893 original size:37 final size:36
Alignment explanation
Indices: 5057843--5057921 Score: 122
Period size: 37 Copynumber: 2.2 Consensus size: 36
5057833 CCCATCGGCC
5057843 TCTCTCTCTCTTCGCTCAGATCTGAACCTTCCGTCGG
1 TCTCTCTCTCTTCGCTCAGATCT-AACCTTCCGTCGG
**
5057880 TCTCTCTCTCTTCGCTCAGATCTCCCCTTCCGTCGG
1 TCTCTCTCTCTTCGCTCAGATCTAACCTTCCGTCGG
*
5057916 CCTCTC
1 TCTCTC
5057922 CCTTTTCTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 16 0.41
37 23 0.59
ACGTcount: A:0.08, C:0.43, G:0.14, T:0.35
Consensus pattern (36 bp):
TCTCTCTCTCTTCGCTCAGATCTAACCTTCCGTCGG
Found at i:5057938 original size:36 final size:36
Alignment explanation
Indices: 5057837--5057944 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 36
5057827 CCTATTCCCA
* *
5057837 TCGGCCTCTCTCTCTCTTCGCTCAGATCTGAACCTTCCG
1 TCGGCCTCTC-C-CTCTTCGCCCAGATCT-CACCTTCCG
* * * *
5057876 TCGGTCTCTCTCTCTTCGCTCAGATCTCCCCTTCCG
1 TCGGCCTCTCCCTCTTCGCCCAGATCTCACCTTCCG
* * *
5057912 TCGGCCTCTCCCTTTTCTCCCGGATCTCACCTT
1 TCGGCCTCTCCCTCTTCGCCCAGATCTCACCTT
5057945 TTTCTCCTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 33 0.57
37 16 0.28
39 9 0.16
ACGTcount: A:0.07, C:0.44, G:0.14, T:0.35
Consensus pattern (36 bp):
TCGGCCTCTCCCTCTTCGCCCAGATCTCACCTTCCG
Found at i:5058181 original size:9 final size:9
Alignment explanation
Indices: 5058159--5058209 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
5058149 AGCCATCCCG
*
5058159 ATTTTTTTT
1 ATTTTATTT
5058168 A-TTTATTT
1 ATTTTATTT
5058176 ATTTTATTT
1 ATTTTATTT
5058185 AATTTATATTT
1 -ATTT-TATTT
*
5058196 ATATTAATTT
1 AT-TTTATTT
5058206 ATTT
1 ATTT
5058210 AAGTGTCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 10 0.28
10 12 0.33
11 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:5058205 original size:10 final size:9
Alignment explanation
Indices: 5058165--5058211 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
5058155 CCCGATTTTT
5058165 TTTATTT-A
1 TTTATTTAA
*
5058173 TTTATTTTA
1 TTTATTTAA
5058182 TTTAATTTATA
1 TTT-ATTTA-A
5058193 TTTATATTAA
1 TTTAT-TTAA
5058203 TTTATTTAA
1 TTTATTTAA
5058212 GTGTCTACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 7 0.21
9 8 0.24
10 12 0.35
11 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTTAA
Found at i:5064255 original size:45 final size:45
Alignment explanation
Indices: 5064206--5064296 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
5064196 GAAAATGAGT
*
5064206 GGGAAAAGTCAAATGTTTTCCTGCAGAGAAAGAACAAAAAGAAAA
1 GGGAAAAGTCAAACGTTTTCCTGCAGAGAAAGAACAAAAAGAAAA
5064251 GGGAAAAGTCAAACGTTTTCCTGCAGAGAAAGAACAAAAAGAAAA
1 GGGAAAAGTCAAACGTTTTCCTGCAGAGAAAGAACAAAAAGAAAA
5064296 G
1 G
5064297 TAATGGAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (45 bp):
GGGAAAAGTCAAACGTTTTCCTGCAGAGAAAGAACAAAAAGAAAA
Found at i:5070287 original size:23 final size:23
Alignment explanation
Indices: 5070256--5070303 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5070246 GAGAGAAAGA
* * *
5070256 TTGATAAAGAATATTAATTTTTT
1 TTGAGAAAGAATAGTAATATTTT
5070279 TTGAGAAAGAATAGTAATATTTT
1 TTGAGAAAGAATAGTAATATTTT
5070302 TT
1 TT
5070304 AATGAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (23 bp):
TTGAGAAAGAATAGTAATATTTT
Found at i:5071385 original size:220 final size:215
Alignment explanation
Indices: 5070895--5071385 Score: 591
Period size: 220 Copynumber: 2.2 Consensus size: 215
5070885 AATTGTATAA
*
5070895 ATAT-TATATATATATTTAATTTATACATAAGTANTTACTATA-ACTTATAATAAACTTTATTTA
1 ATATATATATATATATTTAATTTATACATAATTA-TTA-TATATACTTATAATAAACTTTATTTA
* * * *
5070958 TTTGATTACACTTAATAACCTTATTAATTATCACCCAAGTTTTTATAATATATTTTTTATAATTA
64 TATGATTACACTTAATAACCTTATTAATTATCACCCAAGATTTTATAACATATTGTTTATAATTA
* *
5071023 GTTATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTGTGACATTAGTTTCATA
129 GTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTGTGACATTAATTTCATA
5071088 TATGCATAATAAAGTAATATATT
194 TAT-CATAATAAAGTAATATATT
* * * * *
5071111 ATATATAGATACATATATTTAATTTTTATATATCAGTATTAT-TGTAACTTATAATAAACTTTAT
1 ATATAT--ATATATATATTTAA--TTTATACATAATTATTATATAT-ACTTATAATAAACTTTAT
** * **
5071175 TTATATGATTACACTTAATAATTTTATTAGTTATCACTTTAA-ATTTTATAACATATTGTTTATA
61 TTATATGATTACACTTAATAACCTTATTAATTATCAC-CCAAGATTTTATAACATATTGTTTATA
*
5071239 ATTAGTTATTATTTATACAAACTTTGATATAAAAATTACAATATTATAACATATAAGTTGTGTCA
125 ATTAGTTATTATTTATACAAACTTTGATAT--AAA--AC---ATTATAACATATAAGTTGTGACA
*
5071304 TTAATTTCATATAT-ATAATAAGGT-A-ATATT
183 TTAATTTCATATATCATAATAAAGTAATATATT
* *
5071334 ATATATATATATATATTTAATTTATACATAATTTTTATATATATTTTATAAT
1 ATATATATATATATATTTAATTTATACATAATTATTATATATA-CTTATAAT
5071386 TATGGATGAA
Statistics
Matches: 234, Mismatches: 24, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
216 4 0.02
217 1 0.00
218 1 0.00
219 29 0.12
220 111 0.47
221 27 0.12
222 3 0.01
223 11 0.05
224 3 0.01
225 9 0.04
227 35 0.15
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (215 bp):
ATATATATATATATATTTAATTTATACATAATTATTATATATACTTATAATAAACTTTATTTATA
TGATTACACTTAATAACCTTATTAATTATCACCCAAGATTTTATAACATATTGTTTATAATTAGT
TATTATTTATACAAACTTTGATATAAAACATTATAACATATAAGTTGTGACATTAATTTCATATA
TCATAATAAAGTAATATATT
Found at i:5075517 original size:10 final size:9
Alignment explanation
Indices: 5075502--5075549 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 9
5075492 TTAAACACAA
5075502 TAACACGAT
1 TAACACGAT
5075511 TAGACACGA-
1 TA-ACACGAT
5075520 TAACACGAT
1 TAACACGAT
5075529 TAAACACGA-
1 T-AACACGAT
*
5075538 TAACATGAT
1 TAACACGAT
5075547 TAA
1 TAA
5075550 ATAAACGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 12 0.35
9 9 0.26
10 13 0.38
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (9 bp):
TAACACGAT
Found at i:5075517 original size:18 final size:18
Alignment explanation
Indices: 5075486--5075550 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
5075476 TATCGCGTAT
* *
5075486 ACACGTTTAAACACAATA
1 ACACGATTAAACACGATA
*
5075504 ACACGATTAGACACGATA
1 ACACGATTAAACACGATA
5075522 ACACGATTAAACACGATA
1 ACACGATTAAACACGATA
*
5075540 ACATGATTAAA
1 ACACGATTAAA
5075551 TAAACGTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:5075525 original size:8 final size:8
Alignment explanation
Indices: 5075495--5075542 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
5075485 TACACGTTTA
*
5075495 AACACAAT
1 AACACGAT
5075503 AACACGATT
1 AACACGA-T
5075512 AGACACGAT
1 A-ACACGAT
5075521 AACACGATT
1 AACACGA-T
5075530 AAACACGAT
1 -AACACGAT
5075539 AACA
1 AACA
5075543 TGATTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 16 0.46
9 6 0.17
10 13 0.37
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.15
Consensus pattern (8 bp):
AACACGAT
Found at i:5085827 original size:106 final size:106
Alignment explanation
Indices: 5085642--5085854 Score: 381
Period size: 106 Copynumber: 2.0 Consensus size: 106
5085632 TATTGTTTAA
* *
5085642 TTACATGAATGGACATTTTTAATTTTCTGAAGTCGTAAGGAATATGATGCTCGGTTGATTTACTA
1 TTACATGAATGGACATTTTTAATTTTCTAAAGTCCTAAGGAATATGATGCTCGGTTGATTTACTA
*
5085707 GGAGTTCCATAATAGGGCTTCTAGAGCTACAATCTTCTTGT
66 GGAGTTCCATAATAGGGCGTCTAGAGCTACAATCTTCTTGT
*
5085748 TTACATGAATGGACTTTTTTAATTTTCTAAAGTCCTAAGGAATATGATGCTCGGTTGATTTACTA
1 TTACATGAATGGACATTTTTAATTTTCTAAAGTCCTAAGGAATATGATGCTCGGTTGATTTACTA
*
5085813 GGAGTTCCATAATAGGGCGTCTAGAGCTTCAATCTTCTTGT
66 GGAGTTCCATAATAGGGCGTCTAGAGCTACAATCTTCTTGT
5085854 T
1 T
5085855 CTGTGTATCG
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (106 bp):
TTACATGAATGGACATTTTTAATTTTCTAAAGTCCTAAGGAATATGATGCTCGGTTGATTTACTA
GGAGTTCCATAATAGGGCGTCTAGAGCTACAATCTTCTTGT
Found at i:5087983 original size:2 final size:2
Alignment explanation
Indices: 5087976--5088000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5087966 CTCTTAGTAA
5087976 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5088001 TACTTTTCAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5096781 original size:31 final size:32
Alignment explanation
Indices: 5096744--5096813 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
5096734 ATTATTAAAC
*
5096744 AAAATAGTGAATAAAAGTAAAAAGAG-AATTA
1 AAAATAGTGAATAAAAGTAAAAAAAGAAATTA
5096775 AAAATAGTGAATAAAAGTAAAAAAAGAAATTA
1 AAAATAGTGAATAAAAGTAAAAAAAGAAATTA
5096807 AATAATA
1 AA-AATA
5096814 ATTATAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 25 0.69
32 7 0.19
33 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (32 bp):
AAAATAGTGAATAAAAGTAAAAAAAGAAATTA
Found at i:5099120 original size:22 final size:22
Alignment explanation
Indices: 5099077--5099121 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5099067 TTGATTCGAT
*
5099077 TTTAATTATTATTAAATATAAA
1 TTTAATTAATATTAAATATAAA
*
5099099 TTTAATTAAT-TTAATTATTAAA
1 TTTAATTAATATTAAATA-TAAA
5099121 T
1 T
5099122 ATTTAAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTAATATTAAATATAAA
Found at i:5100000 original size:6 final size:7
Alignment explanation
Indices: 5099983--5100008 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5099973 TTTTATACAC
5099983 AAAAAAT
1 AAAAAAT
5099990 AAAAAAT
1 AAAAAAT
5099997 AAAAAAT
1 AAAAAAT
5100004 AAAAA
1 AAAAA
5100009 GAAAGTCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:5104320 original size:2 final size:2
Alignment explanation
Indices: 5104313--5104350 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5104303 TAAGTTAAGC
5104313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5104351 ATTTGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5104733 original size:24 final size:26
Alignment explanation
Indices: 5104674--5104733 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
5104664 TTTTACTTTT
**
5104674 TTATATAATTTTAAAAAATATTTTAAA
1 TTAT-TAATTTTAAAAAATATAATAAA
5104701 TTATT--TTTTAAAAAATA-AATAAA
1 TTATTAATTTTAAAAAATATAATAAA
5104724 TT-TTAATTTT
1 TTATTAATTTT
5104734 TTATTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 2 0.07
23 6 0.21
24 16 0.55
26 1 0.03
27 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATTAATTTTAAAAAATATAATAAA
Found at i:5104955 original size:11 final size:10
Alignment explanation
Indices: 5104931--5104964 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5104921 AATAATATTT
5104931 TAATTAATAA
1 TAATTAATAA
5104941 TAATTAATCAA
1 TAATTAAT-AA
*
5104952 TAATTAATTA
1 TAATTAATAA
5104962 TAA
1 TAA
5104965 AAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAATAA
Found at i:5111496 original size:11 final size:11
Alignment explanation
Indices: 5111480--5111504 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5111470 ATCTTATAGA
5111480 TTGTTTACTGC
1 TTGTTTACTGC
5111491 TTGTTTACTGC
1 TTGTTTACTGC
5111502 TTG
1 TTG
5111505 CCTTTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (11 bp):
TTGTTTACTGC
Found at i:5115222 original size:12 final size:12
Alignment explanation
Indices: 5115186--5115222 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5115176 AATTAAAGTA
5115186 ATTATATATATT
1 ATTATATATATT
*
5115198 A--ATATATAAT
1 ATTATATATATT
5115208 ATTATATATATT
1 ATTATATATATT
5115220 ATT
1 ATT
5115223 TTTAAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATATATATT
Found at i:5116543 original size:18 final size:18
Alignment explanation
Indices: 5116516--5116554 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5116506 ACACAATTAA
5116516 TAACACGTTTAA-ATCGAT
1 TAACACGTTTAACA-CGAT
*
5116534 TAACATGTTTAACACGAT
1 TAACACGTTTAACACGAT
5116552 TAA
1 TAA
5116555 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:5116924 original size:31 final size:31
Alignment explanation
Indices: 5116889--5116947 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5116879 CGTTAGATAC
5116889 GAAAATTTTGGTATCTTAACGTGTCAGACAT
1 GAAAATTTTGGTATCTTAACGTGTCAGACAT
* *
5116920 GAAAATTTTTGTGTCTTAACGTGTCAGA
1 GAAAATTTTGGTATCTTAACGTGTCAGA
5116948 TACGATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (31 bp):
GAAAATTTTGGTATCTTAACGTGTCAGACAT
Found at i:5122803 original size:18 final size:18
Alignment explanation
Indices: 5122782--5122818 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5122772 TTAATTTGCT
5122782 AATTTAATATAA-TATATA
1 AATTT-ATATAATTATATA
5122800 AATTTATATAATTATATA
1 AATTTATATAATTATATA
5122818 A
1 A
5122819 CAAACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTATATAATTATATA
Found at i:5130725 original size:2 final size:2
Alignment explanation
Indices: 5130718--5130757 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5130708 CAACTTTTAA
* *
5130718 AT AT AT AT AA AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5130758 GAAATTGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5130757 original size:10 final size:10
Alignment explanation
Indices: 5130715--5130756 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
5130705 TATCAACTTT
5130715 TAAATATATA
1 TAAATATATA
5130725 TAAATATATA
1 TAAATATATA
5130735 TAAATATATA
1 TAAATATATA
*
5130745 TATATATATA
1 TAAATATATA
5130755 TA
1 TA
5130757 TGAAATTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TAAATATATA
Found at i:5132427 original size:25 final size:25
Alignment explanation
Indices: 5132399--5132447 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5132389 AATTACATGT
* *
5132399 TTTTACTTTGTAGTTATTTGGTTTC
1 TTTTACTTGGTAGTTATTTAGTTTC
*
5132424 TTTTACTTGGTGGTTATTTAGTTT
1 TTTTACTTGGTAGTTATTTAGTTT
5132448 TTCATGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.18, T:0.63
Consensus pattern (25 bp):
TTTTACTTGGTAGTTATTTAGTTTC
Found at i:5141680 original size:14 final size:14
Alignment explanation
Indices: 5141661--5141691 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5141651 TTTCCAAATC
5141661 TTGAATGCCACACT
1 TTGAATGCCACACT
5141675 TTGAATGCCACACT
1 TTGAATGCCACACT
5141689 TTG
1 TTG
5141692 TTCAGACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (14 bp):
TTGAATGCCACACT
Found at i:5147543 original size:8 final size:8
Alignment explanation
Indices: 5147530--5147554 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5147520 CATAAGCAAC
5147530 CTTGCTAA
1 CTTGCTAA
5147538 CTTGCTAA
1 CTTGCTAA
5147546 CTTGCTAA
1 CTTGCTAA
5147554 C
1 C
5147555 CTTCCAGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (8 bp):
CTTGCTAA
Done.