Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 170 of 207
Found at i:52547840 original size:90 final size:87
Alignment explanation
Indices: 52547645--52547943 Score: 223
Period size: 87 Copynumber: 3.4 Consensus size: 87
52547635 AAACAGTTGG
** * *
52547645 AATAAATCTTAAAACAGATTTTATTTAA-TTTAATTTCTCGTTTTTGGCAACAAAATCAAAATGT
1 AATAAATCCCAAAACAGATTTTATTTAATTTTAATTACTCGTTTTTGGAAACAAAATCAAAATGT
*
52547709 AATAAATCCGTTGAACGGTGGA
66 AATAAATCCGTTGAACGGCGGA
* * *
52547731 AATAAATCCCGAAACAGATTTTATTTTAATTTTAA-TACTCGTTTTTTGGAAATAAAATCAATAT
1 AATAAATCCCAAAACAGATTTTA-TTTAATTTTAATTACTCG-TTTTTGGAAACAAAATCAAAAT
** *
52547795 -TAGAATAAAATTTGTTGAACGGCGGG
64 GT--AAT-AAATCCGTTGAACGGCGGA
* * * * * * * * *
52547821 AGTAAATCCCAAAATAGATTTTAGTTAAATTTAATTTCCCG--TTCGGAAATAAAATAAAAAATG
1 AATAAATCCCAAAACAGATTTTATTTAATTTTAATTACTCGTTTTTGGAAACAAAAT-CAAAATG
* * * *
52547884 GAATAAAATCCATTAAACAGC-GA
65 TAAT-AAATCCGTTGAACGGCGGA
** ** *
52547907 GAATAAATCCTGAAATGGATTTTATTTACTTTTAATT
1 -AATAAATCCCAAAACAGATTTTATTTAATTTTAATT
52547944 TGAAAAAAAA
Statistics
Matches: 168, Mismatches: 35, Indels: 19
0.76 0.16 0.09
Matches are distributed among these distances:
86 21 0.12
87 68 0.40
88 28 0.17
89 12 0.07
90 39 0.23
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (87 bp):
AATAAATCCCAAAACAGATTTTATTTAATTTTAATTACTCGTTTTTGGAAACAAAATCAAAATGT
AATAAATCCGTTGAACGGCGGA
Found at i:52547955 original size:73 final size:73
Alignment explanation
Indices: 52547876--52548015 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
52547866 GAAATAAAAT
* * ***
52547876 AAAAAATGGAATAAAATCCATTAAAC-AGCGAGAATAAATCCTGAAATGGATTTTATTTACTTTT
1 AAAAAATCGAATAAAATCCATTAAACGA-CGAGAATAAATCCCGAAACAAATTTTATTTACTTTT
52547940 AATTTGAAA
65 AATTTGAAA
* * *
52547949 AAAAAATCGAATAAAATCTATTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAGTTTTA
1 AAAAAATCGAATAAAATCCATTAAACGACGAGAATAAATCCCGAAACAAATTTTATTTACTTTTA
52548014 AT
66 AT
52548016 ATTCTTTTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 57 0.98
74 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (73 bp):
AAAAAATCGAATAAAATCCATTAAACGACGAGAATAAATCCCGAAACAAATTTTATTTACTTTTA
ATTTGAAA
Found at i:52551050 original size:21 final size:21
Alignment explanation
Indices: 52551024--52551076 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
52551014 AGCGGTGGCG
*
52551024 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
*
52551045 GTGAGATTAGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
52551066 GTGAGATTAGA
1 GTGAGATTAGA
52551077 AACAATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:52558572 original size:20 final size:22
Alignment explanation
Indices: 52558547--52558592 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
52558537 GCCGAGACAT
52558547 TTGAGTA-AAGAAACAAG-CGG
1 TTGAGTACAAGAAACAAGTCGG
*
52558567 TTGAGTACAGGAAACAAGTCGG
1 TTGAGTACAAGAAACAAGTCGG
52558589 TTGA
1 TTGA
52558593 TTTCAACTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 7 0.30
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (22 bp):
TTGAGTACAAGAAACAAGTCGG
Found at i:52560443 original size:20 final size:21
Alignment explanation
Indices: 52560420--52560460 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
52560410 TAAATTTCTC
*
52560420 CAAAATATTT-TCTAAGTATT
1 CAAAATATTTATCAAAGTATT
*
52560440 CAAAGTATTTATCAAAGTATT
1 CAAAATATTTATCAAAGTATT
52560461 TGGAGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
CAAAATATTTATCAAAGTATT
Found at i:52568324 original size:14 final size:14
Alignment explanation
Indices: 52568305--52568366 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
52568295 AACATGCAAG
52568305 AAAATA-AAGAAAAT
1 AAAATATAA-AAAAT
*
52568319 AAAATATAAAATAT
1 AAAATATAAAAAAT
52568333 AAAATATATAACAGAAT
1 AAAATATA-AA-A-AAT
52568350 AAAA-AT-AAAAAT
1 AAAATATAAAAAAT
52568362 AAAAT
1 AAAAT
52568367 TAGTTTGCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 7 0.17
13 1 0.02
14 20 0.49
15 4 0.10
16 3 0.07
17 6 0.15
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATATAAAAAAT
Found at i:52568329 original size:7 final size:7
Alignment explanation
Indices: 52568317--52568366 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
52568307 AATAAAGAAA
52568317 ATAAAAT
1 ATAAAAT
52568324 ATAAAAT
1 ATAAAAT
52568331 ATAAAAT
1 ATAAAAT
*
52568338 ATATAACAGA
1 ATA-AA-A-T
52568348 ATAAAA-
1 ATAAAAT
52568354 ATAAAA-
1 ATAAAAT
52568360 ATAAAAT
1 ATAAAAT
52568367 TAGTTTGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 12 0.32
7 17 0.45
8 3 0.08
9 3 0.08
10 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (7 bp):
ATAAAAT
Found at i:52575228 original size:13 final size:13
Alignment explanation
Indices: 52575210--52575270 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
52575200 CTAGTTTAGC
52575210 AATGCTTTTAAAA
1 AATGCTTTTAAAA
52575223 AATGCTTTTAAAA
1 AATGCTTTTAAAA
* *
52575236 AATACTTTTGAAA
1 AATGCTTTTAAAA
* * **
52575249 AGTGCTGTGGAAA
1 AATGCTTTTAAAA
52575262 AATGCTTTT
1 AATGCTTTT
52575271 GAGAAGTACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGCTTTTAAAA
Found at i:52575282 original size:13 final size:13
Alignment explanation
Indices: 52575227--52575290 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
52575217 TTAAAAAATG
* *
52575227 CTTTTAAAAAATA
1 CTTTTGAAAAGTA
*
52575240 CTTTTGAAAAGTG
1 CTTTTGAAAAGTA
* * * *
52575253 CTGTGGAAAAATG
1 CTTTTGAAAAGTA
*
52575266 CTTTTGAGAAGTA
1 CTTTTGAAAAGTA
52575279 CTTTTGAAAAGT
1 CTTTTGAAAAGT
52575291 TTGGTTTAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:52575287 original size:26 final size:26
Alignment explanation
Indices: 52575227--52575288 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
52575217 TTAAAAAATG
* *
52575227 CTTTTAAAAAATACTTTTGAAAAGTG
1 CTTTTGAAAAATACTTTTGAAAAGTA
* * * *
52575253 CTGTGGAAAAATGCTTTTGAGAAGTA
1 CTTTTGAAAAATACTTTTGAAAAGTA
52575279 CTTTTGAAAA
1 CTTTTGAAAA
52575289 GTTTGGTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAATACTTTTGAAAAGTA
Found at i:52575782 original size:13 final size:13
Alignment explanation
Indices: 52575766--52575796 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52575756 TCCTTTTTAG
*
52575766 AAGTGCTTTTGAA
1 AAGTACTTTTGAA
52575779 AAGTACTTTTGAA
1 AAGTACTTTTGAA
52575792 AAGTA
1 AAGTA
52575797 GAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (13 bp):
AAGTACTTTTGAA
Found at i:52576915 original size:30 final size:31
Alignment explanation
Indices: 52576881--52576942 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
52576871 TCTGGTTTCA
*
52576881 TGCATGTAACGTAGG-TTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
*
52576911 TGCATGCAACGTGGGTTTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
52576942 T
1 T
52576943 AAACTTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (31 bp):
TGCATGCAACGTAGGTTTTTGCATGGATTCT
Found at i:52581457 original size:30 final size:31
Alignment explanation
Indices: 52581423--52581484 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
52581413 TTTGGTTTCA
*
52581423 TGCATGTAACGTAGG-TTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
*
52581453 TGCATGCAACGTGGGTTTTTGCATGGATTCT
1 TGCATGCAACGTAGGTTTTTGCATGGATTCT
52581484 T
1 T
52581485 AAACTTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (31 bp):
TGCATGCAACGTAGGTTTTTGCATGGATTCT
Found at i:52593557 original size:40 final size:39
Alignment explanation
Indices: 52593478--52593566 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 39
52593468 AAAATTTATA
* * *
52593478 TTTAATACAATAAAATATTTATTATATTTATTTGTGTTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGTG-TTT
52593518 TTTAATATAATAAAACATTTATTATATTTA-TGGTAGTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGT-GTTT
52593557 TTTAATATAA
1 TTTAATATAA
52593567 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 16 0.36
40 29 0.64
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTATTGGTGTTT
Found at i:52596648 original size:19 final size:21
Alignment explanation
Indices: 52596621--52596660 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
52596611 GCGTTTAGCT
*
52596621 TATT-TTTTATCTCA-CGCTA
1 TATTATTTAATCTCATCGCTA
52596640 TATTATTTAATCTCATCGCTA
1 TATTATTTAATCTCATCGCTA
52596661 CCATTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTATTTAATCTCATCGCTA
Found at i:52600639 original size:19 final size:19
Alignment explanation
Indices: 52600611--52600674 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
52600601 AATTTTAGAG
*
52600611 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52600630 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
52600649 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
52600670 GATAT
1 GATAT
52600675 ATACAATCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 22 0.55
21 18 0.45
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52600693 original size:19 final size:21
Alignment explanation
Indices: 52600612--52600687 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
52600602 ATTTTAGAGG
52600612 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
* *
52600631 ATATGCAATTTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
52600652 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
52600673 ATATACAATCTTAGA
1 ATATACAATCTTAGA
52600688 AGATATGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.33
21 34 0.67
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:52600708 original size:23 final size:24
Alignment explanation
Indices: 52600643--52600710 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 24
52600633 ATGCAATTTT
52600643 AGATATGATATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
*
52600664 AGATATGATATATACAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
*
52600688 AGATATGAT-TTTGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
52600711 GATTTAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
21 20 0.49
23 12 0.29
24 9 0.22
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:52600720 original size:22 final size:23
Alignment explanation
Indices: 52600678--52600720 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52600668 ATGATATATA
*
52600678 CAATCTTAGAAGATATGATTTTG
1 CAATCTTAGAAGATATAATTTTG
*
52600701 CAATCTTAG-AGATTTAATTT
1 CAATCTTAGAAGATATAATTT
52600721 GTAGATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (23 bp):
CAATCTTAGAAGATATAATTTTG
Found at i:52600911 original size:19 final size:21
Alignment explanation
Indices: 52600887--52600925 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
52600877 TGTTTTCTTT
*
52600887 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
52600906 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
52600926 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:52605451 original size:15 final size:15
Alignment explanation
Indices: 52605431--52605464 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52605421 TTTCAAAAAA
*
52605431 AAAAGAGAAAGAAAG
1 AAAAGAAAAAGAAAG
52605446 AAAAGAAAAAGAAAG
1 AAAAGAAAAAGAAAG
52605461 AAAA
1 AAAA
52605465 ATGAGAGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAG
Found at i:52605458 original size:19 final size:20
Alignment explanation
Indices: 52605426--52605463 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52605416 AAATTTTTCA
52605426 AAAAAAAAAGAGAAAGAAAG
1 AAAAAAAAAGAGAAAGAAAG
*
52605446 AAAAGAAAA-AGAAAGAAA
1 AAAAAAAAAGAGAAAGAAA
52605464 AATGAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAGAAAG
Found at i:52607004 original size:131 final size:132
Alignment explanation
Indices: 52606685--52607266 Score: 885
Period size: 131 Copynumber: 4.5 Consensus size: 132
52606675 ACCGGTGAAA
*
52606685 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * * *
52606750 G-AGTAGTGGAACAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGCGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
52606814 GC
131 GC
52606816 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
52606881 GTAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
52606946 GC
131 GC
* * *
52606948 CACCAAGCCTTATCTCCTTGAGCAACAGCGGAGTA-GTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * * *
52607012 GCAGTAGTGAAGCAGATCAAAGATGGTAAATCTTATCTTTCGAAGATAATGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
52607077 GC
131 GC
* * *
52607079 CACAAAGCCTTGTCTCCCTAAGCAGCAGC-G-G-A-G-T-AAG-TTGTAGATCCTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
52607137 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
52607202 GC
131 GC
* * * * *
52607204 CACCAAGCTTTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAATCTTATCTCCCT
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
52607267 GAAGTTGCAG
Statistics
Matches: 409, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
125 107 0.26
126 4 0.01
127 2 0.00
128 3 0.01
129 2 0.00
130 2 0.00
131 183 0.45
132 106 0.26
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:52607485 original size:45 final size:44
Alignment explanation
Indices: 52607250--52607710 Score: 163
Period size: 44 Copynumber: 10.7 Consensus size: 44
52607240 GTTGAAGATG
* * *
52607250 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAA--AA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * * * * * *
52607292 CCGATAATCCTATCACCTTGAAGTTGCAGTGGAGCGGATTAA--AA
1 GC-A-AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* ** * * *
52607336 CCTTGGATCTTATCTCTCTGAAGTTGCAGAG-AGCAGA-T-CGC-A
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * * * *
52607378 TCTAGTCTTATCTCTCTGAAGTTGCAGTGAAGCAGACTCAGCAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * *
52607422 GCAAGTCTTATC-CTCCTGAAGTTGCAGTGAGGTAGACTGAAG-ATA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGAAGCAGACT-AAGCA-A
* * *
52607467 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC-C
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTA-AGCAA
* * * *
52607511 G-ATAATCCTATCTCCCTGAAATTGCAGTGGAGCGGA-TCAA--AA
1 GCA-AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACT-AAGCAA
* *** * ** * *
52607553 CCTTGGGTCTTTTCTATCTGAAGTTGCAGAG-AGCAGA-T-CGC-A
1 GC--AAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * * * * *
52607595 TCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAA
1 GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * * **
52607639 ACAAGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAATAA
1 GCAAATCTTATCTC-CCTGAAGTTGCAGTGAAGCAGACTAAGCAA
* * * *
52607683 ACAAATCCTGTCTCCCT-AAGTTGTAGTG
1 GCAAATCTTATCTCCCTGAAGTTGCAGTG
52607711 GAGTGGATTA
Statistics
Matches: 320, Mismatches: 70, Indels: 57
0.72 0.16 0.13
Matches are distributed among these distances:
40 44 0.14
41 11 0.03
42 8 0.03
43 30 0.09
44 189 0.59
45 37 0.12
46 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
GCAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAA
Found at i:52607575 original size:217 final size:217
Alignment explanation
Indices: 52607242--52607723 Score: 718
Period size: 217 Copynumber: 2.2 Consensus size: 217
52607232 CGGAGTAGGT
* * * *
52607242 TGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCGATAATCCTATCA
1 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCA
* * * *
52607307 CCTTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
66 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
* * *
52607372 ATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGAAGCAGACTCAGCAAGCAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAACAAGTCTTATCCTC
*
52607437 CTGAAGTTGCAGTGAGGTAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
*
52607459 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCT
1 TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCA
* *
52607524 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGGTCTTTTCTATCTGAAGTTGCAGAGAGCAG
66 CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
* * *
52607589 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAACAAGTCTTATCCTC
131 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAACAAGTCTTATCCTC
52607654 CTGAAGTTGCAGTGAGGCAGAC
196 CTGAAGTTGCAGTGAGGCAGAC
* * * * **
52607676 T-AA-ATAAACAAATCCTGTCTCCCT-AAGTTGTAGTGGAGTGGATTAGAG
1 TGAAGAT-AGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAG
52607724 TGATGGATTT
Statistics
Matches: 240, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
215 23 0.10
216 17 0.07
217 200 0.83
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (217 bp):
TGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCA
CCCTGAAATTGCAGTGGAGCGGATCAAAACCTTGGATCTTATCTATCTGAAGTTGCAGAGAGCAG
ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAGCAAACAAGTCTTATCCTC
CTGAAGTTGCAGTGAGGCAGAC
Found at i:52608051 original size:19 final size:19
Alignment explanation
Indices: 52608023--52608086 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
52608013 AATTTTCGAG
*
52608023 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52608042 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
52608061 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
52608082 GATAT
1 GATAT
52608087 ATACATTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52608069 original size:21 final size:21
Alignment explanation
Indices: 52608024--52608088 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
52608014 ATTTTCGAGG
*
52608024 ATATACAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
52608043 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
52608064 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
52608085 ATAT
1 ATAT
52608089 ACATTATTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 18 0.42
21 25 0.58
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:52608098 original size:21 final size:21
Alignment explanation
Indices: 52608024--52608099 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
52608014 ATTTTCGAGG
*
52608024 ATATACAATCTTAGATATG--
1 ATATACAATATTAGATATGAT
* *
52608043 ATATGCAATCTTAGATATGAT
1 ATATACAATATTAGATATGAT
* *
52608064 ATATGCAATCTTAGATATGAT
1 ATATACAATATTAGATATGAT
*
52608085 ATATACATTATTAGA
1 ATATACAATATTAGA
52608100 AGATATGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.35
21 33 0.65
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATACAATATTAGATATGAT
Found at i:52612350 original size:41 final size:41
Alignment explanation
Indices: 52612305--52612387 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
52612295 CAATTTGATT
*
52612305 CTAATATCTAATCAGGTTTCCTACACAATTCAAAATCCATC
1 CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
* *
52612346 CTAATATCTTATCAGCTTTCCTACACAATTCGAAATCCATC
1 CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
52612387 C
1 C
52612388 AAACTCTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (41 bp):
CTAATATCTAATCAGCTTTCCTACACAATTCAAAATCCATC
Found at i:52623357 original size:14 final size:14
Alignment explanation
Indices: 52623321--52623358 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
52623311 CAGAATCTCG
*
52623321 AACCTTGAA-CTTC
1 AACCTTGAACCTTA
52623334 AACCTTGAACCTTA
1 AACCTTGAACCTTA
*
52623348 AACTTTGAACC
1 AACCTTGAACC
52623359 CCAAATCCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (14 bp):
AACCTTGAACCTTA
Found at i:52623436 original size:7 final size:7
Alignment explanation
Indices: 52623424--52623465 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
52623414 TTAAGTTTTG
52623424 GATTCAA
1 GATTCAA
*
52623431 GGTTCAA
1 GATTCAA
*
52623438 TATTCAA
1 GATTCAA
52623445 GATTCAA
1 GATTCAA
*
52623452 TATTCAA
1 GATTCAA
52623459 G-TTCAA
1 GATTCAA
52623465 G
1 G
52623466 GTTTAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (7 bp):
GATTCAA
Found at i:52623442 original size:14 final size:14
Alignment explanation
Indices: 52623425--52623464 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
52623415 TAAGTTTTGG
52623425 ATTCAAGGTTCAAT
1 ATTCAAGGTTCAAT
*
52623439 ATTCAAGATTCAAT
1 ATTCAAGGTTCAAT
52623453 ATTCAA-GTTCAA
1 ATTCAAGGTTCAA
52623465 GGTTTAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (14 bp):
ATTCAAGGTTCAAT
Found at i:52623796 original size:23 final size:23
Alignment explanation
Indices: 52623764--52623809 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52623754 TTGTCTTTAA
*
52623764 ATTTTAATGATGTGGTAAAATTT
1 ATTTTAATGACGTGGTAAAATTT
*
52623787 ATTTTGATGACGTGGTAAAATTT
1 ATTTTAATGACGTGGTAAAATTT
52623810 TATTGGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (23 bp):
ATTTTAATGACGTGGTAAAATTT
Found at i:52627865 original size:3 final size:3
Alignment explanation
Indices: 52627857--52627888 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52627847 TACGTAATTC
52627857 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52627889 TCAAGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:52636580 original size:27 final size:29
Alignment explanation
Indices: 52636550--52636603 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
52636540 CATCTCAAAG
* *
52636550 CACATCACATTGG-T-ATAAGAAATAAAA
1 CACATCACAATGGATAATAAAAAATAAAA
52636577 CACATCACAATGGATAATAAAAAATAA
1 CACATCACAATGGATAATAAAAAATAA
52636604 GATAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 1 0.04
29 10 0.43
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (29 bp):
CACATCACAATGGATAATAAAAAATAAAA
Found at i:52641676 original size:16 final size:16
Alignment explanation
Indices: 52641644--52641690 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
52641634 GTTATGTATG
*
52641644 AATTTTAA-TAATTTA
1 AATTTTAATTAATATA
52641659 AATTTTAATTAATATA
1 AATTTTAATTAATATA
* *
52641675 AAATGTAATTCAATAT
1 AATTTTAATT-AATAT
52641691 TTCTCAGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTTTAATTAATATA
Found at i:52642256 original size:20 final size:20
Alignment explanation
Indices: 52642231--52642280 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
52642221 TGGCTTAAAA
52642231 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
52642251 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
52642268 GTGGTAGTGGATT
1 TTGGTAGTGGATT
52642281 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:52646886 original size:20 final size:20
Alignment explanation
Indices: 52646861--52646910 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
52646851 TGGCTTAAAA
52646861 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
52646881 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
52646898 GTGGTAGTGGATT
1 TTGGTAGTGGATT
52646911 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:52647806 original size:27 final size:26
Alignment explanation
Indices: 52647769--52647823 Score: 101
Period size: 27 Copynumber: 2.1 Consensus size: 26
52647759 TATTAAAACA
52647769 TTAATACTGGATGGAACCACTGGCTG
1 TTAATACTGGATGGAACCACTGGCTG
52647795 TTAAGTACTGGATGGAACCACTGGCTG
1 TTAA-TACTGGATGGAACCACTGGCTG
52647822 TT
1 TT
52647824 CTGGGCGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (26 bp):
TTAATACTGGATGGAACCACTGGCTG
Found at i:52649966 original size:20 final size:19
Alignment explanation
Indices: 52649873--52649967 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 19
52649863 ACGAGATTTG
*
52649873 CACTTCGGTGCCTCTGTATA
1 CACTTCGGTGCCCCTGT-TA
* * *
52649893 CACTTCTGTGTCCCTGTTCG
1 CACTTCGGTGCCCCTGTT-A
* *
52649913 CACTACGGTGCCCTTGTTTA
1 CACTTCGGTGCCCCTG-TTA
*
52649933 CACATTTGG-GCCCCTGTCTA
1 CAC-TTCGGTGCCCCTGT-TA
52649953 CACTTCGGTGCCCCT
1 CACTTCGGTGCCCCT
52649968 ATTATGCATC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 6 0.11
20 46 0.81
21 5 0.09
ACGTcount: A:0.12, C:0.35, G:0.20, T:0.34
Consensus pattern (19 bp):
CACTTCGGTGCCCCTGTTA
Found at i:52652731 original size:57 final size:56
Alignment explanation
Indices: 52652636--52652831 Score: 182
Period size: 57 Copynumber: 3.4 Consensus size: 56
52652626 AGACATTCAC
* * *
52652636 TTAACTAAGATAGCCACAAATGCATCTTTTTAATAGAGATAGCCATAAAGGTTTCCTT
1 TTAACAAAGATAGCCACAAAGGC-TCTTTTTAACAGAGATAGCCATAAAGG-TTCCTT
* * *
52652694 TTAACAAAGATAGCTACAAAGGCTCTTTTTAACAGAGATAGCCACAAAGGCTCC-T
1 TTAACAAAGATAGCCACAAAGGCTCTTTTTAACAGAGATAGCCATAAAGGTTCCTT
* * * * *
52652749 TTAACATAGATTGGCCACAAAGGATTTCTTTTAACATAGATCA-CCATAAAGGCTTCCTT
1 TTAACAAAGA-TAGCCACAAAGGCTCT-TTTTAACAGAGAT-AGCCATAAAGG-TTCCTT
* * *
52652808 ATAATAAAGATCA-CTACAAAGGCT
1 TTAACAAAGAT-AGCCACAAAGGCT
52652832 TTCGTTTTAA
Statistics
Matches: 112, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
55 10 0.09
56 15 0.13
57 45 0.40
58 34 0.30
59 8 0.07
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (56 bp):
TTAACAAAGATAGCCACAAAGGCTCTTTTTAACAGAGATAGCCATAAAGGTTCCTT
Found at i:52652732 original size:28 final size:28
Alignment explanation
Indices: 52652643--52652802 Score: 135
Period size: 29 Copynumber: 5.6 Consensus size: 28
52652633 CACTTAACTA
* *
52652643 AGATAGCCACAAATGCATCTTTTTAATAG
1 AGATAGCCACAAAGGC-TCTTTTTAACAG
* * * *
52652672 AGATAGCCATAAAGGTTTCCTTTTAACAA
1 AGATAGCCACAAAGG-CTCTTTTTAACAG
*
52652701 AGATAGCTACAAAGGCTCTTTTTAACAG
1 AGATAGCCACAAAGGCTCTTTTTAACAG
* *
52652729 AGATAGCCACAAAGGCTC-CTTTAACAT
1 AGATAGCCACAAAGGCTCTTTTTAACAG
* * * *
52652756 AGATTGGCCACAAAGGATTTCTTTTAACAT
1 AGA-TAGCCACAAAGGCTCT-TTTTAACAG
*
52652786 AGATCA-CCATAAAGGCT
1 AGAT-AGCCACAAAGGCT
52652803 TCCTTATAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
27 10 0.10
28 39 0.37
29 45 0.43
30 11 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (28 bp):
AGATAGCCACAAAGGCTCTTTTTAACAG
Found at i:52657295 original size:31 final size:32
Alignment explanation
Indices: 52657231--52657295 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
52657221 GGCAAATTAC
52657231 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
*
52657263 AAGAGTAATTGAATCCTAAT-AAAATTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
52657294 AA
1 AA
52657296 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:52660612 original size:10 final size:10
Alignment explanation
Indices: 52660597--52660626 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
52660587 CTTTAATAAG
*
52660597 AAGAAAACTT
1 AAGAAAACTC
52660607 AAGAAAACTC
1 AAGAAAACTC
52660617 AAGAAAACTC
1 AAGAAAACTC
52660627 TACCCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (10 bp):
AAGAAAACTC
Found at i:52660891 original size:10 final size:9
Alignment explanation
Indices: 52660878--52660928 Score: 57
Period size: 9 Copynumber: 5.2 Consensus size: 9
52660868 TTTTTTGCGC
52660878 TTTTTTGCTT
1 TTTTTTG-TT
52660888 TTTTTTGTT
1 TTTTTTGTT
52660897 TTTTTACTGTT
1 TTTTT--TGTT
*
52660908 TTTGTTGTT
1 TTTTTTGTT
52660917 TTTTTTGCTT
1 TTTTTTG-TT
52660927 TT
1 TT
52660929 ATTTAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 17 0.47
10 11 0.31
11 8 0.22
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:52661527 original size:31 final size:32
Alignment explanation
Indices: 52661468--52661532 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
52661458 GGCAAATTAC
52661468 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
52661500 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
52661531 AA
1 AA
52661533 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:52671348 original size:26 final size:26
Alignment explanation
Indices: 52671319--52671380 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
52671309 TACCTACAAT
*
52671319 AGTTTTAGAAT-ATCATAACATATATC
1 AGTTTCAGAATAAT-ATAACATATATC
* *
52671345 AGTTTCAGAATAATATAGCATGTATC
1 AGTTTCAGAATAATATAACATATATC
52671371 AGTTTCAGAA
1 AGTTTCAGAA
52671381 ACTTACAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATAATATAACATATATC
Found at i:52684722 original size:17 final size:17
Alignment explanation
Indices: 52684700--52684738 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
52684690 TAGAATTGGG
*
52684700 TTGAAAAAATTATTTAA
1 TTGAAAAAATTAATTAA
52684717 TTG-AAAAATTAATTAA
1 TTGAAAAAATTAATTAA
52684733 TT-AAAA
1 TTGAAAA
52684739 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TTGAAAAAATTAATTAA
Found at i:52684740 original size:14 final size:15
Alignment explanation
Indices: 52684704--52684744 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
52684694 ATTGGGTTGA
*
52684704 AAAAATTATTTAATT
1 AAAAATTAATTAATT
52684719 GAAAAATTAATTAATT
1 -AAAAATTAATTAATT
52684735 -AAAATTAATT
1 AAAAATTAATT
52684745 TAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAAATTAATTAATT
Found at i:52705127 original size:12 final size:12
Alignment explanation
Indices: 52705089--52705130 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
52705079 ACTGGTCACA
52705089 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
52705101 GAGGGATATT-TG
1 GAGAGAT-TTGAG
52705113 GAGAGATTTGAG
1 GAGAGATTTGAG
52705125 GAGAGA
1 GAGAGA
52705131 ATATTGGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:52705137 original size:24 final size:24
Alignment explanation
Indices: 52705089--52705135 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
52705079 ACTGGTCACA
*
52705089 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
52705113 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
52705136 GGGGATTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:52705352 original size:55 final size:55
Alignment explanation
Indices: 52705261--52705377 Score: 189
Period size: 55 Copynumber: 2.1 Consensus size: 55
52705251 CACATTGCCT
* **
52705261 GGGAATCAAGGGTGCGATGATCATCGTTTTGTGGAATAAGAGTGTTCGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
* *
52705316 GGGAATCAATGGTGCGATGATCATTGATTTACGGAATAAGAGTGTTCGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
52705371 GGGAATC
1 GGGAATC
52705378 TGCAAATCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.26
Consensus pattern (55 bp):
GGGAATCAAGGGTGCGATGATCATCGATTTACGGAATAAGAGTGTTCGGATCGAA
Found at i:52705856 original size:27 final size:27
Alignment explanation
Indices: 52705805--52705996 Score: 151
Period size: 27 Copynumber: 7.1 Consensus size: 27
52705795 TCGATATCTG
* * * *
52705805 GACCGAAATACCCTTGAAGGTTAAAAA
1 GACCGAAATACCCTCGATGGGTAAAAT
*
52705832 GACCGAAATAACCTCGATGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
** *
52705859 GACTAAAATACCCTTGATGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
* *
52705886 GATCGAAATACCCTCGACGGGTAAAAT
1 GACCGAAATACCCTCGATGGGTAAAAT
** *
52705913 GACTAAAATGCTCC-C-ATAGGGTAAAAT
1 GACCGAAATAC-CCTCGAT-GGGTAAAAT
* *
52705940 GATCGAAATACCCCCG-TAGGGTAAAAT
1 GACCGAAATACCCTCGAT-GGGTAAAAT
* *
52705967 GACTGTAATACCC-CTG-TAGGGTAAAAT
1 GACCGAAATACCCTC-GAT-GGGTAAAAT
52705994 GAC
1 GAC
52705997 TGTAATGCCC
Statistics
Matches: 134, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 4 0.03
27 128 0.96
28 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (27 bp):
GACCGAAATACCCTCGATGGGTAAAAT
Found at i:52705874 original size:54 final size:54
Alignment explanation
Indices: 52705810--52705992 Score: 174
Period size: 54 Copynumber: 3.4 Consensus size: 54
52705800 ATCTGGACCG
* *
52705810 AAATACCCTTGAAGGTTAAAAAGACCGAAATAACCTCGATGGGTAAAATGACTA
1 AAATACCCTTGAAGGGTAAAAAGACCGAAATAACCTCGACGGGTAAAATGACTA
* * * *
52705864 AAATACCCTTGATGGGTAAAATGATCGAAATACCCTCGACGGGTAAAATGACTA
1 AAATACCCTTGAAGGGTAAAAAGACCGAAATAACCTCGACGGGTAAAATGACTA
* * * * * * *
52705918 AAATGCTCC--CATAGGGTAAAATGATCGAAATACCCCCGTA-GGGTAAAATGACTG
1 AAATAC-CCTTGA-AGGGTAAAAAGACCGAAATAACCTCG-ACGGGTAAAATGACTA
* * *
52705972 TAATACCCCTGTAGGGTAAAA
1 AAATACCCTTGAAGGGTAAAA
52705993 TGACTGTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
53 3 0.03
54 103 0.94
55 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (54 bp):
AAATACCCTTGAAGGGTAAAAAGACCGAAATAACCTCGACGGGTAAAATGACTA
Found at i:52705997 original size:27 final size:27
Alignment explanation
Indices: 52705850--52706156 Score: 215
Period size: 27 Copynumber: 11.5 Consensus size: 27
52705840 TAACCTCGAT
** *
52705850 GGGTAAAATGACTAAAATACCCTTG-A
1 GGGTAAAATGACTGTAATACCCCTGTA
*
52705876 TGGGTAAAATGA-TCGAAATA-CCCTCG-A
1 -GGGTAAAATGACT-GTAATACCCCT-GTA
** * *
52705903 CGGGTAAAATGACTAAAATGCTCCC-ATA
1 -GGGTAAAATGACTGTAATAC-CCCTGTA
* *
52705931 GGGTAAAATGA-TCGAAATACCCCCGTA
1 GGGTAAAATGACT-GTAATACCCCTGTA
52705958 GGGTAAAATGACTGTAATACCCCTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
* * *
52705985 GGGTAAAATGACTGTAATGCCCGTATA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
52706012 GGGTAAAATGAGC-GTAAT-CCCCTATA
1 GGGTAAAATGA-CTGTAATACCCCTGTA
* * ** *
52706038 AGGTAAAATGACCGTAACGCCCTTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
52706065 GGGTAAAATGA-TCGTCATACCCCTGTA
1 GGGTAAAATGACT-GTAATACCCCTGTA
* * * * *
52706092 GGATAAAATGGCCGTAATGCCCCTCTA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
52706119 GGGTAAAATGACCGTAATA-CCCTGGT-
1 GGGTAAAATGACTGTAATACCCCT-GTA
52706145 GGGT-AAATGACT
1 GGGTAAAATGACT
52706157 ATTTTTGCCT
Statistics
Matches: 229, Mismatches: 36, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
25 8 0.03
26 37 0.16
27 177 0.77
28 4 0.02
29 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGTAAAATGACTGTAATACCCCTGTA
Found at i:52706235 original size:24 final size:24
Alignment explanation
Indices: 52706200--52706258 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
52706190 TATGTGGTTA
* *
52706200 AATGACTAATTTGTTTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
52706224 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
52706248 AATGACTGATT
1 AATGACTGATT
52706259 CTGAGCATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:52706470 original size:32 final size:32
Alignment explanation
Indices: 52706429--52706706 Score: 260
Period size: 32 Copynumber: 8.7 Consensus size: 32
52706419 ACTACGATGC
*
52706429 TACTGATGGCTTTGTGCTGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
** *
52706461 TACTGATGGCTTTGTATCGATCATAGTACTGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
*
52706493 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * *
52706525 TACTGATGGCTTTGTGTCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * ** *
52706557 TACCGATGG-TTGTGTACCGAT-ATTTTACTGT
1 TACTGATGGCTT-TGTGCCGATCATAGTACCGT
* * *
52706588 TACTGATGGCTATGTGCCGATCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
* *
52706620 CACTAATGGCTTTGTGCCGATCAT-GTTACCGT
1 TACTGATGGCTTTGTGCCGATCATAG-TACCGT
* * * * *
52706652 TACTGATGGCTGTGTGTCGATTATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
* *
52706684 TATTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
52706707 CATTACTATA
Statistics
Matches: 200, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
31 27 0.14
32 172 0.86
33 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:52706530 original size:64 final size:64
Alignment explanation
Indices: 52706426--52706712 Score: 339
Period size: 64 Copynumber: 4.5 Consensus size: 64
52706416 TTTACTACGA
* * *
52706426 TGCTACTGATGGCTTTGTGCTGATCATAGTACCGTTACTGATGGCTTTGTATCGATCATAGT-AC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATA-TCAC
* *
52706490 TGTTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATTA-
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
* * * * * * *
52706553 TCGTTACCGATGG-TTGTGTACCGAT-ATTTTACTGTTACTGATGGCTATGTGCCGATCATATCA
1 T-GCTACTGATGGCTT-TGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCA
52706616 C
64 C
* * * * *
52706617 TGCCACTAATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGTCGATTATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
* * *
52706681 TGCTATTGATGGCTTTGTGCCAATCACATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
52706713 TATACTTATG
Statistics
Matches: 190, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
63 52 0.27
64 138 0.73
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATCAC
Found at i:52706977 original size:28 final size:28
Alignment explanation
Indices: 52706944--52706997 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
52706934 CATACTAATA
* *
52706944 CTGTATT-GGGCTTAGGCCCGCACTATTT
1 CTGTATTAGGG-TAAGGCCCACACTATTT
52706972 CTGTATTAGGGTAAGGCCCACACTAT
1 CTGTATTAGGGTAAGGCCCACACTAT
52706998 ACTGTTACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (28 bp):
CTGTATTAGGGTAAGGCCCACACTATTT
Found at i:52719778 original size:3 final size:3
Alignment explanation
Indices: 52719770--52719795 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52719760 TTTAGAGTAG
52719770 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
52719796 GCATTTAGTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:52720968 original size:49 final size:49
Alignment explanation
Indices: 52720888--52721078 Score: 167
Period size: 49 Copynumber: 3.9 Consensus size: 49
52720878 TCCTAGCACT
* * * *
52720888 CACGCCAA-CTGGTTAGTAACTAAGATACCCTACCAGTGGCTCATCATA
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCATCATA
*
52720936 CACGCCAATCTGGTTAGCAACTAACATGCCCTACCAGTGGC-CTATCATA
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTC-ATCATA
* * * * * * *
52720985 TACTCCCACCTAGTTAGCAACTAGCATGCCTTACCAGTGGTCTAGCA-CATG
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGG-CT--CATCATA
* * * *
52721036 TAC-CC-TTCTAGTTTGCAACTAGCATGCCCTACCAGTGGCTCAT
1 CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCAT
52721079 GATAATCGGA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
46 2 0.02
48 11 0.09
49 97 0.80
50 3 0.02
51 6 0.05
52 1 0.01
53 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (49 bp):
CACGCCAATCTAGTTAGCAACTAACATGCCCTACCAGTGGCTCATCATA
Found at i:52725723 original size:20 final size:20
Alignment explanation
Indices: 52725690--52725729 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52725680 GGTCTCGATA
* *
52725690 CTAAGGGAAGGTATCAATAC
1 CTAAGAGAAAGTATCAATAC
*
52725710 CTAAGAGAAAGTATCGATAC
1 CTAAGAGAAAGTATCAATAC
52725730 TTCAAGCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
CTAAGAGAAAGTATCAATAC
Found at i:52737072 original size:18 final size:17
Alignment explanation
Indices: 52737029--52737075 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
52737019 AAGCTAAAAG
52737029 TAAAAAT-AAAATGCAA
1 TAAAAATAAAAATGCAA
52737045 TAAAAATAAAAATG-AA
1 TAAAAATAAAAATGCAA
52737061 TAAATTAATAAAAAT
1 TAAA--AATAAAAAT
52737076 TGAGTGTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.46
17 6 0.21
18 9 0.32
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (17 bp):
TAAAAATAAAAATGCAA
Found at i:52743786 original size:51 final size:51
Alignment explanation
Indices: 52743710--52743822 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
52743700 AAGACCATAA
* *
52743710 ATGAAAGATGTTATAGTAGTCTAGTATGTGGTACGTAGCGTAAGGTCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
52743761 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
52743812 ATGAAAGATGT
1 ATGAAAGATGT
52743823 CATGGCAGCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (51 bp):
ATGAAAGATGTTATAGTAGTCTAGTATATGGTACGTAGCGTAAGGCCATGG
Found at i:52744047 original size:33 final size:33
Alignment explanation
Indices: 52744010--52744100 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 33
52744000 AGTCCTCCGA
52744010 GACAGTAAACACGAAACAGAGTAAGCCCGTCAG
1 GACAGTAAACACGAAACAGAGTAAGCCCGTCAG
* * * * **
52744043 GACAGTAAACATGGAATAGAGTAAGTCCGTTGG
1 GACAGTAAACACGAAACAGAGTAAGCCCGTCAG
* * *
52744076 GATAGTAAATACAAAACAGAGTAAG
1 GACAGTAAACACGAAACAGAGTAAG
52744101 TCTATTGGAA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.15
Consensus pattern (33 bp):
GACAGTAAACACGAAACAGAGTAAGCCCGTCAG
Found at i:52747461 original size:20 final size:19
Alignment explanation
Indices: 52747421--52747457 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52747411 AAAGTAGTGG
52747421 AAATTTATTTTCTTAGAAT
1 AAATTTATTTTCTTAGAAT
52747440 AAATTTGATTTT-TTAGAA
1 AAATTT-ATTTTCTTAGAA
52747458 ATAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (19 bp):
AAATTTATTTTCTTAGAAT
Found at i:52760954 original size:13 final size:13
Alignment explanation
Indices: 52760936--52760960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52760926 ATGTAGCATC
52760936 CAAGGTGGCCATG
1 CAAGGTGGCCATG
52760949 CAAGGTGGCCAT
1 CAAGGTGGCCAT
52760961 TCAGGGAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (13 bp):
CAAGGTGGCCATG
Found at i:52779515 original size:7 final size:7
Alignment explanation
Indices: 52779497--52779553 Score: 69
Period size: 7 Copynumber: 8.1 Consensus size: 7
52779487 TTTCTTAAGC
52779497 GATGTGG
1 GATGTGG
* *
52779504 AATGTGT
1 GATGTGG
52779511 GATGTGG
1 GATGTGG
52779518 GATGTGG
1 GATGTGG
52779525 GATGTGG
1 GATGTGG
*
52779532 GATATGG
1 GATGTGG
*
52779539 GATATGG
1 GATGTGG
*
52779546 GATATGG
1 GATGTGG
52779553 G
1 G
52779554 TATATATAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.21, C:0.00, G:0.49, T:0.30
Consensus pattern (7 bp):
GATGTGG
Found at i:52779546 original size:14 final size:14
Alignment explanation
Indices: 52779515--52779558 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
52779505 ATGTGTGATG
* *
52779515 TGGGATGTGGGATG
1 TGGGATATGGGATA
52779529 TGGGATATGGGATA
1 TGGGATATGGGATA
52779543 TGGGATATGGGTATA
1 TGGGATATGGG-ATA
52779558 T
1 T
52779559 ATAGACTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (14 bp):
TGGGATATGGGATA
Found at i:52780052 original size:58 final size:58
Alignment explanation
Indices: 52779955--52780125 Score: 267
Period size: 56 Copynumber: 3.0 Consensus size: 58
52779945 CAAAATCTTA
52779955 ATATTTATATATAAAATATTATGTGTTACTATA-AGTGTAAGTTTGTCTTTCTTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATA-TGTAAGTTTGTCTTTCTTTTTTT
* *
52780013 ATATCTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTC-TT-TTTTTAT
1 ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTTT
* * *
52780069 ATATTTATATATAAAATATTCTGTGTTACTATATGTGCAAGTTTGTCTTTCTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTT
52780126 ATTGGACTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
56 49 0.48
57 4 0.04
58 49 0.48
59 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (58 bp):
ATATTTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTTTCTTTTTTT
Found at i:52783779 original size:43 final size:44
Alignment explanation
Indices: 52783731--52783820 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 44
52783721 GCAGGTCAAA
* *
52783731 TAATATTAAAATAACCTACACTAAT-TAAGTTTAAGTGAGAAGC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
* * *
52783774 TAATATTAAAATAGCCTACACTCATCAAAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
52783818 TAA
1 TAA
52783821 AAATAGAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 23 0.56
44 18 0.44
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
Found at i:52783847 original size:25 final size:25
Alignment explanation
Indices: 52783802--52783849 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
52783792 CACTCATCAA
* *
52783802 AGTTTAAGTGGGAAACTAAAAATAG
1 AGTTTAACTGGGAAACGAAAAATAG
52783827 AGTTTAACTGGGAGAA-GAAAAAT
1 AGTTTAACTGGGA-AACGAAAAAT
52783850 CGAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.23
Consensus pattern (25 bp):
AGTTTAACTGGGAAACGAAAAATAG
Found at i:52788799 original size:26 final size:26
Alignment explanation
Indices: 52788760--52788814 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
52788750 TGCATAGTTC
*
52788760 AAGATAGGCTCGTGGTGGGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
*
52788786 AAGATAGGCCCGTGGTGTGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
52788812 AAG
1 AAG
52788815 GATGGCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (26 bp):
AAGATAGGCCCGTGGTGGGCTTTGGA
Found at i:52791132 original size:43 final size:43
Alignment explanation
Indices: 52791032--52791132 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
52791022 TACATGTAAC
* *
52791032 CTCATATCGATGCCAATAGCCCAGCTATAGTCTTACACGAAAT
1 CTCATATCGATGCCAATAGCCCAACTATAGTCTCACACGAAAT
* * * *
52791075 -TACAAATCGCTGCCAAT-GTCCCAAAC-ATGGTCTCACACGAAGT
1 CT-CATATCGATGCCAATAG-CCC-AACTATAGTCTCACACGAAAT
52791118 CTCATATCGATGCCA
1 CTCATATCGATGCCA
52791133 TATCTCAGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.04
43 41 0.89
44 3 0.07
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.24
Consensus pattern (43 bp):
CTCATATCGATGCCAATAGCCCAACTATAGTCTCACACGAAAT
Found at i:52794678 original size:16 final size:17
Alignment explanation
Indices: 52794652--52794683 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52794642 TTTTGGGAAT
52794652 TGGGTGGTACTGCCATG
1 TGGGTGGTACTGCCATG
52794669 TGGG-GGTACTGCCAT
1 TGGGTGGTACTGCCAT
52794684 ATCATGGCTT
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:0.12, C:0.19, G:0.41, T:0.28
Consensus pattern (17 bp):
TGGGTGGTACTGCCATG
Found at i:52794701 original size:30 final size:30
Alignment explanation
Indices: 52794665--52794746 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 30
52794655 GTGGTACTGC
52794665 CATGTGGGGGTACTGCCATATCATGGCTTT
1 CATGTGGGGGTACTGCCATATCATGGCTTT
*
52794695 CATGTGGGGGTA-T----T-T-AT---TTA
1 CATGTGGGGGTACTGCCATATCATGGCTTT
52794715 CATGTGGGGGTACTGCCATATCATGGCTTT
1 CATGTGGGGGTACTGCCATATCATGGCTTT
52794745 CA
1 CA
52794747 ACAAAGCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 20
0.65 0.03 0.32
Matches are distributed among these distances:
20 14 0.35
21 1 0.03
23 2 0.05
24 1 0.03
25 2 0.05
26 1 0.03
27 2 0.05
29 1 0.03
30 16 0.40
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.35
Consensus pattern (30 bp):
CATGTGGGGGTACTGCCATATCATGGCTTT
Found at i:52799395 original size:31 final size:32
Alignment explanation
Indices: 52799341--52799401 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
52799331 TCAAATCTCT
*
52799341 TATATCATAATCCATTGATCCAAATACATTTCA
1 TATATCATAATACATTGATCCAAATA-ATTTCA
52799374 TATATCA-AATACATT-ATCCAAATAATTT
1 TATATCATAATACATTGATCCAAATAATTT
52799402 TTCTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 7 0.26
33 7 0.26
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.38
Consensus pattern (32 bp):
TATATCATAATACATTGATCCAAATAATTTCA
Found at i:52800993 original size:11 final size:11
Alignment explanation
Indices: 52800979--52801003 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52800969 CCATATACAG
52800979 TCCAATGATAT
1 TCCAATGATAT
52800990 TCCAATGATAT
1 TCCAATGATAT
52801001 TCC
1 TCC
52801004 TATTGGCTAG
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:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (11 bp):
TCCAATGATAT
Found at i:52802506 original size:57 final size:57
Alignment explanation
Indices: 52802390--52802535 Score: 172
Period size: 57 Copynumber: 2.5 Consensus size: 57
52802380 TGGCACTTTA
* *
52802390 TTTTTCCTAATTTGGTATCTAAA-TTTTTTGGCTCAATTTGGTACTTGAATTTAACAC
1 TTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTT-ACAC
* *
52802447 TTTTTT-TAAATTTGGTATCTAAACTTTTTTGGGTCATATTTGGTACTTGAACTT-GAC
1 TTTTTTCT-AATTTGGTATCTAAACTTTTTTGGCTCA-ATTTGGTACTTGAACTTACAC
* *
52802504 TTTTTTCCTAATTTGGTACCTAAGCATTTTTT
1 TTTTTT-CTAATTTGGTATCTAAAC-TTTTTT
52802536 TTAGGTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
56 1 0.01
57 28 0.36
58 25 0.32
59 23 0.30
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (57 bp):
TTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTTACAC
Found at i:52802534 original size:59 final size:58
Alignment explanation
Indices: 52802390--52802535 Score: 176
Period size: 58 Copynumber: 2.5 Consensus size: 58
52802380 TGGCACTTTA
*
52802390 TTTTTCCTAATTTGGTATCTAA-ATTTTTTGGCTCAATTTGGTACTTGAATTTAACACT
1 TTTTTCCTAATTTGGTATCTAACATTTTTTGGCTCAATTTGGTACTTGAACTT-ACACT
* *
52802448 TTTTT--TAAATTTGGTATCTAA-ACTTTTTTGGGTCATATTTGGTACTTGAACTT-GACT
1 TTTTTCCT-AATTTGGTATCTAACA-TTTTTTGGCTCA-ATTTGGTACTTGAACTTACACT
*
52802505 TTTTTCCTAATTTGGTACCTAAGCATTTTTT
1 TTTTTCCTAATTTGGTATCTAA-CATTTTTT
52802536 TTAGGTTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
56 1 0.01
57 23 0.30
58 29 0.38
59 23 0.30
60 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (58 bp):
TTTTTCCTAATTTGGTATCTAACATTTTTTGGCTCAATTTGGTACTTGAACTTACACT
Found at i:52802679 original size:25 final size:25
Alignment explanation
Indices: 52802651--52802698 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
52802641 AAAGGAAATT
52802651 TATG-TTAAAAAATTAGATATTAAGC
1 TATGCTTAAAAAATTA-ATATTAAGC
**
52802676 TATGCTTAATGAATTAATATTAA
1 TATGCTTAAAAAATTAATATTAA
52802699 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (25 bp):
TATGCTTAAAAAATTAATATTAAGC
Found at i:52803447 original size:136 final size:136
Alignment explanation
Indices: 52803192--52803567 Score: 506
Period size: 136 Copynumber: 2.8 Consensus size: 136
52803182 TGCATTTAAT
* * * * *
52803192 TGTGCGTTGTGTACCCACAGCAAAAGCATATTCCAACTGCGTCCATTTTACCGTGCAAGCACAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* *
52803257 CCTCTGACAACTTTTATCTGTGAGTATGTTGTGATTCCACTGCAATTGTCAGATTTTATCTGCAT
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACTGCAATTGTAAGATTTTATCTGCAT
*
52803322 TATATG
131 TATATA
* ** *
52803328 TGTGCGCTGTGTATCCACAGAAAAAATAGATTCCAACTGCGTCCATTTTACTGTGTGAGCACAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* * * *
52803393 CCTCTGACAGCTTTTTTCTGCGAGTATGTTGTGTTTCCA-TGGCTATTAG-AAGATTTTATCTGC
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACT-GCAATT-GTAAGATTTTATCTGC
52803456 ATTATATA
129 ATTATATA
* * * *
52803464 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAAATGCGTCCATTTTATTGTACGAGCAGAAC
1 TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
* * *
52803529 CCTCTAACAACTTTTATCTGCGAGCATG-TGTGCTTCCAC
66 CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCAC
52803568 GGCCAGTGGC
Statistics
Matches: 208, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
135 10 0.05
136 197 0.95
137 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (136 bp):
TGTGCGCTGTGTATCCACAGCAAAAGCAGATTCCAACTGCGTCCATTTTACTGTGCGAGCACAAC
CCTCTGACAACTTTTATCTGCGAGTATGTTGTGATTCCACTGCAATTGTAAGATTTTATCTGCAT
TATATA
Found at i:52803954 original size:37 final size:37
Alignment explanation
Indices: 52803870--52804010 Score: 142
Period size: 37 Copynumber: 3.8 Consensus size: 37
52803860 TTTACCATAT
* * * *
52803870 TGAATTGATTGATATGCGAGATTGCTTGTTATTAAGT--
1 TGAATTGATTGACATGCGAAATTGTTTGTCATT--GTAC
* * * *
52803907 TAAATAGATTGATATGCGAAACTGTTTGTCATTGTAC
1 TGAATTGATTGACATGCGAAATTGTTTGTCATTGTAC
*
52803944 TGAATTGATTGACATGTGAAATTGTGTTTGTCATTGTAC
1 TGAATTGATTGACATGCGAAA-T-TGTTTGTCATTGTAC
*
52803983 TGAATTGATTGACATGTGAAATTGTTTG
1 TGAATTGATTGACATGCGAAATTGTTTG
52804011 CTATTACTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
35 2 0.02
37 50 0.56
38 1 0.01
39 36 0.40
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (37 bp):
TGAATTGATTGACATGCGAAATTGTTTGTCATTGTAC
Found at i:52803973 original size:39 final size:39
Alignment explanation
Indices: 52803929--52804007 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
52803919 TATGCGAAAC
52803929 TGTTTGTCATTGTACTGAATTGATTGACATGTGAAATTG
1 TGTTTGTCATTGTACTGAATTGATTGACATGTGAAATTG
52803968 TGTTTGTCATTGTACTGAATTGATTGACATGTGAAATTG
1 TGTTTGTCATTGTACTGAATTGATTGACATGTGAAATTG
52804007 T
1 T
52804008 TTGCTATTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (39 bp):
TGTTTGTCATTGTACTGAATTGATTGACATGTGAAATTG
Found at i:52805160 original size:3 final size:3
Alignment explanation
Indices: 52805152--52805177 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52805142 ATATAATTCA
52805152 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52805178 AAGAAACCAA
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:52814662 original size:29 final size:29
Alignment explanation
Indices: 52814627--52814683 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
52814617 CCATTTAATT
*
52814627 TTATTTCTCTTAATTTATTTTGCAATCAC
1 TTATTTCGCTTAATTTATTTTGCAATCAC
52814656 TTATTTCGCTTAATTTATTTTGCAATCA
1 TTATTTCGCTTAATTTATTTTGCAATCA
52814684 TGTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATTTCGCTTAATTTATTTTGCAATCAC
Found at i:52820921 original size:14 final size:15
Alignment explanation
Indices: 52820899--52820927 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52820889 ATTTATCTAT
52820899 TTAATTTTATTTTGC
1 TTAATTTTATTTTGC
52820914 TTAA-TTTATTTTGC
1 TTAATTTTATTTTGC
52820928 AATCACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
TTAATTTTATTTTGC
Found at i:52821896 original size:26 final size:26
Alignment explanation
Indices: 52821867--52821916 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
52821857 TGTATTTTTA
*
52821867 ATTTCA-TAATAATATAAAAATATAAT
1 ATTTCATTAAAAAT-TAAAAATATAAT
*
52821893 ATTTTATTAAAAATTAAAAATATA
1 ATTTCATTAAAAATTAAAAATATA
52821917 TAGAATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTTCATTAAAAATTAAAAATATAAT
Found at i:52826136 original size:24 final size:24
Alignment explanation
Indices: 52826121--52826172 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52826111 AATCACAATC
52826121 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
52826145 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
52826169 AAAT
1 AAAT
52826173 CTCCTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:52831874 original size:15 final size:14
Alignment explanation
Indices: 52831844--52831883 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
52831834 TAAAAAGAAG
*
52831844 TAATTAAA-ATAAA
1 TAATTAAATAAAAA
52831857 TAATTAAGATAAAAA
1 TAATTAA-ATAAAAA
52831872 TAATTAAATAAA
1 TAATTAAATAAA
52831884 TCAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
TAATTAAATAAAAA
Found at i:52832370 original size:19 final size:19
Alignment explanation
Indices: 52832346--52832387 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
52832336 CAAAATTCAA
52832346 AATAAATACATAATAAA-AT
1 AATAAA-ACATAATAAATAT
*
52832365 AATAAAATATAATAAATAT
1 AATAAAACATAATAAATAT
52832384 AATA
1 AATA
52832388 TTGGGCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAACATAATAAATAT
Found at i:52832383 original size:9 final size:9
Alignment explanation
Indices: 52832355--52832387 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
52832345 AAATAAATAC
52832355 ATAATAAA-
1 ATAATAAAT
52832363 ATAATAAAAT
1 ATAAT-AAAT
52832373 ATAATAAAT
1 ATAATAAAT
52832382 ATAATA
1 ATAATA
52832388 TTGGGCTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATAAAT
Found at i:52834956 original size:99 final size:99
Alignment explanation
Indices: 52834847--52835044 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
52834837 AAAACTACGT
*
52834847 TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCACATAATGCAGAT
1 TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
*
52834912 TTAATATGAAAATTTTTGGCACAAAATTCAACCA
66 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
52834946 TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
1 TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
52835011 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
66 CTAATATGAAAATTTTTGGCACAAAATTCAACCA
52835045 CTAGAATGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (99 bp):
TCGAGGTGTTCCTGATTTCAAAAAATCACAAAATTTAAACTAGAGTTTCCTCAAATAATGCAGAT
CTAATATGAAAATTTTTGGCACAAAATTCAACCA
Found at i:52835107 original size:78 final size:78
Alignment explanation
Indices: 52834978--52835121 Score: 209
Period size: 78 Copynumber: 1.8 Consensus size: 78
52834968 AAATCACAAA
* * *
52834978 ATTTAAACTAGAGTTTCCTCAAATAATGCAGATCTAATATGAAAATTTTTGGCACAAAATTCAAC
1 ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGAAAAGTTTTGGCACAAAATTCAAC
52835043 CACTAGAATGTTT
66 CACTAGAATGTTT
* * * *
52835056 ATTTAAATTGGAGTTTCCTCAAATAACGTAGAACTAATCT-AGAAAGTTTTGGCACAAAATTCAA
1 ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGA-AAAGTTTTGGCACAAAATTCAA
52835120 CC
65 CC
52835122 CACAATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (78 bp):
ATTTAAACTAGAGTTTCCTCAAATAACGCAGAACTAATATGAAAAGTTTTGGCACAAAATTCAAC
CACTAGAATGTTT
Found at i:52836532 original size:17 final size:18
Alignment explanation
Indices: 52836495--52836532 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
52836485 ATTTTTTAAA
*
52836495 AATCAATATTTAGTTTTAT
1 AATCAATATTTAG-CTTAT
52836514 AATCAATATTTA-CTTAT
1 AATCAATATTTAGCTTAT
52836531 AA
1 AA
52836533 AAATTAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
AATCAATATTTAGCTTAT
Found at i:52840985 original size:42 final size:42
Alignment explanation
Indices: 52840938--52841021 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
52840928 ATACGTTATG
52840938 TTAATTCAAGAAAATGTGGAACTGATAATAAAAGTGGTCGAC
1 TTAATTCAAGAAAATGTGGAACTGATAATAAAAGTGGTCGAC
52840980 TTAATTCAAGAAAATGTGGAACTGATAATAAAAGTGGTCGAC
1 TTAATTCAAGAAAATGTGGAACTGATAATAAAAGTGGTCGAC
52841022 AATGGCTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (42 bp):
TTAATTCAAGAAAATGTGGAACTGATAATAAAAGTGGTCGAC
Found at i:52841008 original size:24 final size:24
Alignment explanation
Indices: 52840939--52841008 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 24
52840929 TACGTTATGT
52840939 TAATTCAAGAAAATGTGGAACTGA
1 TAATTCAAGAAAATGTGGAACTGA
* *
52840963 TAA-T--A-AAAGTGGTCG-ACT--
1 TAATTCAAGAAAAT-GTGGAACTGA
52840981 TAATTCAAGAAAATGTGGAACTGA
1 TAATTCAAGAAAATGTGGAACTGA
52841005 TAAT
1 TAAT
52841009 AAAAGTGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
18 3 0.09
19 1 0.03
20 7 0.21
21 8 0.24
22 7 0.21
23 1 0.03
24 7 0.21
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (24 bp):
TAATTCAAGAAAATGTGGAACTGA
Found at i:52843215 original size:17 final size:18
Alignment explanation
Indices: 52843189--52843227 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
52843179 AGAATTGTGG
52843189 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
52843205 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
52843223 AAAAT
1 AAAAT
52843228 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:52843404 original size:15 final size:15
Alignment explanation
Indices: 52843384--52843414 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52843374 AAAACAATAT
52843384 AACTCTAGACCTTTC
1 AACTCTAGACCTTTC
*
52843399 AACTCTTGACCTTTC
1 AACTCTAGACCTTTC
52843414 A
1 A
52843415 CTTACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
AACTCTAGACCTTTC
Found at i:52846785 original size:15 final size:15
Alignment explanation
Indices: 52846775--52846804 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52846765 TCCCTTCTTG
52846775 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
52846790 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
52846805 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:52847575 original size:17 final size:18
Alignment explanation
Indices: 52847549--52847587 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
52847539 CAAATTGTGG
52847549 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
52847565 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
52847583 AAAAT
1 AAAAT
52847588 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:52847764 original size:15 final size:15
Alignment explanation
Indices: 52847744--52847774 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52847734 AAAACAATAT
52847744 AACTCTAGACCTTTC
1 AACTCTAGACCTTTC
*
52847759 AACTCTTGACCTTTC
1 AACTCTAGACCTTTC
52847774 A
1 A
52847775 CTTACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
AACTCTAGACCTTTC
Found at i:52848580 original size:25 final size:26
Alignment explanation
Indices: 52848552--52848604 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
52848542 CACTTTTGAG
52848552 TTAATAAAA-TTCT-TTGAGTTTTCTT
1 TTAA-AAAATTTCTCTTGAGTTTTCTT
*
52848577 TTAAAAAATTTCTCTTGAGTTTTTTT
1 TTAAAAAATTTCTCTTGAGTTTTCTT
52848603 TT
1 TT
52848605 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 8 0.32
26 13 0.52
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (26 bp):
TTAAAAAATTTCTCTTGAGTTTTCTT
Found at i:52849628 original size:20 final size:21
Alignment explanation
Indices: 52849603--52849642 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52849593 TGTCTTTATC
*
52849603 AATTTT-TATATAAATTTTAA
1 AATTTTCTAAATAAATTTTAA
*
52849623 AATTTTCTAAATAAGTTTTA
1 AATTTTCTAAATAAATTTTA
52849643 CTAATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTTTCTAAATAAATTTTAA
Found at i:52849731 original size:24 final size:24
Alignment explanation
Indices: 52849686--52849731 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
52849676 TCATTAACTG
*
52849686 TTAGGTACAAAAATAGTGCAAAGT
1 TTAGGTACAAAAATAGTACAAAGT
*
52849710 TTAGGTACCAAAATGAG-ACAAA
1 TTAGGTACAAAAAT-AGTACAAA
52849732 AATATAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (24 bp):
TTAGGTACAAAAATAGTACAAAGT
Found at i:52850851 original size:62 final size:62
Alignment explanation
Indices: 52850754--52850879 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
52850744 TATTTAGCAA
52850754 AATTTTACAAAATGAGGATTAGGGTTGAACTGTAGAATAAGAAAATCTATTTTTGAGGAATT
1 AATTTTACAAAATGAGGATTAGGGTTGAACTGTAGAATAAGAAAATCTATTTTTGAGGAATT
52850816 AATTTTACAAAATGAGGATTAGGGTTGAACTGTAGAATAAGAAAATCTATTTTTGAGGAATT
1 AATTTTACAAAATGAGGATTAGGGTTGAACTGTAGAATAAGAAAATCTATTTTTGAGGAATT
52850878 AA
1 AA
52850880 ATTATAGAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (62 bp):
AATTTTACAAAATGAGGATTAGGGTTGAACTGTAGAATAAGAAAATCTATTTTTGAGGAATT
Found at i:52856259 original size:24 final size:24
Alignment explanation
Indices: 52856227--52856274 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
52856217 CGAGGAGGTT
*
52856227 AAGCGCGTGGAGCACTAAAATAGA
1 AAGCGCGTGGAGAACTAAAATAGA
*
52856251 AAGCGCGTGGAGAACTAGAATAGA
1 AAGCGCGTGGAGAACTAAAATAGA
52856275 GACCGAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.31, T:0.12
Consensus pattern (24 bp):
AAGCGCGTGGAGAACTAAAATAGA
Found at i:52856873 original size:21 final size:22
Alignment explanation
Indices: 52856818--52856874 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
52856808 TATTAGGTTA
*
52856818 ATTGAATTGGTATGTTTATATATG
1 ATTGAA-T-GTATGTTTAAATATG
* *
52856842 ATTGAA-ATATGTTTAAATCT-
1 ATTGAATGTATGTTTAAATATG
52856862 ATTGAATGTATGT
1 ATTGAATGTATGT
52856875 ACAAATAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
24 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (22 bp):
ATTGAATGTATGTTTAAATATG
Found at i:52857106 original size:54 final size:54
Alignment explanation
Indices: 52857037--52857181 Score: 166
Period size: 54 Copynumber: 2.7 Consensus size: 54
52857027 GTATACTTAT
* * * * * *
52857037 CACACGGTCTGCGACACGACCGTGTGTATCAAGTTAGT-GAGTCACATGGTCTGG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACT-ACATGATATGG
* * *
52857091 CACACAGTCTACGACACAACTGTGTGTATCAAGTCAGTAAACTACATGATATGG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACTACATGATATGG
* * *
52857145 CACATGGTCTACGACATGGCCGTGTGTATCAAGTCAG
1 CACACGGTCTACGACACGACCGTGTGTATCAAGTCAG
52857182 AGAGTTACAC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 73 0.97
55 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (54 bp):
CACACGGTCTACGACACGACCGTGTGTATCAAGTCAGTAAACTACATGATATGG
Found at i:52857212 original size:42 final size:42
Alignment explanation
Indices: 52857153--52857235 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
52857143 GGCACATGGT
*
52857153 CTACGACATGGCCGTGTGTATC-AAGTCAGAGAGTTACACGGC
1 CTACGACAAGGCCGTGTG-ATCTAAGTCAGAGAGTTACACGGC
* *
52857195 CTACGACAAGGTCGTGTGATCTAAGTCAGTGAGTTACACGG
1 CTACGACAAGGCCGTGTGATCTAAGTCAGAGAGTTACACGG
52857236 TTTAAGACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (42 bp):
CTACGACAAGGCCGTGTGATCTAAGTCAGAGAGTTACACGGC
Found at i:52858020 original size:358 final size:358
Alignment explanation
Indices: 52857357--52858036 Score: 1094
Period size: 358 Copynumber: 1.9 Consensus size: 358
52857347 TTTCAATTTT
* *
52857357 TCCTTAGATTTTTTGAATTATTTCAAACTAGTCTCGTTTTGATCCCGAAATATTTTTAGGGCCTC
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTTAGGGCCTC
* * *
52857422 GAAAATTTAATTTAAGGCCTAAATGTTTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
66 GAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
**
52857487 ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCTGTAA
131 ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATAA
* * *
52857552 CCCTAGACCGGCGACGGAAACGGGTTAGGGGTGTTATATTAGGTCGACCTTTTTTAGCCACTGCT
196 CCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGCT
* *
52857617 AGAACTATTATTGATATGGGTACTGGTGAACTTGTGCTTGTGTAGGTGATGAAAAGATTACTCTT
261 AGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTT
52857682 CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
326 CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
* *
52857715 TCCTTAGATTTTCTGAATTATTTCAAATTAGTCCCGTTTTGATCTC-AAACTATTTTTAGGGCCT
1 TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAA-TATTTTTAGGGCCT
*
52857779 CGAAAATTTAATTTAATGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAA
65 CGAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAA
* * * *
52857844 TGTTGAATAGCATTATTAAATTGTTTAGATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATA
130 TATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATA
** * *
52857909 ACCCTAGACTTGCAATGGAAACTGGTTAGGGGTGTTACATTAGGTCGACC-CTTTTAGCCACTGC
195 ACCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGC
* * *
52857973 TAGAATTGTTATTGATATAGGTACTGGTGAACTTGTGCTTCGTGTAGGTGATAAAAATATTACT
260 TAGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTT-GTGTAGGTGATAAAAAGATTACT
52858037 GTGTGCCTCA
Statistics
Matches: 294, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
357 53 0.18
358 241 0.82
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (358 bp):
TCCTTAGATTTTCTGAATTATTTCAAACTAGTCCCGTTTTGATCCCGAAATATTTTTAGGGCCTC
GAAAATTTAATTTAAGGCCCAAATATGTATGTTTGTTGGATTTGTATGAGGTTTAAATAATTAAT
ATTGAATAGCATTATTAAACTATTTAAATGTTAATTGTTCTAATTTTTACGGTAATGCTCCATAA
CCCTAGACCGGCAACGGAAACGGGTTAGGGGTGTTACATTAGGTCGACCTCTTTTAGCCACTGCT
AGAACTATTATTGATATAGGTACTGGTGAACTTGTGCTTGTGTAGGTGATAAAAAGATTACTCTT
CAAGCACATGATTTTGTGAGAGTCCCTAGAGAA
Found at i:52862936 original size:102 final size:102
Alignment explanation
Indices: 52862760--52863125 Score: 619
Period size: 102 Copynumber: 3.6 Consensus size: 102
52862750 TAACCGTTAT
* *
52862760 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
52862825 AATCAGCACATAGCAACCCCCTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
52862862 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
52862927 AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
52862964 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
52863028 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATA
* * * **
52863067 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
52863126 TTTATATACA
Statistics
Matches: 253, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
101 28 0.11
102 159 0.63
103 65 0.26
104 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCATTTCAAAGATA
Found at i:52863026 original size:26 final size:26
Alignment explanation
Indices: 52862996--52863047 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
52862986 CACCAATGAA
*
52862996 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
52863022 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
52863048 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:52863485 original size:29 final size:29
Alignment explanation
Indices: 52863452--52863515 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
52863442 TAATCCACCA
52863452 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
52863481 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
52863511 CCCAA
1 CCCAA
52863516 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:52863489 original size:30 final size:30
Alignment explanation
Indices: 52863459--52863515 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52863449 CCACCCAACT
52863459 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
52863488 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
52863516 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:52865146 original size:22 final size:22
Alignment explanation
Indices: 52865099--52865146 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
52865089 ATGTCTTTTT
52865099 TTTTTCCTTTTTAAATCTATT-
1 TTTTTCCTTTTTAAATCTATTC
* * *
52865120 TTTTTTCTTTTCTTAATTTATTC
1 TTTTTCCTTTT-TAAATCTATTC
52865143 TTTT
1 TTTT
52865147 ATTTCATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTCCTTTTTAAATCTATTC
Found at i:52865195 original size:17 final size:15
Alignment explanation
Indices: 52865173--52865214 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 15
52865163 AATCATATTG
52865173 ATTTTATTTAGTTTTAT
1 ATTTTATTTA--TTTAT
52865190 ATTTTATTTATTTAT
1 ATTTTATTTATTTAT
52865205 ATTTCTATTT
1 ATTT-TATTT
52865215 CTATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTATTTATTTAT
Found at i:52865197 original size:26 final size:26
Alignment explanation
Indices: 52865168--52865246 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
52865158 ACCCCAATCA
*
52865168 TATTGATTTTATTTAGT-TTTATATTT
1 TATTGATTTTATTT-CTATTTATATTT
* *
52865194 TATTTATTTATATTTCTATTTCTATTT
1 TATTGATTT-TATTTCTATTTATATTT
* * * *
52865221 TTTTGTTTTTATTTTTATTTTTATTT
1 TATTGATTTTATTTCTATTTATATTT
52865247 ATGTTTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 24 0.56
27 19 0.44
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.75
Consensus pattern (26 bp):
TATTGATTTTATTTCTATTTATATTT
Found at i:52865199 original size:21 final size:20
Alignment explanation
Indices: 52865175--52865254 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 20
52865165 TCATATTGAT
52865175 TTTATTTAGTTTTATATTTTA
1 TTTATTTAGTTTT-TATTTTA
52865196 TTTATTTA-TATTTCTATTTCTA
1 TTTATTTAGT-TTT-TATTT-TA
*
52865218 TTT-TTTTGTTTTTATTTTTA
1 TTTATTTAGTTTTTA-TTTTA
52865238 TTTTTATTTATGTTTTT
1 --TTTATTTA-GTTTTT
52865255 CTGTTTTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
20 5 0.10
21 25 0.52
22 9 0.19
23 3 0.06
24 6 0.12
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTATTTAGTTTTTATTTTA
Found at i:52865240 original size:32 final size:30
Alignment explanation
Indices: 52865196--52865304 Score: 101
Period size: 32 Copynumber: 3.5 Consensus size: 30
52865186 TTATATTTTA
* *
52865196 TTTATTTATATTTCTATTTCTATTTTTTTGTT
1 TTTATTTTTATTTTTATTT-T-TTTTTTTGTT
*
52865228 TTTATTTTTATTTTTATTTATGTTTTTCTGTT
1 TTTATTTTTATTTTTATTT-T-TTTTTTTGTT
* * * **
52865260 TTTCTTCTTTGTTTTTGTTTTTGCTTTTGTT
1 TTTATT-TTTATTTTTATTTTTTTTTTTGTT
52865291 TTTATTTTTATTTT
1 TTTATTTTTATTTT
52865305 ATTATGCACT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 7 0.11
31 12 0.19
32 33 0.52
33 11 0.17
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (30 bp):
TTTATTTTTATTTTTATTTTTTTTTTTGTT
Done.