Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 95 of 228
Found at i:27710486 original size:33 final size:33
Alignment explanation
Indices: 27710435--27710503 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
27710425 GGGTTTGGGC
* *
27710435 AAAATCATTAGGCCCGAAAAATGGGCTTGAGCA
1 AAAATCATTAAGCACGAAAAATGGGCTTGAGCA
* * *
27710468 AAAATTATTAAGCACGAAACATGGGCTTGGGCA
1 AAAATCATTAAGCACGAAAAATGGGCTTGAGCA
27710501 AAA
1 AAA
27710504 TAATTAGGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (33 bp):
AAAATCATTAAGCACGAAAAATGGGCTTGAGCA
Found at i:27714321 original size:21 final size:21
Alignment explanation
Indices: 27714293--27714339 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
27714283 AATAAAAATT
*
27714293 ATAAAAATTATT-AAATTTTA
1 ATAAAAAATATTAAAATTTTA
27714313 ATAAAAAATATTAAAATTTTA
1 ATAAAAAATATTAAAATTTTA
*
27714334 TTAAAA
1 ATAAAA
27714340 TCAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAAAATATTAAAATTTTA
Found at i:27714625 original size:10 final size:10
Alignment explanation
Indices: 27714612--27714758 Score: 69
Period size: 10 Copynumber: 15.1 Consensus size: 10
27714602 CTTTATAAAA
27714612 TTTTATAATT
1 TTTTATAATT
*
27714622 TTTTCT-ATAT
1 TTTTATAAT-T
*
27714632 TTCTAT-ATT
1 TTTTATAATT
*
27714641 TTTTTTAATT
1 TTTTATAATT
*
27714651 TTTTATGA-T
1 TTTTATAATT
27714660 TTTTAT--TT
1 TTTTATAATT
*
27714668 TTTT-TAAGAT
1 TTTTATAA-TT
27714678 TTTTAT-ATT
1 TTTTATAATT
*
27714687 TTTTATGATT
1 TTTTATAATT
* *
27714697 TTTATAAAAAT
1 TTT-TATAATT
*
27714708 TTTTCTAATT
1 TTTTATAATT
* *
27714718 TTTAATAA-A
1 TTTTATAATT
27714727 TTTTA-AATGT
1 TTTTATAAT-T
27714737 TTTTATATATT
1 TTTTATA-ATT
* *
27714748 TCTTAAAATT
1 TTTTATAATT
27714758 T
1 T
27714759 AATATTTTTT
Statistics
Matches: 102, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
7 1 0.01
8 7 0.07
9 25 0.25
10 52 0.51
11 15 0.15
12 2 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:27714662 original size:18 final size:18
Alignment explanation
Indices: 27714642--27714702 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
27714632 TTCTATATTT
27714642 TTTTTA-ATTTTTTATGA
1 TTTTTATATTTTTTATGA
* *
27714659 TTTTTATTTTTTTTAAGA
1 TTTTTATATTTTTTATGA
27714677 TTTTTATATTTTTTATGA
1 TTTTTATATTTTTTATGA
27714695 TTTTTATA
1 TTTTTATA
27714703 AAAATTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 6 0.15
18 33 0.85
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTTATATTTTTTATGA
Found at i:27714673 original size:26 final size:26
Alignment explanation
Indices: 27714622--27714689 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
27714612 TTTTATAATT
*
27714622 TTTTCTATATTTCTATATTTTTTTTAA-T
1 TTTT-TATATTT-T-TATTTTTTTTAAGA
27714650 TTTTTATGATTTTTATTTTTTTTAAGA
1 TTTTTAT-ATTTTTATTTTTTTTAAGA
27714677 TTTTTATATTTTT
1 TTTTTATATTTTT
27714690 TATGATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 18 0.49
27 11 0.30
28 8 0.22
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (26 bp):
TTTTTATATTTTTATTTTTTTTAAGA
Found at i:27714691 original size:9 final size:9
Alignment explanation
Indices: 27714612--27714699 Score: 63
Period size: 9 Copynumber: 9.3 Consensus size: 9
27714602 CTTTATAAAA
27714612 TTTTATAATT
1 TTTTAT-ATT
*
27714622 TTTTCTATAT
1 TTTTATAT-T
*
27714632 TTCTATATT
1 TTTTATATT
*
27714641 TTTTTTAATT
1 TTTTAT-ATT
27714651 TTTTATGA-T
1 TTTTAT-ATT
*
27714660 TTTTATTTT
1 TTTTATATT
*
27714669 TTTTA-AGAT
1 TTTTATA-TT
27714678 TTTTATATT
1 TTTTATATT
27714687 TTTTATGATT
1 TTTTAT-ATT
27714697 TTT
1 TTT
27714700 ATAAAAATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 33 0.54
10 28 0.46
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTTATATT
Found at i:27714710 original size:21 final size:21
Alignment explanation
Indices: 27714686--27714743 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
27714676 ATTTTTATAT
27714686 TTTTTATGATTTTTATAAAAA
1 TTTTTATGATTTTTATAAAAA
* * *
27714707 TTTTTCTAATTTTTA-ATAAA
1 TTTTTATGATTTTTATAAAAA
*
27714727 TTTTAAATG-TTTTTATA
1 TTTT-TATGATTTTTATA
27714744 TATTTCTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTATGATTTTTATAAAAA
Found at i:27715434 original size:30 final size:28
Alignment explanation
Indices: 27715379--27715435 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
27715369 AATTGTAGAA
*
27715379 TAAATTGTAAACTTTGAGATATAGGGAC
1 TAAATTGTAAACTTTGAAATATAGGGAC
* *
27715407 TAAATTGTGAAATTTTTGAAATTTAGGGA
1 TAAATTGT-AAA-CTTTGAAATATAGGGA
27715436 TTTAAGTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 3 0.12
30 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (28 bp):
TAAATTGTAAACTTTGAAATATAGGGAC
Found at i:27715452 original size:18 final size:19
Alignment explanation
Indices: 27715423--27715458 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27715413 GTGAAATTTT
*
27715423 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
27715442 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
27715459 ATCTAGCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:27716018 original size:41 final size:38
Alignment explanation
Indices: 27715967--27716088 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 38
27715957 TTCTTCGACT
27715967 TTAAGTCGATGAGACACTAGGTGTCAATTTACTACTTCGAA
1 TTAA-TCGATGAGACACT-GGTGTCAATTTA-TACTTCGAA
* * * **
27716008 TTAATTCGATGAGGCATTGAGTGCCAA-TT-TACTTCGGT
1 TTAA-TCGATGAGACACTG-GTGTCAATTTATACTTCGAA
* *
27716046 TTAACCGATGAGACACTGGTTGTCAATTTATTACTTTGAA
1 TTAATCGATGAGACACTGG-TGTCAATTTA-TACTTCGAA
27716086 TTA
1 TTA
27716089 TCCAATGAGG
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
36 1 0.02
37 16 0.25
38 13 0.21
40 12 0.19
41 21 0.33
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (38 bp):
TTAATCGATGAGACACTGGTGTCAATTTATACTTCGAA
Found at i:27721898 original size:32 final size:31
Alignment explanation
Indices: 27721862--27721922 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
27721852 GTGCAAAATC
* *
27721862 TAAAACAATATTAACAACTAATTAAAATAAAA
1 TAAAACAATAATAACAA-TAATAAAAATAAAA
*
27721894 TAAAATAATAATAACAATAATAAAAATAA
1 TAAAACAATAATAACAATAATAAAAATAA
27721923 TTAACTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.25
Consensus pattern (31 bp):
TAAAACAATAATAACAATAATAAAAATAAAA
Found at i:27725987 original size:20 final size:20
Alignment explanation
Indices: 27725943--27725987 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
27725933 ACCAAAAAAA
*
27725943 CGATACCAAAATAAACTTAT
1 CGATACCAAAATAAAATTAT
*
27725963 TGATACC-AAATAAAATGTAT
1 CGATACCAAAATAAAAT-TAT
27725983 CGATA
1 CGATA
27725988 TTGGATCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.27
Consensus pattern (20 bp):
CGATACCAAAATAAAATTAT
Found at i:27728847 original size:27 final size:28
Alignment explanation
Indices: 27728809--27728861 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
27728799 AAACAATTTC
27728809 AAGTCATAAAATAT-TTTGAAAACAACT
1 AAGTCATAAAATATATTTGAAAACAACT
* *
27728836 AAGTGCAT-AAATTTATTTGAACACAA
1 AAGT-CATAAAATATATTTGAAAACAA
27728862 AATCAAGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.30
Consensus pattern (28 bp):
AAGTCATAAAATATATTTGAAAACAACT
Found at i:27735344 original size:40 final size:39
Alignment explanation
Indices: 27735260--27735444 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 39
27735250 TTGAATGATG
* * *
27735260 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
27735300 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* **
27735340 TCCGGGCTAAGCCCGAAGGCATTTGTGCGATTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
*
27735379 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
*
27735420 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
27735445 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.27
40 77 0.62
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:27735396 original size:79 final size:81
Alignment explanation
Indices: 27735260--27735444 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
27735250 TTGAATGATG
*
27735260 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
27735324 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * * **
27735339 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GATTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
27735401 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
27735419 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27735445 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 2 0.02
79 56 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:27735466 original size:79 final size:79
Alignment explanation
Indices: 27735313--27735477 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
27735303 GGACTAAGAT
* ** **
27735313 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGATTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAA
*
27735378 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
27735392 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGA-GGAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGATGGA-
* *
27735454 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
27735471 CCGAAGG
1 CCGAAGG
27735478 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.63
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAA
ATCCGGGTTAAATC
Found at i:27743232 original size:40 final size:39
Alignment explanation
Indices: 27743148--27743332 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 39
27743138 TTGAATGATG
* * *
27743148 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
27743188 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* **
27743228 TCCGGGCTAAGCCCGAAGGCATTTGTGCGATTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
*
27743267 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
*
27743308 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
27743333 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 34 0.27
40 77 0.62
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:27743284 original size:79 final size:81
Alignment explanation
Indices: 27743148--27743332 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
27743138 TTGAATGATG
*
27743148 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
27743212 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * * **
27743227 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GATTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
27743289 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
27743307 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27743333 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 2 0.02
79 56 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:27743354 original size:79 final size:79
Alignment explanation
Indices: 27743201--27743365 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
27743191 GGACTAAGAT
* ** **
27743201 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGATTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAA
*
27743266 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
27743280 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGA-GGAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGATGGA-
* *
27743342 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
27743359 CCGAAGG
1 CCGAAGG
27743366 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.63
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAA
ATCCGGGTTAAATC
Found at i:27750016 original size:15 final size:15
Alignment explanation
Indices: 27749996--27750043 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
27749986 ACTATCTTAA
27749996 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
27750011 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* * *
27750025 AGTTTATGGTTTAAG
1 GGTTTATGGATTATG
27750040 GGTT
1 GGTT
27750044 GTGGTTTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:27751496 original size:86 final size:86
Alignment explanation
Indices: 27751349--27751627 Score: 380
Period size: 86 Copynumber: 3.2 Consensus size: 86
27751339 TCCTTCTACT
* * * **
27751349 TTATAAAAGTTGAAAATTTGGTCTGGTTGTTGGTGAATGCATGAACTTGAACTGTTGATTTTTTC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTTC
*
27751414 TAATTTGTTGCACATGAGTTG
66 TAATTTGTTGCACATAAGTTG
*
27751435 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTTC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTTC
*
27751500 TAATTTGTTGCATATAAGTTG
66 TAATTTGTTGCACATAAGTTG
* * * * * *
27751521 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTTC
* *
27751586 TAATTTGTTGCATATAAATCT-
66 TAATTTGTTGCACATAAGT-TG
* *
27751607 TTATAGAAATTGAAGATTTAG
1 TTATAAAAATTGAAAATTTAG
27751628 CCCTATTGCC
Statistics
Matches: 172, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
86 171 0.99
87 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.43
Consensus pattern (86 bp):
TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTTC
TAATTTGTTGCACATAAGTTG
Found at i:27751642 original size:86 final size:85
Alignment explanation
Indices: 27751349--27751705 Score: 351
Period size: 86 Copynumber: 4.1 Consensus size: 85
27751339 TCCTTCTACT
* * * * ** *
27751349 TTATAAAAGTTGAAAATTTGGTCTGGTTGTTGGTGAATGCATGAACTTGAACTGTTGATTTTTTC
1 TTATAAAA-TTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
* *
27751414 TAATTTGTTGCACATGAGTTG
65 TAATTTGTTGCACATAAATTG
* * * *
27751435 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTTC
1 TTAT-AAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
* *
27751500 TAATTTGTTGCATATAAGTTG
65 TAATTTGTTGCACATAAATTG
* *
27751521 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
1 TTATAAA-ATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
*
27751586 TAATTTGTTGCATATAAATCT-
65 TAATTTGTTGCACATAAAT-TG
* * ** * * *
27751607 TTATAGAAATTGAAGATTTAGCCCT-ATTGCCGGTAAATATATGAACTATGAA-TAGTTGATTTG
1 TTATA-AAATTGAAAATTTAG-TCTGATTGTTGGTAAATACATGAACT-TGAACCA-TTGATTTT
* * *
27751670 TGCTATTTTGTTTCACATAAACTG
62 TGCTAATTTGTTGCACATAAATTG
* *
27751694 TTGTAAGATTGA
1 TTATAAAATTGA
27751706 TTTTTGATAA
Statistics
Matches: 234, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
85 3 0.01
86 189 0.81
87 42 0.18
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (85 bp):
TTATAAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCT
AATTTGTTGCACATAAATTG
Found at i:27751786 original size:40 final size:40
Alignment explanation
Indices: 27751702--27751778 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
27751692 TGTTGTAAGA
* *
27751702 TTGATTTTTGATAATTTCTTGCATATAAATTATTGAAATG
1 TTGATTTTTGATAATTGCTTACATATAAATTATTGAAATG
27751742 TTGATTTTTGATAATTGCTTACATATTAAA-TATTGAA
1 TTGATTTTTGATAATTGCTTACATA-TAAATTATTGAA
27751779 GTTTTGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (40 bp):
TTGATTTTTGATAATTGCTTACATATAAATTATTGAAATG
Found at i:27755378 original size:43 final size:43
Alignment explanation
Indices: 27755027--27755381 Score: 399
Period size: 43 Copynumber: 8.3 Consensus size: 43
27755017 ACAGTACTTT
* * * *
27755027 TAGCGGCGTTTTTGGGTAAAGCACCGCT-AAAGATCATGTTCTT
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAG-TCATGATCTA
* * * * * * * *
27755070 TAGCAGTGTTTG-GTGGTAAAGCGCTGCTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTG-GGAAAAGCACCGCTAAAAGTCATGATCTA
* * * * * *
27755113 TAGCGGCATTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
* * *
27755156 TAGCGGCATTTGTGGGTAAAGCGCCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
* * * *
27755199 TAGCAGCGTTTGTGGGAAAAGTACCGCTAAAAGTCATGTTTTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
* *
27755242 TAACGGCGTTTGTGGGAAAAGCATCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
* *
27755285 TAGCGGCGTTTGTGGGAAAAGCGCCACTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
* *
27755328 TAGCGGCGTTTGTGGGAAAAGCACTGCTATAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
27755371 TAGCGGCGTTT
1 TAGCGGCGTTT
27755382 ATTTTTAAAA
Statistics
Matches: 275, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.00
43 270 0.98
44 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAGTCATGATCTA
Found at i:27757023 original size:39 final size:38
Alignment explanation
Indices: 27756935--27757024 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
27756925 TTTGAATATT
* * * * * *
27756935 GTGATATATACTTGAATGTTATGTGATTTTAGAGTATT
1 GTGATATATGCTTAAATGTCATGGGATTATAGAGTATG
* * *
27756973 ATGACACATGCTTAAATGTCATGGGATTATATGAGTATG
1 GTGATATATGCTTAAATGTCATGGGATTATA-GAGTATG
27757012 GTGATATATGCTT
1 GTGATATATGCTT
27757025 GTATGCTAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
38 23 0.59
39 16 0.41
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (38 bp):
GTGATATATGCTTAAATGTCATGGGATTATAGAGTATG
Found at i:27760565 original size:26 final size:26
Alignment explanation
Indices: 27760535--27760610 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
27760525 TCTCATCCCT
*
27760535 ATTTTACCCTC-GATAATATTTTGATG
1 ATTTTACCC-CAGATAAAATTTTGATG
**
27760561 ATTTTACCCCAGATAAAATTTTGACA
1 ATTTTACCCCAGATAAAATTTTGATG
*
27760587 ATTTTGCCCCA-AGTAAAATTTTGA
1 ATTTTACCCCAGA-TAAAATTTTGA
27760611 AAAAATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.05
26 42 0.95
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCAGATAAAATTTTGATG
Found at i:27762571 original size:26 final size:26
Alignment explanation
Indices: 27762532--27762611 Score: 124
Period size: 26 Copynumber: 3.1 Consensus size: 26
27762522 ATGGTGGTCT
* * *
27762532 TTACGGACTAATACTTGAAATAGTCC
1 TTACGGACTCATACATGGAATAGTCC
*
27762558 TTACAGACTCATACATGGAATAGTCC
1 TTACGGACTCATACATGGAATAGTCC
27762584 TTACGGACTCATACATGGAATAGTCC
1 TTACGGACTCATACATGGAATAGTCC
27762610 TT
1 TT
27762612 GTGGAGTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (26 bp):
TTACGGACTCATACATGGAATAGTCC
Found at i:27765187 original size:20 final size:20
Alignment explanation
Indices: 27765162--27765201 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27765152 ACATCAATGC
27765162 CCCTTTGGTAATTAGATATG
1 CCCTTTGGTAATTAGATATG
27765182 CCCTTTGGTAATTAGATATG
1 CCCTTTGGTAATTAGATATG
27765202 GTACTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
CCCTTTGGTAATTAGATATG
Found at i:27769715 original size:24 final size:24
Alignment explanation
Indices: 27769683--27769729 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
27769673 TTATAAATAA
27769683 CATTCAACAAAGGGAGGTAATTAG
1 CATTCAACAAAGGGAGGTAATTAG
*
27769707 CATTCAACAAAGGGAGGTTATTA
1 CATTCAACAAAGGGAGGTAATTA
27769730 CTTATTAGCA
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:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (24 bp):
CATTCAACAAAGGGAGGTAATTAG
Found at i:27770046 original size:22 final size:22
Alignment explanation
Indices: 27769999--27770043 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27769989 ATGCAATCTT
*
27769999 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCCTAGA
* *
27770021 AGATATGACTTTGTAATCCTAGA
1 AGATATGA-TATGCAATCCTAGA
27770044 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
AGATATGATATGCAATCCTAGA
Found at i:27770661 original size:36 final size:36
Alignment explanation
Indices: 27770586--27770661 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
27770576 CATACATACG
*
27770586 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
27770623 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
27770659 TTT
1 TTT
27770662 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:27770766 original size:31 final size:30
Alignment explanation
Indices: 27770728--27770808 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 30
27770718 GTATATTTAT
27770728 ATATATATTTTATTTTTTATAATTCACATAC
1 ATATATATTTTATTTTTTATAATT-ACATAC
* *
27770759 ATATATA--TT-TTTCTTAT-ATGTACATAT
1 ATATATATTTTATTTTTTATAAT-TACATAC
*
27770786 ATATAT-TTTTATATTTTATAATT
1 ATATATATTTTATTTTTTATAATT
27770809 TTTATCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
27 13 0.32
28 10 0.24
29 9 0.22
30 2 0.05
31 7 0.17
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (30 bp):
ATATATATTTTATTTTTTATAATTACATAC
Found at i:27770785 original size:23 final size:22
Alignment explanation
Indices: 27770756--27770799 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
27770746 ATAATTCACA
*
27770756 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
27770779 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
27770800 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:27772462 original size:11 final size:11
Alignment explanation
Indices: 27772448--27772478 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
27772438 TAAAAAAAGT
27772448 ATTTTAAAAAC
1 ATTTTAAAAAC
*
27772459 ATTTTAAAAAT
1 ATTTTAAAAAC
27772470 ATTTTAAAA
1 ATTTTAAAA
27772479 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTTAAAAAC
Found at i:27772504 original size:41 final size:40
Alignment explanation
Indices: 27772459--27772536 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 40
27772449 TTTTAAAAAC
27772459 ATTTTAAAAATATTTTAAAATTAAAAAATAATAAAAAAAGT
1 ATTTTAAAAATATTTTAAAATTAAAAAA-AATAAAAAAAGT
*
27772500 ATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAA
1 ATTTTAAAAATATTTTAAAATTAAAAAAAATAAAAAA
27772537 TAAATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (40 bp):
ATTTTAAAAATATTTTAAAATTAAAAAAAATAAAAAAAGT
Found at i:27773266 original size:17 final size:17
Alignment explanation
Indices: 27773230--27773265 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27773220 CAACCTTTAA
27773230 TTTCCATTAAATAATTT
1 TTTCCATTAAATAATTT
*
27773247 TTTCCTTTAAAT-ATTT
1 TTTCCATTAAATAATTT
27773263 TTT
1 TTT
27773266 TTAAATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTCCATTAAATAATTT
Found at i:27773727 original size:12 final size:12
Alignment explanation
Indices: 27773710--27773739 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
27773700 TAATCCTCTC
27773710 AATTTCCTTCCA
1 AATTTCCTTCCA
27773722 AATTTCCTTCCA
1 AATTTCCTTCCA
27773734 AATTTC
1 AATTTC
27773740 TCTCAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (12 bp):
AATTTCCTTCCA
Found at i:27773782 original size:51 final size:51
Alignment explanation
Indices: 27773708--27773829 Score: 192
Period size: 51 Copynumber: 2.4 Consensus size: 51
27773698 TCTAATCCTC
*
27773708 TCAATTTCCT-TCCAAATTTCCTTCCAAATTTCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCT-C-AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
27773760 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
27773811 TCAATTTCCCCTCAATTTC
1 TCAATTTCCTCTCAATTTC
27773830 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 54 0.82
52 11 0.17
53 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:27773873 original size:30 final size:31
Alignment explanation
Indices: 27773837--27773894 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
27773827 TTCATTTTTT
27773837 AAAATAA-TTTAAATTTTTTTATATTTTTAA
1 AAAATAATTTTAAATTTTTTTATATTTTTAA
27773867 AAAATAATTTTAAATTTTTTTATATTTT
1 AAAATAATTTTAAATTTTTTTATATTTT
27773895 CATCAATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
AAAATAATTTTAAATTTTTTTATATTTTTAA
Found at i:27774984 original size:7 final size:7
Alignment explanation
Indices: 27774972--27774996 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27774962 AGTCGATTGA
27774972 TATTTAG
1 TATTTAG
27774979 TATTTAG
1 TATTTAG
27774986 TATTTAG
1 TATTTAG
27774993 TATT
1 TATT
27774997 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:27776115 original size:25 final size:25
Alignment explanation
Indices: 27776086--27776271 Score: 85
Period size: 25 Copynumber: 7.7 Consensus size: 25
27776076 TTTAAATTTA
27776086 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
** *
27776111 TTATTTGATGTAATACGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
27776137 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
27776156 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
* ** *
27776182 TTATTTGATATAATAGGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
27776208 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
*
27776227 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
27776253 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
27776272 ACCCTAATTT
Statistics
Matches: 116, Mismatches: 24, Indels: 41
0.64 0.13 0.23
Matches are distributed among these distances:
19 2 0.02
20 10 0.09
21 13 0.11
23 4 0.03
24 6 0.05
25 41 0.35
26 40 0.34
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:27776172 original size:71 final size:71
Alignment explanation
Indices: 27776084--27776268 Score: 334
Period size: 71 Copynumber: 2.6 Consensus size: 71
27776074 TATTTAAATT
27776084 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
27776149 TTTTGA
66 TTTTGA
* *
27776155 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
27776220 TTTTGA
66 TTTTGA
*
27776226 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
27776269 AAAACCCTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
71 96 0.88
72 13 0.12
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
TTTTGA
Found at i:27776316 original size:29 final size:29
Alignment explanation
Indices: 27776274--27776481 Score: 320
Period size: 30 Copynumber: 7.3 Consensus size: 29
27776264 TAATAAAAAC
27776274 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
27776303 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
27776333 TCTAATTTAATTAAAAACCCTAAAACCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
27776363 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
27776392 CCTAATTTAATT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
27776415 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
27776444 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
27776474 CCTAATTT
1 CCTAATTT
27776482 TACATAATTT
Statistics
Matches: 166, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
23 20 0.12
25 3 0.02
27 3 0.02
29 68 0.41
30 72 0.43
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:27776325 original size:23 final size:23
Alignment explanation
Indices: 27776295--27776439 Score: 110
Period size: 23 Copynumber: 5.4 Consensus size: 23
27776285 TAAAAACCCT
27776295 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
27776318 AACCCTAAACCCTAATCTAATTTAATTAAA
1 AACCCT-AA--C----CTAATTTAATTAAA
27776348 AACCCTAAAACCTAACCTAATTTAATTAAAA
1 AA-CC------CTAACCTAATTTAATT-AAA
27776379 ACCCTAACCCTAACCTAATTTAATTAAA
1 A----A-CCCTAACCTAATTTAATTAAA
27776407 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
27776430 AACCCTAACC
1 AACCCTAACC
27776440 CTAACCTAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 38
0.72 0.01 0.27
Matches are distributed among these distances:
23 37 0.36
24 3 0.03
26 1 0.01
28 4 0.04
29 16 0.16
30 27 0.26
31 6 0.06
34 1 0.01
35 3 0.03
36 2 0.02
37 2 0.02
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:27776418 original size:52 final size:52
Alignment explanation
Indices: 27776354--27776462 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
27776344 TAAAAACCCT
27776354 AAAA-CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
27776405 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
27776457 AAAACC
1 AAAACC
27776463 TTAAACCCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 4 0.07
52 53 0.93
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.28
Consensus pattern (52 bp):
AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
Found at i:27776426 original size:82 final size:82
Alignment explanation
Indices: 27776324--27776481 Score: 273
Period size: 82 Copynumber: 1.9 Consensus size: 82
27776314 TAAAAACCCT
*
27776324 AAACCCTAATCTAATTTAATTAAAAACCCTAAAACCTAACCTAATTTAATTAAAAACCCT-AACC
1 AAACCCTAACCTAATTTAATTAAAAACCCT-AAACCTAACCTAATTTAATTAAAAACCCTAAACC
27776388 CTAACCTAATTTAATTAA
65 CTAACCTAATTTAATTAA
* *
27776406 AAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCTTAAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCCTAAACCTAACCTAATTTAATTAAAAACCCTAAACCC
27776471 TAACCTAATTT
66 TAACCTAATTT
27776482 TACATAATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
81 27 0.38
82 45 0.62
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (82 bp):
AAACCCTAACCTAATTTAATTAAAAACCCTAAACCTAACCTAATTTAATTAAAAACCCTAAACCC
TAACCTAATTTAATTAA
Found at i:27776545 original size:10 final size:10
Alignment explanation
Indices: 27776530--27776554 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27776520 TTTGGACTTA
27776530 ATAATTTTAC
1 ATAATTTTAC
27776540 ATAATTTTAC
1 ATAATTTTAC
27776550 ATAAT
1 ATAAT
27776555 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:27779212 original size:124 final size:124
Alignment explanation
Indices: 27779040--27779387 Score: 536
Period size: 124 Copynumber: 2.8 Consensus size: 124
27779030 CAAACTTCCT
* * * * **
27779040 ACTGTAGCAAAATCGCGTCCACGAAGGCGCGATTTCACAATTTTTTCTCAAATAGCATTCTAATA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* *
27779105 GAAGCGATATTATACTATTTGCTTAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
*
27779164 ACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
*
27779229 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
*** * *
27779288 ACTGTAATGAAACCGCGTCCACGAGGGCGA-GATTTCGCAATTTCTTCTCAAATAGCATCCTGGT
1 ACTGTAGCAAAATCGCGTCCACGAGGGC-ACGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
*
27779352 AGAACCGATTTTATACTATTTGCTCAGAAACGTCAA
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
27779388 CTCGAAATAA
Statistics
Matches: 206, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
124 205 1.00
125 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
Found at i:27782340 original size:12 final size:12
Alignment explanation
Indices: 27782315--27782353 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27782305 ACTCGCTTCT
* *
27782315 TTACTTACTCAC
1 TTACTTGCTTAC
*
27782327 TTACTTGTTTAC
1 TTACTTGCTTAC
27782339 TTACTTGCTTAC
1 TTACTTGCTTAC
27782351 TTA
1 TTA
27782354 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:27782678 original size:50 final size:50
Alignment explanation
Indices: 27782602--27782747 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
27782592 TTTTCTGTAT
* * **
27782602 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
27782652 TGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
27782702 CGCCAACCCCATGTCCCAGACATGGACTTAAATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
27782748 ATCTCAATAA
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:27783118 original size:43 final size:43
Alignment explanation
Indices: 27783007--27783097 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
27782997 GTACAAAATA
*
27783007 TGATCAAATCTAGCACTTTAGTCTTCAACCTTTTTTCTTTCCC
1 TGATCAAATCTAGCACTTTTGTCTTCAACCTTTTTTCTTTCCC
27783050 TGATCAAATCTAGCACTTTTGTCTTCAACCTTTTTTCTTTCCC
1 TGATCAAATCTAGCACTTTTGTCTTCAACCTTTTTTCTTTCCC
27783093 TGATC
1 TGATC
27783098 TAACTCTGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.45
Consensus pattern (43 bp):
TGATCAAATCTAGCACTTTTGTCTTCAACCTTTTTTCTTTCCC
Found at i:27789925 original size:12 final size:12
Alignment explanation
Indices: 27789900--27789938 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27789890 ACTCGCTTCT
* *
27789900 TTACTTACTCAC
1 TTACTTGCTTAC
*
27789912 TTACTTGTTTAC
1 TTACTTGCTTAC
27789924 TTACTTGCTTAC
1 TTACTTGCTTAC
27789936 TTA
1 TTA
27789939 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:27790266 original size:50 final size:49
Alignment explanation
Indices: 27790200--27790332 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 49
27790190 CAATGTCATA
* ** *
27790200 TCCCAGATATGGTCTTACATAGGAGTTCTCATATCGGTGCGC-ATGCCATG
1 TCCCAGACATGGTCTTACAT-GGACCTCTCATATCGGTGC-CAACGCCATG
** * *
27790250 TCTTAGACATGGTCTTACGGTGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTAC-ATGGACCTCTCATATCGGTGCCAACGCCATG
27790300 TCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TCCCAGACATGGTCTTACAT-GGACCTCTCATA
27790333 ATCTCAATAA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
49 2 0.03
50 65 0.96
51 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:27792266 original size:28 final size:27
Alignment explanation
Indices: 27792231--27792320 Score: 64
Period size: 26 Copynumber: 3.4 Consensus size: 27
27792221 CATATTTGTA
*
27792231 ATATTAT-TAGTATTTATTTTTAAATT
1 ATATTATATTGTATTTATTTTTAAATT
* * *
27792257 ATATTATATTTTAACTTATCTTT-AATT
1 ATATTATATTGT-ATTTATTTTTAAATT
*
27792284 -TATTATATTG--TTAATTTTTTAAATTT
1 ATATTATATTGTATTTA-TTTTTAAA-TT
27792310 ATAATTATATT
1 AT-ATTATATT
27792321 AGTAATCTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
23 2 0.04
24 4 0.08
25 2 0.04
26 18 0.37
27 7 0.14
28 16 0.33
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTATATTGTATTTATTTTTAAATT
Found at i:27793116 original size:20 final size:21
Alignment explanation
Indices: 27793079--27793117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27793069 TCATGAAGTT
* *
27793079 AAGAAAATAACTCTTAATTTA
1 AAGAAAATAACACGTAATTTA
27793100 AAGAAAATAA-ACGTAATT
1 AAGAAAATAACACGTAATT
27793118 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (21 bp):
AAGAAAATAACACGTAATTTA
Found at i:27794831 original size:22 final size:22
Alignment explanation
Indices: 27794798--27794848 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
27794788 CTTAATTTTT
27794798 TTTTGCTTTTGTTTTACTATCA
1 TTTTGCTTTTGTTTTACTATCA
* *
27794820 TTTTG-TTGTTGTTTTGCTGTCA
1 TTTTGCTT-TTGTTTTACTATCA
27794842 TTTTGCT
1 TTTTGCT
27794849 ATTATACTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 22 0.88
23 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.16, T:0.65
Consensus pattern (22 bp):
TTTTGCTTTTGTTTTACTATCA
Found at i:27796307 original size:78 final size:78
Alignment explanation
Indices: 27796178--27796336 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 78
27796168 TTAGCTGTCA
27796178 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
1 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
27796243 TTAATATTCAAAC
66 TTAATATTCAAAC
*
27796256 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTTATTGTCTATATAATACGTGGATCTT
1 CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
27796321 TTAATATTCAAAC
66 TTAATATTCAAAC
27796334 CTT
1 CTT
27796337 TGGAGTATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (78 bp):
CTTGCCATGCATGACTTTGCATGTTTCTTGTCCCTATTTGATTGTCTATATAATACGTGGATCTT
TTAATATTCAAAC
Found at i:27812139 original size:15 final size:15
Alignment explanation
Indices: 27812121--27812152 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27812111 GGCTAGGGGT
27812121 ATTGGGCTTAGGCTA
1 ATTGGGCTTAGGCTA
*
27812136 ATTGGGTTTAGGCTA
1 ATTGGGCTTAGGCTA
27812151 AT
1 AT
27812153 AGGGTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (15 bp):
ATTGGGCTTAGGCTA
Found at i:27812157 original size:15 final size:15
Alignment explanation
Indices: 27812128--27812161 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
27812118 GGTATTGGGC
*
27812128 TTAGGCTAATTGGGT
1 TTAGGCTAATAGGGT
27812143 TTAGGCTAATAGGGT
1 TTAGGCTAATAGGGT
27812158 TTAG
1 TTAG
27812162 TTTACTGGGC
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:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (15 bp):
TTAGGCTAATAGGGT
Found at i:27813307 original size:18 final size:18
Alignment explanation
Indices: 27813272--27813310 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27813262 GAAAAAATGA
*
27813272 AAAAATAATTAAAAAAAT
1 AAAAATAAATAAAAAAAT
* *
27813290 AAAAATAAATAGATAAAT
1 AAAAATAAATAAAAAAAT
27813308 AAA
1 AAA
27813311 TGAAGGTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATAAATAAAAAAAT
Found at i:27814697 original size:20 final size:20
Alignment explanation
Indices: 27814672--27814716 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27814662 CCATGAATTG
*
27814672 TTTTATTGATAAGATTATAA
1 TTTTATTGATAAAATTATAA
* *
27814692 TTTTATTTATAAAATTATTA
1 TTTTATTGATAAAATTATAA
27814712 TTTTA
1 TTTTA
27814717 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTATTGATAAAATTATAA
Found at i:27816980 original size:3 final size:3
Alignment explanation
Indices: 27816963--27817003 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
27816953 TCGCCTTTGC
*
27816963 CTT C-T CTT CCTT CTT CTT CTC CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
27817004 CTTTGTCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:27818361 original size:23 final size:23
Alignment explanation
Indices: 27818312--27818361 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
27818302 AAAATTAAGT
*
27818312 AAAACATTAAAGCATTCCAATAT
1 AAAACATTAAAGCATTCCAATAC
* *
27818335 AAAACATT-AAGACATTTCAATCC
1 AAAACATTAAAG-CATTCCAATAC
27818358 AAAA
1 AAAA
27818362 GTAACCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAACATTAAAGCATTCCAATAC
Found at i:27820110 original size:26 final size:26
Alignment explanation
Indices: 27820081--27820131 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
27820071 ATATACCCAT
*
27820081 GAACTGCTTA-ATACCCCAATGAACAA
1 GAACTG-TTATATACCCCAACGAACAA
27820107 GAACTGTTATATACCCCAACGAACA
1 GAACTGTTATATACCCCAACGAACA
27820132 TTGCTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (26 bp):
GAACTGTTATATACCCCAACGAACAA
Found at i:27827566 original size:20 final size:20
Alignment explanation
Indices: 27827521--27827566 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
27827511 GGTGATATTT
27827521 TCTTTATAATATTAACAACA
1 TCTTTATAATATTAACAACA
* *
27827541 TATTTATACTATTAATCAA-A
1 TCTTTATAATATTAA-CAACA
27827561 TCTTTA
1 TCTTTA
27827567 ATTGAGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
TCTTTATAATATTAACAACA
Found at i:27827904 original size:37 final size:37
Alignment explanation
Indices: 27827855--27827927 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
27827845 TAATCTTTTT
*
27827855 TATTTTAATATTT-TATATATTTTATTTT-TAAACTATA
1 TATTTTAATATTTAT-TATATATTATTTTAT-AACTATA
*
27827892 TATTTTATTATTTATTATATATTATTTTATAACTAT
1 TATTTTAATATTTATTATATATTATTTTATAACTAT
27827928 GGTTTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (37 bp):
TATTTTAATATTTATTATATATTATTTTATAACTATA
Found at i:27833921 original size:92 final size:92
Alignment explanation
Indices: 27833751--27833931 Score: 249
Period size: 92 Copynumber: 2.0 Consensus size: 92
27833741 ACAGAGGAAG
* *
27833751 TAGTCGACAGTTCATTTGCTCGACCAGTGGTTTATCCACAATATATTAGCAACTTTTATCTACAC
1 TAGTCGACAGTTCATCTGCTCGACCAGTGGTTTATCAACAATATATTAGCAACTTTTATCTACAC
27833816 AAATGAATGGTTCATCCACCAATACTC
66 AAATGAATGGTTCATCCACCAATACTC
* * **
27833843 TAGTCGGCAG-TCATCTGCTCGACTAGTGGTTTATCAACAACT-TATTAGCATTTTTTTATCTAC
1 TAGTCGACAGTTCATCTGCTCGACCAGTGGTTTATCAACAA-TATATTAGCA-ACTTTTATCTAC
* * *
27833906 ACAGATGGATGGTTCATCCATCAATA
64 ACAAATGAATGGTTCATCCACCAATA
27833932 TATTTATCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
91 35 0.45
92 43 0.55
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (92 bp):
TAGTCGACAGTTCATCTGCTCGACCAGTGGTTTATCAACAATATATTAGCAACTTTTATCTACAC
AAATGAATGGTTCATCCACCAATACTC
Found at i:27836285 original size:71 final size:71
Alignment explanation
Indices: 27836101--27836381 Score: 253
Period size: 71 Copynumber: 4.0 Consensus size: 71
27836091 GAAATGATTT
* ** * **
27836101 CACACATA-TTAGTCGGTTTTACTGACCAATGCAGGGCGCATTTATTGTCAGTTATATTGACCAG
1 CACACATATTTA-TCGGTTTTACCGACCAGCGCAGGACGCATTTATTGTCAGTTATACCGACCAG
*
27836165 TGCGGGG
65 TGCTGGG
* * * * * * **
27836172 AACACATATTTGTCAGTTTTACCGACCAGCGTA-CATCACATTTATTGTTGGTTATACCGACCAG
1 CACACATATTTATCGGTTTTACCGACCAGCGCAGGA-CGCATTTATTGTCAGTTATACCGACCAG
27836236 TGCTGGG
65 TGCTGGG
* * * ** *
27836243 CACACATATTTATCGGTTTTATCGACTAGTGCAGGGTGCATTTATTGTCAATTATACCGACCAGT
1 CACACATATTTATCGGTTTTACCGACCAGCGCAGGACGCATTTATTGTCAGTTATACCGACCAGT
*
27836308 GCTGTG
66 GCTGGG
* * * * * * *
27836314 CACACATATTTTTTGGTTCTACCGACCAGCGCAAGACGCATTTATTAT-TGTTTATACCGACCAA
1 CACACATATTTATCGGTTTTACCGACCAGCGCAGGACGCATTTATTGTCAG-TTATACCGACCAG
27836378 TGCT
65 TGCT
27836382 ACGAACACTC
Statistics
Matches: 163, Mismatches: 43, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
71 161 0.99
72 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (71 bp):
CACACATATTTATCGGTTTTACCGACCAGCGCAGGACGCATTTATTGTCAGTTATACCGACCAGT
GCTGGG
Found at i:27836357 original size:142 final size:142
Alignment explanation
Indices: 27836101--27836381 Score: 343
Period size: 142 Copynumber: 2.0 Consensus size: 142
27836091 GAAATGATTT
* **
27836101 CACACATATTAGTCGGTTTTACTGACCAATGCAGGGCGCATTTATTGTCAGTTATATTGACCAGT
1 CACACATATTAGTCGGTTTTACTGACCAATGCAGGGCGCATTTATTGTCAATTATACCGACCAGT
* * * *
27836166 GCGGGGAACACATATTTGTCAGTTTTACCGACCAGCGTACATCACATTTATTGTTGGTTATACCG
66 GCGGGGAACACATATTTGTCAGTTCTACCGACCAGCGCACAACACATTTATTATTGGTTATACCG
*
27836231 ACCAGTGCTGGG
131 ACCAATGCTGGG
* * *
27836243 CACACATATTTA-TCGGTTTTA-TCGACTAGTGCAGGGTGCATTTATTGTCAATTATACCGACCA
1 CACACATA-TTAGTCGGTTTTACT-GACCAATGCAGGGCGCATTTATTGTCAATTATACCGACCA
* * * * ** * *
27836306 GTGCTGTGCACACATATTTTTTGGTTCTACCGACCAGCGCA-AGACGCATTTATTATTGTTTATA
64 GTGCGGGGAACACATATTTGTCAGTTCTACCGACCAGCGCACA-ACACATTTATTATTGGTTATA
27836370 CCGACCAATGCT
128 CCGACCAATGCT
27836382 ACGAACACTC
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
141 2 0.02
142 112 0.96
143 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (142 bp):
CACACATATTAGTCGGTTTTACTGACCAATGCAGGGCGCATTTATTGTCAATTATACCGACCAGT
GCGGGGAACACATATTTGTCAGTTCTACCGACCAGCGCACAACACATTTATTATTGGTTATACCG
ACCAATGCTGGG
Found at i:27840775 original size:29 final size:29
Alignment explanation
Indices: 27840751--27840809 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
27840741 GTCACATGGT
27840751 CATGTGTCACACACAGCCTACCACACGGC
1 CATGTGTCACACACAGCCTACCACACGGC
* * *
27840780 CATGTGTTACACACATCCTACCACAAGGC
1 CATGTGTCACACACAGCCTACCACACGGC
27840809 C
1 C
27840810 TGGCACACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.39, G:0.15, T:0.17
Consensus pattern (29 bp):
CATGTGTCACACACAGCCTACCACACGGC
Found at i:27841359 original size:13 final size:13
Alignment explanation
Indices: 27841334--27841370 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27841324 ACGAAAGGAC
27841334 AAAAGAAAGAAAAA
1 AAAAGAAA-AAAAA
27841348 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
*
27841361 CAAAGAAAAA
1 AAAAGAAAAA
27841371 TCAATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:27856711 original size:7 final size:7
Alignment explanation
Indices: 27856699--27856751 Score: 74
Period size: 7 Copynumber: 7.7 Consensus size: 7
27856689 CTTTTCAACA
*
27856699 AAAAAAC
1 AAAAAAT
27856706 AAAAAAT
1 AAAAAAT
27856713 AAAAAAAT
1 -AAAAAAT
27856721 AAAAAAT
1 AAAAAAT
27856728 AAAAAAT
1 AAAAAAT
27856735 -AAAAAT
1 AAAAAAT
27856741 -AAAAAT
1 AAAAAAT
27856747 AAAAA
1 AAAAA
27856752 TACTCCTCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 12 0.28
7 24 0.56
8 7 0.16
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:27856716 original size:6 final size:6
Alignment explanation
Indices: 27856715--27856753 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
27856705 CAAAAAATAA
27856715 AAAAAT AAAAAAT AAAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT A
27856754 CTCCTCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:27856718 original size:15 final size:14
Alignment explanation
Indices: 27856698--27856751 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
27856688 TCTTTTCAAC
27856698 AAAAAAACAAAAAAT
1 AAAAAAA-AAAAAAT
27856713 AAAAAAATAAAAAAT
1 AAAAAAA-AAAAAAT
*
27856728 -AAAAAATAAAAAT
1 AAAAAAAAAAAAAT
27856741 AAAAATAAAAA
1 AAAAA-AAAAA
27856752 TACTCCTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.18
14 10 0.29
15 18 0.53
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:27859010 original size:22 final size:21
Alignment explanation
Indices: 27858984--27859029 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27858974 ATTTTATCAA
*
27858984 TTTTGAACTCAAGTATGGATAT
1 TTTTGAA-TCAAGTATCGATAT
* *
27859006 TTTTGTATCTAGTATCGATAT
1 TTTTGAATCAAGTATCGATAT
27859027 TTT
1 TTT
27859030 ATCATATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTTGAATCAAGTATCGATAT
Found at i:27860773 original size:5 final size:5
Alignment explanation
Indices: 27860765--27860794 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
27860755 TCTAATCTAG
*
27860765 ACTAT ACTAT ACTAT ACTAT ATTAT ACTAT
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT
27860795 TTATTAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (5 bp):
ACTAT
Found at i:27884448 original size:19 final size:19
Alignment explanation
Indices: 27884424--27884463 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27884414 ATTAATTTTG
*
27884424 ATCAAATGAAATGAAATTA
1 ATCAAATGAAATAAAATTA
* *
27884443 ATCAAATTAATTAAAATTA
1 ATCAAATGAAATAAAATTA
27884462 AT
1 AT
27884464 ATGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCAAATGAAATAAAATTA
Found at i:27885212 original size:13 final size:12
Alignment explanation
Indices: 27885172--27885209 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27885162 TGTGGCTGGT
27885172 AATTTTTGTGAA
1 AATTTTTGTGAA
*
27885184 AATTTTT-TGCGA
1 AATTTTTGTG-AA
27885196 AATTTTTGTGAA
1 AATTTTTGTGAA
27885208 AA
1 AA
27885210 ATTATCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (12 bp):
AATTTTTGTGAA
Found at i:27886122 original size:91 final size:92
Alignment explanation
Indices: 27885969--27886200 Score: 337
Period size: 91 Copynumber: 2.6 Consensus size: 92
27885959 TTAATGGTGC
* * *
27885969 AAAAAA-ACCCTCAAACTTTTTC-AAAAAAAGCAATTTAGCCTCTGCTTTTTTTTTGCACTCAAT
1 AAAAAAGACCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAAT
*
27886032 TGGGTACTTGAACTTTCAAAATGCAT-
66 TGGGTACTTGAACCTTCAAAATGCATA
* * *
27886058 CAAAAAGGCCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACTCAAT
1 AAAAAAGACCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAAT
27886123 TGGGTACTTGAACCTTCAAAATGCATA
66 TGGGTACTTGAACCTTCAAAATGCATA
* * *
27886150 AAAAAATACCCTCAAA-CTTATTAAAAAAAAAGTAATTAAGCCCCTGCTTTT
1 AAAAAAGACCCTCAAACCTT-TTCAAAAAAAAGCAATTAAGCCCCTGCTTTT
27886201 ATTAAAAATT
Statistics
Matches: 126, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
89 5 0.04
90 14 0.11
91 66 0.52
92 41 0.33
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (92 bp):
AAAAAAGACCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTGCACTCAAT
TGGGTACTTGAACCTTCAAAATGCATA
Found at i:27886319 original size:17 final size:19
Alignment explanation
Indices: 27886297--27886333 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
27886287 AAATTTATTA
27886297 AAAATT-AGAAAAA-ATAT
1 AAAATTCAGAAAAATATAT
*
27886314 AAAATTCATAAAAATATAT
1 AAAATTCAGAAAAATATAT
27886333 A
1 A
27886334 TAAAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAATTCAGAAAAATATAT
Found at i:27886366 original size:19 final size:20
Alignment explanation
Indices: 27886310--27886407 Score: 69
Period size: 21 Copynumber: 4.9 Consensus size: 20
27886300 ATTAGAAAAA
*
27886310 ATATAAAATTCATAAAAATAT
1 ATATAAAAATCAT-AAAATAT
**
27886331 ATATAAAAAATTGTAAAAT-T
1 ATAT-AAAAATCATAAAATAT
*
27886351 TTATAAAAATCATAAAATAT
1 ATATAAAAATCATAAAATAT
* *
27886371 AATATATATATC-TAGAAATAT
1 -ATATAAAAATCATA-AAATAT
*
27886392 A-A-AAAAATTATAAAAT
1 ATATAAAAATCATAAAAT
27886408 TTTATAAAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
18 8 0.13
19 15 0.25
20 8 0.13
21 23 0.38
22 6 0.10
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAAAATCATAAAATAT
Found at i:27886642 original size:19 final size:19
Alignment explanation
Indices: 27886613--27886726 Score: 78
Period size: 19 Copynumber: 6.2 Consensus size: 19
27886603 TCGTTAATTT
*
27886613 TTTTATGATTTTTATAAAA
1 TTTTATAATTTTTATAAAA
* *
27886632 TTTTGTAATTTTT-T--AT
1 TTTTATAATTTTTATAAAA
* *
27886648 TTTTTTACGTTTTTATAAAA
1 TTTTATA-ATTTTTATAAAA
** *
27886668 -AATATAAATTTTA-ATAAA
1 TTTTATAATTTTTATA-AAA
27886686 TTTTAT-ATTTTTATTAAAA
1 TTTTATAATTTTTA-TAAAA
*
27886705 TTTAATAATTTTTATAAAA
1 TTTTATAATTTTTATAAAA
27886724 TTT
1 TTT
27886727 ATTATTTATT
Statistics
Matches: 71, Mismatches: 15, Indels: 18
0.68 0.14 0.17
Matches are distributed among these distances:
16 7 0.10
17 6 0.08
18 16 0.23
19 33 0.46
20 9 0.13
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTATAATTTTTATAAAA
Found at i:27886717 original size:20 final size:18
Alignment explanation
Indices: 27886666--27886738 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 18
27886656 GTTTTTATAA
* *
27886666 AAAATATAA-ATTTTAAT
1 AAAATTTAATATTTTTAT
*
27886683 -AAATTTTATATTTTTATT
1 AAAATTTAATATTTTTA-T
27886701 AAAATTTAATAATTTTTAT
1 AAAATTTAAT-ATTTTTAT
*
27886720 AAAATTTATTATTTATTAT
1 AAAATTTAATATTT-TTAT
27886739 TTTTATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.13
17 6 0.13
18 5 0.11
19 22 0.48
20 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAAATTTAATATTTTTAT
Found at i:27886738 original size:19 final size:18
Alignment explanation
Indices: 27886675--27886738 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
27886665 AAAAATATAA
* *
27886675 ATTTTAATAAATTTTA-T
1 ATTTTTATAAAATTTATT
*
27886692 ATTTTTATTAAAATTTAATA
1 ATTTTTA-TAAAATTT-ATT
27886712 ATTTTTATAAAATTTATT
1 ATTTTTATAAAATTTATT
27886730 ATTTATTAT
1 ATTT-TTAT
27886739 TTTTATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.15
18 13 0.33
19 13 0.33
20 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTATAAAATTTATT
Found at i:27886854 original size:89 final size:90
Alignment explanation
Indices: 27886758--27886927 Score: 270
Period size: 90 Copynumber: 1.9 Consensus size: 90
27886748 TTTTAATAAG
* * *
27886758 AGCAGGGGCTTAATTGC-ATTTTTGAAAAAATTTGAGGGTCTTTTTTATGCATTTTGAAAGTTTA
1 AGCAGGGGCTTAATTGCTATTTTTGAAAAAATTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
*
27886822 AGTGGCCAATTGAGTGGGGGAAAAA
66 AGTGCCCAATTGAGTGGGGGAAAAA
* * *
27886847 AGCAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
1 AGCAGGGGCTTAATTGCTATTTTTGAAAAAATTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
27886912 AGTGCCCAATTGAGTG
66 AGTGCCCAATTGAGTG
27886928 CAAAAAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 17 0.23
90 56 0.77
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (90 bp):
AGCAGGGGCTTAATTGCTATTTTTGAAAAAATTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
AGTGCCCAATTGAGTGGGGGAAAAA
Found at i:27886935 original size:89 final size:91
Alignment explanation
Indices: 27886758--27886985 Score: 261
Period size: 90 Copynumber: 2.5 Consensus size: 91
27886748 TTTTAATAAG
* * * * *
27886758 AGCAGGGGCTTAATTGC-ATTTTTGAAAAAATTTGAGGGTCTTTTTTATGCATTTTGAAAGTTTA
1 AGCAGGGGCTTAATTGCTTTTTTTG-AAAAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
* ***
27886822 AGTGGCCAATTGAGTGG-GGGAA-AAA
65 AGTGCCCAATTGAGTGGCAAAAAGAAA
27886847 AGCAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
1 AGCAGGGGCTTAATTGCTTTTTTTGAA-AAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCA
27886912 AGTGCCCAATTGAGT-GCAAAAAAAGAAA
65 AGTGCCCAATTGAGTGGC--AAAAAGAAA
* *
27886940 AGAAGAGGGGCTTAATTGCTTTTTTT-TAAAGTTTAAGGG-CTTTTTA
1 AG--CAGGGGCTTAATTGCTTTTTTTGAAAAGTTTAAGGGTCTTTTTA
27886986 CACCCTTAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
89 20 0.17
90 53 0.44
92 9 0.08
93 16 0.13
94 1 0.01
95 21 0.17
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.36
Consensus pattern (91 bp):
AGCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTAAGGGTCTTTTTAATGCATTTTGAAAGTTCAA
GTGCCCAATTGAGTGGCAAAAAGAAA
Found at i:27891703 original size:20 final size:21
Alignment explanation
Indices: 27891669--27891707 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27891659 ACTTGAATTA
27891669 AAAAAATCCATATTAAAAACC
1 AAAAAATCCATATTAAAAACC
*
27891690 AAAAAATCGA-ATTAAAAA
1 AAAAAATCCATATTAAAAA
27891708 TTTTCAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.18
Consensus pattern (21 bp):
AAAAAATCCATATTAAAAACC
Found at i:27892408 original size:13 final size:13
Alignment explanation
Indices: 27892390--27892414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27892380 TTTTTGGGTT
27892390 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
27892403 TTTTTTCTTTTT
1 TTTTTTCTTTTT
27892415 GTGTCATAGT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:27894729 original size:15 final size:15
Alignment explanation
Indices: 27894706--27894736 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27894696 TTATTTAACT
27894706 TTATAAATTAAAAAA
1 TTATAAATTAAAAAA
*
27894721 TTATTAATTAAAAAA
1 TTATAAATTAAAAAA
27894736 T
1 T
27894737 AAATTAAAAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTATAAATTAAAAAA
Found at i:27894813 original size:47 final size:48
Alignment explanation
Indices: 27894721--27894814 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
27894711 AATTAAAAAA
*
27894721 TTATTAATTAAAAAATAAATTAAAATAAAAAACTTGAAAATAATATAT
1 TTATTAATTAAAAAATAAATTAAAATAAAAAACTTGAAAACAATATAT
* *
27894769 TTATTAATTAAAAATATTAAATT-AGA-AAAAAGCTTG-AAACAATATA
1 TTATTAATTAAAAA-A-TAAATTAAAATAAAAAACTTGAAAACAATATA
27894815 AAATAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 9 0.22
48 23 0.56
49 3 0.07
50 6 0.15
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (48 bp):
TTATTAATTAAAAAATAAATTAAAATAAAAAACTTGAAAACAATATAT
Found at i:27911907 original size:23 final size:22
Alignment explanation
Indices: 27911862--27911904 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
27911852 TAACAGATCA
27911862 TCTATAAAAAATGAATAAATTG
1 TCTATAAAAAATGAATAAATTG
27911884 TCTATAAAAAATGAATAAATT
1 TCTATAAAAAATGAATAAATT
27911905 TGTTAACGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (22 bp):
TCTATAAAAAATGAATAAATTG
Found at i:27917566 original size:20 final size:22
Alignment explanation
Indices: 27917541--27917591 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
27917531 AAATTAAAGA
27917541 AAAAATTGATCATT-TAT-ATT
1 AAAAATTGATCATTGTATAATT
* *
27917561 AAAAATTTTATCTTTGTATAATT
1 AAAAA-TTGATCATTGTATAATT
27917584 AAAAATTG
1 AAAAATTG
27917592 GCATGATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 5 0.20
21 7 0.28
22 5 0.20
23 8 0.32
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
AAAAATTGATCATTGTATAATT
Found at i:27927391 original size:8 final size:8
Alignment explanation
Indices: 27927365--27927422 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
27927355 GGATGGAGAG
*
27927365 AAAATCGA
1 AAAATAGA
*
27927373 AAGAT-GA
1 AAAATAGA
27927380 AAAATAGA
1 AAAATAGA
27927388 AAAAGTAGA
1 AAAA-TAGA
*
27927397 AAAGTAGA
1 AAAATAGA
*
27927405 AAAGTAGA
1 AAAATAGA
*
27927413 AAAGTAGA
1 AAAATAGA
27927421 AA
1 AA
27927423 GGTTTTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
7 6 0.13
8 32 0.71
9 7 0.16
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.12
Consensus pattern (8 bp):
AAAATAGA
Found at i:27927407 original size:16 final size:16
Alignment explanation
Indices: 27927378--27927422 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
27927368 ATCGAAAGAT
*
27927378 GAAAAATAGAAAAAGTA
1 GAAAAGTAG-AAAAGTA
27927395 GAAAAGTAGAAAAGTA
1 GAAAAGTAGAAAAGTA
27927411 GAAAAGTAGAAA
1 GAAAAGTAGAAA
27927423 GGTTTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (16 bp):
GAAAAGTAGAAAAGTA
Found at i:27943002 original size:12 final size:13
Alignment explanation
Indices: 27942981--27943009 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
27942971 TGAGATAATG
27942981 TTTTATTTTTTAT
1 TTTTATTTTTTAT
27942994 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
27943006 TTTT
1 TTTT
27943010 TCTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:27943750 original size:18 final size:17
Alignment explanation
Indices: 27943707--27943754 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
27943697 AGGCCAATCT
*
27943707 GGGCATGTGGGCTACAC
1 GGGCATGTGGGCCACAC
* *
27943724 GTGCGTGTGGGTCCACAC
1 GGGCATGTGGG-CCACAC
27943742 GGGCATGTGGGCC
1 GGGCATGTGGGCC
27943755 TAGGATTCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.12, C:0.25, G:0.44, T:0.19
Consensus pattern (17 bp):
GGGCATGTGGGCCACAC
Found at i:27956412 original size:22 final size:21
Alignment explanation
Indices: 27956386--27956428 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
27956376 ATGACCTTAA
27956386 AATTT-ATCTGTTCGAACGTGTT
1 AATTTCAT-TGTTC-AACGTGTT
*
27956408 AATTTCATTGTTCAATGTGTT
1 AATTTCATTGTTCAACGTGTT
27956429 GTTATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (21 bp):
AATTTCATTGTTCAACGTGTT
Found at i:27957473 original size:34 final size:34
Alignment explanation
Indices: 27957430--27957494 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
27957420 AATGCTTTAG
27957430 ATGTGAATCGATATACATATAGTTAGAATAGAGA
1 ATGTGAATCGATATACATATAGTTAGAATAGAGA
* * *
27957464 ATGTGAATCGGTATATATATAGTTGGAATAG
1 ATGTGAATCGATATACATATAGTTAGAATAG
27957495 GTTAATAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (34 bp):
ATGTGAATCGATATACATATAGTTAGAATAGAGA
Found at i:27961042 original size:37 final size:37
Alignment explanation
Indices: 27960990--27961094 Score: 158
Period size: 37 Copynumber: 2.8 Consensus size: 37
27960980 TAGTGCTGTG
*
27960990 GCGTGTTATCTGTTGGATTAGCTCTTATGAGCATTTA
1 GCGTGTTATCGGTTGGATTAGCTCTTATGAGCATTTA
* * *
27961027 GCGTGTTATCGGTTGGATTATCTCTTATGAGCGTTTG
1 GCGTGTTATCGGTTGGATTAGCTCTTATGAGCATTTA
27961064 GCGTGTTATCAGG-TGGATTAGCTCTTATGAG
1 GCGTGTTATC-GGTTGGATTAGCTCTTATGAG
27961095 AAATTGATGT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 60 0.97
38 2 0.03
ACGTcount: A:0.17, C:0.13, G:0.29, T:0.41
Consensus pattern (37 bp):
GCGTGTTATCGGTTGGATTAGCTCTTATGAGCATTTA
Found at i:27961107 original size:37 final size:35
Alignment explanation
Indices: 27960991--27961107 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 35
27960981 AGTGCTGTGG
* * *
27960991 CGTGTTATCTGTTGGATTAGCTCTTATGAGCATTTA
1 CGTGTTATC-GGTGGATTAGCTCTTATGAGAATTGA
* ** *
27961027 GCGTGTTATCGGTTGGATTATCTCTTATGAGCGTTTGG
1 -CGTGTTATCGG-TGGATTAGCTCTTATGAG-AATTGA
27961065 CGTGTTATCAGGTGGATTAGCTCTTATGAGAAATTGA
1 CGTGTTATC-GGTGGATTAGCTCTTATGAG-AATTGA
*
27961102 TGTGTT
1 CGTGTT
27961108 TCTGTTGGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
36 1 0.02
37 60 0.92
38 4 0.06
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (35 bp):
CGTGTTATCGGTGGATTAGCTCTTATGAGAATTGA
Found at i:27962264 original size:54 final size:54
Alignment explanation
Indices: 27962124--27962270 Score: 188
Period size: 54 Copynumber: 2.7 Consensus size: 54
27962114 GTGGCTTGAC
* *
27962124 TCAGTGAGTTACACGGGCAGGGACATAGGCTAGGACATGACAGTATGGCCCGAA
1 TCAGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTATGGCCCAAA
* * * * *
27962178 TGAGTCAGTTACACGGGCAGGGACATAGGCTGGGACTTGACCGTGTGGCCCAAA
1 TCAGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTATGGCCCAAA
* * *
27962232 TCAGTGAGTTACATGGGCAGGGGCA-CGAGCTGGGACATG
1 TCAGTGAGTTACACGGGCAGGGACATAG-GCTGGGACATG
27962271 GTCGTGTGTC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 78 0.99
ACGTcount: A:0.26, C:0.20, G:0.36, T:0.18
Consensus pattern (54 bp):
TCAGTGAGTTACACGGGCAGGGACATAGGCTGGGACATGACAGTATGGCCCAAA
Found at i:27963807 original size:152 final size:152
Alignment explanation
Indices: 27963526--27963832 Score: 524
Period size: 152 Copynumber: 2.0 Consensus size: 152
27963516 ACATATCACC
* *
27963526 TTATTACTTGATTCGACGTGTATACTTGTACAAATCACGTATCATTTCACACGTGAAAAGTTTTT
1 TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATATCATTTCACACGTGAAAAGTTTTT
** *
27963591 GGCGTTGTTACCGGGGATCAACAATTTGATGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
66 GGCGCCGTTACCAGGGATCAACAATTTGATGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
27963656 GTTTTATTTAACTTAGTTTAAT
131 GTTTTATTTAACTTAGTTTAAT
* *
27963678 TTATTACTTGATTCGATGTGTATACTTGCACAAATCACATATCATTTCACACGTGACAAGTTTTT
1 TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATATCATTTCACACGTGAAAAGTTTTT
* * *
27963743 GGCGCCGTTGCCAGGGATCAACAATTTGGTGTAATTTGGTTTGGTTATTTTACTTAATTTCATTA
66 GGCGCCGTTACCAGGGATCAACAATTTGATGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
27963808 GTTTTATTTAACTTAGTTTAAT
131 GTTTTATTTAACTTAGTTTAAT
27963830 TTA
1 TTA
27963833 ATTTCTACAG
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 145 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (152 bp):
TTATTACTTGATTCGACGTGTATACTTGCACAAATCACATATCATTTCACACGTGAAAAGTTTTT
GGCGCCGTTACCAGGGATCAACAATTTGATGTAATTTGGTTTGGTTATTTTACTTAATTCCATTA
GTTTTATTTAACTTAGTTTAAT
Found at i:27963825 original size:15 final size:15
Alignment explanation
Indices: 27963796--27963833 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27963786 GTTATTTTAC
*
27963796 TTAATTTCA-TTAGT
1 TTAATTTAACTTAGT
*
27963810 TTTATTTAACTTAGT
1 TTAATTTAACTTAGT
27963825 TTAATTTAA
1 TTAATTTAA
27963834 TTTCTACAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (15 bp):
TTAATTTAACTTAGT
Found at i:27974739 original size:20 final size:20
Alignment explanation
Indices: 27974679--27974767 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
27974669 TATCAATCAT
* * *
27974679 AGTGCAATCAGAGGCACTAG
1 AGTGCAAACAGAGGCACCAA
* * *
27974699 AGTGCAAATAGAGACAACAA
1 AGTGCAAACAGAGGCACCAA
*
27974719 AGTGTGAAA-AGAGGCACCAA
1 AGTG-CAAACAGAGGCACCAA
* *
27974739 AATGCAAACAGAGGCACCGA
1 AGTGCAAACAGAGGCACCAA
27974759 AGTGCAAAC
1 AGTGCAAAC
27974768 TCGTACAAGC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
AGTGCAAACAGAGGCACCAA
Found at i:27977513 original size:25 final size:25
Alignment explanation
Indices: 27977485--27977559 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
27977475 ATTTATACCT
27977485 GAATACATAGCTAATACATACATTC
1 GAATACATAGCTAATACATACATTC
*
27977510 GAATATATA--T-ATACAT--ATTC
1 GAATACATAGCTAATACATACATTC
*
27977530 GAATACATAGCTAATACATACATTT
1 GAATACATAGCTAATACATACATTC
27977555 GAATA
1 GAATA
27977560 TATATATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 12 0.29
22 7 0.17
23 7 0.17
25 16 0.38
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (25 bp):
GAATACATAGCTAATACATACATTC
Found at i:27977538 original size:45 final size:45
Alignment explanation
Indices: 27977485--27977574 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
27977475 ATTTATACCT
27977485 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
*
27977530 GAATACATAGCTAATACATACATTTGAATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
27977575 ATCATATACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (45 bp):
GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
Found at i:27978026 original size:41 final size:41
Alignment explanation
Indices: 27977924--27978032 Score: 146
Period size: 41 Copynumber: 2.7 Consensus size: 41
27977914 ACCGGCTTTT
* * * * * *
27977924 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
*
27977965 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
*
27978006 AGCCTGCTAGACGTAAAGTCTGTATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTA
27978033 CATTTGATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
Found at i:27984589 original size:18 final size:18
Alignment explanation
Indices: 27984566--27984602 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27984556 CAACCAGAAC
27984566 ACAAACCCACAAAATCAA
1 ACAAACCCACAAAATCAA
*
27984584 ACAAACCCTCAAAATCAA
1 ACAAACCCACAAAATCAA
27984602 A
1 A
27984603 ATCAGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.32, G:0.00, T:0.08
Consensus pattern (18 bp):
ACAAACCCACAAAATCAA
Found at i:27988915 original size:14 final size:14
Alignment explanation
Indices: 27988896--27988922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27988886 TGATCCCTAA
27988896 GTAGTAACAGTCTG
1 GTAGTAACAGTCTG
27988910 GTAGTAACAGTCT
1 GTAGTAACAGTCT
27988923 AGGCCTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (14 bp):
GTAGTAACAGTCTG
Found at i:27988917 original size:42 final size:42
Alignment explanation
Indices: 27988870--27988952 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
27988860 TACAACATAC
* * *
27988870 AGTAACAATCTGGGACTGATCCCTAAGTAGTAACAGTCTGGT
1 AGTAACAATCTAGGACTGAGCCCTAAGCAGTAACAGTCTGGT
* * *
27988912 AGTAACAGTCTAGGCCTGAGCCCTAAGCAGTAATAGTCTGG
1 AGTAACAATCTAGGACTGAGCCCTAAGCAGTAACAGTCTGG
27988953 GCCTGAGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (42 bp):
AGTAACAATCTAGGACTGAGCCCTAAGCAGTAACAGTCTGGT
Found at i:27988955 original size:28 final size:28
Alignment explanation
Indices: 27988912--27989017 Score: 133
Period size: 28 Copynumber: 3.8 Consensus size: 28
27988902 ACAGTCTGGT
27988912 AGTAACAGTCTAGGCCTGAGCCCTAAGC
1 AGTAACAGTCTAGGCCTGAGCCCTAAGC
* * *
27988940 AGTAATAGTCTGGGCCTGAGCCATAAGC
1 AGTAACAGTCTAGGCCTGAGCCCTAAGC
* * *
27988968 AGTAATAGTCTAGGCCTTAGCCCAAAGC
1 AGTAACAGTCTAGGCCTGAGCCCTAAGC
* *
27988996 AGTAACAGTGT-GGCCTTAGCCC
1 AGTAACAGTCTAGGCCTGAGCCC
27989018 AATACAGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
27 11 0.16
28 58 0.84
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21
Consensus pattern (28 bp):
AGTAACAGTCTAGGCCTGAGCCCTAAGC
Found at i:27989029 original size:27 final size:27
Alignment explanation
Indices: 27988980--27989031 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
27988970 TAATAGTCTA
*
27988980 GGCCTTAGCCCAAAGCAGTAACAGTGT
1 GGCCTTAGCCCAAAGCAGAAACAGTGT
27989007 GGCCTTAGCCCAATA-CAGAAACAGT
1 GGCCTTAGCCCAA-AGCAGAAACAGT
27989032 ACAGTGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (27 bp):
GGCCTTAGCCCAAAGCAGAAACAGTGT
Found at i:27989397 original size:27 final size:26
Alignment explanation
Indices: 27989367--27989641 Score: 246
Period size: 27 Copynumber: 10.2 Consensus size: 26
27989357 TATAAAAATT
**
27989367 ATTTTACCCTAT-AGTGGTATTTTGGTC
1 ATTTTACCCT-TCAG-GGTATTTCAGTC
* * *
27989394 ATTTTATCCTTCAGGGGTATTTCGGTT
1 ATTTTACCCTTCA-GGGTATTTCAGTC
* * *
27989421 ATTTTACCCTTCGGGGAATTTCGGTC
1 ATTTTACCCTTCAGGGTATTTCAGTC
* * * *
27989447 ATTGTACCTTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTC-AGGGTATTTCAGTC
27989474 ATTTTACCCTTCGAGGGTATTTCAGTC
1 ATTTTACCCTTC-AGGGTATTTCAGTC
* *
27989501 ATTTTACCCTTTGAGGGTATTTCAGTT
1 ATTTTACCC-TTCAGGGTATTTCAGTC
*
27989528 ATTTTACCCTTCGAGGGTATTTTAGTC
1 ATTTTACCCTTC-AGGGTATTTCAGTC
* * * *
27989555 ATTTTACACTTCGATGGCATTTTAGTC
1 ATTTTACCCTTC-AGGGTATTTCAGTC
* * *
27989582 ATTTTACCCTTTAAGGGCATTTTAGTC
1 ATTTTACCC-TTCAGGGTATTTCAGTC
*
27989609 ATTTTACCCTTCAAGGGTATTTCTGTC
1 ATTTTACCCTTC-AGGGTATTTCAGTC
27989636 ATTTTA
1 ATTTTA
27989642 GACCTATTAC
Statistics
Matches: 210, Mismatches: 31, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
26 26 0.12
27 179 0.85
28 5 0.02
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (26 bp):
ATTTTACCCTTCAGGGTATTTCAGTC
Found at i:27989561 original size:81 final size:81
Alignment explanation
Indices: 27989382--27989641 Score: 301
Period size: 81 Copynumber: 3.2 Consensus size: 81
27989372 ACCCTATAGT
* * * * *
27989382 GGTATTTTGGTCATTTTATCCTTC-AGGGGTATTTCGGTTATTTTACCCTTCG-GGGAATTTCGG
1 GGTATTTTGGTCATTTTACCCTTCGA-GGGTATTTCAGTCATTTTACCCTTTGAGGGAATTTCAG
* *
27989445 TCATTGTACCTTTCGAG
65 TCATTTTACCCTTCGAG
* * *
27989462 GGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCAGT
1 GGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTGAGGGAATTTCAGT
*
27989527 TATTTTACCCTTCGAG
66 CATTTTACCCTTCGAG
* * * * * * * *
27989543 GGTATTTTAGTCATTTTACACTTCGATGGCATTTTAGTCATTTTACCCTTTAAGGGCATTTTAGT
1 GGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTGAGGGAATTTCAGT
*
27989608 CATTTTACCCTTCAAG
66 CATTTTACCCTTCGAG
27989624 GGTATTTCT-GTCATTTTA
1 GGTATTT-TGGTCATTTTA
27989642 GACCTATTAC
Statistics
Matches: 154, Mismatches: 23, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
80 44 0.29
81 109 0.71
82 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (81 bp):
GGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTTGAGGGAATTTCAGT
CATTTTACCCTTCGAG
Found at i:28001061 original size:29 final size:29
Alignment explanation
Indices: 28001003--28001061 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
28000993 CTAGGTTTTC
*
28001003 TTTATTTTTTCTCTGTTCTTTACTTGGGTT
1 TTTATTTTTTCTC-GTTCTTTACTTAGGTT
28001033 TTTA-TTTTTCTC-TTCTTCTACCTTAGGTT
1 TTTATTTTTTCTCGTTCTT-TA-CTTAGGTT
28001062 AGAGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.19
28 2 0.08
29 15 0.58
30 4 0.15
ACGTcount: A:0.08, C:0.17, G:0.10, T:0.64
Consensus pattern (29 bp):
TTTATTTTTTCTCGTTCTTTACTTAGGTT
Found at i:28002073 original size:15 final size:15
Alignment explanation
Indices: 28002053--28002082 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28002043 TGGTTCGCTG
28002053 TATTGGATTAGAGGT
1 TATTGGATTAGAGGT
28002068 TATTGGATTAGAGGT
1 TATTGGATTAGAGGT
28002083 GTAATAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (15 bp):
TATTGGATTAGAGGT
Found at i:28002342 original size:18 final size:17
Alignment explanation
Indices: 28002321--28002355 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28002311 TTATTATCAA
*
28002321 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28002339 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28002356 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28002408 original size:157 final size:157
Alignment explanation
Indices: 28002208--28002524 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
28002198 TAGAATACCC
28002208 TTAGCAAAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
28002273 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATCAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATCAAATATATTATAATTAAAA
28002338 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* * *
28002365 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
28002430 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATCAAATATATTATAATTAAAA
28002495 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
28002522 TTA
1 TTA
28002525 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAAAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATCAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:28002495 original size:16 final size:16
Alignment explanation
Indices: 28002458--28002499 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28002448 TTAATCATAT
*
28002458 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28002474 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28002489 TTAAAATATAT
1 TTAAAATATAT
28002500 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28002506 original size:14 final size:15
Alignment explanation
Indices: 28002467--28002508 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28002457 TTTAAACATA
*
28002467 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28002482 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28002496 A-TATAATTTAATA
1 ATTATAATTAAATA
28002509 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Done.