Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, whole genome shotgun sequence
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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 13 of 22
Found at i:5312146 original size:2 final size:2
Alignment explanation
Indices: 5312139--5312175 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5312129 ATAATCAAGT
5312139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5312176 GTACCTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5325147 original size:16 final size:18
Alignment explanation
Indices: 5325126--5325162 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5325116 GATAAGATTT
5325126 AACAAGA-AAG-AAGAAG
1 AACAAGAGAAGAAAGAAG
5325142 AACAAGATGAAGAAAGAAG
1 AACAAGA-GAAGAAAGAAG
5325161 AA
1 AA
5325163 AATTTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (18 bp):
AACAAGAGAAGAAAGAAG
Found at i:5342080 original size:13 final size:13
Alignment explanation
Indices: 5342058--5342090 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5342048 AAATTATAAC
5342058 TTAT-AAAAAAAT
1 TTATAAAAAAAAT
5342070 TTATAAAAAAAAT
1 TTATAAAAAAAAT
5342083 TTACTAAA
1 TTA-TAAA
5342091 CAACTTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 11 0.58
14 4 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TTATAAAAAAAAT
Found at i:5342081 original size:14 final size:14
Alignment explanation
Indices: 5342062--5342090 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5342052 TATAACTTAT
5342062 AAAAAAATTTA-TA
1 AAAAAAATTTACTA
5342075 AAAAAAATTTACTA
1 AAAAAAATTTACTA
5342089 AA
1 AA
5342091 CAACTTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAAATTTACTA
Found at i:5347962 original size:16 final size:16
Alignment explanation
Indices: 5347941--5347978 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5347931 TCCTTTTCTA
5347941 TTTTTT-TTTATATTTG
1 TTTTTTGTTT-TATTTG
*
5347957 TTTTTTGTTTTTTTTG
1 TTTTTTGTTTTATTTG
5347973 TTTTTT
1 TTTTTT
5347979 CGTAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (16 bp):
TTTTTTGTTTTATTTG
Found at i:5350470 original size:19 final size:19
Alignment explanation
Indices: 5350418--5350471 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5350408 TATCTACATA
*
5350418 AAAATTTTAAAATTTTTTT
1 AAAATTTTATAATTTTTTT
* *
5350437 AACATATTT-TGATTTTTTT
1 AAAAT-TTTATAATTTTTTT
5350456 AAAATTTTATAATTTT
1 AAAATTTTATAATTTT
5350472 GACCTTACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AAAATTTTATAATTTTTTT
Found at i:5351216 original size:18 final size:18
Alignment explanation
Indices: 5351185--5351222 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5351175 TTATCTAAAA
*
5351185 ATTAAAGTTATTATCATT
1 ATTAAAGTTATTATAATT
5351203 ATTAAA-TTATTTATAATT
1 ATTAAAGTTA-TTATAATT
5351221 AT
1 AT
5351223 ACTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTAAAGTTATTATAATT
Found at i:5366839 original size:56 final size:56
Alignment explanation
Indices: 5366768--5366875 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
5366758 GTTCAAGGAT
5366768 GACTTAATATCTTCAAATG-TCTAAAATAAAATATTCAAATGAGATCTTTTTAGGGC
1 GACTTAATATCTTCAAA-GATCTAAAATAAAATATTCAAATGAGATCTTTTTAGGGC
* * * *
5366824 GACTTAATTTTTTCAAAGATCTAAAGTAAAATATTTAAATGAGATCTTTTTA
1 GACTTAATATCTTCAAAGATCTAAAATAAAATATTCAAATGAGATCTTTTTA
5366876 TTGAAATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (56 bp):
GACTTAATATCTTCAAAGATCTAAAATAAAATATTCAAATGAGATCTTTTTAGGGC
Found at i:5367118 original size:25 final size:26
Alignment explanation
Indices: 5367067--5367119 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
5367057 GTTGGAGACG
* *
5367067 TAAAAAAATTATGATTTATGTATTTT
1 TAAAAAAATTATGATATATGTAGTTT
* *
5367093 TAAAAAAATTATTA-ATATTTAGTTT
1 TAAAAAAATTATGATATATGTAGTTT
5367118 TA
1 TA
5367120 TCTTATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (26 bp):
TAAAAAAATTATGATATATGTAGTTT
Found at i:5367312 original size:22 final size:20
Alignment explanation
Indices: 5367253--5367312 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 20
5367243 TGTCAATGTA
5367253 TTAA-ATATAAATTATATTTT
1 TTAATATATAAA-TATATTTT
*
5367273 TTAATATAATTAATTATATTATT
1 TTAATAT-A-TAAATATATT-TT
*
5367296 ATTATTATATAAATATA
1 -TTAATATATAAATATA
5367313 AAATCTCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 6 0.19
24 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATATATAAATATATTTT
Found at i:5368952 original size:33 final size:31
Alignment explanation
Indices: 5368876--5368974 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
5368866 TAAAAAACTC
*
5368876 AATTTAATATTTTGATAGAGTATGAA-GACTA
1 AATTTAATATTTTGATAAAGTAT-AAGGACTA
* *
5368907 AATTAAACATTTTGATAAAAG-ATAAGGACTGCA
1 AATTTAATATTTTGAT-AAAGTATAAGGACT--A
* *
5368940 AATTTAATATTTTTATAAAGTATAAGGATTA
1 AATTTAATATTTTGATAAAGTATAAGGACTA
5368971 AATT
1 AATT
5368975 CATAATTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
30 2 0.04
31 25 0.45
32 7 0.12
33 22 0.39
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.37
Consensus pattern (31 bp):
AATTTAATATTTTGATAAAGTATAAGGACTA
Found at i:5391356 original size:15 final size:15
Alignment explanation
Indices: 5391333--5391378 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5391323 AATATAATTG
*
5391333 AAAAATATAAATAAT
1 AAAAATATAAATAAA
*
5391348 AATAATATAAATAAA
1 AAAAATATAAATAAA
5391363 AAAAAT-TAAATAAA
1 AAAAATATAAATAAA
5391377 AA
1 AA
5391379 TTTGATCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATATAAATAAA
Found at i:5391498 original size:19 final size:18
Alignment explanation
Indices: 5391459--5391502 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
5391449 AAAATTCAAA
5391459 AAAATTTAAAAGTTTGAGT
1 AAAATTTAAAAGTTT-AGT
5391478 AAAATTTAATAAAGTTT-GT
1 AAAATTT-A-AAAGTTTAGT
5391497 AAAATT
1 AAAATT
5391503 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 15 0.65
20 1 0.04
21 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
AAAATTTAAAAGTTTAGT
Found at i:5391549 original size:16 final size:15
Alignment explanation
Indices: 5391528--5391558 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5391518 TAATTATATT
5391528 AATTATTTAATAAAAA
1 AATTATTTAA-AAAAA
5391544 AATTATTTAAAAAAA
1 AATTATTTAAAAAAA
5391559 TTAATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTATTTAAAAAAA
Found at i:5391556 original size:13 final size:16
Alignment explanation
Indices: 5391537--5391576 Score: 59
Period size: 13 Copynumber: 2.7 Consensus size: 16
5391527 TAATTATTTA
5391537 ATAAAAAAATT-AT-T
1 ATAAAAAAATTAATAT
5391551 -TAAAAAAATTAATAT
1 ATAAAAAAATTAATAT
5391566 ATAAAAAAATT
1 ATAAAAAAATT
5391577 TAAAAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 1 0.04
16 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAAATTAATAT
Found at i:5399991 original size:2 final size:2
Alignment explanation
Indices: 5399984--5400009 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5399974 CGATGATTTA
5399984 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5400010 TCGTGTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5400575 original size:14 final size:14
Alignment explanation
Indices: 5400558--5400613 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
5400548 TATTTATTTA
5400558 TTTTATTTTAATAT
1 TTTTATTTTAATAT
* *
5400572 TTTTAACTTTAATTT
1 TTTT-ATTTTAATAT
5400587 TTTTA-TTTAATGAT
1 TTTTATTTTAAT-AT
5400601 TTTTATTTATAAT
1 TTTTATTT-TAAT
5400614 TTTGATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 6 0.17
14 11 0.31
15 14 0.40
16 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTATTTTAATAT
Found at i:5400595 original size:13 final size:14
Alignment explanation
Indices: 5400546--5400628 Score: 59
Period size: 14 Copynumber: 6.0 Consensus size: 14
5400536 ATAAGTTTGG
5400546 TTTATTT-AT-TTAT
1 TTTATTTAATATT-T
5400559 TTTATTTTAATATTT
1 TTTA-TTTAATATTT
*
5400574 TTAACTTTAAT-TTT
1 TTTA-TTTAATATTT
5400588 TTTATTTAATGA-TT
1 TTTATTTAAT-ATTT
*
5400602 TTTATTT-ATAATT
1 TTTATTTAATATTT
* *
5400615 TTGATTTAAAATTT
1 TTTATTTAATATTT
5400629 ACCGTCTTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.02
13 20 0.35
14 22 0.39
15 12 0.21
16 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTATTTAATATTT
Found at i:5400613 original size:29 final size:29
Alignment explanation
Indices: 5400546--5400616 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
5400536 ATAAGTTTGG
*
5400546 TTTATTTAT--TTATTTTATTTTAATATT
1 TTTATTTATAATTTTTTTATTTTAATATT
*
5400573 TTTAACTT-TAATTTTTTTA-TTTAATGATT
1 TTT-ATTTATAATTTTTTTATTTTAAT-ATT
5400602 TTTATTTATAATTTT
1 TTTATTTATAATTTT
5400617 GATTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 4 0.11
28 12 0.33
29 20 0.56
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (29 bp):
TTTATTTATAATTTTTTTATTTTAATATT
Found at i:5400812 original size:16 final size:18
Alignment explanation
Indices: 5400780--5400815 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
5400770 AATAATTAAG
5400780 TTTTTTATTTGAGATTGT
1 TTTTTTATTTGAGATTGT
5400798 TTTTTTA-TTGA-ATTGT
1 TTTTTTATTTGAGATTGT
5400814 TT
1 TT
5400816 ATTGATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTTTTTATTTGAGATTGT
Found at i:5401003 original size:18 final size:18
Alignment explanation
Indices: 5400972--5401009 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5400962 TTATTTAGAA
5400972 ATTAAGATTATTATCATT
1 ATTAAGATTATTATCATT
5400990 ATTAA-ATTATTTATCATT
1 ATTAAGATTA-TTATCATT
5401008 AT
1 AT
5401010 GCTAGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTAAGATTATTATCATT
Found at i:5401073 original size:25 final size:27
Alignment explanation
Indices: 5401016--5401066 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5401006 TTATGCTAGT
* *
5401016 TAATTTTTTTAAGTACTTTATTAAAAA
1 TAATTTTTTGAAGTAATTTATTAAAAA
5401043 TAATTTTTTGAA-TAATTT-TTAAAA
1 TAATTTTTTGAAGTAATTTATTAAAA
5401067 TTTATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 11 0.50
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
TAATTTTTTGAAGTAATTTATTAAAAA
Found at i:5402472 original size:22 final size:22
Alignment explanation
Indices: 5402418--5402472 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
5402408 TTTGTGAATA
* *
5402418 AAAATAATAAAAATTTTAAATT
1 AAAATAATTAATATTTTAAATT
*
5402440 AAAATAATTAATATTTTATATT
1 AAAATAATTAATATTTTAAATT
* *
5402462 TAAATATTTAA
1 AAAATAATTAA
5402473 CTCTGATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAATTAATATTTTAAATT
Found at i:5402724 original size:19 final size:19
Alignment explanation
Indices: 5402703--5402739 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5402693 AATTTATATT
5402703 TTTTG-TTTTATTTTAAAA
1 TTTTGCTTTTATTTTAAAA
5402721 TTTTGCTTTTATTTTAAAA
1 TTTTGCTTTTATTTTAAAA
5402740 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTGCTTTTATTTTAAAA
Found at i:5402754 original size:24 final size:23
Alignment explanation
Indices: 5402727--5402777 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
5402717 AAAATTTTGC
5402727 TTTTAT-TTTAAAAAAAATTTAAAA
1 TTTTATCTTT-AAAAAAA-TTAAAA
* *
5402751 TTTTATCTTTTAAAATATTAAAA
1 TTTTATCTTTAAAAAAATTAAAA
5402774 TTTT
1 TTTT
5402778 CATTCTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
24 11 0.46
25 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTATCTTTAAAAAAATTAAAA
Found at i:5405683 original size:13 final size:13
Alignment explanation
Indices: 5405665--5405689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5405655 ATATTTATTC
5405665 ATTATAATTTTAA
1 ATTATAATTTTAA
5405678 ATTATAATTTTA
1 ATTATAATTTTA
5405690 TATATTATTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATAATTTTAA
Found at i:5405806 original size:83 final size:81
Alignment explanation
Indices: 5405704--5405855 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 81
5405694 TTATTATTAA
* *
5405704 TAATAAAATTTATTGAATTTGTAAACATAACAAAATTTTAATTGTATTGAATTA-TTT-TTTAAA
1 TAATAAAATTTATTCAATTTG-AAA-AT-A-AAAATTTTAATTGTATTGAATGACTTTCTTTAAA
5405767 AATATTTTTACTATACACAT
62 AATATTTTTACTATACACAT
* * *
5405787 TAATAAAATTTATTCAATTTGCAAATAAGAATTTTAATTGTATTTAATGACTTTCTTTAAAAATA
1 TAATAAAATTTATTCAATTTGAAAATAAAAATTTTAATTGTATTGAATGACTTTCTTTAAAAATA
5405852 TTTT
66 TTTT
5405856 CTCAATTACA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 20 0.32
80 4 0.06
81 16 0.26
82 2 0.03
83 20 0.32
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (81 bp):
TAATAAAATTTATTCAATTTGAAAATAAAAATTTTAATTGTATTGAATGACTTTCTTTAAAAATA
TTTTTACTATACACAT
Found at i:5408067 original size:14 final size:13
Alignment explanation
Indices: 5408043--5408085 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
5408033 TAAAATTAAA
*
5408043 AATTTTTAAAATT
1 AATTATTAAAATT
5408056 AATATATTAAAATT
1 AAT-TATTAAAATT
5408070 AATTATTAATAATT
1 AATTATTAA-AATT
5408084 AA
1 AA
5408086 AAAATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTATTAAAATT
Found at i:5408097 original size:18 final size:18
Alignment explanation
Indices: 5408076--5408117 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5408066 AATTAATTAT
5408076 TAATAATTAAAAAATTTA
1 TAATAATTAAAAAATTTA
* * *
5408094 TAATAAATAATAATTTTA
1 TAATAATTAAAAAATTTA
5408112 T-ATAAT
1 TAATAAT
5408118 ATGTAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATTAAAAAATTTA
Found at i:5408603 original size:16 final size:15
Alignment explanation
Indices: 5408579--5408612 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5408569 ATAAATTTTT
*
5408579 AATTTTTAAAAATTAA
1 AATTATTAAAAA-TAA
5408595 AATTATTAAAAATAA
1 AATTATTAAAAATAA
5408610 AAT
1 AAT
5408613 CCACATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATTAAAAATAA
Found at i:5408905 original size:19 final size:18
Alignment explanation
Indices: 5408866--5408909 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
5408856 AAAATTCAAA
5408866 AAAATTTAAAAGTTTGAGT
1 AAAATTTAAAAGTTT-AGT
5408885 AAAATTTAATAAAGTTT-GT
1 AAAATTT-A-AAAGTTTAGT
5408904 AAAATT
1 AAAATT
5408910 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 15 0.65
20 1 0.04
21 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
AAAATTTAAAAGTTTAGT
Found at i:5408956 original size:16 final size:15
Alignment explanation
Indices: 5408935--5408964 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5408925 TAATTATATT
5408935 AATTATTTAATAAAAA
1 AATTATTTAA-AAAAA
5408951 AATTATTTAAAAAA
1 AATTATTTAAAAAA
5408965 TTATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTATTTAAAAAAA
Found at i:5408971 original size:11 final size:12
Alignment explanation
Indices: 5408947--5408976 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5408937 TTATTTAATA
5408947 AAAAAATTATTT
1 AAAAAATTATTT
5408959 AAAAAATTA-TT
1 AAAAAATTATTT
5408970 AAAAAAT
1 AAAAAAT
5408977 ATAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAATTATTT
Found at i:5415522 original size:27 final size:27
Alignment explanation
Indices: 5415492--5415744 Score: 137
Period size: 27 Copynumber: 9.1 Consensus size: 27
5415482 TAATATATTT
5415492 ATATTTTTTATTATTAATTTTTATATA
1 ATATTTTTTATTATTAATTTTTATATA
** * * *
5415519 ATATCATTTCTTAATATATTTTTAATATC
1 ATATTTTTTATTATTA-ATTTTT-ATATA
*
5415548 ATA-TTTTTATT-TTTATTTATTATTATA
1 ATATTTTTTATTATTAATTT-TTA-TATA
*
5415575 ATATTTTATATT-TT--TTTTTAATATA
1 ATATTTTTTATTATTAATTTTT-ATATA
* *
5415600 TTTATATTTATATTATTAATTTTTATATA
1 -ATAT-TTTTTATTATTAATTTTTATATA
** * * * *
5415629 ATATCATTTCTTAAATATATTTTTAATGTC
1 ATATTTTTTATT-ATTA-ATTTTT-ATATA
*
5415659 ATATATTTTATT-TT-ATTTATTATATA
1 ATATTTTTTATTATTAATTT-TTATATA
*
5415685 A-ATATTTTTATT-TTTATTTTTAATATA
1 ATAT-TTTTTATTATTAATTTTT-ATATA
* *
5415712 TTTATATTTATATTATTAATTTTTATATA
1 -ATAT-TTTTTATTATTAATTTTTATATA
5415741 ATAT
1 ATAT
5415745 CATTTCTTAA
Statistics
Matches: 173, Mismatches: 32, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
25 8 0.05
26 31 0.18
27 44 0.25
28 32 0.18
29 33 0.19
30 25 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTTTTTATTATTAATTTTTATATA
Found at i:5415534 original size:48 final size:48
Alignment explanation
Indices: 5415481--5415650 Score: 137
Period size: 55 Copynumber: 3.2 Consensus size: 48
5415471 AAATATAAGT
5415481 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTC
1 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTC
* * *
5415529 TTAATATATTTTTAATATCATATTTTTATT-TTTATTTATTATTATAATATTTTATATTTTTTT
1 TTAATATA---TT--TAT-AT-TTTTTATTATTAATTT-TTA-TATAATA---T-CA---TTTC
*
5415592 TTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATTTC
1 TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTC
5415639 TTAAATATATTT
1 TT-AATATATTT
5415651 TTAATGTCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 36
0.69 0.05 0.26
Matches are distributed among these distances:
47 5 0.05
48 17 0.18
50 1 0.01
51 3 0.03
53 3 0.03
54 15 0.15
55 21 0.22
56 13 0.13
57 1 0.01
58 3 0.03
59 1 0.01
60 3 0.03
63 11 0.11
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (48 bp):
TTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTC
Found at i:5415546 original size:29 final size:27
Alignment explanation
Indices: 5415480--5415763 Score: 111
Period size: 29 Copynumber: 10.1 Consensus size: 27
5415470 AAAATATAAG
* *
5415480 TTTAATATATTTATATTTTTTATTATTAATT
1 TTTAATATA-ATATA-TTTTTAATA-T-ATT
5415511 TTT-ATATAATATCATTTCTTAATATATT
1 TTTAATATAATAT-ATTT-TTAATATATT
* * *
5415539 TTTAATAT--CATATTTTTATTTTTATT
1 TTTAATATAATATATTTTTA-ATATATT
* * * *
5415565 TATTATTATAATAT-TTTAT-ATTTTTT
1 T-TTAATATAATATATTTTTAATATATT
* * *
5415591 TTTAATATATTTATATTTATATTATTAATT
1 TTTAATATA-ATATATTTTTAATA-T-ATT
5415621 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATATAATAT-ATTT-TT-AATATATT
* * * *
5415650 TTTAATGTCATATA-TTTTATTTTATT
1 TTTAATATAATATATTTTTAATATATT
* *
5415676 TATT-ATATAA-ATATTTTTATTTTTATT
1 T-TTAATATAATATATTTTTA-ATATATT
* * *
5415703 TTTAATATATTTATATTTATATTATTAATT
1 TTTAATATA-ATATATTTTTAATA-T-ATT
5415733 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATATAATAT-ATTT-TT-AATATATT
5415762 TT
1 TT
5415764 AAGGTCATAT
Statistics
Matches: 196, Mismatches: 30, Indels: 56
0.70 0.11 0.20
Matches are distributed among these distances:
25 13 0.07
26 37 0.19
27 30 0.15
28 21 0.11
29 53 0.27
30 33 0.17
31 9 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTAATATAATATATTTTTAATATATT
Found at i:5415579 original size:21 final size:22
Alignment explanation
Indices: 5415555--5415627 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
5415545 ATCATATTTT
5415555 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
*
5415576 TATTTTATATTT-TT-TTTTAA
1 TATTTTATATTTATTATTATAA
5415596 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTATTA-TAA
5415619 T-TTTTATAT
1 TATTTTATAT
5415628 AATATCATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 8 0.18
21 25 0.56
22 8 0.18
23 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:5415613 original size:34 final size:37
Alignment explanation
Indices: 5415482--5415749 Score: 127
Period size: 35 Copynumber: 7.3 Consensus size: 37
5415472 AATATAAGTT
**
5415482 TAATATATTTA-TATT-TTTTATTATTAATTTTTATA
1 TAATATATTTATTATTATAATATTATTAATTTTTATA
* * * *
5415517 TAATATCATTTCTTAATATATTTTTAATATCATATTTTTAT-
1 TAATAT-ATTTATTATTATAATATT-AT-T-A-ATTTTTATA
* * *
5415558 T--TTTATTTATTATTATAATATT-TTATATTTTTTTT
1 TAATATATTTATTATTATAATATTATTA-ATTTTTATA
5415593 TAATATATTTA-TATT-T-ATATTATTAATTTTTATA
1 TAATATATTTATTATTATAATATTATTAATTTTTATA
* * * * *
5415627 TAATATCATTTCTTA-AAT-ATATTTTTAA-TGTCATA
1 TAATAT-ATTTATTATTATAATATTATTAATTTTTATA
* * * *
5415662 TATTTTATTTTATTTATTATATAAATATT-TTTATTTTTATTTT
1 TAATATA-TTTA-TTA-T-TAT-AATATTATTAATTTTTA--TA
5415705 TAATATATTTA-TATT-T-ATATTATTAATTTTTATA
1 TAATATATTTATTATTATAATATTATTAATTTTTATA
5415739 TAATATCATTT
1 TAATAT-ATTT
5415750 CTTAAATATA
Statistics
Matches: 177, Mismatches: 30, Indels: 52
0.68 0.12 0.20
Matches are distributed among these distances:
34 35 0.20
35 37 0.21
36 33 0.19
37 11 0.06
38 20 0.11
39 7 0.04
40 6 0.03
41 10 0.06
42 12 0.07
43 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (37 bp):
TAATATATTTATTATTATAATATTATTAATTTTTATA
Found at i:5415616 original size:15 final size:15
Alignment explanation
Indices: 5415554--5415627 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
5415544 TATCATATTT
*
5415554 TTATTTTTATTTATTA
1 TTATTTATATTTA-TA
*
5415570 TTA-TAATATTTTATA
1 TTATTTATA-TTTATA
5415585 TT-TTT-T-TTTA-A
1 TTATTTATATTTATA
5415596 TATATTTATATTTATA
1 T-TATTTATATTTATA
* *
5415612 TTATTAATTTTTATA
1 TTATTTATATTTATA
5415627 T
1 T
5415628 AATATCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
11 2 0.04
12 5 0.11
13 3 0.07
14 2 0.04
15 25 0.54
16 9 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTTATATTTATA
Found at i:5415661 original size:111 final size:112
Alignment explanation
Indices: 5415480--5415812 Score: 540
Period size: 111 Copynumber: 3.0 Consensus size: 112
5415470 AAAATATAAG
*
5415480 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAA
1 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
5415544 TATCATAT-TTTTATTTTTATTTATTATTATAATATTTTATATTTTTT
65 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTTT
5415591 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
5415656 GTCATATATTTTA-TTTTATTTATTA-TATAAATATTTT-TATTTTTATT
66 GTCATATATTTTATTTTTATTTATTATTAT-AATATTTTATA-TTTT-TT
*
5415703 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTAAG
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
5415767 GTCATATATTTTATTTTTATTT-TTATTAT-A-ATTTTATATTTTTT
66 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTTT
5415811 TT
1 TT
5415813 CATTTCTTTA
Statistics
Matches: 211, Mismatches: 3, Indels: 19
0.91 0.01 0.08
Matches are distributed among these distances:
108 4 0.02
109 9 0.04
110 42 0.20
111 81 0.38
112 75 0.36
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (112 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTTT
Found at i:5415709 original size:21 final size:22
Alignment explanation
Indices: 5415661--5415739 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
5415651 TTAATGTCAT
5415661 ATATTTTAT-TTTATTTATTATATAA
1 ATATTTTATATTTA--TATTAT-T-A
* *
5415686 ATATTTT-TATTTTTATTTTTA
1 ATATTTTATATTTATATTATTA
5415707 ATATATTTATATTTATATTATTA
1 ATAT-TTTATATTTATATTATTA
5415730 AT-TTTTATAT
1 ATATTTTATAT
5415740 AATATCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 12 0.26
22 5 0.11
23 19 0.40
24 1 0.02
25 10 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATTTTATATTTATATTATTA
Found at i:5415730 original size:112 final size:112
Alignment explanation
Indices: 5415480--5415812 Score: 538
Period size: 112 Copynumber: 3.0 Consensus size: 112
5415470 AAAATATAAG
*
5415480 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAA
1 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
5415544 TATCATAT-TTTTATTTTTATTTATTATTATAATA-TTTTATATTTTTT
65 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTTAT-TTTTTT
5415591 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
5415656 GTCATATATTTTA-TTTTATTTATTA-TATAAATATTTTTATTTTTATT
66 GTCATATATTTTATTTTTATTTATTATTAT-AATATTTTTATTTTT-TT
*
5415703 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTAAG
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
5415767 GTCATATATTTTATTTTTATTT-TTATTATAAT-TTTATATTTTTTT
66 GTCATATATTTTATTTTTATTTATTATTATAATATTTTTATTTTTTT
5415812 T
1 T
5415813 CATTTCTTTA
Statistics
Matches: 211, Mismatches: 4, Indels: 16
0.91 0.02 0.07
Matches are distributed among these distances:
109 3 0.01
110 47 0.22
111 80 0.38
112 81 0.38
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (112 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTTATTTATTATTATAATATTTTTATTTTTTT
Found at i:5415831 original size:30 final size:30
Alignment explanation
Indices: 5415771--5415849 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
5415761 TTTAAGGTCA
* *
5415771 TATATTTTATTTTTATTTTTATTATAATTT
1 TATATTTTATTTTCATTTTTAATATAATTT
5415801 TATATTTT-TTTTCATTTCTTTAATAT-ATTT
1 TATATTTTATTTTCA-TT-TTTAATATAATTT
* *
5415831 TTTATATATATTTT-ATTTT
1 TATAT-TTTATTTTCATTTT
5415850 AATTTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
29 7 0.17
30 20 0.49
31 10 0.24
32 4 0.10
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (30 bp):
TATATTTTATTTTCATTTTTAATATAATTT
Found at i:5415854 original size:24 final size:24
Alignment explanation
Indices: 5415827--5415910 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 24
5415817 TCTTTAATAT
5415827 ATTTTTTATATATATTTTATTTTA
1 ATTTTTTATATATATTTTATTTTA
* *
5415851 ATTTGTTTTATCTATATTATATAAATATTA
1 A-TT-TTTTATATATATT-T-T--ATTTTA
*
5415881 ATTTTTTATATTTTATTTTA-TTTA
1 ATTTTTTATA-TATATTTTATTTTA
5415905 ATTTTT
1 ATTTTT
5415911 ATTCTTATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
24 10 0.21
25 3 0.06
26 12 0.25
27 2 0.04
28 8 0.17
29 7 0.15
30 6 0.12
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (24 bp):
ATTTTTTATATATATTTTATTTTA
Found at i:5415921 original size:24 final size:25
Alignment explanation
Indices: 5415770--5415934 Score: 66
Period size: 24 Copynumber: 6.6 Consensus size: 25
5415760 TTTTAAGGTC
*
5415770 ATATATTTTATTTTTAT-TTTTATT
1 ATATATTTAATTTTTATATTTTATT
*
5415794 ATA-ATTTTATATTTTTTTTCATTTCT-TT
1 ATATA-TTTA-A-TTTTTAT-ATTT-TATT
5415822 AATATATTT--TTTATATATATTTTATT
1 -ATATATTTAATTT-T-TATATTTTATT
* * * *
5415848 TTA-ATTT-GTTTTATCTATATTA-T
1 ATATATTTAATTTT-TATATTTTATT
*
5415871 ATAAATATTAATTTTTTATATTTTATT
1 ATATAT-TTAA-TTTTTATATTTTATT
5415898 -T-TATTTAATTTTTAT-TCTTATATT
1 ATATATTTAATTTTTATAT-TT-TATT
5415922 ATATATTT-ATTTT
1 ATATATTTAATTTT
5415935 AATTATAATA
Statistics
Matches: 109, Mismatches: 11, Indels: 41
0.68 0.07 0.25
Matches are distributed among these distances:
22 1 0.01
23 13 0.12
24 29 0.27
25 20 0.18
26 26 0.24
27 7 0.06
28 5 0.05
29 7 0.06
30 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (25 bp):
ATATATTTAATTTTTATATTTTATT
Found at i:5415933 original size:25 final size:26
Alignment explanation
Indices: 5415899--5415949 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5415889 TATTTTATTT
* * *
5415899 TATTTAATTTTTATTCTTATATTATA
1 TATTTAATTTTAATTATAATATTATA
5415925 TATTT-ATTTTAATTATAATATTATA
1 TATTTAATTTTAATTATAATATTATA
5415950 AATATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTTAATTTTAATTATAATATTATA
Found at i:5416450 original size:44 final size:44
Alignment explanation
Indices: 5416322--5416496 Score: 138
Period size: 44 Copynumber: 4.0 Consensus size: 44
5416312 TGTCATGTTA
* * * *
5416322 TCATATCATATATAAAATTGTCAAATTTAGTGATGAG-TTAGAT
1 TCATATCATATACAAAATTGTCAAGTTTAGTGATAAGTTTAAAT
* * * *
5416365 TCATATTATATACAAAATTATCAAGTTTACTGATAAATTTAAAT
1 TCATATCATATACAAAATTGTCAAGTTTAGTGATAAGTTTAAAT
* * * *
5416409 TCTTGTCATATGCAAAATTGTCAAGTTTAGTGA-ATAGTTTAAAC
1 TCATATCATATACAAAATTGTCAAGTTTAGTGATA-AGTTTAAAT
* * * ** * * * *
5416453 TCGTATCACACATGAAATTGTCAAATTTAATAATGAGTTTAAAT
1 TCATATCATATACAAAATTGTCAAGTTTAGTGATAAGTTTAAAT
5416497 CCGTTTCGTG
Statistics
Matches: 101, Mismatches: 28, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
43 31 0.31
44 70 0.69
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (44 bp):
TCATATCATATACAAAATTGTCAAGTTTAGTGATAAGTTTAAAT
Found at i:5429266 original size:34 final size:33
Alignment explanation
Indices: 5429220--5429288 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 33
5429210 TATGTGTGAA
* *
5429220 TTATGATTTTTTAATATAATGATCTGATTTTGAG
1 TTATGATGTTTTAATATAATCATCTGATTTT-AG
*
5429254 TTATGATGTTTTAATGTAATCATCTGATTTTAG
1 TTATGATGTTTTAATATAATCATCTGATTTTAG
5429287 TT
1 TT
5429289 TCTATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.28, C:0.04, G:0.14, T:0.54
Consensus pattern (33 bp):
TTATGATGTTTTAATATAATCATCTGATTTTAG
Found at i:5437084 original size:28 final size:27
Alignment explanation
Indices: 5437027--5437310 Score: 523
Period size: 27 Copynumber: 10.4 Consensus size: 27
5437017 ACTGTTTTAA
*
5437027 GAATACCTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437054 GAATAACTTTACTCATCAAAAAGTGAAT
1 GAATAACTTTACTCATC-AAAAGTGAAT
5437082 GAATAACTTTACTCATCAAAAAGTGAAT
1 GAATAACTTTACTCATC-AAAAGTGAAT
5437110 GAATAACTTTACTCATCAAAAAGTGAAT
1 GAATAACTTTACTCATC-AAAAGTGAAT
5437138 GAATAACTTTACTCATCAAAAAGTGAAT
1 GAATAACTTTACTCATC-AAAAGTGAAT
5437166 GAATAACTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437193 GAATAACTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437220 GAATAACTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437247 GAATAACTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437274 GAATAACTTTACTCATCAAAAGTGAAT
1 GAATAACTTTACTCATCAAAAGTGAAT
5437301 GAATAACTTT
1 GAATAACTTT
5437311 TTTATCCACC
Statistics
Matches: 255, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
27 144 0.56
28 111 0.44
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (27 bp):
GAATAACTTTACTCATCAAAAGTGAAT
Found at i:5437554 original size:40 final size:40
Alignment explanation
Indices: 5437499--5437584 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
5437489 CAGAGAGTTA
*
5437499 AATGAATACCTTTACTCACCATAATTGGATGGATACATTT
1 AATGACTACCTTTACTCACCATAATTGGATGGATACATTT
5437539 AATGACTACCTTTACTCACCATAATTGGATGGATACATTT
1 AATGACTACCTTTACTCACCATAATTGGATGGATACATTT
5437579 AATGAC
1 AATGAC
5437585 CAGAAATGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (40 bp):
AATGACTACCTTTACTCACCATAATTGGATGGATACATTT
Found at i:5437598 original size:32 final size:32
Alignment explanation
Indices: 5437562--5437626 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5437552 ACTCACCATA
5437562 ATTGGATGGATACATTTAATGACCAGAAATGG
1 ATTGGATGGATACATTTAATGACCAGAAATGG
5437594 ATTGGATGGATACATTTAATGACCAGAAATGG
1 ATTGGATGGATACATTTAATGACCAGAAATGG
5437626 A
1 A
5437627 ATGTGGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (32 bp):
ATTGGATGGATACATTTAATGACCAGAAATGG
Found at i:5437873 original size:60 final size:60
Alignment explanation
Indices: 5437780--5437899 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
5437770 AGTTCCTTCA
5437780 ATAAAAGAGTGCTATGTAATAGTGAAGTGGTGGTTATGGATTTATGGAAGCATGTATGAG
1 ATAAAAGAGTGCTATGTAATAGTGAAGTGGTGGTTATGGATTTATGGAAGCATGTATGAG
5437840 ATAAAAGAGTGCTATGTAATAGTGAAGTGGTGGTTATGGATTTATGGAAGCATGTATGAG
1 ATAAAAGAGTGCTATGTAATAGTGAAGTGGTGGTTATGGATTTATGGAAGCATGTATGAG
5437900 TTGGTTTGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (60 bp):
ATAAAAGAGTGCTATGTAATAGTGAAGTGGTGGTTATGGATTTATGGAAGCATGTATGAG
Found at i:5442672 original size:15 final size:17
Alignment explanation
Indices: 5442638--5442670 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5442628 CTTCTTATCA
5442638 TATGGATAAGAATTTTT
1 TATGGATAAGAATTTTT
5442655 TATGG-TAAGAATTTTT
1 TATGGATAAGAATTTTT
5442671 ATACAAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (17 bp):
TATGGATAAGAATTTTT
Found at i:5450948 original size:6 final size:7
Alignment explanation
Indices: 5450925--5450961 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
5450915 GAAGTAAGAA
5450925 TTTAGTTT
1 TTTA-TTT
5450933 TATTATTT
1 T-TTATTT
5450941 TTTATTT
1 TTTATTT
5450948 TTTATTT
1 TTTATTT
5450955 TTTATTT
1 TTTATTT
5450962 GCCAGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.71
8 5 0.18
9 3 0.11
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (7 bp):
TTTATTT
Found at i:5451375 original size:3 final size:3
Alignment explanation
Indices: 5451367--5451391 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5451357 ATATTTAAAG
5451367 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5451392 ATCCTTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5460826 original size:50 final size:50
Alignment explanation
Indices: 5460751--5460851 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
5460741 TGAAGAAAGC
5460751 AGAATTAAACAAATGATGAACAGAAAGCCAAAGATTCATATCTCTTACAA
1 AGAATTAAACAAATGATGAACAGAAAGCCAAAGATTCATATCTCTTACAA
5460801 AGAATTAAACAAATGATGAACAGAAAGCCAAAGATTCATATCTCTTACAA
1 AGAATTAAACAAATGATGAACAGAAAGCCAAAGATTCATATCTCTTACAA
5460851 A
1 A
5460852 TATGTATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (50 bp):
AGAATTAAACAAATGATGAACAGAAAGCCAAAGATTCATATCTCTTACAA
Found at i:5461298 original size:37 final size:37
Alignment explanation
Indices: 5461242--5461316 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
5461232 TCTAACTTTC
*
5461242 TATATGCAGCCTAGGTTTACCGTGTGCATCATAAATT
1 TATATGCAGCCTAGCTTTACCGTGTGCATCATAAATT
* **
5461279 TATATGCAGTCTAGCTTTACTTTGTGCATCATAAATT
1 TATATGCAGCCTAGCTTTACCGTGTGCATCATAAATT
5461316 T
1 T
5461317 CTTTTCCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (37 bp):
TATATGCAGCCTAGCTTTACCGTGTGCATCATAAATT
Found at i:5463652 original size:2 final size:2
Alignment explanation
Indices: 5463647--5463672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5463637 TCCTTTTTTC
5463647 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5463673 ATGATCCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5468578 original size:26 final size:26
Alignment explanation
Indices: 5468547--5468600 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
5468537 NNNNNNNNAA
*
5468547 ATTATATTAAAAAATAAAAATAAAAT
1 ATTATAATAAAAAATAAAAATAAAAT
* *
5468573 ATTATAATAAGAAATGAAAATAAAAT
1 ATTATAATAAAAAATAAAAATAAAAT
5468599 AT
1 AT
5468601 ATGACATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
ATTATAATAAAAAATAAAAATAAAAT
Found at i:5468919 original size:16 final size:16
Alignment explanation
Indices: 5468898--5468928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5468888 TTCAATACTA
5468898 CATTAACAAGAAAATC
1 CATTAACAAGAAAATC
*
5468914 CATTAATAAGAAAAT
1 CATTAACAAGAAAAT
5468929 ATAATATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (16 bp):
CATTAACAAGAAAATC
Found at i:5469943 original size:2 final size:2
Alignment explanation
Indices: 5469938--5469967 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5469928 TAAAAAAAGG
5469938 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5469968 AATTGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5475660 original size:13 final size:13
Alignment explanation
Indices: 5475642--5475667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5475632 TCCAGGCTTA
5475642 AGGGGTTCGCAAC
1 AGGGGTTCGCAAC
5475655 AGGGGTTCGCAAC
1 AGGGGTTCGCAAC
5475668 CTGCAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
AGGGGTTCGCAAC
Found at i:5484682 original size:106 final size:106
Alignment explanation
Indices: 5484540--5484805 Score: 356
Period size: 106 Copynumber: 2.5 Consensus size: 106
5484530 ATTCAATTTT
* ** * *
5484540 ACCTACTCATCAAGCAGTCTCAAGTCACTTGGAAAAGGGGAGGTGGAATCCTATGCAGTAGAGCA
1 ACCTACTCAACAAGCAGTCTCAAGTTGCTTGAAAAAGGGGAGGTGGAATCCTATGAAGTAGAGCA
5484605 AATGTGATGAAGGCCTATTTTGAAATTTTTGACTTGCTTTC
66 AATGTGATGAAGGCCTATTTTGAAATTTTTGACTTGCTTTC
* *
5484646 ACCTACTCAACAAGCAGTCTCAAGTTGCTTGAAAAAGGGGAGATGGGAA-CCTACGAAGTAGAGC
1 ACCTACTCAACAAGCAGTCTCAAGTTGCTTGAAAAAGGGGAGGT-GGAATCCTATGAAGTAGAGC
* * * * *
5484710 GAGTGTGATGAAGGCCTATTTTGAGATTTTTTATTTGCTTTC
65 AAATGTGATGAAGGCCTATTTTGAAATTTTTGACTTGCTTTC
* * * * *
5484752 AGCTACTCAACAAGCAGTCTCCAGCTGCTTGAAAAA-GAGAGGTGGGATCCTATG
1 ACCTACTCAACAAGCAGTCTCAAGTTGCTTGAAAAAGGGGAGGTGGAATCCTATG
5484806 TTTAACTCAA
Statistics
Matches: 139, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
104 3 0.02
105 10 0.07
106 122 0.88
107 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (106 bp):
ACCTACTCAACAAGCAGTCTCAAGTTGCTTGAAAAAGGGGAGGTGGAATCCTATGAAGTAGAGCA
AATGTGATGAAGGCCTATTTTGAAATTTTTGACTTGCTTTC
Found at i:5502993 original size:2 final size:2
Alignment explanation
Indices: 5502982--5503015 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5502972 AGTCTCTATC
*
5502982 TA TA -A TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5503016 GTCTCTGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5503993 original size:21 final size:23
Alignment explanation
Indices: 5503956--5504004 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5503946 TGATTAATGC
5503956 TTTTATTTCTTGTTATA-TGTTT
1 TTTTATTTCTTGTTATACTGTTT
*
5503978 TTTTATTT-TT-TATATACTTTTT
1 TTTTATTTCTTGT-TATACTGTTT
5504000 TTTTA
1 TTTTA
5504005 AATAATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 6 0.25
22 17 0.71
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTATTTCTTGTTATACTGTTT
Found at i:5511849 original size:27 final size:27
Alignment explanation
Indices: 5511811--5511865 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5511801 TAGACAGAAA
5511811 GCCTAAAATTAACCTTTAATATTCTAT
1 GCCTAAAATTAACCTTTAATATTCTAT
5511838 GCCTAAAATTAACCTTTAATATTCTAT
1 GCCTAAAATTAACCTTTAATATTCTAT
5511865 G
1 G
5511866 ATTCCTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.40
Consensus pattern (27 bp):
GCCTAAAATTAACCTTTAATATTCTAT
Found at i:5525803 original size:115 final size:112
Alignment explanation
Indices: 5525634--5525863 Score: 273
Period size: 115 Copynumber: 2.0 Consensus size: 112
5525624 AAATTTATCG
* * * *
5525634 TTTTATTTAAGACGGTGATCATATATTAGTAATTATCTTTAAAGGAATGTAATTTTAGTATCT-T
1 TTTTATTTAAGACGATGATCATATATAAGTAATTATCATTAAAGGAATGTAATTTTAATAT-TAT
* * *
5525698 AGTTTTGCTTTGATTCAAGAATAATCACAAATTAAGAGTAAAAAAATA
65 AATTTTACTTTGATTCAAGAACAATCACAAATTAAGAGTAAAAAAATA
* * * ** *
5525746 TTTTATTTAAGATGATGATCATCATATAATTATGATTATCATTAAATGCGTGTAATTTTAATGTT
1 TTTTATTTAAGACGATGATCAT-ATATAAGTA--ATTATCATTAAAGGAATGTAATTTTAATATT
* * *
5525811 ATAATTTTATTTTGGTTCAAGAACAATCACAAATTAAGAGTAAGAAAATA
63 ATAATTTTACTTTGATTCAAGAACAATCACAAATTAAGAGTAAAAAAATA
5525861 TTT
1 TTT
5525864 GAAAATATTT
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
112 20 0.20
113 7 0.07
114 1 0.01
115 70 0.71
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (112 bp):
TTTTATTTAAGACGATGATCATATATAAGTAATTATCATTAAAGGAATGTAATTTTAATATTATA
ATTTTACTTTGATTCAAGAACAATCACAAATTAAGAGTAAAAAAATA
Found at i:5527892 original size:16 final size:17
Alignment explanation
Indices: 5527857--5527894 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5527847 TAATTTGGGT
* *
5527857 TTTATGTTTTTTATTTA
1 TTTATGTTTTGTATTAA
5527874 TTTATGTTTTGT-TTAA
1 TTTATGTTTTGTATTAA
5527890 TTTAT
1 TTTAT
5527895 TGGAAGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTATGTTTTGTATTAA
Found at i:5536619 original size:2 final size:2
Alignment explanation
Indices: 5536612--5536636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5536602 TTTTGCTTGT
5536612 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5536637 TTGGGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5544244 original size:3 final size:3
Alignment explanation
Indices: 5544216--5544305 Score: 58
Period size: 3 Copynumber: 30.0 Consensus size: 3
5544206 ATGGTCGGAT
* * * * * *
5544216 CTG CTT CTG CTG TTG CTG TTG TTG CTG CTG CTG CTG CTG TTG TTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
* * * *
5544264 CTG -TGG CTG TTG CTG TTG TTG -TGG TTG CTG CTG CTG CTG CTG
1 CTG CT-G CTG CTG CTG CTG CTG CT-G CTG CTG CTG CTG CTG CTG
5544306 TTGTTGTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.03
3 67 0.94
4 2 0.03
ACGTcount: A:0.00, C:0.21, G:0.34, T:0.44
Consensus pattern (3 bp):
CTG
Found at i:5544293 original size:21 final size:22
Alignment explanation
Indices: 5544223--5544299 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
5544213 GATCTGCTTC
* *
5544223 TGCTGTTGCTGTTGTTGCT-GC
1 TGCTGCTGCTGTTGTTGCTGGT
5544244 TGCTGCTGCTGTTGTTGCTGCTGT
1 TGCTGCTGCTGTTGTTGCTG--GT
* *
5544268 GGCTGTTGCTGTTGTTG-TGGT
1 TGCTGCTGCTGTTGTTGCTGGT
5544289 TGCTGCTGCTG
1 TGCTGCTGCTG
5544300 CTGCTGTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 29 0.62
23 2 0.04
24 16 0.34
ACGTcount: A:0.00, C:0.18, G:0.36, T:0.45
Consensus pattern (22 bp):
TGCTGCTGCTGTTGTTGCTGGT
Found at i:5544525 original size:6 final size:6
Alignment explanation
Indices: 5544514--5544585 Score: 60
Period size: 6 Copynumber: 12.5 Consensus size: 6
5544504 GAGAAGAAAT
* * * *
5544514 TGTTGC TGTTGC TG-T-- TGTTGA TGTTGA TGATGC TGTTGA TGTTGC
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC
* * *
5544559 TGCTGA TGTTGC TGCTGC TGTTGC TGT
1 TGTTGC TGTTGC TGTTGC TGTTGC TGT
5544586 AAGAGAAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 48 0.92
ACGTcount: A:0.07, C:0.12, G:0.33, T:0.47
Consensus pattern (6 bp):
TGTTGC
Found at i:5544552 original size:12 final size:12
Alignment explanation
Indices: 5544529--5544585 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
5544519 CTGTTGCTGT
*
5544529 TGTTGATGTTGA
1 TGTTGCTGTTGA
*
5544541 TGATGCTGTTGA
1 TGTTGCTGTTGA
*
5544553 TGTTGCTGCTGA
1 TGTTGCTGTTGA
* *
5544565 TGTTGCTGCTGC
1 TGTTGCTGTTGA
5544577 TGTTGCTGT
1 TGTTGCTGT
5544586 AAGAGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.09, C:0.12, G:0.33, T:0.46
Consensus pattern (12 bp):
TGTTGCTGTTGA
Found at i:5549442 original size:29 final size:29
Alignment explanation
Indices: 5549396--5549463 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
5549386 GTATCTTTTT
*
5549396 ACTATTCATCTACTCCTTGGTAGGTTAAA
1 ACTATTCATCTACTCCTTAGTAGGTTAAA
*
5549425 ACTATTCATCTA-TCCCTTAGTGGGTTAAA
1 ACTATTCATCTACT-CCTTAGTAGGTTAAA
5549454 ACTATTCATC
1 ACTATTCATC
5549464 CAGTTCTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 1 0.03
29 35 0.97
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (29 bp):
ACTATTCATCTACTCCTTAGTAGGTTAAA
Found at i:5550249 original size:23 final size:25
Alignment explanation
Indices: 5550199--5550250 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5550189 TATTTATAAG
* *
5550199 TTTACATAAATGGAGGTGGAATGAA
1 TTTACATAAATAGAGGAGGAATGAA
5550224 TTTACATAAATAGA-GAGG-ATGAA
1 TTTACATAAATAGAGGAGGAATGAA
5550247 TTTA
1 TTTA
5550251 GTAGATATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.36
24 3 0.12
25 13 0.52
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (25 bp):
TTTACATAAATAGAGGAGGAATGAA
Found at i:5574885 original size:4 final size:4
Alignment explanation
Indices: 5574878--5574934 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
5574868 ACACACATGC
* *
5574878 ATGT ATGT ATGT ATGT ATGT GTAG- ATGT A--T ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT
5574924 ATGT ATGT ATG
1 ATGT ATGT ATG
5574935 CATACGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 42 0.91
5 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:5574905 original size:16 final size:18
Alignment explanation
Indices: 5574879--5574931 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
5574869 CACACATGCA
5574879 TGTATGTATGTATGTATG
1 TGTATGTATGTATGTATG
* *
5574897 TGTA-G-ATGTATATATA
1 TGTATGTATGTATGTATG
5574913 TGTATGTATGTATGTATG
1 TGTATGTATGTATGTATG
5574931 T
1 T
5574932 ATGCATACGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.45
17 2 0.07
18 14 0.48
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (18 bp):
TGTATGTATGTATGTATG
Found at i:5586785 original size:26 final size:26
Alignment explanation
Indices: 5586751--5586823 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
5586741 CACTTCCAAC
*
5586751 ACTTGATCAAATATGATACAACTAAT
1 ACTTAATCAAATATGATACAACTAAT
5586777 ACTTAATCAAATATGATACAACTAAT
1 ACTTAATCAAATATGATACAACTAAT
5586803 ACTTAATCAAATATGATACAA
1 ACTTAATCAAATATGATACAA
5586824 TTATCGATAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.30
Consensus pattern (26 bp):
ACTTAATCAAATATGATACAACTAAT
Found at i:5600805 original size:26 final size:27
Alignment explanation
Indices: 5600768--5600824 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
5600758 AATGTACTGA
* *
5600768 AAAAAAATGTTGTTACAAGTTATGTTG
1 AAAAAAATGTTGTTACAAGCTATGTTC
*
5600795 AAAAAAA-GTTGTTACATGCTATGTTC
1 AAAAAAATGTTGTTACAAGCTATGTTC
5600821 AAAA
1 AAAA
5600825 TATTGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (27 bp):
AAAAAAATGTTGTTACAAGCTATGTTC
Found at i:5600830 original size:24 final size:25
Alignment explanation
Indices: 5600770--5600832 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
5600760 TGTACTGAAA
* *
5600770 AAAAATGTTGTTACAAGTTATGTTG
1 AAAAATATTGTTACAAGCTATGTTG
* *
5600795 AAAAAAAGTTGTTACATGCTATGTT-
1 AAAAATA-TTGTTACAAGCTATGTTG
*
5600820 CAAAATATTGTTA
1 AAAAATATTGTTA
5600833 TATACCATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.19
25 10 0.32
26 15 0.48
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (25 bp):
AAAAATATTGTTACAAGCTATGTTG
Found at i:5600846 original size:50 final size:51
Alignment explanation
Indices: 5600792--5600939 Score: 131
Period size: 52 Copynumber: 2.9 Consensus size: 51
5600782 ACAAGTTATG
* * * **
5600792 TTGAAAAAAAGTTGTTACATGCTATGTTCAAAATATTGTTA-T-ATACCATA
1 TTGAAAAAAAGTTGTTACATGCCATATT-AAAAAAAAGTTATTCATACCATA
* * *
5600842 TTGAACAAAAGTTGCTATATGCCATATTAAAAAAAAGTTATTGCATACCATA
1 TTGAAAAAAAGTTGTTACATGCCATATTAAAAAAAAGTTATT-CATACCATA
* * *** *
5600894 TTGAAAAAAAATTATTACATATTATATTGAAAAAAAGTTATT-ATAC
1 TTGAAAAAAAGTTGTTACATGCCATATTAAAAAAAAGTTATTCATAC
5600940 AGTATGTTAA
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
49 9 0.12
50 28 0.36
52 41 0.53
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.35
Consensus pattern (51 bp):
TTGAAAAAAAGTTGTTACATGCCATATTAAAAAAAAGTTATTCATACCATA
Found at i:5600861 original size:26 final size:26
Alignment explanation
Indices: 5600831--5600938 Score: 99
Period size: 26 Copynumber: 4.2 Consensus size: 26
5600821 AAAATATTGT
* *
5600831 TATATACCATATTGAACAAAAGTTGC
1 TATATACCATATTGAAAAAAAGTTAC
* * *
5600857 TATATGCCATATTAAAAAAAAGTTAT
1 TATATACCATATTGAAAAAAAGTTAC
** * *
5600883 TGCATACCATATTGAAAAAAAATTAT
1 TATATACCATATTGAAAAAAAGTTAC
* ** *
5600909 TACATATTATATTGAAAAAAAGTTAT
1 TATATACCATATTGAAAAAAAGTTAC
5600935 TATA
1 TATA
5600939 CAGTATGTTA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (26 bp):
TATATACCATATTGAAAAAAAGTTAC
Found at i:5600875 original size:24 final size:25
Alignment explanation
Indices: 5600796--5600876 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
5600786 GTTATGTTGA
* * *
5600796 AAAAAAGTTGTTACATGCTATGTTC
1 AAAAAAGTTGTTATATGCCATATTC
* * *
5600821 AAAATA-TTGTTATATACCATATTG
1 AAAAAAGTTGTTATATGCCATATTC
* *
5600845 AACAAAAGTTGCTATATGCCATATTA
1 AA-AAAAGTTGTTATATGCCATATTC
5600871 AAAAAA
1 AAAAAA
5600877 AGTTATTGCA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 15 0.34
25 12 0.27
26 17 0.39
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (25 bp):
AAAAAAGTTGTTATATGCCATATTC
Found at i:5600974 original size:29 final size:27
Alignment explanation
Indices: 5600904--5600981 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 27
5600894 TTGAAAAAAA
* * *
5600904 ATTATTACATATTATATTGAAAAAAAGTT
1 ATTATTACA-GTTATGTT-AAAAAAAATT
5600933 ATTA-TACAG-TATGTTAAAAAAATATT
1 ATTATTACAGTTATGTTAAAAAAA-ATT
*
5600959 ATTATTACACGTTATGTTTAAAA
1 ATTATTACA-GTTATGTTAAAAA
5600982 TGTTATTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.17
26 11 0.27
27 4 0.10
28 5 0.12
29 14 0.34
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTATTACAGTTATGTTAAAAAAAATT
Found at i:5601032 original size:26 final size:26
Alignment explanation
Indices: 5600863--5601061 Score: 100
Period size: 26 Copynumber: 7.5 Consensus size: 26
5600853 TTGCTATATG
* *
5600863 CCATATTAAAAAAAAGTTATTGCATA
1 CCATATTAAAAAAATGTTATTACATA
*
5600889 CCATATTGAAAAAAA-ATTATTACATA
1 CCATATT-AAAAAAATGTTATTACATA
** * *
5600915 TTATATTGAAAAAAA-GTTATTATACA
1 CCATATT-AAAAAAATGTTATTACATA
** * * *
5600941 GTATGTTAAAAAAATATTATTA-TTA
1 CCATATTAAAAAAATGTTATTACATA
* ** *
5600966 CACGTTATGT-TTAAAATGTTATTATATA
1 C-C-ATAT-TAAAAAAATGTTATTACATA
* * *
5600994 TCATGTTGCAAAAAATGTTATTACATA
1 CCATATT-AAAAAAATGTTATTACATA
**
5601021 CCATATTAAAAAAAAATTATTACATA
1 CCATATTAAAAAAATGTTATTACATA
* *
5601047 TCATGTTAAAGAAAA
1 CCATATTAAA-AAAA
5601062 AAAAATTCTT
Statistics
Matches: 131, Mismatches: 33, Indels: 17
0.72 0.18 0.09
Matches are distributed among these distances:
25 9 0.07
26 74 0.56
27 45 0.34
28 3 0.02
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
CCATATTAAAAAAATGTTATTACATA
Found at i:5601084 original size:30 final size:29
Alignment explanation
Indices: 5601028--5601090 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
5601018 ATACCATATT
*
5601028 AAAAAAAAATTATTACATATCATGTTAAAG
1 AAAAAAAAATTATTACACATCATGTT-AAG
* * *
5601058 AAAAAAAAATTCTTACACGTCTTGTTAAG
1 AAAAAAAAATTATTACACATCATGTTAAG
5601087 AAAA
1 AAAA
5601091 TGTTGTAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (29 bp):
AAAAAAAAATTATTACACATCATGTTAAG
Found at i:5601811 original size:37 final size:38
Alignment explanation
Indices: 5601761--5601834 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 38
5601751 GTAATGAGTC
5601761 ACTCAAAAGTCTTTTCT-TCATTTCTTGTGCAATTATT
1 ACTCAAAAGTCTTTTCTCTCATTTCTTGTGCAATTATT
*
5601798 ACTCAAAAGTCTTTTCTCCCTCTTTTCTTGTGCAATT
1 ACTCAAAAGTCTTTTCT--CTCATTTCTTGTGCAATT
5601835 TCCTTAGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 17 0.52
40 16 0.48
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47
Consensus pattern (38 bp):
ACTCAAAAGTCTTTTCTCTCATTTCTTGTGCAATTATT
Found at i:5607643 original size:21 final size:21
Alignment explanation
Indices: 5607619--5607661 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5607609 ACCCTAAGTG
*
5607619 TTAAATTTTTTC-TCAACTCTT
1 TTAAATTTCTTCGT-AACTCTT
*
5607640 TTAAGTTTCTTCGTAACTCTT
1 TTAAATTTCTTCGTAACTCTT
5607661 T
1 T
5607662 CCATCTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.56
Consensus pattern (21 bp):
TTAAATTTCTTCGTAACTCTT
Found at i:5608450 original size:33 final size:33
Alignment explanation
Indices: 5608413--5608475 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
5608403 TAAAAATAAA
5608413 TATATTTGCTTCTTTTCGTTCCATCCAAATGAG
1 TATATTTGCTTCTTTTCGTTCCATCCAAATGAG
5608446 TATATTTGCTTCTTTTCGTTCCATCCAAAT
1 TATATTTGCTTCTTTTCGTTCCATCCAAAT
5608476 TCAATGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.48
Consensus pattern (33 bp):
TATATTTGCTTCTTTTCGTTCCATCCAAATGAG
Found at i:5612105 original size:19 final size:19
Alignment explanation
Indices: 5612061--5612105 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5612051 AGAGAAATAT
5612061 AAGAGAAAGTATTTAGAAGG
1 AAGAGAAAGTATTTA-AAGG
5612081 AA-AGAAAGTATTT-AAGG
1 AAGAGAAAGTATTTAAAGG
5612098 AGAGAGAA
1 A-AGAGAA
5612106 GAAAATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 15 0.65
20 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (19 bp):
AAGAGAAAGTATTTAAAGG
Found at i:5613195 original size:11 final size:11
Alignment explanation
Indices: 5613179--5613203 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5613169 GTTGTAATGT
5613179 TAAATTATCAA
1 TAAATTATCAA
5613190 TAAATTATCAA
1 TAAATTATCAA
5613201 TAA
1 TAA
5613204 TGACATATTT
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATTATCAA
Found at i:5613912 original size:23 final size:24
Alignment explanation
Indices: 5613867--5613965 Score: 78
Period size: 25 Copynumber: 3.9 Consensus size: 24
5613857 ATATCTAAAC
*
5613867 ACATGTAAAAAGAATATTATTACATG
1 ACATGTTAAAA-AA-ATTATTACATG
*
5613893 -CTATGTT-AAAAAATTATTACACG
1 AC-ATGTTAAAAAAATTATTACATG
*
5613916 ACATGTTAAAAAAAATTATTACATATA
1 ACATGTT-AAAAAAATTATTAC--ATG
5613943 ATCAT-TTGAAAAAAATTATTACA
1 A-CATGTT-AAAAAAATTATTACA
5613966 CGTTATGTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
23 15 0.25
24 3 0.05
25 18 0.30
26 4 0.07
27 18 0.30
28 3 0.05
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (24 bp):
ACATGTTAAAAAAATTATTACATG
Found at i:5613934 original size:25 final size:25
Alignment explanation
Indices: 5613867--5613938 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
5613857 ATATCTAAAC
*
5613867 ACATG-TAAAAAGAATATTATTACATG
1 ACATGTTAAAAA-AA-ATTATTACACG
5613893 -CTATGTT--AAAAAATTATTACACG
1 AC-ATGTTAAAAAAAATTATTACACG
5613916 ACATGTTAAAAAAAATTATTACA
1 ACATGTTAAAAAAAATTATTACA
5613939 TATAATCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
23 15 0.38
24 3 0.08
25 18 0.45
26 3 0.08
27 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (25 bp):
ACATGTTAAAAAAAATTATTACACG
Found at i:5613979 original size:27 final size:26
Alignment explanation
Indices: 5613900--5613981 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
5613890 ATGCTATGTT
*
5613900 AAAAAATTATTACACG-ACATG-TTAA
1 AAAAAATTATTACACGTA-ATGTTTGA
** *
5613925 AAAAAATTATTACATATAATCATTTGA
1 AAAAAATTATTACACGTAAT-GTTTGA
*
5613952 AAAAAATTATTACACGTTATGTTGTGA
1 AAAAAATTATTACACGTAATGTT-TGA
5613979 AAA
1 AAA
5613982 TGTTGTTGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
25 16 0.36
26 3 0.07
27 26 0.58
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (26 bp):
AAAAAATTATTACACGTAATGTTTGA
Found at i:5614034 original size:26 final size:25
Alignment explanation
Indices: 5613996--5614058 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
5613986 GTTGTTATTC
* *
5613996 AAAATGTTGTTATACATTATGTTAAA
1 AAAAAGTTATTATACATTATGTT-AA
**
5614022 AAAAAGTTATTATATGTTATGTTAA
1 AAAAAGTTATTATACATTATGTTAA
5614047 AAAAAGTTATTA
1 AAAAAGTTATTA
5614059 CATGAAACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 14 0.42
26 19 0.58
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (25 bp):
AAAAAGTTATTATACATTATGTTAA
Found at i:5614968 original size:28 final size:27
Alignment explanation
Indices: 5614868--5614973 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
5614858 ATTCAAAATG
*
5614868 TTATTACAAGTCATGTTAAAAAAAAAA
1 TTATTACATGTCATGTTAAAAAAAAAA
* * *
5614895 TTATTATATGTTATGTTAGAAAAAAAA
1 TTATTACATGTCATGTTAAAAAAAAAA
* * *
5614922 TTGTTAGATGTTATGTTAAAAAAAAAAA
1 TTATTACATGTCATGTT-AAAAAAAAAA
* *
5614950 TTATTACACGTCATATTAAAAAAA
1 TTATTACATGTCATGTTAAAAAAA
5614974 TATTATAATC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 45 0.68
28 21 0.32
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (27 bp):
TTATTACATGTCATGTTAAAAAAAAAA
Found at i:5615063 original size:11 final size:11
Alignment explanation
Indices: 5615047--5615071 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5615037 AACATTTTCT
5615047 TTAAGAAATCA
1 TTAAGAAATCA
5615058 TTAAGAAATCA
1 TTAAGAAATCA
5615069 TTA
1 TTA
5615072 GGAAGTGACA
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
TTAAGAAATCA
Found at i:5619354 original size:28 final size:28
Alignment explanation
Indices: 5619322--5619383 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
5619312 CAATAGAATA
* * *
5619322 CCTTTTAAAGGTTCAAGCATAATCATTG
1 CCTTTTAAAGGATCAAACATAACCATTG
* *
5619350 CCTTTTCAAGGATCAAATATAACCATTG
1 CCTTTTAAAGGATCAAACATAACCATTG
*
5619378 ACTTTT
1 CCTTTT
5619384 CTAAGTTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (28 bp):
CCTTTTAAAGGATCAAACATAACCATTG
Found at i:5619938 original size:21 final size:21
Alignment explanation
Indices: 5619909--5619949 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5619899 AATTGGAAAT
*
5619909 CATTCAAGCAATTTTGAAACG
1 CATTCAAGCAATTTTAAAACG
*
5619930 CATTTAAGCAATTTTAAAAC
1 CATTCAAGCAATTTTAAAAC
5619950 TTTTCATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
CATTCAAGCAATTTTAAAACG
Found at i:5620013 original size:21 final size:22
Alignment explanation
Indices: 5619989--5620075 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 22
5619979 AAACTTAACT
5619989 AAACAAG-TCTAAAAACT-ATTC
1 AAACAAGTTC-AAAAACTCATTC
5620010 AAACAAGTTCAAAAACTCATTC
1 AAACAAGTTCAAAAACTCATTC
* * * * *
5620032 ATATAACTT-TAAAGCTCATTC
1 AAACAAGTTCAAAAACTCATTC
* *
5620053 AAATAAGTTCAAACA-TCATTC
1 AAACAAGTTCAAAAACTCATTC
5620074 AA
1 AA
5620076 GTAATTTTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 39 0.74
22 14 0.26
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.28
Consensus pattern (22 bp):
AAACAAGTTCAAAAACTCATTC
Found at i:5623114 original size:80 final size:80
Alignment explanation
Indices: 5622944--5623132 Score: 188
Period size: 81 Copynumber: 2.4 Consensus size: 80
5622934 GTTACACAAC
* * * * *
5622944 ATATTAAAAAAAATATTGTTGTTATACGTTATGTACAAAAACATGTTACATAGCATGGTTAAACA
1 ATATTAAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTACATAGCATGGTTAAAAA
* * *
5623009 AGGTTGTTTCATGAT
66 AAGTTATTTCACGAT
* * *
5623024 ATATTGAAAAAAAATATTATTGTTACATATCATGTAC-AAAATATGTTACA-CGTCATGGTTAAA
1 ATATT-AAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTACATAG-CATGGTT-AA
5623087 AAAAAGTTATTTCACG-T
63 AAAAAGTTATTTCACGAT
* * *
5623104 CATGTT-AAAAAAATATTATTATTGCACAT
1 -ATATTAAAAAAAATATTATTGTTACACAT
5623133 TATGCGTAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
79 21 0.23
80 25 0.28
81 44 0.49
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (80 bp):
ATATTAAAAAAAATATTATTGTTACACATCATGTACAAAAACATGTTACATAGCATGGTTAAAAA
AAGTTATTTCACGAT
Found at i:5625027 original size:148 final size:147
Alignment explanation
Indices: 5624688--5625199 Score: 666
Period size: 148 Copynumber: 3.4 Consensus size: 147
5624678 TTATAGTATT
* * *
5624688 CATTGCAGCAGGCCCCTACGTGTTTCTCACTCATCTCCAAGCCTTTTATAAAACCGCCGCCTTCA
1 CATTGCAACAGGCCCCTACGTGTTTCTCAC-CATCTCCAAGCCTTCTATAAAACCGCCACCTTCA
* * * * *
5624753 CTCTCCATGTCTGTAGCAATTTTGAAATGTCCAACTTTCTGTTCTCACCCATAATTCTTCTATCC
65 CTCTCCTTGTCTGCAGCAATTTCGAAATGT-CAACTTTCTGTTCTCACCCATTATTCTGCTATCC
* *
5624818 ATGTTCCAATAAGATTCTG
129 AAGTTCAAATAAGATTCTG
* * *
5624837 CGTTGCAACAGGCCCCTACGTGTTTCTCACGCATCTCCATGCCTTGTATAAAACCGCCACCTTCA
1 CATTGCAACAGGCCCCTACGTGTTTCTCAC-CATCTCCAAGCCTTCTATAAAACCGCCACCTTCA
* * * * *
5624902 CTCTCCTTGTCTGCAGCAATTGCGAAATGTCAAGTTTCTGTTCTCAACCATTATTGTGCTATCTA
65 CTCTCCTTGTCTGCAGCAATTTCGAAATGTCAACTTTCTGTTCTCACCCATTATTCTGCTATCCA
*
5624967 AGTTCAAATAAGATTTTG
130 AGTTCAAATAAGATTCTG
* * * * *
5624985 CATTGCAACAGGTCTCTACGTGTTTCTCACCGATCTCTATGCCTTCTATAAAACCGCCACCTTTA
1 CATTGCAACAGGCCCCTACGTGTTTCTCACC-ATCTCCAAGCCTTCTATAAAACCGCCACCTTCA
* * * *
5625050 CTCTCCTTATCCGCAGCAATTTCGAAATGTCATCTTTCTGTTCTCACCCA-TAGTTCTGCTATCG
65 CTCTCCTTGTCTGCAGCAATTTCGAAATGTCAACTTTCTGTTCTCACCCATTA-TTCTGCTATCC
* *
5625114 AAGTTCATATCAGATTCTG
129 AAGTTCAAATAAGATTCTG
* * *
5625133 CATTGCAGCTGGCCTCTACGTGTTTCTCATCCATCTCCAAGCCTTCTATAAAACCGCCACCTTCA
1 CATTGCAACAGGCCCCTACGTGTTTCTCA-CCATCTCCAAGCCTTCTATAAAACCGCCACCTTCA
5625198 CT
65 CT
5625200 TTCTCAATTG
Statistics
Matches: 318, Mismatches: 42, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
147 3 0.01
148 228 0.72
149 87 0.27
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (147 bp):
CATTGCAACAGGCCCCTACGTGTTTCTCACCATCTCCAAGCCTTCTATAAAACCGCCACCTTCAC
TCTCCTTGTCTGCAGCAATTTCGAAATGTCAACTTTCTGTTCTCACCCATTATTCTGCTATCCAA
GTTCAAATAAGATTCTG
Found at i:5625931 original size:45 final size:45
Alignment explanation
Indices: 5625882--5626015 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 45
5625872 GTTATACACT
* * * * *
5625882 ATGTACAAAAACATGTTATACGTCATGATTAGGTTTTTATACGTC
1 ATGTATAAAAACATGTGACACGTCATGATTAGGTTATTACACGTC
* * * * **
5625927 ATGTATAAAAACGTGTGACAAGCCATGATTAGGTTGTTACACACC
1 ATGTATAAAAACATGTGACACGTCATGATTAGGTTATTACACGTC
*
5625972 ATGTATAAAAACATGTGAGACGTCATGATTAGGTTATTACACGT
1 ATGTATAAAAACATGTGACACGTCATGATTAGGTTATTACACGT
5626016 TATGGTTAGA
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (45 bp):
ATGTATAAAAACATGTGACACGTCATGATTAGGTTATTACACGTC
Found at i:5626015 original size:21 final size:21
Alignment explanation
Indices: 5625991--5626040 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
5625981 AACATGTGAG
*
5625991 ACGTCATGATTAGGTTATTAC
1 ACGTCATGATTAGATTATTAC
* * *
5626012 ACGTTATGGTTAGATTGTTAC
1 ACGTCATGATTAGATTATTAC
*
5626033 ACATCATG
1 ACGTCATG
5626041 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (21 bp):
ACGTCATGATTAGATTATTAC
Found at i:5626120 original size:80 final size:81
Alignment explanation
Indices: 5626025--5626197 Score: 210
Period size: 82 Copynumber: 2.1 Consensus size: 81
5626015 TTATGGTTAG
* * *
5626025 ATTGTTACACATCATGTT-AAAAAAAATACTATTATTACACG-CTATGTATC-AAAATATGTTAC
1 ATTGTTACACGTCATGTTAAAAAAAAATACTATTATTACAAGTC-ATATA-CAAAAATATGTTAC
* *
5626087 ATG-TCATGGTTAAAAAAG
64 ACGCT-ATGGTTAAAAAAA
* * *
5626105 GTTGTTACACGTCATGTTGAAAAAAAAATACTGTTGTTACAAGTCATATACAAAAATATGTTACA
1 ATTGTTACACGTCATGTT-AAAAAAAAATACTATTATTACAAGTCATATACAAAAATATGTTACA
5626170 CGCTATGGTTAAAAAAA
65 CGCTATGGTTAAAAAAA
5626187 ATTGTTACACG
1 ATTGTTACACG
5626198 CCATATTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
80 16 0.20
81 1 0.01
82 60 0.76
83 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (81 bp):
ATTGTTACACGTCATGTTAAAAAAAAATACTATTATTACAAGTCATATACAAAAATATGTTACAC
GCTATGGTTAAAAAAA
Found at i:5626209 original size:26 final size:27
Alignment explanation
Indices: 5626156--5626210 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
5626146 AGTCATATAC
* *
5626156 AAAAATATGTTACACGCTATGGTTAAA
1 AAAAATATGTTACACGCCATGATTAAA
*
5626183 AAAAAT-TGTTACACGCCAT-ATTCAA
1 AAAAATATGTTACACGCCATGATTAAA
5626208 AAA
1 AAA
5626211 TATTTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 12 0.48
27 6 0.24
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (27 bp):
AAAAATATGTTACACGCCATGATTAAA
Found at i:5638148 original size:12 final size:12
Alignment explanation
Indices: 5638131--5638155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5638121 TTTCAATGAT
5638131 TATATATATATG
1 TATATATATATG
5638143 TATATATATATG
1 TATATATATATG
5638155 T
1 T
5638156 TGGACTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATATATG
Found at i:5641445 original size:16 final size:17
Alignment explanation
Indices: 5641424--5641462 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5641414 TTTTTAAAAT
5641424 AAATATTTTATT-TTAA
1 AAATATTTTATTATTAA
*
5641440 AAATATTTTTTTATTAA
1 AAATATTTTATTATTAA
*
5641457 ATATAT
1 AAATAT
5641463 AAATCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTTTATTATTAA
Found at i:5645739 original size:26 final size:28
Alignment explanation
Indices: 5645691--5645742 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
5645681 TGAGTTGTAG
*
5645691 TAAAAAGAGTAAAATAAAAACAAAAAAA
1 TAAAAAGAGTAAAAGAAAAACAAAAAAA
*
5645719 TAAAAA-AG-AAAAGAAAGACAAAAA
1 TAAAAAGAGTAAAAGAAAAACAAAAA
5645743 GAAAGAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 2 0.09
28 6 0.27
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.08
Consensus pattern (28 bp):
TAAAAAGAGTAAAAGAAAAACAAAAAAA
Found at i:5653664 original size:2 final size:2
Alignment explanation
Indices: 5653659--5653683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5653649 ATAGAGACCT
5653659 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5653684 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5653688 original size:2 final size:2
Alignment explanation
Indices: 5653683--5653712 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5653673 TATATATATA
5653683 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5653713 GCATATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5653943 original size:23 final size:25
Alignment explanation
Indices: 5653903--5653948 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
5653893 GAAAAATCTC
5653903 AAAAATAAATAATCATAATTTTTTT
1 AAAAATAAATAATCATAATTTTTTT
5653928 AAAAA-AAA-AATCATAATTTTT
1 AAAAATAAATAATCATAATTTTT
5653949 AAAGTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAATAAATAATCATAATTTTTTT
Found at i:5654912 original size:21 final size:21
Alignment explanation
Indices: 5654886--5654966 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 21
5654876 TAATTTTTTT
5654886 ATTTTTAATATATTTAATTAA
1 ATTTTTAATATATTTAATTAA
* *
5654907 ATTTTT-ATATTTTTATTTTAA
1 ATTTTTAATATATTTA-ATTAA
*
5654928 A--TTAAATATA-TT-ATT-A
1 ATTTTTAATATATTTAATTAA
* *
5654944 ATTATTATTATTATTTAATTAA
1 ATTTTTAATA-TATTTAATTAA
5654966 A
1 A
5654967 ATAACACATA
Statistics
Matches: 44, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
16 2 0.05
17 2 0.05
18 4 0.09
19 6 0.14
20 14 0.32
21 14 0.32
22 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTAATATATTTAATTAA
Found at i:5654946 original size:16 final size:18
Alignment explanation
Indices: 5654913--5654966 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
5654903 TTAAATTTTT
*
5654913 ATATTTTTATTTTAAATTAA
1 ATATTATTA-TTT-AATTAA
5654933 ATA-TATTA-TTAATT-A
1 ATATTATTATTTAATTAA
*
5654948 TTATTATTATTTAATTAA
1 ATATTATTATTTAATTAA
5654966 A
1 A
5654967 ATAACACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
15 3 0.11
16 9 0.32
17 8 0.29
18 1 0.04
19 4 0.14
20 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATTATTTAATTAA
Found at i:5670207 original size:8 final size:8
Alignment explanation
Indices: 5670194--5670223 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5670184 TTCTTGAATA
5670194 TATATATC
1 TATATATC
5670202 TATATATC
1 TATATATC
*
5670210 TATATATA
1 TATATATC
5670218 TATATA
1 TATATA
5670224 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATATC
Found at i:5678086 original size:164 final size:165
Alignment explanation
Indices: 5677814--5678144 Score: 531
Period size: 164 Copynumber: 2.0 Consensus size: 165
5677804 TTAATTCTAG
* *
5677814 TACTCTATTTCTTTTTATGCTTATAAACTTGGAAAAGTTTGCTTGTTTGATTATGTTTTATGCAT
1 TACTCTATTTCTTTTCATGCTTATAAACTTGGAAAAGTTTGCTTGCTTGATTATGTTTTATGCAT
* *
5677879 CTCATGATTTGCTATTAATTCTTTGTTTGACTTATTCTGTTCTTT-CCTTTTTTTCACCAAGATA
66 CTCATGACTTGCTATTAATTCTTTGTTTGACTTATTCTGTTCTTTACC-TTCTTTCACCAAGATA
*
5677943 TTCACTA-TTTTGGCACTATGGAATATATATATATA
130 TTCACTATTTTTGGCACTATGAAATATATATATATA
*
5677978 TACTCTATTTCTTTTCATGCTTATAAACTTGGAAAAGTTTGCTTGCTTGATTATGTTTTGTGCAT
1 TACTCTATTTCTTTTCATGCTTATAAACTTGGAAAAGTTTGCTTGCTTGATTATGTTTTATGCAT
* * * * *
5678043 CTTATGACTTGTTATTGATTTTTTGTTTGACTTATTTTGTTCTTTACCTTCTTTCACCAAGATAT
66 CTCATGACTTGCTATTAATTCTTTGTTTGACTTATTCTGTTCTTTACCTTCTTTCACCAAGATAT
*
5678108 TCACTATTTTTGGCACTATGAAATATATATATGTA
131 TCACTATTTTTGGCACTATGAAATATATATATATA
5678143 TA
1 TA
5678145 TATATATATA
Statistics
Matches: 153, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
164 123 0.80
165 30 0.20
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (165 bp):
TACTCTATTTCTTTTCATGCTTATAAACTTGGAAAAGTTTGCTTGCTTGATTATGTTTTATGCAT
CTCATGACTTGCTATTAATTCTTTGTTTGACTTATTCTGTTCTTTACCTTCTTTCACCAAGATAT
TCACTATTTTTGGCACTATGAAATATATATATATA
Found at i:5690803 original size:2 final size:2
Alignment explanation
Indices: 5690798--5690835 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5690788 TATATACATA
* *
5690798 AG AG AG AG TG AG AG AG AG AG AG AG AA AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5690836 TTAGAGTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:5691308 original size:19 final size:21
Alignment explanation
Indices: 5691267--5691308 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
5691257 ACTCGGTTGA
*
5691267 ACATAATATTTTTTAATTTAAG
1 ACATAATATTTTTT-ATTGAAG
5691289 ACATAAT-TTTTTT-TTGAAG
1 ACATAATATTTTTTATTGAAG
5691308 A
1 A
5691309 TTAAAGTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
ACATAATATTTTTTATTGAAG
Found at i:5692480 original size:2 final size:2
Alignment explanation
Indices: 5692473--5692499 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5692463 CATCAACAAC
5692473 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5692500 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5692724 original size:2 final size:2
Alignment explanation
Indices: 5692717--5692755 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5692707 TTAAATAAAA
5692717 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5692756 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.