Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 28 of 45
Found at i:4958001 original size:20 final size:20
Alignment explanation
Indices: 4957973--4958022 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
4957963 TAAACCTTGA
*
4957973 TCATTCATTTTTACTGTGCT
1 TCATGCATTTTTACTGTGCT
4957993 TCATGCATTTTTACTGTGCT
1 TCATGCATTTTTACTGTGCT
4958013 TCATGCATTT
1 TCATGCATTT
4958023 ATAGCATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.12, T:0.52
Consensus pattern (20 bp):
TCATGCATTTTTACTGTGCT
Found at i:4971622 original size:19 final size:20
Alignment explanation
Indices: 4971581--4971623 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
4971571 CTTTTTCCCT
4971581 TGAAG-ACAGAGAAAACATA
1 TGAAGAACAGAGAAAACATA
*
4971600 -GAAGAACAGA-AAAATATA
1 TGAAGAACAGAGAAAACATA
4971618 TGAAGA
1 TGAAGA
4971624 TAAGAGACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.60, C:0.07, G:0.21, T:0.12
Consensus pattern (20 bp):
TGAAGAACAGAGAAAACATA
Found at i:4973535 original size:14 final size:16
Alignment explanation
Indices: 4973505--4973536 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
4973495 GTAAAAGGGA
4973505 AATTTTCAACTAGTAT
1 AATTTTCAACTAGTAT
4973521 AATTTTC-AC-AGTAT
1 AATTTTCAACTAGTAT
4973535 AA
1 AA
4973537 GTAACCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTTTCAACTAGTAT
Found at i:4976252 original size:19 final size:18
Alignment explanation
Indices: 4976225--4976272 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
4976215 TTCCATGTCA
* *
4976225 TAAACATAATATAAATTAT
1 TAAATATAATATAAACT-T
4976244 TAAATATAATA-AAACTT
1 TAAATATAATATAAACTT
*
4976261 TAAATATGATAT
1 TAAATATAATAT
4976273 GTATATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAATATAATATAAACTT
Found at i:4977220 original size:2 final size:2
Alignment explanation
Indices: 4977213--4977252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4977203 GATGCAAATC
4977213 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
4977253 GTGATATGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4981607 original size:19 final size:19
Alignment explanation
Indices: 4981579--4981634 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
4981569 CACAGTACCG
*
4981579 TATACATGAATAGTGCCTA
1 TATACGTGAATAGTGCCTA
4981598 TATACGTGAATAGTGCCTA
1 TATACGTGAATAGTGCCTA
*
4981617 TATACGTAAATAGTGCCT
1 TATACGTGAATAGTGCCT
4981635 CGACAACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
TATACGTGAATAGTGCCTA
Found at i:4982641 original size:2 final size:2
Alignment explanation
Indices: 4982636--4982692 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
4982626 TTTAAAAAAA
4982636 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
4982678 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4982693 AAACAGGTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4983631 original size:17 final size:16
Alignment explanation
Indices: 4983607--4983647 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4983597 AACTAATTAT
*
4983607 TTTA-AAATATAGTTAA
1 TTTATAAATATA-TAAA
4983623 TTTATAAATATATAAA
1 TTTATAAATATATAAA
4983639 TTT-TAAATA
1 TTTATAAATA
4983648 ATTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTATAAATATATAAA
Found at i:4983647 original size:15 final size:16
Alignment explanation
Indices: 4983605--4983647 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
4983595 TGAACTAATT
*
4983605 ATTTTAAAATATAGTTA
1 ATTTT-AAATATAGTAA
4983622 ATTTATAAATATA-TAA
1 ATTT-TAAATATAGTAA
4983638 ATTTTAAATA
1 ATTTTAAATA
4983648 ATTTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 6 0.25
17 11 0.46
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTTTAAATATAGTAA
Found at i:4983985 original size:21 final size:21
Alignment explanation
Indices: 4983940--4983983 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4983930 TAGTTCTAAT
*
4983940 AAAT-TTTATTTTTTAACCAA
1 AAATCTTTATTCTTTAACCAA
4983960 AAATCTTTATTCTTTAATCCAA
1 AAATCTTTATTCTTTAA-CCAA
4983982 AA
1 AA
4983984 TCCCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATCTTTATTCTTTAACCAA
Found at i:4984800 original size:27 final size:26
Alignment explanation
Indices: 4984761--4984811 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
4984751 TTTATTTTTG
*
4984761 TATTAAATTATTATTTTAATATAAAAA
1 TATTAAATAATTA-TTTAATATAAAAA
*
4984788 TATTTAATAATTATTTAATATAAA
1 TATTAAATAATTATTTAATATAAA
4984812 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTAAATAATTATTTAATATAAAAA
Found at i:4984828 original size:24 final size:22
Alignment explanation
Indices: 4984798--4984863 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
4984788 TATTTAATAA
4984798 TTATTTAATATAAATATAATTT
1 TTATTTAATATAAATATAATTT
*
4984820 TTAGTTTTA-ATAAATAT--TTT
1 TTA-TTTAATATAAATATAATTT
*
4984840 ATTATTTAATAAAAATATAATTT
1 -TTATTTAATATAAATATAATTT
4984863 T
1 T
4984864 AATAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
20 7 0.19
21 10 0.28
22 12 0.33
23 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTTAATATAAATATAATTT
Found at i:4984847 original size:19 final size:19
Alignment explanation
Indices: 4984786--4984852 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 19
4984776 TTAATATAAA
*
4984786 AATATTTAATAATTA-TTT
1 AATATTTAATAAATATTTT
*
4984804 AATA-TAAATATAAT-TTTT
1 AATATTTAATA-AATATTTT
*
4984822 AGT-TTTAATAAATATTTT
1 AATATTTAATAAATATTTT
*
4984840 ATTATTTAATAAA
1 AATATTTAATAAA
4984853 AATATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 8 0.21
18 22 0.56
19 9 0.23
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
AATATTTAATAAATATTTT
Found at i:4984927 original size:37 final size:36
Alignment explanation
Indices: 4984825--4985051 Score: 119
Period size: 35 Copynumber: 6.5 Consensus size: 36
4984815 AATTTTTAGT
*
4984825 TTTAATAAATATTTT-ATTAT-TT-AATAAAAATATAA
1 TTTAAT-AAT-TTTTAATTATATTCAATATAAATATAA
**
4984860 TTTTAATAA--TTTAATT-T-TT-AATATGGATATAA
1 -TTTAATAATTTTTAATTATATTCAATATAAATATAA
*
4984892 TTTAGTAATTTTTAATTAGTATTCAATATAAATATAA
1 TTTAATAATTTTTAATTA-TATTCAATATAAATATAA
* * * *
4984929 TTTTATTTATATTTT-ATTAT-TT-AATATAATTAAAA
1 -TTTAATAAT-TTTTAATTATATTCAATATAAATATAA
* * *
4984964 TATAATAAATTTTAATTATTATTCAACATAAAT-T--
1 TTTAATAATTTTTAATTA-TATTCAATATAAATATAA
** * *
4984998 TTTGTTTATATTTT-ATTA-ATT-AATATAAATATATT
1 TTTAATAAT-TTTTAATTATATTCAATATAAATATA-A
4985033 TTTAATAATTTTTAATTAT
1 TTTAATAATTTTTAATTAT
4985052 TTATTATGTA
Statistics
Matches: 145, Mismatches: 26, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
31 15 0.10
32 20 0.14
33 14 0.10
34 21 0.14
35 29 0.20
36 12 0.08
37 19 0.13
38 11 0.08
39 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (36 bp):
TTTAATAATTTTTAATTATATTCAATATAAATATAA
Found at i:4984978 original size:72 final size:71
Alignment explanation
Indices: 4984842--4985025 Score: 184
Period size: 72 Copynumber: 2.7 Consensus size: 71
4984832 AATATTTTAT
* * * * * * * * *
4984842 TATTTAATAAAAATATAATTTTA-ATA-ATTTAATT-TTTAATATGGATATAATTTAGTAATTTT
1 TATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATAT-AATAAAATATAATAAATTT
4984904 TAATTAG
65 TAATTAG
4984911 TATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATATAATTAAAATATAATAAATTT
1 TATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATATAA-TAAAATATAATAAATTT
*
4984976 TAATTAT
65 TAATTAG
* * *
4984983 TATTCAACAT-AA-AT--TTTTGTTTATATTTTATTAATTAATATAA
1 TATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATATAA
4985026 ATATATTTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
68 27 0.28
69 21 0.21
70 4 0.04
71 10 0.10
72 36 0.37
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (71 bp):
TATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATATAATAAAATATAATAAATTTT
AATTAG
Found at i:4985043 original size:68 final size:71
Alignment explanation
Indices: 4984890--4985052 Score: 197
Period size: 68 Copynumber: 2.3 Consensus size: 71
4984880 ATATGGATAT
* * * *
4984890 AATTTAGTAATTTTTAATTAGTATTCAATATAAATATAATTTTATTTATATTTTATTATTTAATA
1 AATTTAATAATTTTTAATTATTATTCAACATAAATAT-ATTTTATTTATATTTTATTAATTAATA
*
4984955 TAATTAA
65 TAAATAA
* * *
4984962 AATATAATAAATTTTAATTATTATTCAACAT-AA-AT-TTTTGTTTATATTTTATTAATTAATAT
1 AATTTAATAATTTTTAATTATTATTCAACATAAATATATTTTATTTATATTTTATTAATTAATAT
4985024 AAATATA
66 AAATA-A
**
4985031 TTTTTAATAATTTTTAATTATT
1 AATTTAATAATTTTTAATTATT
4985053 TATTATGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
68 29 0.37
69 19 0.24
70 2 0.03
71 2 0.03
72 26 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (71 bp):
AATTTAATAATTTTTAATTATTATTCAACATAAATATATTTTATTTATATTTTATTAATTAATAT
AAATAA
Found at i:4985214 original size:18 final size:17
Alignment explanation
Indices: 4985193--4985226 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4985183 TTAATCTAAC
4985193 TATTATAATAATTAATTT
1 TATTATAATAA-TAATTT
*
4985211 TATTATTATAATAATT
1 TATTATAATAATAATT
4985227 AATCTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATAATAATAATTT
Found at i:4985239 original size:21 final size:22
Alignment explanation
Indices: 4985162--4985240 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 22
4985152 ACTGTAAATT
4985162 TTAATCTCACTAA-TATAATAA
1 TTAATCTCACTAATTATAATAA
*
4985183 TTAATCTAACT-ATTATAATAA
1 TTAATCTCACTAATTATAATAA
* * *
4985204 TTAATTTTA-TTATTATAATAA
1 TTAATCTCACTAATTATAATAA
4985225 TTAATCTCA-TAATTAT
1 TTAATCTCACTAATTAT
4985241 TATTATTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.04
21 48 0.96
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAATCTCACTAATTATAATAA
Found at i:4986433 original size:11 final size:12
Alignment explanation
Indices: 4986417--4986445 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4986407 ATTAAATTAA
4986417 TTAAAAA-AATT
1 TTAAAAATAATT
4986428 TTAAAAATAATT
1 TTAAAAATAATT
4986440 TTAAAA
1 TTAAAA
4986446 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAATAATT
Found at i:4986445 original size:20 final size:20
Alignment explanation
Indices: 4986422--4986476 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
4986412 ATTAATTAAA
*
4986422 AAAATTTTAAAAATAATTTT
1 AAAATTTTAAAAATAATATT
4986442 AAAATTTTATAAAA-AATATT
1 AAAATTTTA-AAAATAATATT
*
4986462 AAATTCTTTAAAAAT
1 AAAAT-TTTAAAAAT
4986477 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTTTAAAAATAATATT
Found at i:4986490 original size:19 final size:18
Alignment explanation
Indices: 4986423--4986515 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 18
4986413 TTAATTAAAA
* *
4986423 AAATTTTAAAAATAATTTT
1 AAATTTTTAAAA-AATATT
4986442 AAAATTTTATAAAAAATATT
1 -AAATTTT-TAAAAAATATT
*
4986462 AAATTCTTTAAAAATTATT
1 AAATT-TTTAAAAAATATT
* **
4986481 ATTATTTTTAATCAA-ATT
1 A-AATTTTTAAAAAATATT
*
4986499 AAATTAATTAAAAAATA
1 AAATT-TTTAAAAAATA
4986516 AATAAAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.05
18 10 0.18
19 23 0.40
20 17 0.30
21 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTTTAAAAAATATT
Found at i:4989211 original size:31 final size:31
Alignment explanation
Indices: 4989173--4989260 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
4989163 TTCCAAAAAA
*
4989173 ATGATGCTCCTAAATAAGAGCTTAAACTGTT
1 ATGATGCTCCTAAACAAGAGCTTAAACTGTT
* *
4989204 ATGATGCTCCTAAGCAATAGCTTAAACTGTT
1 ATGATGCTCCTAAACAAGAGCTTAAACTGTT
* * * *
4989235 ATGATTCTCTTAAGCATGAGCTTAAA
1 ATGATGCTCCTAAACAAGAGCTTAAA
4989261 TTGCCCATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (31 bp):
ATGATGCTCCTAAACAAGAGCTTAAACTGTT
Found at i:4994423 original size:6 final size:6
Alignment explanation
Indices: 4994413--4994452 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
4994403 TGCCTTAGCT
* *
4994413 CATCAT CATCAC CATTAC CATCAC CATCAC CATCAC CATC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATC
4994453 CTCATGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (6 bp):
CATCAC
Found at i:4994630 original size:63 final size:63
Alignment explanation
Indices: 4994553--4994748 Score: 313
Period size: 63 Copynumber: 3.1 Consensus size: 63
4994543 GTCGTAGGCA
*
4994553 AACTT-CACTACTTTACTGGCATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAAC
1 AACTTCCACCACTTTACTGGCATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAAC
* * *
4994615 AACTTCCACCACTTTACAGGCATTCGTTGCTTGTTCACTGCCATCATCGTGTGAATGATTAAC
1 AACTTCCACCACTTTACTGGCATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAAC
* * * *
4994678 AACTTCCGCCACTTTACTGGCATTCGTTGCTTGTTCACTGCGATCATCGACTGAATGCTTAAA
1 AACTTCCACCACTTTACTGGCATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAAC
4994741 AACTTCCA
1 AACTTCCA
4994749 TGTCTTGCTC
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
62 5 0.04
63 116 0.96
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (63 bp):
AACTTCCACCACTTTACTGGCATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAAC
Found at i:4995751 original size:2 final size:2
Alignment explanation
Indices: 4995744--4995768 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4995734 ATAGCCTCAA
4995744 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
4995769 TTTATGCTTA
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:4996756 original size:3 final size:3
Alignment explanation
Indices: 4996748--4996804 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
4996738 AGATCGGAAC
4996748 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4996796 TAT TAT TAT
1 TAT TAT TAT
4996805 GATATACTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4996994 original size:12 final size:12
Alignment explanation
Indices: 4996962--4997030 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
4996952 ATATTTACAA
*
4996962 ATTAAATTATTT
1 ATTATATTATTT
4996974 ATT-TAATTATTT
1 ATTAT-ATTATTT
*
4996986 ATTATATTATTA
1 ATTATATTATTT
*
4996998 AATATTATT-TTT
1 ATTA-TATTATTT
* *
4997010 ATAATAATATTT
1 ATTATATTATTT
4997022 ATATATATT
1 AT-TATATT
4997031 TTAAATAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
11 3 0.07
12 31 0.72
13 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATATTATTT
Found at i:5001895 original size:2 final size:2
Alignment explanation
Indices: 5001888--5001930 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5001878 CTAATTATTC
5001888 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5001930 A
1 A
5001931 ATACAAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5006009 original size:19 final size:19
Alignment explanation
Indices: 5005978--5006041 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
5005968 TTAATATAAA
*
5005978 TAATATATA-ATAATTATT
1 TAATATAAATATAATTATT
*
5005996 TAATATAAATATAATTTTT
1 TAATATAAATATAATTATT
* * *
5006015 TAATATATATTTTATTATT
1 TAATATAAATATAATTATT
5006034 TAATATAA
1 TAATATAA
5006042 TTAGAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 8 0.21
19 30 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATAAATATAATTATT
Found at i:5006032 original size:38 final size:36
Alignment explanation
Indices: 5005988--5006146 Score: 136
Period size: 34 Copynumber: 4.6 Consensus size: 36
5005978 TAATATATAA
5005988 TAATTATTTAATATAAATATAATTTTTTAATATATATT
1 TAATTATTTAATATAAATATAA-TTTTTAATA-ATATT
* * *
5006026 TTATTATTTAATATAATTAGAA--TTTAATAAT-TT
1 TAATTATTTAATATAAATATAATTTTTAATAATATT
* * * *
5006059 TAATTA-TT-AT-TCAATATAAATTTTATTTATATT
1 TAATTATTTAATATAAATATAATTTTTAATAATATT
* * *
5006092 TTATTATTTCATATAAATAT-ATTTTTAATAA-CTT
1 TAATTATTTAATATAAATATAATTTTTAATAATATT
* *
5006126 TAATTATTTATTATATATATA
1 TAATTATTTAATATAAATATA
5006147 TACAATCATT
Statistics
Matches: 95, Mismatches: 19, Indels: 17
0.73 0.15 0.13
Matches are distributed among these distances:
30 6 0.06
31 2 0.02
32 9 0.09
33 14 0.15
34 22 0.23
35 17 0.18
36 6 0.06
38 19 0.20
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (36 bp):
TAATTATTTAATATAAATATAATTTTTAATAATATT
Found at i:5007311 original size:6 final size:6
Alignment explanation
Indices: 5007300--5007345 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
5007290 TGCCTCAGCT
*
5007300 CATCAC CATCAC CATCAC CATCAC CGTCAC CATCAC CATCAC CATC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATC
5007346 CTCATGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.30, C:0.50, G:0.02, T:0.17
Consensus pattern (6 bp):
CATCAC
Found at i:5007634 original size:3 final size:3
Alignment explanation
Indices: 5007626--5007682 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
5007616 TTGCCTGAGC
* * * * *
5007626 TCA TCA TCA TCA TCA TCA GCA GCA GCA GCA GCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
5007674 TCA CCA TCA
1 TCA TCA TCA
5007683 CCAGCCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.23
Consensus pattern (3 bp):
TCA
Found at i:5007955 original size:342 final size:321
Alignment explanation
Indices: 5007189--5008182 Score: 1182
Period size: 342 Copynumber: 3.0 Consensus size: 321
5007179 ATGGTTCAAT
* ** * * ** *
5007189 TGTCCGCATTTTTCTCTGTTTGTTTGGCAAAATATAACTTTTCAC-CTACCATTTCTGCTAACAG
1 TGTCCACATTTTTCTGGGTTTGCTTGGCAAAAAATAACTTTTC-CTCTAAAATTTCTGCTACCAG
* * * * * * * *
5007253 GACTCTGTTAACCTTAGCAATAAATTCTTCAATTTTTTGCCTCAGCTCATCACCATCACCATCAC
65 GCCTCTGCTAACCTTAGCAACAAATTCTTCAATTCTTTGCCTCAGCTCTTTATCAT--CC-TCAT
* * *
5007318 CATCACCGTCACCATCACCATCACCATCCTCATGATTTTCATCCTTGTCATCCGTATTGTAGTTT
127 CATCA---TCACCATCACCATCACCATCCTCATGATTTTCATCCTTATCATCCGTATTGTAATTG
5007383 TTGTCACTATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGCAACTACGGTCTCGTTGTTGACACG
189 TTGTCACTATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGCAACTACGGTCTCGTTGTTGACACG
* * *
5007448 TAGCACTACTTTACTGGTATTCGTTGCTTGTTCACTGCCATTATCGAGTGAATGCCTAACTGCTT
254 TAGCACTACTTTACTGGTATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAACTACTT
5007513 CCA
319 CCA
* ** * *
5007516 TGTCCACCTTTTTCTGTTTTTGTTTGGCAAAAAATAACTTTTCCTCTAACATTTCTGCTACCAGG
1 TGTCCACATTTTTCTGGGTTTGCTTGGCAAAAAATAACTTTTCCTCTAAAATTTCTGCTACCAGG
* * * *
5007581 TCTCTGTTAACCTTAGCAATAAATTCTTCAATTCTTTGCCTGAGCTCATCATCATCATCATCAGC
66 CCTCTGCTAACCTTAGCAACAAATTCTTCAATTCTTTGCCTCAGCTC-T--T--T-ATCAT----
* * *
5007646 AGCAGCAGCAGCATCATCATCATCATCATCACCATCACCAGCCTCGTGATTTTCATCCTTATCAT
121 --------C--C-TCATCATCATCACCATCACCATCACCATCCTCATGATTTTCATCCTTATCAT
* * *
5007711 CCGTATCGTAATTGTTGTCACTATAATCCTCTTCGCTTGCTTTGCTGTCTGCAGCAACTACAGTC
175 CCGTATTGTAATTGTTGTCACTATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGCAACTACGGTC
* * * * * *
5007776 TCGTCGTAGACACATAGCACTACTTTACTGGTATTTGTTGCTTGTTCACTGCCATCATCAAGCGA
240 TCGTTGTTGACACGTAGCACTACTTTACTGGTATTCGTTGCTTGTTCACTGCCATCATCGAGTGA
*
5007841 ATGCTTAACTACTTCCG
305 ATGCTTAACTACTTCCA
* * * * **
5007858 TGTCCGCATTTTTCTGGGTTTGCTTGGCAAAACATAACTTTTTCTTTAAAATTTCTGCTTTCAGG
1 TGTCCACATTTTTCTGGGTTTGCTTGGCAAAAAATAACTTTTCCTCTAAAATTTCTGCTACCAGG
*
5007923 CCTCTGCTAACCTTAGCAACAAATTCTTCAATTCTTTGCCTCTGCTCTTTATCATCCTCATCATC
66 CCTCTGCTAACCTTAGCAACAAATTCTTCAATTCTTTGCCTCAGCTCTTTATCATCCTCATCATC
*
5007988 ATCACCATCACCATCACCATCCTCATGATTTTCATCCTTATCATCCGTATTGTAATTGTTTTCAC
131 ATCACCATCACCATCACCATCCTCATGATTTTCATCCTTATCATCCGTATTGTAATTGTTGTCAC
* ** *
5008053 TATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGTAACTGTGGTCTTGTTGTTGACACGTAGCACT
196 TATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGCAACTACGGTCTCGTTGTTGACACGTAGCACT
* * *
5008118 ACTTCACTGGCT-TTCGTTGCTTGTTCACTGCCATCCTCGAGTGAATGCTTAACAACTTCCA
261 ACTTTACTGG-TATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAACTACTTCCA
5008179 TGTC
1 TGTC
5008183 TTGCTCGTCT
Statistics
Matches: 575, Mismatches: 72, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
321 180 0.31
322 2 0.00
324 1 0.00
326 1 0.00
327 100 0.17
330 1 0.00
333 4 0.01
336 5 0.01
337 1 0.00
339 1 0.00
341 1 0.00
342 267 0.46
343 1 0.00
345 10 0.02
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (321 bp):
TGTCCACATTTTTCTGGGTTTGCTTGGCAAAAAATAACTTTTCCTCTAAAATTTCTGCTACCAGG
CCTCTGCTAACCTTAGCAACAAATTCTTCAATTCTTTGCCTCAGCTCTTTATCATCCTCATCATC
ATCACCATCACCATCACCATCCTCATGATTTTCATCCTTATCATCCGTATTGTAATTGTTGTCAC
TATAATCCTCTTCGCCTGCTTTGCTGTCTGCAGCAACTACGGTCTCGTTGTTGACACGTAGCACT
ACTTTACTGGTATTCGTTGCTTGTTCACTGCCATCATCGAGTGAATGCTTAACTACTTCCA
Found at i:5009175 original size:2 final size:2
Alignment explanation
Indices: 5009168--5009212 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5009158 ATAGCCTCAA
5009168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5009210 TC T
1 TC T
5009213 TTTTAATGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5010079 original size:20 final size:20
Alignment explanation
Indices: 5010044--5010093 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5010034 ATCCCGTCTC
* **
5010044 ATTTAATATTTATTATTTAT
1 ATTTAATTTTTATTATAAAT
* *
5010064 TTTTAATTTTTTTTATAAAT
1 ATTTAATTTTTATTATAAAT
5010084 ATTTAATTTT
1 ATTTAATTTT
5010094 ATTCCAGGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTAATTTTTATTATAAAT
Found at i:5016179 original size:4 final size:4
Alignment explanation
Indices: 5016170--5016219 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
5016160 ACAAACCAGA
5016170 AAAG AAAG AAAG -AAG -AAG AAAG -AAG AAAG -AAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5016213 AAAG AAA
1 AAAG AAA
5016220 TAAGTAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 15 0.36
4 27 0.64
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5016188 original size:14 final size:13
Alignment explanation
Indices: 5016167--5016219 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 13
5016157 ATAACAAACC
5016167 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
5016180 AGAAGAAGAAAG-A
1 AGAA-AAGAAAGAA
5016193 AG-AAAG-AAGAA
1 AGAAAAGAAAGAA
5016204 AG--AAGAAAGAA
1 AGAAAAGAAAGAA
5016215 AGAAA
1 AGAAA
5016220 TAAGTAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.17
11 13 0.37
12 1 0.03
13 8 0.23
14 7 0.20
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:5016190 original size:10 final size:10
Alignment explanation
Indices: 5016175--5016214 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
5016165 CCAGAAAAGA
5016175 AAGAAAGAAG
1 AAGAAAGAAG
5016185 AAGAAAGAAG
1 AAGAAAGAAG
5016195 AA-AGAAGAAAG
1 AAGA-AAG-AAG
5016206 AAGAAAGAA
1 AAGAAAGAA
5016215 AGAAATAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 17 0.63
11 8 0.30
12 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:5016192 original size:7 final size:7
Alignment explanation
Indices: 5016171--5016219 Score: 73
Period size: 7 Copynumber: 6.9 Consensus size: 7
5016161 CAAACCAGAA
5016171 AAGAAAG
1 AAGAAAG
5016178 AA-AGAAG
1 AAGA-AAG
5016185 AAGAAAG
1 AAGAAAG
5016192 AAGAAAG
1 AAGAAAG
5016199 AAGAAAG
1 AAGAAAG
5016206 AAGAAAG
1 AAGAAAG
5016213 AAAGAAA
1 -AAGAAA
5016220 TAAGTAGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 1 0.03
7 31 0.79
8 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:5018954 original size:11 final size:11
Alignment explanation
Indices: 5018938--5018964 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5018928 TAAGTTAATT
5018938 TTTAATTTAAA
1 TTTAATTTAAA
5018949 TTTAATTTAAA
1 TTTAATTTAAA
5018960 TTTAA
1 TTTAA
5018965 ATCAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5019145 original size:30 final size:30
Alignment explanation
Indices: 5019094--5019172 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
5019084 TATTTTATTA
* *
5019094 AAATTA-AATTAAATTAAAATTTAATAAAAT
1 AAATTATAATAAAATT-TAATTTAATAAAAT
5019124 -AATTATAATAATAATTTAATTTAATAAAAT
1 AAATTATAATAA-AATTTAATTTAATAAAAT
*
5019154 AAATTATTATAAAATTTAA
1 AAATTATAATAAAATTTAA
5019173 ATCTTTTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.12
30 24 0.56
31 14 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATTATAATAAAATTTAATTTAATAAAAT
Found at i:5019292 original size:15 final size:16
Alignment explanation
Indices: 5019275--5019335 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
5019265 TTGTATCAAA
5019275 ATTTTATAAAATAAA-
1 ATTTTATAAAATAAAT
5019290 A--TTAT--AATAAATT
1 ATTTTATAAAATAAA-T
5019303 ATTTTATAAAATAAAT
1 ATTTTATAAAATAAAT
* *
5019319 ATTTAATAAATTAAAT
1 ATTTTATAAAATAAAT
5019335 A
1 A
5019336 ATTATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 6 0.16
13 5 0.13
15 5 0.13
16 16 0.42
17 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTATAAAATAAAT
Found at i:5019306 original size:28 final size:28
Alignment explanation
Indices: 5019275--5019331 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
5019265 TTGTATCAAA
5019275 ATTTTATAAAATAAA-ATTATAATAAATT
1 ATTTTATAAAATAAATATT-TAATAAATT
5019303 ATTTTATAAAATAAATATTTAATAAATT
1 ATTTTATAAAATAAATATTTAATAAATT
5019331 A
1 A
5019332 AATAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTTATAAAATAAATATTTAATAAATT
Found at i:5019360 original size:26 final size:23
Alignment explanation
Indices: 5019318--5019368 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
5019308 ATAAAATAAA
*
5019318 TATTTAATAAATTAAATAATTATAT
1 TATTTAATAAA-TAAA-ATTTATAT
*
5019343 TATTATAATACATAAAATTTATAT
1 TATT-TAATAAATAAAATTTATAT
5019367 TA
1 TA
5019369 AATAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 9 0.39
25 8 0.35
26 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAATAAATAAAATTTATAT
Found at i:5019377 original size:15 final size:15
Alignment explanation
Indices: 5019345--5019385 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5019335 AATTATATTA
*
5019345 TTATAATACATAAAAT
1 TTATAATAAAT-AAAT
*
5019361 TTATATTAAATAAAT
1 TTATAATAAATAAAT
5019376 TTATAATAAA
1 TTATAATAAA
5019386 ATAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATAATAAATAAAT
Found at i:5020531 original size:2 final size:2
Alignment explanation
Indices: 5020526--5020567 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5020516 TATAAAATAC
5020526 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
5020568 CAACAATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5021430 original size:2 final size:2
Alignment explanation
Indices: 5021423--5021452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5021413 CACGGACTAC
5021423 AT AT 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 AT AT
5021453 GTGTGTGTGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5022772 original size:21 final size:21
Alignment explanation
Indices: 5022747--5022786 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5022737 TATTAAAAAT
5022747 TATTTTA-AATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
5022768 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
5022787 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:5023082 original size:21 final size:21
Alignment explanation
Indices: 5023057--5023125 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 21
5023047 ATTTTTAATA
5023057 TAAATATAATTTTAATAATTT
1 TAAATATAATTTTAATAATTT
* *
5023078 TAAATAT-ATTTTATTATTTAAT
1 TAAATATAATTTTAATAATT--T
*
5023100 ATAAATATAAATTTAATAAATTT
1 -TAAATATAATTTTAAT-AATTT
5023123 TAA
1 TAA
5023126 TTATTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
20 10 0.26
21 7 0.18
22 4 0.11
23 8 0.21
24 6 0.16
25 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATATAATTTTAATAATTT
Found at i:5023105 original size:44 final size:42
Alignment explanation
Indices: 5023025--5023125 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 42
5023015 TTAAATTTTT
* *
5023025 TTTTAA-AATTTTTAATTTATATATTTTTAATATAAATATAA
1 TTTTAATAATTTTAAATATATATATTTTTAATATAAATATAA
*
5023066 TTTTAATAATTTTAAATATATTTTATTATTTAATATAAATATAA
1 TTTTAATAATTTTAAATATA-TATATT-TTTAATATAAATATAA
*
5023110 ATTTAATAAATTTTAA
1 TTTTAAT-AATTTTAA
5023126 TTATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 6 0.12
42 11 0.21
43 5 0.10
44 22 0.42
45 8 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (42 bp):
TTTTAATAATTTTAAATATATATATTTTTAATATAAATATAA
Found at i:5023130 original size:38 final size:41
Alignment explanation
Indices: 5023046--5023142 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 41
5023036 TTAATTTATA
* *
5023046 TATT-TTTAATATAAATATAATTTTAATAATTTTAAATATATTT
1 TATTATTTAATATAAATATAAATTTAATAAATTT--ATATA-TT
5023089 TATTATTTAATATAAATATAAATTTAATAAATTT-TA-A-T
1 TATTATTTAATATAAATATAAATTTAATAAATTTATATATT
5023127 TATTTATTTATATATA
1 TA-TTATTTA-ATATA
5023143 TTTTTTAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
38 3 0.06
39 7 0.14
40 6 0.12
41 2 0.04
43 4 0.08
44 27 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (41 bp):
TATTATTTAATATAAATATAAATTTAATAAATTTATATATT
Found at i:5023581 original size:42 final size:40
Alignment explanation
Indices: 5023487--5023587 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 40
5023477 TAAATCTTCA
* *
5023487 AATTATTTTATTTTTAATATAAATATAGTTTTAATAATTT
1 AATTATTTTATTTTTAACATAAATATAGATTTAATAATTT
5023527 AGATATATTTTATTATTTAACATAAATAT-GAATTTAATAATTTTT
1 A-AT-TATTTTATT-TTTAACATAAATATAG-ATTTAATAA--TTT
5023572 AATTA-TTTATTCTTTA
1 AATTATTTTATT-TTTA
5023588 TATATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 20 0.38
43 23 0.44
44 2 0.04
45 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (40 bp):
AATTATTTTATTTTTAACATAAATATAGATTTAATAATTT
Found at i:5026544 original size:32 final size:32
Alignment explanation
Indices: 5026504--5026572 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
5026494 GATAAAAAAA
* *
5026504 ATAAAGATTAGT-TTATTTTATGTATACAA-AG
1 ATAAAGATTA-TCTTATCTTATCTATACAAGAG
5026535 ATAAGAGATTATCTTATCTTATCTATACAAGAG
1 ATAA-AGATTATCTTATCTTATCTATACAAGAG
5026568 ATAAA
1 ATAAA
5026573 TAATTAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 5 0.15
32 22 0.67
33 6 0.18
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (32 bp):
ATAAAGATTATCTTATCTTATCTATACAAGAG
Found at i:5032082 original size:12 final size:12
Alignment explanation
Indices: 5032065--5032102 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
5032055 CTCCATTTCA
5032065 TTTTTTTTTCTT
1 TTTTTTTTTCTT
5032077 TTTTTTTTTCTT
1 TTTTTTTTTCTT
5032089 TTTCTTTCTTTCTT
1 TTT-TTT-TTTCTT
5032103 CTTCATCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.62
13 3 0.12
14 6 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:5032104 original size:17 final size:17
Alignment explanation
Indices: 5032069--5032122 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
5032059 ATTTCATTTT
* *
5032069 TTTTTCTTTTTTTTTTTC
1 TTTTTC-TTTCTTTCTTC
5032087 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
5032104 TTCATCTTCTTTCTTTCTT
1 TT--T-TTCTTTCTTTCTT
5032123 TCTTACCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 11 0.35
18 6 0.19
19 1 0.03
20 13 0.42
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:5033526 original size:29 final size:28
Alignment explanation
Indices: 5033432--5033809 Score: 487
Period size: 28 Copynumber: 13.2 Consensus size: 28
5033422 TTAGATGGGT
* * *
5033432 TGCCACTGGCTTGTGTGGGTTTTAAAATGG
1 TGCCACTGACTTGTG-GGCTTTGAAAA-GG
5033462 TGCCACTGACTTGTGGGCTTTG-AAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
5033489 ATGCCACTGATTTGTGGGCTTTGAAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAAG-G
*
5033519 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAAG-G
* *
5033548 TGCCACTGACTTGTGGCCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
5033576 TGCCACTGACTTGTGGGCTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAA-GG
5033605 TGCCACTGACTTGTGGGCTTTG-AAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
5033632 CTGCCACTGACTTGTAGGCTTTGAAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAA-GG
*
5033662 TGCCACTGTCTTGTGGGCTTTGAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
5033690 TGACACTGACTTGTGGGCTTTG-AAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
5033717 CTGCCACTGACTCGTGGGCTTTG-AAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGG
* *
5033745 CTGCCACTAACTCGTGGGCTTT-AAAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGG
*
5033773 ATGCCACTAACTTGTGGGCTTTGAAAAGAG
1 -TGCCACTGACTTGTGGGCTTTGAAAAG-G
5033803 TGCCACT
1 TGCCACT
5033810 TTGAAAGTTT
Statistics
Matches: 318, Mismatches: 19, Indels: 23
0.88 0.05 0.06
Matches are distributed among these distances:
27 9 0.03
28 166 0.52
29 125 0.39
30 18 0.06
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGG
Found at i:5033742 original size:56 final size:56
Alignment explanation
Indices: 5033414--5034629 Score: 967
Period size: 56 Copynumber: 21.8 Consensus size: 56
5033404 CACCCACTTG
** * * * *
5033414 TGTGGGCTTTAGATGGGTTGCCACTGGCTTGTGTGGGTTTTAAAATGGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACTTGTG-GGCTTTGAAAA-GGTGCCACTGACT
* *
5033473 TGTGGGCTTTGAAAGGATGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * *
5033530 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGCCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
*
5033587 TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGCTGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * *
5033644 TGTAGGCTTTGAAAAGGGTGCCACTGTCTTGTGGGCTTTGAAAAGGTGACACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
5033701 TGTGGGCTTTGAAAGGCTGCCACTGACTCGTGGGCTTTG-AAAGGCTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * *
5033757 CGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAGTG-C-C--A--
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
** * * *
5033808 ------CTTTGAAAGTTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGTCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * *
5033859 TGTGGGCTTTGAAAAGTTGCCACCGACTCGTGGGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * *
5033915 TGTGGGCTTTGAAAGGTTGCCA-TCGACTCGTGGGCTTT-AAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
5033971 TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
*
5034028 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGCCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * *
5034084 TGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTCGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* *
5034140 TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * * *
5034197 TGTGGGTTTTGAAAGGATGCCACTGACTTGTGTGGAC-TTAAAAAGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTG-GG-CTTTGAAAAGGTGCCACTGACT
* * * * *
5034254 TGTGGAC-TTAAAAGGATGTCACAATG--TTGTGGACTTT-AAAAGAGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGATG-C-CACTGACTTGTGGGCTTTGAAAAG-GTGCCACT-GACT
* *** * * * * * * **
5034309 TGTGGACTCAAAAAGG-TGCCACGGAGTTAT-GGATTTTAAAAGGATGCCACAGTGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * * * * * * *
5034364 TGTGGAC-TTAAAAGGGTGCCACGGAGTGGTGGACTTT-AAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * * * * * *
5034419 TGTGGAC-TTAAAAGGGTGCCAC-GAAGTTGTGGACTTT-AAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * * * * *
5034473 TGTGGAC-TTAAAAGGGTGCCAC-GAAGTTGTGGAC-TT-AAAAGGGTGCCACGGATT
1 TGTGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAA-GGTGCCACTGACT
* * * * * * * *
5034527 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGAGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACT
* * * * * *
5034582 TGTGGACTTTAAAAAGAAATGCCACTGAATCGTGGACTTTGAAAAGGT
1 TGTGGGCTTT-GAAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGGT
5034630 CACAGTACTA
Statistics
Matches: 1000, Mismatches: 104, Indels: 107
0.83 0.09 0.09
Matches are distributed among these distances:
45 39 0.04
46 1 0.00
49 1 0.00
53 9 0.01
54 110 0.11
55 140 0.14
56 302 0.30
57 297 0.30
58 85 0.09
59 16 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:5033840 original size:28 final size:28
Alignment explanation
Indices: 5033808--5034271 Score: 556
Period size: 28 Copynumber: 16.5 Consensus size: 28
5033798 AAGAGTGCCA
** *
5033808 CTTTGAAAGTTTGCCACTAACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* * *
5033836 CTTTGAAAAGAGTGTCATTGACTTGTGGG
1 CTTTGAAAGGA-TGCCACTGACTTGTGGG
* * * *
5033865 CTTTGAAAAGTTGCCACCGACTCGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
5033893 CTTTAAAAGGATGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* *
5033921 CTTTGAAAGGTTGCCA-TCGACTCGTGGG
1 CTTTGAAAGGATGCCACT-GACTTGTGGG
* *
5033949 CTTTAAAAGGATGCCACTGATTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* *
5033977 CTTTGAAAGGTTGCCACTAACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
5034005 CTTTGAAAAGAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGA-TGCCACTGACTTGTGGG
5034034 CTTTGAAAGGATGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
5034062 CTTTGAAAGGATGCCACTGCCTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
5034090 CTTTGAAAGGATGCCACTGACTTATGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* * *
5034118 CTTCGAAAAGATGCCACTGATTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* *
5034146 CTTTGAAAGGTTGCCACTAACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
5034174 CTTTGAAAAGAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGA-TGCCACTGACTTGTGGG
*
5034203 TTTTGAAAGGATGCCACTGACTTGTGTGG
1 CTTTGAAAGGATGCCACTGACTTGTG-GG
* * * * *
5034232 AC-TTAAAAAGATGCCACGGAGTTGTGGA
1 -CTTTGAAAGGATGCCACTGACTTGTGGG
*
5034260 C-TTAAAAGGATG
1 CTTTGAAAGGATG
5034272 TCACAATGTT
Statistics
Matches: 374, Mismatches: 55, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
27 12 0.03
28 264 0.71
29 98 0.26
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
CTTTGAAAGGATGCCACTGACTTGTGGG
Found at i:5033881 original size:73 final size:73
Alignment explanation
Indices: 5033735--5033874 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
5033725 GACTCGTGGG
5033735 CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
1 CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
5033800 GAGTGCCA
66 GAGTGCCA
** * * * *
5033808 CTTTGAAAGTTTGCCACTAACTTGTGGGCTTTGAAAA-GAGTGTCATTGACTTGTGGGCTTTGAA
1 CTTTGAAAGGCTGCCACTAACTCGTGGGCTTT-AAAAGGA-TGCCACTAACTTGTGGGCTTTGAA
5033872 AAG
64 AAG
5033875 TTGCCACCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 31 0.53
74 28 0.47
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (73 bp):
CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
GAGTGCCA
Found at i:5033901 original size:101 final size:101
Alignment explanation
Indices: 5033707--5033910 Score: 236
Period size: 102 Copynumber: 2.0 Consensus size: 101
5033697 GACTTGTGGG
*
5033707 CTTTGAAAGGCTGCCACTGACTCGTGGGCTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAG
1 CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAG
* *
5033772 GATGCCACTAACTTGTGGGCTTTGAAAA-GAGTGCCA
66 GATGCCACCAACTCGTGGGCTTTGAAAAGGA-TGCCA
** * * * * *
5033808 CTTTGAAAGTTTGCCACTAACTTGTGGGCTTTGAAAAGAG-TGTCATTGACTTGTGGGCTTTGAA
1 CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTG-AAAG-GCTGCCACTAACTCGTGGGCTTT-AA
* *
5033872 AA-GTTGCCACCGACTCGTGGGCTTT-AAAAGGATGCCA
63 AAGGATGCCACCAACTCGTGGGCTTTGAAAAGGATGCCA
5033909 CT
1 CT
5033911 GACTTGTGGG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
101 40 0.46
102 42 0.48
103 5 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (101 bp):
CTTTGAAAGGCTGCCACTAACTCGTGGGCTTTGAAAGGCTGCCACTAACTCGTGGGCTTTAAAAG
GATGCCACCAACTCGTGGGCTTTGAAAAGGATGCCA
Found at i:5034088 original size:169 final size:169
Alignment explanation
Indices: 5033808--5034271 Score: 693
Period size: 169 Copynumber: 2.7 Consensus size: 169
5033798 AAGAGTGCCA
* * *
5033808 CTTTGAAAGTTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGTCATTGACTTGTGGGCTTTGAAA
1 CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * * *
5033873 AGTTGCCACCGACTCGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCA-
66 GGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* *
5033937 TCGACTCGTGGGCTT-TAAAAGGATGCCACTGATTTGTGGG
131 T-GACTCATGGGCTTCGAAAA-GATGCCACTGATTTGTGGG
5033977 CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* *
5034042 GGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGCCTTGTGGGCTTTGAAAGGATGCCAC
66 GGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
*
5034107 TGACTTATGGGCTTCGAAAAGATGCCACTGATTTGTGGG
131 TGACTCATGGGCTTCGAAAAGATGCCACTGATTTGTGGG
*
5034146 CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGTTTTGAAA
1 CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * * *
5034211 GGATGCCACTGACTTGTGTGGAC-TTAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGATG
66 GGATGCCACTGACTTGTG-GG-CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATG
5034272 TCACAATGTT
Statistics
Matches: 270, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
169 241 0.89
170 28 0.10
171 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (169 bp):
CTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
GGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
TGACTCATGGGCTTCGAAAAGATGCCACTGATTTGTGGG
Found at i:5034265 original size:27 final size:27
Alignment explanation
Indices: 5033895--5034595 Score: 439
Period size: 28 Copynumber: 25.2 Consensus size: 27
5033885 CTCGTGGGCT
* * *
5033895 TTAAAAGGATGCCACTGACTTGTGGGC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* * * * *
5033922 TTTGAAAGGTTGCCATC-GACTCGTGGGC
1 -TTAAAAGGATGCCA-CGGAGTTGTGGAC
* * *
5033950 TTTAAAAGGATGCCACTGATTTGTGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * ** * *
5033978 TTTGAAAGGTTGCCACTAACTTGTGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * *
5034006 TTTGAAAA-GAGTGCCACTGACTTGTGGGC
1 -TT-AAAAGGA-TGCCACGGAGTTGTGGAC
* * * *
5034035 TTTGAAAGGATGCCACTGACTTGTGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * ** *
5034063 TTTGAAAGGATGCCACTGCCTTGTGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * * * *
5034091 TTTGAAAGGATGCCACTGACTTATGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * *
5034119 TTCGAAAA-GATGCCACTGATTTGTGGGC
1 TT--AAAAGGATGCCACGGAGTTGTGGAC
* * ** * *
5034147 TTTGAAAGGTTGCCACTAACTTGTGGGC
1 -TTAAAAGGATGCCACGGAGTTGTGGAC
* * **
5034175 TTTGAAAA-GAGTGCCACTGACTTGTGGGTT
1 -TT-AAAAGGA-TGCCACGGAGTTGT-GGAC
* * *
5034205 TTGAAAGGATGCCACTGACTTGTGTGGAC
1 TTAAAAGGATGCCACGGA-GT-TGTGGAC
*
5034234 TTAAAAAGATGCCACGGAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
5034261 TTAAAAGGATGTCAC-AATGTTGTGGAC
1 TTAAAAGGATGCCACGGA-GTTGTGGAC
*
5034288 TTTAAAA-GAGTGCCATGGAGTTGTGGAC
1 -TTAAAAGGA-TGCCACGGAGTTGTGGAC
* * *
5034316 TCAAAAAGG-TGCCACGGAGTTATGGATT
1 T-TAAAAGGATGCCACGGAGTTGTGGA-C
* *
5034344 TTAAAAGGATGCCACAGTGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
5034371 TTAAAAGGGTGCCACGGAGTGGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
5034398 TTTAAAA-GAGTGCCACGGAGTTGTGGAC
1 -TTAAAAGGA-TGCCACGGAGTTGTGGAC
* *
5034426 TTAAAAGGGTGCCACGAAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
5034453 TTTAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
5034480 TTAAAAGGGTGCCACGAAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
* *
5034507 TTAAAAGGGTGCCACGGATTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
*
5034534 TTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAGGATGCCACGGAGTTGTGGAC
*
5034561 TTTAAAA-GAGTGCCACAGAGTTGTGGAC
1 -TTAAAAGGA-TGCCACGGAGTTGTGGAC
5034589 TTTAAAA
1 -TTAAAA
5034596 AGAAATGCCA
Statistics
Matches: 575, Mismatches: 70, Indels: 56
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.00
27 208 0.36
28 290 0.50
29 71 0.12
30 5 0.01
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (27 bp):
TTAAAAGGATGCCACGGAGTTGTGGAC
Found at i:5034308 original size:55 final size:55
Alignment explanation
Indices: 5033944--5034595 Score: 532
Period size: 55 Copynumber: 11.7 Consensus size: 55
5033934 CCATCGACTC
* * * * * * * *
5033944 GTGGGCTTTAAAAG-GATGCCACTGATTTGTGGGCTTTGAAAGGTTGCCACTAACTT
1 GTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGAAGTT
* * * * * * *
5034000 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTG-ACTT
1 GTGGACTTT-AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC-GAAGTT
* * * ** * * * *
5034057 GTGGGCTTTGAAAG-GATGCCACTGCCTTGTGGGCTTTGAAAGGATGCCACTG-ACTT
1 GTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC-GAAGTT
* * * * * * * * * *
5034113 ATGGGCTTCGAAAAGA-TGCCACTGATTTGTGGGCTTTGAAAGGTTGCCACTAACTT
1 GTGGACTT-TAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGAAGTT
* * * ** * * **
5034169 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGTTTTGAAAGGATGCCACTGACTTGT
1 GTGGACTTT-AAAAGAGTGCCACGGAGTTGT-GGACTTAAAAGGGTGCCAC-GAAGT-T
* * *
5034228 GTGGACTTAAAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGATGTCAC-AATGTT
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAA-GTT
* * * *
5034282 GTGGACTTTAAAAGAGTGCCATGGAGTTGTGGACTCAAAAAGGTGCCACGGAGTT
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
* * * * * *
5034337 ATGGATTTTAAAAG-GATGCCACAGTGTTGTGGACTTAAAAGGGTGCCACGGAGTG
1 GTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
5034392 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
*
5034447 GTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
* * *
5034501 GTGGAC-TTAAAAGGGTGCCACGGATTTGTGGACTTAAAAGGGTGCCACGGAGTT
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
*
5034555 GTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTTTAAAA
1 GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAA
5034596 AGAAATGCCA
Statistics
Matches: 518, Mismatches: 58, Indels: 40
0.84 0.09 0.06
Matches are distributed among these distances:
53 2 0.00
54 116 0.22
55 158 0.31
56 130 0.25
57 93 0.18
58 11 0.02
59 8 0.02
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.27
Consensus pattern (55 bp):
GTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTT
Found at i:5034331 original size:82 final size:82
Alignment explanation
Indices: 5034227--5034595 Score: 503
Period size: 82 Copynumber: 4.5 Consensus size: 82
5034217 CACTGACTTG
* *
5034227 TGTGGACTTAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGATGTCAC-AATGTTGTGGACTTT
1 TGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAATGTTGTGGAC-TT
* *
5034291 AAAAGAGTGCCATGGAGT
65 AAAAGGGTGCCACGGAGT
* * * *
5034309 TGTGGACTCAAAAAGGTGCCACGGAGTTATGGATTTTAAAAGGATGCCAC-AGTGTTGTGGACTT
1 TGTGGACTTAAAAAGGTGCCACGGAGTTGTGGA-CTTAAAAGGATGCCACGAATGTTGTGGACTT
5034373 AAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGT
* * *
5034391 GGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAA-GTTGTGGACTT
1 TGTGGACTTAAAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAATGTTGTGGACTT
*
5034455 TAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGT
* * * *
5034473 TGTGGACTTAAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGGAT-TTGTGGACTTA
1 TGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAATGTTGTGGACTTA
5034537 AAAGGGTGCCACGGAGT
66 AAAGGGTGCCACGGAGT
* *
5034554 TGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTTTAAAA
1 TGTGGACTTAAAAAG-GTGCCACGGAGTTGTGGAC-TTAAAA
5034596 AGAAATGCCA
Statistics
Matches: 255, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
81 75 0.29
82 131 0.51
83 49 0.19
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (82 bp):
TGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAATGTTGTGGACTTA
AAAGGGTGCCACGGAGT
Found at i:5034617 original size:30 final size:28
Alignment explanation
Indices: 5034228--5034627 Score: 131
Period size: 27 Copynumber: 14.5 Consensus size: 28
5034218 ACTGACTTGT
* * * *
5034228 GTGGACTTAAAAAG-ATGCCACGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
* * * *
5034255 GTGGAC-TTAAAAGGATGTCACA-ATGTT
1 GTGGACTTTAAAAGAATGCCACAGA-ATC
* ** * *
5034282 GTGGACTTTAAAAGAGTGCCATGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
** * * * *
5034310 GTGGACTCAAAAAG-GTGCCACGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
* * * ** *
5034337 ATGGATTTTAAAAGGATGCCACAGTGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
** * * *
5034365 GTGGAC-TTAAAAGGGTGCCACGGAGTG
1 GTGGACTTTAAAAGAATGCCACAGAATC
* * * *
5034392 GTGGACTTTAAAAGAGTGCCACGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
** *
5034420 GTGGAC-TTAAAAGGGTGCCAC-GAAGTT
1 GTGGACTTTAAAAGAATGCCACAGAA-TC
** * * *
5034447 GTGGACTTT-AAAGGGTGCCACGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
** *
5034474 GTGGAC-TTAAAAGGGTGCCAC-GAAGTT
1 GTGGACTTTAAAAGAATGCCACAGAA-TC
** * * *
5034501 GTGGAC-TTAAAAGGGTGCCACGGATTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
** * * *
5034528 GTGGAC-TTAAAAGGGTGCCACGGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
* * *
5034555 GTGGACTTTAAAAGAGTGCCACAGAGTT
1 GTGGACTTTAAAAGAATGCCACAGAATC
*
5034583 GTGGACTTTAAAAAGAAATGCCACTGAATC
1 GTGGACTTT-AAAAG-AATGCCACAGAATC
5034613 GTGGACTTTGAAAAG
1 GTGGACTTT-AAAAG
5034628 GTCACAGTAC
Statistics
Matches: 319, Mismatches: 39, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.04
27 177 0.55
28 99 0.31
29 6 0.02
30 24 0.08
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (28 bp):
GTGGACTTTAAAAGAATGCCACAGAATC
Found at i:5035977 original size:23 final size:24
Alignment explanation
Indices: 5035951--5035996 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5035941 TGCTTTTACA
*
5035951 CTTTTTCTTTTCA-TTTTTTTGTG
1 CTTTTGCTTTTCACTTTTTTTGTG
*
5035974 CTTTTGCTTTTGACTTTTTTTGT
1 CTTTTGCTTTTCACTTTTTTTGT
5035997 CATTTTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (24 bp):
CTTTTGCTTTTCACTTTTTTTGTG
Found at i:5043114 original size:22 final size:22
Alignment explanation
Indices: 5043088--5043130 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5043078 CATTTTCCCT
*
5043088 TTTTTTTCTTTGTTTTTTGTTTC
1 TTTTTTT-ATTGTTTTTTGTTTC
*
5043111 TTTTTTTATTTTTTTTTGTT
1 TTTTTTTATTGTTTTTTGTT
5043131 AGTTTATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (22 bp):
TTTTTTTATTGTTTTTTGTTTC
Found at i:5045941 original size:113 final size:113
Alignment explanation
Indices: 5045735--5045946 Score: 275
Period size: 113 Copynumber: 1.9 Consensus size: 113
5045725 ATGAATATAC
* * * * * * *
5045735 TATACCTAATAATATTCATGTATGTTTATGGTTTATGAATATTGAAAGCTCATGAATGTTCATAA
1 TATACCTAATAATAATCATGTATGATCATAGTTAATAAATATTCAAAGCTCATGAATGTTCATAA
* * *
5045800 TAGCATTTATGTTTATTACATAATAATTAATGTAATAAAATTCACGAA
66 TAACATTTATATTTATTACATAAAAATTAATGTAATAAAATTCACGAA
* *
5045848 TATACTTAATAATAATCATGTATGATCATAGTTAATAAATATTCAAAGTTCATGAATGTTCATAA
1 TATACCTAATAATAATCATGTATGATCATAGTTAATAAATATTCAAAGCTCATGAATGTTCATAA
*
5045913 TAATATTTATATTTA-T-CATACCAAAATTAATGTA
66 TAACATTTATATTTATTACATA--AAAATTAATGTA
5045947 TTGATTCATG
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
111 4 0.05
112 1 0.01
113 79 0.94
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (113 bp):
TATACCTAATAATAATCATGTATGATCATAGTTAATAAATATTCAAAGCTCATGAATGTTCATAA
TAACATTTATATTTATTACATAAAAATTAATGTAATAAAATTCACGAA
Found at i:5052938 original size:59 final size:58
Alignment explanation
Indices: 5052764--5053016 Score: 310
Period size: 59 Copynumber: 4.3 Consensus size: 58
5052754 TATAACACTG
*
5052764 CAAACTTAAATCGCCACCAAGGCGACCAGATTCACACACTAAGTGACGCCAAGTCACC
1 CAAACTTAGATCGCCACCAAGGCGACCAGATTCACACACTAAGTGACGCCAAGTCACC
* * * *
5052822 CAAAATTAGATCGCCACCAAGGCAACCAGATTCATACACTAAGTGACGCCAAATCACC
1 CAAACTTAGATCGCCACCAAGGCGACCAGATTCACACACTAAGTGACGCCAAGTCACC
* * * * * * *
5052880 TAAACTTTGATCCCCACCAAGGCGATCTAGATTCCCGCACTAAGTGACACCAAGTCACC
1 CAAACTTAGATCGCCACCAAGGCGA-CCAGATTCACACACTAAGTGACGCCAAGTCACC
* * * *
5052939 CAAACTTAGATTGCCACCAAGGCAACCCAGATTTACACACTACA-TGACGCCAAGTCACT
1 CAAACTTAGATCGCCACCAAGGCGA-CCAGATTCACACACTA-AGTGACGCCAAGTCACC
* *
5052998 CAAACTTGGATCACCACCA
1 CAAACTTAGATCGCCACCA
5053017 GCGTGATCCC
Statistics
Matches: 162, Mismatches: 31, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
58 73 0.45
59 88 0.54
60 1 0.01
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Consensus pattern (58 bp):
CAAACTTAGATCGCCACCAAGGCGACCAGATTCACACACTAAGTGACGCCAAGTCACC
Found at i:5057876 original size:51 final size:51
Alignment explanation
Indices: 5057819--5057945 Score: 161
Period size: 51 Copynumber: 2.5 Consensus size: 51
5057809 AAAAAAAGCT
* *
5057819 GAGTATCCCCGATTATGGAAAATT-G-GTATTTCGAAAATAAAATC-GGAGTTG
1 GAGTATCCCCGATTATGAAAAATTAGTGT-TTTAG-AAATAAAA-CGGGAGTTG
* *
5057870 GAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACGGGGGTTG
1 GAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACGGGAGTTG
*
5057921 GAGTACCCCCGATTATGAAAAATTA
1 GAGTATCCCCGATTATGAAAAATTA
5057946 AGAAACTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
50 1 0.01
51 59 0.88
52 5 0.07
53 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACGGGAGTTG
Found at i:5060780 original size:17 final size:17
Alignment explanation
Indices: 5060758--5060792 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5060748 AGGTATGAAG
*
5060758 AGTTCATAAACATAAGT
1 AGTTCATAAACACAAGT
5060775 AGTTCATAAACACAAGT
1 AGTTCATAAACACAAGT
5060792 A
1 A
5060793 CAAAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (17 bp):
AGTTCATAAACACAAGT
Found at i:5062395 original size:2 final size:2
Alignment explanation
Indices: 5062390--5062424 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5062380 AATTTTTTCT
5062390 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 T
5062425 TCCCGTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5064705 original size:25 final size:24
Alignment explanation
Indices: 5064673--5064744 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 24
5064663 TAAATTAAAA
5064673 TAATAAATTAT-TTTGAAAATATTT
1 TAATAAATTATATTT-AAAATATTT
5064697 TAATAAAATTAAATATTTAAAAT-TTT
1 TAAT-AAATT--ATATTTAAAATATTT
5064723 TAATAAATTATATTTTAAAATA
1 TAATAAATTATA-TTTAAAATA
5064745 ACATTTAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 10 0.24
26 7 0.17
27 7 0.17
28 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
TAATAAATTATATTTAAAATATTT
Found at i:5066368 original size:23 final size:23
Alignment explanation
Indices: 5066325--5066368 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5066315 ATTTGAATAA
* *
5066325 TTATTTTATAAATTATTTTTATT
1 TTATTTTATAAAATATATTTATT
5066348 TTATTTT-TAATAATATATTTA
1 TTATTTTATAA-AATATATTTA
5066369 AAGAGTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTTTATAAAATATATTTATT
Found at i:5067066 original size:13 final size:13
Alignment explanation
Indices: 5067029--5067104 Score: 72
Period size: 13 Copynumber: 6.2 Consensus size: 13
5067019 TTGTTTTACG
*
5067029 AATATTTAAAGAT
1 AATATTTAAATAT
5067042 AAT-TTTAAATAT
1 AATATTTAAATAT
*
5067054 AATATTAAAATAT
1 AATATTTAAATAT
5067067 AATA--TAAATAT
1 AATATTTAAATAT
*
5067078 AATATATTTAATA-
1 AATAT-TTAAATAT
*
5067091 AATA-TAAAATAT
1 AATATTTAAATAT
5067103 AA
1 AA
5067105 ATAATATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 15 0.29
12 13 0.25
13 19 0.37
14 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:5067093 original size:29 final size:29
Alignment explanation
Indices: 5067061--5067117 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
5067051 TATAATATTA
*
5067061 AAATATAATATA-AATATAATATATTTAAT
1 AAATATAAAATATAA-ATAATATATTTAAT
5067090 AAATATAAAATATAAATAATATATTTAA
1 AAATATAAAATATAAATAATATATTTAA
5067118 ATATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATATAAAATATAAATAATATATTTAAT
Found at i:5067105 original size:13 final size:11
Alignment explanation
Indices: 5067047--5067121 Score: 59
Period size: 11 Copynumber: 6.6 Consensus size: 11
5067037 AAGATAATTT
5067047 TAAATATAATA
1 TAAATATAATA
5067058 TTAAAATATAATA
1 -T-AAATATAATA
5067071 TAAATATAATA
1 TAAATATAATA
5067082 TATTTAATA-AATA
1 TA---AATATAATA
5067095 TAAAATATAA-A
1 T-AAATATAATA
*
5067106 T-AATAT-ATT
1 TAAATATAATA
5067115 TAAATAT
1 TAAATAT
5067122 GATAAATTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
8 1 0.02
9 6 0.11
10 5 0.09
11 18 0.33
12 4 0.07
13 15 0.28
14 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATATAATA
Found at i:5067113 original size:18 final size:17
Alignment explanation
Indices: 5067047--5067112 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 17
5067037 AAGATAATTT
5067047 TAAATATAATATTAAAATA
1 TAAATA-AATA-TAAAATA
*
5067066 TAATATAAATATAATATA
1 TAA-ATAAATATAAAATA
*
5067084 TTTAATAAATATAAAATA
1 -TAAATAAATATAAAATA
5067102 TAAAT-AATATA
1 TAAATAAATATA
5067113 TTTAAATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.15
17 4 0.10
18 19 0.46
19 9 0.22
20 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATAAATATAAAATA
Found at i:5067170 original size:20 final size:21
Alignment explanation
Indices: 5067142--5067189 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
5067132 ATTATATATA
*
5067142 ATATTTATTTTTTAA-AATTT
1 ATATATATTTTTTAATAATTT
5067162 ATATATA---TTTAATAATTT
1 ATATATATTTTTTAATAATTT
5067180 ATATATATTT
1 ATATATATTT
5067190 ATATGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 5 0.22
18 12 0.52
20 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATATTTTTTAATAATTT
Found at i:5067171 original size:10 final size:10
Alignment explanation
Indices: 5067158--5067193 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5067148 ATTTTTTAAA
5067158 ATTTATATAT
1 ATTTATATAT
5067168 ATTTA-ATA-
1 ATTTATATAT
5067176 ATTTATATAT
1 ATTTATATAT
5067186 ATTTATAT
1 ATTTATAT
5067194 GAAAAACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.21
9 6 0.25
10 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTATATAT
Found at i:5067180 original size:18 final size:17
Alignment explanation
Indices: 5067152--5067190 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
5067142 ATATTTATTT
5067152 TTTAAAATTTATATATA
1 TTTAAAATTTATATATA
5067169 TTTAATAATTTATATATA
1 TTTAA-AATTTATATATA
5067187 TTTA
1 TTTA
5067191 TATGAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATTTATATATA
Found at i:5068386 original size:17 final size:17
Alignment explanation
Indices: 5068364--5068398 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5068354 AGGTATGAAG
*
5068364 AGTTCATAAACATAAGT
1 AGTTCATAAACACAAGT
5068381 AGTTCATAAACACAAGT
1 AGTTCATAAACACAAGT
5068398 A
1 A
5068399 CAAAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (17 bp):
AGTTCATAAACACAAGT
Found at i:5068546 original size:10 final size:10
Alignment explanation
Indices: 5068528--5068588 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
5068518 TTTAATATAT
*
5068528 TATATATTTA
1 TATAAATTTA
5068538 TATAAATTT-
1 TATAAATTTA
5068547 TGATAAA-TTA
1 T-ATAAATTTA
5068557 -AT-AATTTA
1 TATAAATTTA
5068565 TATAAATTT-
1 TATAAATTTA
5068574 TAATAAATTTA
1 T-ATAAATTTA
5068585 TATA
1 TATA
5068589 TTTATATCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 6 0.14
10 29 0.67
11 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TATAAATTTA
Found at i:5068556 original size:27 final size:27
Alignment explanation
Indices: 5068518--5068595 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
5068508 CACAATTATA
*
5068518 TTTAATATATTATATATTTATATAAAT
1 TTTAATAAATTATATATTTATATAAAT
*
5068545 TTTGATAAATTA-ATAATTTATATAAAT
1 TTTAATAAATTATAT-ATTTATATAAAT
5068572 TTTAATAAATTTATATATTTATAT
1 TTTAATAAA-TTATATATTTATAT
5068596 CATATTTGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.04
27 30 0.67
28 11 0.24
29 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTAATAAATTATATATTTATATAAAT
Found at i:5070033 original size:2 final size:2
Alignment explanation
Indices: 5070028--5070056 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5070018 AATTTTTTCT
5070028 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 T
5070057 TCCCGTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5072251 original size:27 final size:26
Alignment explanation
Indices: 5072212--5072272 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
5072202 TGCTTATAAG
* *
5072212 AAATTGAGCACATGTGGACCTAATGC
1 AAATTAAGCACATGTGAACCTAATGC
* * *
5072238 AAATTAAGACACATGTGAACTTAGTGT
1 AAATTAAG-CACATGTGAACCTAATGC
5072265 AAATTAAG
1 AAATTAAG
5072273 TCTTGAGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (26 bp):
AAATTAAGCACATGTGAACCTAATGC
Found at i:5078607 original size:22 final size:20
Alignment explanation
Indices: 5078567--5078639 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
5078557 CTCAGCAAGC
*
5078567 AGAAAAAAAATAGAG--AAAG
1 AGAAAAAAAA-AGAGCAAAAA
* *
5078586 AGAATAAAAAAGAGTAAAAA
1 AGAAAAAAAAAGAGCAAAAA
*
5078606 AGAAAAGAAAAGAGCAAAAA
1 AGAAAAAAAAAGAGCAAAAA
*
5078626 AAAAAAAGAAAAGA
1 AGAAAAA-AAAAGA
5078640 AAAAGAAAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 4 0.09
19 9 0.20
20 25 0.57
21 6 0.14
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (20 bp):
AGAAAAAAAAAGAGCAAAAA
Found at i:5078638 original size:21 final size:20
Alignment explanation
Indices: 5078593--5078643 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
5078583 AAGAGAATAA
* *
5078593 AAAAGAGTAAAAAAGAAAAG
1 AAAAGAGAAAAAAAAAAAAG
5078613 AAAAGAGCAAAAAAAAAAAAG
1 AAAAGAG-AAAAAAAAAAAAG
5078634 AAAAGA-AAAA
1 AAAAGAGAAAA
5078644 GAAAGCGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 7 0.25
21 17 0.61
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAGAGAAAAAAAAAAAAG
Found at i:5079432 original size:58 final size:57
Alignment explanation
Indices: 5079367--5079501 Score: 150
Period size: 58 Copynumber: 2.4 Consensus size: 57
5079357 TCATTTTAGC
* * * *
5079367 TATTCATTTTAGAGTTATTT-AGATTATTTTAAATAATTTAGGTCATTTTAGAACTTTT
1 TATTCATTTTAGAGATATTTAAG-GTATTTTAAATAATCTAGGTAATTTTAGAA-TTTT
* *
5079425 TATTCATTTTAG-GACTATTTAAGGTATTTTATATAATCTAGGTAATTTTAGCATTTT
1 TATTCATTTTAGAGA-TATTTAAGGTATTTTAAATAATCTAGGTAATTTTAGAATTTT
*
5079482 TCA-TCATTTTAAAGATATTT
1 T-ATTCATTTTAGAGATATTT
5079502 TTATTTTACA
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 19 0.29
58 45 0.68
59 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (57 bp):
TATTCATTTTAGAGATATTTAAGGTATTTTAAATAATCTAGGTAATTTTAGAATTTT
Found at i:5079445 original size:19 final size:19
Alignment explanation
Indices: 5079409--5079445 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5079399 ATAATTTAGG
*
5079409 TCATTTTAGAACTTTTTAT
1 TCATTTTAGAACTATTTAT
*
5079428 TCATTTTAGGACTATTTA
1 TCATTTTAGAACTATTTA
5079446 AGGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (19 bp):
TCATTTTAGAACTATTTAT
Found at i:5079654 original size:9 final size:9
Alignment explanation
Indices: 5079640--5079664 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5079630 ATCTAGGATC
5079640 ATTTTAATA
1 ATTTTAATA
5079649 ATTTTAATA
1 ATTTTAATA
5079658 ATTTTAA
1 ATTTTAA
5079665 AATCATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTAATA
Found at i:5079710 original size:29 final size:28
Alignment explanation
Indices: 5079637--5079712 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
5079627 ATAATCTAGG
5079637 ATCATTTTAATAATTTTAATAATTTTAAA
1 ATCA-TTTAATAATTTTAATAATTTTAAA
* * *
5079666 ATCATTTATGTTATTTTACATAA-TTTAAG
1 ATCATTTA-ATAATTTTA-ATAATTTTAAA
*
5079695 GTCATTTAACTAATTTTA
1 ATCATTTAA-TAATTTTA
5079713 TCATTTAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.11
29 30 0.79
30 4 0.11
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (28 bp):
ATCATTTAATAATTTTAATAATTTTAAA
Found at i:5081060 original size:11 final size:11
Alignment explanation
Indices: 5081044--5081068 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5081034 AATAAACACA
5081044 AAAAATAACAT
1 AAAAATAACAT
5081055 AAAAATAACAT
1 AAAAATAACAT
5081066 AAA
1 AAA
5081069 CATATCAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAACAT
Found at i:5083951 original size:34 final size:34
Alignment explanation
Indices: 5083907--5084089 Score: 228
Period size: 34 Copynumber: 5.4 Consensus size: 34
5083897 AAAAACCACT
*
5083907 ATTTAATCAACAATGGCAACCTACCAAATCTCCC
1 ATTTAATCAACAATGGCAACCTACCAAATCACCC
* *
5083941 ATTTAGTCAACAATGGTAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-CAACCTACCAAATCACCC
* * * *
5083975 ATTTAATCAACAATGGTAAGCTACTAAATCTCCC
1 ATTTAATCAACAATGGCAACCTACCAAATCACCC
* *
5084009 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCT
1 ATTTAATCAACAATGGC-AACCTACCAAATCACCC
* *
5084043 ATTTAATCAACAATGGTAAACTACCAAATCA-CC
1 ATTTAATCAACAATGGCAACCTACCAAATCACCC
5084076 ATTTAATCAACAAT
1 ATTTAATCAACAAT
5084090 TCTCCCACTT
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.17
34 99 0.78
35 7 0.06
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
ATTTAATCAACAATGGCAACCTACCAAATCACCC
Found at i:5084016 original size:68 final size:68
Alignment explanation
Indices: 5083907--5084089 Score: 287
Period size: 68 Copynumber: 2.7 Consensus size: 68
5083897 AAAAACCACT
* * *
5083907 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAATCA
1 ATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
5083972 CCC
66 CCC
* *
5083975 ATTTAATCAACAATGGTAAGCTACTAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
*
5084040 CCT
66 CCC
* *
5084043 ATTTAATCAACAATGGTAAACTACCAAATC-ACCATTTAATCAACAAT
1 ATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAGTCAACAAT
5084090 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 15 0.14
68 91 0.86
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.25
Consensus pattern (68 bp):
ATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
CCC
Found at i:5084047 original size:102 final size:101
Alignment explanation
Indices: 5083907--5084089 Score: 296
Period size: 102 Copynumber: 1.8 Consensus size: 101
5083897 AAAAACCACT
* *
5083907 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATCA
5083972 CCCATTTAATCAACAATGGTAAGCTACTAAATCTCCC
66 -CCATTTAATCAACAATGGTAAGCTACTAAATCTCCC
* * *
5084009 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCTATTTAATCAACAATGGTAAACTACCAAATC
1 ATTTAATCAACAATGGC-AACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATC
5084073 ACCATTTAATCAACAAT
65 ACCATTTAATCAACAAT
5084090 TCTCCCACTT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
101 16 0.21
102 55 0.73
103 4 0.05
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCACCCATTTAATCAACAATGGTAAACCACCAAATCA
CCATTTAATCAACAATGGTAAGCTACTAAATCTCCC
Found at i:5087933 original size:34 final size:34
Alignment explanation
Indices: 5087890--5088071 Score: 203
Period size: 34 Copynumber: 5.4 Consensus size: 34
5087880 TAAAAACCAC
*
5087890 CATTTAATCAACAATGGCAACCTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCTCT
*
5087924 CATTTAATCAACAATGGTAAGCC-ACCAAATCACT
1 CATTTAATCAACAATGGTAA-CCTACCAAATCTCT
*
5087958 -ATTTAATCAACAATGGTAAGCTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCTCT
* ** * *
5087991 CATTTAATTAACAATGACAA-ATCATCAAATCATC-
1 CATTTAATCAACAATGGTAACCT-ACCAAATC-TCT
* * *
5088025 CATTTAATCAACAATGATAAACTACCAAATCAC-
1 CATTTAATCAACAATGGTAACCTACCAAATCTCT
5088058 CATTTAATCAACAA
1 CATTTAATCAACAA
5088072 CTCTGGTACA
Statistics
Matches: 128, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
32 1 0.01
33 45 0.35
34 77 0.60
35 5 0.04
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.27
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAACCTACCAAATCTCT
Found at i:5088004 original size:67 final size:68
Alignment explanation
Indices: 5087889--5088071 Score: 244
Period size: 67 Copynumber: 2.7 Consensus size: 68
5087879 ATAAAAACCA
* * ** *
5087889 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAATCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCTCATTTAATCAACAATGACAAACCACCAAAT
5087954 CA-
66 CAT
* * * * *
5087956 CTATTTAATCAACAATGGTAAGCTACCAAATCTCTCATTTAATTAACAATGACAAATCATCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCTCATTTAATCAACAATGACAAACCACCAAAT
5088021 CAT
66 CAT
* *
5088024 CCATTTAATCAACAATGATAAACTACCAAATCAC-CATTTAATCAACAA
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCTCATTTAATCAACAA
5088072 CTCTGGTACA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 71 0.70
68 30 0.30
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTCTCATTTAATCAACAATGACAAACCACCAAAT
CAT
Found at i:5090509 original size:27 final size:26
Alignment explanation
Indices: 5090451--5090511 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
5090441 ATTCTATTTT
*
5090451 AATTTAAAATTAGTTATCAAATTTAA
1 AATTTAAAATTAGTCATCAAATTTAA
*
5090477 ATTTTAAAATTA-TCATCAAAAATTTAA
1 AATTTAAAATTAGTCATC--AAATTTAA
5090504 AATTTAAA
1 AATTTAAA
5090512 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 11 0.37
27 15 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (26 bp):
AATTTAAAATTAGTCATCAAATTTAA
Found at i:5091691 original size:2 final size:2
Alignment explanation
Indices: 5091684--5091717 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5091674 CATGCCTTTA
5091684 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5091718 CACACATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5091726 original size:21 final size:21
Alignment explanation
Indices: 5091685--5091727 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5091675 ATGCCTTTAA
* * *
5091685 TATATATATATATATATATAT
1 TATATATATATACACACATAT
5091706 TATATATATATACACACATAT
1 TATATATATATACACACATAT
5091727 T
1 T
5091728 TTGTGTCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATATATATACACACATAT
Found at i:5097939 original size:20 final size:20
Alignment explanation
Indices: 5097916--5097953 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5097906 ACAATGAGAA
5097916 ATGTATCAATACAATTTCTT
1 ATGTATCAATACAATTTCTT
*
5097936 ATGTATCGATACAATTTC
1 ATGTATCAATACAATTTC
5097954 CTTCCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACAATTTCTT
Found at i:5098027 original size:20 final size:21
Alignment explanation
Indices: 5097999--5098047 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5097989 TTCAGGCATA
*
5097999 TATCAATACATTTG-CTTA-TG
1 TATCGATACA-TTGCCTTATTG
5098019 TATCGATACATTGCCTTATTG
1 TATCGATACATTGCCTTATTG
5098040 TATCGATA
1 TATCGATA
5098048 TAAATTGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
TATCGATACATTGCCTTATTG
Found at i:5100399 original size:25 final size:26
Alignment explanation
Indices: 5100371--5100419 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5100361 CTAAATAAGA
* *
5100371 TATTCTATTTGAA-TTTAAAATTAAT
1 TATTCAATTTAAATTTTAAAATTAAT
5100396 TATTCAATTTAAATTTTAAAATTA
1 TATTCAATTTAAATTTTAAAATTA
5100420 TCATCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTCAATTTAAATTTTAAAATTAAT
Found at i:5100473 original size:13 final size:12
Alignment explanation
Indices: 5100455--5100489 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5100445 TATCTGGGTT
5100455 TTTAAAATCTAAA
1 TTTAAAAT-TAAA
5100468 TTTAAATATTAAA
1 TTTAAA-ATTAAA
5100481 TTTAAAATT
1 TTTAAAATT
5100490 TTGATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 16 0.76
14 2 0.10
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:5101355 original size:165 final size:165
Alignment explanation
Indices: 5101049--5101355 Score: 447
Period size: 165 Copynumber: 1.9 Consensus size: 165
5101039 CAAGGGATGA
*
5101049 GTTGAATTTTCACCCTCCATGCAGAGAGGGTAACGAAAAAAAAATAGACATCAATATTATTAAAT
1 GTTGAATTTTCACCCTCCATGCAGAGAGGGTAACGAAAAAAAAATAGAAATCAATATTATTAAAT
*
5101114 TTAATTTTTACATTAAGATATTAAATTAAAAAAATTAACAGATTTAAATTAATATTTTTAAATAT
66 TTAATTTTTACATTAAGATATTAAATTAAAAAAATTAACAAATTTAAATTAATATTTTTAAATAT
*
5101179 TTTATATTTAAATTCATATTTATTTTAATTTTTGG
131 TTTAAATTTAAATTCATATTTATTTTAATTTTTGG
* * * * * * * *
5101214 GTTGAATTTTTACTCTCTATGTAGATAGGGTAAC-TAAAAAAAATTGAAATTCAATGTTATTAAA
1 GTTGAATTTTCACCCTCCATGCAGAGAGGGTAACGAAAAAAAAATAGAAA-TCAATATTATTAAA
* * * *
5101278 TTTAATTTTTATATTAAGATATTAAATTAAAAGATTATAATAAATTTAAATTAATATTTTTAAAT
65 TTTAATTTTTACATTAAGATATTAAATTAAAAAAAT-TAACAAATTTAAATTAATATTTTTAAAT
5101343 A-TTTAAATTTAAA
129 ATTTTAAATTTAAA
5101356 AGTACATTTA
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
164 12 0.10
165 86 0.69
166 27 0.22
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (165 bp):
GTTGAATTTTCACCCTCCATGCAGAGAGGGTAACGAAAAAAAAATAGAAATCAATATTATTAAAT
TTAATTTTTACATTAAGATATTAAATTAAAAAAATTAACAAATTTAAATTAATATTTTTAAATAT
TTTAAATTTAAATTCATATTTATTTTAATTTTTGG
Found at i:5102934 original size:28 final size:28
Alignment explanation
Indices: 5102900--5102953 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
5102890 TACTTTAATT
*
5102900 TTAAATATATAAAATTAAAA-ATATTTAA
1 TTAAATA-AAAAAATTAAAATATATTTAA
5102928 TTAAATAAAAAAATTAAAATATATTT
1 TTAAATAAAAAAATTAAAATATATTT
5102954 CTCATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TTAAATAAAAAAATTAAAATATATTTAA
Found at i:5106128 original size:15 final size:14
Alignment explanation
Indices: 5106106--5106143 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
5106096 GTAAAACAAG
5106106 CTTTTTTTTTTTCT
1 CTTTTTTTTTTTCT
*
5106120 -TTCTTTTTTTTCT
1 CTTTTTTTTTTTCT
5106133 CTTTTTTTTTT
1 CTTTTTTTTTT
5106144 GGCTATTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
CTTTTTTTTTTTCT
Found at i:5107641 original size:10 final size:10
Alignment explanation
Indices: 5107622--5107652 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5107612 TTATGACCCC
5107622 ATGTATTGAT
1 ATGTATTGAT
*
5107632 ATGTAATGAT
1 ATGTATTGAT
5107642 ATGTATTGAT
1 ATGTATTGAT
5107652 A
1 A
5107653 CATTAAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (10 bp):
ATGTATTGAT
Found at i:5111661 original size:16 final size:16
Alignment explanation
Indices: 5111624--5111662 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
5111614 AACTAAAAAC
5111624 TAAATAAAAGCAAATAA
1 TAAAT-AAAGCAAATAA
5111641 T-AATAAAGCAAATAA
1 TAAATAAAGCAAATAA
5111656 TAAATAA
1 TAAATAA
5111663 TAAAAGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 8 0.38
17 1 0.05
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (16 bp):
TAAATAAAGCAAATAA
Found at i:5114741 original size:64 final size:64
Alignment explanation
Indices: 5114660--5114789 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
5114650 GAAATTAATC
*
5114660 AATTTAGAGAAACAATTGAATGAGATACAAGATAATAACAAAGTCTTAACAAATGAAAACAATG
1 AATTTAAAGAAACAATTGAATGAGATACAAGATAATAACAAAGTCTTAACAAATGAAAACAATG
* *
5114724 AATTTAAAGAAACAATTGAATGAGATACAAGGTAATAATAAAGTCTTAACAAATGAAAACAATG
1 AATTTAAAGAAACAATTGAATGAGATACAAGATAATAACAAAGTCTTAACAAATGAAAACAATG
5114788 AA
1 AA
5114790 CTAGTTAAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.22
Consensus pattern (64 bp):
AATTTAAAGAAACAATTGAATGAGATACAAGATAATAACAAAGTCTTAACAAATGAAAACAATG
Found at i:5114775 original size:37 final size:37
Alignment explanation
Indices: 5114670--5114780 Score: 89
Period size: 37 Copynumber: 3.3 Consensus size: 37
5114660 AATTTAGAGA
* *
5114670 AACAATTGAATGAGATACAAGATAATAACAAAGTCTT
1 AACAATTGAATGAGATACAAGGTAATAATAAAGTCTT
* * * *
5114707 AAC-A---AATGA-AAACAATG-AAT-TTAAAG---A
1 AACAATTGAATGAGATACAAGGTAATAATAAAGTCTT
5114734 AACAATTGAATGAGATACAAGGTAATAATAAAGTCTT
1 AACAATTGAATGAGATACAAGGTAATAATAAAGTCTT
*
5114771 AACAAATGAA
1 AACAATTGAA
5114781 AACAATGAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 20
0.63 0.13 0.24
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
30 4 0.08
31 8 0.15
32 11 0.21
33 8 0.15
34 5 0.09
36 1 0.02
37 12 0.23
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.23
Consensus pattern (37 bp):
AACAATTGAATGAGATACAAGGTAATAATAAAGTCTT
Found at i:5120455 original size:27 final size:27
Alignment explanation
Indices: 5120420--5120473 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5120410 GTTTTAAGAA
*
5120420 GTATGAGTTCTAAAAAGGGTGAGAATT
1 GTATAAGTTCTAAAAAGGGTGAGAATT
5120447 GTATAAGTTCTAAAAAGGGTGAGAATT
1 GTATAAGTTCTAAAAAGGGTGAGAATT
5120474 TGTTAAAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.30
Consensus pattern (27 bp):
GTATAAGTTCTAAAAAGGGTGAGAATT
Found at i:5120493 original size:17 final size:17
Alignment explanation
Indices: 5120460--5120507 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5120450 TAAGTTCTAA
*
5120460 AAAGGGTGAGAATTTGTT
1 AAAGGG-GAGAAGTTGTT
5120478 AAAGGGGAGAAGTTGTT
1 AAAGGGGAGAAGTTGTT
*
5120495 AAAAGGGAGAAGT
1 AAAGGGGAGAAGT
5120508 ATGAGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 22 0.79
18 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.23
Consensus pattern (17 bp):
AAAGGGGAGAAGTTGTT
Found at i:5120540 original size:17 final size:17
Alignment explanation
Indices: 5120520--5120562 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5120510 GAGTTTTAAA
*
5120520 AAGAGGGAGAATTTATT
1 AAGAGAGAGAATTTATT
* *
5120537 AAGAGAGATAATTTGTT
1 AAGAGAGAGAATTTATT
*
5120554 AAGGGAGAG
1 AAGAGAGAG
5120563 TATTAAATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.26
Consensus pattern (17 bp):
AAGAGAGAGAATTTATT
Found at i:5121287 original size:32 final size:33
Alignment explanation
Indices: 5121230--5121292 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
5121220 CACCCAGATG
* *
5121230 TATCGATATATATTGCTTAGTATCGATACATTA
1 TATCAATATATAATGCTTAGTATCGATACATTA
*
5121263 TATCAATATATAAT-CTTGGTATCGATACAT
1 TATCAATATATAATGCTTAGTATCGATACAT
5121293 ATTGAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (33 bp):
TATCAATATATAATGCTTAGTATCGATACATTA
Found at i:5124195 original size:39 final size:38
Alignment explanation
Indices: 5124112--5124195 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
5124102 TTAAATTATA
** *
5124112 AAATATTTAATTTTTATCTTTCAATAAAAATAATTCTT
1 AAATATTTAATTTTTATAATTCAATAAAAATAATTCAT
* *
5124150 ATATATTTAATTTTTATAATT-AATATAAAATTATTTCAT
1 AAATATTTAATTTTTATAATTCAATA-AAAA-TAATTCAT
5124189 AAATATT
1 AAATATT
5124196 AAAGATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 4 0.11
38 22 0.58
39 12 0.32
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (38 bp):
AAATATTTAATTTTTATAATTCAATAAAAATAATTCAT
Found at i:5124793 original size:2 final size:2
Alignment explanation
Indices: 5124786--5124826 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5124776 CACATTTGGA
*
5124786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5124827 ATAAATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5127436 original size:2 final size:2
Alignment explanation
Indices: 5127429--5127454 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5127419 AAATTTTATG
5127429 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
5127455 GCAATAGATT
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:5128236 original size:86 final size:87
Alignment explanation
Indices: 5128139--5128374 Score: 257
Period size: 86 Copynumber: 2.7 Consensus size: 87
5128129 CAAAATAGTG
*
5128139 GGGATGAAGTTTTCCCAAGGATAAAATTGTA-AAAAGAAAAATTTAATTTTTGATGAGCGGGGTT
1 GGGATGAAGTTTTCCCAAAGATAAAATTGTATAAAAGAAAAATTTAATTTTTGATGAGCGGGGTT
*
5128203 GGAATGTC-CTTTCGAAATAATA
66 GGAATGTCTCCTT-GAAATAATA
* * * * ***
5128225 GGGATGGAG-TTTCCCTAAAGATAAAATTGTATTAAA-AAAATTTTAAGTTTTGATGAGTAAGGT
1 GGGATGAAGTTTTCCC-AAAGATAAAATTGTATAAAAGAAAAATTTAATTTTTGATGAGCGGGGT
* * * *
5128288 TGGAGTGTCTCCTTGGAATCATG
65 TGGAATGTCTCCTTGAAATAATA
* * * *
5128311 GGGATAAAGTTTCCCCAAAGATAAAATTGTATGAAAG-AAAATTTAATTTTTTGAAGAGCGGGGT
1 GGGATGAAGTTTTCCCAAAGATAAAATTGTATAAAAGAAAAATTTAA-TTTTTGATGAGCGGGGT
5128375 CGGCTTTAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
85 6 0.05
86 92 0.76
87 23 0.19
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (87 bp):
GGGATGAAGTTTTCCCAAAGATAAAATTGTATAAAAGAAAAATTTAATTTTTGATGAGCGGGGTT
GGAATGTCTCCTTGAAATAATA
Done.