Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 201 of 240
Found at i:61237826 original size:20 final size:21
Alignment explanation
Indices: 61237801--61237842 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
61237791 CCCTTAGAAC
61237801 CCAAAAATTAC-A-GTTTTGAT
1 CCAAAAATT-CTATGTTTTGAT
61237821 CCAAAAATTCTATGTTTTGAT
1 CCAAAAATTCTATGTTTTGAT
61237842 C
1 C
61237843 AATTTAGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 10 0.50
21 9 0.45
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
CCAAAAATTCTATGTTTTGAT
Found at i:61243003 original size:18 final size:18
Alignment explanation
Indices: 61242961--61243004 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
61242951 ACTAAACTTT
* *
61242961 CTTAATGACATAAAAATC
1 CTTAATAACATAAAAATA
* *
61242979 CTAAATAACTTAAAAATA
1 CTTAATAACATAAAAATA
61242997 CTTAATAA
1 CTTAATAA
61243005 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (18 bp):
CTTAATAACATAAAAATA
Found at i:61247603 original size:17 final size:17
Alignment explanation
Indices: 61247577--61247615 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
61247567 TTCTTAATCA
61247577 TTTTTATTATTAA-TAT
1 TTTTTATTATTAATTAT
61247593 TTTTATATTATTAATTAT
1 TTTT-TATTATTAATTAT
61247611 TTTTT
1 TTTTT
61247616 TACAGTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTATTAATTAT
Found at i:61247605 original size:20 final size:19
Alignment explanation
Indices: 61247580--61247639 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
61247570 TTAATCATTT
61247580 TTATTATTAATATTTTTATA
1 TTATTATT-ATATTTTTATA
* *
61247600 TTATTAATTATTTTTTTACA
1 TTATT-ATTATATTTTTATA
* *
61247620 GTATT-CTATATTTTTATA
1 TTATTATTATATTTTTATA
61247638 TT
1 TT
61247640 TCATGGTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
18 11 0.34
20 18 0.56
21 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTATTATATTTTTATA
Found at i:61248883 original size:16 final size:16
Alignment explanation
Indices: 61248846--61248885 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
61248836 TTAATAAAAT
* *
61248846 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
61248862 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
61248878 TAAAATTA
1 TAAAATTA
61248886 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:61248953 original size:58 final size:58
Alignment explanation
Indices: 61248891--61249064 Score: 303
Period size: 58 Copynumber: 3.0 Consensus size: 58
61248881 AATTATCAAA
61248891 TTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAAT
1 TTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAAT
61248949 TTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAAT
1 TTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAAT
* * * *
61249007 TTATCAAATTATTAATTGTATTAATTGTAGTAACAAAATCTAACATTTGATTAGTAAA
1 TTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
61249065 ACAAACTTGA
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 62 0.56
59 49 0.44
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (58 bp):
TTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAAT
Found at i:61248971 original size:16 final size:15
Alignment explanation
Indices: 61248946--61248976 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
61248936 TTGATTAGTA
61248946 AATTTATTAATTGTT
1 AATTTATTAATTGTT
61248961 AATTGTATTAATTGTT
1 AATT-TATTAATTGTT
61248977 GTAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
AATTTATTAATTGTT
Found at i:61249171 original size:22 final size:24
Alignment explanation
Indices: 61249131--61249174 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61249121 ACATAAACTT
61249131 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
61249155 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
61249175 AATTTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:61253643 original size:17 final size:18
Alignment explanation
Indices: 61253606--61253643 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
61253596 TTCAAAATTA
*
61253606 TTTTTCAACTTTATATAT
1 TTTTTCAAATTTATATAT
61253624 TTTTTCAAATTT-TAT-T
1 TTTTTCAAATTTATATAT
61253640 TTTT
1 TTTT
61253644 GAATTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCAAATTTATATAT
Found at i:61259193 original size:16 final size:16
Alignment explanation
Indices: 61259157--61259201 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
61259147 CTTTGATTAA
*
61259157 ATTTATTTTAAAATAT
1 ATTTATATTAAAATAT
61259173 ATTTATATTAAAAT-T
1 ATTTATATTAAAATAT
*
61259188 AGTTTACATTAAAA
1 A-TTTATATTAAAA
61259202 AATTCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTATATTAAAATAT
Found at i:61259437 original size:19 final size:19
Alignment explanation
Indices: 61259409--61259460 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
61259399 AGTAACCTTT
*
61259409 TTAA-CTTGAACCTCGATC
1 TTAACCTTGAACCTCGAAC
*
61259427 TTAACCTTGAACCCCGAAC
1 TTAACCTTGAACCTCGAAC
*
61259446 TTGAGCCTTGAACCT
1 TT-AACCTTGAACCT
61259461 TAAACCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.14
19 14 0.50
20 10 0.36
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (19 bp):
TTAACCTTGAACCTCGAAC
Found at i:61262811 original size:18 final size:18
Alignment explanation
Indices: 61262790--61262829 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
61262780 GTTTGGGCCG
*
61262790 GGGTTATTGATTGGGCTT
1 GGGTTATTGATTGGGCTA
* *
61262808 GGGTTGTTGTTTGGGCTA
1 GGGTTATTGATTGGGCTA
61262826 GGGT
1 GGGT
61262830 AACAATTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.05, G:0.45, T:0.42
Consensus pattern (18 bp):
GGGTTATTGATTGGGCTA
Found at i:61275207 original size:14 final size:13
Alignment explanation
Indices: 61275176--61275212 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
61275166 GTTATGCAAG
61275176 CAATAAC-ATAAT
1 CAATAACAATAAT
61275188 -AATAACAATAAT
1 CAATAACAATAAT
61275200 ACAATAACAATAA
1 -CAATAACAATAA
61275213 ATGTAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
14 11 0.50
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.22
Consensus pattern (13 bp):
CAATAACAATAAT
Found at i:61276434 original size:165 final size:169
Alignment explanation
Indices: 61276219--61276555 Score: 540
Period size: 166 Copynumber: 2.0 Consensus size: 169
61276209 CTGATTTGTA
61276219 AAAGAAGTGAATAAATAAATAAATAAGAAAAAAAGAAAACAGAAAAACAAGAAGAAAAACGATCA
1 AAAGAAGTGAATAAATAAATAAATAAGAAAAAAAGAAAACAGAAAAACAAGAAGAAAAACGATCA
* * *
61276284 GATTTTTCAACCTCTTAAGATATTTGTT-TCGTTTTGATTAACTGAAGCGCGTAAAATATTTACA
66 GATTTTTCAACATCTTAAGATATTTGTTCTAGTTTTGATTAACTGAAGCGCGTAAAAAATTTACA
*
61276348 AAGATAAGATTTAGGCCTTTATA-ACCGGATACAACCATT
131 AAGATAAGATCTAGGCCTTTATACA-CGGATACAACCATT
* *
61276387 AAAGAAGTGAATAAATAAAT-AA-AA-TAAAAAAGAAAACAGAAAAACAAGAGGAAAAACGATCA
1 AAAGAAGTGAATAAATAAATAAATAAGAAAAAAAGAAAACAGAAAAACAAGAAGAAAAACGATCA
* * * *
61276449 GATTTTTCAACATTTTAAGATGTTTGTTCTATTTTTGATTAACTGATGCGCGTAAAAAATTTACA
66 GATTTTTCAACATCTTAAGATATTTGTTCTAGTTTTGATTAACTGAAGCGCGTAAAAAATTTACA
61276514 AAGATAAGATCTAGGCCTTTATACACGGATACAACCATT
131 AAGATAAGATCTAGGCCTTTATACACGGATACAACCATT
61276553 AAA
1 AAA
61276556 ATTTTCCTTT
Statistics
Matches: 157, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
165 61 0.39
166 73 0.46
167 3 0.02
168 20 0.13
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (169 bp):
AAAGAAGTGAATAAATAAATAAATAAGAAAAAAAGAAAACAGAAAAACAAGAAGAAAAACGATCA
GATTTTTCAACATCTTAAGATATTTGTTCTAGTTTTGATTAACTGAAGCGCGTAAAAAATTTACA
AAGATAAGATCTAGGCCTTTATACACGGATACAACCATT
Found at i:61276788 original size:18 final size:18
Alignment explanation
Indices: 61276742--61276796 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
61276732 GCTTCTCTGC
*
61276742 TGTTGGTTTGGGCTGGGGT
1 TGTT-GTTTGGGCTAGGGT
* ** *
61276761 TATTAATTGGGCTTGGGT
1 TGTTGTTTGGGCTAGGGT
61276779 TGTTGTTTGGGCTAGGGT
1 TGTTGTTTGGGCTAGGGT
61276797 AACAATTAGG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
18 25 0.89
19 3 0.11
ACGTcount: A:0.07, C:0.05, G:0.44, T:0.44
Consensus pattern (18 bp):
TGTTGTTTGGGCTAGGGT
Found at i:61282694 original size:18 final size:18
Alignment explanation
Indices: 61282666--61282710 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
61282656 TTGATATGGT
* *
61282666 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
61282684 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
61282702 TGGTGGCGA
1 TGGTGGCGA
61282711 TCATTGCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:61284171 original size:17 final size:17
Alignment explanation
Indices: 61284149--61284181 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
61284139 AGTAAGATGT
61284149 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
61284166 CATGAATATTAGAATA
1 CATGAATATTAGAATA
61284182 ACATCTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:61285519 original size:16 final size:15
Alignment explanation
Indices: 61285498--61285527 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
61285488 TTTTTTCTGT
61285498 TTTTTTATCTTTTTTG
1 TTTTTTA-CTTTTTTG
61285514 TTTTTTACTTTTTT
1 TTTTTTACTTTTTT
61285528 TGATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTACTTTTTTG
Found at i:61285560 original size:27 final size:28
Alignment explanation
Indices: 61285530--61285597 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
61285520 ACTTTTTTTG
61285530 ATATATTTTGGTAAATAAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
61285557 ATATATTTTGGTAAATAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAGTTAT
61285585 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
61285598 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAGTTAT
Found at i:61285620 original size:13 final size:13
Alignment explanation
Indices: 61285602--61285627 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61285592 TGGTAATTTT
61285602 TTATTTTTTTATA
1 TTATTTTTTTATA
61285615 TTATTTTTTTATA
1 TTATTTTTTTATA
61285628 AAACCCATAA
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:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:61286400 original size:10 final size:10
Alignment explanation
Indices: 61286387--61286575 Score: 51
Period size: 10 Copynumber: 20.1 Consensus size: 10
61286377 TCCTTCCCTC
61286387 TTCTTCTTCT
1 TTCTTCTTCT
61286397 TTCTT-TT-T
1 TTCTTCTTCT
61286405 TT-TT-TTC-
1 TTCTTCTTCT
*
61286412 -TCTTCTCCT
1 TTCTTCTTCT
61286421 TTCCTT-TTCT
1 TT-CTTCTTCT
*
61286431 TTC--CTTAT
1 TTCTTCTTCT
61286439 TT-TTCTTTCT
1 TTCTTC-TTCT
*
61286449 TTC--CTCCT
1 TTCTTCTTCT
61286457 TTCCTT-TTCT
1 TT-CTTCTTCT
*
61286467 TTC--CTTAT
1 TTCTTCTTCT
61286475 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
61286485 TTCCTCCCCT
1 TTCTTCTTCT
61286495 TTCCTT-TTCT
1 TT-CTTCTTCT
61286505 TTC--CTTCT
1 TTCTTCTTCT
61286513 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
61286523 TTCCTCTCCT
1 TTCTTCTTCT
*
61286533 TTCCTT-TTCC
1 TT-CTTCTTCT
*
61286543 TTCTTTTTCT
1 TTCTTCTTCT
61286553 TTCTTCCTTTCT
1 TTCTT-C-TTCT
61286565 TTCTTCTTCT
1 TTCTTCTTCT
61286575 T
1 T
61286576 CCCCTCTCCT
Statistics
Matches: 129, Mismatches: 21, Indels: 58
0.62 0.10 0.28
Matches are distributed among these distances:
6 1 0.01
7 6 0.05
8 26 0.20
9 13 0.10
10 62 0.48
11 12 0.09
12 9 0.07
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:61286444 original size:14 final size:13
Alignment explanation
Indices: 61286405--61286555 Score: 51
Period size: 14 Copynumber: 10.9 Consensus size: 13
61286395 CTTTCTTTTT
61286405 TTTTTTCTCTTCTCC
1 TTTTTT-TCTT-TCC
61286420 TTTCCTTTTCTTTCC
1 TTT--TTTTCTTTCC
61286435 TTATTTTTCTTT-C
1 TT-TTTTTCTTTCC
** *
61286448 TTTCCTCCTTTCC
1 TTTTTTTCTTTCC
61286461 ---TTTTCTTTCC
1 TTTTTTTCTTTCC
61286471 TTATTTTTCTTT-C
1 TT-TTTTTCTTTCC
***
61286484 TTTCCTCCCCTTTCC
1 TTT--TTTTCTTTCC
* *
61286499 TTTTCTTTCCTTCT
1 TTTT-TTTCTTTCC
61286513 TTTTCTTTCTTTCC
1 TTTT-TTTCTTTCC
* *
61286527 TCTCCTTTCCTTTTCC
1 T-T-TTTTTC-TTTCC
61286543 TTCTTTTTCTTTC
1 TT-TTTTTCTTTC
61286556 TTCCTTTCTT
Statistics
Matches: 101, Mismatches: 20, Indels: 31
0.66 0.13 0.20
Matches are distributed among these distances:
10 7 0.07
12 7 0.07
13 8 0.08
14 42 0.42
15 22 0.22
16 12 0.12
17 3 0.03
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTTTCTTTCC
Found at i:61286447 original size:18 final size:18
Alignment explanation
Indices: 61286426--61286572 Score: 124
Period size: 18 Copynumber: 8.1 Consensus size: 18
61286416 CTCCTTTCCT
*
61286426 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* *
61286444 TTTCTTTCC-TCCTTTCC
1 TTTCTTTCCTTCTTTTTC
*
61286461 TTTTCTTTCCTTATTTTTC
1 -TTTCTTTCCTTCTTTTTC
* * *
61286480 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
61286499 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
61286518 TTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
61286536 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
61286552 TTTC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
61286571 TT
1 TT
61286573 CTTCCCCTCT
Statistics
Matches: 102, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
16 9 0.09
17 17 0.17
18 47 0.46
19 19 0.19
20 10 0.10
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:61286524 original size:28 final size:28
Alignment explanation
Indices: 61286493--61286572 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
61286483 CTTTCCTCCC
61286493 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
61286521 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTT
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTT
61286555 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
61286573 CTTCCCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.15
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 18 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:61286556 original size:38 final size:38
Alignment explanation
Indices: 61286357--61286563 Score: 230
Period size: 38 Copynumber: 5.5 Consensus size: 38
61286347 ATAAAAATTA
* * *
61286357 CCTTA-TTTTCTTTTTTTCCT-TCCTTCCCTCTTCTTCT
1 CCTTATTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTT-T
* *
61286394 TCTT-TCTTTT-TTTTTTTCTCTTCTCCTTTCCTTTTCTTT
1 CCTTAT-TTTTCTTTCTTTC-C-TCTCCTTTCCTTTTCTTT
61286433 CCTTATTTTTCTTTCTTT-C-CTCCTTTCCTTTTCTTT
1 CCTTATTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT
*
61286469 CCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTT
1 CCTTATTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT
* *
61286507 CCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTT
1 CCTTATTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT
* *
61286545 -CTTTTTCTTTCTTCCTTTC
1 CCTTATT-TTTCTTTCTTTC
61286564 TTTCTTCTTC
Statistics
Matches: 149, Mismatches: 11, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
36 35 0.23
37 17 0.11
38 68 0.46
39 9 0.06
40 20 0.13
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (38 bp):
CCTTATTTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTT
Found at i:61286556 original size:112 final size:112
Alignment explanation
Indices: 61286357--61286563 Score: 262
Period size: 112 Copynumber: 1.8 Consensus size: 112
61286347 ATAAAAATTA
* * *
61286357 CCTTATTTTCTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTTCTTTTTTTTTTTCTCTTCTCCTT
1 CCTTATTTTCTTTCTTTCCTCCCTTCCCTCTTCTTCTTCCTTCTTTTTTTTTTTCTCTTCTCCTT
* *
61286422 TCCTTTTCTTTCCTTATTTTTCTTTCTTTCCTCCTTTCCTTTTCTTT
66 TCCTTTTCCTTCCTTATTTTTCTTCCTTTCCTCCTTTCCTTTTCTTT
* *
61286469 CCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTC-T-TTCCTTCTTTTTCTTTCTTTC-C-TCT
1 CCTTA-TTTTCTTTCTTTCCT-CCCTTCCCTCTTCTTCTTCCTTCTTTTT-TTT-TTTCTCTTCT
*
61286530 CCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
62 CCTTTCCTTTTCCTTCCTTATT-TTTCTTCCTTTC
61286564 TTTCTTCTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
111 5 0.06
112 44 0.54
113 19 0.23
114 14 0.17
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (112 bp):
CCTTATTTTCTTTCTTTCCTCCCTTCCCTCTTCTTCTTCCTTCTTTTTTTTTTTCTCTTCTCCTT
TCCTTTTCCTTCCTTATTTTTCTTCCTTTCCTCCTTTCCTTTTCTTT
Found at i:61286568 original size:22 final size:23
Alignment explanation
Indices: 61286533--61286575 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
61286523 TTCCTCTCCT
*
61286533 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
61286556 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
61286576 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:61286573 original size:28 final size:30
Alignment explanation
Indices: 61286495--61286576 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
61286485 TTCCTCCCCT
*
61286495 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
61286527 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
61286556 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
61286577 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:61286574 original size:18 final size:17
Alignment explanation
Indices: 61286364--61286577 Score: 91
Period size: 18 Copynumber: 12.0 Consensus size: 17
61286354 TTACCTTATT
*
61286364 TTCTTTTT-TTCCTTCC
1 TTCTTTTTCTTTCTTCC
* * *
61286380 TTCCCTCTTC-TTCTTCT
1 TT-CTTTTTCTTTCTTCC
*
61286397 TTCTTTTT-TTTTTTCTC
1 TTCTTTTTCTTTCTTC-C
*
61286414 TTCTCCTTTCCTTTTCTTTCC
1 TTCT--TTTTC-TTTC-TTCC
*
61286435 TTATTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* *
61286453 -TCCTTTCCTTTTCTTTCC
1 TTCTTTTTC-TTTC-TTCC
*
61286471 TTATTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* * *
61286489 TCCCCTTTCCTTTTCTTTCC
1 T-TCTTTTTC-TTTC-TTCC
61286509 TTCTTTTTCTTTCTTTCC
1 TTCTTTTTCTTTC-TTCC
* *
61286527 -TCTCCTTTCCTT-TTCC
1 TTCT-TTTTCTTTCTTCC
61286543 TTCTTTTTCTTTCTTCC
1 TTCTTTTTCTTTCTTCC
61286560 TTTCTTTCTTC-TTCTTCC
1 -TTCTTT-TTCTTTCTTCC
61286578 CCTCTCCTTC
Statistics
Matches: 151, Mismatches: 29, Indels: 34
0.71 0.14 0.16
Matches are distributed among these distances:
16 21 0.14
17 30 0.20
18 56 0.37
19 24 0.16
20 10 0.07
21 7 0.05
22 3 0.02
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTTTTCTTTCTTCC
Found at i:61286586 original size:42 final size:40
Alignment explanation
Indices: 61286474--61286589 Score: 105
Period size: 42 Copynumber: 2.9 Consensus size: 40
61286464 TCTTTCCTTA
* *
61286474 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* * *
61286512 TTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
* *
61286552 TTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
61286590 CCCCCCACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
38 21 0.33
39 2 0.03
40 7 0.11
41 2 0.03
42 32 0.50
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
Found at i:61286761 original size:28 final size:29
Alignment explanation
Indices: 61286729--61286798 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
61286719 TCGTTTTTTG
61286729 ATATATTTTGGTAAATAAAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
61286757 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
61286786 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
61286799 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:61293847 original size:3 final size:3
Alignment explanation
Indices: 61293827--61293861 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
61293817 ATCCCAAAAG
* *
61293827 GGT GGG GGT GGG GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
61293862 GAATAACCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.74, T:0.26
Consensus pattern (3 bp):
GGT
Found at i:61294009 original size:12 final size:12
Alignment explanation
Indices: 61293994--61294075 Score: 119
Period size: 12 Copynumber: 6.8 Consensus size: 12
61293984 TAGATGGAAG
*
61293994 TGATGATGATTT
1 TGATGATGAGTT
61294006 TGATGATGAGTT
1 TGATGATGAGTT
* *
61294018 CGATGATGAATT
1 TGATGATGAGTT
61294030 TGATGATGAGTT
1 TGATGATGAGTT
*
61294042 CGATGATGAGTT
1 TGATGATGAGTT
*
61294054 TGATGATGATTT
1 TGATGATGAGTT
61294066 TGATGATGAG
1 TGATGATGAG
61294076 GAATTTGGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.40
Consensus pattern (12 bp):
TGATGATGAGTT
Found at i:61294724 original size:30 final size:30
Alignment explanation
Indices: 61294690--61294754 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
61294680 CGGTAAGAAT
*
61294690 ATGGGGCAGATGGG-CCAAATGGGAGGTCAG
1 ATGGGGCACATGGGTCC-AATGGGAGGTCAG
* * *
61294720 ATGGGTCACATGGGTTCAATGGGTGGTCAG
1 ATGGGGCACATGGGTCCAATGGGAGGTCAG
61294750 ATGGG
1 ATGGG
61294755 TTATAACATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.45, T:0.20
Consensus pattern (30 bp):
ATGGGGCACATGGGTCCAATGGGAGGTCAG
Found at i:61311587 original size:35 final size:35
Alignment explanation
Indices: 61311541--61311611 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
61311531 CCGATCACCA
*
61311541 TATAAACAAAGACATAATTACATCATCATTCAGCT
1 TATAAACAAAGAAATAATTACATCATCATTCAGCT
61311576 TATAAACAAAGAAATAATTACATCATCATTCAGCT
1 TATAAACAAAGAAATAATTACATCATCATTCAGCT
61311611 T
1 T
61311612 CTTTAGATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (35 bp):
TATAAACAAAGAAATAATTACATCATCATTCAGCT
Found at i:61314997 original size:21 final size:21
Alignment explanation
Indices: 61314971--61315011 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61314961 ATCTGCTCAA
* *
61314971 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
61314992 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
61315012 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:61318036 original size:73 final size:73
Alignment explanation
Indices: 61317917--61318063 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
61317907 TAGGCCAAAC
*
61317917 GAAGAGTTCCCAAGCTCTTTGGTTCCTCTATCTTGCAACACAACAAGGGTGAAATGGACCCTGAA
1 GAAGAGTTCCCAAGCTCTTTGGTTCCTCCATCTTGCAACACAACAAGGGTGAAATGGACCCTGAA
61317982 AATGAATT
66 AATGAATT
61317990 GAAGAGTTCCCAAGCTCTTTGGTTCCTCCATCTTGCAACACAACAAGGGTGAAATGGACCCTGAA
1 GAAGAGTTCCCAAGCTCTTTGGTTCCTCCATCTTGCAACACAACAAGGGTGAAATGGACCCTGAA
61318055 AATGAATT
66 AATGAATT
61318063 G
1 G
61318064 TTTGAAAGAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (73 bp):
GAAGAGTTCCCAAGCTCTTTGGTTCCTCCATCTTGCAACACAACAAGGGTGAAATGGACCCTGAA
AATGAATT
Found at i:61330393 original size:14 final size:16
Alignment explanation
Indices: 61330361--61330393 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
61330351 AATTTTAAAT
61330361 TTTATATTAAAATTCA
1 TTTATATTAAAATTCA
61330377 TTTAT-TTAAAATT-A
1 TTTATATTAAAATTCA
61330391 TTT
1 TTT
61330394 GTTTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATATTAAAATTCA
Found at i:61330683 original size:27 final size:27
Alignment explanation
Indices: 61330653--61330733 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
61330643 GTTAAATCTG
61330653 ATGGTGGGCC-TGCCACAGGCGGCACCA
1 ATGGT-GGCCGTGCCACAGGCGGCACCA
* *
61330680 ATGGT-GCCTGTGGCAGAGGCGGCACCA
1 ATGGTGGCC-GTGCCACAGGCGGCACCA
* *
61330707 ATGGT-GCCTGTGGCAAAGGCGGCACCA
1 ATGGTGGCC-GTGCCACAGGCGGCACCA
61330734 CTTCAATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 3 0.06
27 46 0.94
ACGTcount: A:0.20, C:0.28, G:0.38, T:0.14
Consensus pattern (27 bp):
ATGGTGGCCGTGCCACAGGCGGCACCA
Found at i:61330795 original size:25 final size:25
Alignment explanation
Indices: 61330761--61330809 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
61330751 GATTCAGCCC
61330761 AGCTGAAGGAGAAAAAGAAGAAGAG
1 AGCTGAAGGAGAAAAAGAAGAAGAG
*
61330786 AGCTGAAGGAGAAGAAGAAGAAGA
1 AGCTGAAGGAGAAAAAGAAGAAGA
61330810 AGGTGGTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.55, C:0.04, G:0.37, T:0.04
Consensus pattern (25 bp):
AGCTGAAGGAGAAAAAGAAGAAGAG
Found at i:61331173 original size:13 final size:13
Alignment explanation
Indices: 61331155--61331180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61331145 TTTTACATTA
61331155 TATTATTTTTAGT
1 TATTATTTTTAGT
61331168 TATTATTTTTAGT
1 TATTATTTTTAGT
61331181 AAAACCCTAA
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:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
TATTATTTTTAGT
Found at i:61331204 original size:37 final size:37
Alignment explanation
Indices: 61331077--61331214 Score: 102
Period size: 37 Copynumber: 3.7 Consensus size: 37
61331067 AACTAATATT
* **
61331077 ATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGT-AAAACCCTA
* *** * *
61331115 ATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTA-CATT
1 ATTATTATTGTTAGTTA-T-T-ATTATTAG-TAAAACCCTA
* *
61331154 A-TATTATTTTTAGTTATTATTTTTAGTAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
*
61331190 ATTATTATTGTTAGTTAGTATTATT
1 ATTATTATTGTTAGTTATTATTATT
61331215 TTGAGTAAAA
Statistics
Matches: 75, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
35 2 0.03
36 10 0.13
37 28 0.37
38 17 0.23
39 11 0.15
40 6 0.08
41 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (37 bp):
ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
Found at i:61331235 original size:76 final size:79
Alignment explanation
Indices: 61331030--61331264 Score: 230
Period size: 76 Copynumber: 2.9 Consensus size: 79
61331020 GTTTAGTTAT
* *
61331030 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAA-T--TATTATTATTAT-GTTAGTTAT
61331095 TAGGATTAGTAAAAACCC
62 TAGGATTAGTAAAAACCC
* *** * *
61331113 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATT-T-TTAGTTATTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAATTATTATTATTATGTTAGTTATTAG
**
61331174 TTTTAGT-AAAACCC
65 GATTAGTAAAAACCC
61331188 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAATTATTATTATTGTTATTGTGTTAGT
1 TAATTATTATTGTTAGTTAGTATTATTGTT-AGTAAAAAATTATTATTA---TTA---TGTTAGT
61331252 TATTAGGATTAGT
59 TATTAGGATTAGT
61331265 GGTTAAACGT
Statistics
Matches: 122, Mismatches: 18, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
75 26 0.21
76 36 0.30
78 1 0.01
79 9 0.07
80 2 0.02
82 19 0.16
83 14 0.11
84 15 0.12
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (79 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAATTATTATTATTATGTTAGTTATTAGG
ATTAGTAAAAACCC
Found at i:61334258 original size:156 final size:156
Alignment explanation
Indices: 61334075--61334977 Score: 1346
Period size: 155 Copynumber: 5.8 Consensus size: 156
61334065 TTTAGTAAAA
* * *
61334075 AACCCTTATTTCGGCCTTTTGTTCGTATTTTTTCTCGAATTTTATTACTTTTAATAAAAATATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
*
61334140 TATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTAGTG
66 TATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
61334205 TGTTTTTTAAATAAATTTCAAAAATT
131 TGTTTTTTAAATAAATTTCAAAAATT
* * *
61334231 AACCTTTATTTCGGTCCTTTGTTCGTATTTTTT-CCTAGATTTTATTACTTTCAATAAAAATATA
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGA-ATTTTATTACTTTCAATAAAAATATA
*
61334295 TTATTTTCTATTTTTATTAGTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
65 TTATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
61334360 GTG-TTTTTAAATAAATTTCAAAAATT
130 GTGTTTTTTAAATAAATTTCAAAAATT
* *
61334386 AACTCTTATTTCGGCCCTTTGTTTGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
* * *
61334451 TATTTTATATTTTTATTAGTTTACATTATTTTAATACATTATGTTTGAAATGTATTAATTTAGTG
66 TATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
*
61334516 TGATTTTTAAATAAATTTCAAAAATT
131 TGTTTTTTAAATAAATTTCAAAAATT
* *
61334542 AACCCTTATTTTGGCCATTTGTTCGTA-TTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
* *
61334606 TATTTTCTAATTTTATTATTTTATATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA--G
66 TATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
*
61334669 TGTTTTTTAAATAAATTTAAAAAATT
131 TGTTTTTTAAATAAATTTCAAAAATT
* *
61334695 AACCATTATTTTGGCCCTTTGTTCGTATTCTTTTCCCCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATT-TTTT-CCCGAATTTTATTACTTTCAATAAAAATAT
* * *
61334760 ATTATTTTTTAATTTTATTATTTTATATT-TTTTAGTACATTATGTTTGAAATGTATTAATTTAG
64 ATTATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
*
61334824 TGTGTTTTTAAAATAAATTT-AGTAAAA--
129 TGTGTTTTTTAAATAAATTTCA--AAAATT
* * ** * * *
61334851 AACCCTTATTTCTGCCCTTTGTTCGTATTTTTTACCGAAGCCTCATT-GTTT-TA-AAAAATATA
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAA-TTTTATTACTTTCAATAAAAATATA
* *
61334913 TTATTTTC-ATATTTTATTATTTTACGTTATTTTAGTACATTATGTTTGAAATGCATTAATTTAG
65 TTATTTTCTAT-TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
61334977 T
129 T
61334978 AAAAAAAACC
Statistics
Matches: 690, Mismatches: 44, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
151 1 0.00
152 31 0.04
153 86 0.12
154 9 0.01
155 286 0.41
156 255 0.37
157 18 0.03
158 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (156 bp):
AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATAT
TATTTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
TGTTTTTTAAATAAATTTCAAAAATT
Found at i:61334736 original size:311 final size:307
Alignment explanation
Indices: 61334078--61334977 Score: 1332
Period size: 311 Copynumber: 2.9 Consensus size: 307
61334068 AGTAAAAAAC
* * *
61334078 CCTTATTTCGGCCTTTTGTTCGTATTTTTTCTCGAATTTTATTACTTTTAATAAAAATATATTAT
1 CCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTAT
* *
61334143 TTTCTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTAGTGTGT
66 TTTATATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG-
* * * *
61334208 TTTTTAAATAAATTTCAAAAATTAACCTTTATTTCGGTCCTTTGTTCGTATTTTTTCCTAGATTT
130 TTTTTAAATAAATTTCAAAAATTAACCCTTATTTTGG-CCTTTGTTCGTATTTTTACCGA-ATTT
* *
61334273 TATTACTTTCAATAAAAATATATTATTTTCTATTTTTATTAGTTTACATTATTTTAGTACATTAT
193 TATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTAT
*
61334338 GTTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTCAAAAATTAA
258 GTTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAATTAA
*
61334388 CTCTTATTTCGGCCCTTTGTTTGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTA
1 C-CTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTA
* *
61334453 TTTTATATTTTTATTAGTTTACATTATTTTAATACATTATGTTTGAAATGTATTAATTTAGTGTG
65 TTTTATATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG
*
61334518 ATTTTTAAATAAATTTCAAAAATTAACCCTTATTTTGGCCATTTGTTCGTATTTTTCCCGAATTT
130 -TTTTTAAATAAATTTCAAAAATTAACCCTTATTTTGGCC-TTTGTTCGTATTTTTACCGAATTT
*
61334583 TATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTATATTATTTTAGTACATTAT
193 TATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTAT
61334648 GTTTGAAATGTATTAATTTAGTGT-TTTTTAAATAAATTTAAAAAATTAA
258 GTTTGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAATTAA
*
61334697 CCATTATTTTGGCCCTTTGTTCGTATTCTTTTCCCCGAATTTTATTACTTTCAATAAAAATATAT
1 CC-TTATTTCGGCCCTTTGTTCGTATT-TTTT-CCCGAATTTTATTACTTTCAATAAAAATATAT
* * *
61334762 TATTTTTTAATTTTATTATTTTATATT-TTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
63 TATTTTATATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
*
61334826 TGTTTTTAAAATAAATTT-AGTAAAA--AACCCTTATTTCTGCCCTTTGTTCGTATTTTTTACCG
128 TGTTTTT-AAATAAATTTCA--AAAATTAACCCTTATTT-TGGCCTTTGTTCGTA-TTTTTACCG
** * * * *
61334888 AAGCCTCATT-GTTT-TA-AAAAATATATTATTTTC-ATATTTTATTATTTTACGTTATTTTAGT
188 AA-TTTTATTACTTTCAATAAAAATATATTATTTTCTA-ATTTTATTATTTTACATTATTTTAGT
*
61334949 ACATTATGTTTGAAATGCATTAATTTAGT
251 ACATTATGTTTGAAATGTATTAATTTAGT
61334978 AAAAAAAACC
Statistics
Matches: 544, Mismatches: 34, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
307 1 0.00
308 70 0.13
309 75 0.14
310 162 0.30
311 236 0.43
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (307 bp):
CCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTAT
TTTATATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGT
TTTTAAATAAATTTCAAAAATTAACCCTTATTTTGGCCTTTGTTCGTATTTTTACCGAATTTTAT
TACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTT
TGAAATGTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAATTAA
Found at i:61335408 original size:25 final size:26
Alignment explanation
Indices: 61335380--61335463 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 26
61335370 CTTCCCTCAC
61335380 TCTTCTTC-TTCTTCTCCTTTCCTTT
1 TCTTCTTCTTTCTTCTCCTTTCCTTT
61335405 TCTTTCTTTTTCTTTCTTCTCCTTTCCTTT
1 TC-TTC---TTCTTTCTTCTCCTTTCCTTT
* * *
61335435 CCTT-TTCTTTCTTTTTCTTTCC-TT
1 TCTTCTTCTTTCTTCTCCTTTCCTTT
61335459 TCTTC
1 TCTTC
61335464 CCCAGCTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
24 5 0.10
25 18 0.37
26 3 0.06
29 5 0.10
30 18 0.37
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (26 bp):
TCTTCTTCTTTCTTCTCCTTTCCTTT
Found at i:61335415 original size:10 final size:10
Alignment explanation
Indices: 61335396--61335455 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
61335386 TCTTCTTCTC
*
61335396 CTTTCCTTTT
1 CTTTCTTTTT
61335406 CTTTCTTTTT
1 CTTTCTTTTT
61335416 CTTTCTTCTCCTTT
1 CTTTC-T-T--TTT
*
61335430 CCTTTCCTTTT
1 -CTTTCTTTTT
61335441 CTTTCTTTTT
1 CTTTCTTTTT
61335451 CTTTC
1 CTTTC
61335456 CTTTCTTCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
10 28 0.67
11 4 0.10
12 1 0.02
13 1 0.02
14 3 0.07
15 5 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:61335437 original size:35 final size:36
Alignment explanation
Indices: 61335382--61335455 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
61335372 TCCCTCACTC
*
61335382 TTCTTCTTCTTCTCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTCTCCTTTCCTTTTCTTTCTTTTTCT
61335418 TTCTTCTCCTT-TCCTTTCCTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTCTCCTTTCCTTTTCTTTCTTTTTCT
61335453 TTC
1 TTC
61335456 CTTTCTTCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 27 0.73
36 10 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (36 bp):
TTCTTCTCCTTCTCCTTTCCTTTTCTTTCTTTTTCT
Found at i:61338066 original size:9 final size:9
Alignment explanation
Indices: 61338052--61338095 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
61338042 TTTTGTTACA
61338052 ACAATTAAT
1 ACAATTAAT
61338061 ACAATTAAT
1 ACAATTAAT
61338070 ACAATT-A-
1 ACAATTAAT
61338077 ACAATTAAT
1 ACAATTAAT
61338086 ACAATTAAT
1 ACAATTAAT
61338095 A
1 A
61338096 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 25 0.76
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:61338082 original size:16 final size:16
Alignment explanation
Indices: 61338061--61338098 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
61338051 AACAATTAAT
61338061 ACAATTAATACAATTA
1 ACAATTAATACAATTA
61338077 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
61338093 ATAATT
1 ACAATT
61338099 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:61338189 original size:16 final size:16
Alignment explanation
Indices: 61338168--61338209 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
61338158 AATAATTTGA
*
61338168 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
61338184 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
61338200 TAGTTTTAAT
1 TAATTTTAAT
61338210 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:61340473 original size:3 final size:3
Alignment explanation
Indices: 61340465--61340493 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
61340455 AGACTAGTGT
61340465 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
61340494 GATGGGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:61351116 original size:33 final size:33
Alignment explanation
Indices: 61351074--61351138 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
61351064 TCTTGAAAAT
*
61351074 GAATCTGCCTCAACAAAATGACCTCATTTTTCA
1 GAATCTGCCTCAACAAAATGACATCATTTTTCA
61351107 GAATCTGCCTCAACAAAATGACATCATTTTTC
1 GAATCTGCCTCAACAAAATGACATCATTTTTC
61351139 GACCAACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (33 bp):
GAATCTGCCTCAACAAAATGACATCATTTTTCA
Found at i:61352803 original size:12 final size:11
Alignment explanation
Indices: 61352780--61352814 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
61352770 ATATTATATA
61352780 ATTATTATTTT
1 ATTATTATTTT
*
61352791 ATTGTTAATTTT
1 ATTATT-ATTTT
61352803 ATTATTATTTT
1 ATTATTATTTT
61352814 A
1 A
61352815 GAAATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:61353312 original size:16 final size:16
Alignment explanation
Indices: 61353288--61353341 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
61353278 TTTGGTTCGC
*
61353288 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
61353304 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
61353320 TGTATTGGAATAGAGG
1 TGTAATGGATTAGAGG
61353336 TGTAAT
1 TGTAAT
61353342 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:61353592 original size:16 final size:16
Alignment explanation
Indices: 61353555--61353596 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
61353545 TTAATCATAT
*
61353555 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
61353571 TT-AAATATATTATAA
1 TTAAAATATATTATAA
61353586 TTAAAATATAT
1 TTAAAATATAT
61353597 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:61353603 original size:14 final size:15
Alignment explanation
Indices: 61353564--61353605 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61353554 TTTAAACATA
*
61353564 ATTATTATTAAATAT
1 ATTATAATTAAATAT
61353579 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
61353593 A-TATAATTTAATA
1 ATTATAATTAAATA
61353606 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:61353655 original size:61 final size:60
Alignment explanation
Indices: 61353590--61353776 Score: 195
Period size: 61 Copynumber: 3.1 Consensus size: 60
61353580 TTATAATTAA
61353590 AATATATAATTTAATAAAATTCTTAATAATCAGTATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCA-TATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
61353651 AATATATGATACT-ATAAAATT-TAAATTAA-CATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAT-ATTCTTATATGAATTTACTCA-AATCAT
*
61353710 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAA-TCATATTCTTATATGAATTTACTCAAATCAT
61353771 AATATA
1 AATATA
61353777 AAATCGTGTT
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
58 3 0.03
59 31 0.32
60 22 0.23
61 38 0.39
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATCATATTCTTATATGAATTTACTCAAATCAT
Found at i:61353696 original size:120 final size:120
Alignment explanation
Indices: 61353558--61353776 Score: 420
Period size: 120 Copynumber: 1.8 Consensus size: 120
61353548 ATCATATTTA
*
61353558 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAG
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
61353623 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
*
61353678 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
61353743 TATTCTTATATGAATTTACTCAAATCATAATATA
66 TATTCTTATATGAATTTACTCAAATCATAATATA
61353777 AAATCGTGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
Found at i:61353723 original size:14 final size:15
Alignment explanation
Indices: 61353674--61353725 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
61353664 ATAAAATTTA
61353674 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
61353689 TATTAAATATATTAT
1 AATTAAATATATTAT
61353704 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
61353717 AATTTAATA
1 AATTAAATA
61353726 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:61353776 original size:59 final size:59
Alignment explanation
Indices: 61353593--61353777 Score: 175
Period size: 59 Copynumber: 3.1 Consensus size: 59
61353583 TAATTAAAAT
* *
61353593 ATATAATTTAATAAAATTCTTAATAATCAGTATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * *
61353652 ATAT-ATGATACTATAAAATT-TAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATT-TACTCAAATCA
61353712 T-
58 TA
61353713 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
61353772 ATATAA
1 ATATAA
61353778 AATCGTGTTG
Statistics
Matches: 96, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
56 6 0.06
57 12 0.12
58 8 0.08
59 23 0.24
60 6 0.06
61 17 0.18
62 6 0.06
63 12 0.12
64 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
Found at i:61358924 original size:15 final size:16
Alignment explanation
Indices: 61358906--61358936 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
61358896 AAAAATTTAA
61358906 AAGTTTTTT-ATTTTT
1 AAGTTTTTTAATTTTT
61358921 AAGTTTTTTAATTTTT
1 AAGTTTTTTAATTTTT
61358937 TGGTTAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
AAGTTTTTTAATTTTT
Found at i:61369201 original size:9 final size:9
Alignment explanation
Indices: 61369189--61369217 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
61369179 TTTAATTGGT
61369189 TTATTCGAA
1 TTATTCGAA
61369198 TTATTCGAA
1 TTATTCGAA
61369207 TTATTCGAA
1 TTATTCGAA
61369216 TT
1 TT
61369218 TAAAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:61377270 original size:81 final size:81
Alignment explanation
Indices: 61377134--61377294 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
61377124 ACTCATTGGT
* * *
61377134 CCATCACTTTTTTGCAAACCTTTTCTGCTCTTCAATGGTGACACCAATCTGTTAGCCAAAT-GGG
1 CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCC-AATCGGG
*
61377198 AAGGTGAAAATGATCTG
65 AAGGCGAAAATGATCTG
*
61377215 CCATCACTTCTTTGCAAACTTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
1 CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
61377280 AGGCGAAAATGATCT
66 AGGCGAAAATGATCT
61377295 CCGTAGCTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 3 0.04
81 71 0.96
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (81 bp):
CCATCACTTCTTTGCAAACCTTTTCTGCTCTTCAATGGTGAAACCAATCTATTAGCCAATCGGGA
AGGCGAAAATGATCTG
Found at i:61380402 original size:29 final size:29
Alignment explanation
Indices: 61380360--61380417 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
61380350 AAGCTCAATA
* *
61380360 ACAAGTGCATTTGTAGTTAAATAGTGGAC
1 ACAAGTACAATTGTAGTTAAATAGTGGAC
*
61380389 ACAAGTACAATTGTAGTTAAATGGTGGAC
1 ACAAGTACAATTGTAGTTAAATAGTGGAC
61380418 TATAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (29 bp):
ACAAGTACAATTGTAGTTAAATAGTGGAC
Found at i:61388688 original size:3 final size:3
Alignment explanation
Indices: 61388680--61388705 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61388670 ATCACATGTT
61388680 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
61388706 TGGATGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61393045 original size:3 final size:3
Alignment explanation
Indices: 61393037--61393068 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
61393027 ATCACATGTT
61393037 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61393069 TGGATGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61412743 original size:20 final size:22
Alignment explanation
Indices: 61412697--61412743 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
61412687 GAAATAGTAG
61412697 TAAAATAGTGAAAAAATAACAA
1 TAAAATAGTGAAAAAATAACAA
* *
61412719 GAAAATAGT-AATAAA-AACAA
1 TAAAATAGTGAAAAAATAACAA
61412739 TAAAA
1 TAAAA
61412744 AAAAGCAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (22 bp):
TAAAATAGTGAAAAAATAACAA
Found at i:61412746 original size:23 final size:22
Alignment explanation
Indices: 61412698--61412746 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
61412688 AAATAGTAGT
* * *
61412698 AAAATAGTGAAAAAATAACAAG
1 AAAATAGTAAAAAAACAACAAA
*
61412720 AAAATAGTAATAAAAACAATAAA
1 AAAATAGTAA-AAAAACAACAAA
61412743 AAAA
1 AAAA
61412747 AGCAAAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAATAGTAAAAAAACAACAAA
Found at i:61413070 original size:16 final size:16
Alignment explanation
Indices: 61413049--61413088 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
61413039 GTATAAATTC
* *
61413049 TTTTTAATTTATTTTA
1 TTTTTAAATTATATTA
61413065 TTTTTAAATTATATTA
1 TTTTTAAATTATATTA
61413081 -TTTTAAAT
1 TTTTTAAAT
61413089 ACTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAAATTATATTA
Found at i:61415301 original size:33 final size:35
Alignment explanation
Indices: 61415264--61415360 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
61415254 ATGGTTATAT
61415264 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
61415297 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
61415332 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
61415361 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:61415555 original size:13 final size:13
Alignment explanation
Indices: 61415539--61415591 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
61415529 TTTAAACTGA
61415539 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * * *
61415552 ACTTCTCCACACC
1 ACTTTTCAAAAGC
61415565 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
61415578 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
61415591 A
1 A
61415592 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:61416430 original size:16 final size:16
Alignment explanation
Indices: 61416397--61416430 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61416387 ACTCCCTGTT
* *
61416397 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
61416413 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
61416429 AA
1 AA
61416431 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:61419257 original size:21 final size:21
Alignment explanation
Indices: 61419231--61419271 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61419221 AGACGAGCAA
* *
61419231 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
61419252 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
61419272 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:61421210 original size:16 final size:16
Alignment explanation
Indices: 61421177--61421210 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61421167 GGAGATTGTT
* *
61421177 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
61421193 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
61421209 AA
1 AA
61421211 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:61424341 original size:508 final size:507
Alignment explanation
Indices: 61423332--61424352 Score: 1898
Period size: 508 Copynumber: 2.0 Consensus size: 507
61423322 TTGGAAAGGG
61423332 ATAATAACCTGCTGGTCTGAAAGAAATTTCAAACTTTGATGATCTGTTGTAACACCCCAACCCGT
1 ATAATAACCTGCTGGTCTGAAAGAAATTTCAAACTTTGATGATCTGTTGTAACACCCCAACCCGT
*
61423397 ATCCCTCGCCGAAACCTGGTTACGGAGCATTACCGGAGATTACATATCAAACAGATAGAAATCTC
66 ATCCCTCGCCGAAACCCGGTTACGGAGCATTACCGGAGATTACATATCAAACAGATAGAAATCTC
* *
61423462 AAACATTTTATATCATCAAAATAAGTCATCAAGCATCGTTTTAATCCAAATTATAAATTATCAAA
131 AAACATTTTATATCATCAAAACAAGTCATCAAGCATCGTTTTAATCCAAATTATAAACTATCAAA
*
61423527 AATAGATCTTATAACTTCATTTACAATTAAACACAAAATAACTAATATTTAGACACTCTAGGTAC
196 AATAGATCTTATAACTTCATTTACAATCAAACACAAAATAACTAATATTTAGACACTCTAGGTAC
*
61423592 ATGCCGACACAAAGAAATAAACATCACCATATTTGAGTTCGGAATTGTTGTTGGATGCTGAATCA
261 ATGCCGACACAAAGAAATAAACATCACCATATTTGAGTTCGGAATCGTTGTTGGATGCTGAATCA
* * * **
61423657 GCGATCAAACTTAAGTACTTAACTTGAGCATGAAAAACAAAACCGTATGCTGGGTAAAAACTCAG
326 GCGATCAAACTTAAGTACTTAACCTGAGCACGAAAAACAAAACCATATGCTGAATAAAAACTCAG
*
61423722 TGGTATTTCCATAATCCGAATATTTAAAAATAAAACAATAACATATGTATAATAAAATGTCAAGC
391 TGGTATTTCCATAATCCGAATATTTAAAAATAAAACAATAAAATATGTATAATAAAATGTCAAGC
61423787 ACAATTGAACATTTAAAACCATACGATACTCAATTATCATCACTTGCTATAT
456 ACAATTGAACATTTAAAACCATACGATACTCAATTATCATCACTTGCTATAT
*
61423839 GTAATAACCTGCTGGTCTGAAAGAAATTTCAAACTTTGATGATCTGTTGTAACACCCCCAACCCG
1 ATAATAACCTGCTGGTCTGAAAGAAATTTCAAACTTTGATGATCTGTTGTAACA-CCCCAACCCG
*
61423904 TATCCCTCGTCGAAACCCGGTTACGGAGCATTACCGGAGATTACATATCAAACAGATAGAAATCT
65 TATCCCTCGCCGAAACCCGGTTACGGAGCATTACCGGAGATTACATATCAAACAGATAGAAATCT
61423969 CAAACATTTTATATCATCAAAACAAGTCATCAAGCATCGTTTTAATCCAAATTATAAACTATCAA
130 CAAACATTTTATATCATCAAAACAAGTCATCAAGCATCGTTTTAATCCAAATTATAAACTATCAA
61424034 AAATAGATCTTATAACTTCATTTACAATCAAACACAAAATAACTAATATTTAGACACTCTAGGTA
195 AAATAGATCTTATAACTTCATTTACAATCAAACACAAAATAACTAATATTTAGACACTCTAGGTA
*
61424099 CATGCCGACACAAAGAAATAAACATCACCATATTTGAGTTCGGGATCGTTGTTGGATGCTGAATC
260 CATGCCGACACAAAGAAATAAACATCACCATATTTGAGTTCGGAATCGTTGTTGGATGCTGAATC
61424164 AGCGATCAAACTTAAGTACTTAACCTGAGCACGAAAAACAAAACCATATGCTGAATAAAAACTCA
325 AGCGATCAAACTTAAGTACTTAACCTGAGCACGAAAAACAAAACCATATGCTGAATAAAAACTCA
*
61424229 GTGGTATTTCTATAATCCGAATATTTAAAAATAAAACAATAAAATATGTATAATAAAATGTCAAG
390 GTGGTATTTCCATAATCCGAATATTTAAAAATAAAACAATAAAATATGTATAATAAAATGTCAAG
61424294 CACAATTGAACATTTAAAACCATACGATACTCAATTATCATCACTTGCTATAT
455 CACAATTGAACATTTAAAACCATACGATACTCAATTATCATCACTTGCTATAT
61424347 ATAATA
1 ATAATA
61424353 GCTTTCCACA
Statistics
Matches: 497, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
507 53 0.11
508 444 0.89
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (507 bp):
ATAATAACCTGCTGGTCTGAAAGAAATTTCAAACTTTGATGATCTGTTGTAACACCCCAACCCGT
ATCCCTCGCCGAAACCCGGTTACGGAGCATTACCGGAGATTACATATCAAACAGATAGAAATCTC
AAACATTTTATATCATCAAAACAAGTCATCAAGCATCGTTTTAATCCAAATTATAAACTATCAAA
AATAGATCTTATAACTTCATTTACAATCAAACACAAAATAACTAATATTTAGACACTCTAGGTAC
ATGCCGACACAAAGAAATAAACATCACCATATTTGAGTTCGGAATCGTTGTTGGATGCTGAATCA
GCGATCAAACTTAAGTACTTAACCTGAGCACGAAAAACAAAACCATATGCTGAATAAAAACTCAG
TGGTATTTCCATAATCCGAATATTTAAAAATAAAACAATAAAATATGTATAATAAAATGTCAAGC
ACAATTGAACATTTAAAACCATACGATACTCAATTATCATCACTTGCTATAT
Found at i:61424856 original size:30 final size:31
Alignment explanation
Indices: 61424820--61424892 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
61424810 ATTTTAAAAT
* *
61424820 ATTTTTAAAATACTTTTT-AAGTTTTTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATATTTTTTTA
61424851 A-TTTTAAAATATTTTTAAAATATTTTTTTA
1 ATTTTTAAAATATTTTTAAAATATTTTTTTA
61424881 ATTTTTAAAATA
1 ATTTTTAAAATA
61424893 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 5 0.13
30 22 0.58
31 11 0.29
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
ATTTTTAAAATATTTTTAAAATATTTTTTTA
Found at i:61424881 original size:13 final size:11
Alignment explanation
Indices: 61424811--61424877 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
61424801 TATTTTTTAA
61424811 TTTTAAAATAT
1 TTTTAAAATAT
61424822 TTTTAAAATACT
1 TTTTAAAATA-T
*
61424834 TTTT-AAGT-T
1 TTTTAAAATAT
** *
61424843 TTTT--TTTAA
1 TTTTAAAATAT
61424852 TTTTAAAATAT
1 TTTTAAAATAT
61424863 TTTTAAAATAT
1 TTTTAAAATAT
61424874 TTTT
1 TTTT
61424878 TTAATTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
8 1 0.02
9 9 0.20
11 30 0.67
12 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:61424898 original size:20 final size:20
Alignment explanation
Indices: 61424861--61424899 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61424851 ATTTTAAAAT
**
61424861 ATTTTTAAAATATTTTTTTA
1 ATTTTTAAAATAAATTTTTA
61424881 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
61424900 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:61425037 original size:22 final size:22
Alignment explanation
Indices: 61425003--61425087 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
61424993 GAGCACCTCT
*
61425003 AGCACAGATGTGCTAAACAGAA
1 AGCACTGATGTGCTAAACAGAA
* *
61425025 AGCACTGACGTGCTAAATATCAGAG
1 AGCACTGATGTGCT-AA-A-CAGAA
*
61425050 AGCA-TAGATGTGCTAAACAGAC
1 AGCACT-GATGTGCTAAACAGAA
61425072 AGCACTGA-GTGCTAAA
1 AGCACTGATGTGCTAAA
61425088 TATCAGAGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 8 0.15
22 22 0.42
23 4 0.08
24 4 0.08
25 15 0.28
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (22 bp):
AGCACTGATGTGCTAAACAGAA
Found at i:61425053 original size:25 final size:24
Alignment explanation
Indices: 61425020--61425098 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 24
61425010 ATGTGCTAAA
*
61425020 CAGAAAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGA-GTGCTAAATAT
61425045 CAGAGAGCA-TAGATGTGCT-AA-A-
1 CAGAGAGCACT-GA-GTGCTAAATAT
*
61425067 CAGACAGCACTGAGTGCTAAATAT
1 CAGAGAGCACTGAGTGCTAAATAT
61425091 CAGAGAGC
1 CAGAGAGC
61425099 GCATTAGAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.11
22 12 0.27
23 3 0.07
24 10 0.22
25 15 0.33
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (24 bp):
CAGAGAGCACTGAGTGCTAAATAT
Found at i:61425077 original size:47 final size:46
Alignment explanation
Indices: 61425003--61425098 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 46
61424993 GAGCACCTCT
61425003 AGCACAGATGTGCTAAACAGAAAGCACTGACGTGCTAAATATCAGAG
1 AGCACAGATGTGCTAAACAGAAAGCACTGA-GTGCTAAATATCAGAG
* *
61425050 AGCATAGATGTGCTAAACAGACAGCACTGAGTGCTAAATATCAGAG
1 AGCACAGATGTGCTAAACAGAAAGCACTGAGTGCTAAATATCAGAG
61425096 AGC
1 AGC
61425099 GCATTAGAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 19 0.40
47 28 0.60
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (46 bp):
AGCACAGATGTGCTAAACAGAAAGCACTGAGTGCTAAATATCAGAG
Found at i:61426060 original size:5 final size:5
Alignment explanation
Indices: 61426050--61426095 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
61426040 TTGTTTCTTT
* * *
61426050 TATAA TATAA TATAA TAT-- TATAA TCTAA TATAA TCTAA TCTAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
61426096 TTATACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 3 0.09
5 32 0.91
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:61426072 original size:18 final size:18
Alignment explanation
Indices: 61426049--61426083 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61426039 TTTGTTTCTT
61426049 TTATAATATAATATAATA
1 TTATAATATAATATAATA
*
61426067 TTATAATCTAATATAAT
1 TTATAATATAATATAAT
61426084 CTAATCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATATAATATAATA
Found at i:61441013 original size:38 final size:37
Alignment explanation
Indices: 61440971--61441053 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
61440961 GCCCCGACGC
* * *
61440971 TTTAATTTTGTTTAATTTTTTTATATTTCTTATTATAT
1 TTTAATTTTGTTTAATTTATATAT-TTTCTTACTATAT
* *
61441009 TTTAATGTTGTTTAATTTATATATTTTCTTGCTATAT
1 TTTAATTTTGTTTAATTTATATATTTTCTTACTATAT
*
61441046 TTGAATTT
1 TTTAATTT
61441054 AATATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 17 0.45
38 21 0.55
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (37 bp):
TTTAATTTTGTTTAATTTATATATTTTCTTACTATAT
Found at i:61454576 original size:4 final size:4
Alignment explanation
Indices: 61454567--61454597 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
61454557 AGAAGAAGAC
61454567 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
61454598 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:61460288 original size:24 final size:24
Alignment explanation
Indices: 61460261--61460306 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61460251 TTGAATGTTG
* *
61460261 TATCATGGTAAATCGAAAATTTCT
1 TATCATGGTAAACCAAAAATTTCT
61460285 TATCATGGTAAACCAAAAATTT
1 TATCATGGTAAACCAAAAATTT
61460307 TTTCGTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (24 bp):
TATCATGGTAAACCAAAAATTTCT
Found at i:61461774 original size:7 final size:7
Alignment explanation
Indices: 61461762--61461811 Score: 65
Period size: 6 Copynumber: 7.9 Consensus size: 7
61461752 TGTAAATGAA
61461762 TCATTTC
1 TCATTTC
61461769 TCATTTC
1 TCATTTC
61461776 TCATTT-
1 TCATTTC
61461782 TCATTT-
1 TCATTTC
61461788 TCATTTC
1 TCATTTC
61461795 T-ATTTC
1 TCATTTC
61461801 -CATTTC
1 TCATTTC
61461807 -CATTT
1 TCATTT
61461812 TGAGAAACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.66
7 14 0.34
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (7 bp):
TCATTTC
Found at i:61465503 original size:50 final size:50
Alignment explanation
Indices: 61465437--61465535 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
61465427 ATATTATTCT
* * * *
61465437 AATCAATGTCATATAGAAGGAGAGAAGTT-TTATACGGATTCTACTTGTAC
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTT-TACAGATTCTACTTGTAC
* *
61465487 AATCAATATCAAATAGAAGAAGAGTAGTTCTTTACAGATTCTATTTGTA
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTTTACAGATTCTACTTGTA
61465536 TCATTTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (50 bp):
AATCAATATCAAATAGAAGAAGAGAAGTTCTTTACAGATTCTACTTGTAC
Found at i:61471826 original size:21 final size:21
Alignment explanation
Indices: 61471800--61471861 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
61471790 CGAACACTCT
61471800 TGAACAGAAGCTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
*
61471821 TGAACAGAAGCTCATAAGATC
1 TGAACAGAAGCTCATAAGAGC
*
61471842 TGAACAGAAGCTCAAAAGAG
1 TGAACAGAAGCTCATAAGAG
61471862 TTGATCCACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:61490139 original size:26 final size:24
Alignment explanation
Indices: 61490090--61490139 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
61490080 ACAATAATAC
*
61490090 ATAACATAAAGCATACAGTCATTT
1 ATAACATAAAGCATACAGCCATTT
*
61490114 ATAACATAAGGGCATAACAGCCATTT
1 ATAACATAA-AGCAT-ACAGCCATTT
61490140 TACCACGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 4 0.18
26 9 0.41
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (24 bp):
ATAACATAAAGCATACAGCCATTT
Found at i:61493836 original size:11 final size:11
Alignment explanation
Indices: 61493820--61493848 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
61493810 GACTGTGTTG
61493820 CCCAAGGTTTC
1 CCCAAGGTTTC
61493831 CCCAAGGTTTC
1 CCCAAGGTTTC
61493842 CCCAAGG
1 CCCAAGG
61493849 GAGGTACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (11 bp):
CCCAAGGTTTC
Found at i:61501407 original size:12 final size:12
Alignment explanation
Indices: 61501390--61501423 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
61501380 CGGTCCTCCC
61501390 ATATTAATTTTT
1 ATATTAATTTTT
*
61501402 ATATTATTTTTT
1 ATATTAATTTTT
61501414 ATA-TAATTTT
1 ATATTAATTTT
61501424 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:61504357 original size:23 final size:23
Alignment explanation
Indices: 61504317--61504362 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
61504307 ATTAATTTTT
*
61504317 AAGTTAATCGAATCAAGTTATTC
1 AAGTTAATCGAATCAAGTAATTC
*
61504340 AAGTTAACTTGAAT-AAGTAATTC
1 AAGTTAA-TCGAATCAAGTAATTC
61504363 GAATTTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (23 bp):
AAGTTAATCGAATCAAGTAATTC
Found at i:61504501 original size:20 final size:20
Alignment explanation
Indices: 61504475--61504528 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
61504465 CTCTTTCAAC
*
61504475 AAAAATTACAAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
*
61504495 CAAAATTTCAAAATATTTAT
1 AAAAATTTCAAAATATTTAT
61504515 AAAAATTTCAAAAT
1 AAAAATTTCAAAAT
61504529 TTACATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:61506399 original size:55 final size:55
Alignment explanation
Indices: 61506313--61506421 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
61506303 AAGGAGCCAA
* ** *
61506313 ATGCTTCTTCTATTCTTTTCCTTGGCGCAGCTGGGCCATCCTAGACTTGAACCAG
1 ATGCTTCTTCTAATCTTTTCCTTGGAACAGCTAGGCCATCCTAGACTTGAACCAG
61506368 ATGCTTCTTCTAATCTTTTCCTTGGAACAGCTAGGCCATCCTAGACTTGAACCA
1 ATGCTTCTTCTAATCTTTTCCTTGGAACAGCTAGGCCATCCTAGACTTGAACCA
61506422 AAGATCTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (55 bp):
ATGCTTCTTCTAATCTTTTCCTTGGAACAGCTAGGCCATCCTAGACTTGAACCAG
Found at i:61508170 original size:19 final size:20
Alignment explanation
Indices: 61508126--61508174 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
61508116 CAACACATAA
61508126 AGTGCCTGAAACGACACACGT
1 AGTGCCTGAAACGACACAC-T
*
61508147 GGTGCCT-AATACGACACA-T
1 AGTGCCTGAA-ACGACACACT
61508166 AGTGCCTGA
1 AGTGCCTGA
61508175 TCGGGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (20 bp):
AGTGCCTGAAACGACACACT
Found at i:61509042 original size:5 final size:6
Alignment explanation
Indices: 61509027--61509051 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61509017 CAAATTCTCG
61509027 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
61509052 CCTTTCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:61509127 original size:20 final size:20
Alignment explanation
Indices: 61509095--61509133 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
61509085 TCTTTCCTTA
61509095 ATTTGTTTCTCTTTTATTTC
1 ATTTGTTTCTCTTTTATTTC
61509115 ATTTCGTTT-TCTTTTATTT
1 ATTT-GTTTCTCTTTTATTT
61509134 GTCTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (20 bp):
ATTTGTTTCTCTTTTATTTC
Found at i:61509456 original size:14 final size:17
Alignment explanation
Indices: 61509437--61509474 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
61509427 ATTTATTTCT
61509437 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
61509451 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
61509468 TAATATA
1 TAATATA
61509475 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:61509492 original size:11 final size:11
Alignment explanation
Indices: 61509454--61509492 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
61509444 ATATTTATAA
61509454 TATAATTAATT
1 TATAATTAATT
*
61509465 TAATAATATACTT
1 T-ATAAT-TAATT
61509478 TATAATTAATT
1 TATAATTAATT
61509489 TATA
1 TATA
61509493 TATATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:61509510 original size:17 final size:17
Alignment explanation
Indices: 61509478--61509511 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61509468 TAATATACTT
* *
61509478 TATAATTAATTTATATA
1 TATAATTAAATCATATA
61509495 TATAATTAAATCATATA
1 TATAATTAAATCATATA
61509512 AAAATTTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAATTAAATCATATA
Found at i:61516541 original size:4 final size:4
Alignment explanation
Indices: 61516532--61516556 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
61516522 AACTCACTTG
61516532 TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC T
61516557 CTATATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:61518044 original size:16 final size:18
Alignment explanation
Indices: 61518023--61518062 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
61518013 ACACATAAAA
61518023 TATATAAT-ATAAT-TTT
1 TATATAATGATAATATTT
61518039 TATAT-ATGATAATATTT
1 TATATAATGATAATATTT
61518056 TA-ATAAT
1 TATATAAT
61518063 TTTACAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATAATGATAATATTT
Found at i:61526859 original size:41 final size:40
Alignment explanation
Indices: 61526724--61526858 Score: 134
Period size: 41 Copynumber: 3.4 Consensus size: 40
61526714 ACCAGTTTGG
* * * *
61526724 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGA
1 CACCCAATGCCTCATCGGTTAATCCGAAGTAATAAATTGA
** * * *
61526764 CACTTAGTGTCTCATC-GTCTAAACCGAAG---TAAATTGA
1 CACCCAATGCCTCATCGGT-TAATCCGAAGTAATAAATTGA
61526801 CACCCAATGCCTCATCGAGTTAATCCGAAGTAATAAATTGA
1 CACCCAATGCCTCATCG-GTTAATCCGAAGTAATAAATTGA
*
61526842 CACCCAATGTCTCATCG
1 CACCCAATGCCTCATCG
61526859 ACTCAAAGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
37 19 0.25
38 9 0.12
39 3 0.04
40 21 0.28
41 24 0.32
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (40 bp):
CACCCAATGCCTCATCGGTTAATCCGAAGTAATAAATTGA
Found at i:61527046 original size:24 final size:24
Alignment explanation
Indices: 61527017--61527063 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61527007 TATATATACC
61527017 AATTCAATCA-ATA-TAAATTCAATA
1 AATTC-ATCACATATTAAA-TCAATA
61527041 AATTCATCACATATTAAATCAAT
1 AATTCATCACATATTAAATCAAT
61527064 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCATCACATATTAAATCAATA
Found at i:61527749 original size:16 final size:16
Alignment explanation
Indices: 61527728--61527766 Score: 57
Period size: 13 Copynumber: 2.6 Consensus size: 16
61527718 ACTTTTCTCC
61527728 TTCTTTCTTCCTCTTT
1 TTCTTTCTTCCTCTTT
61527744 TTC--T-TTCCTCTTT
1 TTCTTTCTTCCTCTTT
61527757 TTCTTTCTTC
1 TTCTTTCTTC
61527767 ATTCTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.60
14 1 0.05
15 1 0.05
16 6 0.30
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTCTTCCTCTTT
Found at i:61527753 original size:13 final size:13
Alignment explanation
Indices: 61527731--61527763 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
61527721 TTTCTCCTTC
61527731 TTTC-TTCCTCTT
1 TTTCTTTCCTCTT
61527743 TTTCTTTCCTCTT
1 TTTCTTTCCTCTT
61527756 TTTCTTTC
1 TTTCTTTC
61527764 TTCATTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTTTCCTCTT
Found at i:61527794 original size:24 final size:22
Alignment explanation
Indices: 61527755--61527810 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
61527745 TCTTTCCTCT
61527755 TTTTCTTTCTTCATTC-TATTCTC
1 TTTTCTTT-TTCATTCAT-TTCTC
*
61527778 TGTTTCTTTTTCAATTCATTTTTC
1 T-TTTCTTTTTC-ATTCATTTCTC
61527802 TTTTCTTTT
1 TTTTCTTTT
61527811 ATTTGTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 12 0.41
24 16 0.55
25 1 0.03
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTCTTTTTCATTCATTTCTC
Found at i:61527878 original size:19 final size:20
Alignment explanation
Indices: 61527854--61527892 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
61527844 ATTAATAAGT
61527854 AATACATAT-TTTATTATTA
1 AATACATATATTTATTATTA
61527873 AATACATATATTTATTATTA
1 AATACATATATTTATTATTA
61527893 TTACACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AATACATATATTTATTATTA
Found at i:61527900 original size:21 final size:20
Alignment explanation
Indices: 61527857--61527907 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
61527847 AATAAGTAAT
*
61527857 ACATAT-TTTATTATTAAAT
1 ACATATATTTATTATTAAAC
*
61527876 ACATATATTTATTATTATTAC
1 ACATATATTTATTATTA-AAC
*
61527897 ACATGTATTTA
1 ACATATATTTA
61527908 CCAACACCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 11 0.41
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (20 bp):
ACATATATTTATTATTAAAC
Found at i:61528929 original size:23 final size:25
Alignment explanation
Indices: 61528898--61528951 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
61528888 CATAATTTTG
*
61528898 ATTTATTTAATTT-T-ATATTATTA
1 ATTTTTTTAATTTATAATATTATTA
*
61528921 ATTTTTTTATTTTCATAATATTATTA
1 ATTTTTTTAATTT-ATAATATTATTA
61528947 ATTTT
1 ATTTT
61528952 ATTGTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
25 1 0.04
26 14 0.54
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
ATTTTTTTAATTTATAATATTATTA
Found at i:61528952 original size:23 final size:22
Alignment explanation
Indices: 61528925--61528975 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
61528915 TTATTAATTT
*
61528925 TTTTATTTTCATAATA-TTATTAA
1 TTTTATTGT-ATAATATTTA-TAA
*
61528948 TTTTATTGTATATTATTTATAA
1 TTTTATTGTATAATATTTATAA
61528970 TTTTAT
1 TTTTAT
61528976 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTGTATAATATTTATAA
Found at i:61528974 original size:45 final size:46
Alignment explanation
Indices: 61528887--61528975 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 46
61528877 TTTGGTGAAA
* * * **
61528887 TCATAATTTTGATTTATTTAATTTTATATTATTAATTTTTTTATTT
1 TCATAATATTGATTAATTTAATTGTATATTATTAATAATTTTATTT
* *
61528933 TCATAATATT-ATTAATTTTATTGTATATTATTTATAATTTTAT
1 TCATAATATTGATTAATTTAATTGTATATTATTAATAATTTTAT
61528976 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 27 0.75
46 9 0.25
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (46 bp):
TCATAATATTGATTAATTTAATTGTATATTATTAATAATTTTATTT
Found at i:61536635 original size:17 final size:17
Alignment explanation
Indices: 61536613--61536647 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61536603 AACATAAAAG
61536613 AAAATACAAAAAAATAA
1 AAAATACAAAAAAATAA
* *
61536630 AAAATATAAAAATATAA
1 AAAATACAAAAAAATAA
61536647 A
1 A
61536648 TTTTTACCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATACAAAAAAATAA
Found at i:61536761 original size:11 final size:11
Alignment explanation
Indices: 61536745--61536779 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
61536735 CCCTTCCCCC
61536745 CTCCCTTCTCT
1 CTCCCTTCTCT
61536756 CTCCCTTCTCT
1 CTCCCTTCTCT
61536767 CTTCCC-TCTCT
1 C-TCCCTTCTCT
61536778 CT
1 CT
61536780 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:61549825 original size:69 final size:69
Alignment explanation
Indices: 61549651--61549825 Score: 226
Period size: 70 Copynumber: 2.5 Consensus size: 69
61549641 CTTTCCAAGG
* * *
61549651 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
61549716 TTTT
66 TTTT
* ** * *
61549720 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTT-
61549785 TGTTTT
64 TGTTTT
** *
61549791 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
61549826 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
69 31 0.34
70 56 0.61
71 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
TTTT
Found at i:61550034 original size:72 final size:72
Alignment explanation
Indices: 61549829--61550178 Score: 411
Period size: 72 Copynumber: 4.7 Consensus size: 72
61549819 TAAGCCTTTT
* *
61549829 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
61549893 GTAATTTC
65 GTAATTTC
* **
61549901 AATTTCTGTTGTTAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCT
1 AATTTCTGTT-TT--CAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
61549966 GAGGTAATTTC
62 GAGGTAATTTC
* * * ** * *
61549977 AATTTCTATTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
*
61550042 TATTTTC
66 TAATTTC
*
61550049 AATTTCTGTTTTCAAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACA
1 AATTTCTGTTTTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
*
61550113 TGCTGAGGT-ATTTC
58 CGCTGAGGTAATTTC
*
61550127 AATTTCTGTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
61550179 ATTACACACT
Statistics
Matches: 242, Mismatches: 22, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
71 2 0.01
72 107 0.44
73 5 0.02
75 6 0.02
76 61 0.25
77 35 0.14
78 16 0.07
79 10 0.04
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTC
Found at i:61550156 original size:149 final size:147
Alignment explanation
Indices: 61549829--61550173 Score: 462
Period size: 149 Copynumber: 2.3 Consensus size: 147
61549819 TAAGCCTTTT
* * * *
61549829 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
*
61549894 TAATTTCAATTTCTGTTGTTAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
65 TAATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
61549959 ACACGCTGAGGTAATTTC
130 ACACGCTGAGGTAATTTC
* * * ** *
61549977 AATTTCTATTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
* * **
61550042 TATTTTCAATTTCTGTT-TTCAAAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-
65 TAATTTCAATTTCTGTTGTT--AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
*
61550105 GGTTCACATGCTGAGGT-ATTTC
128 GG---ACACGCTGAGGTAATTTC
61550127 AATTTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AATTTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
61550174 TTCAGATTAC
Statistics
Matches: 170, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
147 6 0.04
148 68 0.40
149 69 0.41
150 16 0.09
151 11 0.06
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (147 bp):
AATTTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT
AATTTCAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
CACGCTGAGGTAATTTC
Found at i:61550694 original size:72 final size:72
Alignment explanation
Indices: 61550577--61550828 Score: 400
Period size: 72 Copynumber: 3.5 Consensus size: 72
61550567 TTTGAAAGAA
*
61550577 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
61550642 TCAAAAT
66 TCAAAAT
*
61550649 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT-TGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
61550713 TTCAAAAT
65 TTCAAAAT
* * *
61550721 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
61550786 TCAAAAAAA
66 TC--AAAAT
61550795 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
61550829 GTTCACATGT
Statistics
Matches: 168, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
71 2 0.01
72 127 0.76
73 5 0.03
74 34 0.20
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Done.