Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 191 of 279
Found at i:62698965 original size:23 final size:23
Alignment explanation
Indices: 62698938--62698989 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
62698928 TTATAAACTT
* *
62698938 TCTTCTTCTTCTTCTTCTTCTTC
1 TCTTCTTCTTCTTCTCCTTCTCC
62698961 TCTTCTTCTTCTTCTCCTTCTCC
1 TCTTCTTCTTCTTCTCCTTCTCC
62698984 TCTTCT
1 TCTTCT
62698990 CCTTTCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (23 bp):
TCTTCTTCTTCTTCTCCTTCTCC
Found at i:62698966 original size:20 final size:20
Alignment explanation
Indices: 62698941--62698989 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
62698931 TAAACTTTCT
*
62698941 TCTTCTTCTTCTTCTTCTTC
1 TCTTCTTCTTCTTCTCCTTC
62698961 TCTTCTTCTTCTTCTCCTTC
1 TCTTCTTCTTCTTCTCCTTC
*
62698981 TCCTCTTCT
1 TCTTCTTCT
62698990 CCTTTCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCTTCTTCTCCTTC
Found at i:62699251 original size:45 final size:45
Alignment explanation
Indices: 62699187--62699277 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 45
62699177 GACCCGACCG
62699187 TATTTTGACCATA-TTTTTTT-AAAAAATATTTAAAAAAATATAAAA
1 TATTTTGACCATATTTTTTTTAAAAAAATA-TT-AAAAAATATAAAA
*
62699232 TATTTTGA-CATGTATTTTTTTAAAAAAATATTAAAAAATATAAAA
1 TATTTTGACCATAT-TTTTTTTAAAAAAATATTAAAAAATATAAAA
62699277 T
1 T
62699278 TATATTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
44 3 0.07
45 22 0.52
46 9 0.21
47 8 0.19
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (45 bp):
TATTTTGACCATATTTTTTTTAAAAAAATATTAAAAAATATAAAA
Found at i:62699296 original size:47 final size:47
Alignment explanation
Indices: 62699187--62699300 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 47
62699177 GACCCGACCG
62699187 TATTTTGACCAT--ATTTTTTT-AAAAAATATTTAAAAAAATATAAAA
1 TATTTTGA-CATAAATTTTTTTAAAAAAATATTTAAAAAAATATAAAA
**
62699232 TATTTTGACATGTATTTTTTTAAAAAAATA-TT-AAAAAATATAAAA
1 TATTTTGACATAAATTTTTTTAAAAAAATATTTAAAAAAATATAAAA
*
62699277 TTATATTTTA-ATAAAATTTTTTTA
1 -TAT-TTTGACAT-AAATTTTTTTA
62699301 TTATTATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
44 3 0.05
45 21 0.35
46 15 0.25
47 21 0.35
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (47 bp):
TATTTTGACATAAATTTTTTTAAAAAAATATTTAAAAAAATATAAAA
Found at i:62699297 original size:46 final size:47
Alignment explanation
Indices: 62699199--62699298 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 47
62699189 TTTTGACCAT
* **
62699199 ATTTTTTTAAAAAATATTTAAAAAAATATAAAATATTTTGACATGTA
1 ATTTTTTAAAAAAATATTTAAAAAAATATAAAATATTTTGACATAAA
* *
62699246 TTTTTTTAAAAAAATA-TT-AAAAAATATAAAATTATATTTTA-ATAAA
1 ATTTTTTAAAAAAATATTTAAAAAAATATAAAA-TAT-TTTGACATAAA
62699292 ATTTTTT
1 ATTTTTT
62699299 TATTATTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
45 13 0.29
46 14 0.31
47 18 0.40
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (47 bp):
ATTTTTTAAAAAAATATTTAAAAAAATATAAAATATTTTGACATAAA
Found at i:62700231 original size:29 final size:29
Alignment explanation
Indices: 62700188--62700243 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
62700178 GAGCATGGAG
* * *
62700188 TTTTATCCCATCTCTCTTATATTTGTAGA
1 TTTTATCCAAGCTCTCCTATATTTGTAGA
62700217 TTTTATCCAAGCTCTCCTATATTTGTA
1 TTTTATCCAAGCTCTCCTATATTTGTA
62700244 AATGACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (29 bp):
TTTTATCCAAGCTCTCCTATATTTGTAGA
Found at i:62708025 original size:3 final size:3
Alignment explanation
Indices: 62708017--62708056 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
62708007 AATAAATCCT
62708017 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62708057 GGCTGGTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:62721008 original size:17 final size:16
Alignment explanation
Indices: 62720978--62721020 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
62720968 GGCGCCAATG
**
62720978 AATAAAATAATAATAA
1 AATAAAATTTTAATAA
62720994 TAATAAAATTTTAATAA
1 -AATAAAATTTTAATAA
*
62721011 AATATAATTT
1 AATAAAATTT
62721021 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAAATTTTAATAA
Found at i:62721276 original size:14 final size:14
Alignment explanation
Indices: 62721254--62721290 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
62721244 GAAAAAAAAG
62721254 AGAGAAAGGAGAAGA
1 AGAG-AAGGAGAAGA
62721269 AGAGAAGGAGAAGA
1 AGAGAAGGAGAAGA
62721283 AGAAGAAG
1 AG-AGAAG
62721291 AAAGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGAAGGAGAAGA
Found at i:62721299 original size:17 final size:17
Alignment explanation
Indices: 62721251--62721300 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
62721241 AGAGAAAAAA
* *
62721251 AAGAGAGAAAGGAGAAG
1 AAGAAAGAAAGAAGAAG
62721268 AAGAGAAGGAGAAGAAGAAG
1 AAGA-AA-GA-AAGAAGAAG
62721288 AAGAAAGAAAGAA
1 AAGAAAGAAAGAA
62721301 AAAAGGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 4 0.14
20 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAGAAGAAG
Found at i:62721487 original size:22 final size:21
Alignment explanation
Indices: 62721460--62721697 Score: 195
Period size: 22 Copynumber: 11.1 Consensus size: 21
62721450 TAGATTAGAA
*
62721460 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
62721482 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
62721503 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
62721521 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
62721542 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
62721564 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
62721585 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
62721604 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
62721626 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
62721651 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
62721675 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
62721696 TT
1 TT
62721698 GTAATTTTGT
Statistics
Matches: 176, Mismatches: 22, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.02
19 30 0.17
20 23 0.13
21 27 0.15
22 61 0.35
23 9 0.05
24 2 0.01
25 4 0.02
26 1 0.01
27 16 0.09
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:62721531 original size:19 final size:19
Alignment explanation
Indices: 62721484--62721540 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
62721474 TTTAAATTTT
* *
62721484 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
62721504 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
62721523 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
62721541 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:62721626 original size:41 final size:40
Alignment explanation
Indices: 62721460--62721700 Score: 186
Period size: 41 Copynumber: 5.7 Consensus size: 40
62721450 TAGATTAGAA
*
62721460 TTTTGTATGAATATTTTAAATTTTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTATAATT
* *
62721503 TTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
* * * *
62721542 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTA-TAATT
62721585 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTAT-AATT
**
62721626 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTG------TA-A-TTTTGTATGAATATTATAA-TT
62721675 TTTTGTATGAATATTGTAATTTTGTA
1 TTTTGTATGAATATTGTAATTTTGTA
62721701 ATTTTGTATG
Statistics
Matches: 162, Mismatches: 14, Indels: 46
0.73 0.06 0.21
Matches are distributed among these distances:
39 22 0.14
40 6 0.04
41 47 0.29
42 34 0.21
43 12 0.07
44 3 0.02
47 2 0.01
48 3 0.02
49 33 0.20
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
Found at i:62721647 original size:30 final size:27
Alignment explanation
Indices: 62721626--62721716 Score: 111
Period size: 27 Copynumber: 3.6 Consensus size: 27
62721616 ATTATAAATT
62721626 TTTTGTATGAATATTGTAATATTATAG
1 TTTTGTATGAATATTGTAATATTATAG
*
62721653 TTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGTAATATTATAG
* * *
62721675 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTATAG
62721702 TTTTGTATGAATATT
1 TTTTGTATGAATATT
62721717 ATATTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
22 16 0.29
23 1 0.02
24 3 0.05
25 4 0.07
26 1 0.02
27 31 0.55
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAG
Found at i:62721662 original size:27 final size:25
Alignment explanation
Indices: 62721594--62721716 Score: 123
Period size: 22 Copynumber: 4.9 Consensus size: 25
62721584 TTTTTGTATG
*
62721594 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
62721621 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
62721643 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
*
62721669 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
62721692 AATTTTGTAATTTTGTATGAATATT
1 AATATT-T-ATTTTGTATGAATATT
62721717 ATATTTTTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
22 34 0.41
23 2 0.02
24 5 0.06
25 6 0.07
26 2 0.02
27 33 0.40
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:62721725 original size:49 final size:49
Alignment explanation
Indices: 62721594--62721726 Score: 205
Period size: 49 Copynumber: 2.7 Consensus size: 49
62721584 TTTTTGTATG
*
62721594 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * **
62721643 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
62721692 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTT
62721727 NGGAGAAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
48 8 0.11
49 66 0.89
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.56
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
Found at i:62722436 original size:22 final size:21
Alignment explanation
Indices: 62722401--62722445 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
62722391 TACCTAATTT
*
62722401 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
62722422 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
62722444 TT
1 TT
62722446 CTTTCTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:62722453 original size:18 final size:18
Alignment explanation
Indices: 62722403--62722454 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
62722393 CCTAATTTTT
62722403 TTCTTC-TT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
62722419 TTCTTTTCTTCTGCTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
62722441 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
62722455 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 8 0.27
19 2 0.07
20 6 0.20
22 11 0.37
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.62
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:62722560 original size:27 final size:27
Alignment explanation
Indices: 62722511--62722610 Score: 141
Period size: 27 Copynumber: 3.7 Consensus size: 27
62722501 AAAATCACAG
*
62722511 CATTGGCGCCTTCTA-ATATGGCACCAC
1 CATTGGCGCCTCCTAGATA-GGCACCAC
62722538 CATTGGCGCCTCCTAGATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
* *
62722565 CATTGGCGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
62722592 CATTGGCGCCTTCC-AGATA
1 CATTGGCGCC-TCCTAGATA
62722611 AGCGCCAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 61 0.91
28 6 0.09
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (27 bp):
CATTGGCGCCTCCTAGATAGGCACCAC
Found at i:62731672 original size:30 final size:31
Alignment explanation
Indices: 62731629--62731699 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
62731619 AATTTTTTTT
* *
62731629 AAAAGAATCAAATTTGACCATCA-ACTTTCA
1 AAAAGAGTTAAATTTGACCATCAGACTTTCA
* *
62731659 AAAAGAGTTAAATTTGACCATCAGTCTTTTA
1 AAAAGAGTTAAATTTGACCATCAGACTTTCA
*
62731690 AAAATAGTTA
1 AAAAGAGTTA
62731700 CTTTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAAGAGTTAAATTTGACCATCAGACTTTCA
Found at i:62733275 original size:31 final size:31
Alignment explanation
Indices: 62733239--62733305 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
62733229 ATTTAGCGGA
62733239 GAGTGACCAAAATAGAAAC-GATCTAAAATGT
1 GAGTGACCAAAATA-AAACTGATCTAAAATGT
*
62733270 GAGTGACCAAAGTAAAACTGATCTAAAATGT
1 GAGTGACCAAAATAAAACTGATCTAAAATGT
*
62733301 TAGTG
1 GAGTG
62733306 GTTAAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (31 bp):
GAGTGACCAAAATAAAACTGATCTAAAATGT
Found at i:62740953 original size:21 final size:22
Alignment explanation
Indices: 62740911--62740959 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
62740901 TAACAGTTAA
62740911 CTAACTATAACTACCATAACTG
1 CTAACTATAACTACCATAACTG
62740933 CTAACTATTAACTA-C-TAACTG
1 CTAACTA-TAACTACCATAACTG
62740954 CTAACT
1 CTAACT
62740960 GTTACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.31
Consensus pattern (22 bp):
CTAACTATAACTACCATAACTG
Found at i:62745457 original size:14 final size:14
Alignment explanation
Indices: 62745434--62745475 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
62745424 GCCATGGCAG
62745434 AAACACAAACAAGA
1 AAACACAAACAAGA
*
62745448 AAACATAAACAAGA
1 AAACACAAACAAGA
*
62745462 AAACACAAAGAAGA
1 AAACACAAACAAGA
62745476 CTAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.71, C:0.17, G:0.10, T:0.02
Consensus pattern (14 bp):
AAACACAAACAAGA
Found at i:62745644 original size:7 final size:7
Alignment explanation
Indices: 62745611--62745660 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
62745601 TTAACAGTTA
62745611 ACTAACT
1 ACTAACT
62745618 A-TAACT
1 ACTAACT
62745624 ACCATAACT
1 A-C-TAACT
*
62745633 GCTAACT
1 ACTAACT
62745640 ACTAACT
1 ACTAACT
62745647 ACTAACT
1 ACTAACT
*
62745654 GCTAACT
1 ACTAACT
62745661 GTCACAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 6 0.16
7 25 0.68
8 1 0.03
9 5 0.14
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (7 bp):
ACTAACT
Found at i:62745654 original size:21 final size:22
Alignment explanation
Indices: 62745612--62745660 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
62745602 TAACAGTTAA
62745612 CTAACTATAACTACCATAACTG
1 CTAACTATAACTACCATAACTG
62745634 CTAACTACTAACTA-C-TAACTG
1 CTAACTA-TAACTACCATAACTG
62745655 CTAACT
1 CTAACT
62745661 GTCACAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.29
Consensus pattern (22 bp):
CTAACTATAACTACCATAACTG
Found at i:62751581 original size:22 final size:22
Alignment explanation
Indices: 62751551--62751596 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62751541 CAAGAGAAAC
* *
62751551 AAGAGAAACC-GAATGAAGCAAA
1 AAGAAAAACCAGAAGGAA-CAAA
62751573 AAGAAAAACCAGAAGGAACAAA
1 AAGAAAAACCAGAAGGAACAAA
62751595 AA
1 AA
62751597 CTCAGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.65, C:0.13, G:0.20, T:0.02
Consensus pattern (22 bp):
AAGAAAAACCAGAAGGAACAAA
Found at i:62752546 original size:22 final size:24
Alignment explanation
Indices: 62752520--62752563 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
62752510 GAAAAATATT
62752520 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
62752542 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
62752564 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:62752677 original size:9 final size:9
Alignment explanation
Indices: 62752663--62752690 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62752653 TTTTGTTACA
62752663 ACAATTAAT
1 ACAATTAAT
62752672 ACAATTAAT
1 ACAATTAAT
62752681 ACAATTAAT
1 ACAATTAAT
62752690 A
1 A
62752691 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:62752744 original size:59 final size:59
Alignment explanation
Indices: 62752672--62752870 Score: 389
Period size: 59 Copynumber: 3.4 Consensus size: 59
62752662 AACAATTAAT
62752672 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
62752731 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
62752790 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
*
62752849 ACAATTAATACAATTAACAATT
1 ACAATTAATACAATTAATAATT
62752871 AATAATTTGA
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 139 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (59 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACA
Found at i:62752902 original size:16 final size:16
Alignment explanation
Indices: 62752881--62752922 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
62752871 AATAATTTGA
*
62752881 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
62752897 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
62752913 TAGTTTTAAT
1 TAATTTTAAT
62752923 TTTATTAAAA
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:62752906 original size:22 final size:22
Alignment explanation
Indices: 62752896--62752945 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
62752886 TTACTAACAA
* * *
62752896 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
62752918 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
62752940 TTAATT
1 TTAATT
62752946 AAAAACGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:62752938 original size:16 final size:17
Alignment explanation
Indices: 62752919--62752950 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62752909 CAATTAGTTT
62752919 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
62752935 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
62752951 CGGGCCGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:62769191 original size:20 final size:20
Alignment explanation
Indices: 62769168--62769211 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
62769158 ATCATACTTA
*
62769168 TATTAATTTTTTATATTATT
1 TATTAATTTTTGATATTATT
* *
62769188 TATTCATTTTTGGTATTATT
1 TATTAATTTTTGATATTATT
62769208 TATT
1 TATT
62769212 TATATCGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTAATTTTTGATATTATT
Found at i:62772850 original size:7 final size:7
Alignment explanation
Indices: 62772840--62772890 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
62772830 AGTATTGAGG
62772840 ATTGAAA
1 ATTGAAA
62772847 ATTGAAA
1 ATTGAAA
62772854 ATTGAAA
1 ATTGAAA
*
62772861 ATTGGAA
1 ATTGAAA
*
62772868 ATTG-AG
1 ATTGAAA
*
62772874 ATTGAAG
1 ATTGAAA
*
62772881 ATTGAGA
1 ATTGAAA
62772888 ATT
1 ATT
62772891 TAGGAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (7 bp):
ATTGAAA
Found at i:62776193 original size:40 final size:40
Alignment explanation
Indices: 62776095--62776357 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
62776085 TCCTCGTTCA
* * * ** *
62776095 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
62776134 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62776174 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
62776214 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
62776254 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
62776294 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
62776334 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
62776358 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:62784143 original size:40 final size:40
Alignment explanation
Indices: 62784045--62784307 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
62784035 TCCTCGTTCA
* * * * *
62784045 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
62784084 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62784124 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
62784164 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
62784204 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
62784244 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
62784284 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
62784308 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:62784316 original size:41 final size:41
Alignment explanation
Indices: 62784239--62784316 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
62784229 TTAGTATCTC
* * *
62784239 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
62784280 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
62784317 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:62787031 original size:18 final size:18
Alignment explanation
Indices: 62787008--62787042 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
62786998 CTTATAGATC
62787008 ATGTTGAAATACTACATA
1 ATGTTGAAATACTACATA
62787026 ATGTTGAAATACTACAT
1 ATGTTGAAATACTACAT
62787043 CTTTTGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
ATGTTGAAATACTACATA
Found at i:62787142 original size:55 final size:55
Alignment explanation
Indices: 62787081--62787188 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
62787071 CAACTTCTTC
* * * *
62787081 TTCTTTTGAATCAATTGTTTATATGTTTAAATTGATTGTTATGTTAGAATACTGT
1 TTCTTTTGAATCAATTATTTATATGTTTAAATCGATTATTATCTTAGAATACTGT
*
62787136 TTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTATCTTAGAATACT
1 TTCTTTTGAATCAATTATTTATATGTTTAAATCGATTATTATCTTAGAATACT
62787189 ACTTTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (55 bp):
TTCTTTTGAATCAATTATTTATATGTTTAAATCGATTATTATCTTAGAATACTGT
Found at i:62787244 original size:36 final size:35
Alignment explanation
Indices: 62787165--62787261 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 35
62787155 TATATGTTTA
* *
62787165 AATCGATTATTATCTTAGAATACTACTTTTTTTTTT
1 AATCGATTGTTATC-TAGAATACTACTTTTTCTTTT
*
62787201 GAATCGATTGTTATGCTAGAATATTA-TTTTTCTTTT
1 -AATCGATTGTTAT-CTAGAATACTACTTTTTCTTTT
*
62787237 AATTCGATTGTTATATTAGAATACT
1 AA-TCGATTGTTAT-CTAGAATACT
62787262 GGTTATTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
35 2 0.04
36 28 0.54
37 21 0.40
38 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.52
Consensus pattern (35 bp):
AATCGATTGTTATCTAGAATACTACTTTTTCTTTT
Found at i:62789163 original size:15 final size:16
Alignment explanation
Indices: 62789137--62789166 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62789127 TCTTAAGCAT
62789137 CTCAGTGAAGATGACA
1 CTCAGTGAAGATGACA
62789153 CTCAG-GAAGATGAC
1 CTCAGTGAAGATGAC
62789167 GATACCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (16 bp):
CTCAGTGAAGATGACA
Found at i:62794606 original size:12 final size:12
Alignment explanation
Indices: 62794589--62794617 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
62794579 ATTTGTGAAC
62794589 ATAAATGATCCA
1 ATAAATGATCCA
62794601 ATAAATGATCCA
1 ATAAATGATCCA
62794613 ATAAA
1 ATAAA
62794618 GATTCTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (12 bp):
ATAAATGATCCA
Found at i:62803966 original size:32 final size:32
Alignment explanation
Indices: 62803926--62803999 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
62803916 CACACATGAT
* *
62803926 GAACAACATAAATGGCGAATAGTCTAATTGGC
1 GAACAACATAAATGGCGAACAGTCTAATTAGC
* *
62803958 GAACAACATAAATGTCGAACAGTTTAATTAGC
1 GAACAACATAAATGGCGAACAGTCTAATTAGC
62803990 GAACACACAT
1 GAACA-ACAT
62804000 GGCGAACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (32 bp):
GAACAACATAAATGGCGAACAGTCTAATTAGC
Found at i:62803976 original size:16 final size:16
Alignment explanation
Indices: 62803926--62804017 Score: 57
Period size: 16 Copynumber: 5.9 Consensus size: 16
62803916 CACACATGAT
62803926 GAACAACATAAATGGC
1 GAACAACATAAATGGC
* * *
62803942 GAATAGTC-TAATTGGC
1 GAACA-ACATAAATGGC
*
62803958 GAACAACATAAATGTC
1 GAACAACATAAATGGC
*** * *
62803974 GAACAGTTTAATTAGC
1 GAACAACATAAATGGC
*
62803990 GAAC-AC--ACATGGC
1 GAACAACATAAATGGC
62804003 GAACAACATAAATGG
1 GAACAACATAAATGG
62804018 AAAACACACA
Statistics
Matches: 52, Mismatches: 19, Indels: 10
0.64 0.23 0.12
Matches are distributed among these distances:
13 8 0.15
14 2 0.04
15 1 0.02
16 40 0.77
17 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (16 bp):
GAACAACATAAATGGC
Found at i:62812662 original size:11 final size:11
Alignment explanation
Indices: 62812646--62812674 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
62812636 GTTGAATTGG
62812646 TGAATTGTTTA
1 TGAATTGTTTA
62812657 TGAATTGTTTA
1 TGAATTGTTTA
62812668 TGAATTG
1 TGAATTG
62812675 GGAATTTTGG
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:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (11 bp):
TGAATTGTTTA
Found at i:62815458 original size:26 final size:25
Alignment explanation
Indices: 62815429--62815486 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
62815419 AAAATATAAA
*
62815429 AATTTGTTTAAAAATTATAAAATTAT
1 AATTT-TTTAAAAATAATAAAATTAT
*
62815455 AATTTATT-AAAATAATAAAATTAT
1 AATTTTTTAAAAATAATAAAATTAT
62815479 -ATTTTTTA
1 AATTTTTTA
62815487 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.21
24 15 0.54
25 2 0.07
26 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTTTTTAAAAATAATAAAATTAT
Found at i:62815469 original size:21 final size:23
Alignment explanation
Indices: 62815440--62815505 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
62815430 ATTTGTTTAA
*
62815440 AAATTATAAAATTATAATTTATT
1 AAATAATAAAATTATAATTTATT
62815463 AAAATAATAAAATTAT-ATTT-TT
1 -AAATAATAAAATTATAATTTATT
* *
62815485 -TATTATAAAAATTATAATTTA
1 AAATAAT-AAAATTATAATTTA
62815506 ATTTCGTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.11
21 8 0.22
22 6 0.17
23 4 0.11
24 14 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATAATAAAATTATAATTTATT
Found at i:62822580 original size:21 final size:22
Alignment explanation
Indices: 62822540--62822580 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
62822530 CAAAAATGAT
62822540 GAAATTATATATAATAAATTTA
1 GAAATTATATATAATAAATTTA
62822562 GAAA-TAT-TATAATTAAATT
1 GAAATTATATATAA-TAAATT
62822581 CAGGTCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
GAAATTATATATAATAAATTTA
Found at i:62824698 original size:31 final size:31
Alignment explanation
Indices: 62824662--62824739 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 31
62824652 AAATAATTTT
* *
62824662 TAATAAATTTATATTTTATATATTTTA-AATA
1 TAATAAATTTAAATATTA-ATATTTTATAATA
* *
62824693 TAATAACTTAAAATATTAATATTTTATAATA
1 TAATAAATTTAAATATTAATATTTTATAATA
62824724 -AA-AAATTTTAAA-ATTA
1 TAATAAA-TTTAAATATTA
62824740 CCAAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 6 0.15
30 15 0.38
31 18 0.46
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
TAATAAATTTAAATATTAATATTTTATAATA
Found at i:62830729 original size:223 final size:223
Alignment explanation
Indices: 62830341--62830786 Score: 883
Period size: 223 Copynumber: 2.0 Consensus size: 223
62830331 AGAGTGATTA
62830341 ATTAATTTGATATATTTGGTGTAGATATGGCGTTGTATGGTGAAAAAGAGTGGTATTTCTTTTCT
1 ATTAATTTGATATATTTGGTGTAGATATGGCGTTGTATGGTGAAAAAGAGTGGTATTTCTTTTCT
62830406 CCAAGGGATCGAAAATACCCAAATGGGTGTCGGCCGAACAGGGCGGCTGGAACCGGATACTGGAA
66 CCAAGGGATCGAAAATACCCAAATGGGTGTCGGCCGAACAGGGCGGCTGGAACCGGATACTGGAA
62830471 AGCGACCGGAGCCGATAAGCCCATCGGAAAGCCCAAGACACTGGGCATAAAAAAAGCACTCGTTT
131 AGCGACCGGAGCCGATAAGCCCATCGGAAAGCCCAAGACACTGGGCATAAAAAAAGCACTCGTTT
62830536 TCTACGCTGGTAAAGCCCCACGCGGTGT
196 TCTACGCTGGTAAAGCCCCACGCGGTGT
62830564 ATTAATTTGATATATTTGGTGTAGATATGGCGTTGTATGGTGAAAAAGAGTGGTATTTCTTTTCT
1 ATTAATTTGATATATTTGGTGTAGATATGGCGTTGTATGGTGAAAAAGAGTGGTATTTCTTTTCT
62830629 CCAAGGGATCGAAAATACCCAAATGGGTGTCGGCCGAACAGGGCGGCTGGAACCGGATACTGGAA
66 CCAAGGGATCGAAAATACCCAAATGGGTGTCGGCCGAACAGGGCGGCTGGAACCGGATACTGGAA
*
62830694 AGCGACTGGAGCCGATAAGCCCATCGGAAAGCCCAAGACACTGGGCATAAAAAAAGCACTCGTTT
131 AGCGACCGGAGCCGATAAGCCCATCGGAAAGCCCAAGACACTGGGCATAAAAAAAGCACTCGTTT
62830759 TCTACGCTGGTAAAGCCCCACGCGGTGT
196 TCTACGCTGGTAAAGCCCCACGCGGTGT
62830787 CAAAACCAAC
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 222 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (223 bp):
ATTAATTTGATATATTTGGTGTAGATATGGCGTTGTATGGTGAAAAAGAGTGGTATTTCTTTTCT
CCAAGGGATCGAAAATACCCAAATGGGTGTCGGCCGAACAGGGCGGCTGGAACCGGATACTGGAA
AGCGACCGGAGCCGATAAGCCCATCGGAAAGCCCAAGACACTGGGCATAAAAAAAGCACTCGTTT
TCTACGCTGGTAAAGCCCCACGCGGTGT
Found at i:62831988 original size:19 final size:19
Alignment explanation
Indices: 62831942--62831989 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
62831932 GTATATATTT
62831942 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
62831960 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
62831979 TAAGTTTTATT
1 TAAATTTTATT
62831990 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:62835955 original size:10 final size:10
Alignment explanation
Indices: 62835888--62835956 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
62835878 ACATTAAACA
*
62835888 AAATAGTTAT
1 AAATAATTAT
62835898 AAATAATCTAT
1 AAATAAT-TAT
*
62835909 ATATAATATATT
1 AAATAAT-TA-T
* *
62835921 AAAAAATTTT
1 AAATAATTAT
*
62835931 AAA-AAATAT
1 AAATAATTAT
62835940 ATAATAATTAT
1 A-AATAATTAT
62835951 AAATAA
1 AAATAA
62835957 CAATTTAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 5 0.11
10 17 0.37
11 18 0.39
12 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
AAATAATTAT
Found at i:62836009 original size:23 final size:21
Alignment explanation
Indices: 62835974--62836021 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
62835964 ATTGTTGATA
62835974 ATTTAAAATATATGTAATAGTTT
1 ATTTAAAATATAT-TAAT-GTTT
*
62835997 ATTT-AAATAATATTTATGTTT
1 ATTTAAAAT-ATATTAATGTTT
62836018 ATTT
1 ATTT
62836022 TCAATCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
ATTTAAAATATATTAATGTTT
Found at i:62841277 original size:19 final size:19
Alignment explanation
Indices: 62841253--62841290 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62841243 TGAAAAAATG
*
62841253 TTTGCTTGTATATAAATAA
1 TTTGCTTGTACATAAATAA
62841272 TTTGCTTGTACATAAATAA
1 TTTGCTTGTACATAAATAA
62841291 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCTTGTACATAAATAA
Found at i:62841290 original size:4 final size:4
Alignment explanation
Indices: 62841283--62841320 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
62841273 TTGCTTGTAC
*
62841283 ATAA ATAA ATAA ATAA ATAAA ATGA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A
62841321 GACTCAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:62841310 original size:17 final size:17
Alignment explanation
Indices: 62841285--62841320 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
62841275 GCTTGTACAT
62841285 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
*
62841302 AAATGAATAAATAAATA
1 AAATAAATAAATAAATA
62841319 AA
1 AA
62841321 GACTCAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:62842042 original size:25 final size:23
Alignment explanation
Indices: 62841987--62842042 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
62841977 TCTCGGCTAG
62841987 AGAAGAAAAGAAAGGAGAAAAGA
1 AGAAGAAAAGAAAGGAGAAAAGA
* * *
62842010 AAATAGAAGAAGAGAGGAGAAGAGA
1 AGA-AGAA-AAGAAAGGAGAAAAGA
62842035 AGGAAGAA
1 A-GAAGAA
62842043 TTCGGCACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 4 0.15
25 19 0.73
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (23 bp):
AGAAGAAAAGAAAGGAGAAAAGA
Found at i:62843733 original size:28 final size:28
Alignment explanation
Indices: 62843702--62843839 Score: 127
Period size: 28 Copynumber: 4.9 Consensus size: 28
62843692 TAATTATATG
** *
62843702 TGGCACTTAACGTGCGAAGTATCGGGGA
1 TGGCACTTAGTGTGCGAAGTATCGAGGA
* * *
62843730 TGGCACTTAGTGTGCGATA-CATCCAGAA
1 TGGCACTTAGTGTGCGA-AGTATCGAGGA
*
62843758 TGGCACTTAGTGTGCGAAGTAACGAGGA
1 TGGCACTTAGTGTGCGAAGTATCGAGGA
* ** * *
62843786 TGGCACATAGTGTGCGAAACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTATCGAGGA
*
62843814 CGGCACTTAGTGTGC-AAGGTATCGAG
1 TGGCACTTAGTGTGCGAA-GTATCGAG
62843840 TATGACATCT
Statistics
Matches: 86, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
27 3 0.03
28 82 0.95
29 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAAGTATCGAGGA
Found at i:62843788 original size:56 final size:56
Alignment explanation
Indices: 62843702--62843863 Score: 202
Period size: 56 Copynumber: 2.9 Consensus size: 56
62843692 TAATTATATG
** *
62843702 TGGCACTTAACGTGCGAAGTATCGGGGATGGCACTTAGTGTGCGATACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATCCAGAA
* * *
62843758 TGGCACTTAGTGTGCGAAGTAACGAGGATGGCACATAGTGTGCGAAACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATCCAGAA
* * * *
62843814 CGGCACTTAGTGTGC-AAGGTATCGAGTATGACA-TCTAGTGTGTGATACAT
1 TGGCACTTAGTGTGCGAA-GTATCGAGGATGGCACT-TAGTGTGCGATACAT
62843864 TGAGTATTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
55 2 0.02
56 89 0.98
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (56 bp):
TGGCACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGATACATCCAGAA
Found at i:62843942 original size:32 final size:32
Alignment explanation
Indices: 62843906--62843979 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
62843896 TAAGTATGAG
*
62843906 ATTGGTACGAGATGATACAGGTATCTACGGAA
1 ATTGGTACAAGATGATACAGGTATCTACGGAA
* * * *
62843938 ATTGGTACAATATGGTATAGGTATGTACGGAA
1 ATTGGTACAAGATGATACAGGTATCTACGGAA
*
62843970 ATTAGTACAA
1 ATTGGTACAA
62843980 TATAGTACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (32 bp):
ATTGGTACAAGATGATACAGGTATCTACGGAA
Found at i:62843980 original size:32 final size:32
Alignment explanation
Indices: 62843921--62844004 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
62843911 TACGAGATGA
* * *
62843921 TACAGGTATCTACGGAAATTGGTACAATATGG
1 TACAGGTATGTACGGAAATTAGTACAATATAG
*
62843953 TATAGGTATGTACGGAAATTAGTACAATATAG
1 TACAGGTATGTACGGAAATTAGTACAATATAG
* *
62843985 TACATGTATGTACGAAAATT
1 TACAGGTATGTACGGAAATT
62844005 CAATTGAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (32 bp):
TACAGGTATGTACGGAAATTAGTACAATATAG
Found at i:62845413 original size:17 final size:17
Alignment explanation
Indices: 62845391--62845424 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62845381 AGAGTTATCG
62845391 CTCTTTCCTACAGTTTA
1 CTCTTTCCTACAGTTTA
62845408 CTCTTTCCTACAGTTTA
1 CTCTTTCCTACAGTTTA
62845425 GAGTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (17 bp):
CTCTTTCCTACAGTTTA
Found at i:62846690 original size:15 final size:15
Alignment explanation
Indices: 62846666--62846705 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
62846656 ATGCTTTCCA
62846666 TAACATGTATTCATT
1 TAACATGTATTCATT
*
62846681 TAATATGTATTCATT
1 TAACATGTATTCATT
62846696 TAACATGTAT
1 TAACATGTAT
62846706 AGACCATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (15 bp):
TAACATGTATTCATT
Found at i:62855038 original size:14 final size:14
Alignment explanation
Indices: 62855019--62855047 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62855009 GTTTCCCCTT
62855019 TCTTAATCAAACAA
1 TCTTAATCAAACAA
62855033 TCTTAATCAAACAA
1 TCTTAATCAAACAA
62855047 T
1 T
62855048 ATATAGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TCTTAATCAAACAA
Found at i:62857237 original size:27 final size:27
Alignment explanation
Indices: 62857207--62857489 Score: 138
Period size: 27 Copynumber: 10.4 Consensus size: 27
62857197 ATTACCAAAG
* * * *
62857207 TACCCCCGATTTACAGAATTTCCGTTC
1 TACCCTCGATTTACAAAATTACCGTTT
* * *
62857234 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
62857261 TACCTTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*****
62857288 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACCGTTT
* ** *****
62857315 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTACAAAATTACCGTTT
* ** * ***
62857342 TACCCCCTGATTTGTAAAATTACTGAAA
1 TACCCTC-GATTTACAAAATTACCGTTT
****
62857370 TACCCTCGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TACAAAATTACCGTTT
* * * *
62857398 TACCCTCGATTTATAGAATCACTGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* **
62857425 TACCCTCGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
62857452 TACCCTTGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
62857479 TACCCTCGATT
1 TACCCTCGATT
62857490 GTGAAATTAT
Statistics
Matches: 210, Mismatches: 41, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
26 3 0.01
27 159 0.76
28 47 0.22
29 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:62857357 original size:28 final size:28
Alignment explanation
Indices: 62857302--62857402 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
62857292 CTCGATTTAC
*
62857302 AAAATTACTAAAATA-CCCCTGGTTTGT
1 AAAATTACTAAAATACCCCCTGATTTGT
62857329 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCCCTGATTTGT
* * *
62857357 AAAATTACTGAAATACCCTC-GACTTGT
1 AAAATTACTAAAATACCCCCTGATTTGT
* *
62857384 AAAAATTACCAAAGTACCC
1 -AAAATTACTAAAATACCC
62857403 TCGATTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 21 0.32
28 44 0.68
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAATTACTAAAATACCCCCTGATTTGT
Found at i:62857624 original size:27 final size:27
Alignment explanation
Indices: 62857302--62857726 Score: 143
Period size: 27 Copynumber: 15.7 Consensus size: 27
62857292 CTCGATTTAC
*
62857302 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACTAAAATACCCCTGATTTGT
62857329 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATA-CCCCTGATTTGT
* *
62857357 AAAATTACTGAAATA-CCCTCGACTTGT
1 AAAATTACTAAAATACCCCT-GATTTGT
* * *
62857384 AAAAATTACCAAAGTA-CCCTCGATTTAT
1 -AAAATTACTAAAATACCCCT-GATTTGT
* * **** **
62857412 AGAATCACTGTTTTA-CCCTCGATTTAC
1 AAAATTACTAAAATACCCCT-GATTTGT
* * **** * *
62857439 AGAATTATTGTTTTACCCTTGATTTAT
1 AAAATTACTAAAATACCCCTGATTTGT
*****
62857466 AAAATTACCGTTTTA-CCCTCGA-TTGT
1 AAAATTACTAAAATACCCCT-GATTTGT
* * * **
62857492 GAAATTATTGAAATACCCCT-ATAGGGT
1 AAAATTACTAAAATACCCCTGAT-TTGT
* * *
62857519 AGAATTACCAAAACACCCCT-AGTTTGT
1 AAAATTACTAAAATACCCCTGA-TTTGT
* * *
62857546 AAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACTAAAATACCCCTGATTTGT
* *
62857573 AAAATTACTGAAATA-CCCTCAATTTGT
1 AAAATTACTAAAATACCCCT-GATTTGT
* **
62857600 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTAAAATACCCCTGATTTGT
* * *
62857627 AAAGTTAC-AGAAATA-CCTTGACTTTCT
1 AAAATTACTA-AAATACCCCTGA-TTTGT
* ** * **
62857654 AAAAATTA-TGGAAATACCATTGGTTTAC
1 -AAAATTACT-AAAATACCCCTGATTTGT
* *
62857682 AAAATTACTGAAATACCCTTGATTTGT
1 AAAATTACTAAAATACCCCTGATTTGT
* * *
62857709 AGATTTACCAAAATACCC
1 AAAATTACTAAAATACCC
62857727 TTATAAGATG
Statistics
Matches: 306, Mismatches: 73, Indels: 38
0.73 0.18 0.09
Matches are distributed among these distances:
25 1 0.00
26 28 0.09
27 203 0.66
28 70 0.23
29 4 0.01
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGATTTGT
Found at i:62857640 original size:54 final size:54
Alignment explanation
Indices: 62857541--62857725 Score: 199
Period size: 54 Copynumber: 3.4 Consensus size: 54
62857531 ACACCCCTAG
**
62857541 TTTGTAAAATTACCAAAATACCACTGGTTTGTAAAATTACTGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
* * * * * * *
62857595 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAATACCTTGAC
1 TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
* *** * **
62857649 TTTCTAAAAATTATGGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGA
1 TTTGT-AAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
* *
62857704 TTTGTAGATTTACCAAAATACC
1 TTTGTAAAATTACCAAAATACC
62857726 CTTATAAGAT
Statistics
Matches: 102, Mismatches: 28, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
54 61 0.60
55 41 0.40
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
Found at i:62857781 original size:27 final size:27
Alignment explanation
Indices: 62857747--62857819 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
62857737 AAATGACTAA
*
62857747 AATACCCCTATAGGGTAAAGAGACAGT
1 AATACCCCTGTAGGGTAAAGAGACAGT
* * *
62857774 AA-AGCCCCTGTAGGATAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAGAGACAGT
*
62857801 AATACCCCTGTATGGTAAA
1 AATACCCCTGTAGGGTAAA
62857820 ATGACGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAGAGACAGT
Found at i:62858556 original size:20 final size:20
Alignment explanation
Indices: 62858531--62858597 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
62858521 GATATGATAT
*
62858531 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
* *
62858551 ACATGATATGTATAAAATAC
1 ACATGATATGTATGAAATGC
62858571 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
62858591 ACATGAT
1 ACATGAT
62858598 GTATTCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:62858676 original size:26 final size:26
Alignment explanation
Indices: 62858647--62858777 Score: 180
Period size: 26 Copynumber: 5.2 Consensus size: 26
62858637 GAGGAAGTGC
62858647 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
62858673 AAAAGGGCATATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
62858699 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
62858725 AAAAGGGCTT-TGCCCAAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
62858750 AAAAGGGCTT-TTCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
62858773 AAAAG
1 AAAAG
62858778 ATGCTAGGCC
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.05
24 4 0.04
25 29 0.31
26 56 0.60
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:62858974 original size:42 final size:42
Alignment explanation
Indices: 62858915--62859006 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
62858905 TAGTCTCCCC
* ** *
62858915 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
62858957 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
62858999 AAATGGGC
1 AAATGGGC
62859007 CTATGGGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:62859068 original size:31 final size:31
Alignment explanation
Indices: 62859030--62859108 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
62859020 CGTTTACAGT
62859030 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
62859061 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
62859092 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
62859109 AACCGTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:62867772 original size:25 final size:23
Alignment explanation
Indices: 62867717--62867772 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
62867707 AATTATAAAG
62867717 ATTTTTTA-AAAAATTATTTTCA
1 ATTTTTTAGAAAAATTATTTTCA
*
62867739 ATTTGTTAGAAAATATTTATTTT-A
1 ATTTTTTAGAAAA-A-TTATTTTCA
62867763 ATGTTTTTAG
1 AT-TTTTTAG
62867773 TGTTTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 4 0.14
25 13 0.46
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (23 bp):
ATTTTTTAGAAAAATTATTTTCA
Found at i:62868657 original size:22 final size:22
Alignment explanation
Indices: 62868629--62868671 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62868619 CTAATAAATA
*
62868629 ATTAAAATTTTATTTTATTTAT
1 ATTAAAATTTTATTGTATTTAT
62868651 ATTAAAATTTTATTGTATTTA
1 ATTAAAATTTTATTGTATTTA
62868672 AATATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTAAAATTTTATTGTATTTAT
Found at i:62868662 original size:17 final size:18
Alignment explanation
Indices: 62868639--62868678 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
62868629 ATTAAAATTT
62868639 TATTTTATT-TATATTAAA
1 TATTTTATTGTAT-TTAAA
62868657 -ATTTTATTGTATTTAAA
1 TATTTTATTGTATTTAAA
62868674 TATTT
1 TATTT
62868679 ATAATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTTATTGTATTTAAA
Found at i:62871283 original size:21 final size:21
Alignment explanation
Indices: 62871259--62871299 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62871249 TTTTTTCCTG
62871259 TAAAAATTCAAGTTCTTCTCA
1 TAAAAATTCAAGTTCTTCTCA
* *
62871280 TAAAAGTTCAAGTTTTTCTC
1 TAAAAATTCAAGTTCTTCTC
62871300 TTGGGAAAAA
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:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TAAAAATTCAAGTTCTTCTCA
Found at i:62872211 original size:29 final size:29
Alignment explanation
Indices: 62872156--62872213 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
62872146 CATTCAATTA
*
62872156 ATTTTTAATTTTTACAAATTTTAAAAAAT
1 ATTTTTAATTATTACAAATTTTAAAAAAT
*
62872185 ATTTTTAATTATTA-AAATTATTTAAAAAT
1 ATTTTTAATTATTACAAATT-TTAAAAAAT
62872214 TATATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTTTAATTATTACAAATTTTAAAAAAT
Found at i:62872230 original size:29 final size:29
Alignment explanation
Indices: 62872171--62872235 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
62872161 TAATTTTTAC
* *
62872171 AAAT-TTTAAAAAATATTTTTAATTATTAA
1 AAATATTTAAAAAATATTATTAATTA-GAA
* *
62872200 AATTATTTAAAAATTA-TATTAATTAGAA
1 AAATATTTAAAAAATATTATTAATTAGAA
62872228 AAATATTT
1 AAATATTT
62872236 TTTAACATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 9 0.30
29 11 0.37
30 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
AAATATTTAAAAAATATTATTAATTAGAA
Found at i:62872825 original size:30 final size:32
Alignment explanation
Indices: 62872789--62872856 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 32
62872779 ACACTTTATA
*
62872789 TTTAAAAATAATAATAAT-T-TAATTTAATTT
1 TTTAAAAATAATAAAAATATATAATTTAATTT
*
62872819 TTTAAAAATTATAAAAATATAAATAATTTAATTT
1 TTTAAAAATAATAAAAATAT--ATAATTTAATTT
62872853 TTTA
1 TTTA
62872857 CCACTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 16 0.50
31 1 0.03
34 15 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTAAAAATAATAAAAATATATAATTTAATTT
Found at i:62879707 original size:20 final size:21
Alignment explanation
Indices: 62879658--62879708 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
62879648 TCTCCTCTTG
* * *
62879658 AATTATGTTATTTAAGTTTTT
1 AATTATATTATTTAAGATTTA
62879679 AATTATATTATTTAA-ATTTA
1 AATTATATTATTTAAGATTTA
*
62879699 AATTTTATTA
1 AATTATATTA
62879709 ATTATGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTATATTATTTAAGATTTA
Found at i:62889926 original size:20 final size:20
Alignment explanation
Indices: 62889885--62889926 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
62889875 TTTTAAAAAA
* *
62889885 TTAAAAACTATAAAAGTTAT
1 TTAAAAACTATAAAAATAAT
*
62889905 TTAAAAATTATAAAAATAAT
1 TTAAAAACTATAAAAATAAT
62889925 TT
1 TT
62889927 TTAGTATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAAACTATAAAAATAAT
Found at i:62894252 original size:122 final size:124
Alignment explanation
Indices: 62894120--62894371 Score: 364
Period size: 122 Copynumber: 2.0 Consensus size: 124
62894110 TGTAAAAAAA
*
62894120 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACCAT
1 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
* * * *
62894185 GTATAAA-TAGTGCTAAAGTTGCTATTATGCTAATTTTAAAAGTTACCATGTCA-ACAT
66 ATATAAATTAATGCTAAAGTTGCTATTATGCCAATTTTAAAAATTACCATGTCAGACAT
* * * * *
62894242 TTAAATTACAAATGTGTAAATGTTGAAGGTTAGATTTTTTTAAATCAAGAATAATTTAACACAAT
1 TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
* *
62894307 ATATAAATGTTAATGTTAAAGTTGCTATTATGCCAATTTTAAAAATTACCATGTCAGTCAT
66 ATATAAA--TTAATGCTAAAGTTGCTATTATGCCAATTTTAAAAATTACCATGTCAGACAT
62894368 TTAA
1 TTAA
62894372 TGGCGGGATG
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 65 0.57
125 42 0.37
126 7 0.06
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (124 bp):
TTAAATTACAAATGTGTAAATGTTGAAAGTTAAATTTTTTAAAATCAAAAATAAATTAACACAAT
ATATAAATTAATGCTAAAGTTGCTATTATGCCAATTTTAAAAATTACCATGTCAGACAT
Found at i:62903677 original size:23 final size:24
Alignment explanation
Indices: 62903647--62903697 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
62903637 TAATTAGATT
**
62903647 AAAAAAATTAAATTTTA-AAAATA
1 AAAAAAATTAAATTCCACAAAATA
*
62903670 AAAAAAATTAGATTCCACAAAATA
1 AAAAAAATTAAATTCCACAAAATA
62903694 AAAA
1 AAAA
62903698 TAAAAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAAAATTAAATTCCACAAAATA
Found at i:62911528 original size:47 final size:46
Alignment explanation
Indices: 62911449--62911543 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 46
62911439 CAAAACTTTG
62911449 AAGAGAAATATTCAATTTGTATTTCAACCTTATCTCATCTGTGTAC
1 AAGAGAAATATTCAATTTGTATTTCAACCTTATCTCATCTGTGTAC
62911495 AAGAGAAATATTCAATTTTGTATTTCAACCTTATCTCATCTGTGTAC
1 AAGAGAAATATTCAA-TTTGTATTTCAACCTTATCTCATCTGTGTAC
62911542 AA
1 AA
62911544 TGACTTGATA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 15 0.31
47 33 0.69
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (46 bp):
AAGAGAAATATTCAATTTGTATTTCAACCTTATCTCATCTGTGTAC
Found at i:62911699 original size:16 final size:16
Alignment explanation
Indices: 62911678--62911708 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62911668 TTTTAAATGT
62911678 TTTTAAAAATAATATA
1 TTTTAAAAATAATATA
*
62911694 TTTTAAAAATTATAT
1 TTTTAAAAATAATAT
62911709 TAATATTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATAATATA
Found at i:62914358 original size:18 final size:18
Alignment explanation
Indices: 62914324--62914360 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
62914314 GGAAACTGGG
* *
62914324 AATGAAGAGGGAGCTGAA
1 AATGAAGAGGAACCTGAA
62914342 AATGAAGAGGAACCTGAA
1 AATGAAGAGGAACCTGAA
62914360 A
1 A
62914361 CTGATGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.32, T:0.11
Consensus pattern (18 bp):
AATGAAGAGGAACCTGAA
Found at i:62921202 original size:20 final size:20
Alignment explanation
Indices: 62921179--62921217 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62921169 AAATGGGTCA
*
62921179 TAGATATGTATGCTAGAAAT
1 TAGAAATGTATGCTAGAAAT
* *
62921199 TAGAAATTTATGTTAGAAA
1 TAGAAATGTATGCTAGAAA
62921218 ATGAAAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (20 bp):
TAGAAATGTATGCTAGAAAT
Found at i:62932308 original size:13 final size:13
Alignment explanation
Indices: 62932290--62932321 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
62932280 AAATATTTTT
62932290 CTATAAAAAATTA
1 CTATAAAAAATTA
62932303 CTAT--AAAATTA
1 CTATAAAAAATTA
62932314 CTATAAAA
1 CTATAAAA
62932322 TTTCTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (13 bp):
CTATAAAAAATTA
Found at i:62932312 original size:11 final size:11
Alignment explanation
Indices: 62932296--62932323 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
62932286 TTTTCTATAA
62932296 AAAATTACTAT
1 AAAATTACTAT
62932307 AAAATTACTAT
1 AAAATTACTAT
62932318 AAAATT
1 AAAATT
62932324 TCTTTATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATTACTAT
Found at i:62934673 original size:40 final size:40
Alignment explanation
Indices: 62934618--62934781 Score: 190
Period size: 40 Copynumber: 4.1 Consensus size: 40
62934608 TGAGCGTTAC
* *
62934618 CTACTGAAATGTATGCACTATTGAGCCATACCTACTAAAT
1 CTACTAAAATGTATGCACTATTGAGCCATACCTACTGAAT
*
62934658 CTACTAAAATGTATGCACTATTGAGCCATACCTACTGATT
1 CTACTAAAATGTATGCACTATTGAGCCATACCTACTGAAT
* * ** *
62934698 CTGCTGAAA-GTATGTTCTATCGAGCCATACCTA-TCGAAT
1 CTACTAAAATGTATGCACTATTGAGCCATACCTACT-GAAT
* * *
62934737 TTACTAAAATGTATGCGCT-TTCGAGCCATACCTACTGATT
1 CTACTAAAATGTATGCACTATT-GAGCCATACCTACTGAAT
62934777 CTACT
1 CTACT
62934782 GAAAGTTGCT
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 31 0.30
40 70 0.68
41 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (40 bp):
CTACTAAAATGTATGCACTATTGAGCCATACCTACTGAAT
Found at i:62934730 original size:79 final size:79
Alignment explanation
Indices: 62934618--62934787 Score: 236
Period size: 79 Copynumber: 2.1 Consensus size: 79
62934608 TGAGCGTTAC
*
62934618 CTACTGAAATGTATGCACTATTGAGCCATACCTA-CTAAATCTACTAAAATGTATGCACTATT-G
1 CTACTGAAA-GTATGCACTATCGAGCCATACCTATC-AAATCTACTAAAATGTATGCACT-TTCG
62934681 AGCCATACCTACTGATT
63 AGCCATACCTACTGATT
* ** * * *
62934698 CTGCTGAAAGTATGTTCTATCGAGCCATACCTATCGAATTTACTAAAATGTATGCGCTTTCGAGC
1 CTACTGAAAGTATGCACTATCGAGCCATACCTATCAAATCTACTAAAATGTATGCACTTTCGAGC
62934763 CATACCTACTGATT
66 CATACCTACTGATT
62934777 CTACTGAAAGT
1 CTACTGAAAGT
62934788 TGCTCAAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.03
79 69 0.86
80 9 0.11
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (79 bp):
CTACTGAAAGTATGCACTATCGAGCCATACCTATCAAATCTACTAAAATGTATGCACTTTCGAGC
CATACCTACTGATT
Found at i:62936687 original size:27 final size:27
Alignment explanation
Indices: 62936652--62936774 Score: 167
Period size: 27 Copynumber: 4.6 Consensus size: 27
62936642 ACATAGGGAT
* * *
62936652 AAAACAGTCATCTTACCATAAAAGGGC
1 AAAATAGTCATTTTACCACAAAAGGGC
62936679 AAAATAGTCATTTTACCACAAAAGGGC
1 AAAATAGTCATTTTACCACAAAAGGGC
*
62936706 AAAATAGTCATTTTACC-CTATAAGGGC
1 AAAATAGTCATTTTACCAC-AAAAGGGC
* *
62936733 AAAATAGTCATTTTACCCCATAAGGGC
1 AAAATAGTCATTTTACCACAAAAGGGC
*
62936760 GAAATAGTCATTTTA
1 AAAATAGTCATTTTA
62936775 TTAATTAGGG
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
26 1 0.01
27 87 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
AAAATAGTCATTTTACCACAAAAGGGC
Found at i:62942240 original size:13 final size:13
Alignment explanation
Indices: 62942222--62942249 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
62942212 TGGTCCAATG
62942222 GAAAATTGGACTT
1 GAAAATTGGACTT
62942235 GAAAATTGGACTT
1 GAAAATTGGACTT
62942248 GA
1 GA
62942250 GATTGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (13 bp):
GAAAATTGGACTT
Found at i:62942607 original size:19 final size:19
Alignment explanation
Indices: 62942583--62942647 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
62942573 GTTTCAAAAA
*
62942583 TAATATTATTTTAATAGTT
1 TAATATTAATTTAATAGTT
62942602 TAATATTAATTTAA-A-TT
1 TAATATTAATTTAATAGTT
**
62942619 TAATACTTAGCTTAATAGTT
1 TAATA-TTAATTTAATAGTT
62942639 TAATATTAA
1 TAATATTAA
62942648 AATGATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 17 0.44
20 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATATTAATTTAATAGTT
Found at i:62942735 original size:12 final size:12
Alignment explanation
Indices: 62942718--62942742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62942708 TTTTAATAAG
62942718 ATTTAATATTAA
1 ATTTAATATTAA
62942730 ATTTAATATTAA
1 ATTTAATATTAA
62942742 A
1 A
62942743 GTGGTTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:62945279 original size:8 final size:9
Alignment explanation
Indices: 62945257--62945353 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 9
62945247 CCAGTTCAAG
*
62945257 TTTTTATGAT
1 TTTTTAT-AA
62945267 TTTTTATAA
1 TTTTTATAA
62945276 TTTTTATAA
1 TTTTTATAA
* *
62945285 GTTTATATTAG
1 -TTTTTA-TAA
* *
62945296 TTTTAATAC
1 TTTTTATAA
62945305 TTTTT-TGATA
1 TTTTTAT-A-A
*
62945315 TTTTTATGA
1 TTTTTATAA
62945324 TTTTTATAGAA
1 TTTTTAT--AA
*
62945335 TTTTAATACA
1 TTTTTATA-A
62945345 TTTTTATAA
1 TTTTTATAA
62945354 AATTTTAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
8 1 0.01
9 27 0.40
10 29 0.43
11 10 0.15
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:62945309 original size:39 final size:38
Alignment explanation
Indices: 62945266--62945353 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
62945256 GTTTTTATGA
62945266 TTTTTTATAATTTTTATAAGTTTATATTAG-TTTTAATAC
1 TTTTTTATAATTTTTATAA-TTTATA-TAGATTTTAATAC
* *
62945305 TTTTTTGAT-ATTTTTATGATTTTTATAGAATTTTAATAC
1 TTTTTT-ATAATTTTTATAATTTATATAG-ATTTTAATAC
*
62945344 ATTTTTATAA
1 TTTTTTATAA
62945354 AATTTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 3 0.07
38 7 0.17
39 30 0.71
40 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (38 bp):
TTTTTTATAATTTTTATAATTTATATAGATTTTAATAC
Found at i:62945626 original size:28 final size:26
Alignment explanation
Indices: 62945592--62945666 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 26
62945582 ATTAAGAGAG
*
62945592 AAACTTACTTAATTATTTTAATTAACA
1 AAACTTAATTAATTATTTTAATTAA-A
*
62945619 AAGACTTAATTAATGTAAATTTAATTAAA
1 AA-ACTTAATTAAT-T-ATTTTAATTAAA
*
62945648 AAACTTAATTATTTATTTT
1 AAACTTAATTAATTATTTT
62945667 TATATTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 20 0.49
29 4 0.10
30 10 0.24
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (26 bp):
AAACTTAATTAATTATTTTAATTAAA
Found at i:62946131 original size:24 final size:24
Alignment explanation
Indices: 62946090--62946159 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
62946080 TGATTATTAA
62946090 TATTTAAATTTAGT-TTTAATTTTT
1 TATTT-AATTTAGTATTTAATTTTT
*
62946114 TATTTAATTTAGTATTTAA-GTTT
1 TATTTAATTTAGTATTTAATTTTT
*
62946137 AATTTTAATGTT-GTATTTAATTT
1 TA-TTTAAT-TTAGTATTTAATTT
62946160 ATCCTAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 12 0.31
24 24 0.62
25 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TATTTAATTTAGTATTTAATTTTT
Found at i:62946143 original size:36 final size:36
Alignment explanation
Indices: 62946090--62946160 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
62946080 TGATTATTAA
* * *
62946090 TATTTAAATTTAGTTTTAATTTTTTATTTAATTTAG
1 TATTTAAATTTAATTTTAATGTTGTATTTAATTTAG
*
62946126 TATTTAAGTTTAATTTTAATGTTGTATTTAATTTA
1 TATTTAAATTTAATTTTAATGTTGTATTTAATTTA
62946161 TCCTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (36 bp):
TATTTAAATTTAATTTTAATGTTGTATTTAATTTAG
Found at i:62963127 original size:12 final size:13
Alignment explanation
Indices: 62963110--62963146 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
62963100 GAACCGGACA
62963110 CGAACCGAA-CTC
1 CGAACCGAAGCTC
62963122 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
62963134 CGAACCGTAGCTC
1 CGAACCGAAGCTC
62963147 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:62984005 original size:206 final size:206
Alignment explanation
Indices: 62983638--62984028 Score: 590
Period size: 206 Copynumber: 1.9 Consensus size: 206
62983628 TAAAACCTAC
* * * * * *
62983638 AATCTAAAAGTCCTAAAATCTAATTTCTAGAAATTTAATCGAAAAATGCCTACTATTTAGATTCA
1 AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAAAATGCATACTATTTAAATCCA
* * * *
62983703 AAATCCTAAAATGAACTAATTTAAAACCTAATATAAAAAAAATTAAAGTATGAAATTCAAAAATA
66 AAATCCTAAAATGAACTAATTTAAAACCGAAGATAAAAAAAATTAAAGGATGAAATTCAAAAAGA
* * *
62983768 TGCTAACATACTATAAAGTACACAGTCCTAAAGAGAAAACCTT-AAATAATCCTAATACTTAATT
131 AGCTAACATACTATAAAATACACAATCCTAAAGAGAAAA-CTTCAAATAATCCTAATACTTAATT
62983832 TTTTTAAAAAAT
195 TTTTTAAAAAAT
* *
62983844 AATCTAAAAGTATTAAAATCTAATTTCTAGAAATTTAACCAAAAGAAT-CATAGTATTTAAATCC
1 AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAA-AATGCATACTATTTAAATCC
*
62983908 AAGATCCTAAAATGAACTAATTTAAAACCGAAGATAAAAAAAATTAAAGGATGAAATTCAAAAAG
65 AAAATCCTAAAATGAACTAATTTAAAACCGAAGATAAAAAAAATTAAAGGATGAAATTCAAAAAG
62983973 AAGCTAACCA-ACTATAAAATACACAATCCTAAAGAGAAAACTTCAAATAATCCTAA
130 AAGCTAA-CATACTATAAAATACACAATCCTAAAGAGAAAACTTCAAATAATCCTAA
62984029 GACATAAAAA
Statistics
Matches: 166, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
205 3 0.02
206 158 0.95
207 5 0.03
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (206 bp):
AATCTAAAAGTACTAAAATCTAATTTCTAGAAATTTAACCAAAAAATGCATACTATTTAAATCCA
AAATCCTAAAATGAACTAATTTAAAACCGAAGATAAAAAAAATTAAAGGATGAAATTCAAAAAGA
AGCTAACATACTATAAAATACACAATCCTAAAGAGAAAACTTCAAATAATCCTAATACTTAATTT
TTTTAAAAAAT
Found at i:62984915 original size:67 final size:67
Alignment explanation
Indices: 62984823--62984957 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 67
62984813 AAACAACAAA
* * * *
62984823 TTCTAAAATAGTAAGTAGAAATAAAATATGAG-AATTACCATGGGATATAATACAAATCTAACAT
1 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATAC-AATCTAACAT
62984887 TAC
65 TAC
62984890 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
1 TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
62984955 AC
66 AC
62984957 T
1 T
62984958 CAAACAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 44 0.70
68 19 0.30
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (67 bp):
TTCTAAAATAGAAAGTAAAAATAAAATATGAGAAATTACCATGGAATAAAATACAATCTAACATT
AC
Found at i:62985821 original size:282 final size:281
Alignment explanation
Indices: 62985116--62985894 Score: 1066
Period size: 280 Copynumber: 2.8 Consensus size: 281
62985106 TAAAACGGAG
* * *
62985116 AAATCTAAATAAAAAATGAAATTAAAAAAGGATTTAAAATCGAAAT-AAAAAACGTACGAAGCAA
1 AAATCAAAATAAAAAATGAAATTAAAAAAGGATTTAAAATCGAAATAAAAAAATGTAAGAAGCAA
* * * ** *
62985180 AGGACCTATTTGGCACTTAATTTGCCTGAAATTTCAAAATCTGGGAGAAACCAAAACCAAAGGGA
66 AGTACCTATTTGGCAATTAATTTGCCTGAAATTTCAAAATCGGGGAGAATTCAAAAGCAAAGGGA
* * * ** * * *
62985245 CGAGAACTACAATTAGCCCATGCGGCGATCCTTTTCTGCT-GATGGCAGGATTTAGAAGGAATTA
131 CAAGAACTGCAATTAGTCCATGCGGCGATCCTTTT-TTATAAAAGGCAGGATGTAGAAGGAATTA
62985309 TGTAGAAAATATCCCTTTATATAACCCTATAAATAACCCTAAAACACCAAAAAAAAAAGAGAGAA
195 TGTAGAAAATATCCCTTTATATAACCCTATAAATAACCCTAAAACACCAAAAAAAAAAGAGAGAA
**
62985374 ATGTAAATCAATAGGATAAAAT
260 ATCAAAATCAATAGGATAAAAT
* * * *
62985396 AAATTAAAATAAAAAATGAGATTAAAAAAAGATTTAAAATC-AAA-ACAAAAAATGTAAGAAGCT
1 AAATCAAAATAAAAAATGAAATTAAAAAAGGATTTAAAATCGAAATA-AAAAAATGTAAGAAGCA
* * * * * *
62985459 GAGTACCTATGTGGCAATTAATTTGCCTGAAATTTCAAAATTGAGGAGAATTTAAAAGCAAACGG
65 AAGTACCTATTTGGCAATTAATTTGCCTGAAATTTCAAAATCGGGGAGAATTCAAAAGCAAAGGG
* * *
62985524 ACAAGAGCTGCAATTAGTCCATGCGACGATCCTTTTTTATAAAAGGCAGGAGGTAGAAGGAATTA
130 ACAAGAACTGCAATTAGTCCATGCGGCGATCCTTTTTTATAAAAGGCAGGATGTAGAAGGAATTA
* * *
62985589 TGTAGAAAATATCTCTTTATATAACCTTATAAATAACCTTAAAACACCAAAAAAAAAAG-GAGAA
195 TGTAGAAAATATCCCTTTATATAACCCTATAAATAACCCTAAAACACCAAAAAAAAAAGAGAGAA
62985653 ATCAAAATCAATAGGATAAAAT
260 ATCAAAATCAATAGGATAAAAT
* *
62985675 AAATCAAAATAAAAAATGATATTAAAAAAGGATTTAAAATCGAAATTAAAAAAAATGTAAGAAGA
1 AAATCAAAATAAAAAATGAAATTAAAAAAGGATTTAAAATCGAAA-T-AAAAAAATGTAAGAAGC
* *
62985740 AAAGTACCTATTTGGCAATTAATTTGCATGAAATTTCAAAATCGGGGAGAATTCAAAAGC-AGGG
64 AAAGTACCTATTTGGCAATTAATTTGCCTGAAATTTCAAAATCGGGGAGAATTCAAAAGCAAAGG
* ** * *
62985804 AGACAAGAACTGCAATTAGTCCATGCGGCGATCCTTTTCTGCAAAAGGCGGGATGTAGAAAGAAT
129 -GACAAGAACTGCAATTAGTCCATGCGGCGATCCTTTTTTATAAAAGGCAGGATGTAGAAGGAAT
*
62985869 TATGTAGAAAATATCCCTTTACATAA
193 TATGTAGAAAATATCCCTTTATATAA
62985895 TGTTATGGAA
Statistics
Matches: 433, Mismatches: 58, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
279 68 0.16
280 214 0.49
281 2 0.00
282 148 0.34
283 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (281 bp):
AAATCAAAATAAAAAATGAAATTAAAAAAGGATTTAAAATCGAAATAAAAAAATGTAAGAAGCAA
AGTACCTATTTGGCAATTAATTTGCCTGAAATTTCAAAATCGGGGAGAATTCAAAAGCAAAGGGA
CAAGAACTGCAATTAGTCCATGCGGCGATCCTTTTTTATAAAAGGCAGGATGTAGAAGGAATTAT
GTAGAAAATATCCCTTTATATAACCCTATAAATAACCCTAAAACACCAAAAAAAAAAGAGAGAAA
TCAAAATCAATAGGATAAAAT
Found at i:62993111 original size:43 final size:43
Alignment explanation
Indices: 62993037--62993126 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
62993027 CTTTGAAACA
* * * * * *
62993037 AAAATACAGTAGAAATGAAAATGGACTTCACAACTAAGTCACT
1 AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
* *
62993080 AAAACACAATAGAAATGTAAACGAACCTCACAACTAAGCCTCT
1 AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
62993123 AAAA
1 AAAA
62993127 TGCAAGAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (43 bp):
AAAACACAATAGAAATGAAAACGAACCTCACAACTAAGCCACT
Found at i:62993337 original size:86 final size:86
Alignment explanation
Indices: 62993245--62993408 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 86
62993235 AATGCAACAA
* * * *
62993245 AAACAT-AAATAGATCACACAACTAGGCCTCTAAAATGCAATAGAATGTAAGATGGACATCACAA
1 AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAA-ATGAACATCACAA
*
62993309 CTAGGCCTCTAAAATATAATGG
65 CTAAGCCTCTAAAATATAATGG
* * * *
62993331 AAACATAAAATGGATCTCACAACTAAGCCTTTAAAATGAAATAAAATGTAAATGAACCTCACAAC
1 AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGAACATCACAAC
62993396 TAAGCCTCTAAAA
66 TAAGCCTCTAAAA
62993409 AGAAAACTGA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 30 0.44
87 38 0.56
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (86 bp):
AAACATAAAATAGATCACACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGAACATCACAAC
TAAGCCTCTAAAATATAATGG
Found at i:62993397 original size:42 final size:42
Alignment explanation
Indices: 62993261--62993413 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 42
62993251 AAATAGATCA
* * * *
62993261 CACAACTAGGCCTCTAAAATGCAATAGAATGTAAGATGGACAT
1 CACAACTAAGCCTCTAAAATGAAATAAAATGTAA-ATGGACCT
* * *
62993304 CACAACTAGGCCTCTAAAAT-ATAATGGAAACAT-AAAATGGATCT
1 CACAACTAAGCCTCTAAAATGA-AAT--AAA-ATGTAAATGGACCT
* *
62993348 CACAACTAAGCCTTTAAAATGAAATAAAATGTAAATGAACCT
1 CACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGGACCT
*
62993390 CACAACTAAGCCTCTAAAAAGAAA
1 CACAACTAAGCCTCTAAAATGAAA
62993414 ACTGAACTCC
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.02
42 33 0.36
43 23 0.25
44 27 0.29
45 5 0.05
46 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (42 bp):
CACAACTAAGCCTCTAAAATGAAATAAAATGTAAATGGACCT
Found at i:62994965 original size:26 final size:25
Alignment explanation
Indices: 62994936--62994985 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
62994926 ATTTCTCCTA
* *
62994936 TTTTTTCCTCTTTCTTTTTTTTTCTT
1 TTTTTTCCT-TTTCCTTTTATTTCTT
62994962 TTTTTTCCTTTTCCTTTTATTTCT
1 TTTTTTCCTTTTCCTTTTATTTCT
62994986 CTCTCCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTCCTTTTCCTTTTATTTCTT
Found at i:62995546 original size:7 final size:7
Alignment explanation
Indices: 62995534--62995559 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62995524 CAGAAATATA
62995534 ACAAAAT
1 ACAAAAT
62995541 ACAAAAT
1 ACAAAAT
62995548 ACAAAAT
1 ACAAAAT
62995555 ACAAA
1 ACAAA
62995560 TAGAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (7 bp):
ACAAAAT
Found at i:62996061 original size:12 final size:12
Alignment explanation
Indices: 62996044--62996076 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
62996034 TTGAAGAACC
62996044 ATTAATCATGTT
1 ATTAATCATGTT
62996056 ATTAATCATGTT
1 ATTAATCATGTT
62996068 ATTAATCAT
1 ATTAATCAT
62996077 ATATGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
ATTAATCATGTT
Found at i:62996211 original size:83 final size:83
Alignment explanation
Indices: 62996116--62996275 Score: 320
Period size: 83 Copynumber: 1.9 Consensus size: 83
62996106 AAAGTACCAT
62996116 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACATGCAGAAT
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACATGCAGAAT
62996181 TTACAGTATTTAAGCTCC
66 TTACAGTATTTAAGCTCC
62996199 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACATGCAGAAT
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACATGCAGAAT
62996264 TTACAGTATTTA
66 TTACAGTATTTA
62996276 CATGCATCAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (83 bp):
TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTACATGCAGAAT
TTACAGTATTTAAGCTCC
Found at i:62996446 original size:89 final size:89
Alignment explanation
Indices: 62996338--62996829 Score: 984
Period size: 89 Copynumber: 5.5 Consensus size: 89
62996328 TTTAAGCTCC
62996338 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
62996403 CCAGAAAATGAAACAATGTACCAT
66 CCAGAAAATGAAACAATGTACCAT
62996427 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
62996492 CCAGAAAATGAAACAATGTACCAT
66 CCAGAAAATGAAACAATGTACCAT
62996516 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
62996581 CCAGAAAATGAAACAATGTACCAT
66 CCAGAAAATGAAACAATGTACCAT
62996605 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
62996670 CCAGAAAATGAAACAATGTACCAT
66 CCAGAAAATGAAACAATGTACCAT
62996694 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
62996759 CCAGAAAATGAAACAATGTACCAT
66 CCAGAAAATGAAACAATGTACCAT
62996783 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATG
1 TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATG
62996830 AATTATGATT
Statistics
Matches: 403, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 403 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (89 bp):
TTAGAATTATACTTTTGAATCATCTTTTGCATCAAGTGAATTATATGCCCATTTAGAATTTAATG
CCAGAAAATGAAACAATGTACCAT
Found at i:63002395 original size:15 final size:15
Alignment explanation
Indices: 63002348--63002396 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
63002338 CCCCTATCAC
*
63002348 CACCTCTTCCACCAC
1 CACCTCTTCCACCAT
* *
63002363 CTCCTCTTCC-TC-T
1 CACCTCTTCCACCAT
63002376 C-CCTCTTCCACCAT
1 CACCTCTTCCACCAT
63002390 CACCTCT
1 CACCTCT
63002397 GCCCCTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 3 0.11
15 14 0.52
ACGTcount: A:0.12, C:0.57, G:0.00, T:0.31
Consensus pattern (15 bp):
CACCTCTTCCACCAT
Found at i:63003679 original size:21 final size:21
Alignment explanation
Indices: 63003653--63003737 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
63003643 ACTCCTAAAC
*
63003653 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* *
63003674 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
63003699 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
63003720 CTTAAACAATAAACCATA
1 CTTAAACCATAAACCATA
63003738 AACTATAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
24 3 0.06
25 15 0.29
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:63003690 original size:46 final size:46
Alignment explanation
Indices: 63003637--63003726 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
63003627 CTTCAAACAC
*
63003637 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
63003683 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
63003727 AATAAACCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:63004094 original size:81 final size:81
Alignment explanation
Indices: 63003902--63004078 Score: 277
Period size: 81 Copynumber: 2.2 Consensus size: 81
63003892 GTTATATGAC
*
63003902 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGC
63003967 GCCGCTAATGCTCTGT
66 GCCGCTAATGCTCTGT
* *
63003983 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-GTTTTTTGCGGCGTTTTTTACTAAAA
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG--TTTTACCAAAA
*
63004047 -CGCCGCTATTGCTCTGT
64 GCGCCGCTAATGCTCTGT
*
63004064 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
63004079 TGGTAAAACG
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
80 12 0.13
81 68 0.76
82 9 0.10
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAAAAGC
GCCGCTAATGCTCTGT
Found at i:63004109 original size:41 final size:40
Alignment explanation
Indices: 63003902--63004078 Score: 275
Period size: 41 Copynumber: 4.4 Consensus size: 40
63003892 GTTATATGAC
63003902 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-GT
63003943 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
63003983 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
* * * *
63004023 TTTTTGCGGCGTTTTTTACTAAAA-CGCCGCTATTGCTCTGT
1 TTTTAGCGGCG--TTTTGCCAAAAGCGCCGCTAATGCTCTGT
*
63004064 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
63004079 TGGTAAAACG
Statistics
Matches: 128, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
39 4 0.03
40 52 0.41
41 63 0.49
42 9 0.07
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGT
Found at i:63005651 original size:21 final size:20
Alignment explanation
Indices: 63005621--63005659 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
63005611 CAGGCCTAGA
*
63005621 AATAAGTCCAAAAACAAAAAT
1 AATAAATCCAAAAA-AAAAAT
63005642 AATAAATCCAAAAAAAAA
1 AATAAATCCAAAAAAAAA
63005660 GTCCAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.13
Consensus pattern (20 bp):
AATAAATCCAAAAAAAAAAT
Found at i:63005849 original size:35 final size:37
Alignment explanation
Indices: 63005776--63005864 Score: 128
Period size: 35 Copynumber: 2.4 Consensus size: 37
63005766 AATCTTCAAC
63005776 GATATGCAATCTTAGATATAATATGCAATCTTAAATAT
1 GATA-GCAATCTTAGATATAATATGCAATCTTAAATAT
* *
63005814 GATA-CAATCTTAGATATGAT-TGCAATCTTAGATAT
1 GATAGCAATCTTAGATATAATATGCAATCTTAAATAT
63005849 GATATGCAATCTTAGA
1 GATA-GCAATCTTAGA
63005865 AGATATGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 18 0.38
36 15 0.32
37 10 0.21
38 4 0.09
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (37 bp):
GATAGCAATCTTAGATATAATATGCAATCTTAAATAT
Done.