Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 38
Found at i:3443460 original size:7 final size:7
Alignment explanation
Indices: 3443448--3443505 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
3443438 AATTTTATAG
3443448 AAACCCT
1 AAACCCT
3443455 AAACCCT
1 AAACCCT
**
3443462 AAACTTT
1 AAACCCT
*
3443469 AAACCAT
1 AAACCCT
*
3443476 AAACACT
1 AAACCCT
*
3443483 AACCCCT
1 AAACCCT
* *
3443490 AAATCAT
1 AAACCCT
3443497 AAACCCT
1 AAACCCT
3443504 AA
1 AA
3443506 TATAAATGGA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:3443867 original size:15 final size:15
Alignment explanation
Indices: 3443866--3443901 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3443856 ACTATATATA
* *
3443866 TATATATATATAACC
1 TATATATATAAAAAC
3443881 TATATATATAAAAAC
1 TATATATATAAAAAC
3443896 TATATA
1 TATATA
3443902 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (15 bp):
TATATATATAAAAAC
Found at i:3443877 original size:23 final size:24
Alignment explanation
Indices: 3443842--3443890 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
3443832 ATAAACCATG
3443842 TATAGTATATATAAACTATATATA
1 TATAGTATATATAAACTATATATA
*
3443866 TATA-TATATATAACCTATATATA
1 TATAGTATATATAAACTATATATA
3443889 TA
1 TA
3443891 AAAACTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
TATAGTATATATAAACTATATATA
Found at i:3444026 original size:21 final size:20
Alignment explanation
Indices: 3443998--3444040 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3443988 CTAAATTATA
3443998 AACCCTAAACCATAAACACT
1 AACCCTAAACCATAAACACT
*
3444018 AACCTCTAAACCATAAACCCT
1 AACC-CTAAACCATAAACACT
3444039 AA
1 AA
3444041 TATAAATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (20 bp):
AACCCTAAACCATAAACACT
Found at i:3444040 original size:14 final size:14
Alignment explanation
Indices: 3443976--3444019 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3443966 TAGTTTATAA
3443976 AAACCATAAACCCT
1 AAACCATAAACCCT
**
3443990 AAATTATAAACCCT
1 AAACCATAAACCCT
*
3444004 AAACCATAAACACT
1 AAACCATAAACCCT
3444018 AA
1 AA
3444020 CCTCTAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:3445127 original size:19 final size:19
Alignment explanation
Indices: 3445103--3445153 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3445093 GAAAATATTC
3445103 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
3445122 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3445141 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3445154 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3446762 original size:44 final size:43
Alignment explanation
Indices: 3446670--3446765 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
3446660 GCATGGTCTT
* * *
3446670 ATGCATCGATGCATATTCAAGGCATGCATCGGTGCATCATGGTG
1 ATGCATCGATACATATTCAAGGCATGCATCGATGCAT-ATGGTA
* *
3446714 ATGCATCGATACATATTCAAAGGGATGCATCGATGCAT-TGTTAA
1 ATGCATCGATACATATTC-AAGGCATGCATCGATGCATATGGT-A
3446758 ATGCATCG
1 ATGCATCG
3446766 GTGCATGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
43 3 0.07
44 25 0.56
45 17 0.38
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
ATGCATCGATACATATTCAAGGCATGCATCGATGCATATGGTA
Found at i:3450621 original size:22 final size:21
Alignment explanation
Indices: 3450579--3450618 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3450569 GAGTTTGTTT
*
3450579 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3450600 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3450619 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3452614 original size:64 final size:64
Alignment explanation
Indices: 3452561--3452723 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
3452551 CGGTGCACCA
3452561 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAA-ATAGCTTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCTTGGTGCATCGATGCATGG
** * * * * *
3452625 CTTGTGCATCGATGCATCAAATGCATTTGATGTTTTGAAAATATTCATAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATGCTTGGTGCATCGATGCATGG
* * *
3452690 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
3452724 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 30 0.36
65 51 0.61
66 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCTTGGTGCATCGATGCATGG
Found at i:3452633 original size:19 final size:20
Alignment explanation
Indices: 3452604--3452641 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3452594 TTGAAAAATA
3452604 GCTTGGTGCATCGATGCATG
1 GCTTGGTGCATCGATGCATG
3452624 GCTT-GTGCATCGATGCAT
1 GCTTGGTGCATCGATGCAT
3452642 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GCTTGGTGCATCGATGCATG
Found at i:3452697 original size:19 final size:18
Alignment explanation
Indices: 3452673--3452721 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
3452663 AAATATTCAT
3452673 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
3452691 GAGTGCATCGGTGCATGGA
1 -AGTGCATCGATGCATGGA
3452710 A-TGCATTCGATG
1 AGTGCA-TCGATG
3452722 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 17 0.63
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:3453239 original size:16 final size:16
Alignment explanation
Indices: 3453220--3453274 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3453210 AAATATCATA
*
3453220 TCAGGTTATTAACAAG
1 TCAGGTTATTAACAGG
* * *
3453236 TCAGATCATTTACAGG
1 TCAGGTTATTAACAGG
**
3453252 TCAGGTTAAAAACAGG
1 TCAGGTTATTAACAGG
3453268 TCAGGTT
1 TCAGGTT
3453275 GAAAATAGGT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (16 bp):
TCAGGTTATTAACAGG
Found at i:3453279 original size:16 final size:16
Alignment explanation
Indices: 3453247--3453284 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3453237 CAGATCATTT
3453247 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
3453263 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
*
3453279 ATAGGT
1 ACAGGT
3453285 TTGGTAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:3459573 original size:4 final size:4
Alignment explanation
Indices: 3459556--3459590 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3459546 GCGAGTTTTT
*
3459556 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3459591 ATGTCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:3468447 original size:29 final size:31
Alignment explanation
Indices: 3468405--3468466 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
3468395 TAAAAATGCA
*
3468405 ATTTTCCAGAAAAATG-ATCGATCCC-TTGC
1 ATTTTCCAGAAAAAAGAATCGATCCCTTTGC
* *
3468434 ATTTTCTAGGAAAAAGAATCGATCCCTTTGC
1 ATTTTCCAGAAAAAAGAATCGATCCCTTTGC
3468465 AT
1 AT
3468467 AAAGGATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 9 0.32
31 6 0.21
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (31 bp):
ATTTTCCAGAAAAAAGAATCGATCCCTTTGC
Found at i:3468455 original size:30 final size:30
Alignment explanation
Indices: 3468405--3468466 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3468395 TAAAAATGCA
3468405 ATTTTCCAGAAAAATGATCGATCCC-TTGC
1 ATTTTCCAGAAAAATGATCGATCCCTTTGC
*
3468434 ATTTTCTAGGAAAAA-GAATCGATCCCTTTGC
1 ATTTTCCA-GAAAAATG-ATCGATCCCTTTGC
3468465 AT
1 AT
3468467 AAAGGATCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.28
30 15 0.52
31 6 0.21
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (30 bp):
ATTTTCCAGAAAAATGATCGATCCCTTTGC
Found at i:3468475 original size:21 final size:21
Alignment explanation
Indices: 3468446--3468525 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
3468436 TTTCTAGGAA
* *
3468446 AAAGAATCGATCCCTTTGCAT
1 AAAGGATCGATCCCTTTTCAT
*
3468467 AAAGGATCGATCCTTTTTTCA-
1 AAAGGATCGATCC-CTTTTCAT
**
3468488 AAAGGATCGATCCCTTTTTGT
1 AAAGGATCGATCCCTTTTCAT
*
3468509 AAATGATCGATCCCTTT
1 AAAGGATCGATCCCTTT
3468526 AGGCCAAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.08
21 41 0.82
22 5 0.10
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTTCAT
Found at i:3470226 original size:20 final size:21
Alignment explanation
Indices: 3470201--3470246 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3470191 TCTAGCTCAA
3470201 ATCCCTTAGA-AAAGGAATCG
1 ATCCCTTAGACAAAGGAATCG
* *
3470221 ATCCCTTTGACCAAGGAATCG
1 ATCCCTTAGACAAAGGAATCG
3470242 ATCCC
1 ATCCC
3470247 CTTGTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCCCTTAGACAAAGGAATCG
Found at i:3470315 original size:21 final size:21
Alignment explanation
Indices: 3470286--3470359 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
3470276 GTAGGTTTGT
*
3470286 GATCAATCCCTTTACAAAAAG
1 GATCGATCCCTTTACAAAAAG
* **
3470307 GATCGATCCC-TCATGTAAAAG
1 GATCGATCCCTTTA-CAAAAAG
* * *
3470328 GATCGATTCCTTTACCAAAAT
1 GATCGATCCCTTTACAAAAAG
3470349 GATCGATCCCT
1 GATCGATCCCT
3470360 CAATGAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (21 bp):
GATCGATCCCTTTACAAAAAG
Found at i:3470370 original size:21 final size:20
Alignment explanation
Indices: 3470302--3470368 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
3470292 TCCCTTTACA
3470302 AAAAGGATCGATCCCTCATG
1 AAAAGGATCGATCCCTCATG
* * **
3470322 TAAAAGGATCGATTCCTTTACC
1 -AAAAGGATCGA-TCCCTCATG
*
3470344 AAAATGATCGATCCCTCAATG
1 AAAAGGATCGATCCCTC-ATG
3470365 AAAA
1 AAAA
3470369 TGTTGAGTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.11
21 26 0.74
22 5 0.14
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (20 bp):
AAAAGGATCGATCCCTCATG
Found at i:3471185 original size:64 final size:65
Alignment explanation
Indices: 3471072--3471206 Score: 177
Period size: 64 Copynumber: 2.1 Consensus size: 65
3471062 TGGACCCTTA
* * *
3471072 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGGCTT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGGATTG
** *
3471136 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCAATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-GC-ATGAGTGCATCGATGCATGGAT
3471199 TG
64 TG
3471201 GTGCAT
1 GTGCAT
3471207 TGGTACACTC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
63 6 0.10
64 48 0.77
65 8 0.13
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCATGAGTGCATCGATGCATGGATTG
Found at i:3474616 original size:77 final size:75
Alignment explanation
Indices: 3474530--3474683 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 75
3474520 GTTTCTCATT
3474530 TTCCAATCCAAACTTCTTGAGCATGTCTTTGACGTACTTAGTTTGATTGATGAAGATTCCATCTT
1 TTCCAATCCAAACTTCTTGAGCATGTCTTTGACGTAC-TAGTTTGATTGATG-AGATTCCATCTT
3474595 TTCTTTGCTTGA
64 TTCTTTGCTTGA
3474607 TTCCAATCCAAACTTCTTGAGCATGTCTTTGACGTACTAGTTTGATTGATGAGATTCCATCTTTT
1 TTCCAATCCAAACTTCTTGAGCATGTCTTTGACGTACTAGTTTGATTGATGAGATTCCATCTTTT
3474672 CTTTGCTTGA
66 CTTTGCTTGA
3474682 TT
1 TT
3474684 TGGAGTCCCA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 26 0.34
76 14 0.18
77 37 0.48
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (75 bp):
TTCCAATCCAAACTTCTTGAGCATGTCTTTGACGTACTAGTTTGATTGATGAGATTCCATCTTTT
CTTTGCTTGA
Found at i:3478749 original size:11 final size:11
Alignment explanation
Indices: 3478733--3478758 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3478723 GTTTGATGTT
3478733 TTCTCTCTTGA
1 TTCTCTCTTGA
3478744 TTCTCTCTTGA
1 TTCTCTCTTGA
3478755 TTCT
1 TTCT
3478759 TGTTGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:3479125 original size:67 final size:64
Alignment explanation
Indices: 3478998--3479159 Score: 184
Period size: 67 Copynumber: 2.5 Consensus size: 64
3478988 TGCACTAAGA
* * * * *
3478998 GTGCATTGATGCATAAAATGTATTCAATGTTTTAAAATAGCCTGAGTGCATCAATTCATGGCT-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCGGAGTGCATCAATACATGG-TAT
*
3479062 GTGCATCGATGCATATATAATGCATTCGATGTTTTCATAAATA-CCGGAGTGCATCGATACATGG
1 GTGCATCGATGCATA-A-AATGCATTCGATGTTTT-A-AAATAGCCGGAGTGCATCAATACATGG
3479126 TAT
62 TAT
** *
3479129 GTGTTTCGATGCATAAAATGCATTTGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
3479160 CAATTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
64 14 0.17
65 15 0.18
66 17 0.20
67 33 0.39
68 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCGGAGTGCATCAATACATGGTAT
Found at i:3483604 original size:12 final size:12
Alignment explanation
Indices: 3483575--3483638 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
3483565 AAACGGAGAT
* *
3483575 ATCAGAAATCAT
1 ATCAGAATTCAG
*
3483587 AACAGAATTCAG
1 ATCAGAATTCAG
*
3483599 ATCAGAATCCAG
1 ATCAGAATTCAG
*
3483611 ATCAGAAATCAG
1 ATCAGAATTCAG
* *
3483623 AACATAATTCAG
1 ATCAGAATTCAG
3483635 ATCA
1 ATCA
3483639 TGTATCAGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.20
Consensus pattern (12 bp):
ATCAGAATTCAG
Found at i:3484035 original size:27 final size:27
Alignment explanation
Indices: 3483992--3484052 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3483982 ATTCTTATCC
3483992 ATAGATCATATTCGGAATCATCACTGA
1 ATAGATCATATTCGGAATCATCACTGA
* * *
3484019 ATAGATCATCTTGGGAATCATTACTGA
1 ATAGATCATATTCGGAATCATCACTGA
3484046 ATAGATC
1 ATAGATC
3484053 TTAAGGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (27 bp):
ATAGATCATATTCGGAATCATCACTGA
Found at i:3485343 original size:15 final size:15
Alignment explanation
Indices: 3485323--3485353 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3485313 AGGTATTCTC
3485323 ATAATTTATCATCCA
1 ATAATTTATCATCCA
3485338 ATAATTTATCATCCA
1 ATAATTTATCATCCA
3485353 A
1 A
3485354 GTACCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATTTATCATCCA
Found at i:3486015 original size:30 final size:30
Alignment explanation
Indices: 3485981--3486068 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
3485971 AACTTTTTTG
3485981 TCAAAGTCAACGGTCAATGGGTTGACCCGA
1 TCAAAGTCAACGGTCAATGGGTTGACCCGA
* *
3486011 TCAAAGTCAACGGTCAATGGGTTAACCCGG
1 TCAAAGTCAACGGTCAATGGGTTGACCCGA
* * *
3486041 TCAAAGTCAACAGTCAACGAGTTGACCC
1 TCAAAGTCAACGGTCAATGGGTTGACCC
3486069 AGTGAGTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
TCAAAGTCAACGGTCAATGGGTTGACCCGA
Found at i:3488252 original size:24 final size:24
Alignment explanation
Indices: 3488223--3488316 Score: 91
Period size: 24 Copynumber: 3.9 Consensus size: 24
3488213 AACGAAGATT
*
3488223 TCAGAAATTAAAATAGAATTCAGA
1 TCAGAAATCAAAATAGAATTCAGA
* * *
3488247 TCAGAAATCATAACAGAATCCAGA
1 TCAGAAATCAAAATAGAATTCAGA
* * *
3488271 TCATAAATCAGAATAGAATTTAGA
1 TCAGAAATCAAAATAGAATTCAGA
* *
3488295 TCATG-TATCAGAATAGAATTCA
1 TCA-GAAATCAAAATAGAATTCA
3488317 AGGGTATTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (24 bp):
TCAGAAATCAAAATAGAATTCAGA
Found at i:3489079 original size:19 final size:20
Alignment explanation
Indices: 3489040--3489084 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3489030 TAAGTGTTAA
*
3489040 TGAATTGTAAGATTTTATAT
1 TGAATTGTAAGATTATATAT
*
3489060 TGAATTTTAA-ATTATATAT
1 TGAATTGTAAGATTATATAT
*
3489079 TCAATT
1 TGAATT
3489085 AAATTATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (20 bp):
TGAATTGTAAGATTATATAT
Found at i:3489303 original size:20 final size:20
Alignment explanation
Indices: 3489280--3489334 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3489270 AGAGGGAACA
3489280 GATTCCCCCCAGGTGGTACC
1 GATTCCCCCCAGGTGGTACC
*
3489300 GATTCCCCCCAGGGGGTACC
1 GATTCCCCCCAGGTGGTACC
*
3489320 GATTCTCCCCTAGGT
1 GATTC-CCCCCAGGT
3489335 TTTTGGCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (20 bp):
GATTCCCCCCAGGTGGTACC
Found at i:3491369 original size:31 final size:31
Alignment explanation
Indices: 3491334--3491424 Score: 166
Period size: 31 Copynumber: 3.0 Consensus size: 31
3491324 TGACTTTTTT
3491334 GTCAAAGTCAACGGTCAACGGGGTTGACCCG
1 GTCAAAGTCAACGGTCAACGGGGTTGACCCG
3491365 GTCAAAGTCAACGGTCAACGGGGTTGACCCG
1 GTCAAAGTCAACGGTCAACGGGGTTGACCCG
*
3491396 GTCAAAGTCAATGGTCAAC-GGGTTGACCC
1 GTCAAAGTCAACGGTCAACGGGGTTGACCC
3491425 AGTGAGTTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 10 0.17
31 49 0.83
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (31 bp):
GTCAAAGTCAACGGTCAACGGGGTTGACCCG
Found at i:3491493 original size:18 final size:18
Alignment explanation
Indices: 3491464--3491535 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
3491454 CGCAGGTTGA
3491464 CTCAGTCGGCTTGGCTC-G
1 CTCAG-CGGCTTGGCTCAG
3491482 TCTCAGCGGCTTGGCTCAG
1 -CTCAGCGGCTTGGCTCAG
3491501 CTCAGCGGCTTGGCTCAG
1 CTCAGCGGCTTGGCTCAG
* *
3491519 CTCAGTGGCTCGGCTCA
1 CTCAGCGGCTTGGCTCA
3491536 ACTGTTGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
18 44 0.88
19 6 0.12
ACGTcount: A:0.10, C:0.33, G:0.32, T:0.25
Consensus pattern (18 bp):
CTCAGCGGCTTGGCTCAG
Found at i:3491839 original size:25 final size:25
Alignment explanation
Indices: 3491811--3491859 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3491801 CACGATGGAC
*
3491811 CGGGAGGTGTCGAAAATGGATGGTG
1 CGGGAGGTGTCGAAAACGGATGGTG
*
3491836 CGGGAGGTGTTGAAAACGGATGGT
1 CGGGAGGTGTCGAAAACGGATGGT
3491860 CGGATTGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.47, T:0.20
Consensus pattern (25 bp):
CGGGAGGTGTCGAAAACGGATGGTG
Found at i:3492814 original size:17 final size:17
Alignment explanation
Indices: 3492794--3492888 Score: 75
Period size: 17 Copynumber: 5.2 Consensus size: 17
3492784 AAAAGTTAGC
*
3492794 AAAAAAGAAAAAAAATT
1 AAAAAAGAAAATAAATT
* *
3492811 AAAAATTAAAAAATTAAAAT
1 AAAAA--AGAAAA-TAAATT
3492831 AAATAAAGAAAATAAA-T
1 AAA-AAAGAAAATAAATT
*
3492848 AAATAAAGAAAATAAATA
1 AAA-AAAGAAAATAAATT
*
3492866 AATAAAATTAAAATAAATT
1 AA-AAAA-GAAAATAAATT
3492885 AAAA
1 AAAA
3492889 CAGTTAGTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
17 22 0.34
18 11 0.17
19 22 0.34
20 7 0.11
21 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAAAGAAAATAAATT
Found at i:3492833 original size:13 final size:13
Alignment explanation
Indices: 3492812--3492883 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 13
3492802 AAAAAAATTA
3492812 AAAATTAAA-AAATT
1 AAAA-TAAATAAA-T
*
3492826 AAAATAAATAAAG
1 AAAATAAATAAAT
3492839 AAAATAAATAAAT
1 AAAATAAATAAAT
3492852 AAAGA-AAATAAAT
1 AAA-ATAAATAAAT
*
3492865 -AAAT-AA-AATT
1 AAAATAAATAAAT
3492875 AAAATAAAT
1 AAAATAAAT
3492884 TAAAACAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
10 3 0.06
11 7 0.14
12 4 0.08
13 27 0.55
14 8 0.16
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:3492883 original size:4 final size:4
Alignment explanation
Indices: 3492827--3492871 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
3492817 TAAAAAATTA
* *
3492827 AAAT AAAT AAAGA AAAT AAAT AAAT AAAGA AAAT AAAT AAAT AAA
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAA
3492872 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 29 0.83
5 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:3492915 original size:11 final size:11
Alignment explanation
Indices: 3492899--3492934 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3492889 CAGTTAGTTA
3492899 AAAAATAAAAT
1 AAAAATAAAAT
3492910 AAAAATAAAA-
1 AAAAATAAAAT
3492920 AAAGAATAAAAT
1 AAA-AATAAAAT
3492932 AAA
1 AAA
3492935 TATTTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3494815 original size:33 final size:33
Alignment explanation
Indices: 3494743--3494958 Score: 337
Period size: 33 Copynumber: 6.6 Consensus size: 33
3494733 CTTGAAGGTC
3494743 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGG-TT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTT
3494775 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
* *
3494808 TTTGTGTTTCAAAAGAAACAATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
* *
3494841 TTTGTGCTTCAAGAGAAACTATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
* *
3494874 TTTGTGTTTCAAGAGGAACGATTTTAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
* *
3494907 TTTGTGTTTCAAGAGAAACTATTTCAAAAGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
3494940 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
3494959 ATTCTCGAGG
Statistics
Matches: 169, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
32 28 0.17
33 141 0.83
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
Found at i:3495098 original size:36 final size:36
Alignment explanation
Indices: 3495011--3495335 Score: 380
Period size: 36 Copynumber: 9.1 Consensus size: 36
3495001 CAAAGATTGG
3495011 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
3495048 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
3495084 TGTTTCAAGAGAAACTGTCTCAAGATAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
3495121 AGTTCCAAAAGAAACTGCCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
3495157 TATTTTAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
3495186 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
3495222 TGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
3495258 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
3495294 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
3495331 TGTTT
1 TGTTT
3495336 AGAGTAAATT
Statistics
Matches: 245, Mismatches: 30, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
28 2 0.01
29 16 0.07
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 2 0.01
36 149 0.61
37 69 0.28
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:3495100 original size:73 final size:73
Alignment explanation
Indices: 3495011--3495335 Score: 411
Period size: 73 Copynumber: 4.6 Consensus size: 73
3495001 CAAAGATTGG
*
3495011 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGGG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
3495076 ACAAAATT
66 ACAAAATT
* * * ** * *
3495084 TGTTTCAAGAGAAACTGTCTCAAGATAGACAAAACTTAGTTCCAAAAGAAACTGCCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
3495149 ACGAAATT
66 ACAAAATT
* * * *
3495157 TATTTTAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
3495212 AGACAAAATT
64 AGACAAAATT
* * *
3495222 TGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAA-TTTGTTTAAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
3495286 ACAAAATT
66 ACAAAATT
3495294 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
3495336 AGAGTAAATT
Statistics
Matches: 213, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
64 2 0.01
65 45 0.21
66 2 0.01
67 1 0.00
68 2 0.01
70 2 0.01
71 1 0.00
72 71 0.33
73 85 0.40
74 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:3495209 original size:138 final size:137
Alignment explanation
Indices: 3495046--3495294 Score: 383
Period size: 138 Copynumber: 1.8 Consensus size: 137
3495036 GAGACAAAAC
* *
3495046 TTTGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGATA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* *
3495111 GACAAAACTTAGTTCCAAA-AGAAACTGCCTCAAGGGAGACGAAATTTATTTTAAGGAAAACATA
66 GACAAAA-TTAGTT-CAAAGAGAAACTGCCTCAAGAGAGACAAAATTTATTTTAAGGAAAACATA
3495175 TTCAAAGAT
129 TTCAAAGAT
* *
3495184 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTTTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * *
3495249 GACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATTT
66 GACAAAATTAGTTCAAAGAGAAACTGCCTCAAGAGAGACAAAATTT
3495295 GTTTCAAGAG
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
136 3 0.03
137 29 0.29
138 68 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTCAAAGAGAAACTGCCTCAAGAGAGACAAAATTTATTTTAAGGAAAACATATT
CAAAGAT
Found at i:3495255 original size:174 final size:175
Alignment explanation
Indices: 3494983--3495323 Score: 535
Period size: 174 Copynumber: 2.0 Consensus size: 175
3494973 CAAAATTTTG
3494983 TTTTAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TTTTAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * *
3495048 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGATAGA
66 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGA
*
3495113 CAAAACTTAGTTCCAAAAGAAACTGCCTCAAGGGAGACGAAATTTA
131 CAAAA-TTAGTTCCAAAAGAAACTGCCTCAAGAGAGACGAAATTTA
* *
3495159 TTTTAAG-GAAAACATATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
1 TTTTAAGAG-AAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
* *
3495221 TTGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAG
65 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAG
* * * *
3495286 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
130 ACAAAATTAGTTCCAAAAGAAACTGCCTCAAGAGAGAC
3495324 AAAACTTTGT
Statistics
Matches: 152, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
173 27 0.18
174 67 0.44
175 34 0.22
176 24 0.16
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (175 bp):
TTTTAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGA
CAAAATTAGTTCCAAAAGAAACTGCCTCAAGAGAGACGAAATTTA
Found at i:3495303 original size:21 final size:21
Alignment explanation
Indices: 3495205--3495305 Score: 82
Period size: 21 Copynumber: 5.4 Consensus size: 21
3495195 GGAAACTGTC
3495205 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
*
3495226 TCAAG-G-G---AAA-CTGTT
1 TCAAGAGAGACAAAATTTGTT
3495241 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
3495262 T-AA-AG-G--GAAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
3495277 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
3495298 TCAAGAGA
1 TCAAGAGA
3495306 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
15 13 0.22
16 9 0.15
17 3 0.05
18 2 0.03
19 3 0.05
20 9 0.15
21 21 0.35
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:3495360 original size:37 final size:34
Alignment explanation
Indices: 3495196--3495353 Score: 199
Period size: 36 Copynumber: 4.4 Consensus size: 34
3495186 TGTTTCAAGG
*
3495196 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTT--AGA
* *
3495232 GAAACTGTTTCAAGAGAGACAAAATTTGTTTAAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTT--AGA
3495268 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTT--AGA
3495304 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTAGA
*
3495339 GTAAATTAGTCTCAA
1 G-AAACT-GTCTCAA
3495354 ACGAGACGAC
Statistics
Matches: 113, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
35 4 0.04
36 95 0.84
37 14 0.12
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (34 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTAGA
Found at i:3500698 original size:13 final size:13
Alignment explanation
Indices: 3500680--3500709 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3500670 CTTTATGGAG
3500680 AAAATTAAAAATT
1 AAAATTAAAAATT
*
3500693 AAAATTAAAATTT
1 AAAATTAAAAATT
3500706 AAAA
1 AAAA
3500710 CATCGATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:3500903 original size:18 final size:16
Alignment explanation
Indices: 3500846--3500903 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
3500836 AAAAGTTAGC
*
3500846 AAAAAGAAAATAAAAA
1 AAAAATAAAATAAAAA
*
3500862 ATAAATTAAAATAAAGAA
1 A-AAAATAAAATAAA-AA
3500880 AGAAAATAAAATGAATAAA
1 A-AAAATAAAAT-AA-AAA
3500899 AAAAA
1 AAAAA
3500904 AGTAAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.03
17 11 0.32
18 16 0.47
19 5 0.15
20 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAATAAAATAAAAA
Found at i:3502248 original size:21 final size:21
Alignment explanation
Indices: 3502224--3502264 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3502214 GCGAAACATT
**
3502224 AAAAGACATATTTATTAAAAA
1 AAAAGACATACATATTAAAAA
*
3502245 AAAATACATACATATTAAAA
1 AAAAGACATACATATTAAAA
3502265 TATTTCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAGACATACATATTAAAAA
Found at i:3504982 original size:19 final size:19
Alignment explanation
Indices: 3504960--3505023 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
3504950 TTAGGAAACA
*
3504960 ATTTTTAGGCTGCAACCTG
1 ATTTTTAGGTTGCAACCTG
* * *
3504979 ATTTTTCA-TTTAGAAACCCG
1 ATTTTT-AGGTT-GCAACCTG
3504999 ATTTTTAGGTTGCAACCTG
1 ATTTTTAGGTTGCAACCTG
3505018 ATTTTT
1 ATTTTT
3505024 TATATGAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (19 bp):
ATTTTTAGGTTGCAACCTG
Found at i:3505023 original size:20 final size:20
Alignment explanation
Indices: 3504961--3505025 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
3504951 TAGGAAACAA
*
3504961 TTTTTAGGCTGCAACCTGAT
1 TTTTTAGGTTGCAACCTGAT
* * * *
3504981 TTTTCA-TTTAGAAACCCGA-
1 TTTTTAGGTT-GCAACCTGAT
3505000 TTTTTAGGTTGCAACCTGAT
1 TTTTTAGGTTGCAACCTGAT
3505020 TTTTTA
1 TTTTTA
3505026 TATGAAAACT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTTTAGGTTGCAACCTGAT
Found at i:3505074 original size:19 final size:21
Alignment explanation
Indices: 3505050--3505091 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3505040 TCTATTCATA
*
3505050 TGGAAAC-A-ATATTTTCGGT
1 TGGAAACTAGATATTTTAGGT
3505069 TGGAAACTAGATATTTTAGGT
1 TGGAAACTAGATATTTTAGGT
3505090 TG
1 TG
3505092 AAGCCCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (21 bp):
TGGAAACTAGATATTTTAGGT
Found at i:3507845 original size:15 final size:15
Alignment explanation
Indices: 3507825--3507872 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3507815 CTTTAGGGTT
*
3507825 TTTATTCCAAATTTA
1 TTTATTTCAAATTTA
*
3507840 TTTATTTGAAATTT-
1 TTTATTTCAAATTTA
*
3507854 TATCATTTCAAATTTA
1 T-TTATTTCAAATTTA
3507870 TTT
1 TTT
3507873 CTATTAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTATTTCAAATTTA
Found at i:3515354 original size:36 final size:37
Alignment explanation
Indices: 3515303--3515374 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
3515293 TGCTCATAGC
*
3515303 GGGTCAATTCAATATGTTGTTCTTTAACAACATACTT
1 GGGTCAATTCAATATGTTGTTCTCTAACAACATACTT
3515340 GGGTCAA-TCAATATGTTGTTCTCTAACAACATACT
1 GGGTCAATTCAATATGTTGTTCTCTAACAACATACT
3515375 CATGCATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (37 bp):
GGGTCAATTCAATATGTTGTTCTCTAACAACATACTT
Found at i:3519131 original size:19 final size:20
Alignment explanation
Indices: 3519063--3519129 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
3519053 CTTGGGTACC
*
3519063 AATACTAATCCCTTAGTATA
1 AATACTAATCCCTTAGTATT
*
3519083 AATACTAATCCCTTAGTATC
1 AATACTAATCCCTTAGTATT
* *
3519103 AGTACTAA-CCCTGAGTATT
1 AATACTAATCCCTTAGTATT
*
3519122 GATACTAA
1 AATACTAA
3519130 CCTTTGGGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (20 bp):
AATACTAATCCCTTAGTATT
Found at i:3519141 original size:39 final size:41
Alignment explanation
Indices: 3519053--3519147 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 41
3519043 TAAAACTATT
* *
3519053 CTTGGGTACCAATACTAATCCCTTAGTATAAATACTAATCC
1 CTTGGGTATCAATACTAATCCCTGAGTATAAATACTAATCC
* * **
3519094 CTT-AGTATCAGTACTAA-CCCTGAGTATTGATACTAA-CC
1 CTTGGGTATCAATACTAATCCCTGAGTATAAATACTAATCC
*
3519132 TTTGGGTATCAATACT
1 CTTGGGTATCAATACT
3519148 GACTAATTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
38 4 0.09
39 26 0.59
40 11 0.25
41 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (41 bp):
CTTGGGTATCAATACTAATCCCTGAGTATAAATACTAATCC
Found at i:3531869 original size:10 final size:10
Alignment explanation
Indices: 3531854--3531932 Score: 89
Period size: 10 Copynumber: 8.3 Consensus size: 10
3531844 CCGATTTTCA
3531854 ACCGGTTCTG
1 ACCGGTTCTG
3531864 ACCGGTTC-G
1 ACCGGTTCTG
*
3531873 ACCGGTTTTG
1 ACCGGTTCTG
3531883 ACCGGTTC-G
1 ACCGGTTCTG
3531892 AACCGGTT-TG
1 -ACCGGTTCTG
3531902 ACCGG-TCTG
1 ACCGGTTCTG
3531911 AACCGGTT-TG
1 -ACCGGTTCTG
3531921 ACCGG-TCTG
1 ACCGGTTCTG
3531930 ACC
1 ACC
3531933 CGACCCGACT
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
8 2 0.03
9 26 0.43
10 31 0.52
11 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:3531878 original size:19 final size:19
Alignment explanation
Indices: 3531833--3531926 Score: 113
Period size: 19 Copynumber: 4.8 Consensus size: 19
3531823 GAGGGCTGGA
*
3531833 AACCGGTTTGACCGATTTTC-
1 AACCGGTTTGACCG--GTTCG
3531853 AACCGGTTCTGACCGGTTCG
1 AACCGGTT-TGACCGGTTCG
3531873 -ACCGGTTTTGACCGGTTCG
1 AACCGG-TTTGACCGGTTCG
3531892 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
3531911 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
3531927 CTGACCCGAC
Statistics
Matches: 67, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
18 2 0.03
19 44 0.66
20 15 0.22
21 6 0.09
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:3531896 original size:29 final size:31
Alignment explanation
Indices: 3531833--3531932 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 31
3531823 GAGGGCTGGA
*
3531833 AACCGGTTTGACCGATTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
* *
3531864 -ACCGGTTCGACCGGTTTT-GACCGGTTC-G
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
* *
3531892 AACCGGTTTGACCGG-TCTGAACCGGTT-TG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
*
3531921 -ACCGGTCTGACC
1 AACCGGTTTGACC
3531933 CGACCCGACT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 14 0.24
29 29 0.49
30 16 0.27
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (31 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCTG
Found at i:3539092 original size:9 final size:9
Alignment explanation
Indices: 3539053--3539140 Score: 59
Period size: 10 Copynumber: 9.1 Consensus size: 9
3539043 GTTGGAAACT
3539053 GGTTTGACC
1 GGTTTGACC
*
3539062 GGTTTTCAACC
1 GG-TTT-GACC
3539073 GGTTCTGACC
1 GGTT-TGACC
3539083 GGTTTGACC
1 GGTTTGACC
3539092 GGTTTCGACC
1 GGTTT-GACC
* *
3539102 GATTCGAACC
1 GGTTTG-ACC
*
3539112 GATTTGACC
1 GGTTTGACC
* **
3539121 GATCCGAACC
1 GGTTTG-ACC
3539131 GGTTTGACC
1 GGTTTGACC
3539140 G
1 G
3539141 ATCTGACCCG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
9 24 0.38
10 33 0.52
11 6 0.10
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (9 bp):
GGTTTGACC
Found at i:3539094 original size:19 final size:20
Alignment explanation
Indices: 3539053--3539140 Score: 76
Period size: 19 Copynumber: 4.5 Consensus size: 20
3539043 GTTGGAAACT
* *
3539053 GGTTTGACCGGTTTTCAACC
1 GGTTTGACCGGTTCTGAACC
3539073 GGTTCTGACCGGTT-TG-ACC
1 GGTT-TGACCGGTTCTGAACC
*
3539092 GGTTTCGACCGATTC-GAACC
1 GGTTT-GACCGGTTCTGAACC
* * *
3539112 GATTTGACC-GATCCGAACC
1 GGTTTGACCGGTTCTGAACC
3539131 GGTTTGACCG
1 GGTTTGACCG
3539141 ATCTGACCCG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.05
19 32 0.57
20 12 0.21
21 9 0.16
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (20 bp):
GGTTTGACCGGTTCTGAACC
Found at i:3539112 original size:29 final size:30
Alignment explanation
Indices: 3539053--3539121 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
3539043 GTTGGAAACT
*
3539053 GGTTTGACCGGTTTTCAACCGGTTCTGACC
1 GGTTTGACCGGTTTTCAACCGATTCTGACC
*
3539083 GGTTTGACCGG-TTTCGACCGATTC-GAACC
1 GGTTTGACCGGTTTTCAACCGATTCTG-ACC
*
3539112 GATTTGACCG
1 GGTTTGACCG
3539122 ATCCGAACCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 23 0.66
30 11 0.31
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (30 bp):
GGTTTGACCGGTTTTCAACCGATTCTGACC
Found at i:3539141 original size:19 final size:19
Alignment explanation
Indices: 3539089--3539143 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
3539079 GACCGGTTTG
*
3539089 ACCGGTTTCGACCGATTCGA
1 ACCGGTTT-GACCGATCCGA
*
3539109 ACCGATTTGACCGATCCGA
1 ACCGGTTTGACCGATCCGA
3539128 ACCGGTTTGACCGATC
1 ACCGGTTTGACCGATC
3539144 TGACCCGACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 25 0.78
20 7 0.22
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (19 bp):
ACCGGTTTGACCGATCCGA
Found at i:3539181 original size:7 final size:7
Alignment explanation
Indices: 3539169--3539205 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
3539159 GACACGACCC
3539169 GACCGTT
1 GACCGTT
3539176 GACCGTT
1 GACCGTT
3539183 GACCG-T
1 GACCGTT
3539189 GACCGTT
1 GACCGTT
3539196 GACCGTT
1 GACCGTT
3539203 GAC
1 GAC
3539206 TTCCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:3539193 original size:13 final size:13
Alignment explanation
Indices: 3539169--3539201 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3539159 GACACGACCC
3539169 GACCGTTGACCGTT
1 GACCG-TGACCGTT
3539183 GACCGTGACCGTT
1 GACCGTGACCGTT
3539196 GACCGT
1 GACCGT
3539202 TGACTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:3540929 original size:20 final size:20
Alignment explanation
Indices: 3540901--3540950 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3540891 TTTGACTCAA
3540901 TATCGATACCACACTGCGAG
1 TATCGATACCACACTGCGAG
* * *
3540921 TATCAATACCATACTGTGAG
1 TATCGATACCACACTGCGAG
3540941 TATCGATACC
1 TATCGATACC
3540951 CTATCTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
TATCGATACCACACTGCGAG
Found at i:3551781 original size:2 final size:2
Alignment explanation
Indices: 3551774--3551865 Score: 170
Period size: 2 Copynumber: 47.0 Consensus size: 2
3551764 ACGGAGGAGA
3551774 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3551815 AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3551856 AT AT AT AT AT
1 AT AT AT AT AT
3551866 GACTCCCTCC
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 86 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3552586 original size:23 final size:24
Alignment explanation
Indices: 3552541--3552586 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3552531 TTTTATAGTT
*
3552541 TTTTTTAGATGAGAAGACGATTTAA
1 TTTTTTAGATGAAAAGAC-ATTTAA
*
3552566 TTTTTTAGATTAAAAGA-ATTT
1 TTTTTTAGATGAAAAGACATTT
3552587 TTCAGACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
25 15 0.79
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (24 bp):
TTTTTTAGATGAAAAGACATTTAA
Found at i:3554093 original size:18 final size:18
Alignment explanation
Indices: 3554070--3554161 Score: 139
Period size: 18 Copynumber: 5.1 Consensus size: 18
3554060 CGTGAGGATT
*
3554070 GGGCAGTGGTCTAGCATG
1 GGGCAGTGGTCCAGCATG
*
3554088 GGGCAGTGGTTCAGCATG
1 GGGCAGTGGTCCAGCATG
* * *
3554106 GTGCAGTGATCCAGCATA
1 GGGCAGTGGTCCAGCATG
3554124 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
3554142 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
3554160 GG
1 GG
3554162 CATCTGACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.18, C:0.20, G:0.42, T:0.20
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:3558612 original size:18 final size:18
Alignment explanation
Indices: 3558585--3558694 Score: 175
Period size: 18 Copynumber: 6.1 Consensus size: 18
3558575 CGTGAGGATT
*
3558585 GGGCAATGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
3558603 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
* *
3558621 GTGCAGTGATCCAGCATG
1 GGGCAGTGGTCCAGCATG
*
3558639 GGGCAGTGGTCCAGTATG
1 GGGCAGTGGTCCAGCATG
3558657 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
*
3558675 GGGCAGTGGTCCAACATG
1 GGGCAGTGGTCCAGCATG
3558693 GG
1 GG
3558695 CATCTGACAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 84 1.00
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.18
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:3559030 original size:20 final size:20
Alignment explanation
Indices: 3558993--3559035 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3558983 ATTCCACCAC
*
3558993 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
3559013 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
3559033 ATG
1 ATG
3559036 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:3560037 original size:165 final size:165
Alignment explanation
Indices: 3559765--3560094 Score: 660
Period size: 165 Copynumber: 2.0 Consensus size: 165
3559755 ATTCGTCATC
3559765 AAGGAATGAAAAATGCACCTCCATATAAGCGGACTATTATTTATCTACAACAGTTCGTATTATAT
1 AAGGAATGAAAAATGCACCTCCATATAAGCGGACTATTATTTATCTACAACAGTTCGTATTATAT
3559830 CCTACCATATTTCTTCTTTCTTTTAAGGTTGTACATGCACTGATTGAACGTTGGAGACCCGAAAC
66 CCTACCATATTTCTTCTTTCTTTTAAGGTTGTACATGCACTGATTGAACGTTGGAGACCCGAAAC
3559895 TCATACGTTTAATTTTCCTAGTGGTGAAGCGGCAA
131 TCATACGTTTAATTTTCCTAGTGGTGAAGCGGCAA
3559930 AAGGAATGAAAAATGCACCTCCATATAAGCGGACTATTATTTATCTACAACAGTTCGTATTATAT
1 AAGGAATGAAAAATGCACCTCCATATAAGCGGACTATTATTTATCTACAACAGTTCGTATTATAT
3559995 CCTACCATATTTCTTCTTTCTTTTAAGGTTGTACATGCACTGATTGAACGTTGGAGACCCGAAAC
66 CCTACCATATTTCTTCTTTCTTTTAAGGTTGTACATGCACTGATTGAACGTTGGAGACCCGAAAC
3560060 TCATACGTTTAATTTTCCTAGTGGTGAAGCGGCAA
131 TCATACGTTTAATTTTCCTAGTGGTGAAGCGGCAA
3560095 TTAATTTGGA
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (165 bp):
AAGGAATGAAAAATGCACCTCCATATAAGCGGACTATTATTTATCTACAACAGTTCGTATTATAT
CCTACCATATTTCTTCTTTCTTTTAAGGTTGTACATGCACTGATTGAACGTTGGAGACCCGAAAC
TCATACGTTTAATTTTCCTAGTGGTGAAGCGGCAA
Found at i:3563278 original size:18 final size:18
Alignment explanation
Indices: 3563251--3563286 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3563241 TAATTTGAGT
*
3563251 TGACTCGAATAACTCAAA
1 TGACTAGAATAACTCAAA
3563269 TGACTAGAATAACTCAAA
1 TGACTAGAATAACTCAAA
3563287 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (18 bp):
TGACTAGAATAACTCAAA
Found at i:3563511 original size:60 final size:60
Alignment explanation
Indices: 3563418--3563542 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
3563408 TAAAGTGCGT
* * * *
3563418 AAATGATCCCATAACTATATAATATTATTTTGTTAAATCCTTCGACTATTGAAAA-CTACA
1 AAATGATCCCATAACTATAAAATATTACTTTGTTAAATCCATCGAATATT-AAAAGCTACA
* * * * * *
3563478 AAATGATCCCCTTACTATAAAATATTGCTTTGTTGAATTCATCGAATATTAAAAGTTACA
1 AAATGATCCCATAACTATAAAATATTACTTTGTTAAATCCATCGAATATTAAAAGCTACA
3563538 AAATG
1 AAATG
3563543 GTCACTTGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (60 bp):
AAATGATCCCATAACTATAAAATATTACTTTGTTAAATCCATCGAATATTAAAAGCTACA
Found at i:3566845 original size:29 final size:29
Alignment explanation
Indices: 3566800--3566857 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3566790 GTGTTGGCCG
3566800 TAGGTCGCCATGCCTTCCAGGCGACCTAC
1 TAGGTCGCCATGCCTTCCAGGCGACCTAC
* * *
3566829 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCAGGCGACCTAC
3566858 AAGAGATTGT
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:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCAGGCGACCTAC
Found at i:3566919 original size:14 final size:14
Alignment explanation
Indices: 3566900--3566941 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
3566890 CGCTGGGCAT
*
3566900 CCGAGGCCATCTGA
1 CCGAGGCCATCCGA
3566914 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
3566928 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
3566942 GACCATCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:3566941 original size:24 final size:23
Alignment explanation
Indices: 3566914--3566974 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
3566904 GGCCATCTGA
*
3566914 CCGAGGCCATCCGACCGAGGCCAT
1 CCGAGGCCATCCGAACGA-GCCAT
* *
3566938 CCGAGACCATCCGAACGAGCTAT
1 CCGAGGCCATCCGAACGAGCCAT
* *
3566961 GCGAGGGCATCCGA
1 CCGAGGCCATCCGA
3566975 GGGCAACCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.25, C:0.36, G:0.30, T:0.10
Consensus pattern (23 bp):
CCGAGGCCATCCGAACGAGCCAT
Found at i:3566972 original size:33 final size:33
Alignment explanation
Indices: 3566929--3567008 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
3566919 GCCATCCGAC
* *
3566929 CGAGGCCATCCGAGACCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGACCAACCGAACGAGCTATG
** *
3566962 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGACCAACCGAACGAGCTATG
*
3566995 CGAGGGAATCCGAG
1 CGAGGGCATCCGAG
3567009 CGAGGGTAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.26, C:0.29, G:0.35, T:0.10
Consensus pattern (33 bp):
CGAGGGCATCCGAGACCAACCGAACGAGCTATG
Found at i:3567049 original size:29 final size:29
Alignment explanation
Indices: 3567016--3567071 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3567006 GAGCGAGGGT
* *
3567016 AGGTCGCCCGGAGTGTATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
3567045 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
3567072 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:3567187 original size:29 final size:29
Alignment explanation
Indices: 3567142--3567198 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3567132 GAGCAAGGGT
*
3567142 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAATGCATGGCGACCTACA
*
3567171 AGGTCGTCCGGAATGCATGGCGACCTAC
1 AGGTCGCCCGGAATGCATGGCGACCTAC
3567199 GACCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAATGCATGGCGACCTACA
Found at i:3570982 original size:37 final size:37
Alignment explanation
Indices: 3570932--3571005 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
3570922 AACTTAACGT
*
3570932 TAAATTTTGAA-TGGGTACTAAAATGAAATAAAAAAC
1 TAAATTTTGAAGTGGGTACTAAAATGAAACAAAAAAC
*
3570968 TAAAGTTTTTAATGGTGGGTACTAAAATGAAACAAAAA
1 TAAA-TTTTGAA--GTGGGTACTAAAATGAAACAAAAA
3571006 TTAAATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.12
37 6 0.19
40 22 0.69
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.28
Consensus pattern (37 bp):
TAAATTTTGAAGTGGGTACTAAAATGAAACAAAAAAC
Found at i:3571891 original size:768 final size:759
Alignment explanation
Indices: 3570645--3572151 Score: 2533
Period size: 768 Copynumber: 2.0 Consensus size: 759
3570635 GAGGCAGGGC
3570645 GGGCCAGGGCAGGAGGGGCACCCGCCCAGAGCCTACAAATTAATTATTTTAAGTATAATATTTTT
1 GGGCCAGGGCAGGAGGGGCACCCGCCCAGAGCCTACAAATTAATTATTTTAAGTATAATATTTTT
* *
3570710 TTATTTTTCTGATAATAAATTAAAAATAGGGTAATTTATGCATTTAGCATCTAAACTATCAGTTT
66 TTATTTTTCTGACAATAAATTAAAAATAGGGTAATTTATGCATTTAGCACCTAAACTATCAGTTT
3570775 TAGTACCTAAACTTTTAATTTTTCCAAAATCATATCTAATGTTTAGTTTTCATTTCATTTTAGTA
131 TAGTACCTAAACTTTTAATTTTTCCAAAATCATATCTAATGTTTAGTTTTCATTTCATTTTAGTA
* *
3570840 CCTCGCCGTTAAAAACTTAATGTGTTTAGTACCTAAACTATCAGTTTTGGTTTGTTTTAGTACAT
196 CCCCGCCGTTAAAAACTTAATGTGTTTAGTACATAAACTATCAGTTTTGGTTTGTTTTAGTACAT
*
3570905 AAAATAAAAAAAATTAAAACTTAACGTTAAATTTTGAATGGGTACTAAAATGAAATAAAAAACTA
261 AAAATAAAAAAAATTAAAACTTAACGTTAAATTTTGAATAGGTACTAAAATGAAATAAAAAACTA
*
3570970 AAGTTTTTAATGGTGGGTACTAAAATGAAACAAAAATTAAATCTTAGGTATGATTTTGAAATAAA
326 AAGTTTTTAACGGTGGGTACTAAAATGAAACAAAAATTAAATCTTAGGTATGATTTTGAAATAAA
** *
3571035 TTGAAAGTTTAGGTGCTAAAACGGGTCAAACCTTATAGTTTAGATACTAAACACATAATTTACCC
391 TTGAAAGTTTAGGTAATAAAACGGGTCAAAACTTATAGTTTAGATACTAAACACATAATTTACCC
3571100 AATAAAATAATGGGGCCCATGAATTTATTAAGGTGTCAATTGTCATTATTGAATTTTATATTAAC
456 AATAAAATAATGGGGCCCATGAATTTATTAAGGTGTCAATTGTCATTATTGAATTTTATATTAAC
* * *
3571165 GTTAATAATTTGTTCTTCTATAAAATTCTAATTCAATATTTTTTTCCTAAAATTAAAAAAAATCA
521 ATTAATAATTTCTTCTTCTATAAAATTCTAATTCAATATTTCTTTCCTAAAATTAAAAAAAATCA
* *
3571230 ATTGAATATCTTTAATTTTGGTATTTCCAAATTCCCACCATAAATTCACCAAATCTCTTTCCCGA
586 ATTGAATATATTTAATTTTGATATTTCCAAATTCCCACCATAAATTCACCAAATCTCTTTCCCGA
* *
3571295 TTTTTCATATCAATGAACAAATTTGTTAACGTAATTTTTTTCTTCAAACCTTAATGA-GAGGAAA
651 TTTTTCATATCAATGAACAAATTTATTAACGTAATTTTTTTCTTCAAAACTTAAT-ATGAGGAAA
3571359 AAATTTAAGTATAATTAGCATGTTTGGTGAGGCAAGGTCGTCCCT
715 AAATTTAAGTATAATTAGCATGTTTGGTGAGGCAAGGTCGTCCCT
* * *
3571404 GGGCCTGGGTAGGAGGGGCATCCC-CCCAGGGCCTACAAATTAATTATTTTAAGTATAATA-TTT
1 GGGCCAGGGCAGGAGGGGCA-CCCGCCCAGAGCCTACAAATTAATTATTTTAAGTATAATATTTT
* *
3571467 TTTATTTTTTTGACAATAAATTCAAAATAGGGTAATTTATGCATTTAGCACCTAAACTATATGTT
65 TTTATTTTTCTGACAATAAATTAAAAATAGGGTAATTTATGCATTTAGCACCTAAAC--------
* *
3571532 TTGATCCGTTTTAGTACCTAAACTTTTAATTTTTTCAAAATCATATCTAATGTTTAGTTTTCATT
122 -T-ATCAGTTTTAGTACCTAAACTTTTAATTTTTCCAAAATCATATCTAATGTTTAGTTTTCATT
3571597 TCATTTTAGTACCCCCGCCGTT-AAAACTTAATGTGTTTAGTACATAAACTATCAGTTTTGGTTT
185 TCATTTTAGTA-CCCCGCCGTTAAAAACTTAATGTGTTTAGTACATAAACTATCAGTTTTGGTTT
*
3571661 GTTTTAGTACATAAAATAAAAAAAATTAAAACTTAACGTTAAATTTTGAATAGGTATTAAAATGA
249 GTTTTAGTACATAAAATAAAAAAAATTAAAACTTAACGTTAAATTTTGAATAGGTACTAAAATGA
*
3571726 AATAAAAAAGCTAAAGTTTTTAACGGCT-TGTACTAAAATGAAACAAAAATTAAATCTTAGGTAT
314 AATAAAAAA-CTAAAGTTTTTAACGG-TGGGTACTAAAATGAAACAAAAATTAAATCTTAGGTAT
*
3571790 GATTTTGAAATAAATTGAAAGTTTAGGTAATAAAACGGG-CTAAAACTTATAGTTTAGGTACTAA
377 GATTTTGAAATAAATTGAAAGTTTAGGTAATAAAACGGGTC-AAAACTTATAGTTTAGATACTAA
*
3571854 ACACATAATTTACCCAATAAAATAAT-GGGCTCATGAATTTATTAAGGTGTCAATTGTCATTATT
441 ACACATAATTTACCCAATAAAATAATGGGGCCCATGAATTTATTAAGGTGTCAATTGTCATTATT
*
3571918 GAATTTTATATTAACATTAATAATTTCTTCTTCTATAAAATTCTAATTCGATATTTCTTTCCTAA
506 GAATTTTATATTAACATTAATAATTTCTTCTTCTATAAAATTCTAATTCAATATTTCTTTCCTAA
* * *
3571983 AATTAAAAAAAATTAATTGAATATATTTAATTTTGATCTTTCTAAATTCCCACCATAAATTCACC
571 AATTAAAAAAAATCAATTGAATATATTTAATTTTGATATTTCCAAATTCCCACCATAAATTCACC
3572048 AAATCTCTTTCCCGATTTTTCATATCAATGAACAAATTTATTAACGTAATTTTTTTCTTCAAAAC
636 AAATCTCTTTCCCGATTTTTCATATCAATGAACAAATTTATTAACGTAATTTTTTTCTTCAAAAC
*
3572113 TTAATATGAGGAAAATATTTAAGTATAATTAGCATGTTT
701 TTAATATGAGGAAAAAATTTAAGTATAATTAGCATGTTT
3572152 CTTTTCTCTT
Statistics
Matches: 700, Mismatches: 32, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
758 56 0.08
759 53 0.08
760 3 0.00
767 2 0.00
768 442 0.63
769 143 0.20
770 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (759 bp):
GGGCCAGGGCAGGAGGGGCACCCGCCCAGAGCCTACAAATTAATTATTTTAAGTATAATATTTTT
TTATTTTTCTGACAATAAATTAAAAATAGGGTAATTTATGCATTTAGCACCTAAACTATCAGTTT
TAGTACCTAAACTTTTAATTTTTCCAAAATCATATCTAATGTTTAGTTTTCATTTCATTTTAGTA
CCCCGCCGTTAAAAACTTAATGTGTTTAGTACATAAACTATCAGTTTTGGTTTGTTTTAGTACAT
AAAATAAAAAAAATTAAAACTTAACGTTAAATTTTGAATAGGTACTAAAATGAAATAAAAAACTA
AAGTTTTTAACGGTGGGTACTAAAATGAAACAAAAATTAAATCTTAGGTATGATTTTGAAATAAA
TTGAAAGTTTAGGTAATAAAACGGGTCAAAACTTATAGTTTAGATACTAAACACATAATTTACCC
AATAAAATAATGGGGCCCATGAATTTATTAAGGTGTCAATTGTCATTATTGAATTTTATATTAAC
ATTAATAATTTCTTCTTCTATAAAATTCTAATTCAATATTTCTTTCCTAAAATTAAAAAAAATCA
ATTGAATATATTTAATTTTGATATTTCCAAATTCCCACCATAAATTCACCAAATCTCTTTCCCGA
TTTTTCATATCAATGAACAAATTTATTAACGTAATTTTTTTCTTCAAAACTTAATATGAGGAAAA
AATTTAAGTATAATTAGCATGTTTGGTGAGGCAAGGTCGTCCCT
Found at i:3577403 original size:33 final size:34
Alignment explanation
Indices: 3577361--3577427 Score: 109
Period size: 33 Copynumber: 1.9 Consensus size: 34
3577351 CTATAATTTA
3577361 CTAAAATTAGAGCTAA-TTTAGGTTTAGTCCTTT
1 CTAAAATTAGAGCTAATTTTAGGTTTAGTCCTTT
3577394 CTAAAATTAGAGCTAATTTTTTAGGTTTAGTCCT
1 CTAAAATTAGAGCTAA--TTTTAGGTTTAGTCCT
3577428 CTAGATCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 16 0.52
36 15 0.48
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (34 bp):
CTAAAATTAGAGCTAATTTTAGGTTTAGTCCTTT
Found at i:3579478 original size:25 final size:25
Alignment explanation
Indices: 3579450--3579520 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 25
3579440 TAATGCATTG
3579450 TTATGCATTTTCATTTATGGCATCT
1 TTATGCATTTTCATTTATGGCATCT
* * * *
3579475 TTATGC-----CAATAAT-GCACCA
1 TTATGCATTTTCATTTATGGCATCT
3579494 TTATGCATTTTCATTTATGGCATCT
1 TTATGCATTTTCATTTATGGCATCT
3579519 TT
1 TT
3579521 CTGTCAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 10 0.31
20 5 0.16
24 5 0.16
25 12 0.38
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.46
Consensus pattern (25 bp):
TTATGCATTTTCATTTATGGCATCT
Found at i:3579484 original size:44 final size:44
Alignment explanation
Indices: 3579436--3579648 Score: 311
Period size: 44 Copynumber: 4.8 Consensus size: 44
3579426 CACTTTTTTC
* *
3579436 CCAATAATGCATTGTTATGCATTTTCATTTATGGCATCTTTATG
1 CCAATAATGCACTGTTATGCATTTTCATTTATGGCATCTTTCTG
**
3579480 CCAATAATGCACCATTATGCATTTTCATTTATGGCATCTTTCTG
1 CCAATAATGCACTGTTATGCATTTTCATTTATGGCATCTTTCTG
* * * *
3579524 TCAATAATGCACTATTATGCATTTTCATTTATGACACCTTTCTG
1 CCAATAATGCACTGTTATGCATTTTCATTTATGGCATCTTTCTG
* *
3579568 CCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CATTTCTT
1 CCAATAATGCACTGTTATGCATTTTCATTTATGGCATC-TTTCTG
*
3579612 CCAATAATACACTGTTATGCATTTTCATTTATGGCAT
1 CCAATAATGCACTGTTATGCATTTTCATTTATGGCAT
3579649 GTTGAAAACA
Statistics
Matches: 152, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.01
44 151 0.99
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (44 bp):
CCAATAATGCACTGTTATGCATTTTCATTTATGGCATCTTTCTG
Found at i:3585753 original size:20 final size:20
Alignment explanation
Indices: 3585728--3585809 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
3585718 TTTTGGTGTA
3585728 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
* * *
3585748 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATACCCCC-AT
* * *
3585769 AAAGGGGAATCGATTCCCCCCAC
1 -GA-GGGAATCGA-TACCCCCAT
*
3585792 GGGGGAATCGATACCCCC
1 GAGGGAATCGATACCCCC
3585810 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 22 0.47
21 10 0.21
22 1 0.02
23 8 0.17
24 6 0.13
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:3586515 original size:12 final size:12
Alignment explanation
Indices: 3586483--3586516 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3586473 ACACCGTCAA
*
3586483 CCAAATCCACCT
1 CCAAATCCTCCT
3586495 CCAAATCCTCCT
1 CCAAATCCTCCT
3586507 CCAAATCCTC
1 CCAAATCCTC
3586517 GTCCTATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:3587816 original size:17 final size:17
Alignment explanation
Indices: 3587783--3587816 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3587773 TTGAATATTT
* *
3587783 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
3587800 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
3587817 GATTTGTTTG
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:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:3589321 original size:44 final size:43
Alignment explanation
Indices: 3589253--3589386 Score: 180
Period size: 44 Copynumber: 3.0 Consensus size: 43
3589243 TTAACTCAAC
* * *
3589253 ATGGCACATTTCTTCCAATGATGCACCGTTATGCATTTTCATTT
1 ATGGCAC-TTTCTACCAATAATGCACAGTTATGCATTTTCATTT
*
3589297 ATGGCATCTTTCTACCAATAATGCACAGTTATACATTTTCATTT
1 ATGGCA-CTTTCTACCAATAATGCACAGTTATGCATTTTCATTT
*
3589341 ATGGCACCTTTCTGCCAATAATGCACTA-TTATGCATTTTCATTT
1 ATGGCA-CTTTCTACCAATAATGCAC-AGTTATGCATTTTCATTT
3589385 AT
1 AT
3589387 TTCGGTAACA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 79 0.98
45 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (43 bp):
ATGGCACTTTCTACCAATAATGCACAGTTATGCATTTTCATTT
Found at i:3590102 original size:21 final size:21
Alignment explanation
Indices: 3590076--3590143 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
3590066 TATATATATA
3590076 TTTTTAATTATATTTTTTATT
1 TTTTTAATTATATTTTTTATT
*
3590097 TTTTT-ACTATATTCCTTTT-TT
1 TTTTTAATTATATT--TTTTATT
*
3590118 TATTTATATTATATTATTTTTATT
1 TTTTTA-ATTATA-T-TTTTTATT
3590142 TT
1 TT
3590144 ATATATCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 4 0.11
23 9 0.25
24 4 0.11
25 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTAATTATATTTTTTATT
Found at i:3590137 original size:20 final size:19
Alignment explanation
Indices: 3590074--3590147 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
3590064 CCTATATATA
* *
3590074 TATTTTTAATTATATTTTT
1 TATTTTTATTTATATTTAT
**
3590093 TATTTTT-TTACTATATTCCT
1 TATTTTTATT--TATATTTAT
3590113 T-TTTTTATTTATATTATAT
1 TATTTTTATTTATATT-TAT
3590132 TATTTTTATTTTATAT
1 TATTTTTA-TTTATAT
3590148 ATCTTATATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 7 0.16
19 14 0.32
20 16 0.36
21 7 0.16
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTATTTATATTTAT
Found at i:3590148 original size:23 final size:21
Alignment explanation
Indices: 3590074--3590149 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 21
3590064 CCTATATATA
3590074 TATTTTTA-ATTATA-TTTTT
1 TATTTTTATATTATATTTTTT
* *
3590093 TATTTTTTTACTATATTCCTTTT
1 TATTTTTATATTATATT--TTTT
3590116 T-TTATTTATATTATATTATTTT
1 TATT-TTTATATTATATT-TTTT
3590138 TATTTTATATAT
1 TATTTT-TATAT
3590150 CTTATATCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.16
20 5 0.11
21 1 0.02
22 9 0.20
23 23 0.51
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTTATATTATATTTTTT
Found at i:3590244 original size:39 final size:40
Alignment explanation
Indices: 3590196--3590277 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 40
3590186 TTTTTCTCCA
3590196 TTTACTATGTATCTATATATAGTTTTTCTTAATATTATAT
1 TTTACTATGTATCTATATATAGTTTTTCTTAATATTATAT
* * * *
3590236 TTTA-TATGTTTTTATATATATTTTTTCTTAATATTCTAT
1 TTTACTATGTATCTATATATAGTTTTTCTTAATATTATAT
3590275 TTT
1 TTT
3590278 TGTTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (40 bp):
TTTACTATGTATCTATATATAGTTTTTCTTAATATTATAT
Found at i:3590460 original size:18 final size:17
Alignment explanation
Indices: 3590428--3590472 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
3590418 TGTACACATT
3590428 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
3590445 ATTTCTTTTACCTTTTTA
1 ATTT-TTTTACCTTTTTA
3590463 ATTTTTTTAC
1 ATTTTTTTAC
3590473 TCCATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:3590589 original size:26 final size:27
Alignment explanation
Indices: 3590529--3590595 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
3590519 ATTCATTTTG
* *
3590529 TTTATTTTTTTTTTATTTTTTACGTGT
1 TTTATTTATTTTCTATTTTTTACGTGT
* *
3590556 TTT-GTTATTTTCTATTTTTT-CTTGT
1 TTTATTTATTTTCTATTTTTTACGTGT
3590581 TTTATTTATTATTCT
1 TTTATTTATT-TTCT
3590596 CACGTTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 7 0.21
26 19 0.58
27 7 0.21
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (27 bp):
TTTATTTATTTTCTATTTTTTACGTGT
Found at i:3592443 original size:7 final size:7
Alignment explanation
Indices: 3592423--3592463 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
3592413 GAACATTTCA
3592423 TGCATTTT
1 TGCA-TTT
3592431 TGCATTT
1 TGCATTT
*
3592438 TTCATTT
1 TGCATTT
*
3592445 TGCATCT
1 TGCATTT
3592452 TGCATTT
1 TGCATTT
3592459 TGCAT
1 TGCAT
3592464 ATACATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:3593730 original size:27 final size:25
Alignment explanation
Indices: 3593700--3593751 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
3593690 CAAAAAGAGA
3593700 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
3593727 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
3593752 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:3593732 original size:13 final size:13
Alignment explanation
Indices: 3593702--3593750 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
3593692 AAAAGAGAAA
3593702 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
3593716 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
3593729 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
3593742 AAAG-GAAAA
1 AAAGAGAAAA
3593751 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:3595539 original size:36 final size:37
Alignment explanation
Indices: 3595492--3595821 Score: 126
Period size: 36 Copynumber: 9.5 Consensus size: 37
3595482 ATTGAAAACA
** * *
3595492 TTTCCCTTGAAA-TGAATTTTGT-CTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTT-TCCTCCCTTGAGACAG
3595528 TTTCCCTTGAAACAAAATTTTTCCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTTCCTCCCTTGAGACAG
* * *
3595565 TTTCTCTTGAAACATAAA---------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTTCCTCCCTTG-AGACAG
* ** *
3595594 TTTCCCTTGAAA-TAAATATCGT-CTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAAT-TTTTCCTCCCTTGAGACAG
*
3595630 TTTCCCTTGAAAC-AAATTTTGT-CTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTT-TCCTCCCTTGAGACAG
* *
3595666 TTTCCCTTGAAACAAAA----T-AT---TTGA-ATATG
1 TTTCCCTTGAAACAAAATTTTTCCTCCCTTGAGACA-G
*** *
3595695 TTTTATTTGAAAC-AAATTTCAT-CTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTT-TTCCTCCCTTGAGACAG
** * * * *
3595731 TTTCTTTTGGAACTAAGTTTTGT-CTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTT-TCCTCCCTTGAGACAG
* * *
3595768 TTTCTCTTGAAAC-AAATTTCGT-CTCTCTTGAGACAG
1 TTTCCCTTGAAACAAAATTT-TTCCTCCCTTGAGACAG
3595804 TTTCCCTTGAAACAAAAT
1 TTTCCCTTGAAACAAAAT
3595822 CTTTGAATTT
Statistics
Matches: 231, Mismatches: 32, Indels: 61
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 30 0.13
30 4 0.02
32 2 0.01
33 2 0.01
35 5 0.02
36 107 0.46
37 70 0.30
38 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTTCCTCCCTTGAGACAG
Found at i:3595559 original size:37 final size:37
Alignment explanation
Indices: 3595492--3595578 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
3595482 ATTGAAAACA
** * *
3595492 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3595528 TTTCCCTTGAAACAAAATTTT-TCCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGT-CTCCCTTGAGACAG
*
3595565 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
3595579 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 13 0.30
37 31 0.70
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3595581 original size:102 final size:102
Alignment explanation
Indices: 3595405--3595781 Score: 456
Period size: 102 Copynumber: 3.7 Consensus size: 102
3595395 TAAAAAGAAG
* * * *
3595405 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTT-TCTCCCTTGAGACAATTTCTC
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTGTCTCCCTTGAGACAGTTTCTC
*
3595469 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
65 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
** *
3595507 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTT-TCCTCCCTTGAGACAGTTTCTC
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGT-CTCCCTTGAGACAGTTTCTC
3595571 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
65 TTGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
* * * *
3595609 ATATCGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* * ** *** *
3595673 TGAAACA-AAATATTTGAATATGTTTTATTTGAAACAA
66 TGAAACATAAACA-TTGAAAACATTTCCCTTGAAATAA
* ** * * * *
3595710 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
3595775 TGAAACA
66 TGAAACA
3595782 AATTTCGTCT
Statistics
Matches: 246, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
100 4 0.02
101 82 0.33
102 160 0.65
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
Found at i:3595727 original size:203 final size:204
Alignment explanation
Indices: 3595411--3595781 Score: 471
Period size: 203 Copynumber: 1.8 Consensus size: 204
3595401 GAAGATTTTA
* *
3595411 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTTTCTCCCTTGAGACAATTTCTCTTGAAAC
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTTTCTCCCTTGAGACAATTTCCCTTGAAAC
* ** ** * *
3595476 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
66 ATAAACATTGAAAACATTTCACTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAAC
3595541 AAAATTTT-TCCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
131 AAAATTTTGT-CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
3595605 ATAAATATCG
195 ATAAATATCG
* * *
3595615 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAT-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTT-TCTCCCTTGAGACAATTTCCCTTGAAA
* * ** * * ** *
3595678 CA-AAATATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGA
65 CATAAACA-TTGAAAACATTTCACTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAA
* * *
3595742 ACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
129 ACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
3595782 AATTTCGTCT
Statistics
Matches: 140, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
202 7 0.05
203 106 0.76
204 27 0.19
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (204 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTTTCTCCCTTGAGACAATTTCCCTTGAAAC
ATAAACATTGAAAACATTTCACTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAAC
AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
TAAATATCG
Found at i:3595756 original size:138 final size:138
Alignment explanation
Indices: 3595614--3595873 Score: 416
Period size: 138 Copynumber: 1.9 Consensus size: 138
3595604 AATAAATATC
*
3595614 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* *
3595679 AAAATATTTGAATATGT-TTTAT-TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGA
66 AAAATATTTGAAT-T-TATTTATCCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGA
3595742 ACTAAGTTTT
129 ACTAAGTTTT
*
3595752 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * **
3595817 AAAATCTTTGAATTTATTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATTTATTTATCCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
3595874 CTTGAAACAC
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
136 1 0.01
137 5 0.04
138 106 0.95
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATTTATTTATCCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:3595771 original size:37 final size:36
Alignment explanation
Indices: 3595701--3595819 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 36
3595691 TATGTTTTAT
* * *
3595701 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
* * *
3595737 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAATTTCGTCTCTCTTGAGACAGTTTCTC
*
3595774 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
3595810 TTGAAACAAA
1 TTGAAACAAA
3595820 ATCTTTGAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 42 0.58
37 30 0.42
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
Found at i:3595872 original size:65 final size:67
Alignment explanation
Indices: 3595768--3595939 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 67
3595758 CTTGAGACAG
* * * * **
3595768 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
3595831 TA
66 TA
*
3595833 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
3595898 TA
66 TA
* *
3595900 TTTC-CCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT
1 TTTCTCC-TAAAAC-AAATTTTGTCTCCCTTGAGACAGTTT
3595940 TTCATGAAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 40 0.43
66 4 0.04
67 26 0.28
68 24 0.26
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (67 bp):
TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:3596868 original size:110 final size:108
Alignment explanation
Indices: 3596660--3596926 Score: 292
Period size: 110 Copynumber: 2.5 Consensus size: 108
3596650 ACGAAGGGGC
* * * *
3596660 TTCCCAG-T-TTCAGAGCCAATTTCAACTTCATAGCGAGGGATATTGGACTCAAGACAACACAAG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAG
* * * * *
3596723 CTCAACTTCACAATGAAGGGGCAATTGATTGTCAACAAACAACT
66 CTCAACTTCACAACGAAGAGGCAACTGACTATCAACAAACAA-T
* * * *
3596767 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGATAACACA
1 TTCCCAG-TTC-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
* ** * *
3596831 AGCTCAACTTCACAGCGAAGAGGCGGCTGGCTATCAACAAATAAT
64 AGCTCAACTTCACAACGAAGAGGCAACTGACTATCAACAAACAAT
* *
3596876 TTCCCAGTTC--CAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
3596927 GAAAAATACT
Statistics
Matches: 132, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
106 40 0.30
107 2 0.02
108 1 0.01
109 6 0.05
110 83 0.63
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (108 bp):
TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAG
CTCAACTTCACAACGAAGAGGCAACTGACTATCAACAAACAAT
Found at i:3598311 original size:23 final size:22
Alignment explanation
Indices: 3598263--3598330 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
3598253 TATATTTTTA
*
3598263 ATTATATTTTTTATTTATTTACTAT
1 ATTAT-TTTTTTATTTA--TATTAT
*
3598288 ATTCCTTTTTTTATTTATATTAT
1 ATT-ATTTTTTTATTTATATTAT
*
3598311 ATTATTTTTATTATATATAT
1 ATTATTTTT-TTATTTATAT
3598331 CTTATATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 5 0.14
23 17 0.46
25 14 0.38
26 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTATTTTTTTATTTATATTAT
Found at i:3598317 original size:14 final size:14
Alignment explanation
Indices: 3598298--3598337 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3598288 ATTCCTTTTT
3598298 TTATTTATATTATA
1 TTATTTATATTATA
*
3598312 TTATTTTTATTATA
1 TTATTTATATTATA
3598326 TATATCTTATAT
1 T-TAT-TTATAT
3598338 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:3598318 original size:21 final size:21
Alignment explanation
Indices: 3598267--3598328 Score: 54
Period size: 25 Copynumber: 2.8 Consensus size: 21
3598257 TTTTTAATTA
*
3598267 TATTTTTTATTTATTTACTATAT
1 TATTTTTTATTTA--TATTATAT
*
3598290 TCCTTTTTTTATTTATATTATAT
1 T--ATTTTTTATTTATATTATAT
3598313 TA-TTTTTATTATATAT
1 TATTTTTTATT-TATAT
3598329 ATCTTATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 8 0.24
21 5 0.15
23 9 0.27
25 11 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTTTTATTTATATTATAT
Found at i:3598423 original size:17 final size:19
Alignment explanation
Indices: 3598393--3598454 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
3598383 TTTACTATGT
*
3598393 ATATATATAGTTTTTCTTA
1 ATATATATACTTTTTCTTA
*
3598412 ATAT-TATA-TTTTATACGTTT
1 ATATATATACTTTT-T-C-TTA
*
3598432 TTATATATACTTTTTCTTA
1 ATATATATACTTTTTCTTA
3598451 ATAT
1 ATAT
3598455 TCTATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 10 0.29
20 6 0.18
21 5 0.15
22 4 0.12
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (19 bp):
ATATATATACTTTTTCTTA
Found at i:3598732 original size:11 final size:11
Alignment explanation
Indices: 3598702--3598738 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
3598692 TTTTTTAACA
3598702 TTTTATTCATTT
1 TTTTATT-ATTT
3598714 TGTTTATTATTT
1 T-TTTATTATTT
3598726 TTTTATTATTT
1 TTTTATTATTT
3598737 TT
1 TT
3598739 ACGTGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 12 0.50
12 6 0.25
13 6 0.25
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:3599553 original size:22 final size:22
Alignment explanation
Indices: 3599510--3599564 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
3599500 GTACCCCTAC
* *
3599510 TATGGTATCGATACTTCTTTTT
1 TATGGTATCGATACTCCCTTTT
3599532 TATGGTA-CTGATACTCCC-TTT
1 TATGGTATC-GATACTCCCTTTT
3599553 TA--GTATCGATAC
1 TATGGTATCGATAC
3599565 CATTTCTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 6 0.21
22 14 0.48
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (22 bp):
TATGGTATCGATACTCCCTTTT
Found at i:3605833 original size:44 final size:44
Alignment explanation
Indices: 3605779--3606027 Score: 372
Period size: 44 Copynumber: 5.6 Consensus size: 44
3605769 ATACCATGAG
*
3605779 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
3605823 TGGCATCTTTCTGCTAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
3605867 TGGCACCACCTTTCTACCAATAATGCACCGTTATGTATTTTCATTTA
1 TGG---CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** * *
3605914 TGGCACAGTTCTGCTAACAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
3605958 TGGCACCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
3606002 TGGCACCTTTCTGCCAATAATGCACC
1 TGGCACCTTTCTGCCAATAATGCACC
3606028 TTTTCTGCCA
Statistics
Matches: 182, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
44 142 0.78
47 40 0.22
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:3605937 original size:91 final size:87
Alignment explanation
Indices: 3605779--3606027 Score: 381
Period size: 91 Copynumber: 2.8 Consensus size: 87
3605769 ATACCATGAG
3605779 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGGCATCTTTCTGCTAATAAT
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CTTTCTGCTAATAAT
3605844 GCACCGTTATGCATTTTCATTTA
65 GCACCGTTATGCATTTTCATTTA
* * *
3605867 TGGCACCACCTTTCTACCAATAATGCACCGTTATGTATTTTCATTTATGGCACAGTTCTGCTAAC
1 TGG---CACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGGCAC-TTTCTGCTAAT
3605932 AATGCACCGTTATGCATTTTCATTTA
62 AATGCACCGTTATGCATTTTCATTTA
* * * *
3605958 TGGCACCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTCTGCCAATAAT
1 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CTTTCTGCTAATAAT
3606023 GCACC
65 GCACC
3606028 TTTTCTGCCA
Statistics
Matches: 146, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
88 61 0.42
89 1 0.01
90 1 0.01
91 83 0.57
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (87 bp):
TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGGCACTTTCTGCTAATAATG
CACCGTTATGCATTTTCATTTA
Found at i:3606028 original size:19 final size:20
Alignment explanation
Indices: 3606004--3606047 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3605994 TTCATTTATG
3606004 GCACC-TTTCTGCCAATAAT
1 GCACCTTTTCTGCCAATAAT
3606023 GCACCTTTTCTGCCAATAAT
1 GCACCTTTTCTGCCAATAAT
3606043 GCACC
1 GCACC
3606048 GTTATGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (20 bp):
GCACCTTTTCTGCCAATAAT
Found at i:3606048 original size:64 final size:63
Alignment explanation
Indices: 3605960--3606088 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 63
3605950 TTCATTTATG
3605960 GCACCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTCTGCCAATAAT
1 GCACCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTCTGCCAATAAT
* *
3606023 GCACCTTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATTGCACCTTTCTGCCAATAAT
1 GCACCTTTT-TGCCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTCTGCCAATAAT
3606087 GC
1 GC
3606089 CTCATTATGA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 9 0.14
64 54 0.86
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (63 bp):
GCACCTTTTTGCCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTCTGCCAATAAT
Found at i:3606086 original size:44 final size:45
Alignment explanation
Indices: 3606022--3606111 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
3606012 CTGCCAATAA
* *
3606022 TGCACCTTTTCTGCCAATAATGCAC-CGTTATGCATTTTCATTTAT
1 TGCACCTTTTCTGCCAATAATGC-CTCATTATGAATTTTCATTTAT
3606067 TGCACC-TTTCTGCCAATAATGCCTCATTATGAATTTTCATTTAT
1 TGCACCTTTTCTGCCAATAATGCCTCATTATGAATTTTCATTTAT
3606111 T
1 T
3606112 TCGGTAACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 35 0.83
45 6 0.14
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (45 bp):
TGCACCTTTTCTGCCAATAATGCCTCATTATGAATTTTCATTTAT
Found at i:3609850 original size:20 final size:19
Alignment explanation
Indices: 3609813--3609850 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3609803 TTTCTTCAAT
3609813 AAAATTTTTAAAAGAAGAA
1 AAAATTTTTAAAAGAAGAA
3609832 AAAATATTTTCAAAA-AAGA
1 AAAAT-TTTT-AAAAGAAGA
3609851 TAATTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAATTTTTAAAAGAAGAA
Found at i:3610541 original size:116 final size:115
Alignment explanation
Indices: 3610380--3610707 Score: 342
Period size: 116 Copynumber: 2.8 Consensus size: 115
3610370 AATGTAATGG
** * *
3610380 TCATAATGGGAAGAACTCGTTGGATGAGGGAGAAGAA-TTTCCTAATGAGAAGAACTTGTTCAAT
1 TCATAAT-GGAAGAACTCGTCCGATCAGGGAGAAGAAGTTT-CTAATGAGAAGAACTTGTTCAAC
** * *
3610444 ATTGGCTTGTCCATCACAGAATGAGGTGGATC-AGTATTTCCAACAAAAGGGT
64 ATTGGCTCATCCATCACAGAATGAGGTGGATCGA-CATTTCCAACAAAAGGGC
* *
3610496 TTATAATAGGAAGAACTCGTCCGATCAGGGAGAAGAAGTTTCTAATGAGAAGAACTTGTTCAACC
1 TCATAAT-GGAAGAACTCGTCCGATCAGGGAGAAGAAGTTTCTAATGAGAAGAACTTGTTCAACA
* * * *
3610561 TTGGCTCATCCATCACATAATGATGTGGATCGACATTTCCAATAGAAGGGC
65 TTGGCTCATCCATCACAGAATGAGGTGGATCGACATTTCCAACAAAAGGGC
* * * * *
3610612 TCATAATGAGAAAAACTCGTCCGA-CAAGGGAAAAGATG-TTCATAATGAGAAAAAATTGTTCAA
1 TCATAATG-GAAGAACTCGTCCGATC-AGGGAGAAGAAGTTTC-TAATGAGAAGAACTTGTTCAA
* * * *
3610675 -ACTTGACTCATCCATCACATAAGGAGTTGGATC
63 CA-TTGGCTCATCCATCACAGAATGAGGTGGATC
3610708 ATCATCATCT
Statistics
Matches: 180, Mismatches: 26, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
115 5 0.03
116 171 0.95
117 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (115 bp):
TCATAATGGAAGAACTCGTCCGATCAGGGAGAAGAAGTTTCTAATGAGAAGAACTTGTTCAACAT
TGGCTCATCCATCACAGAATGAGGTGGATCGACATTTCCAACAAAAGGGC
Found at i:3610940 original size:36 final size:35
Alignment explanation
Indices: 3610817--3610977 Score: 144
Period size: 36 Copynumber: 4.5 Consensus size: 35
3610807 TTCACTAAAG
*
3610817 ATTTTATCTCACTTGAGATTATTTTCCTTAAAACA
1 ATTTTATCTCACTTGAGATTATTTTTCTTAAAACA
* ** *
3610852 CATTTTGTCT-ATCTCAAGATTATTTTTCTTTACAACAA
1 -ATTTTATCTCA-CTTGAGATTATTTTTC-TTAAAAC-A
** *
3610890 ATTTCCTCTCACTTGAGATTATTTTTCTCAAAACGA
1 ATTTTATCTCACTTGAGATTATTTTTCTTAAAAC-A
* * * *
3610926 ATTTTATCTTACTTGAGATTGTTTTTCTAAAAATA
1 ATTTTATCTCACTTGAGATTATTTTTCTTAAAACA
*
3610961 AGTTTTGTCTCACTTGA
1 A-TTTTATCTCACTTGA
3610978 AACAGTTTCC
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
35 3 0.03
36 68 0.68
37 27 0.27
38 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.47
Consensus pattern (35 bp):
ATTTTATCTCACTTGAGATTATTTTTCTTAAAACA
Found at i:3615278 original size:138 final size:139
Alignment explanation
Indices: 3615029--3615310 Score: 300
Period size: 138 Copynumber: 2.0 Consensus size: 139
3615019 TTCTAGGTGG
* * * * ** *
3615029 ATATTTGATTTGGTCATCGCATTAATGTGCAAGGATCCATTTCGAGTATTTTATTCAATAATAGG
1 ATATTTGATTTAGCCATCGCATTAATGTCCAAGGATCCATTTCGAGTACTCGATTCAATAATAGA
* * * * *
3615094 TTAAAATTAATTAGGATTAATGATGAGAGCCTATACTTAAGATTAATTTTAC-TTTAGTCCCTTA
66 TCAAAATTAAATAGGATTAATAATGAGAGCCTATACTTAAGATTAATATCACTTTTAGTCCCTTA
*
3615158 ATTTAGGGA
131 ATTTAAGGA
* * * * * * *
3615167 CTATTTGATTTAGCCCTCGCCTTAATGTCCAAGGGTTCATTTCGATTACTCGATTCAATAATTGA
1 ATATTTGATTTAGCCATCGCATTAATGTCCAAGGATCCATTTCGAGTACTCGATTCAATAATAGA
* * * * *
3615232 TCATAATTAAATAGGATTAATAATTAGAGCCTCCA-ACTT-ATATTAATATCGCTTTTAGTCCTT
66 TCAAAATTAAATAGGATTAATAATGAGAGCCT--ATACTTAAGATTAATATCACTTTTAGTCCCT
3615295 TAATTTAAGGA
129 TAATTTAAGGA
3615306 ATATT
1 ATATT
3615311 CAATTTGGCA
Statistics
Matches: 115, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
138 87 0.76
139 27 0.23
140 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (139 bp):
ATATTTGATTTAGCCATCGCATTAATGTCCAAGGATCCATTTCGAGTACTCGATTCAATAATAGA
TCAAAATTAAATAGGATTAATAATGAGAGCCTATACTTAAGATTAATATCACTTTTAGTCCCTTA
ATTTAAGGA
Done.