Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 4 of 109
Found at i:502207 original size:17 final size:17
Alignment explanation
Indices: 502185--502219 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
502175 TTACTTTTCA
**
502185 TTTCATTTTTAAAAATT
1 TTTCATTTAAAAAAATT
502202 TTTCATTTAAAAAAATT
1 TTTCATTTAAAAAAATT
502219 T
1 T
502220 AATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTCATTTAAAAAAATT
Found at i:502346 original size:41 final size:41
Alignment explanation
Indices: 502301--502559 Score: 254
Period size: 41 Copynumber: 6.2 Consensus size: 41
502291 ATGACTCCTT
* *
502301 TGTTTAGAGGAGCATTTTATTTTTCAAAGTTGTGATGCATC
1 TGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGCCTC
* *
502342 TGTTTAGATGAGCAATTTATTTTTCAAAGTTGTGGTGCCTC
1 TGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGCCTC
* *
502383 TGTTTAGAGGAACAATTTATTTTTCTCAAAGTTAT-AGTGCCTC
1 TGTTTAGAGGAGCAATTTA-TTTT-TCAAAGTTGTGA-TGCCTC
* * * * * * *
502426 TGTTTAAATGAGCAATTTTATGTTTCAATGTTGTGGTACCTT
1 TGTTTAGAGGAGCAA-TTTATTTTTCAAAGTTGTGATGCCTC
* * *
502468 TATTTAGAGGAGCAATTTA-TTTTCAAAAGTTATGATGCTTC
1 TGTTTAGAGGAGCAATTTATTTTTC-AAAGTTGTGATGCCTC
* * * * *
502509 TATTTAGAGGAGTATTTTATTTTTCAAAGTCGTTGA-ACCTC
1 TGTTTAGAGGAGCAATTTATTTTTCAAAGTTG-TGATGCCTC
502550 TGTTTAGAGG
1 TGTTTAGAGG
502560 TGTTTTGTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
40 4 0.02
41 102 0.58
42 36 0.20
43 30 0.17
44 4 0.02
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.44
Consensus pattern (41 bp):
TGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGATGCCTC
Found at i:502459 original size:126 final size:125
Alignment explanation
Indices: 502301--502533 Score: 288
Period size: 126 Copynumber: 1.9 Consensus size: 125
502291 ATGACTCCTT
* * * * *
502301 TGTTTAGAGGAGCATTTTATTTTTCAAAGTTGTGATGCATCTGTTTAGATGAGCAATTTATTTTT
1 TGTTTAAAGGAGCATTTTATGTTTCAAAGTTGTGATACATCTATTTAGAGGAGCAATTTA-TTTT
* * *
502366 C-AAAGTTGTGGTGCCTCTGTTTAGAGGAACAATTTATTTTTCTCAAAGTTATAGTGCCTC
65 CAAAAGTTATGATGCCTCTATTTAGAGGAACAATTTATTTTTCTCAAAGTTATAGTGCCTC
* * * * *
502426 TGTTTAAATGAGCAATTTTATGTTTCAATGTTGTGGTACCTTTATTTAGAGGAGCAATTTATTTT
1 TGTTTAAAGGAGC-ATTTTATGTTTCAAAGTTGTGATACATCTATTTAGAGGAGCAATTTATTTT
* ** *
502491 CAAAAGTTATGATGCTTCTATTTAGAGGAGTATTTTATTTTTC
65 CAAAAGTTATGATGCCTCTATTTAGAGGAACAATTTATTTTTC
502534 AAAGTCGTTG
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
125 16 0.18
126 73 0.82
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (125 bp):
TGTTTAAAGGAGCATTTTATGTTTCAAAGTTGTGATACATCTATTTAGAGGAGCAATTTATTTTC
AAAAGTTATGATGCCTCTATTTAGAGGAACAATTTATTTTTCTCAAAGTTATAGTGCCTC
Found at i:502799 original size:24 final size:24
Alignment explanation
Indices: 502767--502812 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
502757 AAAAAATAGG
502767 AGGAGTTTAAGTGGGATTAAAATT
1 AGGAGTTTAAGTGGGATTAAAATT
*
502791 AGGAGTTTAGGTGGGATTAAAA
1 AGGAGTTTAAGTGGGATTAAAA
502813 GTTGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (24 bp):
AGGAGTTTAAGTGGGATTAAAATT
Found at i:503205 original size:12 final size:12
Alignment explanation
Indices: 503188--503224 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
503178 TTTCCAAAAA
503188 TCGATGAACTTT
1 TCGATGAACTTT
503200 TCGATGAACTTT
1 TCGATGAACTTT
503212 TCGATGAACTTT
1 TCGATGAACTTT
503224 T
1 T
503225 GACGAACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (12 bp):
TCGATGAACTTT
Found at i:503887 original size:59 final size:60
Alignment explanation
Indices: 503752--504048 Score: 277
Period size: 59 Copynumber: 4.9 Consensus size: 60
503742 AAAATTTGAA
*
503752 AAAAAAT-TTTTTAAAGG-AAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAAAAAAAAGATTT
1 AAAAAATATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-----AAAAAGATTT
503815 C
60 C
*** * * *
503816 AAGAAGGGATTTTTAAGGAAAAGTTGAAAGTATTAATTTCCCTTGAAAATAAAAA-TTTTC
1 AA-AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAGATTTC
* * * *
503876 AAAAAATATTTTTAAGAAAAAGTTTAAAATAACAATTTTCCTTGAAAA-AAAAAGATTTC
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAGATTTC
*** * *
503935 AAGAAGGGATTTTTAA-GAAAAGGTTGAAAGTATCAATTTTTCTTGAAAAT--AAA-ATTTGA
1 AA-AAAATATTTTTAAGGAAAA-GTTGAAAGTATCAATTTTCCTTGAAAATAAAAAGATTT-C
* *
503994 AGAAAAATATTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAA
1 A-AAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAA
504049 CCTTAAAATG
Statistics
Matches: 194, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
58 9 0.05
59 89 0.46
60 45 0.23
61 8 0.04
64 2 0.01
65 6 0.03
66 35 0.18
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (60 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAGATTTC
Found at i:503963 original size:119 final size:119
Alignment explanation
Indices: 503736--504048 Score: 373
Period size: 119 Copynumber: 2.6 Consensus size: 119
503726 TGATCTCTTT
* * * * *
503736 AAAATGAAAATTTGAAAAAAAAT-TTTTTAAAGGAAAGTTGAAAGTATCAATTTCCCTTGAAAAT
1 AAAAT-AAAATTTGAAGAAAAATATTTTTAAAGAAAAGTTGAAAATAACAATTTTCCTTG-----
*
503800 AAAAAAAAAAGATTTCAAGAAGGGATTTTTAAGGAAAAGTTGAAAGTATTAATTTCCCTTG
60 -AAAAAAAAAGATTTCAAGAAGGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTCCCTTG
** *
503861 AAAATAAAAATTTTCA-AAAAATATTTTT-AAGAAAAAGTTTAAAATAACAATTTTCCTTGAAAA
1 AAAAT-AAAATTTGAAGAAAAATATTTTTAAAG-AAAAGTTGAAAATAACAATTTTCCTTGAAAA
**
503924 AAAAAGATTTCAAGAAGGGATTTTTAA-GAAAAGGTTGAAAGTATCAATTTTTCTTG
64 AAAAAGATTTCAAGAAGGGATTTTTAAGGAAAA-GTTGAAAGTATCAATTTCCCTTG
* * *
503980 AAAATAAAATTTGAAGAAAAATATTTTTAAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATA
1 AAAATAAAATTTGAAGAAAAATATTTTTAAAGAAAAGTTGAAAATAACAATTTTCCTTGAAAA-A
504045 AAAA
65 AAAA
504049 CCTTAAAATG
Statistics
Matches: 165, Mismatches: 17, Indels: 17
0.83 0.09 0.09
Matches are distributed among these distances:
118 13 0.08
119 95 0.58
120 8 0.05
124 9 0.05
125 40 0.24
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (119 bp):
AAAATAAAATTTGAAGAAAAATATTTTTAAAGAAAAGTTGAAAATAACAATTTTCCTTGAAAAAA
AAAGATTTCAAGAAGGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTCCCTTG
Found at i:506062 original size:38 final size:38
Alignment explanation
Indices: 506011--506083 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
506001 ACACTGTGAC
*
506011 AGATCATGATAGTTTTTCGTTATTCCAATTAGATTGAG
1 AGATCATAATAGTTTTTCGTTATTCCAATTAGATTGAG
*
506049 AGATCATAATAGTTTTTGGTTATTCCAATTAGATT
1 AGATCATAATAGTTTTTCGTTATTCCAATTAGATT
506084 TTTTTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (38 bp):
AGATCATAATAGTTTTTCGTTATTCCAATTAGATTGAG
Found at i:511432 original size:170 final size:170
Alignment explanation
Indices: 511127--511440 Score: 445
Period size: 170 Copynumber: 1.8 Consensus size: 170
511117 AAATATATTC
* * * *
511127 TTTTTATGACTAGATATTTTGCACTTCAATCTTGATACCTTTATTTTAAAGATGTGCTGCTTCAT
1 TTTTTATGACTAAATATTTTGCACTGCAAGCTTGATACCTATATTTTAAAGATGTGCTGCTTCAT
* * * * * *
511192 AATTCTTTGACAAGGAATGGGGAGGATGCATGAAGGGCTAGAAGTAAAATGAATCTACATCATGA
66 AATTCTTTGACAAGGAATGGGCAGGATGAATGAAGGGCCAGAAGTAAAAAGAATCTACAACATAA
*
511257 AACTAGTGGGAAAGGCTTTTTTTTCCCCTTCAATCTATAT
131 AACTAGTAGGAAAGGCTTTTTTTTCCCCTTCAATCTATAT
* *
511297 TTTTTGTGACTAAATATTTTGCACTGC-AGCATTGATACCTATATTTTAAAGATTTGCTGC-TCT
1 TTTTTATGACTAAATATTTTGCACTGCAAGC-TTGATACCTATATTTTAAAGATGTGCTGCTTC-
* *
511360 ATAATTTTTTGACACGGAATGGTGCA-GATGAATGAAGGGCCAGAAGTAAAAAGAATCTACAACA
64 ATAATTCTTTGACAAGGAATGG-GCAGGATGAATGAAGGGCCAGAAGTAAAAAGAATCTACAACA
511424 TAAAACTAGTAGGAAAG
128 TAAAACTAGTAGGAAAG
511441 TCTTGTATGT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
169 4 0.03
170 120 0.95
171 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (170 bp):
TTTTTATGACTAAATATTTTGCACTGCAAGCTTGATACCTATATTTTAAAGATGTGCTGCTTCAT
AATTCTTTGACAAGGAATGGGCAGGATGAATGAAGGGCCAGAAGTAAAAAGAATCTACAACATAA
AACTAGTAGGAAAGGCTTTTTTTTCCCCTTCAATCTATAT
Found at i:511973 original size:2 final size:2
Alignment explanation
Indices: 511966--511994 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
511956 GTATGTATGT
511966 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
511995 ATAACCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:516244 original size:2 final size:2
Alignment explanation
Indices: 516237--516262 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
516227 GCTAGATTGC
516237 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
516263 AACATGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:517180 original size:14 final size:15
Alignment explanation
Indices: 517159--517193 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
517149 GGTTCGTTAC
517159 TAAAATTTTAA-AAT
1 TAAAATTTTAATAAT
*
517173 TTAAATTTTAATAAT
1 TAAAATTTTAATAAT
517188 TAAAAT
1 TAAAAT
517194 ATAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAATTTTAATAAT
Found at i:519209 original size:2 final size:2
Alignment explanation
Indices: 519202--519235 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
519192 ATAAACTCAT
519202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
519236 TTCCATCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:521817 original size:28 final size:30
Alignment explanation
Indices: 521786--521856 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
521776 GTTTAATAAA
521786 TTTATAATTTAAATATTATATT-AA-ATTT
1 TTTATAATTTAAATATTATATTAAATATTT
*
521814 TTTAAAATTTAAATATTATATTAAATATTT
1 TTTATAATTTAAATATTATATTAAATATTT
521844 TATTATAATTTAA
1 T-TTATAATTTAA
521857 CGATGATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 21 0.55
29 2 0.05
30 5 0.13
31 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATAATTTAAATATTATATTAAATATTT
Found at i:526333 original size:18 final size:19
Alignment explanation
Indices: 526310--526359 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
526300 AATTATTTTA
*
526310 AAAATAAATTA-AAAAATT
1 AAAATAAATAACAAAAATT
526328 AAAATAAAATAACAAAAATT
1 AAAAT-AAATAACAAAAATT
526348 ATAAATATAATA
1 A-AAATA-AATA
526360 TATTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 9 0.33
21 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAAATAACAAAAATT
Found at i:526353 original size:21 final size:20
Alignment explanation
Indices: 526321--526359 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
526311 AAATAAATTA
526321 AAAAATTAAAATAAAATAAC
1 AAAAATTAAAATAAAATAAC
*
526341 AAAAATTATAAATATAATA
1 AAAAATTA-AAATAAAATA
526360 TATTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATTAAAATAAAATAAC
Found at i:530443 original size:26 final size:26
Alignment explanation
Indices: 530414--530465 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
530404 AATAAATATC
**
530414 ATTAAATTAAAATTTTCATATAATAA
1 ATTAAATTAAAATTTGAATATAATAA
* *
530440 ATTAATTTAAAGTTTGAATATAATAA
1 ATTAAATTAAAATTTGAATATAATAA
530466 TTTTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTAAATTAAAATTTGAATATAATAA
Found at i:537023 original size:15 final size:16
Alignment explanation
Indices: 536993--537026 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
536983 TTATTAATTT
536993 TTAAAATTAAATTAGA
1 TTAAAATTAAATTAGA
*
537009 TTAAATTTAAA-TAGA
1 TTAAAATTAAATTAGA
537024 TTA
1 TTA
537027 TTTAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
TTAAAATTAAATTAGA
Found at i:543587 original size:9 final size:9
Alignment explanation
Indices: 543573--543617 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
543563 TTATCATTTA
543573 TATTATATT
1 TATTATATT
543582 TATTATATT
1 TATTATATT
543591 TATT-TA--
1 TATTATATT
543597 TATTATATT
1 TATTATATT
543606 TATT-T-TT
1 TATTATATT
543613 TATTA
1 TATTA
543618 AATTAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
6 4 0.12
7 8 0.25
8 3 0.09
9 17 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTATATT
Found at i:543596 original size:24 final size:22
Alignment explanation
Indices: 543568--543616 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
543558 ATAAGTTATC
543568 ATTTATATTATATTTATTATATTT
1 ATTTATATTATATTTATT-T-TTT
543592 ATTTATATTATATTTATTTTTT
1 ATTTATATTATATTTATTTTTT
543614 ATT
1 ATT
543617 AAATTAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 6 0.24
23 1 0.04
24 18 0.72
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTATATTATATTTATTTTTT
Found at i:543600 original size:15 final size:14
Alignment explanation
Indices: 543570--543615 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
543560 AAGTTATCAT
543570 TTATA-TTATATTTA
1 TTATATTTAT-TTTA
543584 TTATATTTATTTATA
1 TTATATTTATTT-TA
543599 TTATATTTATTTT-
1 TTATATTTATTTTA
543612 TTAT
1 TTAT
543616 TAAATTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 18 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTTATTTTA
Found at i:547348 original size:23 final size:24
Alignment explanation
Indices: 547303--547348 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
547293 AAACTAGAAA
* **
547303 AATAAAAATTATTAAAATTATTAC
1 AATAAAAATAATTAAAAAAATTAC
547327 AATAAAAA-AATTAAAAAAATTA
1 AATAAAAATAATTAAAAAAATTA
547349 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAAAATAATTAAAAAAATTAC
Found at i:548411 original size:45 final size:44
Alignment explanation
Indices: 548332--548420 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 44
548322 GATTCTGAAG
*
548332 CAGGTAAGTGTTTGATTTTCCTTGTTCTTGTTAAATCAGCTTCT
1 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
*
548376 CAGGTAAGTGTTTGATTATTCCTTGTTCGTGTTAAATTAGCTTCT
1 CAGGTAAGTGTTTGATT-TTCCTTGTTCGTGTTAAATCAGCTTCT
548421 TTTATAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 17 0.40
45 25 0.60
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (44 bp):
CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
Found at i:551039 original size:52 final size:52
Alignment explanation
Indices: 550961--551091 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 52
550951 AAATTTGTTC
* * * **
550961 ATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCC-TGTAAGTTAAACTTGTCT
1 ATTAAGAATCTCTCTTCTCTTAGAATTCTTC-CCTTGCAAGTCAAACTTACCT
* * *
551013 ATTAAAAATCTCTCTTCTTTTAGAATTCTTCCCTTGCAAGTCAAATTTACCT
1 ATTAAGAATCTCTCTTCTCTTAGAATTCTTCCCTTGCAAGTCAAACTTACCT
551065 ATTAAGAATCTACT-TTCTCTTAGAATT
1 ATTAAGAATCT-CTCTTCTCTTAGAATT
551092 TTTTTTTTGC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
51 2 0.03
52 63 0.94
53 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (52 bp):
ATTAAGAATCTCTCTTCTCTTAGAATTCTTCCCTTGCAAGTCAAACTTACCT
Found at i:551145 original size:11 final size:11
Alignment explanation
Indices: 551132--551182 Score: 84
Period size: 11 Copynumber: 4.6 Consensus size: 11
551122 CAATATCAAT
*
551132 AAATCTCAAAT
1 AAATCTCAAAC
*
551143 AAATCTCTAAC
1 AAATCTCAAAC
551154 AAATCTCAAAC
1 AAATCTCAAAC
551165 AAATCTCAAAC
1 AAATCTCAAAC
551176 AAATCTC
1 AAATCTC
551183 TTATGAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATCTCAAAC
Found at i:552155 original size:52 final size:52
Alignment explanation
Indices: 552061--552213 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 52
552051 ATAATCATAC
* * * * *
552061 AAACTTA-CTCATTAAGAATCTCTCTCCTCTTAAAATTTTTCTCTTGTAAGTT
1 AAACTTACCT-ATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTT
** *
552113 AAACTTGTCTATTAAGAATCTCTTTTCTTTTAGAATTCTTCTCTTGCAAGTT
1 AAACTTACCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTT
* *
552165 AAACTTACCTATTAAGAATCTCCTTTCTCTTAGAATTCTTCTTTTGCAA
1 AAACTTACCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAA
552214 ATCTTCTTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 86 0.98
53 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (52 bp):
AAACTTACCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTT
Found at i:552257 original size:11 final size:11
Alignment explanation
Indices: 552241--552271 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
552231 GCAATATTTG
*
552241 ACAAATCTTAA
1 ACAAATCTCAA
552252 ACAAATCTCAA
1 ACAAATCTCAA
552263 ACAAATCTC
1 ACAAATCTC
552272 TTATGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:553610 original size:10 final size:11
Alignment explanation
Indices: 553584--553608 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
553574 ACTAACTATC
553584 TTTTCTCTTTT
1 TTTTCTCTTTT
553595 TTTTCTCTTTT
1 TTTTCTCTTTT
553606 TTT
1 TTT
553609 CTTAGCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:561348 original size:58 final size:57
Alignment explanation
Indices: 561247--561363 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 57
561237 ATTTATTTTA
*
561247 ATTTAATATAAATATATAAAAATTATTTTAATGTTTTAATTATAATACACAATTACAT
1 ATTTAATATAAATATATAAAAATTATTTTAATGATTTAATTATAATACACAATTA-AT
* * * * *
561305 ATTTAATATAATTATGTAAAAATTATTTTAAAT-ATTTATTTATAATGCACATTTAAT
1 ATTTAATATAAATATATAAAAATTATTTT-AATGATTTAATTATAATACACAATTAAT
561362 AT
1 AT
561364 GCAATTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 4 0.08
58 45 0.87
59 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (57 bp):
ATTTAATATAAATATATAAAAATTATTTTAATGATTTAATTATAATACACAATTAAT
Found at i:561779 original size:24 final size:23
Alignment explanation
Indices: 561748--561792 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
561738 ACATATATAA
* *
561748 AAATTATATTATTTTGATATTAC
1 AAATTATATTAATTTAATATTAC
561771 AAATATATATTAATTTAATATT
1 AAAT-TATATTAATTTAATATT
561793 TTCAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTATATTAATTTAATATTAC
Found at i:565562 original size:23 final size:24
Alignment explanation
Indices: 565516--565562 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
565506 AAACTAGAAT
**
565516 AATAAAAAATTATTAAAATTATTAC
1 AATAAAAAA-TATTAAAAAAATTAC
565541 AATAAAAAA-ATTAAAAAAATTA
1 AATAAAAAATATTAAAAAAATTA
565563 ATTTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAAAAATATTAAAAAAATTAC
Found at i:565769 original size:18 final size:19
Alignment explanation
Indices: 565742--565782 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
565732 TTAATTAATT
* *
565742 TTAAATTTTTATTAAAATA
1 TTAAATTTTTAATAAAAAA
565761 TTAAA-TTTTAATAAAAAA
1 TTAAATTTTTAATAAAAAA
565779 TTAA
1 TTAA
565783 TTATACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATTTTTAATAAAAAA
Found at i:566626 original size:44 final size:44
Alignment explanation
Indices: 566563--566650 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
566553 GATTCTGAAG
*
566563 CAGGTAAGTGTTTGATTTTCCTTGTTCTTGTTAAATCAGCTTCT
1 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
*
566607 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATTAGCTTCT
1 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
566651 TTTATAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.48
Consensus pattern (44 bp):
CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
Found at i:567187 original size:56 final size:56
Alignment explanation
Indices: 567101--567229 Score: 249
Period size: 56 Copynumber: 2.3 Consensus size: 56
567091 GAAGGTAAAG
567101 AAAATATGATATCATTTTTTTTTCCTTTTAGCATATAATTATAACTATAAATCAAT
1 AAAATATGATATCATTTTTTTTTCCTTTTAGCATATAATTATAACTATAAATCAAT
*
567157 AAAATATGATATCATTTTTTTTTTCTTTTAGCATATAATTATAACTATAAATCAAT
1 AAAATATGATATCATTTTTTTTTCCTTTTAGCATATAATTATAACTATAAATCAAT
567213 AAAATATGATATCATTT
1 AAAATATGATATCATTT
567230 CCATTAATGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (56 bp):
AAAATATGATATCATTTTTTTTTCCTTTTAGCATATAATTATAACTATAAATCAAT
Found at i:569326 original size:52 final size:52
Alignment explanation
Indices: 569245--569373 Score: 152
Period size: 52 Copynumber: 2.5 Consensus size: 52
569235 AACCCTCTCT
* * * * *
569245 TCTTAGAATTCTTTTTTTGTAAGTTAAACTTGCCTATTAAGAATC-TCTCTCC
1 TCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCTTCT-TCC
* * * *
569297 TTTTATAATTTTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCTTCTTTC
1 TCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCTTCTTCC
*
569349 TCTTAGAATTCTTCTTTTGCAAGTC
1 TCTTAGAATTCTTCTCTTGCAAGTC
569374 TTCTTATCCA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
52 60 0.95
53 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (52 bp):
TCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAATCTTCTTCC
Found at i:569700 original size:25 final size:25
Alignment explanation
Indices: 569666--569776 Score: 104
Period size: 24 Copynumber: 4.5 Consensus size: 25
569656 GCACTTTTCA
569666 AACTTTTAGCTCTTTTCACATCTCG
1 AACTTTTAGCTCTTTTCACATCTCG
**
569691 AACTTTTAGCTC-TTTCATGTCTCG
1 AACTTTTAGCTCTTTTCACATCTCG
* * *
569715 AACCTTTGGCTCTTTTCACATCTTG
1 AACTTTTAGCTCTTTTCACATCTCG
* * *
569740 AATTTTTAAC-CTTCTT-ACATTTCG
1 AACTTTTAGCTCTT-TTCACATCTCG
569764 AA-TTTTCAGCTCT
1 AACTTTT-AGCTCT
569777 GATACCACTT
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
23 4 0.06
24 33 0.49
25 31 0.46
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.46
Consensus pattern (25 bp):
AACTTTTAGCTCTTTTCACATCTCG
Found at i:569713 original size:24 final size:24
Alignment explanation
Indices: 569666--569747 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 24
569656 GCACTTTTCA
569666 AACTTTTAGCTCTTTTCACATCTCG
1 AACTTTTAGCTC-TTTCACATCTCG
**
569691 AACTTTTAGCTCTTTCATGTCTCG
1 AACTTTTAGCTCTTTCACATCTCG
* * *
569715 AACCTTTGGCTCTTTTCACATCTTG
1 AACTTTTAGCTC-TTTCACATCTCG
*
569740 AATTTTTA
1 AACTTTTA
569748 ACCTTCTTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
24 20 0.43
25 26 0.57
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (24 bp):
AACTTTTAGCTCTTTCACATCTCG
Found at i:570380 original size:52 final size:52
Alignment explanation
Indices: 570294--570450 Score: 172
Period size: 52 Copynumber: 3.0 Consensus size: 52
570284 TATAATCATA
** * *
570294 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTACTTATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
570346 TAAACTT-GTCTATTAAGAATCTCTCTCTTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACT-TATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * * * *
570398 CAAACTTACTTATTAAGAATCTTTTTTCTCTTAAAATTCTTTTTTTGCAAGT
1 CAAACTTACTTATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCTTGCAAGT
570450 C
1 C
570451 TTCTTGTCTA
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
52 84 0.99
53 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.44
Consensus pattern (52 bp):
CAAACTTACTTATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:574214 original size:58 final size:58
Alignment explanation
Indices: 574111--574392 Score: 331
Period size: 58 Copynumber: 4.8 Consensus size: 58
574101 TTGCGTAGGA
* * * *
574111 AAAATTGATACCTTCAACTTTT-TTTCGAAAATA-TTTTTTGGAAATTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTCCTT-AAAAATATTTTTTTGAAAATTTATTTTTAAAG
*
574168 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGGAAATTTATTTTT-AAG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTATTTTTAAAG
* * *
574225 AAAAATTGATACTTTCAACTTTTCCTTAAAAAT-TCATTTTTGAAAATTTATTTCTAAGG
1 -AAAATTGATACTTTCAACTTTTCCTTAAAAATAT-TTTTTTGAAAATTTATTTTTAAAG
* * * * *
574284 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTCGAAAATTTTGATTCTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAA-TTT-ATTTTTAAAG
* *
574343 AAAATTGATACTTTCAACATTTCCTCAAAAATATTTCTCTTTGAAAATTT
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTT-T-TTTGAAAATTT
574393 TTATTTTTTT
Statistics
Matches: 197, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
57 40 0.20
58 105 0.53
59 39 0.20
60 2 0.01
61 4 0.02
62 7 0.04
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTATTTTTAAAG
Found at i:574314 original size:27 final size:27
Alignment explanation
Indices: 574225--574315 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
574215 TATTTTTAAG
*
574225 AAAAATTGATACTTTCAACTTTTCCTT
1 AAAAATTGATACTTTCAACTTTTCCCT
* * * * **
574252 AAAAATTCAT-TTTTGAAAATTTATTTCT
1 AAAAATTGATACTTT-CAACTTT-TCCCT
574280 AAGGAAAATTGATACTTTCAACTTTTCCCT
1 -A--AAAATTGATACTTTCAACTTTTCCCT
574310 AAAAAT
1 AAAAAT
574316 ATTTTTCGAA
Statistics
Matches: 45, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
26 3 0.07
27 19 0.42
28 2 0.04
29 2 0.04
30 3 0.07
31 13 0.29
32 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.42
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTCCCT
Found at i:576562 original size:53 final size:55
Alignment explanation
Indices: 576495--576604 Score: 143
Period size: 57 Copynumber: 2.0 Consensus size: 55
576485 CTTTTCTCTC
*
576495 CTATTCGGACTCTTC-CTCT-TATTCAGATTTCTCCTCCATCTTTTTTCCGTTTT
1 CTATTCGGACTCTTCTCTCTCTATCCAGATTTCTCCTCCATCTTTTTTCCGTTTT
* * * *
576548 CTATTCGGATTCTTCTTCTCTCCTATCCCGATTTCTCTTCCATCTTTTTTTCGTTTT
1 CTATTCGGACTCTTC-TCTCT-CTATCCAGATTTCTCCTCCATCTTTTTTCCGTTTT
576605 ATAAAACCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 14 0.29
55 4 0.08
57 30 0.62
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (55 bp):
CTATTCGGACTCTTCTCTCTCTATCCAGATTTCTCCTCCATCTTTTTTCCGTTTT
Found at i:577081 original size:8 final size:9
Alignment explanation
Indices: 577060--577096 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
577050 TAGGCAACTT
577060 TTTTTGTTA
1 TTTTTGTTA
577069 TTTTTGTTA
1 TTTTTGTTA
*
577078 TTTTTTTTA
1 TTTTTGTTA
*
577087 TTTTTTTTA
1 TTTTTGTTA
577096 T
1 T
577097 ATATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTTGTTA
Found at i:577120 original size:129 final size:126
Alignment explanation
Indices: 576978--577217 Score: 365
Period size: 129 Copynumber: 1.9 Consensus size: 126
576968 TTAATAAAAA
* *
576978 AAATCTTGATCAAAGCTCCTCTAAACAGAAGTTCAATGATTTTGAAAAACATAAACAAAGCTCCT
1 AAATCTTGATCAAAGCTCCTCTAAACAGAAGCTCAATGACTTTGAAAAACATAAACAAAGCTCCT
* *
577043 CTAAATATAGGCAACTTTTTTTGTTATTTTTGTTATTTTTTTTATTTTTTTTATATATATATTTT
66 CTAAATAGACGCAACTTTTTTTG---TTTTT-TTATTTTTTTTATTTTTTTTATATATATATTTT
* * * *
577108 AAAT-TTGATCAAAGTTCCTCTAAGCAGAGGCTCAATGACTTTGAGAAACATAAACAAAGCTCCT
1 AAATCTTGATCAAAGCTCCTCTAAACAGAAGCTCAATGACTTTGAAAAACATAAACAAAGCTCCT
577172 CTAAATAGACGCAACTTTTTTTGTTTTTTTATTTTTTTTATTTTTT
66 CTAAATAGACGCAACTTTTTTTGTTTTTTTATTTTTTTTATTTTTT
577218 GATTTTTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
125 18 0.18
126 5 0.05
129 75 0.74
130 4 0.04
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (126 bp):
AAATCTTGATCAAAGCTCCTCTAAACAGAAGCTCAATGACTTTGAAAAACATAAACAAAGCTCCT
CTAAATAGACGCAACTTTTTTTGTTTTTTTATTTTTTTTATTTTTTTTATATATATATTTT
Found at i:577193 original size:1 final size:1
Alignment explanation
Indices: 577187--577253 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
577177 TAGACGCAAC
* * * ** * * *
577187 TTTTTTTGTTTTTTTATTTTTTTTATTTTTTGATTTTTTTTGTTTTTTTGTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
577252 TT
1 TT
577254 CAAAGCTCCT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:577200 original size:8 final size:8
Alignment explanation
Indices: 577187--577251 Score: 78
Period size: 8 Copynumber: 7.9 Consensus size: 8
577177 TAGACGCAAC
577187 TTTTTTTG
1 TTTTTTTG
*
577195 TTTTTTTA
1 TTTTTTTG
577203 TTTTTTT-
1 TTTTTTTG
577210 TATTTTTTG
1 T-TTTTTTG
577219 ATTTTTTTTG
1 --TTTTTTTG
577229 TTTTTTTG
1 TTTTTTTG
*
577237 TTTTTTTA
1 TTTTTTTG
577245 TTTTTTT
1 TTTTTTT
577252 TTCAAAGCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
7 1 0.02
8 42 0.82
10 7 0.14
11 1 0.02
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:577209 original size:17 final size:17
Alignment explanation
Indices: 577187--577252 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
577177 TAGACGCAAC
577187 TTTTTTTGTTTTTTTAT
1 TTTTTTTGTTTTTTTAT
* *
577204 TTTTTTTATTTTTTGAT
1 TTTTTTTGTTTTTTTAT
*
577221 TTTTTTTGTTTTTTTGT
1 TTTTTTTGTTTTTTTAT
577238 TTTTTTAT-TTTTTTT
1 TTTTTT-TGTTTTTTT
577253 TCAAAGCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTAT
Found at i:577347 original size:42 final size:42
Alignment explanation
Indices: 577258--577668 Score: 558
Period size: 42 Copynumber: 10.0 Consensus size: 42
577248 TTTTTTCAAA
* * *
577258 GCTCCTCTAAATAGAGGCTCAACGACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
577299 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
577341 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAG-AAAGTAAATT
* * *
577383 GCTCCTTTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
*
577425 GCTTCTCTAAACAGAGGCACCACGACTTTTGA-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAGAAAGTAAATT
** * *
577467 GCTCCTCTAAACAGAGATACCACGATTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
* *
577509 GCTCCTCTAAATAGAGGCACCACGACTTT-TGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
*
577550 GCTCCTCTAAACAGAGGCACCACAACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
577591 GCTCCTCTAAACAGAGGCA--ACGAAC-TTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAGAAAGTAAATT
* *
577630 GCTCCTCTAAACAAAGGCA--ACGAACTTGGA-AAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAGAAAGTAAAT
577669 ACTCCTAGAC
Statistics
Matches: 337, Mismatches: 24, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
39 40 0.12
40 13 0.04
41 100 0.30
42 179 0.53
43 5 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
Found at i:578942 original size:8 final size:8
Alignment explanation
Indices: 578886--578951 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
578876 AATTTGAATC
578886 TCTTTTTT
1 TCTTTTTT
*
578894 TATTTTTT
1 TCTTTTTT
*
578902 TCATTTTT
1 TCTTTTTT
*
578910 TCATTTTTC
1 TC-TTTTTT
*
578919 CCTTTTTT
1 TCTTTTTT
578927 TCATTTTTTT
1 TC--TTTTTT
578937 TCTTTTTT
1 TCTTTTTT
578945 CTCTTTT
1 -TCTTTT
578952 CTCATTTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
8 27 0.59
9 11 0.24
10 8 0.17
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (8 bp):
TCTTTTTT
Found at i:578942 original size:17 final size:17
Alignment explanation
Indices: 578884--578963 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
578874 TCAATTTGAA
*
578884 TCTCTTTTTTTATTTTT
1 TCTCTTTTTTCATTTTT
578901 T-TCATTTTTTCA-TTTT
1 TCTC-TTTTTTCATTTTT
*
578917 TCCCTTTTTTTCATTTTT
1 TCTC-TTTTTTCATTTTT
* *
578935 TTTCTTTTTTC-TCTTT
1 TCTCTTTTTTCATTTTT
*
578951 TCTCATTTTTCAT
1 TCTCTTTTTTCAT
578964 CCATATCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
16 20 0.39
17 25 0.49
18 6 0.12
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTCTTTTTTCATTTTT
Found at i:578960 original size:9 final size:9
Alignment explanation
Indices: 578895--578961 Score: 52
Period size: 9 Copynumber: 7.8 Consensus size: 9
578885 CTCTTTTTTT
*
578895 ATTTTTTTC
1 ATTTTTCTC
578904 ATTTTT-TC
1 ATTTTTCTC
578912 ATTTTTC-C
1 ATTTTTCTC
* *
578920 CTTTTTTTC
1 ATTTTTCTC
*
578929 ATTTTTTTTC
1 A-TTTTTCTC
*
578939 TTTTTTCTC
1 ATTTTTCTC
578948 --TTTTCTC
1 ATTTTTCTC
578955 ATTTTTC
1 ATTTTTC
578962 ATCCATATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.15
8 14 0.29
9 19 0.40
10 8 0.17
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (9 bp):
ATTTTTCTC
Found at i:582892 original size:58 final size:58
Alignment explanation
Indices: 582802--583089 Score: 321
Period size: 58 Copynumber: 4.9 Consensus size: 58
582792 TCTTGCGTAG
**
582802 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAATTTATTTCCAA
* *
582860 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACATTGATTTCCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTT-AAAAATTTATTTCCAA
* * * * *
582921 GGAAAATTGATACTTTCAACTTTTCCTTAAAAAT-TCATTTTTGAAAATTTATTTCTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTAAAAATTTATTTCCAA
* * * *
582979 GAAAAATTGATACTTTCAACTTTT-TTCTAAAAATA-TTTTTCAGAAATTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTA-AAAATTT-ATTTCCAA
* * * *
583038 GGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTCTCTTTGAAAATTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTT-T-TTTAAAAATTT
583090 TTATTTTTTT
Statistics
Matches: 192, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
57 5 0.03
58 83 0.43
59 41 0.21
60 10 0.05
61 51 0.27
62 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAATTTATTTCCAA
Found at i:583083 original size:119 final size:119
Alignment explanation
Indices: 582804--583089 Score: 402
Period size: 119 Copynumber: 2.4 Consensus size: 119
582794 TTGCGTAGGA
* * *
582804 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTT-TTTTAAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTCTTTTGAAAATTTATTTCTAAGAAAAATT
**
582868 GATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAACATTGATTTCCAAGG
66 GATACTTTCAACTTTTCCTCAAAAATA-TTTTTTCAGAAACATTGATTTCCAAGG
*
582923 AAAATTGATACTTTCAACTTTTCCTTAAAAAT-TCAT-TTTTGAAAATTTATTTCTAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATAT-TTCTTTTGAAAATTTATTTCTAAGAAAAAT
* ** *
582986 TGATACTTTCAACTTTT-TTCTAAAAATA-TTTTTCAGAAATTTTGATTTTCAAGG
65 TGATACTTTCAACTTTTCCTC-AAAAATATTTTTTCAGAAACATTGATTTCCAAGG
*
583040 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTCTCTTTGAAAATTT
1 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTCT-TTTGAAAATTT
583090 TTATTTTTTT
Statistics
Matches: 150, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
117 53 0.35
118 5 0.03
119 92 0.61
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (119 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTCTTTTGAAAATTTATTTCTAAGAAAAATT
GATACTTTCAACTTTTCCTCAAAAATATTTTTTCAGAAACATTGATTTCCAAGG
Found at i:591313 original size:30 final size:30
Alignment explanation
Indices: 591277--591373 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
591267 TTTTTTATAT
591277 TTATTTTAATTTAATATAAATATATAAAAA
1 TTATTTTAATTTAATATAAATATATAAAAA
*
591307 TTATTTTAAAGTTTTAAT-T--ATA-ATACACAA
1 TTATTTT-AA--TTTAATATAAATATATA-AAAA
** *
591337 TTA-CAT-ATTTAATATAATTATATAAAAA
1 TTATTTTAATTTAATATAAATATATAAAAA
591365 TTATTTTAA
1 TTATTTTAA
591374 ATATTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
25 6 0.12
26 1 0.02
27 1 0.02
28 8 0.16
29 8 0.16
30 17 0.34
31 2 0.04
32 1 0.02
33 6 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (30 bp):
TTATTTTAATTTAATATAAATATATAAAAA
Found at i:591811 original size:24 final size:24
Alignment explanation
Indices: 591778--591830 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
591768 ATAACATAAC
* *
591778 ATATATAAAAAT-TATATTAGTTTG
1 ATAT-TAAAAATATATATTAATTTA
591802 ATATTAAAAATATATATTAATTTA
1 ATATTAAAAATATATATTAATTTA
591826 ATATT
1 ATATT
591831 TTCAATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATTAAAAATATATATTAATTTA
Found at i:592418 original size:2 final size:2
Alignment explanation
Indices: 592411--592436 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
592401 ACATGCTATC
592411 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
592437 CATGTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:594852 original size:13 final size:14
Alignment explanation
Indices: 594834--594875 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
594824 TTCTTATCAA
*
594834 AAAAAAATAT-TTT
1 AAAAAAATATAATT
594847 AAAAAAATATAATT
1 AAAAAAATATAATT
594861 AAAATAAATAATAAT
1 AAAA-AAAT-ATAAT
594876 GCTTATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
14 6 0.24
15 4 0.16
16 5 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAAATATAATT
Found at i:595635 original size:23 final size:24
Alignment explanation
Indices: 595589--595635 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
595579 AAACTAGAAT
**
595589 AATAAAAAATTATTAAAATTATTAC
1 AATAAAAAA-TATTAAAAAAATTAC
595614 AATAAAAAA-ATTAAAAAAATTA
1 AATAAAAAATATTAAAAAAATTA
595636 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAAAAATATTAAAAAAATTAC
Found at i:596706 original size:44 final size:44
Alignment explanation
Indices: 596638--596725 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
596628 GATTCTGAAG
*
596638 CAGGTAAGTGTTTGATTTTCCTTGTTCTTGTTAAATCAGCTTCT
1 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
* *
596682 CAGGTAAGTGTTTGATTTTTCTTGTTCGTGTTAAATTAGCTTCT
1 CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
596726 TTTATAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (44 bp):
CAGGTAAGTGTTTGATTTTCCTTGTTCGTGTTAAATCAGCTTCT
Found at i:601226 original size:25 final size:25
Alignment explanation
Indices: 601170--601229 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
601160 CTTTTATTTT
* * *
601170 AGGCCTTCATTGTTGAACGCGGTTT
1 AGGCCTTCATTATTGAACCCGGTTA
* *
601195 AGACCTTCATTATTGAACCCTGTTA
1 AGGCCTTCATTATTGAACCCGGTTA
601220 AGGCCTTCAT
1 AGGCCTTCAT
601230 AGTCATTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (25 bp):
AGGCCTTCATTATTGAACCCGGTTA
Found at i:604924 original size:22 final size:22
Alignment explanation
Indices: 604899--604942 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
604889 CTATGTATTT
*
604899 ATATTTGTATCTCTAGAATTAA
1 ATATTTGAATCTCTAGAATTAA
*
604921 ATATTTGAATTTCTAGAATTAA
1 ATATTTGAATCTCTAGAATTAA
604943 GGACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (22 bp):
ATATTTGAATCTCTAGAATTAA
Found at i:607743 original size:24 final size:23
Alignment explanation
Indices: 607712--607756 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
607702 ACATATATAT
* *
607712 AAATTATATTAGTTTGATATTAA
1 AAATTATATTAATATGATATTAA
607735 AAATGTATATTAATATGATATT
1 AAAT-TATATTAATATGATATT
607757 TTCAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (23 bp):
AAATTATATTAATATGATATTAA
Found at i:608921 original size:202 final size:202
Alignment explanation
Indices: 608573--608982 Score: 721
Period size: 202 Copynumber: 2.0 Consensus size: 202
608563 GACTTGTGAA
608573 ATATATATCCCAAAATTATTTATTTCAGCTCAATGTTATGGATGGTTTGGAACTCAATGAATTAT
1 ATATATATCCCAAAATTATTTATTTCAGCTCAATGTTATGGATGGTTTGGAACTCAATGAATTAT
608638 TGGACGATCCGTTATCTAATGAAGAGGTATGATAATTGCGTATATTCGTTTTGAATGCATTTGTT
66 TGGACGATCCGTTATCTAATGAAGAGGTATGATAATTGCGTATATTCGTTTTGAATGCATTTGTT
* * *
608703 TTGAGAAATCTGAAAAGATTATCATTTCTTTTGAAAGTATCTTTTAGATATTTTTACTTAAATAT
131 TTGAGAAATCTGAAAAGATTATCATTACTTTTGAAAGTATCTTTTAGACACTTTTACTTAAATAT
608768 TATCTTT
196 TATCTTT
* *
608775 ATATATATCCCAAAATTATTTATTTCAGCTCGATGTTATGGATGGTTTGGAGCTCAATGAATTAT
1 ATATATATCCCAAAATTATTTATTTCAGCTCAATGTTATGGATGGTTTGGAACTCAATGAATTAT
* *
608840 TGGACGATCCGTTGTCTAATGAAGAGGTATGATAATTGCGTATATTGGTTTTGAATGCATTTGTT
66 TGGACGATCCGTTATCTAATGAAGAGGTATGATAATTGCGTATATTCGTTTTGAATGCATTTGTT
* * *
608905 TTGAGAAATTTGAAAAGATTATCATTACTTTTGAGAGTATCTTTTAGACGCTTTTACTTAAATAT
131 TTGAGAAATCTGAAAAGATTATCATTACTTTTGAAAGTATCTTTTAGACACTTTTACTTAAATAT
608970 TATCTTT
196 TATCTTT
*
608977 ACATAT
1 ATATAT
608983 TTATTAATGT
Statistics
Matches: 197, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
202 197 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (202 bp):
ATATATATCCCAAAATTATTTATTTCAGCTCAATGTTATGGATGGTTTGGAACTCAATGAATTAT
TGGACGATCCGTTATCTAATGAAGAGGTATGATAATTGCGTATATTCGTTTTGAATGCATTTGTT
TTGAGAAATCTGAAAAGATTATCATTACTTTTGAAAGTATCTTTTAGACACTTTTACTTAAATAT
TATCTTT
Found at i:610168 original size:21 final size:21
Alignment explanation
Indices: 610144--610183 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
610134 ATCAACTAAT
610144 TATAATGAAGTCATCAGAAAA
1 TATAATGAAGTCATCAGAAAA
610165 TATAATGAAGTCATCAGAA
1 TATAATGAAGTCATCAGAA
610184 GGGAGAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (21 bp):
TATAATGAAGTCATCAGAAAA
Found at i:613750 original size:24 final size:24
Alignment explanation
Indices: 613718--613765 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
613708 GCGGCATCCC
*
613718 TCTGGGGGGCATTCCTCCCATGTT
1 TCTGGGGGGCATCCCTCCCATGTT
613742 TCTGGGGGGCATCCCTCCCATGTT
1 TCTGGGGGGCATCCCTCCCATGTT
613766 GGATGGCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.31, G:0.29, T:0.31
Consensus pattern (24 bp):
TCTGGGGGGCATCCCTCCCATGTT
Found at i:613796 original size:24 final size:23
Alignment explanation
Indices: 613744--613822 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
613734 CCCATGTTTC
* *
613744 TGGGGGGCATCCCTCCCA--TGT
1 TGGGTGGCATCCCTCCTAGTTGT
*
613765 TGGATGGCATCCCTCTCGTA-TTGT
1 TGGGTGGCATCCCTC-C-TAGTTGT
613789 TGGGTGGCATCCCTCCTATGTTGT
1 TGGGTGGCATCCCTCCTA-GTTGT
613813 TGGGTGGCAT
1 TGGGTGGCAT
613823 TCCAACTGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
21 13 0.27
22 3 0.06
23 2 0.04
24 31 0.63
ACGTcount: A:0.10, C:0.25, G:0.32, T:0.33
Consensus pattern (23 bp):
TGGGTGGCATCCCTCCTAGTTGT
Found at i:616429 original size:21 final size:21
Alignment explanation
Indices: 616405--616450 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
616395 AAAAGGAACG
*
616405 TTTTAAATACATTATCAATTT
1 TTTTAAATACATTATAAATTT
* * *
616426 TTTTATATACCTTTTAAATTT
1 TTTTAAATACATTATAAATTT
616447 TTTT
1 TTTT
616451 TCAAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAATACATTATAAATTT
Found at i:616681 original size:24 final size:25
Alignment explanation
Indices: 616639--616689 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
616629 TTTATTTTTG
616639 AAAATACATAAATACATTTAATCTT
1 AAAATACATAAATACATTTAATCTT
* * *
616664 AAAATATAT-AATATATTTAATTTT
1 AAAATACATAAATACATTTAATCTT
616688 AA
1 AA
616690 TTTAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATACATAAATACATTTAATCTT
Found at i:634045 original size:30 final size:30
Alignment explanation
Indices: 633975--634082 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
633965 TTGATTTATG
* *
633975 TTAAAGGCTTATTTAGG-TAGAAATTAAA-T
1 TTAAGGGCTTATTT-GGATACAAATTAAAGT
* *
634004 GCTAAGCGCTTATTTGGATACAAATTAAAGT
1 -TTAAGGGCTTATTTGGATACAAATTAAAGT
* * * *
634035 TTAAGGGCTTATTTGGGTGCAAAGTAAAGG
1 TTAAGGGCTTATTTGGATACAAATTAAAGT
*
634065 TCAAGGGCTTATTTGGAT
1 TTAAGGGCTTATTTGGAT
634083 GCAATAAAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.03
30 61 0.95
31 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.34
Consensus pattern (30 bp):
TTAAGGGCTTATTTGGATACAAATTAAAGT
Found at i:634086 original size:30 final size:30
Alignment explanation
Indices: 634011--634086 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
634001 AATGCTAAGC
* * * *
634011 GCTTATTTGGATACAAATTAAAGTTTAAGG
1 GCTTATTTGGATGCAAAGTAAAGGTCAAGG
*
634041 GCTTATTTGGGTGCAAAGTAAAGGTCAAGG
1 GCTTATTTGGATGCAAAGTAAAGGTCAAGG
634071 GCTTATTTGGATGCAA
1 GCTTATTTGGATGCAA
634087 TAAAAGTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (30 bp):
GCTTATTTGGATGCAAAGTAAAGGTCAAGG
Found at i:641562 original size:24 final size:25
Alignment explanation
Indices: 641527--641585 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 25
641517 CGATATCCTA
**
641527 TTTTATATTATATTTTAAAT-ATAT
1 TTTTATATTATAAATTAAATAATAT
641551 TTTTAGTA-TATAAATTAAATAATAT
1 TTTTA-TATTATAAATTAAATAATAT
641576 TAATTTATAT
1 T--TTTATAT
641586 ATTTACACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 15 0.54
25 7 0.25
26 2 0.07
27 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTATATTATAAATTAAATAATAT
Found at i:649211 original size:24 final size:24
Alignment explanation
Indices: 649159--649203 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
649149 AGTTATTGAA
* *
649159 AATATTAAATTAATATATATTTGT
1 AATATCAAAATAATATATATTTGT
649183 AATATCAAAATAATATA-ATTT
1 AATATCAAAATAATATATATTT
649204 TTATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATCAAAATAATATATATTTGT
Found at i:658834 original size:52 final size:52
Alignment explanation
Indices: 658749--658894 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 52
658739 TAGACAAGAA
* * * **
658749 GACTTGCAAAAGAAGAATTTTAAGAGAAAAGAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAGAGGAGAGAGATTCTTAATAGACAAGTTT
* *
658801 GACTTGCAAGAGAAGAATTCTAAAAGGAGAGAGATTCTTAATAGACAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAGAGGAGAGAGATTCTTAATAGACAAGTTT
* * * *
658853 AACTTACAACAGAAGAATTCTAAGAGGAGAGGGATTCTTAAT
1 GACTTGCAAAAGAAGAATTCTAAGAGGAGAGAGATTCTTAAT
658895 GGATAAATTT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTCTAAGAGGAGAGAGATTCTTAATAGACAAGTTT
Found at i:659412 original size:31 final size:31
Alignment explanation
Indices: 659377--659458 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
659367 CTTTTAACCC
*
659377 AACAAATGGTATCAGAGCTGTGGTGTTCCCT
1 AACAAATGGTATCAGAGCTGTGGTATTCCCT
* *
659408 AACAAATGATATCAGAGCTGTGGTATTTCCT
1 AACAAATGGTATCAGAGCTGTGGTATTCCCT
*
659439 AACAAGTGGTATCAGAGCTG
1 AACAAATGGTATCAGAGCTG
659459 AAGGTTCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (31 bp):
AACAAATGGTATCAGAGCTGTGGTATTCCCT
Found at i:659539 original size:24 final size:25
Alignment explanation
Indices: 659512--659562 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
659502 GAGCCGAAGA
659512 TTCGAGACATGA-AAGAGCTAAAAG
1 TTCGAGACATGAGAAGAGCTAAAAG
**
659536 TTCGAGATGTGAGAAGAGCTAAAAG
1 TTCGAGACATGAGAAGAGCTAAAAG
659561 TT
1 TT
659563 TGAAAAGTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (25 bp):
TTCGAGACATGAGAAGAGCTAAAAG
Found at i:659828 original size:11 final size:11
Alignment explanation
Indices: 659812--659851 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
659802 CCCATAAAAA
*
659812 ATTTGTTTAAG
1 ATTTGTTTGAG
659823 ATTTGTTTGAG
1 ATTTGTTTGAG
659834 ATTTGTTTGAG
1 ATTTGTTTGAG
659845 ATTTGTT
1 ATTTGTT
659852 AGATATTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (11 bp):
ATTTGTTTGAG
Found at i:659992 original size:52 final size:52
Alignment explanation
Indices: 659885--659997 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
659875 GACTTGTAAA
* * * * *
659885 AGAAGAATTCTAAGAGAAAGAAGATTCTTAATAGGTAAATTTGACTTGCAAG
1 AGAAAAATTCTAAAAGAAAGAAGATTCTTAATAGGCAAATTTAACTTACAAG
* * *
659937 AGAAAAATTCTAAAAGAAA-AGAGATTCTTAATAGGCAAGTTTAACTTATAGG
1 AGAAAAATTCTAAAAGAAAGA-AGATTCTTAATAGGCAAATTTAACTTACAAG
659989 AGAAAAATT
1 AGAAAAATT
659998 TTAGGAAGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 1 0.02
52 51 0.98
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.27
Consensus pattern (52 bp):
AGAAAAATTCTAAAAGAAAGAAGATTCTTAATAGGCAAATTTAACTTACAAG
Found at i:662620 original size:44 final size:44
Alignment explanation
Indices: 662555--662642 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
662545 TTTCTATAAA
* *
662555 AGAAGCTAATTTAACACGAACAAGGATAATCAAACACTTACCTG
1 AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
*
662599 AGAAGCTGATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
1 AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
662643 CTTCAGAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (44 bp):
AGAAGCTAATTTAACAAGAACAAGGAAAATCAAACACTTACCTG
Found at i:663449 original size:18 final size:18
Alignment explanation
Indices: 663422--663478 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
663412 TTAGGTATAA
*
663422 TTAATTTTTTATTAAAAT
1 TTAATATTTTATTAAAAT
*
663440 TTAATATTTTAATAAAAAT
1 TTAATATTTT-ATTAAAAT
* *
663459 TTAA-AATTAATTAAAAT
1 TTAATATTTTATTAAAAT
663476 TTA
1 TTA
663479 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 10 0.30
18 12 0.36
19 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATATTTTATTAAAAT
Found at i:663457 original size:19 final size:18
Alignment explanation
Indices: 663422--663462 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
663412 TTAGGTATAA
* *
663422 TTAATTTTTTATTAAAAT
1 TTAATTTTTAATAAAAAT
663440 TTAATATTTTAATAAAAAT
1 TTAAT-TTTTAATAAAAAT
663459 TTAA
1 TTAA
663463 AATTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTTTTAATAAAAAT
Found at i:663474 original size:17 final size:19
Alignment explanation
Indices: 663432--663478 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
663422 TTAATTTTTT
*
663432 ATTAAAATTTAATATTTTA
1 ATTAAAATTTAATATATTA
*
663451 ATAAAAATTTAA-A-ATTA
1 ATTAAAATTTAATATATTA
663468 ATTAAAATTTA
1 ATTAAAATTTA
663479 TAAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.52
18 1 0.04
19 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAAATTTAATATATTA
Found at i:667419 original size:24 final size:24
Alignment explanation
Indices: 667367--667411 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
667357 AGTTATTGAA
* *
667367 AATATTAAATTAATATATATTTGT
1 AATATCAAAATAATATATATTTGT
667391 AATATCAAAATAATATA-ATTT
1 AATATCAAAATAATATATATTT
667412 TTATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATCAAAATAATATATATTTGT
Found at i:676357 original size:54 final size:54
Alignment explanation
Indices: 676228--676488 Score: 391
Period size: 56 Copynumber: 4.7 Consensus size: 54
676218 TTTCAAAGAG
*
676228 AAATATTTTTAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAA
1 AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTG-AAAT--AAATTTCAAA
676285 AAATATTTTTA-GAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC-AA
1 AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAATAAATTTCAAA
676338 AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATAAATTTTCAAAAA
1 AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATAAA-TTTC--AAA
* *
676395 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTAAAA
1 AAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAATAAATTTCAAA
*
676451 AAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCT
1 AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCT
676489 ACCAAAGAAA
Statistics
Matches: 193, Mismatches: 3, Indels: 18
0.90 0.01 0.08
Matches are distributed among these distances:
53 21 0.11
54 38 0.20
55 27 0.14
56 44 0.23
57 24 0.12
58 32 0.17
59 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (54 bp):
AAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATAAATTTCAAA
Found at i:680313 original size:23 final size:24
Alignment explanation
Indices: 680270--680315 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 24
680260 TGAGCAAAGA
680270 CATGCTCATGATGAAGCAATGGAAT
1 CATGCTCATGA-GAAGCAATGGAAT
680295 CATGCTACATGA-AAG-AATGGA
1 CATGCT-CATGAGAAGCAATGGA
680316 TGAAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 6 0.30
26 5 0.25
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (24 bp):
CATGCTCATGAGAAGCAATGGAAT
Found at i:680352 original size:10 final size:10
Alignment explanation
Indices: 680332--680362 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
680322 ATGAAAAGAG
680332 AAAAAAG-AA
1 AAAAAAGAAA
680341 AAAAAAGAAA
1 AAAAAAGAAA
680351 AAAAAAGAAA
1 AAAAAAGAAA
680361 AA
1 AA
680363 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:680354 original size:26 final size:27
Alignment explanation
Indices: 680325--680380 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
680315 ATGAAAAATG
*
680325 AAAAGAGAAAAAAGAAAAAAAA-GAAA
1 AAAAAAGAAAAAAGAAAAAAAATGAAA
*
680351 AAAAAAGAAAAATGAAAAAAAATGAAA
1 AAAAAAGAAAAAAGAAAAAAAATGAAA
680378 AAA
1 AAA
680381 TAAAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (27 bp):
AAAAAAGAAAAAAGAAAAAAAATGAAA
Found at i:680371 original size:10 final size:9
Alignment explanation
Indices: 680325--680380 Score: 69
Period size: 9 Copynumber: 6.2 Consensus size: 9
680315 ATGAAAAATG
*
680325 AAAAGAGAA
1 AAAAGAAAA
680334 AAAAGAAAA
1 AAAAGAAAA
680343 AAAAGAAAA
1 AAAAGAAAA
*
680352 AAAA-AGAA
1 AAAAGAAAA
*
680360 AAATGAAAA
1 AAAAGAAAA
680369 AAAATGAAAA
1 AAAA-GAAAA
680379 AA
1 AA
680381 TAAAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
8 6 0.15
9 27 0.68
10 7 0.17
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:680385 original size:7 final size:7
Alignment explanation
Indices: 680317--680389 Score: 60
Period size: 7 Copynumber: 10.3 Consensus size: 7
680307 AAGAATGGAT
*
680317 GAAAAAT
1 GAAAAAA
*
680324 GAAAAGA
1 GAAAAAA
680331 GAAAAAA
1 GAAAAAA
680338 GAAAAAA
1 GAAAAAA
*
680345 -AAGAAA
1 GAAAAAA
680351 -AAAAAA
1 GAAAAAA
680357 GAAAAATGA
1 GAAAAA--A
*
680366 AAAAAAA
1 GAAAAAA
680373 TGAAAAAA
1 -GAAAAAA
*
680381 TAAAAAA
1 GAAAAAA
680388 GA
1 GA
680390 GATTCAAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 10 0.19
7 31 0.58
8 6 0.11
9 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:680385 original size:17 final size:17
Alignment explanation
Indices: 680318--680387 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
680308 AGAATGGATG
*
680318 AAAAATGAAAAGAGAAA
1 AAAAATGAAAAAAGAAA
680335 AAAGAA--AAAAAAGAAA
1 AAA-AATGAAAAAAGAAA
* *
680351 AAAAAAGAAAAATGAAA
1 AAAAATGAAAAAAGAAA
*
680368 AAAAATGAAAAAATAAA
1 AAAAATGAAAAAAGAAA
680385 AAA
1 AAA
680388 GAGATTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 2 0.04
16 12 0.27
17 29 0.64
18 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAATGAAAAAAGAAA
Found at i:681774 original size:81 final size:82
Alignment explanation
Indices: 681591--681915 Score: 522
Period size: 81 Copynumber: 4.0 Consensus size: 82
681581 GTCTAGGAGT
*
681591 ATTTACTTTTCCAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTAC-TTTC-AAGTCGT--TG
1 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
681650 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
*
681668 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTCGTGGTGC
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGC
681732 CTCTGTTTAGAGGAGCA
66 CTCTGTTTAGAGGAGCA
681749 ATTTACTTTTCAAA-TCGTGGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTACTTTTCAAAGTCGTGG-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
*
681813 CCTCTGTTTAGAGAAGCA
65 CCTCTGTTTAGAGGAGCA
*
681831 ATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT
1 ATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGT
681896 GCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCA
681915 A
1 A
681916 GTGCCTCTGT
Statistics
Matches: 232, Mismatches: 6, Indels: 13
0.92 0.02 0.05
Matches are distributed among these distances:
76 4 0.02
77 13 0.06
78 30 0.13
79 7 0.03
80 6 0.03
81 59 0.25
82 38 0.16
83 38 0.16
84 37 0.16
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (82 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGC
CTCTGTTTAGAGGAGCA
Found at i:681842 original size:42 final size:41
Alignment explanation
Indices: 681591--681915 Score: 522
Period size: 41 Copynumber: 8.0 Consensus size: 41
681581 GTCTAGGAGT
*
681591 ATTTACTTTTCCAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
681631 ATTTAC-TTTC-AAGTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
681668 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
681709 ATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
681749 ATTTACTTTTCAAA-TCGTGGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGG-TGCCTCTGTTTAGAGGAGCA
*
681790 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGAAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
681831 ATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
681873 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
681915 A
1 A
681916 GTGCCTCTGT
Statistics
Matches: 270, Mismatches: 6, Indels: 16
0.92 0.02 0.05
Matches are distributed among these distances:
37 30 0.11
38 6 0.02
39 11 0.04
40 51 0.19
41 95 0.35
42 77 0.29
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:681922 original size:22 final size:22
Alignment explanation
Indices: 681894--681937 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
681884 CAAAGTCGTG
681894 GTGCCTCTGTTTAGAGGAGCAA
1 GTGCCTCTGTTTAGAGGAGCAA
681916 GTGCCTCTGTTTAGAGGAGCAA
1 GTGCCTCTGTTTAGAGGAGCAA
681938 TTTACTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (22 bp):
GTGCCTCTGTTTAGAGGAGCAA
Found at i:681978 original size:63 final size:64
Alignment explanation
Indices: 681852--681978 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 64
681842 CAAAGTCGTG
681852 GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
1 GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
681916 GTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
1 GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
681979 TTTACTTTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 32 0.51
64 31 0.49
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (64 bp):
GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
Found at i:681993 original size:105 final size:106
Alignment explanation
Indices: 681810--682020 Score: 381
Period size: 105 Copynumber: 2.0 Consensus size: 106
681800 CAAAGTCGTG
*
681810 GTGCCTCTGTTTAGAGAAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
1 GTGCCTCTGTTTAGAGAAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
681875 TTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
66 TTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
*
681916 GTGCCTCTGTTTAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
1 GTGCCTCTGTTTAGAGAAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
681980 TTAC-TTTCTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
66 TTACTTTTC-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
682021 TTTATTTCCA
Statistics
Matches: 102, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
104 4 0.04
105 73 0.72
106 25 0.25
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GTGCCTCTGTTTAGAGAAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
TTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
Found at i:682005 original size:42 final size:42
Alignment explanation
Indices: 681916--682055 Score: 236
Period size: 42 Copynumber: 3.5 Consensus size: 42
681906 AGAGGAGCAA
681916 GTGCCTCTGTTTAGAGGAGCAATTTACTTT-TCAAAGTCGTG
1 GTGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTG
681957 GTGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTG
1 GTGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTG
681999 GTGCCTCTGTTTAGAGGAGCAATTTA-TTTC-CAAAGTCGT-
1 GTGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTG
*
682038 GAGCCTCT-TTTAGAGGAG
1 GTGCCTCTGTTTAGAGGAG
682056 TTTGAATCAA
Statistics
Matches: 97, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
38 10 0.10
39 7 0.07
40 9 0.09
41 34 0.35
42 37 0.38
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (42 bp):
GTGCCTCTGTTTAGAGGAGCAATTTACTTTCTCAAAGTCGTG
Found at i:689783 original size:22 final size:22
Alignment explanation
Indices: 689758--689817 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
689748 ATTCAAAGTT
*
689758 TTGAAATTCAATGATTCCCAAC
1 TTGAAATTCAATGATTCACAAC
* * *
689780 TTGAAATTCAAAGGTTCACAAT
1 TTGAAATTCAATGATTCACAAC
689802 TTGAAATTCAATGATT
1 TTGAAATTCAATGATT
689818 AGGAATTACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TTGAAATTCAATGATTCACAAC
Found at i:689992 original size:18 final size:19
Alignment explanation
Indices: 689964--690007 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
689954 ACAAAGCTTT
689964 AAAGATTTGCAAGAATTCA
1 AAAGATTTGCAAGAATTCA
*
689983 AAAG-TTTGCAAGATTTC-
1 AAAGATTTGCAAGAATTCA
690000 AAAGATTT
1 AAAGATTT
690008 ACAAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (19 bp):
AAAGATTTGCAAGAATTCA
Found at i:690077 original size:34 final size:35
Alignment explanation
Indices: 690033--690126 Score: 104
Period size: 34 Copynumber: 2.8 Consensus size: 35
690023 TTCAGAAAAC
*
690033 TTTCAGATTTGCAAAAGTTGATA-ATTTGCAAGAT
1 TTTCAGATTTGCAAAAATTGATAGATTTGCAAGAT
* * * * *
690067 TTTTATATTTGTAAAAATTG-TAGCTTTGTAAGAT
1 TTTCAGATTTGCAAAAATTGATAGATTTGCAAGAT
*
690101 TTTCAGATTTGCAAAACTTGA-AGATT
1 TTTCAGATTTGCAAAAATTGATAGATT
690127 CATAAGAACT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
33 2 0.04
34 45 0.96
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (35 bp):
TTTCAGATTTGCAAAAATTGATAGATTTGCAAGAT
Found at i:690145 original size:16 final size:16
Alignment explanation
Indices: 690124--690175 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
690114 AAACTTGAAG
690124 ATTCATAAGAACTCAT
1 ATTCATAAGAACTCAT
* *
690140 ATTCATAAGAATTGAT
1 ATTCATAAGAACTCAT
690156 GATTCATAAGAACTCAT
1 -ATTCATAAGAACTCAT
690173 ATT
1 ATT
690176 TGCAAGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (16 bp):
ATTCATAAGAACTCAT
Found at i:690162 original size:17 final size:17
Alignment explanation
Indices: 690118--690167 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
690108 TTTGCAAAAC
*
690118 TTGAAGATTCATAAGAA
1 TTGATGATTCATAAGAA
* *
690135 CTCAT-ATTCATAAGAA
1 TTGATGATTCATAAGAA
690151 TTGATGATTCATAAGAA
1 TTGATGATTCATAAGAA
690168 CTCATATTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (17 bp):
TTGATGATTCATAAGAA
Found at i:690260 original size:33 final size:33
Alignment explanation
Indices: 690118--690261 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
690108 TTTGCAAAAC
* **
690118 TTGAAGATTCATAAGAACTCATATTCATAAGAA
1 TTGAAGATTCATAAGAACTCAAATTCGCAAGAA
* * * *
690151 TTGATGATTCATAAGAACTCATATTTGCAAGCA
1 TTGAAGATTCATAAGAACTCAAATTCGCAAGAA
* ** * *
690184 TTGGAGATTTGTAA-AATTTTCAAAGTT-GCAAGATT
1 TTGAAGATTCATAAGAA--CTCAAA-TTCGCAAGA-A
* *
690219 TTGAAAGATTCATAAGAACTTAAATTCGTAAGAA
1 TTG-AAGATTCATAAGAACTCAAATTCGCAAGAA
690253 TTGAAGATT
1 TTGAAGATT
690262 TGAAAGAAAT
Statistics
Matches: 84, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
32 2 0.02
33 44 0.52
34 14 0.17
35 14 0.17
36 8 0.10
37 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGAAGATTCATAAGAACTCAAATTCGCAAGAA
Found at i:690361 original size:21 final size:22
Alignment explanation
Indices: 690322--690366 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
690312 TCACAATTGT
690322 AATTTTTAGAAATTAACATCCAA
1 AATTTTTA-AAATTAACATCCAA
*
690345 AATTTTT-AAATTTACATCCAA
1 AATTTTTAAAATTAACATCCAA
690366 A
1 A
690367 TTTCTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTTTTAAAATTAACATCCAA
Found at i:690382 original size:21 final size:21
Alignment explanation
Indices: 690331--690382 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
690321 TAATTTTTAG
* *
690331 AAATTAACATCCAAAATTTTT
1 AAATTCACATCCAAAATTTCT
*
690352 AAATTTACATCC-AAATTTCT
1 AAATTCACATCCAAAATTTCT
690372 AAGATTCACAT
1 AA-ATTCACAT
690383 TCGAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATTCACATCCAAAATTTCT
Found at i:690391 original size:24 final size:23
Alignment explanation
Indices: 690364--690554 Score: 98
Period size: 23 Copynumber: 8.2 Consensus size: 23
690354 ATTTACATCC
690364 AAATTTCTAAGATTCACATTCGAA
1 AAATTTCTAAGATTCACATTC-AA
*
690388 AAATTTTTGTTAAAGATTCACATT-AA
1 AAA--TTT-CT-AAGATTCACATTCAA
* * *
690414 AAA-TTCAAAGGTTCCCATTCGAA
1 AAATTTCTAAGATTCACATTC-AA
690437 AAA-TTC-AAGAATTCACATCTC-A
1 AAATTTCTAAG-ATTCACAT-TCAA
* *
690459 AAATTTCAAAG-CTCACATTCATA
1 AAATTTCTAAGATTCACATTCA-A
* *
690482 AAATTT-TAAAGATTCACATTTGAG
1 AAATTTCT-AAGATTCACA-TTCAA
*
690506 AAATTT-TAAAGATTCACA-TCCA
1 AAATTTCT-AAGATTCACATTCAA
690528 AAATTT-TAAAGA-TCACATTTCAA
1 AAATTTCT-AAGATTCACA-TTCAA
690551 AAAT
1 AAAT
690555 CTTAGAGACT
Statistics
Matches: 134, Mismatches: 16, Indels: 35
0.72 0.09 0.19
Matches are distributed among these distances:
21 17 0.13
22 26 0.19
23 36 0.27
24 31 0.23
25 3 0.02
26 8 0.06
27 1 0.01
28 12 0.09
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (23 bp):
AAATTTCTAAGATTCACATTCAA
Found at i:690461 original size:23 final size:22
Alignment explanation
Indices: 690399--690554 Score: 113
Period size: 22 Copynumber: 6.9 Consensus size: 22
690389 AATTTTTGTT
690399 AAAGATTCACATT-AAAAATTC
1 AAAGATTCACATTCAAAAATTC
* *
690420 AAAGGTTCCCATTCGAAAAATTC
1 AAAGATTCACATTC-AAAAATTC
*
690443 -AAGAATTCACATCTCAAAATTTC
1 AAAG-ATTCACAT-TCAAAAATTC
* *
690466 AAAG-CTCACATTCATAAAATTTT
1 AAAGATTCACATTCA-AAAA-TTC
* * *
690489 AAAGATTCACATTTGAGAAATTTT
1 AAAGATTCACA-TTCA-AAAATTC
* * *
690513 AAAGATTCACATCCAAAATTTT
1 AAAGATTCACATTCAAAAATTC
690535 AAAGA-TCACATTTCAAAAAT
1 AAAGATTCACA-TTCAAAAAT
690555 CTTAGAGACT
Statistics
Matches: 109, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
21 19 0.17
22 31 0.28
23 29 0.27
24 24 0.22
25 6 0.06
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.31
Consensus pattern (22 bp):
AAAGATTCACATTCAAAAATTC
Found at i:690474 original size:22 final size:23
Alignment explanation
Indices: 690397--690552 Score: 112
Period size: 24 Copynumber: 6.9 Consensus size: 23
690387 AAAATTTTTG
*
690397 TTAAAGATTCACAT-T-AAAAAT
1 TTAAAGATTCACATCTCAAAATT
* * * *
690418 TCAAAGGTTCCCAT-TCGAAAA-A
1 TTAAAGATTCACATCTC-AAAATT
*
690440 TTCAAGAATTCACATCTCAAAATT
1 TTAAAG-ATTCACATCTCAAAATT
* *
690464 TCAAAG-CTCACAT-TCATAAAATT
1 TTAAAGATTCACATCTC--AAAATT
* *
690487 TTAAAGATTCACATTTGAGAAATT
1 TTAAAGATTCACATCTCA-AAATT
690511 TTAAAGATTCACATC-CAAAATT
1 TTAAAGATTCACATCTCAAAATT
*
690533 TTAAAGA-TCACATTTCAAAA
1 TTAAAGATTCACATCTCAAAA
690553 ATCTTAGAGA
Statistics
Matches: 106, Mismatches: 18, Indels: 21
0.73 0.12 0.14
Matches are distributed among these distances:
21 20 0.19
22 27 0.25
23 27 0.25
24 31 0.29
25 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAGATTCACATCTCAAAATT
Found at i:690498 original size:46 final size:45
Alignment explanation
Indices: 690364--690552 Score: 147
Period size: 46 Copynumber: 4.1 Consensus size: 45
690354 ATTTACATCC
*
690364 AAATTTCTAAGATTCACATTCGAAAAATTTTTGTTAAAGATTCACA-TT-A
1 AAATTTCAAAG-TTCACATTC-AAAAA---TT-TTAAAGATTCACATTTCA
* * * *
690413 AAAATTCAAAGGTTCCCATTCGAAAAA--TTCAAGAATTCACATCTCA
1 AAATTTCAAA-GTTCACATTC-AAAAATTTTAAAG-ATTCACATTTCA
* *
690459 AAATTTCAAAGCTCACATTCATAAAATTTTAAAGATTCACATTTGA
1 AAATTTCAAAGTTCACATTCA-AAAATTTTAAAGATTCACATTTCA
* *
690505 GAAATTTTAAAGATTCACA-TCCAAAATTTTAAAGA-TCACATTTCA
1 -AAATTTCAAAG-TTCACATTCAAAAATTTTAAAGATTCACATTTCA
690550 AAA
1 AAA
690553 ATCTTAGAGA
Statistics
Matches: 116, Mismatches: 15, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
43 5 0.04
44 11 0.09
45 22 0.19
46 33 0.28
47 17 0.15
48 5 0.04
49 22 0.19
50 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (45 bp):
AAATTTCAAAGTTCACATTCAAAAATTTTAAAGATTCACATTTCA
Found at i:690815 original size:21 final size:20
Alignment explanation
Indices: 690790--690841 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
690780 TATCTAAGAT
690790 TCAAATATTTTCATTTGAAAC
1 TCAAA-ATTTTCATTTGAAAC
**
690811 TCAAAGATTCGCATTTGAAAC
1 TCAAA-ATTTTCATTTGAAAC
*
690832 TTAAAATTTT
1 TCAAAATTTT
690842 GAAAATTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (20 bp):
TCAAAATTTTCATTTGAAAC
Found at i:692044 original size:18 final size:18
Alignment explanation
Indices: 692023--692083 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 18
692013 TAAGTTTTCT
692023 TTTTCTTTCATTTTTTTA
1 TTTTCTTTCATTTTTTTA
*
692041 TTTTCATTC-TTTATTTT-
1 TTTTCTTTCATTT-TTTTA
*
692058 TTTTC--ACATATTTTTTA
1 TTTTCTTTCAT-TTTTTTA
692075 TTTT-TTTCA
1 TTTTCTTTCA
692084 CTTTATCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 14 0.41
18 14 0.41
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTTTCATTTTTTTA
Found at i:693793 original size:60 final size:59
Alignment explanation
Indices: 693504--693817 Score: 347
Period size: 59 Copynumber: 5.3 Consensus size: 59
693494 ATTTTTTTAA
* * *
693504 TTTT-AAAATTTTATTTTCAAGAAAAAATT-ATACTTTCAGCTTTTCCT-TAAAAATATTT
1 TTTTGAAATTTTTATTTT-AAG-AAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTT
* * * *
693562 TTTTAAAACTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTC-AAAAATATTT
1 TTTTGAAATTTTTATTTT-AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTT
* *
693621 TTTTGAAATTTTTATCTTTAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAAATATTT
1 TTTTGAAATTTTTAT-TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTT
* *
693681 TTCTTGATAATTTTTATTCTTAAGAAAAATTGGTACTTCCAACTTTTCCTCAAAAATATATTTT
1 TT-TTGA-AATTTTTATT-TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-ATA-TTT
* * * *
693745 TTTTGAAA-TTTTAATTTAAAAAAAATTGATACTTTCAACTTTTTCTC--AAAATA-CT
1 TTTTGAAATTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTT
693800 TTTTGAAAATTTTTATTT
1 TTTTG-AAATTTTTATTT
693818 CTAAAATTTT
Statistics
Matches: 223, Mismatches: 21, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
55 6 0.03
56 3 0.01
57 10 0.04
58 13 0.06
59 81 0.36
60 43 0.19
61 11 0.05
62 44 0.20
63 7 0.03
64 5 0.02
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.48
Consensus pattern (59 bp):
TTTTGAAATTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTT
Found at i:693901 original size:60 final size:62
Alignment explanation
Indices: 693810--693971 Score: 215
Period size: 60 Copynumber: 2.6 Consensus size: 62
693800 TTTTGAAAAT
* *
693810 TTTTATTTCTAAAAT-TTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTTTCCAAAA-ACA
1 TTTT-TTT-TAAAATCTTTATTTTCAAGAAAAATTGATACTTCCAACTTTTTTTCAAAAATACA
* *
693871 TTTTTTTTAAAATCTTTATTTTTAAGAAAAATTGATACTTCCAACTTTTTTTCAAAAATATA
1 TTTTTTTTAAAATCTTTATTTTCAAGAAAAATTGATACTTCCAACTTTTTTTCAAAAATACA
*
693933 TTTTTTTTCTAAA-CTTTTATTTTCAAGAAAAATTGATAC
1 TTTTTTTT-AAAATC-TTTATTTTCAAGAAAAATTGATAC
693972 AGTTGCATCT
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
59 6 0.07
60 31 0.34
61 16 0.18
62 11 0.12
63 26 0.29
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.49
Consensus pattern (62 bp):
TTTTTTTTAAAATCTTTATTTTCAAGAAAAATTGATACTTCCAACTTTTTTTCAAAAATACA
Found at i:694157 original size:45 final size:44
Alignment explanation
Indices: 694085--694665 Score: 566
Period size: 45 Copynumber: 12.9 Consensus size: 44
694075 CACCCCCAAG
* * * *
694085 CAGAGGTTC-ACAACTTTTTAGAGAATAAACAAAACTCCTCTAAAT
1 CAGAGGCTCAACAACTTTTGA-AAAATAAACAAAGCTCCTCT-AAT
** *
694130 -AGAGGCTCAACAACTTTTTGAAAAATAAACAAAATTCCTCTAAA
1 CAGAGGCTCAACAAC-TTTTGAAAAATAAACAAAGCTCCTCTAAT
** *
694174 CAGAGGCTCAATGACTTTTGAAAAATAAACAAAGCTCCTTTAA-
1 CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTCTAAT
* *
694217 CAGAGGCTTAACAAC-TTTGAAAAAATAAACAAAGCCCATCTAAACAAAGGCTCAAT
1 CAGAGGCTCAACAACTTTTG-AAAAATAAACAAAG--C-TC----C----TCT-AAT
* * * *
694273 CAAAGGCTCAATAACTTTTGAAAAATAAATAAAACTCCTCTAAT
1 CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTCTAAT
*
694317 CAGAGGCTCAACAACTTTTGAAAAAATAAACAAAGCTCCTCTAAA
1 CAGAGGCTCAACAACTTTTG-AAAAATAAACAAAGCTCCTCTAAT
* * *
694362 CAGAAGCTCAACAACTTTTAAAAAAATAAACAAAGCTCATCTAAT
1 CAGAGGCTCAACAACTTTT-GAAAAATAAACAAAGCTCCTCTAAT
* * *** *
694407 CAAAGGCTTAGTGACATTTTAAAAAATAAACAAAGCTCCTCTAAT
1 CAGAGGCTCAACAAC-TTTTGAAAAATAAACAAAGCTCCTCTAAT
* ** * *
694452 CAAAGGCTCAATGACTTTGTGAAAAATAAATAAAG-TCCTTTAAAT
1 CAGAGGCTCAACAACTTT-TGAAAAATAAACAAAGCTCCTCT-AAT
694497 -AGAGGCTCAACAACTTTTGAAAAAATAAACAAAGCTCCTCTAAT
1 CAGAGGCTCAACAACTTTTG-AAAAATAAACAAAGCTCCTCTAAT
* * * *
694541 CAGAAGCTTAACAACTTTTGAAAAATAAACAAAGCTCTTTTAAT
1 CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTCTAAT
** *
694585 CAGAGGCTCAATGACTTTT-AAAAATAAATAAAGCTCCTCTAAT
1 CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTCTAAT
694628 CAGAGGCTCAACAAC-TTTGAAAAATAAACAAAGCTCCT
1 CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
694666 TGACAATCAT
Statistics
Matches: 448, Mismatches: 61, Indels: 56
0.79 0.11 0.10
Matches are distributed among these distances:
42 7 0.02
43 80 0.18
44 130 0.29
45 184 0.41
46 11 0.02
49 1 0.00
50 1 0.00
53 2 0.00
54 2 0.00
55 2 0.00
56 24 0.05
57 4 0.01
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (44 bp):
CAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTCTAAT
Found at i:694178 original size:89 final size:89
Alignment explanation
Indices: 694085--694665 Score: 458
Period size: 89 Copynumber: 6.4 Consensus size: 89
694075 CACCCCCAAG
* *
694085 CAGAGGTTCACAACTTTTTAGAGAATAAACAAAACTCCTCTAAAT-AGAGGCTCAACAACTTTTT
1 CAGAGGCTCACAACTTTTTAGAAAATAAACAAAACTCCTCT-AATCAGAGGCTCAACAAC-TTTT
**
694149 G-AAAAATAAACAAAATTCCTCTAAA
64 GAAAAAATAAACAAAGCTCCTCTAAA
* * * *
694174 CAGAGGCTCA-ATGACTTTTGA-AAAATAAACAAAGCTCCTTTAA-CAGAGGCTTAACAAC-TTT
1 CAGAGGCTCACA--ACTTTTTAGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACAACTTTT
694235 GAAAAAATAAACAAAGC-CCATCTAAA
64 GAAAAAATAAACAAAGCTCC-TCTAAA
* * *
694261 CAAAGGCTCAATCAAAGGCTCAATAACTTTTGAAAAATAAATAAAACTCCTCTAATCAGAGGCTC
1 CAGAGGCTC-A-C-AA--CT---T---TTTAG-AAAATAAACAAAACTCCTCTAATCAGAGGCTC
694326 AACAACTTTTGAAAAAATAAACAAAGCTCCTCTAAA
54 AACAACTTTTGAAAAAATAAACAAAGCTCCTCTAAA
* * * * * * * ***
694362 CAGAAGCTCAACAACTTTTAAAAAAATAAACAAAGCTCATCTAATCAAAGGCTTAGTGACATTTT
1 CAGAGGCTC-ACAACTTTTTAGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACAAC-TTTT
*
694427 -AAAAAATAAACAAAGCTCCTCTAAT
64 GAAAAAATAAACAAAGCTCCTCTAAA
* * * * *
694452 CAAAGGCTCA-ATGACTTTGT-GAAAAATAAA-TAAAGTCCTTTAAAT-AGAGGCTCAACAACTT
1 CAGAGGCTCACA--ACTTTTTAG-AAAATAAACAAAACTCCTCT-AATCAGAGGCTCAACAACTT
*
694513 TTGAAAAAATAAACAAAGCTCCTCTAAT
62 TTGAAAAAATAAACAAAGCTCCTCTAAA
* * * * * * **
694541 CAGAAGCTTAACAACTTTTGA-AAAATAAACAAAGCTCTTTTAATCAGAGGCTCAATGACTTTT-
1 CAGAGGC-TCACAACTTTTTAGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACAACTTTTG
* *
694604 -AAAAATAAATAAAGCTCCTCTAAT
65 AAAAAATAAACAAAGCTCCTCTAAA
* *
694628 CAGAGGCTCAACAAC-TTTGA-AAAATAAACAAAGCTCCT
1 CAGAGGCTC-ACAACTTTTTAGAAAATAAACAAAACTCCT
694666 TGACAATCAT
Statistics
Matches: 399, Mismatches: 59, Indels: 71
0.75 0.11 0.13
Matches are distributed among these distances:
86 29 0.07
87 61 0.15
88 33 0.08
89 101 0.25
90 86 0.22
91 10 0.03
94 2 0.01
97 4 0.01
99 21 0.05
100 15 0.04
101 35 0.09
102 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (89 bp):
CAGAGGCTCACAACTTTTTAGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACAACTTTTGA
AAAAATAAACAAAGCTCCTCTAAA
Found at i:694289 original size:56 final size:56
Alignment explanation
Indices: 694220--694327 Score: 130
Period size: 56 Copynumber: 1.9 Consensus size: 56
694210 CCTTTAACAG
* *
694220 AGGCTTAACAAC-TTTGAAAAAATAAACAAAGC-CCATCTAAACAAAGGCTCAATCAA
1 AGGCTCAACAACTTTTG-AAAAATAAACAAAACTCC-TCTAAACAAAGGCTCAATCAA
* * * *
694276 AGGCTCAATAACTTTTGAAAAATAAATAAAACTCCTCTAATCAGAGGCTCAA
1 AGGCTCAACAACTTTTGAAAAATAAACAAAACTCCTCTAAACAAAGGCTCAA
694328 CAACTTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
56 38 0.86
57 6 0.14
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.21
Consensus pattern (56 bp):
AGGCTCAACAACTTTTGAAAAATAAACAAAACTCCTCTAAACAAAGGCTCAATCAA
Found at i:694523 original size:179 final size:175
Alignment explanation
Indices: 694270--694666 Score: 582
Period size: 179 Copynumber: 2.2 Consensus size: 175
694260 ACAAAGGCTC
* *
694270 AATCAAAGGCTCAATAACTTTTGAAAAATAAATAAAACTCCTCTAATCAGAGGCTCAACAACTTT
1 AATCAAAGGCTCAATAACTTTTGAAAAATAAAT-AAAGTCCTTTAATCAGAGGCTCAACAACTTT
694335 TGAAAAAATAAACAAAGCTCCTCTAAACAGAAGCTCAACAACTTTTAAAAAAATAAACAAAGCTC
65 TGAAAAAATAAACAAAGCTCCTCTAAACAGAAGCTCAACAACTTTT-AAAAAATAAACAAAGCTC
* *
694400 ATCTAATCAAAGGCTTAGTGACATTTTAAAAAATAAACAAAGCTCCTCT
129 ATCTAATCAAAGGCTCAATGAC-TTTT-AAAAATAAACAAAGCTCCTCT
*
694449 AATCAAAGGCTCAATGACTTTGTGAAAAATAAATAAAGTCCTTTAAAT-AGAGGCTCAACAACTT
1 AATCAAAGGCTCAATAACTTT-TGAAAAATAAATAAAGTCCTTT-AATCAGAGGCTCAACAACTT
* * *
694513 TTGAAAAAATAAACAAAGCTCCTCTAATCAGAAGCTTAACAACTTTTGAAAAATAAACAAAGCTC
64 TTGAAAAAATAAACAAAGCTCCTCTAAACAGAAGCTCAACAACTTTTAAAAAATAAACAAAGCTC
* * * *
694578 TTTTAATCAGAGGCTCAATGACTTTTAAAAATAAATAAAGCTCCTCT
129 ATCTAATCAAAGGCTCAATGACTTTTAAAAATAAACAAAGCTCCTCT
* * *
694625 AATCAGAGGCTCAACAAC-TTTGAAAAATAAACAAAGCTCCTT
1 AATCAAAGGCTCAATAACTTTTGAAAAATAAATAAAG-TCCTT
694667 GACAATCATA
Statistics
Matches: 199, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
174 15 0.08
175 7 0.04
176 35 0.18
177 4 0.02
178 34 0.17
179 89 0.45
180 15 0.08
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (175 bp):
AATCAAAGGCTCAATAACTTTTGAAAAATAAATAAAGTCCTTTAATCAGAGGCTCAACAACTTTT
GAAAAAATAAACAAAGCTCCTCTAAACAGAAGCTCAACAACTTTTAAAAAATAAACAAAGCTCAT
CTAATCAAAGGCTCAATGACTTTTAAAAATAAACAAAGCTCCTCT
Found at i:695687 original size:23 final size:22
Alignment explanation
Indices: 695660--695708 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
695650 TGAGTCATCC
* *
695660 TTTTTATTTTTTTTATTTTTATT
1 TTTTTATCTTTTTTATCTTT-TT
*
695683 TTTTTCTCTTTTTTATCTTTTT
1 TTTTTATCTTTTTTATCTTTTT
695705 TTTT
1 TTTT
695709 CTTTTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTATCTTTTTTATCTTTTT
Found at i:695711 original size:10 final size:10
Alignment explanation
Indices: 695659--695715 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
695649 TTGAGTCATC
695659 CTTTTTATTTT
1 CTTTTT-TTTT
*
695670 -TTTTATTTT
1 CTTTTTTTTT
*
695679 -TATTTTTTT
1 CTTTTTTTTT
*
695688 CTCTTTTTTAT
1 CT-TTTTTTTT
695699 CTTTTTTTTT
1 CTTTTTTTTT
695709 CTTTTTT
1 CTTTTTT
695716 CAAGCATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 11 0.29
10 19 0.50
11 8 0.21
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:699079 original size:12 final size:12
Alignment explanation
Indices: 699059--699088 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
699049 TATGACATAC
699059 TCTTCAGAATCA
1 TCTTCAGAATCA
*
699071 TCTTTAGAATCA
1 TCTTCAGAATCA
699083 TCTTCA
1 TCTTCA
699089 TTGTCAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (12 bp):
TCTTCAGAATCA
Found at i:702310 original size:15 final size:14
Alignment explanation
Indices: 702288--702317 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
702278 TGTATCATCA
702288 TATTTTTTAAATTT
1 TATTTTTTAAATTT
702302 TATTATTTTAAATTT
1 TATT-TTTTAAATTT
702317 T
1 T
702318 GGTAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTTAAATTT
Found at i:704811 original size:58 final size:59
Alignment explanation
Indices: 704689--704992 Score: 304
Period size: 58 Copynumber: 5.2 Consensus size: 59
704679 TTTTAATGTT
* * *
704689 AAAATTTTATTTTCAAG-AAAATTAATGC-TTCGACTTTTTCTCAAAAATATTTTTTT-
1 AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTG
* * *
704745 AAACTTTTATTTTTAA-AGAAAATTGATACTTTTAACTTTTT-TCAAAAATATTTTTTTG
1 AAAATTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTG
* * *
704803 AAAATTTTATCTTCAAGAAAAATTGATACTCTCAACTTTTTCATAAAAAATATTTTTCTTG
1 AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTT-TTG
* * * * * *
704864 ATAATTTTATTCTT-AAGAAAAATT-AGTACTTCCAACTTTTCCTTAAAAGTGTTTTTTT-
1 AAAATTTTATT-TTCAAGAAAAATTGA-TACTTTCAACTTTTTCTCAAAAATATTTTTTTG
*** * *
704922 TTTATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATA-CTTTTTG
1 AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTG
704979 AAAATTTTTATTTT
1 AAAA-TTTTATTTT
704993 AGAAATTTTA
Statistics
Matches: 201, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
56 19 0.09
57 32 0.16
58 84 0.42
59 4 0.02
60 25 0.12
61 35 0.17
62 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.49
Consensus pattern (59 bp):
AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTG
Found at i:704894 original size:119 final size:113
Alignment explanation
Indices: 704687--704986 Score: 288
Period size: 119 Copynumber: 2.6 Consensus size: 113
704677 TTTTTTAATG
* * * *
704687 TTAAAATTTTATTTTCAAG-AAAATTAATGCTTCGACTTTTTCTCAAAAATATTTTTTTAAACTT
1 TTAAAATTTTA-TTTCAAGAAAAATTGATACTTCAACTTTTTCTAAAAAATATTTTTTTAAACTT
* **
704751 TTATTTTTAAAGAAAATTGATACTTTTAACTTTT-TTCAAAAATATTTTT
65 TTATTCTTAAAGAAAATTGATACTTCCAACTTTTCTT-AAAAATATTTTT
704800 TTGAAAATTTTATCTTCAAGAAAAATTGATACTCTCAACTTTTTCATAAAAAATATTTTTCTTGA
1 TT-AAAATTTTAT-TTCAAGAAAAATTGATACT-TCAACTTTTTC-TAAAAAATATTTTT-TT-A
* *
704865 TAA-TTTTATTCTT-AAGAAAAATT-AGTACTTCCAACTTTTCCTTAAAAGTGTTTTT
60 -AACTTTTATTCTTAAAG-AAAATTGA-TACTTCCAACTTTT-CTTAAAAATATTTTT
*** * * * *
704920 TTTTTATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCT-CAAAATACTTTTTGAAAAT
1 TTAAAATTTT-ATTTCAAGAAAAATTGATAC-TTCAACTTTTTCTAAAAAATATTTTTTTAAACT
704984 TTT
64 TTT
704987 TATTTTAGAA
Statistics
Matches: 157, Mismatches: 15, Indels: 28
0.79 0.08 0.14
Matches are distributed among these distances:
113 3 0.02
114 17 0.11
115 15 0.10
116 11 0.07
117 23 0.15
118 7 0.04
119 62 0.39
120 17 0.11
121 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (113 bp):
TTAAAATTTTATTTCAAGAAAAATTGATACTTCAACTTTTTCTAAAAAATATTTTTTTAAACTTT
TATTCTTAAAGAAAATTGATACTTCCAACTTTTCTTAAAAATATTTTT
Done.