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 82 of 109
Found at i:16572248 original size:21 final size:22
Alignment explanation
Indices: 16572208--16572287 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 22
16572198 TCTTTGAATC
*
16572208 TTTTATGAATTTTTGAAATTTT
1 TTTTATGAATCTTTGAAATTTT
*
16572230 TTTTATGGATCTTTG-AATTTT
1 TTTTATGAATCTTTGAAATTTT
* * *
16572251 TTTCA--AAACTTTGAAA--TC
1 TTTTATGAATCTTTGAAATTTT
*
16572269 TTTTATGAATCATTGAAAT
1 TTTTATGAATCTTTGAAAT
16572288 CATTTTTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
18 5 0.11
19 6 0.13
20 11 0.24
21 10 0.22
22 13 0.29
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTTATGAATCTTTGAAATTTT
Found at i:16572487 original size:23 final size:23
Alignment explanation
Indices: 16572461--16572505 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16572451 TCTAGATTTG
*
16572461 AATCTTTAAAATTTTTAAATGTA
1 AATCTATAAAATTTTTAAATGTA
* *
16572484 AATCTATGAAATTTTTATATGT
1 AATCTATAAAATTTTTAAATGT
16572506 GCATTTCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (23 bp):
AATCTATAAAATTTTTAAATGTA
Found at i:16572626 original size:21 final size:21
Alignment explanation
Indices: 16572600--16572667 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
16572590 GAATCGTTGA
16572600 AAATTTTAAATGTGAATTTCT
1 AAATTTTAAATGTGAATTTCT
**
16572621 AAATTTTTCAAATGAAAATCTT-T
1 AAA-TTTT-AAATGTGAAT-TTCT
** *
16572644 ATTTTTTAAATGTGAATCTCT
1 AAATTTTAAATGTGAATTTCT
16572665 AAA
1 AAA
16572668 CCCATTATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 8 0.24
23 10 0.29
24 2 0.06
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (21 bp):
AAATTTTAAATGTGAATTTCT
Found at i:16572633 original size:23 final size:22
Alignment explanation
Indices: 16572603--16572667 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
16572593 TCGTTGAAAA
16572603 TTTTAAATGTGAATTTCTAAAT
1 TTTTAAATGTGAATTTCTAAAT
** *
16572625 TTTTCAAATGAAAATCTT-T-ATT
1 TTTT-AAATGTGAAT-TTCTAAAT
*
16572647 TTTTAAATGTGAATCTCTAAA
1 TTTTAAATGTGAATTTCTAAA
16572668 CCCATTATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
20 1 0.03
21 9 0.28
22 11 0.34
23 9 0.28
24 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (22 bp):
TTTTAAATGTGAATTTCTAAAT
Found at i:16573005 original size:91 final size:90
Alignment explanation
Indices: 16572855--16573038 Score: 289
Period size: 91 Copynumber: 2.0 Consensus size: 90
16572845 TTTTCAGAAG
*
16572855 GCATTTGTATCATGGGAAGGACACTTGCATTTGCATTATTAGTAACCATTTTTGCAGAATATCTA
1 GCATTTGTATCATGAGAAGGACACTTGCATTTGCATTATTAGTAACCATTTTTGCAGAATATCTA
*
16572920 TATTTGCATAAGAACTTTTGCATTT
66 CATTTGCATAAGAACTTTTGCATTT
* **
16572945 GCATATTGTATCATGAGAAGGACACTTGCATTTGCATTGTTCA-TAACCATTTTTTTAGAATATC
1 GCAT-TTGTATCATGAGAAGGACACTTGCATTTGCATTATT-AGTAACCATTTTTGCAGAATATC
*
16573009 TGCATTTGCATAAGAACTTTTGCATTT
64 TACATTTGCATAAGAACTTTTGCATTT
16573036 GCA
1 GCA
16573039 CCATCATTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
90 4 0.05
91 81 0.94
92 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (90 bp):
GCATTTGTATCATGAGAAGGACACTTGCATTTGCATTATTAGTAACCATTTTTGCAGAATATCTA
CATTTGCATAAGAACTTTTGCATTT
Found at i:16576829 original size:20 final size:20
Alignment explanation
Indices: 16576806--16576844 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16576796 ACCACAATTG
*
16576806 AATCAGTCAAATCACAACTA
1 AATCAATCAAATCACAACTA
16576826 AATCAATCAAATCACAACT
1 AATCAATCAAATCACAACT
16576845 GAATTGGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (20 bp):
AATCAATCAAATCACAACTA
Found at i:16577744 original size:514 final size:502
Alignment explanation
Indices: 16576904--16577903 Score: 1574
Period size: 514 Copynumber: 2.0 Consensus size: 502
16576894 AACTGAATCA
**
16576904 GACTATCATTGAAACATTGACCAATTTTGATTAGTTTTATTAGGTAATTTTTTTTTTTTACTTTG
1 GACTATCATTGAAACATTGACCAATTTTGATTAGTCCTATTAGGTAATTTTTTTTTTTTACTTTG
* *
16576969 TTAAGTTATTTTGTTTATCTATGCATTTTTAAATTTTTAAAAATAAATAAATATTTTTAAAAAAT
66 TTAAGTTATTTTGTTTATCTATGCACTTTTAAATTTTTAAAAATAAATAAATATTTTCAAAAAAT
16577034 GTTAAAAGATTTTTGTAAAAAAAAAATTAAACCCTCCGATGATGAGATATTAAGAAAATGTGAGT
131 GTTAAAAGATTTTTGTAAAAAAAAAATTAAACCCTCCGATGATGAGATATTAAGAAAATGTGAGT
* *
16577099 AATGATTCCTTAAAAATCTTTAAGTGAGGATATTTTCTAAAATGCTATCAAAGTACTATAGTATT
196 AATGATTCCTTAAAAATCTTTAAGTGAGGATATTTTCTAAAATGCAATCAAAGTACTATAGTACT
* * * * *
16577164 TAGAAAGTTATTCAACATAAGAGGTTTTTGTTTATTTATTTTTTATATTGTTAAAATTGAAAAAG
261 TAGAAAGATATTCAACACAAGAGGTTTTCGTTTATTTATTTTTTATATTATTAAAATAGAAAAAG
*
16577229 AATTAAAGAATGAGTTATTTTAGGAATAAAATTACATATAATAA-TATGAATATTATTGGCATTA
326 AATTAAAGAATAAGTTATTTTAGGAATAAAATTACATATAATAATTATGAA-ATTATTGGCATTA
* *
16577293 ATTAATTAAAAAATATGAGCCGAAGATGATACTCTAAGAAAATCCAAGTGGTGATTCTTAAAAAA
390 ATTAATTAAAAAATACGAGCAGAAGATGATACTCTAAGAAAATCCAAGTGGTGATTCTTAAAAAA
*
16577358 TCTC-TAGGTGAGAAAATTT-TTTCTAATATTACTGATGTACTAGAATTG
455 TC-CATAGGTAAGAAAATTTCTTT-TAATATTACTGATGTACTAGAATTG
* *
16577406 GACTATCATTGAAACATTGACCAGTTTTGATTAGTCCTATTGGGTAATTTTTTTTTATTTCTTTT
1 GACTATCATTGAAACATTGACCAATTTTGATTAGTCCTATTAGGTAA----TTTTT-TTT-TTTT
*
16577471 ACTTTGTTAAGTTATTTATTTGTTTATCTATGCACTTTTAAATTTTTAAAAATAAATATATATTT
60 ACTTTGTTAAGTTA--T-TTTGTTTATCTATGCACTTTTAAATTTTTAAAAATAAATAAATATTT
** * * *
16577536 TCAAAAAATGTTAAAATTTTTTTGTAAAAAAAAAAAATTAAATCTTCTGATGATGAGATATTAAG
122 TCAAAAAATGTTAAAAGATTTTTGT--AAAAAAAAAATTAAACCCTCCGATGATGAGATATTAAG
16577601 AAAATGTGAGTAATGATTCCTTAAAAATCTTTAAGTGAGGATATTTTTCTAAAATGCAATCAAAG
185 AAAATGTGAGTAATGATTCCTTAAAAATCTTTAAGTGAGGATA-TTTTCTAAAATGCAATCAAAG
* *
16577666 TACTATAGTACTTAGGAAGATATTCAACACAAGAGGTTTTCGTTTATTTATTTTTTGTATTATTA
249 TACTATAGTACTTAGAAAGATATTCAACACAAGAGGTTTTCGTTTATTTATTTTTTATATTATTA
*
16577731 AAATAGAAAAAGAATTAAAGAATAAGTTGTTTTAGGAATAAAATTACATATAATAATTTATGAAA
314 AAATAGAAAAAGAATTAAAGAATAAGTTATTTTAGGAATAAAATTACATATAATAA-TTATGAAA
* *
16577796 TTATTGGCATTAATTAATTAAAAAATACGAGCAGAAGATGATAGTCTAAGAAAATCTAAGTGGTG
378 TTATTGGCATTAATTAATTAAAAAATACGAGCAGAAGATGATACTCTAAGAAAATCCAAGTGGTG
*
16577861 ATTTTTAAAAAATCCATAGGTAAGAAAATTTCTTTTAATATTA
443 ATTCTTAAAAAATCCATAGGTAAGAAAATTTCTTTTAATATTA
16577904 TCAATGTATT
Statistics
Matches: 453, Mismatches: 29, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
502 43 0.09
506 5 0.01
507 3 0.01
508 18 0.04
510 1 0.00
511 67 0.15
513 78 0.17
514 132 0.29
515 97 0.21
516 9 0.02
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (502 bp):
GACTATCATTGAAACATTGACCAATTTTGATTAGTCCTATTAGGTAATTTTTTTTTTTTACTTTG
TTAAGTTATTTTGTTTATCTATGCACTTTTAAATTTTTAAAAATAAATAAATATTTTCAAAAAAT
GTTAAAAGATTTTTGTAAAAAAAAAATTAAACCCTCCGATGATGAGATATTAAGAAAATGTGAGT
AATGATTCCTTAAAAATCTTTAAGTGAGGATATTTTCTAAAATGCAATCAAAGTACTATAGTACT
TAGAAAGATATTCAACACAAGAGGTTTTCGTTTATTTATTTTTTATATTATTAAAATAGAAAAAG
AATTAAAGAATAAGTTATTTTAGGAATAAAATTACATATAATAATTATGAAATTATTGGCATTAA
TTAATTAAAAAATACGAGCAGAAGATGATACTCTAAGAAAATCCAAGTGGTGATTCTTAAAAAAT
CCATAGGTAAGAAAATTTCTTTTAATATTACTGATGTACTAGAATTG
Found at i:16577991 original size:22 final size:22
Alignment explanation
Indices: 16577955--16577997 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16577945 TTCTAATTTA
*
16577955 TTTTTTAAATAAAAAATAATAT
1 TTTTTTAAATAAAAAAGAATAT
16577977 TTTTTTAAA-AGAAAAAGAATA
1 TTTTTTAAATA-AAAAAGAATA
16577998 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
TTTTTTAAATAAAAAAGAATAT
Found at i:16579610 original size:2 final size:2
Alignment explanation
Indices: 16579603--16579633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16579593 TTAAAGTGTT
16579603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16579634 TCGGCCAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16584133 original size:19 final size:20
Alignment explanation
Indices: 16584111--16584155 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
16584101 AACCTTTAAT
*
16584111 TTTTTGACG-ATTTTTTCAG
1 TTTTCGACGTATTTTTTCAG
*
16584130 TTTTCGACGTCTTTTTTCAG
1 TTTTCGACGTATTTTTTCAG
*
16584150 ATTTCG
1 TTTTCG
16584156 GTAAACATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.56
Consensus pattern (20 bp):
TTTTCGACGTATTTTTTCAG
Found at i:16584518 original size:13 final size:13
Alignment explanation
Indices: 16584500--16584530 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16584490 TTTTGTTATT
16584500 TATTTTATTTAAG
1 TATTTTATTTAAG
*
16584513 TATTTTATTTATG
1 TATTTTATTTAAG
16584526 TATTT
1 TATTT
16584531 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (13 bp):
TATTTTATTTAAG
Found at i:16590267 original size:9 final size:9
Alignment explanation
Indices: 16590253--16590305 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
16590243 CTATGCTTAA
16590253 AAAAAAAAG
1 AAAAAAAAG
*
16590262 AAAAAAAGGGG
1 AAAAAAA--AG
*
16590273 AAAAATGAAAA
1 AAAAA--AAAG
16590284 AAAAAAAAG
1 AAAAAAAAG
16590293 AAAAAAAAG
1 AAAAAAAAG
16590302 AAAA
1 AAAA
16590306 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 23 0.64
11 11 0.31
13 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:16590304 original size:29 final size:29
Alignment explanation
Indices: 16590251--16590316 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
16590241 TACTATGCTT
*
16590251 AAAAAAAAAAGAAAAAAAGGGGAAAAATGAA
1 AAAAAAAAAAGAAAAAAA-GAG-AAAATGAA
*
16590282 AAAAAAAAAAGAAAAAAA-AGAAAATTAA
1 AAAAAAAAAAGAAAAAAAGAGAAAATGAA
16590310 AAAAAAA
1 AAAAAAA
16590317 GACTCAAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 14 0.42
29 1 0.03
31 18 0.55
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAAGAAAAAAAGAGAAAATGAA
Found at i:16591236 original size:21 final size:21
Alignment explanation
Indices: 16591207--16591278 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
16591197 AGAGAAATTG
*
16591207 TGAACTTTTTAATGAAAATCTT
1 TGAA-TTTTCAATGAAAATCTT
* * *
16591229 TGAATTTTGAATGAGAGTCTT
1 TGAATTTTCAATGAAAATCTT
*
16591250 TGAA-TTTCAAAGAAAAATCTT
1 TGAATTTTCAATG-AAAATCTT
*
16591271 TGAGTTTT
1 TGAATTTT
16591279 AAGTTTCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.15
21 27 0.68
22 7 0.17
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (21 bp):
TGAATTTTCAATGAAAATCTT
Found at i:16591636 original size:41 final size:41
Alignment explanation
Indices: 16591526--16591658 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
16591516 GGTTGTCGAT
*
16591526 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAGAG
1 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTTAGAG
* * * * *
16591567 GTGCTATTTATTTTTTAAAAGTTCTGTTGCCTCTATTTAGAT
1 GAGCCATTTA-TTTTTCAAAGTTTTGTTGCCTCTATTTAGAG
*
16591609 GAACCATTTATTTTTCAAAGTTTTGTTGCCTCTATTTAGAG
1 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTTAGAG
16591650 GAGCCATTT
1 GAGCCATTT
16591659 CTATTGCCTT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 44 0.56
42 34 0.44
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (41 bp):
GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTTAGAG
Found at i:16591674 original size:69 final size:69
Alignment explanation
Indices: 16591588--16591727 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
16591578 TTTTTAAAAG
* * *
16591588 TTCTGTTGCCTCTATTTAGATGAACCATTTATTTTTCAAAGTTTTGTTGCCTCTATTTAGAGGAG
1 TTCTATTGCCTCTATTTAGAAGAACCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAGAGGAG
16591653 CCAT
66 CCAT
* * **
16591657 TTCTATTGCCTTTATTTAGAAGAGCCATTTATTTTTTGAAGTTTTGTTGCCTCTATTCAGAGGAG
1 TTCTATTGCCTCTATTTAGAAGAACCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAGAGGAG
16591722 CCAT
66 CCAT
16591726 TT
1 TT
16591728 ATTTTTCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (69 bp):
TTCTATTGCCTCTATTTAGAAGAACCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAGAGGAG
CCAT
Found at i:16591707 original size:41 final size:41
Alignment explanation
Indices: 16591662--16591751 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
16591652 GCCATTTCTA
* * **
16591662 TTGCCTTTATTTAGAAGAGCCATTTATTTTTTGAAGTTTTG
1 TTGCCTCTATTCAGAAGAGCCATTTATTTTTCAAAGTTTTG
*
16591703 TTGCCTCTATTCAGAGGAGCCATTTATTTTTCAAAGTTTTG
1 TTGCCTCTATTCAGAAGAGCCATTTATTTTTCAAAGTTTTG
16591744 TTGCCTCT
1 TTGCCTCT
16591752 GTTTAAAGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (41 bp):
TTGCCTCTATTCAGAAGAGCCATTTATTTTTCAAAGTTTTG
Found at i:16591762 original size:41 final size:41
Alignment explanation
Indices: 16591678--16591763 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
16591668 TTATTTAGAA
** *
16591678 GAGCCATTTATTTTTTGAAGTTTTGTTGCCTCTATTCAGAG
1 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAAAG
* *
16591719 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTGTTTAAAG
1 GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAAAG
16591760 GAGC
1 GAGC
16591764 TTTGCTTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (41 bp):
GAGCCATTTATTTTTCAAAGTTTTGTTGCCTCTATTCAAAG
Found at i:16591994 original size:9 final size:9
Alignment explanation
Indices: 16591978--16592025 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
16591968 AACTGACCAT
16591978 TTTA-TTTA
1 TTTATTTTA
16591986 TTTATTTTA
1 TTTATTTTA
16591995 TTTATTTTTAA
1 TTTA-TTTT-A
16592006 TTTATTTT-
1 TTTATTTTA
16592014 TATTATTTTA
1 T-TTATTTTA
16592024 TT
1 TT
16592026 ATCTGATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.14
9 16 0.46
10 9 0.26
11 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:16592009 original size:24 final size:23
Alignment explanation
Indices: 16591977--16592021 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
16591967 CAACTGACCA
16591977 TTTTATTTATTTATT-TTATTTAT
1 TTTTATTTATTT-TTATTATTTAT
16592000 TTTTAATTTATTTTTATTATTT
1 TTTT-ATTTATTTTTATTATTT
16592022 TATTATCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATTTATTTTTATTATTTAT
Found at i:16592010 original size:20 final size:20
Alignment explanation
Indices: 16591985--16592062 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
16591975 CATTTTATTT
16591985 ATTTA-TTTTATTTATTTTTA
1 ATTTATTTTTA-TTATTTTTA
16592005 ATTTATTTTTATTA-TTTT-
1 ATTTATTTTTATTATTTTTA
*
16592023 A-TTATCTGATTTCTTATTTTTA
1 ATTTAT-T--TTTATTATTTTTA
* *
16592045 ATTTAATGTTATTATTTT
1 ATTTATTTTTATTATTTT
16592063 ATCATATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.09
18 2 0.04
19 4 0.09
20 23 0.49
21 9 0.19
22 2 0.04
23 3 0.06
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (20 bp):
ATTTATTTTTATTATTTTTA
Found at i:16593261 original size:24 final size:26
Alignment explanation
Indices: 16593198--16593262 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
16593188 GTTCATAGTT
*
16593198 TAACAATCCTTATACTTTACACATAC
1 TAACAATTCTTATACTTTACACATAC
* * *
16593224 TAAGCAATTTTTATACTTTA-A-TTCC
1 TAA-CAATTCTTATACTTTACACATAC
16593249 TAACAATTCTTATA
1 TAACAATTCTTATA
16593263 TTTTCTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 10 0.30
25 5 0.15
26 4 0.12
27 14 0.42
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.42
Consensus pattern (26 bp):
TAACAATTCTTATACTTTACACATAC
Found at i:16597925 original size:22 final size:22
Alignment explanation
Indices: 16597897--16597945 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
16597887 CCATTTTATT
16597897 AATAAACAAAACAAAA-AAACAA
1 AATAAAC-AAACAAAAGAAACAA
*
16597919 AATAAACAAACAAAAGAAACAG
1 AATAAACAAACAAAAGAAACAA
16597941 AATAA
1 AATAA
16597946 GATAGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.78, C:0.12, G:0.04, T:0.06
Consensus pattern (22 bp):
AATAAACAAACAAAAGAAACAA
Found at i:16597938 original size:13 final size:13
Alignment explanation
Indices: 16597900--16597939 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16597890 TTTTATTAAT
*
16597900 AAACAAAACAAAA
1 AAACAAAACAAAC
*
16597913 AAACAAAATAAAC
1 AAACAAAACAAAC
*
16597926 AAACAAAAGAAAC
1 AAACAAAACAAAC
16597939 A
1 A
16597940 GAATAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.15, G:0.03, T:0.03
Consensus pattern (13 bp):
AAACAAAACAAAC
Found at i:16598019 original size:12 final size:12
Alignment explanation
Indices: 16597982--16598032 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
16597972 GCCGCTGTCG
16597982 CCAG-CCCCCGA
1 CCAGCCCCCCGA
* ** *
16597993 CCAACTACCCTA
1 CCAGCCCCCCGA
16598005 CCAGCCCCCCGA
1 CCAGCCCCCCGA
*
16598017 CCAGCCTCCCGA
1 CCAGCCCCCCGA
16598029 CCAG
1 CCAG
16598033 TCACCCTACA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
11 3 0.10
12 27 0.90
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (12 bp):
CCAGCCCCCCGA
Found at i:16598031 original size:24 final size:23
Alignment explanation
Indices: 16597982--16598032 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
16597972 GCCGCTGTCG
*
16597982 CCAGCCCCCGACCAACTACCCTA
1 CCAGCCCCCGACCAACTACCCGA
*
16598005 CCAGCCCCCCGACCAGCCT-CCCGA
1 CCAG-CCCCCGACCA-ACTACCCGA
16598029 CCAG
1 CCAG
16598033 TCACCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.75
25 2 0.08
ACGTcount: A:0.22, C:0.59, G:0.14, T:0.06
Consensus pattern (23 bp):
CCAGCCCCCGACCAACTACCCGA
Found at i:16599818 original size:193 final size:192
Alignment explanation
Indices: 16599567--16599948 Score: 669
Period size: 193 Copynumber: 2.0 Consensus size: 192
16599557 GCATGGCATG
* *
16599567 CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACAT-ATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
16599632 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
16599697 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTAA
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTA-TTTTCTCGAGAAT-AATTTTTTTAA
*
16599762 CATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCTCCAAAGATGAGATTTTAAAAGTATTCCG
1 CATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
*
16599825 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGA
*
16599890 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTGATTTATTTTCTCGAGAATAATTTTT
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTT
16599949 AATAAATAAA
Statistics
Matches: 181, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
191 7 0.04
192 13 0.07
193 151 0.83
194 2 0.01
195 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (192 bp):
CATGACATATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGA
GTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAATTCTTTTAATGTTACCAACGTACTGGAA
CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTCTCGAGAATAATTTTTTTAA
Found at i:16611529 original size:48 final size:48
Alignment explanation
Indices: 16611465--16611896 Score: 434
Period size: 48 Copynumber: 8.8 Consensus size: 48
16611455 AAATTTGAAA
*
16611465 AAGATGAG-AATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
1 AAGA-GAGAAATTTTAAAGTTGT-GAGCCTCTGCTGAGAGGAGCTTTTTC
*
16611514 AAGA-AGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGAGAGAAATTTTAAAGTTG-TGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
16611562 AAGATGAG-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGA-GAGAAATTTTAAAGTTG-TGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
16611611 AAGATGAGAATTTTTAAAGTTGTTGGAACCTCTGCTGAGAGGAGC-TTTTC
1 AAGA-GAGAAATTTTAAAGTTG-T-GAGCCTCTGCTGAGAGGAGCTTTTTC
* *
16611661 AAGATGAGAATTTTTAAAGTTGTGAACCTCTGCTGGAAAGAGGAGC-TTTTC
1 AAGA-GAGAAATTTTAAAGTTGTGAGCCTCTGCT-G--AGAGGAGCTTTTTC
16611712 AAGATGAGAGAATTTTAAAGTTGTGA-CCTCTGCTGAGAGGAGC-TTTTC
1 AAGA-GAGA-AATTTTAAAGTTGTGAGCCTCTGCTGAGAGGAGCTTTTTC
** * *
16611760 AAGATGAGATTTTTTTAAAGTTGTGAACCTCTGCTGAGAGGAGCTTTTCC
1 AAGA-GAGA-AATTTTAAAGTTGTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * *
16611810 AAGA-TGAAATTTTAAAGTTGTTAGCCTCTACTGAAAATAGAGGCTTTTTC
1 AAGAGAGAAATTTTAAAGTTGTGAGCCTCTGCTG-AGA-GGA-GCTTTTTC
* * *
16611860 AAGTGAG-AATTTT-AAGTTGTTGAGCTTTTGCTGAGAG
1 AAGAGAGAAATTTTAAAGTTG-TGAGCCTCTGCTGAGAG
16611897 CAGAGGAGCT
Statistics
Matches: 339, Mismatches: 27, Indels: 35
0.85 0.07 0.09
Matches are distributed among these distances:
47 23 0.07
48 92 0.27
49 82 0.24
50 77 0.23
51 50 0.15
52 15 0.04
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (48 bp):
AAGAGAGAAATTTTAAAGTTGTGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:16611595 original size:49 final size:48
Alignment explanation
Indices: 16611465--16611896 Score: 522
Period size: 49 Copynumber: 8.8 Consensus size: 48
16611455 AAATTTGAAA
* *
16611465 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
1 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTC
*
16611514 AAGAAGA-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-C
*
16611562 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-C
*
16611611 AAGATGAGAATTTTTAAAGTTGTTGGAACCTCTGCTGAGAGGAGCTTTTC
1 AAGATGAGAA-TTTTAAAGTTGTT-GAGCCTCTGCTGAGAGGAGCTTTTC
*
16611661 AAGATGAGAATTTTTAAAGTTG-TGAACCTCTGCTGGAAAGAGGAGCTTTTC
1 AAGATGAGAA-TTTTAAAGTTGTTGAGCCTCTGCT-G--AGAGGAGCTTTTC
16611712 AAGATGAGAGAATTTTAAAGTTG-TGA-CCTCTGCTGAGAGGAGCTTTTC
1 AAGAT--GAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTC
* *
16611760 AAGATGAGATTTTTTTAAAGTTG-TGAACCTCTGCTGAGAGGAGCTTTTCC
1 AAGATGAGA--ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-C
* * *
16611810 AAGATGA-AATTTTAAAGTTGTT-AGCCTCTACTGAAAATAGAGGCTTTTTC
1 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTG-AGA-GGA-GC-TTTTC
* *
16611860 AAG-TGAGAATTTT-AAGTTGTTGAGCTTTTGCTGAGAG
1 AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAG
16611897 CAGAGGAGCT
Statistics
Matches: 345, Mismatches: 18, Indels: 41
0.85 0.04 0.10
Matches are distributed among these distances:
46 4 0.01
47 24 0.07
48 86 0.25
49 94 0.27
50 65 0.19
51 53 0.15
52 14 0.04
53 5 0.01
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (48 bp):
AAGATGAGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTC
Found at i:16611857 original size:99 final size:97
Alignment explanation
Indices: 16611465--16611843 Score: 522
Period size: 99 Copynumber: 3.9 Consensus size: 97
16611455 AAATTTGAAA
* * * * *
16611465 AAGATGAGA-ATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAGA-AATTTTA
1 AAGATGAGATTTTTTAAAGTTGT-GAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTA
16611528 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
65 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-C
*
16611562 AAGATGAGA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTT
1 AAGATGAGATTTTTTAAAGTTG-TGAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAA-TTTT
*
16611626 AAAGTTGTTGGAACCTCTGCTGAGAGGAGCTTTTC
64 AAAGTTGTT-GAGCCTCTGCTGAGAGGAGCTTTTC
*
16611661 AAGATGAGAATTTTTAAAGTTGTGAACCTCTGCTGGAAAGAGGAGCTTTT-CAAGATGAGAGAAT
1 AAGATGAGATTTTTTAAAGTTGTGAACCTCTGCT-G--AGAGGAGCTTTTCCAAGAT--GAGAAT
16611725 TTTAAAGTTG-TGA-CCTCTGCTGAGAGGAGCTTTTC
61 TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTC
16611760 AAGATGAGATTTTTTTAAAGTTGTGAACCTCTGCTGAGAGGAGCTTTTCCAAGATGA-AATTTTA
1 AAGATGAGA-TTTTTTAAAGTTGTGAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTA
*
16611824 AAGTTGTT-AGCCTCTACTGA
65 AAGTTGTTGAGCCTCTGCTGA
16611844 AAATAGAGGC
Statistics
Matches: 260, Mismatches: 8, Indels: 29
0.88 0.03 0.10
Matches are distributed among these distances:
95 14 0.05
96 12 0.05
97 62 0.24
98 9 0.03
99 66 0.25
100 62 0.24
101 7 0.03
102 23 0.09
103 5 0.02
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (97 bp):
AAGATGAGATTTTTTAAAGTTGTGAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTAA
AGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTC
Found at i:16611910 original size:199 final size:197
Alignment explanation
Indices: 16611465--16611879 Score: 561
Period size: 199 Copynumber: 2.1 Consensus size: 197
16611455 AAATTTGAAA
* *
16611465 AAGATGAGAA-TTTTAAAGTTGTGGAGCCTCTG-TTG--AGAGGAGCTTTTTCAAGAAGAAATTT
1 AAGATGAGAATTTTTAAAGTTGT-GAACCTCTGCTGGAAAGAGGAGC-TTTTCAAGAAGAAATTT
*
16611526 TAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGTTGAGCCT
64 TAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGTTGAACCT
* * *
16611591 CTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTTAAAGTTGTTGGAACCTCTGCTGAGAGGAGC
129 CTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTTAAAGTTGTT-GAACCTCTACTGAAAAGAGC
16611656 TTTTC
193 TTTTC
16611661 AAGATGAGAATTTTTAAAGTTGTGAACCTCTGCTGGAAAGAGGAGCTTTTCAAGATGAGAGAATT
1 AAGATGAGAATTTTTAAAGTTGTGAACCTCTGCTGGAAAGAGGAGCTTTTCAAGA--AGA-AATT
16611726 TTAAAGTTG-TGA-CCTCTGCTGAGAGGAGCTTTT-CAAGATGAGATTTTTTTAAAGTTG-TGAA
63 TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGA--TTTTTAAAGTTGTTGAA
*
16611787 CCTCTGCTGAGAGGAGCTTTTCCAAGATGA-AA-TTTTAAAGTTGTT-AGCCTCTACTGAAAATA
126 CCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAATTTTTAAAGTTGTTGAACCTCTACTG-AAA-A
16611849 GAGGCTTTTTC
189 GA-GC-TTTTC
16611860 AAG-TGAGAA-TTTT-AAGTTGT
1 AAGATGAGAATTTTTAAAGTTGT
16611880 TGAGCTTTTG
Statistics
Matches: 199, Mismatches: 7, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
195 9 0.05
196 27 0.14
197 33 0.17
198 29 0.15
199 70 0.35
200 18 0.09
201 13 0.07
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (197 bp):
AAGATGAGAATTTTTAAAGTTGTGAACCTCTGCTGGAAAGAGGAGCTTTTCAAGAAGAAATTTTA
AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGTTGAACCTCT
GCTGAGAGGAGCTTTTCCAAGATGAGAATTTTTAAAGTTGTTGAACCTCTACTGAAAAGAGCTTT
TC
Found at i:16612087 original size:22 final size:22
Alignment explanation
Indices: 16612059--16612107 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
16612049 CCATTTTATT
16612059 AATAAACAAAACAAAA-AAACAA
1 AATAAAC-AAACAAAAGAAACAA
*
16612081 AATAAACAAACAAAAGAAACAG
1 AATAAACAAACAAAAGAAACAA
16612103 AATAA
1 AATAA
16612108 GATAGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.78, C:0.12, G:0.04, T:0.06
Consensus pattern (22 bp):
AATAAACAAACAAAAGAAACAA
Found at i:16612100 original size:13 final size:13
Alignment explanation
Indices: 16612062--16612101 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16612052 TTTTATTAAT
*
16612062 AAACAAAACAAAA
1 AAACAAAACAAAC
*
16612075 AAACAAAATAAAC
1 AAACAAAACAAAC
*
16612088 AAACAAAAGAAAC
1 AAACAAAACAAAC
16612101 A
1 A
16612102 GAATAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.15, G:0.03, T:0.03
Consensus pattern (13 bp):
AAACAAAACAAAC
Found at i:16612179 original size:11 final size:11
Alignment explanation
Indices: 16612144--16612192 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
16612134 GCCGCTGTCG
16612144 CCAGCCCCCGA
1 CCAGCCCCCGA
* ** *
16612155 CCAACTACCTA
1 CCAGCCCCCGA
16612166 CCAGCCCCCGA
1 CCAGCCCCCGA
16612177 CCAGCCTCCCGA
1 CCAGCC-CCCGA
16612189 CCAG
1 CCAG
16612193 TCACCCTACA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.22, C:0.57, G:0.14, T:0.06
Consensus pattern (11 bp):
CCAGCCCCCGA
Found at i:16614099 original size:19 final size:19
Alignment explanation
Indices: 16614070--16614133 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
16614060 GGTCTGACTG
16614070 GACCAGAACCGAACCGCCCA
1 GACC-GAACCGAACCGCCCA
16614090 GACCGAACCGAA----CC-
1 GACCGAACCGAACCGCCCA
16614104 G---GAACCGAACCGCCCA
1 GACCGAACCGAACCGCCCA
16614120 GACCGAACCGAACC
1 GACCGAACCGAACC
16614134 AGTACTGGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 17
0.68 0.00 0.32
Matches are distributed among these distances:
11 8 0.22
14 1 0.03
15 4 0.11
16 1 0.03
19 18 0.50
20 4 0.11
ACGTcount: A:0.34, C:0.44, G:0.22, T:0.00
Consensus pattern (19 bp):
GACCGAACCGAACCGCCCA
Found at i:16614111 original size:30 final size:30
Alignment explanation
Indices: 16614075--16614164 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
16614065 GACTGGACCA
16614075 GAACCGAACCGCCCAGACCGAACCGAACCG
1 GAACCGAACCGCCCAGACCGAACCGAACCG
*
16614105 GAACCGAACCGCCCAGACCGAACCGAACCA
1 GAACCGAACCGCCCAGACCGAACCGAACCG
* * * *
16614135 GTACTGGACCGTCCAGACCGAACCGAACCG
1 GAACCGAACCGCCCAGACCGAACCGAACCG
16614165 TCGAACCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.32, C:0.41, G:0.23, T:0.03
Consensus pattern (30 bp):
GAACCGAACCGCCCAGACCGAACCGAACCG
Found at i:16615188 original size:191 final size:190
Alignment explanation
Indices: 16614861--16615210 Score: 630
Period size: 191 Copynumber: 1.8 Consensus size: 190
16614851 TAAATTTAGA
16614861 CCTCCAAAGATGAGATTCTAAAAGTATTCGAGTAGAGAAGCTTTAAGGAAATCTCTAGGTGAGAA
1 CCTCCAAAGATGAGATTCTAAAAGTATTCGAGTAGAGAAGCTTTAAGGAAATCTCTAGGTGAGAA
*
16614926 AGAATTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATTAAAAGGTTTTA
66 AGAATTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTA
16614991 ATTTATTTTCTCGAGAATAAATTTTTTAATATTGATATTTTCTTATGAAAAATAAATTCGAG
131 ATTTATTTTCTCGAGAAT-AA-TTTTTAATATTGATATTTTCTTATGAAAAATAAATTCGAG
* *
16615053 CCTCCAAAGATGAGATTTTAAAAGTATTCGAGTAGAGATGCTTTAA-GAAATCTCTAGGTGAGAA
1 CCTCCAAAGATGAGATTCTAAAAGTATTCGAGTAGAGAAGCTTTAAGGAAATCTCTAGGTGAGAA
* *
16615117 AGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTG
66 AGAATTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTA
16615182 ATTTATTTTCTCGAGAATAATTTTTAATA
131 ATTTATTTTCTCGAGAATAATTTTTAATA
16615211 AATAAAAATC
Statistics
Matches: 153, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
189 9 0.06
190 2 0.01
191 98 0.64
192 44 0.29
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (190 bp):
CCTCCAAAGATGAGATTCTAAAAGTATTCGAGTAGAGAAGCTTTAAGGAAATCTCTAGGTGAGAA
AGAATTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTA
ATTTATTTTCTCGAGAATAATTTTTAATATTGATATTTTCTTATGAAAAATAAATTCGAG
Found at i:16627935 original size:62 final size:62
Alignment explanation
Indices: 16627838--16627961 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
16627828 GAATAAGTAA
16627838 AAGTTTCACACCACTTCTTTATTGCAGTAACCCTAGTGTTTCCCTCAAAAAGTTTTTAGCCT
1 AAGTTTCACACCACTTCTTTATTGCAGTAACCCTAGTGTTTCCCTCAAAAAGTTTTTAGCCT
16627900 AAGTTTCACACCACTTCTTTATTGCAGTAACCCTAGTGTTTCCCTCAAAAAGTTTTTAGCCT
1 AAGTTTCACACCACTTCTTTATTGCAGTAACCCTAGTGTTTCCCTCAAAAAGTTTTTAGCCT
16627962 TCCTTCCGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (62 bp):
AAGTTTCACACCACTTCTTTATTGCAGTAACCCTAGTGTTTCCCTCAAAAAGTTTTTAGCCT
Found at i:16628820 original size:27 final size:27
Alignment explanation
Indices: 16628767--16628822 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
16628757 TCACAAATTG
* **
16628767 ATACACTAATTGATATAAATTTTTTTA
1 ATACACTAATTGATATAAAGTAATTTA
*
16628794 ATACACTAATTGATATTAAGTAATTTA
1 ATACACTAATTGATATAAAGTAATTTA
16628821 AT
1 AT
16628823 CTTTTTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (27 bp):
ATACACTAATTGATATAAAGTAATTTA
Found at i:16628927 original size:27 final size:27
Alignment explanation
Indices: 16628872--16628928 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
16628862 AATGACTTTC
***
16628872 AATAATTATATAATAAATATAATCTTT
1 AATAATTATATAATAAATATAAGAATT
16628899 AATAATTATATAA-AAATAATAAGAATT
1 AATAATTATATAATAAAT-ATAAGAATT
16628926 AAT
1 AAT
16628929 CTAATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AATAATTATATAATAAATATAAGAATT
Found at i:16629369 original size:15 final size:15
Alignment explanation
Indices: 16629346--16629376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16629336 TCACTCTCTC
16629346 TTCTATTCTTTTTCT
1 TTCTATTCTTTTTCT
*
16629361 TTCTGTTCTTTTTCT
1 TTCTATTCTTTTTCT
16629376 T
1 T
16629377 CATGCCTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (15 bp):
TTCTATTCTTTTTCT
Found at i:16635312 original size:8 final size:8
Alignment explanation
Indices: 16635301--16635357 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
16635291 GAAAAATAAG
16635301 AAAAGCAA
1 AAAAGCAA
*
16635309 AAAAGCTA
1 AAAAGCAA
16635317 AAAAGCTAA
1 AAAAGC-AA
16635326 AAAA-C-A
1 AAAAGCAA
16635332 AAAAGCAA
1 AAAAGCAA
16635340 AAGAA--AA
1 AA-AAGCAA
16635347 AAAAG-AA
1 AAAAGCAA
16635354 AAAA
1 AAAA
16635358 CCAAGGAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 7 0.17
7 11 0.26
8 17 0.40
9 7 0.17
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.04
Consensus pattern (8 bp):
AAAAGCAA
Found at i:16635349 original size:15 final size:14
Alignment explanation
Indices: 16635301--16635357 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
16635291 GAAAAATAAG
*
16635301 AAAAGCAAAAAAGCTA
1 AAAAGCAAAAAA--AA
*
16635317 AAAAGCTAAAAAACA
1 AAAAGC-AAAAAAAA
16635332 AAAAGCAAAAGAAAA
1 AAAAGCAAAA-AAAA
16635347 AAAAG-AAAAAA
1 AAAAGCAAAAAA
16635358 CCAAGGAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 2 0.05
14 8 0.22
15 15 0.41
16 6 0.16
17 6 0.16
ACGTcount: A:0.77, C:0.09, G:0.11, T:0.04
Consensus pattern (14 bp):
AAAAGCAAAAAAAA
Found at i:16640918 original size:16 final size:17
Alignment explanation
Indices: 16640891--16640922 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16640881 ATTTTTTACT
16640891 TTTAATATGTGAATCTC
1 TTTAATATGTGAATCTC
16640908 TTTAA-ATGTGAATCT
1 TTTAATATGTGAATCT
16640923 TTGAATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTAATATGTGAATCTC
Found at i:16640985 original size:22 final size:23
Alignment explanation
Indices: 16640937--16640991 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
16640927 ATTCCAAATC
*
16640937 TGAATCTCTAAAATTTTCATATG
1 TGAATCTCTAAAATTTTCAGATG
*
16640960 TGAATCTCTGAAATTTT-AGATG
1 TGAATCTCTAAAATTTTCAGATG
16640982 TGAATCTCTA
1 TGAATCTCTA
16640992 GATTCTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (23 bp):
TGAATCTCTAAAATTTTCAGATG
Found at i:16641030 original size:40 final size:40
Alignment explanation
Indices: 16640982--16641058 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
16640972 ATTTTAGATG
* ** *
16640982 TGAATCTCTAGATTCTTCAAATAAGAATCTTTGATTTTTA
1 TGAATCTCTAAACCCTTCAAATAAGAATATTTGATTTTTA
**
16641022 TGAATCTCTAAACCCTTCAAATGTGAATATTTGATTT
1 TGAATCTCTAAACCCTTCAAATAAGAATATTTGATTT
16641059 CTAGATGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (40 bp):
TGAATCTCTAAACCCTTCAAATAAGAATATTTGATTTTTA
Found at i:16641180 original size:23 final size:22
Alignment explanation
Indices: 16641121--16641237 Score: 78
Period size: 23 Copynumber: 5.3 Consensus size: 22
16641111 AGATTTTTTT
16641121 ATTTTTAAATGTGAATCTCTGAA
1 ATTTTTAAATGTGAATCTCT-AA
** *
16641144 CCTATTATAA-GTGAATCTCTAAA
1 ATTTTTA-AATGTGAATCTCT-AA
* *
16641167 ATTTTTAGATGTGAATGTCTAA
1 ATTTTTAAATGTGAATCTCTAA
* *
16641189 ATTTTTCAAATGAGAATCT-TTA
1 ATTTTT-AAATGTGAATCTCTAA
* **
16641211 A-TTTTGAATAAGAATCTCTAA
1 ATTTTTAAATGTGAATCTCTAA
*
16641232 GTTTTT
1 ATTTTT
16641238 GTTTTTTTCA
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.14
21 6 0.08
22 16 0.22
23 38 0.53
24 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (22 bp):
ATTTTTAAATGTGAATCTCTAA
Found at i:16641987 original size:50 final size:50
Alignment explanation
Indices: 16641897--16642036 Score: 137
Period size: 50 Copynumber: 2.8 Consensus size: 50
16641887 TCACAGGTTG
* * * * *
16641897 AAATTTTTAAAGTTCAATGCCTTTAATTA-AAGGAGACTTTTTTAGTAT-A
1 AAATTTTAAAATTTCAATGCCTTTGATTAGAAGGAGCCTTTTTTA-AATGA
*
16641946 AAATTTCTAAAATTTCAATGCCTTTGACTAGAA-GAGCC-TTTTTAAATGA
1 AAATTT-TAAAATTTCAATGCCTTTGATTAGAAGGAGCCTTTTTTAAATGA
* * *
16641995 AAATTTTAAAATTTC-TTAGCCTTTGTTTAGAATGAGCCTTTT
1 AAATTTTAAAATTTCAAT-GCCTTTGATTAGAAGGAGCCTTTT
16642037 GGATGAAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
47 1 0.01
48 23 0.30
49 24 0.32
50 26 0.34
51 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (50 bp):
AAATTTTAAAATTTCAATGCCTTTGATTAGAAGGAGCCTTTTTTAAATGA
Found at i:16642044 original size:48 final size:48
Alignment explanation
Indices: 16641897--16642036 Score: 124
Period size: 49 Copynumber: 2.9 Consensus size: 48
16641887 TCACAGGTTG
* * * * * *
16641897 AAATTTTTAAAGTTCAATGCCTTTAATTA-AAGGAGACTTTTTTAGTAT-A
1 AAATTTTAAAATTTCAATGCCTTTGACTAGAA-GAG-CCTTTTTA-AATGA
16641946 AAATTTCTAAAATTTCAATGCCTTTGACTAGAAGAGCCTTTTTAAATGA
1 AAATTT-TAAAATTTCAATGCCTTTGACTAGAAGAGCCTTTTTAAATGA
* **
16641995 AAATTTTAAAATTTC-TTAGCCTTTGTTTAGAATGAGCCTTTT
1 AAATTTTAAAATTTCAAT-GCCTTTGACTAGAA-GAGCCTTTT
16642037 GGATGAAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
47 1 0.01
48 23 0.30
49 29 0.38
50 22 0.29
51 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (48 bp):
AAATTTTAAAATTTCAATGCCTTTGACTAGAAGAGCCTTTTTAAATGA
Found at i:16642453 original size:16 final size:17
Alignment explanation
Indices: 16642428--16642467 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
16642418 AAAAAACATA
**
16642428 AAAAACAAAGGTAAAAT
1 AAAAACAAAGAAAAAAT
16642445 AAAAA-AAAGAAAAAAT
1 AAAAACAAAGAAAAAAT
16642461 AAAAACA
1 AAAAACA
16642468 TGTTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAACAAAGAAAAAAT
Found at i:16649592 original size:42 final size:43
Alignment explanation
Indices: 16649540--16649624 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
16649530 CTCTCAGTTT
* * *
16649540 TAAGTGTATTTTTGTGGCGTTT-TTAAAAGAAAACGCCACTAAA
1 TAAGTGTA-TTTAGTGGCATTTGTAAAAAGAAAACGCCACTAAA
16649583 TAAG-GTATTTAGTGGCATTTGTAAAAAGAAAACGCCACTAAA
1 TAAGTGTATTTAGTGGCATTTGTAAAAAGAAAACGCCACTAAA
16649625 AATTTCTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 23 0.61
43 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (43 bp):
TAAGTGTATTTAGTGGCATTTGTAAAAAGAAAACGCCACTAAA
Found at i:16650828 original size:13 final size:13
Alignment explanation
Indices: 16650810--16650836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16650800 AAGAATAATT
16650810 TAATTATTAGCTC
1 TAATTATTAGCTC
16650823 TAATTATTAGCTC
1 TAATTATTAGCTC
16650836 T
1 T
16650837 TTCATCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TAATTATTAGCTC
Found at i:16656876 original size:1 final size:1
Alignment explanation
Indices: 16656870--16656894 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16656860 ACTTTGAAAC
16656870 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
16656895 CTTTGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16657016 original size:28 final size:28
Alignment explanation
Indices: 16656983--16657038 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16656973 TTTAAGAAAG
* *
16656983 AAAAAATATATATTTTTTGGCTAAAAAAT
1 AAAAAA-ATATATATTTTGGCAAAAAAAT
16657012 AAAAAAATATATATTTTGGCAAAAAAA
1 AAAAAAATATATATTTTGGCAAAAAAA
16657039 AGAACCCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAAATATATATTTTGGCAAAAAAAT
Found at i:16657323 original size:21 final size:23
Alignment explanation
Indices: 16657289--16657330 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16657279 TTTTGTCATC
16657289 ATTTCCAATAATTCAATAAATCT
1 ATTTCCAATAATTCAATAAATCT
*
16657312 ATTT-CAA-AATTCTATAAAT
1 ATTTCCAATAATTCAATAAAT
16657331 AGTATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 3 0.17
23 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTCCAATAATTCAATAAATCT
Found at i:16667517 original size:23 final size:22
Alignment explanation
Indices: 16667456--16667518 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
16667446 AAGTTTAACC
16667456 TAACAAAAACTTAACAAATATA
1 TAACAAAAACTTAACAAATATA
* *
16667478 TAACAAGAAACTCAACAAATTTA
1 TAACAA-AAACTTAACAAATATA
*
16667501 TAACAAAAAGTTTAACAA
1 TAACAAAAA-CTTAACAA
16667519 TAAACTTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.26
23 26 0.74
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.22
Consensus pattern (22 bp):
TAACAAAAACTTAACAAATATA
Found at i:16667916 original size:22 final size:23
Alignment explanation
Indices: 16667872--16667918 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16667862 ATAACCCAAT
* *
16667872 AAAAACTCAACAAATATATAACA
1 AAAAACTAAACAAATATACAACA
*
16667895 AAAAACTAAACAAATCT-CAACA
1 AAAAACTAAACAAATATACAACA
16667917 AA
1 AA
16667919 CTTATAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.66, C:0.19, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAACTAAACAAATATACAACA
Found at i:16669571 original size:14 final size:13
Alignment explanation
Indices: 16669551--16669604 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
16669541 AAATTAATTC
*
16669551 CTTTTTTTTCTTT
1 CTTTTTTTTTTTT
16669564 CTTTTTTTTTTTCT
1 CTTTTTTTTTTT-T
16669578 CTTTTTTGTTTTTT
1 CTTTTTT-TTTTTT
*
16669592 GTTTTTATTTTTT
1 CTTTTT-TTTTTT
16669605 GAAACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
13 11 0.31
14 19 0.53
15 6 0.17
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.85
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:16670542 original size:17 final size:17
Alignment explanation
Indices: 16670516--16670551 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16670506 ACCATTCTCC
16670516 AATTTCTATATTTTTTT
1 AATTTCTATATTTTTTT
*
16670533 AATTTTTATATTTTTTT
1 AATTTCTATATTTTTTT
16670550 AA
1 AA
16670552 ATAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTCTATATTTTTTT
Found at i:16670973 original size:14 final size:14
Alignment explanation
Indices: 16670951--16670980 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16670941 GTCTTACACA
16670951 TTGCCTTTTTTTTT
1 TTGCCTTTTTTTTT
16670965 TTG-CTTTTTTTTT
1 TTGCCTTTTTTTTT
16670978 TTG
1 TTG
16670981 TAAATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (14 bp):
TTGCCTTTTTTTTT
Found at i:16671096 original size:51 final size:51
Alignment explanation
Indices: 16671037--16671144 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 51
16671027 GAGGCTTTAT
* * * *
16671037 AACTTTTTAAAAATAAATTGAAATGAAAATTGCTCCCACCAAAAGGTCCAC
1 AACTTTTTAAAAACAAATTGAAATGAAAAATCCTCCCACCAAAAGCTCCAC
* * *
16671088 AACTTTTTAAAACCAAATTGAAATGAAAAATCCTCTCACCATAAGCTCCAC
1 AACTTTTTAAAAACAAATTGAAATGAAAAATCCTCCCACCAAAAGCTCCAC
16671139 AACTTT
1 AACTTT
16671145 AAAATAGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (51 bp):
AACTTTTTAAAAACAAATTGAAATGAAAAATCCTCCCACCAAAAGCTCCAC
Found at i:16671655 original size:49 final size:50
Alignment explanation
Indices: 16671519--16671731 Score: 166
Period size: 49 Copynumber: 4.3 Consensus size: 50
16671509 CAAATGCTAA
* * * * * * * * * *
16671519 GAAATTTTGAAAATCTTATCTGAAAAAAAACTCCTTTAATCAAAAGTATT
1 GAAACTTTAAAAATCTTATATGAAAAAGAGCTCATCTAATTAAAGGCATT
* * * ** *
16671569 GAAATTTTAAAAATCTCATCTG-AAAAGAGCTCATCTAATTTGAGGTATT
1 GAAACTTTAAAAATCTTATATGAAAAAGAGCTCATCTAATTAAAGGCATT
16671618 -AGAACTTTAAAAATCTTATATGAAAAAG-GCTTC-TCTAATTAAAGGCATT
1 GA-AACTTTAAAAATCTTATATGAAAAAGAGC-TCATCTAATTAAAGGCATT
* * * * * *
16671667 GAAACTTTAAATATCTTATATGGAAAA-AGTTCTTCTAATCAAAGCCATT
1 GAAACTTTAAAAATCTTATATGAAAAAGAGCTCATCTAATTAAAGGCATT
*
16671716 AAAACTTTAAAAATCT
1 GAAACTTTAAAAATCT
16671732 CATTTGACAG
Statistics
Matches: 134, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
48 3 0.02
49 103 0.77
50 28 0.21
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (50 bp):
GAAACTTTAAAAATCTTATATGAAAAAGAGCTCATCTAATTAAAGGCATT
Found at i:16672498 original size:19 final size:21
Alignment explanation
Indices: 16672476--16672520 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16672466 TACACGTGTA
16672476 AAAAAC-AA-ATTCACACTTG
1 AAAAACAAATATTCACACTTG
* *
16672495 AAAACCAAATATTCACATTTG
1 AAAAACAAATATTCACACTTG
16672516 AAAAA
1 AAAAA
16672521 TTTTAGAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAAACAAATATTCACACTTG
Found at i:16672669 original size:37 final size:37
Alignment explanation
Indices: 16672592--16672674 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
16672582 TCATTTGAAA
* * * * *
16672592 ATTTTCAAATATTCATATTTAAAAGTAAAACATTCTC
1 ATTTTAAAAGATTCATATCTAAAAATAAAACATTCAC
* *
16672629 ATTTTAAAAGATTCATATCTAAAAATCAAATATTCAC
1 ATTTTAAAAGATTCATATCTAAAAATAAAACATTCAC
*
16672666 ATTTGAAAA
1 ATTTTAAAA
16672675 TTTTCAGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (37 bp):
ATTTTAAAAGATTCATATCTAAAAATAAAACATTCAC
Found at i:16672767 original size:155 final size:155
Alignment explanation
Indices: 16672495--16672775 Score: 370
Period size: 155 Copynumber: 1.8 Consensus size: 155
16672485 TTCACACTTG
* *
16672495 AAAACCAAATATTCACATTTGAAAAATTTTAGAGATCTACATCTAAAAGTTAAAGATTCTTATTT
1 AAAACCAAATATTCACATTTGAAAAATTTTAGAGATCTACATCTAAAAGTAAAAGATTCTCATTT
* * * * * * *
16672560 GACATACAAATATCAAAGATTCTCATTTGAAAATTTTCAAATATTCATATTTAAAAGTAAAACAT
66 CACATACAAAAATAAAAAATTCTCATTTAAAAATTTTCAAAGATTCACATTTAAAAGTAAAACAT
16672625 TCTCATTTTAAAAGATTCATATCTA
131 TCTCATTTTAAAAGATTCATATCTA
* * * *
16672650 AAAATCAAATATTCACATTTG-AAAATTTTCAGAGAT-TAATATTTTAAAGTAAAAGATTCTCAC
1 AAAACCAAATATTCACATTTGAAAAATTTT-AGAGATCT-ACATCTAAAAGTAAAAGATTCTCA-
** *
16672713 TTTCACATGTAAAAATAAAAAATTCTCATTTAAAAATTTT-AGAGATTCACATTTAAAAGTAAA
63 TTTCACATACAAAAATAAAAAATTCTCATTTAAAAATTTTCAAAGATTCACATTTAAAAGTAAA
16672776 GATTCTTATT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
154 9 0.08
155 65 0.61
156 33 0.31
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.36
Consensus pattern (155 bp):
AAAACCAAATATTCACATTTGAAAAATTTTAGAGATCTACATCTAAAAGTAAAAGATTCTCATTT
CACATACAAAAATAAAAAATTCTCATTTAAAAATTTTCAAAGATTCACATTTAAAAGTAAAACAT
TCTCATTTTAAAAGATTCATATCTA
Found at i:16672988 original size:156 final size:157
Alignment explanation
Indices: 16672794--16673122 Score: 511
Period size: 156 Copynumber: 2.1 Consensus size: 157
16672784 TTTGAAATAT
* * * * *
16672794 TCAAAGATTATCATTTAGGAAAGTTTAGAGACTAATATCTAAAAGTTAAAGATTCTTATTTTAAA
1 TCAAAGATTATTATTTAGGAAAGTTTAGAAACTAATATCTAAAAGTCAAAGAATCTCATTTTAAA
16672859 AATTCAAAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
66 AATTCAAAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
16672924 CAAAGTTTAGAGATTTC-TTCTAAAA-C
131 CAAAGTTTAGAGA-TTCATTCTAAAAGC
* *
16672950 TCAAAGATTTTTATTTAGGAAAGTTTAGAAACTGATATCTAAAAGTCAAAGAATCTCATTTTAAA
1 TCAAAGATTATTATTTAGGAAAGTTTAGAAACTAATATCTAAAAGTCAAAGAATCTCATTTTAAA
* * *
16673015 AATTCAAAGATTCACATTTTAAACTCAAATGTTCTTATTTGAAAAGTTCAATGATTCACATTTGG
66 AATTCAAAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
*
16673080 CAAAGTTTAGATATTCATTTCTAAAAGC
131 CAAAGTTTAGAGATTCA-TTCTAAAAGC
*
16673108 -CAAAGATTCTTATTT
1 TCAAAGATTATTATTT
16673123 GAAAATTTCA
Statistics
Matches: 158, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
155 3 0.02
156 132 0.84
157 22 0.14
158 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (157 bp):
TCAAAGATTATTATTTAGGAAAGTTTAGAAACTAATATCTAAAAGTCAAAGAATCTCATTTTAAA
AATTCAAAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
CAAAGTTTAGAGATTCATTCTAAAAGC
Found at i:16673016 original size:23 final size:23
Alignment explanation
Indices: 16672990--16673037 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
16672980 ACTGATATCT
*
16672990 AAAAGTCAAAGAATCTCATTTTA
1 AAAAGTCAAAGAATCACATTTTA
* *
16673013 AAAATTCAAAGATTCACATTTTA
1 AAAAGTCAAAGAATCACATTTTA
16673036 AA
1 AA
16673038 CTCAAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (23 bp):
AAAAGTCAAAGAATCACATTTTA
Found at i:16673085 original size:112 final size:110
Alignment explanation
Indices: 16672967--16673368 Score: 368
Period size: 112 Copynumber: 3.6 Consensus size: 110
16672957 TTTTTATTTA
* * * * *
16672967 GGAAAGTTTAGAAACTGATATCTAAAAGTCAAAGAATCTCATTTTAAAAATTCAAAGATTCACAT
1 GGAAAGTTTAGAAATTCACATCTAAAAGTCAAAGATTCTCATTTGAAAAATTCAAAGATTCACAT
* * *
16673032 TTTAAACTCAAATGTTCTTATTTGAAAAGTTCAATGATTCACATTT
66 TTAAAACTCAAAGGTTCTCATTTGAAAAGTTCAATGATTCACA-TT
* ** * * * *
16673078 GGCAAAGTTTAGATATTCATTTCTAAAAGCCAAAGATTCTTATTTGAAAATTTCAGAA-ATTTAC
1 GG-AAAGTTTAGAAATTCACATCTAAAAGTCAAAGATTCTCATTTGAAAAATTCA-AAGATTCAC
* * * *
16673142 ATATAAAACTCATAGGTTCTCATTTGAAAAGTTTAAAGATTCACATT
64 ATTTAAAACTCAAAGGTTCTCATTTGAAAAGTTCAATGATTCACATT
* * * *
16673189 GGGAAATGTTTA-AAGATTCACATCTAGAAGTC-ATGCATTCTCATTTGAAAAATTTAGAGATTC
1 -GGAAA-GTTTAGAA-ATTCACATCTAAAAGTCAAAG-ATTCTCATTTGAAAAATTCAAAGATTC
*
16673252 ACATCTTAAAAC-CAAAGGTT-TACATTT-AAAACGATCAAAT-ATTCACATT
62 ACAT-TTAAAACTCAAAGGTTCT-CATTTGAAAA-GTTC-AATGATTCACATT
* * * * * * *
16673301 GAGAAGGTTCAGAGATTCACATTTAAAAGTAAAAGATTCCCATTTAAAAAATTCAAAGATTCACA
1 G-GAAAGTTTAGAAATTCACATCTAAAAGTCAAAGATTCTCATTTGAAAAATTCAAAGATTCACA
16673366 TTT
65 TTT
16673369 GGGAAAGTTT
Statistics
Matches: 233, Mismatches: 44, Indels: 29
0.76 0.14 0.09
Matches are distributed among these distances:
110 2 0.01
111 62 0.27
112 159 0.68
113 10 0.04
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (110 bp):
GGAAAGTTTAGAAATTCACATCTAAAAGTCAAAGATTCTCATTTGAAAAATTCAAAGATTCACAT
TTAAAACTCAAAGGTTCTCATTTGAAAAGTTCAATGATTCACATT
Found at i:16673136 original size:156 final size:155
Alignment explanation
Indices: 16672794--16673188 Score: 499
Period size: 156 Copynumber: 2.5 Consensus size: 155
16672784 TTTGAAATAT
* * * * * * *
16672794 TCAAAGATTATCATTTAGGAAAGTTTAGAGACTAATATCTAAAAGTTAAAGATTCTTATTTTAAA
1 TCAAAGATTCTTATTTA-GAAAATTTAGAAACTGATATCTAAAAGTCAAAGATTCTCATTTTAAA
*
16672859 AATTCAAAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
65 AATTCAAAGATTCACATTTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
16672924 CAAAGTTTAGAGATTTCTTCTAAAAC
130 CAAAGTTTAGAGATTTCTTCTAAAAC
* * *
16672950 TCAAAGATTTTTATTTAGGAAAGTTTAGAAACTGATATCTAAAAGTCAAAGAATCTCATTTTAAA
1 TCAAAGATTCTTATTTA-GAAAATTTAGAAACTGATATCTAAAAGTCAAAGATTCTCATTTTAAA
* *
16673015 AATTCAAAGATTCACATTTTAAACTCAAATGTTCTTATTTGAAAAGTTCAATGATTCACATTTGG
65 AATTCAAAGATTCACATTTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGG
*
16673080 CAAAGTTTAGATA-TTCATTTCTAAAAGC
130 CAAAGTTTAGAGATTTC--TTCTAAAA-C
* * * * * * * *
16673108 -CAAAGATTCTTATTT-GAAAATTTCAGAAATTTACATATAAAACTCATAGGTTCTCATTTGAAA
1 TCAAAGATTCTTATTTAGAAAATTT-AGAAACTGATATCTAAAAGTCAAAGATTCTCATTTTAAA
* *
16673171 AGTTTAAAGATTCACATT
65 AATTCAAAGATTCACATT
16673189 GGGAAATGTT
Statistics
Matches: 211, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
155 10 0.05
156 178 0.84
157 22 0.10
158 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (155 bp):
TCAAAGATTCTTATTTAGAAAATTTAGAAACTGATATCTAAAAGTCAAAGATTCTCATTTTAAAA
ATTCAAAGATTCACATTTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGGC
AAAGTTTAGAGATTTCTTCTAAAAC
Found at i:16673188 original size:23 final size:23
Alignment explanation
Indices: 16673162--16673385 Score: 90
Period size: 23 Copynumber: 9.9 Consensus size: 23
16673152 CATAGGTTCT
16673162 CATTTGAAAAGTTTAAAGATTCA
1 CATTTGAAAAGTTTAAAGATTCA
* *
16673185 CATTGGGAAATGTTTAAAGATTCA
1 CATT-TGAAAAGTTTAAAGATTCA
* * * * *
16673209 CATCT-AGAAG--TCATGCATTCT
1 CATTTGAAAAGTTTAAAG-ATTCA
* *
16673230 CATTTGAAAAATTTAGAGATTCA
1 CATTTGAAAAGTTTAAAGATTCA
** * *
16673253 CATCTT-AAAA--CCAAAGGTTTA
1 CAT-TTGAAAAGTTTAAAGATTCA
* * *
16673274 CATTT-AAAACGATCAAATATTCA
1 CATTTGAAAA-GTTTAAAGATTCA
* * *
16673297 CA-TTGAGAAGGTTCAGAGATTCA
1 CATTTGA-AAAGTTTAAAGATTCA
* *
16673320 CATTT-AAAAG-TAAAAGATTCC
1 CATTTGAAAAGTTTAAAGATTCA
* * *
16673341 CATTTAAAAAATTCAAAGATTCA
1 CATTTGAAAAGTTTAAAGATTCA
* *
16673364 CATTTGGGAAAGTTTAGAGATT
1 CATTT-GAAAAGTTTAAAGATT
16673386 TGCATATAAA
Statistics
Matches: 145, Mismatches: 41, Indels: 29
0.67 0.19 0.13
Matches are distributed among these distances:
20 9 0.06
21 30 0.21
22 15 0.10
23 52 0.36
24 39 0.27
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (23 bp):
CATTTGAAAAGTTTAAAGATTCA
Found at i:16673300 original size:268 final size:267
Alignment explanation
Indices: 16672736--16673268 Score: 582
Period size: 268 Copynumber: 2.0 Consensus size: 267
16672726 AATAAAAAAT
* * *
16672736 TCTCA-TTTAAAAATTTTAGAGATTCACATTTAAAAGTAAAGATTCTTATTTGAAATATTCAAAG
1 TCTCATTTTAAAAA-TTCAAAGATTCACATTTAAAACTAAAGATTCTTATTTGAAATATTCAAAG
** *
16672800 ATTATCATTTAGGAAAGTTTAGAGACTAATATCTAAAAGTTAAAGATTCTTATTTTAAAAATTCA
65 ATTATCATTTAGGAAAGTTTAGAGACTAATATCTAAAAGCCAAAGATTCTTATTTGAAAAATTCA
* * *
16672865 AAGATTCACATCTAAAACTCAAATGTTCTCATTTGAAAAGTTCAATGATTCACATTTGGCAAAGT
130 AAGATTCACATATAAAACTCAAAGGTTCTCATTTGAAAAGTTCAAAGATTCACATTTGGCAAAGT
* * * * * * * * *
16672930 TTAGAGATTTCTTCTAAAACTCAAAGATTTTTATTTAGGAAAGTTTAGAAACTGATATCTAAAAG
195 TTAAAGATTACATCTAAAACTCAAAGATTCTCATTTAGAAAAATTTAGAAACTCACATCTAAAAG
*
16672995 TCAAAGAA
260 CCAAAGAA
*
16673003 TCTCATTTTAAAAATTCAAAGATTCACATTTTAAACTCAAATG-TTCTTATTTGAAA-AGTTCAA
1 TCTCATTTTAAAAATTCAAAGATTCACATTTAAAACT-AAA-GATTCTTATTTGAAATA-TTCAA
* * * * * *
16673066 TGATTCA-CATTT-GGCAAAGTTTAGATATTCATTTCTAAAAGCCAAAGATTCTTATTTGAAAAT
63 AGATT-ATCATTTAGG-AAAGTTTAGAGACTAATATCTAAAAGCCAAAGATTCTTATTTGAAAAA
* * * *
16673129 TTCAGAA-ATTTACATATAAAACTCATAGGTTCTCATTTGAAAAGTTTAAAGATTCACA-TTGGG
126 TTCA-AAGATTCACATATAAAACTCAAAGGTTCTCATTTGAAAAGTTCAAAGATTCACATTTGGC
* * * * *
16673192 AAATGTTTAAAGATTCACATCTAGAAGTC-ATGCATTCTCATTT-GAAAAATTTAGAGATTCACA
190 AAA-GTTTAAAGATT-ACATCTAAAACTCAAAG-ATTCTCATTTAGAAAAATTTAGAAACTCACA
16673255 TCTTAAAA-CCAAAG
252 TC-TAAAAGCCAAAG
16673269 GTTTACATTT
Statistics
Matches: 220, Mismatches: 35, Indels: 21
0.80 0.13 0.08
Matches are distributed among these distances:
267 34 0.15
268 160 0.73
269 26 0.12
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (267 bp):
TCTCATTTTAAAAATTCAAAGATTCACATTTAAAACTAAAGATTCTTATTTGAAATATTCAAAGA
TTATCATTTAGGAAAGTTTAGAGACTAATATCTAAAAGCCAAAGATTCTTATTTGAAAAATTCAA
AGATTCACATATAAAACTCAAAGGTTCTCATTTGAAAAGTTCAAAGATTCACATTTGGCAAAGTT
TAAAGATTACATCTAAAACTCAAAGATTCTCATTTAGAAAAATTTAGAAACTCACATCTAAAAGC
CAAAGAA
Found at i:16673419 original size:68 final size:67
Alignment explanation
Indices: 16673286--16673432 Score: 161
Period size: 68 Copynumber: 2.2 Consensus size: 67
16673276 TTTAAAACGA
* * *
16673286 TCAAATATTCACATTGAGAAGGTTCAGAGATTCACATTTAAAAGTAAAAGATTCCCATTTAAAAA
1 TCAAAGATTCACATTGAGAAAGTTCAGAGATTCACATATAAAAGTAAAAGATTCCCATTTAAAAA
16673351 AT
66 AT
* * ** * * ** *
16673353 TCAAAGATTCACATTTGGGAAAGTTTAGAGATTTGCATATAAAAGTCAAATATTCTTATTTGAAA
1 TCAAAGATTCACA-TTGAGAAAGTTCAGAGATTCACATATAAAAGTAAAAGATTCCCATTTAAAA
16673418 AAT
65 AAT
16673421 T-AAAGGATTCAC
1 TCAAA-GATTCAC
16673433 TTCGAAGGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
67 15 0.23
68 51 0.77
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (67 bp):
TCAAAGATTCACATTGAGAAAGTTCAGAGATTCACATATAAAAGTAAAAGATTCCCATTTAAAAA
AT
Found at i:16678518 original size:12 final size:11
Alignment explanation
Indices: 16678501--16678539 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16678491 ATAACTTAAC
*
16678501 AAAAAAATATA
1 AAAAAAAAATA
*
16678512 AAAAAAAAACA
1 AAAAAAAAATA
16678523 AAAAATAAAATA
1 AAAAA-AAAATA
16678535 AAAAA
1 AAAAA
16678540 TTATCTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:16678525 original size:18 final size:19
Alignment explanation
Indices: 16678481--16678539 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
16678471 GTTTATAGAT
** *
16678481 AAACAAATAAATAACTTAAC
1 AAACAAA-AAATAAAATAAA
*
16678501 AAA-AAAATATAAAA-AAA
1 AAACAAAAAATAAAATAAA
16678518 AAACAAAAAATAAAATAAA
1 AAACAAAAAATAAAATAAA
16678537 AAA
1 AAA
16678540 TTATCTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.16
18 15 0.47
19 9 0.28
20 3 0.09
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.14
Consensus pattern (19 bp):
AAACAAAAAATAAAATAAA
Found at i:16678525 original size:20 final size:20
Alignment explanation
Indices: 16678502--16678539 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16678492 TAACTTAACA
16678502 AAAAAATATAAA-AAAAAAAC
1 AAAAAATA-AAATAAAAAAAC
16678522 AAAAAATAAAATAAAAAA
1 AAAAAATAAAATAAAAAA
16678540 TTATCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAATAAAATAAAAAAAC
Found at i:16679216 original size:16 final size:16
Alignment explanation
Indices: 16679195--16679225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16679185 TGTTTTTTTT
16679195 TGGTTTTCTTTGTGTG
1 TGGTTTTCTTTGTGTG
*
16679211 TGGTTTTTTTTGTGT
1 TGGTTTTCTTTGTGT
16679226 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.03, G:0.29, T:0.68
Consensus pattern (16 bp):
TGGTTTTCTTTGTGTG
Found at i:16679925 original size:22 final size:22
Alignment explanation
Indices: 16679897--16679940 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16679887 TGTCAAAATC
16679897 TTGAATAAAAATTAAGATTTAT
1 TTGAATAAAAATTAAGATTTAT
*
16679919 TTGAATAAAAATTAATATTTAT
1 TTGAATAAAAATTAAGATTTAT
16679941 ATATAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
TTGAATAAAAATTAAGATTTAT
Found at i:16679954 original size:12 final size:12
Alignment explanation
Indices: 16679931--16679964 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16679921 GAATAAAAAT
16679931 TAATATTTATATA
1 TAATA-TTATATA
16679944 TAATATTATATA
1 TAATATTATATA
*
16679956 TAAGATTAT
1 TAATATTAT
16679965 CGAGTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TAATATTATATA
Found at i:16682632 original size:29 final size:28
Alignment explanation
Indices: 16682588--16682646 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
16682578 AAATTAAATA
** *
16682588 TTATATTTTGATTTTGTTATTTACTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
16682616 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
16682645 TT
1 TT
16682647 TTTTATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:16686356 original size:18 final size:18
Alignment explanation
Indices: 16686244--16686359 Score: 91
Period size: 18 Copynumber: 6.7 Consensus size: 18
16686234 ATAGTTATTA
* *
16686244 TCCACCACAAATGTATCC
1 TCCACCTCAAATATATCC
**
16686262 TCCACCTCAAACGTATCC
1 TCCACCTCAAATATATCC
* *
16686280 TCTACCTCAAAT-TATTC
1 TCCACCTCAAATATATCC
* *
16686297 TCC-CCATCATATGTATCC
1 TCCACC-TCAAATATATCC
* *
16686315 -CCACCACAAATATATCA
1 TCCACCTCAAATATATCC
16686332 T---CCTCAAATATATCC
1 TCCACCTCAAATATATCC
16686347 TCCACCTCAAATA
1 TCCACCTCAAATA
16686360 CATTAAGAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
15 13 0.17
16 2 0.03
17 21 0.27
18 41 0.53
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.28
Consensus pattern (18 bp):
TCCACCTCAAATATATCC
Found at i:16689476 original size:16 final size:17
Alignment explanation
Indices: 16689455--16689529 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 17
16689445 GATTCGTAGG
*
16689455 TTTTTTCTTTTCT-TTT
1 TTTTTTATTTTCTATTT
16689471 TTTTTTATTTTCTATTT
1 TTTTTTATTTTCTATTT
* *
16689488 TGATTTTGATTTT-GATTT
1 T--TTTTTATTTTCTATTT
* *
16689506 TTTTTTGTTTT-TATGCT
1 TTTTTTATTTTCTAT-TT
16689523 TTTTTTA
1 TTTTTTA
16689530 ATATAATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
16 22 0.47
17 11 0.23
18 5 0.11
19 9 0.19
ACGTcount: A:0.09, C:0.05, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTCTATTT
Found at i:16690341 original size:51 final size:50
Alignment explanation
Indices: 16690228--16690341 Score: 120
Period size: 51 Copynumber: 2.3 Consensus size: 50
16690218 AATAGGTTGA
* ** *
16690228 GATGATCCTAAAACTTATTCAAAACTTTTAAGATTTCACCGAAGAGTCGG
1 GATGATCCTAAAACTTATTCAAAAATTTTAAGAACTCACCAAAGAGTCGG
* * * * * *
16690278 GATAATCTTAAAACTTGTTTAATAAATTTTAGGAACTCACCAAATAGTCGG
1 GATGATCCTAAAACTTATTCAA-AAATTTTAAGAACTCACCAAAGAGTCGG
*
16690329 GATGTTCCTAAAA
1 GATGATCCTAAAA
16690342 TCCTTTTCGA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
50 18 0.36
51 32 0.64
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (50 bp):
GATGATCCTAAAACTTATTCAAAAATTTTAAGAACTCACCAAAGAGTCGG
Found at i:16697856 original size:36 final size:37
Alignment explanation
Indices: 16697788--16697861 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
16697778 AATTTTGAGG
16697788 ATTAAAGGAAAATGACAATGAAAAAAAAAAGAAAGAA
1 ATTAAAGGAAAATGACAATGAAAAAAAAAAGAAAGAA
16697825 ATTAAAGGAAAATGACAATG-AAAAAAAAAGAAAGAA
1 ATTAAAGGAAAATGACAATGAAAAAAAAAAGAAAGAA
16697861 A
1 A
16697862 GAAGATGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.70, C:0.03, G:0.16, T:0.11
Consensus pattern (37 bp):
ATTAAAGGAAAATGACAATGAAAAAAAAAAGAAAGAA
Found at i:16698160 original size:39 final size:38
Alignment explanation
Indices: 16698108--16698529 Score: 349
Period size: 39 Copynumber: 10.8 Consensus size: 38
16698098 CCATTACTTC
* *
16698108 TGGTCAGAAGAGCTTTTAATATTTAAAGTTTGTTGCCTT
1 TGGTTAGAGGAGCTTTTAA-ATTTAAAGTTTGTTGCCTT
* * *
16698147 TGGTTAAAGGAGCTTCTGAAATTTAAAGTTTGTTGCATT
1 TGGTTAGAGGAGCTT-TTAAATTTAAAGTTTGTTGCCTT
* * **
16698186 TGGTCAGAGGAGCCTTTGAAATTTAAAGTTTGTTATCTT
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTT
* * * ** * * *
16698225 TGGTTAAAGAAGTTTTTTGGATTTAAAGTTCGTTACCTC
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTT
* * *
16698264 TGGTCAGTGGAGCTTTTAATATTTAAAGTTTGTTACCTT
1 TGGTTAGAGGAGCTTTTAA-ATTTAAAGTTTGTTGCCTT
* * ** *
16698303 TGGCTAAAAAAGCTTTTGAAATGTAAAGTTTGTTGCCTT
1 TGGTTAGAGGAGCTTTT-AAATTTAAAGTTTGTTGCCTT
* *
16698342 TGGTCAGAGGAGCCTTTAAAATTTAAAGTTTGTTGCCTT
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTT
* * * *
16698381 TGGTTAAATGAGCTTTTAGGATTTAAAGTTTGTTGCCTC
1 TGGTTAGAGGAGCTTTTA-AATTTAAAGTTTGTTGCCTT
* * *
16698420 TGGTGAGAGGAGCCTTTTGAATTTAAAATTTGTTGCCTT
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTT
** * * * *
16698459 TAATGAGAGGAGCCTTTTGAATTTAAAATTTGTTGCCTC
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTGTTGCCTT
* * * *
16698498 TGATGAGAGGAGCCTTTTAAATTAAAAATTTG
1 TGGTTAGAGGAG-CTTTTAAATTTAAAGTTTG
16698530 CATAACCTCA
Statistics
Matches: 312, Mismatches: 64, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
38 9 0.03
39 286 0.92
40 17 0.05
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (38 bp):
TGGTTAGAGGAGCTTTTAAATTTAAAGTTTGTTGCCTT
Found at i:16698218 original size:78 final size:78
Alignment explanation
Indices: 16698106--16698529 Score: 462
Period size: 78 Copynumber: 5.4 Consensus size: 78
16698096 GTCCATTACT
* *
16698106 TCTGGTCAGAAGAG-CTTTTAATATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTCTGAAATT
1 TCTGGTCAGAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGAAATT
*
16698170 TAAAGTTTGTTGCA
65 TAAAGTTTGTTGCC
* * ** * * *
16698184 TTTGGTCAGAGGAGCCTTTGAAATTTAAAGTTTGTTATCTTTGGTTAAAGAAGTTTTTTG-GATT
1 TCTGGTCAGAGGAGCCTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTTTTGAAATT
* *
16698248 TAAAGTTCGTTACC
65 TAAAGTTTGTTGCC
* * * ** *
16698262 TCTGGTCAGTGGAG-CTTTTAATATTTAAAGTTTGTTACCTTTGGCTAAAAAAGCTTTTGAAATG
1 TCTGGTCAGAGGAGCCTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGAAATT
16698326 TAAAGTTTGTTGCC
65 TAAAGTTTGTTGCC
* * * *
16698340 TTTGGTCAGAGGAGCCTTTAAAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTT-AGGATT
1 TCTGGTCAGAGGAGCCTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA-AATT
16698404 TAAAGTTTGTTGCC
65 TAAAGTTTGTTGCC
* * * ** * *
16698418 TCTGGTGAGAGGAGCCTTTTGAATTTAAAATTTGTTGCCTTTAATGAGAGGAGCCTTTTG-AATT
1 TCTGGTCAGAGGAGCCTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAG-CTTTTGAAATT
*
16698482 TAAAATTTGTTGCC
65 TAAAGTTTGTTGCC
* * * *
16698496 TCTGATGAGAGGAGCCTTTTAAATTAAAAATTTG
1 TCTGGTCAGAGGAGCCTTTTAAATTTAAAGTTTG
16698530 CATAACCTCA
Statistics
Matches: 291, Mismatches: 47, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
77 12 0.04
78 258 0.89
79 21 0.07
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (78 bp):
TCTGGTCAGAGGAGCCTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGAAATTT
AAAGTTTGTTGCC
Found at i:16698366 original size:156 final size:156
Alignment explanation
Indices: 16698082--16698459 Score: 526
Period size: 156 Copynumber: 2.4 Consensus size: 156
16698072 GCCTCTAAGA
* * * *
16698082 TTTTTGGATTTAAAGTCCATTACTTCTGGTCAGAAGAGCTTTTAATATTTAAAGTTTGTTGCCTT
1 TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
* ** * *
16698147 TGGTTAAAGGAGCTTCTGAAATTTAAAGTTTGTTGCATTTGGTCAGAGGAGCCTTTGAAATTTAA
66 TGGCTAAAAAAGCTTCTGAAATGTAAAGTTTGTTGCATTTGGTCAGAGGAGCCTTTAAAATTTAA
* *
16698212 AGTTTGTTATCTTTGGTTAAA-GAAGT
131 AGTTTGTTACCTTTGGTTAAATG-AGC
* *
16698238 TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGTGGAGCTTTTAATATTTAAAGTTTGTTACCTT
1 TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
* *
16698303 TGGCTAAAAAAGCTTTTGAAATGTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTTAA
66 TGGCTAAAAAAGCTTCTGAAATGTAAAGTTTGTTGCATTTGGTCAGAGGAGCCTTTAAAATTTAA
*
16698368 AGTTTGTTGCCTTTGGTTAAATGAGC
131 AGTTTGTTACCTTTGGTTAAATGAGC
* * * * * *
16698394 TTTTAGGATTTAAAGTTTGTTGCCTCTGGTGAGAGGAGCCTTTTGA-ATTTAAAATTTGTTGCCT
1 TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAG-CTTTTAATATTTAAAGTTTGTTGCCT
16698458 TT
65 TT
16698460 AATGAGAGGA
Statistics
Matches: 196, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
156 189 0.96
157 7 0.04
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (156 bp):
TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
TGGCTAAAAAAGCTTCTGAAATGTAAAGTTTGTTGCATTTGGTCAGAGGAGCCTTTAAAATTTAA
AGTTTGTTACCTTTGGTTAAATGAGC
Found at i:16698491 original size:156 final size:155
Alignment explanation
Indices: 16698082--16698529 Score: 524
Period size: 156 Copynumber: 2.9 Consensus size: 155
16698072 GCCTCTAAGA
* * * * *
16698082 TTTTTGGATTTAAAGTCCATTACTTCTGGTCAGAAGAGCTTTTAATATTTAAAGTTTGTTGCCTT
1 TTTTAGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
* * * *
16698147 TGGTTAAAGGAGCTTCTGAAATTTAAAGTTTGTTGCATTTGGTCAGAGGAGCCTTTGAAATTTAA
66 T-GATAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTTAA
* *
16698212 AGTTTGTTATCTTTGGTTAAAGAAGT
130 AGTTTGTTACCTTTGGTTAAAGAAGC
* * *
16698238 TTTTTGGATTTAAAGTTCGTTACCTCTGGTCAGTGGAGCTTTTAATATTTAAAGTTTGTTACCTT
1 TTTTAGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
* ** *
16698303 TGGCTAAAAAAGCTTTTGAAATGTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTTAA
66 T-GATAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTTAA
*
16698368 AGTTTGTTGCCTTTGGTTAAATG-AGC
130 AGTTTGTTACCTTTGGTTAAA-GAAGC
* * * * *
16698394 TTTTAGGATTTAAAGTTTGTTGCCTCTGGTGAGAGGAGCCTTTTGA-ATTTAAAATTTGTTGCCT
1 TTTTAGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAG-CTTTTAATATTTAAAGTTTGTTGCCT
* * * * * * * *
16698458 TTAATGAGAGGAGCCTTTTG-AATTTAAAATTTGTTGCCTCTGATGAGAGGAGCCTTTTAAATTA
65 TTGAT-AAAGGAG-CTTTTGAAATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTT
*
16698522 AAAATTTG
128 AAAGTTTG
16698530 CATAACCTCA
Statistics
Matches: 251, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
155 1 0.00
156 237 0.94
157 13 0.05
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (155 bp):
TTTTAGGATTTAAAGTTCGTTACCTCTGGTCAGAGGAGCTTTTAATATTTAAAGTTTGTTGCCTT
TGATAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTTTGGTCAGAGGAGCCTTTAAAATTTAAA
GTTTGTTACCTTTGGTTAAAGAAGC
Found at i:16699617 original size:18 final size:18
Alignment explanation
Indices: 16699585--16699639 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
16699575 ATTTTGCAGG
16699585 TTTTTCATTTT-ATTTTT
1 TTTTTCATTTTGATTTTT
*
16699602 TTTTTCATTTTGATTTTG
1 TTTTTCATTTTGATTTTT
* *
16699620 ATTTTGATTTTGATTTTT
1 TTTTTCATTTTGATTTTT
16699638 TT
1 TT
16699640 ATGTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTCATTTTGATTTTT
Found at i:16699618 original size:12 final size:12
Alignment explanation
Indices: 16699603--16699636 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
16699593 TTTATTTTTT
*
16699603 TTTTCATTTTGA
1 TTTTGATTTTGA
16699615 TTTTGATTTTGA
1 TTTTGATTTTGA
16699627 TTTTGATTTT
1 TTTTGATTTT
16699637 TTTATGTTAT
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:0.15, C:0.03, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTGATTTTGA
Found at i:16699763 original size:11 final size:11
Alignment explanation
Indices: 16699724--16699772 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
16699714 AATTTTTATT
16699724 TAAAAAT-AAA
1 TAAAAATAAAA
*
16699734 TAAATAAATAGAA
1 T-AA-AAATAAAA
16699747 TAAAAATAAAA
1 TAAAAATAAAA
*
16699758 TTAAAATAAAA
1 TAAAAATAAAA
16699769 TAAA
1 TAAA
16699773 GACTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 1 0.03
11 22 0.69
12 6 0.19
13 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:16699806 original size:22 final size:21
Alignment explanation
Indices: 16699726--16699807 Score: 53
Period size: 22 Copynumber: 3.8 Consensus size: 21
16699716 TTTTTATTTA
* *
16699726 AAAATAAATAAATAAATAGAATAA
1 AAAA-AAATTAAT-AATA-AATAT
16699750 AAATAAAATTAA-AATAAA-AT
1 AAA-AAAATTAATAATAAATAT
* * *
16699770 -AAAGACTTAAAAATATAATAT
1 AAAAAAATTAATAATA-AATAT
16699791 AAAAAAATTAATAATAA
1 AAAAAAATTAATAATAA
16699808 CTTTTATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
18 6 0.13
19 6 0.13
20 3 0.07
21 5 0.11
22 16 0.35
24 9 0.20
25 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAAATTAATAATAAATAT
Found at i:16699918 original size:17 final size:17
Alignment explanation
Indices: 16699898--16699945 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
16699888 TAATTTTTGT
16699898 TAAAAAATAATAAATTA
1 TAAAAAATAATAAATTA
*
16699915 TAAAAAATGATAAA-TA
1 TAAAAAATAATAAATTA
16699931 -AAATAAA-AATAAATT
1 TAAA-AAATAATAAATT
16699946 GTTTAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
17 13 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAAATAATAAATTA
Found at i:16700861 original size:9 final size:10
Alignment explanation
Indices: 16700839--16700872 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
16700829 CCTAAACTTC
16700839 TTTTAATAAT
1 TTTTAATAAT
*
16700849 TTTTAATTAT
1 TTTTAATAAT
16700859 TTTTAA-AAT
1 TTTTAATAAT
16700868 TTTTA
1 TTTTA
16700873 CTAAAAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:16704030 original size:16 final size:16
Alignment explanation
Indices: 16704011--16704043 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16704001 AAAAAAGCAT
*
16704011 ATCTTAAAAAATAAAA
1 ATCTAAAAAAATAAAA
16704027 ATCTAAAAAAATAAAA
1 ATCTAAAAAAATAAAA
16704043 A
1 A
16704044 AAAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
ATCTAAAAAAATAAAA
Found at i:16704534 original size:14 final size:14
Alignment explanation
Indices: 16704517--16704565 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
16704507 AAGAAGATAA
*
16704517 AAAAAAGGAAAAAC
1 AAAAAAGAAAAAAC
*
16704531 AAAAAATAAAAAAC
1 AAAAAAGAAAAAAC
* *
16704545 AAAAAACAAAAAAA
1 AAAAAAGAAAAAAC
16704559 AAAAAAG
1 AAAAAAG
16704566 GAAAGAAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAAC
Found at i:16704541 original size:21 final size:21
Alignment explanation
Indices: 16704515--16704569 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
16704505 AAAAGAAGAT
16704515 AAAAAAAAGGAAAAACAAAAA
1 AAAAAAAAGGAAAAACAAAAA
* **
16704536 ATAAAAAACAAAAAACAAAAA
1 AAAAAAAAGGAAAAACAAAAA
16704557 AAAAAAAAGGAAA
1 AAAAAAAAGGAAA
16704570 GAAAGGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGGAAAAACAAAAA
Found at i:16704564 original size:7 final size:7
Alignment explanation
Indices: 16704525--16704563 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
16704515 AAAAAAAAGG
16704525 AAAAACA
1 AAAAACA
*
16704532 AAAAATA
1 AAAAACA
16704539 AAAAACA
1 AAAAACA
16704546 AAAAACA
1 AAAAACA
16704553 AAAAA-A
1 AAAAACA
16704559 AAAAA
1 AAAAA
16704564 AGGAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAACA
Found at i:16708467 original size:17 final size:17
Alignment explanation
Indices: 16708441--16708473 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16708431 TCGAGAAGAA
16708441 TAGTGACATTTTTTAAT
1 TAGTGACATTTTTTAAT
*
16708458 TAGTGGCATTTTTTAA
1 TAGTGACATTTTTTAA
16708474 AAAACGTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (17 bp):
TAGTGACATTTTTTAAT
Found at i:16708856 original size:19 final size:19
Alignment explanation
Indices: 16708818--16708855 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16708808 TTTAATATTT
*
16708818 ATTATTATAATTAAATAAA
1 ATTATTATAAATAAATAAA
16708837 ATTATTA-AAATAAATAAA
1 ATTATTATAAATAAATAAA
16708855 A
1 A
16708856 AATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTATTATAAATAAATAAA
Found at i:16724106 original size:20 final size:17
Alignment explanation
Indices: 16724071--16724104 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16724061 TGTTATTTTA
16724071 TAAAAAAAAATTATAAT
1 TAAAAAAAAATTATAAT
16724088 TAAAAAAAAATTATAAT
1 TAAAAAAAAATTATAAT
16724105 AAATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAAAAATTATAAT
Found at i:16724107 original size:16 final size:16
Alignment explanation
Indices: 16724070--16724107 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
16724060 ATGTTATTTT
16724070 ATAAAAAAAAATTATA
1 ATAAAAAAAAATTATA
16724086 ATTAAAAAAAAATTATA
1 A-TAAAAAAAAATTATA
16724103 ATAAA
1 ATAAA
16724108 TTATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAAAAATTATA
Found at i:16725412 original size:16 final size:16
Alignment explanation
Indices: 16725391--16725424 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16725381 ATAAAATCTC
16725391 GACTTTATGAATACTT
1 GACTTTATGAATACTT
*
16725407 GACTTTGTGAATACTT
1 GACTTTATGAATACTT
16725423 GA
1 GA
16725425 GTATGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (16 bp):
GACTTTATGAATACTT
Found at i:16733660 original size:23 final size:23
Alignment explanation
Indices: 16733634--16733706 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
16733624 TAGGAGATAC
16733634 TTTCTCTTTAACTCTTTTTTCAT
1 TTTCTCTTTAACTCTTTTTTCAT
* *** *
16733657 TTTCTC-TTAAGT-TACAATT-AC
1 TTTCTCTTTAACTCT-TTTTTCAT
*
16733678 TTTCTCTTCAACTCTTTTTTCAT
1 TTTCTCTTTAACTCTTTTTTCAT
16733701 TTTCTC
1 TTTCTC
16733707 CTAAGTTACA
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 8 0.23
22 13 0.37
23 14 0.40
ACGTcount: A:0.16, C:0.23, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTCTCTTTAACTCTTTTTTCAT
Found at i:16733681 original size:44 final size:44
Alignment explanation
Indices: 16733631--16733717 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
16733621 ATCTAGGAGA
* *
16733631 TACTTTCTCTTTAACTCTTTTTTCATTTTCTCTTAAGTTACAAT
1 TACTTTCTCTTCAACTCTTTTTTCATTTTCTCCTAAGTTACAAT
16733675 TACTTTCTCTTCAACTCTTTTTTCATTTTCTCCTAAGTTACAA
1 TACTTTCTCTTCAACTCTTTTTTCATTTTCTCCTAAGTTACAA
16733718 ATTGTCTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (44 bp):
TACTTTCTCTTCAACTCTTTTTTCATTTTCTCCTAAGTTACAAT
Found at i:16740105 original size:744 final size:745
Alignment explanation
Indices: 16738678--16740166 Score: 2703
Period size: 744 Copynumber: 2.0 Consensus size: 745
16738668 AATAACATAC
16738678 TACAAGGTAGTCCCCTGCTTGCCCTTTTCTCTTTTTCAATCTCTAACCATGGTCACACATTTCTT
1 TACAAGGTAGTCCCCTGCTTGCCCTTTTCTCTTTTTCAATCTCTAACCATGGTCACACATTTCTT
*
16738743 GGTTTTTATATTTAAATGAAAGTTGTAAATGTTATATATCTTGTATTATCATTTCAACATTGGTA
66 GGTTTTTATAGTTAAATGAAAGTTGTAAATGTTATATATCTTGTATTATCATTTCAACATTGGTA
16738808 GCAATTTAGGTTTGTATCTTATTTAATTCTTTTGTGTTAAGATGTTTGCTTTTTTTTTTTTATTG
131 GCAATTTAGGTTTGTATCTTATTTAATTCTTTTGTGTTAAGATGTTTGCTTTTTTTTTTTTATTG
16738873 AAAGATGGCTCCATAGTTAGATCATTTTATTCAACTCATGAACATAGGTTTATTAATTATATTTC
196 AAAGATGGCTCCATAGTTAGATCATTTTATTCAACTCATGAACATAGGTTTATTAATTATATTTC
16738938 TTTCCAAGTACCTGGTGACTCTTCCTTAGATATTATTAATGGTATAGGGATATCAAGAAGATTCA
261 TTTCCAAGTACCTGGTGACTCTTCCTTAGATATTATTAATGGTATAGGGATATCAAGAAGATTCA
16739003 TGCATAGTTTCAACAACAGTATTGAGTTTGCTTTTGTTATTTAATGATTCAGTCTTCACCTTTTA
326 TGCATAGTTTCAACAACAGTATTGAGTTTGCTTTTGTTATTTAATGATTCAGTCTTCACCTTTTA
* *
16739068 AGTTTGAGCTTTTTAGGATGTTTTCTAACTCAATTAATCCTTTTTAAAAAAAATCTAAAACAAAA
391 AGTTAGAACTTTTTAGGATGTTTTCTAACTCAATTAATCCTTTTTAAAAAAAATCTAAAACAAAA
* * * *
16739133 AAGTCAAATTGTTTTGTTATTAAATGAAACAATTGCCTCTGAAAGCTCTAAAAGATCTTTTATGA
456 AAGTCAAATTATTTTGTTATTAAATGAAACAATTACCTCTAAAAGCTCTAAAAGATCTTTTATAA
* *
16739198 TGATCATCCAAGTTAATTATATCTCTTTTATGTCTATTTTAAGATCCACTTCTTTAAACCTCTAG
521 TGATCATCCAAGTTAATGATATCTCATTTATGTCTATTTTAAGATCCACTTCTTTAAACCTCTAG
16739263 AATTTAAATCAATTAAAGGTAAATGTTTCTTCAGGCAGATCCTAACCATACTCCTTTGACTAAAT
586 AATTTAAATCAATTAAAGGTAAATGTTTCTTCAGGCAGATCCTAACCATACTCCTTTGACTAAAT
*
16739328 GATTGATAAGACCTTTAACTTTATTATTTTTGCTGCTCAATATTTTTAGATGTCAAATTAAGACT
651 GATTGATAAGACCTTTAACTTTATTATTTTTGCTGCTCAATATTTTTAAATGTCAAATTAAGACT
*
16739393 AATATAAAACCAACTAAAAAAATGTATTCA
716 AATACAAAACCAACTAAAAAAATGTATTCA
* * * *
16739423 TACAAGGTAGTCCCTTGGTTGCCCTTTTCTTTTTTTCAATCTCTAACCTTGGTCACACATTTCTT
1 TACAAGGTAGTCCCCTGCTTGCCCTTTTCTCTTTTTCAATCTCTAACCATGGTCACACATTTCTT
16739488 GGTTTTTATAGTTAAATGAAAGTTGTAAATGTTATATATCTTGTATTATCATTTCAACATTGGTA
66 GGTTTTTATAGTTAAATGAAAGTTGTAAATGTTATATATCTTGTATTATCATTTCAACATTGGTA
16739553 GCAATTTAGGTTTGTATCTTATTTAATTCTTTTGTGTTAAGATGTTTGCTTTTTTTTTTTT-TTG
131 GCAATTTAGGTTTGTATCTTATTTAATTCTTTTGTGTTAAGATGTTTGCTTTTTTTTTTTTATTG
*
16739617 AAAGATGGCTCCATAGTTAGATCATTTTATTCGACTCATGAACATAGGTTTATTAATTATATTTC
196 AAAGATGGCTCCATAGTTAGATCATTTTATTCAACTCATGAACATAGGTTTATTAATTATATTTC
* * *
16739682 TTTCCAAGTACTTGGTGACTCTTCTTTAGATATTATTAATGGTATAGGGATGTCAAGAAGATTCA
261 TTTCCAAGTACCTGGTGACTCTTCCTTAGATATTATTAATGGTATAGGGATATCAAGAAGATTCA
*
16739747 TGCATAGTTTCAACAACAGTATTGAGTTTGCTTTTGTTATTTAATGATTCAGTCTTCGCCTTTTA
326 TGCATAGTTTCAACAACAGTATTGAGTTTGCTTTTGTTATTTAATGATTCAGTCTTCACCTTTTA
*
16739812 AGTTAGAACTTTTTAGGATGTTTTCTAACTCAATTGATCCTTTTTTAAAAAAAATCTAAAAC-AA
391 AGTTAGAACTTTTTAGGATGTTTTCTAACTCAATTAATCC-TTTTTAAAAAAAATCTAAAACAAA
16739876 AAAGTCAAATTATTTTGTTATTAAATGAAACAATTACCTCTAAAAGCTCTAAAAGATCTTTTATA
455 AAAGTCAAATTATTTTGTTATTAAATGAAACAATTACCTCTAAAAGCTCTAAAAGATCTTTTATA
* * *
16739941 ATGATCATCCAAGTTAATGATCTCTCATTTGTGTCTATTTTAAGATCCACTTCTTTAAACCTTTA
520 ATGATCATCCAAGTTAATGATATCTCATTTATGTCTATTTTAAGATCCACTTCTTTAAACCTCTA
* *
16740006 GAATTTAAATCAATTAAAGGTAAATGTTTCTTCTGGCATATCCTAACCATACTCCTTTGACTAAA
585 GAATTTAAATCAATTAAAGGTAAATGTTTCTTCAGGCAGATCCTAACCATACTCCTTTGACTAAA
* *
16740071 TGATTGATAGGACCTTTAACTTTATTATTTTTGCTGTTCAATATTTTTAAATGTCAAATTAAGAC
650 TGATTGATAAGACCTTTAACTTTATTATTTTTGCTGCTCAATATTTTTAAATGTCAAATTAAGAC
16740136 TAATACAAAACCAACTAAAAAAATGTATTCA
715 TAATACAAAACCAACTAAAAAAATGTATTCA
16740167 AGTTGCATGG
Statistics
Matches: 715, Mismatches: 28, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
744 508 0.71
745 207 0.29
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (745 bp):
TACAAGGTAGTCCCCTGCTTGCCCTTTTCTCTTTTTCAATCTCTAACCATGGTCACACATTTCTT
GGTTTTTATAGTTAAATGAAAGTTGTAAATGTTATATATCTTGTATTATCATTTCAACATTGGTA
GCAATTTAGGTTTGTATCTTATTTAATTCTTTTGTGTTAAGATGTTTGCTTTTTTTTTTTTATTG
AAAGATGGCTCCATAGTTAGATCATTTTATTCAACTCATGAACATAGGTTTATTAATTATATTTC
TTTCCAAGTACCTGGTGACTCTTCCTTAGATATTATTAATGGTATAGGGATATCAAGAAGATTCA
TGCATAGTTTCAACAACAGTATTGAGTTTGCTTTTGTTATTTAATGATTCAGTCTTCACCTTTTA
AGTTAGAACTTTTTAGGATGTTTTCTAACTCAATTAATCCTTTTTAAAAAAAATCTAAAACAAAA
AAGTCAAATTATTTTGTTATTAAATGAAACAATTACCTCTAAAAGCTCTAAAAGATCTTTTATAA
TGATCATCCAAGTTAATGATATCTCATTTATGTCTATTTTAAGATCCACTTCTTTAAACCTCTAG
AATTTAAATCAATTAAAGGTAAATGTTTCTTCAGGCAGATCCTAACCATACTCCTTTGACTAAAT
GATTGATAAGACCTTTAACTTTATTATTTTTGCTGCTCAATATTTTTAAATGTCAAATTAAGACT
AATACAAAACCAACTAAAAAAATGTATTCA
Found at i:16742558 original size:12 final size:12
Alignment explanation
Indices: 16742550--16742598 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 12
16742540 TTTATTATAT
16742550 AATAAATTAATA
1 AATAAATTAATA
16742562 AATAAATTTTATTATA
1 AATAAA--TTA--ATA
16742578 TAATAAATTAATA
1 -AATAAATTAATA
16742591 AATAAATT
1 AATAAATT
16742599 TATTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 14 0.44
13 3 0.09
14 3 0.09
15 3 0.09
16 3 0.09
17 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAAATTAATA
Found at i:16742579 original size:29 final size:29
Alignment explanation
Indices: 16742539--16742599 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
16742529 CATTTTAATT
16742539 TTTTATTATATAATAAATTAATAAATAAA
1 TTTTATTATATAATAAATTAATAAATAAA
16742568 TTTTATTATATAATAAATTAATAAATAAA
1 TTTTATTATATAATAAATTAATAAATAAA
16742597 TTT
1 TTT
16742600 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTATTATATAATAAATTAATAAATAAA
Found at i:16742582 original size:17 final size:17
Alignment explanation
Indices: 16742539--16742586 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
16742529 CATTTTAATT
16742539 TTTTATTATATAATAAA
1 TTTTATTATATAATAAA
16742556 --TTA--ATA-AATAAA
1 TTTTATTATATAATAAA
16742568 TTTTATTATATAATAAA
1 TTTTATTATATAATAAA
16742585 TT
1 TT
16742587 AATAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 3 0.12
15 3 0.12
16 3 0.12
17 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATTATATAATAAA
Found at i:16743860 original size:23 final size:23
Alignment explanation
Indices: 16743833--16743877 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
16743823 TATAGAATAT
* *
16743833 ACAAAATTAAGATCATACTAAAC
1 ACAAAATTAAAATCACACTAAAC
16743856 ACAAAATTAAAATCACACTAAA
1 ACAAAATTAAAATCACACTAAA
16743878 AATGAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (23 bp):
ACAAAATTAAAATCACACTAAAC
Found at i:16746052 original size:37 final size:37
Alignment explanation
Indices: 16746011--16746082 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
16746001 CCCACTGACA
* **
16746011 TTTCTTTTCAATTCTGCTGGTCAGGCAATGGCATTGG
1 TTTCTTTTCAATTCTGATCATCAGGCAATGGCATTGG
*
16746048 TTTCTTTTCAATTCTGATCATCAGGCAATTGCATT
1 TTTCTTTTCAATTCTGATCATCAGGCAATGGCATT
16746083 TCCAGTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (37 bp):
TTTCTTTTCAATTCTGATCATCAGGCAATGGCATTGG
Found at i:16751242 original size:12 final size:12
Alignment explanation
Indices: 16751234--16751282 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 12
16751224 TTTATTATAT
16751234 AATAAATTAATA
1 AATAAATTAATA
16751246 AATAAATTTTATTATA
1 AATAAA--TTA--ATA
16751262 TAATAAATTAATA
1 -AATAAATTAATA
16751275 AATAAATT
1 AATAAATT
16751283 TATTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 14 0.44
13 3 0.09
14 3 0.09
15 3 0.09
16 3 0.09
17 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAAATTAATA
Found at i:16751263 original size:29 final size:29
Alignment explanation
Indices: 16751223--16751283 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
16751213 CATTTTAATT
16751223 TTTTATTATATAATAAATTAATAAATAAA
1 TTTTATTATATAATAAATTAATAAATAAA
16751252 TTTTATTATATAATAAATTAATAAATAAA
1 TTTTATTATATAATAAATTAATAAATAAA
16751281 TTT
1 TTT
16751284 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTATTATATAATAAATTAATAAATAAA
Found at i:16751266 original size:17 final size:17
Alignment explanation
Indices: 16751223--16751270 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
16751213 CATTTTAATT
16751223 TTTTATTATATAATAAA
1 TTTTATTATATAATAAA
16751240 --TTA--ATA-AATAAA
1 TTTTATTATATAATAAA
16751252 TTTTATTATATAATAAA
1 TTTTATTATATAATAAA
16751269 TT
1 TT
16751271 AATAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 3 0.12
15 3 0.12
16 3 0.12
17 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATTATATAATAAA
Found at i:16752543 original size:23 final size:23
Alignment explanation
Indices: 16752516--16752560 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
16752506 TATAGAATAT
* *
16752516 ACAAAATTAAGATCATACTAAAC
1 ACAAAATTAAAATCACACTAAAC
16752539 ACAAAATTAAAATCACACTAAA
1 ACAAAATTAAAATCACACTAAA
16752561 AATGAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (23 bp):
ACAAAATTAAAATCACACTAAAC
Found at i:16754744 original size:37 final size:37
Alignment explanation
Indices: 16754703--16754774 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
16754693 CCCACTGACA
* **
16754703 TTTCTTTTCAATTCTGCTGGTCAGGCAATGGCATTGG
1 TTTCTTTTCAATTCTGATCATCAGGCAATGGCATTGG
*
16754740 TTTCTTTTCAATTCTGATCATCAGGCAATTGCATT
1 TTTCTTTTCAATTCTGATCATCAGGCAATGGCATT
16754775 TCCAGTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (37 bp):
TTTCTTTTCAATTCTGATCATCAGGCAATGGCATTGG
Found at i:16756358 original size:25 final size:25
Alignment explanation
Indices: 16756316--16756363 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
16756306 TTTTATTTTC
*
16756316 TTTTTGTATTTTATTAAAATTTATT
1 TTTTTGAATTTTATTAAAATTTATT
*
16756341 TTTTTGAATATTTA-TAAATTTTA
1 TTTTTGAAT-TTTATTAAAATTTA
16756364 GTAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTTGAATTTTATTAAAATTTATT
Found at i:16757789 original size:2 final size:2
Alignment explanation
Indices: 16757782--16757825 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
16757772 TGTCAAAATC
* * *
16757782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC 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
16757824 AT
1 AT
16757826 TACAATATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:16757833 original size:14 final size:16
Alignment explanation
Indices: 16757781--16757834 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
16757771 GTGTCAAAAT
*
16757781 CATATATATATATATA
1 CATATATATATATACA
*
16757797 TATATATATATATACA
1 CATATATATATATACA
*
16757813 CACATATATATATTACA
1 CATATATATATA-TACA
16757830 -ATATA
1 CATATA
16757835 CATGAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 28 0.88
17 4 0.12
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
CATATATATATATACA
Found at i:16758803 original size:21 final size:21
Alignment explanation
Indices: 16758777--16758832 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
16758767 AATTCATTGG
16758777 TAATAATTAAAATTCCACCGA
1 TAATAATTAAAATTCCACCGA
*
16758798 TAATAATTAAAATTCCACTGA
1 TAATAATTAAAATTCCACCGA
16758819 TAATAA-TAAAATTC
1 TAATAATTAAAATTC
16758833 TATCAGTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (21 bp):
TAATAATTAAAATTCCACCGA
Found at i:16761782 original size:16 final size:16
Alignment explanation
Indices: 16761761--16761792 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16761751 ATATAAAGTT
16761761 TTAAACCTTTGTATTG
1 TTAAACCTTTGTATTG
*
16761777 TTAAACCTTTTTATTG
1 TTAAACCTTTGTATTG
16761793 ATTGACTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TTAAACCTTTGTATTG
Done.