Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 98 of 113
Found at i:19813173 original size:22 final size:22
Alignment explanation
Indices: 19813125--19813231 Score: 100
Period size: 22 Copynumber: 5.1 Consensus size: 22
19813115 CCAAAAAAAG
*
19813125 AAAAAA-AATAA-CAGAT-AAT
1 AAAAAATAATAATAAGATAAAT
*
19813144 TAAAAATAATAATAAGATAAAT
1 AAAAAATAATAATAAGATAAAT
* *
19813166 AAAAAAT-ATTACAAGATAAAT
1 AAAAAATAATAATAAGATAAAT
19813187 AAAAAATAATAATAA-ATAAACT
1 AAAAAATAATAATAAGATAAA-T
* * *
19813209 ATAATATAATAATAA-ATATAT
1 AAAAAATAATAATAAGATAAAT
19813230 AA
1 AA
19813232 CTAGATAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 30 0.42
22 32 0.44
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAAAATAATAATAAGATAAAT
Found at i:19813204 original size:53 final size:55
Alignment explanation
Indices: 19813130--19813245 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 55
19813120 AAAAGAAAAA
* * *
19813130 AAATAACAGATAATTAAAAATAATAATA-AGATA-AATAA-AAA-ATATTACAAGAT
1 AAATAAAAAATAATTAAAAATAA-AATATA-ATATAATAATAAATATATAACAAGAT
* *
19813183 AAATAAAAAATAA-TAATAAATAAACTATAATATAATAATAAATATATAACTAGAT
1 AAATAAAAAATAATTAA-AAATAAAATATAATATAATAATAAATATATAACAAGAT
19813238 AAATAAAA
1 AAATAAAA
19813246 TACATATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
52 9 0.17
53 23 0.43
54 3 0.06
55 18 0.34
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (55 bp):
AAATAAAAAATAATTAAAAATAAAATATAATATAATAATAAATATATAACAAGAT
Found at i:19813213 original size:60 final size:55
Alignment explanation
Indices: 19813127--19813245 Score: 123
Period size: 55 Copynumber: 2.1 Consensus size: 55
19813117 AAAAAAAGAA
* *
19813127 AAAAAATAACAGATAATTAAAAATAATAATAAGATAAATAAAAAATATTACAAGATAAAT
1 AAAAAATAACAGATAAATAAAAATAAT-AT-A-AT-AAT-AAAAATATAACAAGATAAAT
* * * *
19813187 AAAAAATAATA-ATAAATAAACTATAATATAATAATAAATATATAACTAGATAAAT
1 AAAAAATAACAGATAAATAAA-AATAATATAATAATAAAAATATAACAAGATAAAT
19813242 AAAA
1 AAAA
19813246 TACATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
55 21 0.40
56 3 0.06
57 2 0.04
58 1 0.02
59 10 0.19
60 15 0.29
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (55 bp):
AAAAAATAACAGATAAATAAAAATAATATAATAATAAAAATATAACAAGATAAAT
Found at i:19813233 original size:25 final size:25
Alignment explanation
Indices: 19813181--19813255 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
19813171 ATATTACAAG
* *
19813181 ATAAATAAAAAATAATAAT-AA-AT
1 ATAACTAATAAATAATAATAAATAT
19813204 A-AACT-ATAATATAATAATAAATAT
1 ATAACTAATAA-ATAATAATAAATAT
*
19813228 ATAACTAGATAAATAA-AATACATAT
1 ATAACTA-ATAAATAATAATAAATAT
19813253 ATA
1 ATA
19813256 GATATTAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.07
22 11 0.26
23 3 0.07
24 3 0.07
25 15 0.35
26 4 0.09
27 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (25 bp):
ATAACTAATAAATAATAATAAATAT
Found at i:19813257 original size:21 final size:19
Alignment explanation
Indices: 19813126--19813259 Score: 84
Period size: 21 Copynumber: 6.8 Consensus size: 19
19813116 CAAAAAAAGA
* * *
19813126 AAAAAAATAACAGATAATT
1 AAAATAATAATAGATAAAT
19813145 AAAAATAATAATAAGATAAAT
1 -AAAATAATAAT-AGATAAAT
*
19813166 AAAA-AATATTACAAGATAAAT
1 AAAATAATA--A-TAGATAAAT
19813187 AAAA-AATAATA-ATAAAT
1 AAAATAATAATAGATAAAT
19813204 AAACTATAAT-ATA-AT-AAT
1 AAA--ATAATAATAGATAAAT
19813222 -AAATATATAACTAGATAAAT
1 AAAATA-ATAA-TAGATAAAT
19813242 AAAATACATATATAGATA
1 AAAATA-ATA-ATAGATA
19813260 TTAACAGAAG
Statistics
Matches: 94, Mismatches: 6, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.03
16 2 0.02
17 12 0.13
18 6 0.06
19 13 0.14
20 19 0.20
21 38 0.40
22 1 0.01
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATAATAATAGATAAAT
Found at i:19813343 original size:18 final size:18
Alignment explanation
Indices: 19813320--19813373 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
19813310 TAGCAAATAC
19813320 ATAAAATACAAAGAA-AAA
1 ATAAAATACAAA-AATAAA
* * *
19813338 ATAAAAAATAAAAATAAT
1 ATAAAATACAAAAATAAA
19813356 ATAAAATAC-AAAATAAA
1 ATAAAATACAAAAATAAA
19813373 A
1 A
19813374 GTCAAATTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.17
Consensus pattern (18 bp):
ATAAAATACAAAAATAAA
Found at i:19813361 original size:16 final size:17
Alignment explanation
Indices: 19813333--19813371 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19813323 AAATACAAAG
19813333 AAAA-AATAAAAAATA-
1 AAAATAATAAAAAATAC
*
19813348 AAAATAATATAAAATAC
1 AAAATAATAAAAAATAC
19813365 AAAATAA
1 AAAATAA
19813372 AAGTCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAAAATAC
Found at i:19820938 original size:13 final size:13
Alignment explanation
Indices: 19820920--19820945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19820910 TTAGTCAAAG
19820920 AAAAATCAAAATA
1 AAAAATCAAAATA
19820933 AAAAATCAAAATA
1 AAAAATCAAAATA
19820946 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:19821182 original size:61 final size:61
Alignment explanation
Indices: 19820982--19821229 Score: 326
Period size: 59 Copynumber: 4.1 Consensus size: 61
19820972 CTGTGTAGGA
*** *
19820982 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTT-CGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTAAGG
* * *
19821041 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTGAAAATTTA---TTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTTTTTTAAGG
19821100 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTAAGG
* * *
19821161 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTTTATTTTTATTTAAAG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAA--ATTTATTTTT-TTTAAGG
19821226 AAAA
1 AAAA
19821230 CAGAATAATA
Statistics
Matches: 169, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
58 16 0.09
59 69 0.41
61 54 0.32
62 11 0.07
64 9 0.05
65 10 0.06
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (61 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTAAGG
Found at i:19821259 original size:7 final size:8
Alignment explanation
Indices: 19821249--19821299 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 8
19821239 AAAAAAAGTC
19821249 AAAATAAA
1 AAAATAAA
19821257 AAAATAAA
1 AAAATAAA
19821265 AAAATTAAA
1 AAAA-TAAA
19821274 GAAAAGTAAA
1 -AAAA-TAAA
19821284 ACAAA-AATA
1 A-AAATAA-A
19821293 AAAATAA
1 AAAATAA
19821300 GATAAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
8 17 0.46
9 9 0.24
10 11 0.30
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:19821305 original size:22 final size:21
Alignment explanation
Indices: 19821249--19821314 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
19821239 AAAAAAAGTC
19821249 AAAATAAA-AAAA-T-AA-AA
1 AAAATAAAGAAAAGTAAAGAA
*
19821266 AAATTAAAGAAAAGTAAA-ACA
1 AAAATAAAGAAAAGTAAAGA-A
19821287 AAAATAAA-AATAAGATAAAGAA
1 AAAATAAAGAA-AAG-TAAAGAA
19821309 AAAATA
1 AAAATA
19821315 TTAAATGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 1 0.03
20 5 0.12
21 11 0.28
22 11 0.28
23 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.14
Consensus pattern (21 bp):
AAAATAAAGAAAAGTAAAGAA
Found at i:19821345 original size:10 final size:10
Alignment explanation
Indices: 19821332--19821372 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
19821322 AATTTAATCT
19821332 AATAAATAAA
1 AATAAATAAA
19821342 AATAAATAAA
1 AATAAATAAA
* *
19821352 GATAAA-ACA
1 AATAAATAAA
19821361 AATAAATAAA
1 AATAAATAAA
19821371 AA
1 AA
19821373 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
AATAAATAAA
Found at i:19822235 original size:31 final size:30
Alignment explanation
Indices: 19822200--19822299 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
19822190 AATCAAATAA
19822200 AAAAAGAAAAAATAATAGATAATTAGAAAAG
1 AAAAAGAAAAAATAATAGATAATTA-AAAAG
* *
19822231 AAAAA-AAATAATAATCAGATAATAAAAAAG
1 AAAAAGAAAAAATAAT-AGATAATTAAAAAG
** * * *
19822261 AATCAGATAAAATTAACAGATAATTTAAAAAA
1 AAAAAGA-AAAAATAATAGATAA-TTAAAAAG
19822293 AAAAAGA
1 AAAAAGA
19822300 TAAACCCAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
30 17 0.31
31 20 0.37
32 17 0.31
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (30 bp):
AAAAAGAAAAAATAATAGATAATTAAAAAG
Found at i:19822244 original size:23 final size:25
Alignment explanation
Indices: 19822201--19822270 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 25
19822191 ATCAAATAAA
*
19822201 AAAAGAAAAAATAATAGATAATTAG
1 AAAAGAAAAAATAATAGATAATCAG
19822226 AAAAGAAAAAA-AATA-ATAATCAG
1 AAAAGAAAAAATAATAGATAATCAG
* * *
19822249 ATAATAAAAAAGAATCAGATAA
1 AAAAGAAAAAATAAT-AGATAA
19822271 AATTAACAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 16 0.41
24 7 0.18
25 12 0.31
26 4 0.10
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (25 bp):
AAAAGAAAAAATAATAGATAATCAG
Found at i:19822260 original size:30 final size:31
Alignment explanation
Indices: 19822200--19822299 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 31
19822190 AATCAAATAA
*
19822200 AAAAAGAAAAAATAATAGATAATTAGAAAAG
1 AAAAAGAAAAAATAATAGATAATTAAAAAAG
*
19822231 AAAAA-AAATAATAATCAGATAA-TAAAAAAG
1 AAAAAGAAAAAATAAT-AGATAATTAAAAAAG
** * *
19822261 AATCAGATAAAATTAACAGATAATTTAAAAAA-
1 AAAAAGA-AAAAATAATAGATAA-TTAAAAAAG
19822293 AAAAAGA
1 AAAAAGA
19822300 TAAACCCAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
30 19 0.35
31 18 0.33
32 11 0.20
33 7 0.13
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (31 bp):
AAAAAGAAAAAATAATAGATAATTAAAAAAG
Found at i:19822332 original size:3 final size:3
Alignment explanation
Indices: 19822324--19822357 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
19822314 TATTACAAAA
19822324 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19822358 ATATATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19822342 original size:14 final size:14
Alignment explanation
Indices: 19822325--19822353 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19822315 ATTACAAAAA
19822325 ATAATAATAATAAT
1 ATAATAATAATAAT
19822339 ATAATAATAATAAT
1 ATAATAATAATAAT
19822353 A
1 A
19822354 ATAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:19822630 original size:4 final size:4
Alignment explanation
Indices: 19822611--19822647 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
19822601 TTTTATATTT
*
19822611 TTTG -TTG TTT- TTTG TTTG TTTG TTTG TTTT TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
19822648 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (4 bp):
TTTG
Found at i:19822651 original size:8 final size:8
Alignment explanation
Indices: 19822608--19822667 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 8
19822598 TATTTTTATA
19822608 TTTTTTG-
1 TTTTTTGT
*
19822615 TTGTTT-T
1 TTTTTTGT
*
19822622 TTGTTTGT
1 TTTTTTGT
*
19822630 TTGTTTGT
1 TTTTTTGT
19822638 TTTTTTGT
1 TTTTTTGT
19822646 TTTTTT-T
1 TTTTTTGT
*
19822653 TATTTTTAT
1 T-TTTTTGT
19822662 TTTTTT
1 TTTTTT
19822668 TTACCAAAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
7 13 0.28
8 32 0.68
9 2 0.04
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTGT
Found at i:19822653 original size:12 final size:12
Alignment explanation
Indices: 19822608--19822668 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
19822598 TATTTTTATA
*
19822608 TTTTTTGTTGTTT
1 TTTTTTTTTG-TT
19822621 TTTGTTTGTTTGTT
1 TTT-TTT-TTTGTT
*
19822635 TGTTTTTTTGTT
1 TTTTTTTTTGTT
19822647 TTTTTTTATT-TT
1 TTTTTTT-TTGTT
19822659 TATTTTTTTT
1 T-TTTTTTTT
19822669 TACCAAAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 17 0.41
13 14 0.34
14 7 0.17
15 3 0.07
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:19822797 original size:41 final size:41
Alignment explanation
Indices: 19822676--19823165 Score: 756
Period size: 41 Copynumber: 12.0 Consensus size: 41
19822666 TTTTACCAAA
* *
19822676 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19822717 GCTCCTCTAAACAGA-GCA--ACGAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGAAAAGTAAATT
*
19822757 GCTCTTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
19822798 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19822839 GCTCCTCTAAACAGAGGCATCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19822880 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
19822921 GCTCCTTTAAACAGAGGCACCACGGCTTTGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
19822962 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
19823003 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19823044 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
19823085 GCTCCTATCAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19823126 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAA-TAAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAAT
19823166 ACTCCTTGAC
Statistics
Matches: 413, Mismatches: 28, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.01
40 36 0.09
41 361 0.87
42 10 0.02
43 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:19824400 original size:20 final size:21
Alignment explanation
Indices: 19824375--19824430 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
19824365 TTTGAATCTC
**
19824375 TTTTTTCATTTTCTTTTTT-T
1 TTTTTTCATCATCTTTTTTCT
19824395 TTTTTTCATCATCTTTTTTCT
1 TTTTTTCATCATCTTTTTTCT
19824416 TTTTTTC-TCAT-TTTT
1 TTTTTTCATCATCTTTT
19824431 CATCAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 21 0.64
21 8 0.24
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCATCATCTTTTTTCT
Found at i:19828221 original size:13 final size:13
Alignment explanation
Indices: 19828203--19828228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19828193 TTAGTCAAAG
19828203 AAAAATCAAAATA
1 AAAAATCAAAATA
19828216 AAAAATCAAAATA
1 AAAAATCAAAATA
19828229 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:19828461 original size:63 final size:63
Alignment explanation
Indices: 19828266--19828516 Score: 243
Period size: 59 Copynumber: 4.1 Consensus size: 63
19828256 TTGTGTAGGA
* * * *** *
19828266 AAAATTGATATTTTCAACTTTTTCTCAAAAATA-TTTTTTGAAAA--T-TTCGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTTTAAGG
* * * * *
19828325 AAAATTGATACTTTTAACTTTTCCTCAAAAATCCTTTATTTGAAAATTTA-----TTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTTTTTTTTAAGG
* *
19828384 AAAATTGATTCTTTCAATTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTTTAAGG
* * *
19828447 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTG-AAATTTTTTATTTTTATTTAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAAATTTATT-TTTTT-TTTAAG
19828511 G
63 G
19828512 AAAAT
1 AAAAT
19828517 AGAATAATAA
Statistics
Matches: 160, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
58 15 0.09
59 64 0.40
61 10 0.06
63 47 0.29
64 13 0.08
65 11 0.07
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (63 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTTTAAGG
Found at i:19828489 original size:122 final size:118
Alignment explanation
Indices: 19828266--19828491 Score: 287
Period size: 122 Copynumber: 1.9 Consensus size: 118
19828256 TTGTGTAGGA
*
19828266 AAAATTGATATTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAATT
1 AAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAATT
* *
19828331 GATACTTTTAACTTTTCCTCAAAAATCCTTTATTTGAAAATTTATTTCTAAGG
66 GATACTTTCAACTTTTCCTCAAAAATACTTTATTTGAAAATTTATTTCTAAGG
*** *
19828384 AAAATTGAT-TCTTTCAA-TTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTTTAAGG
1 AAAATTGATAT-TTTCAACTTTTT-CCCAAAAATA-TTTTTTGAAAA--T-TTCGATTTTCAAGG
* *
19828447 AAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTTGAAA
60 AAAATTGATACTTTCAACTTTTCCTC-AAAAATACTTTATTTGAAA
19828492 TTTTTTATTT
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
117 6 0.07
118 24 0.26
119 11 0.12
121 2 0.02
122 49 0.53
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (118 bp):
AAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAATACTTTATTTGAAAATTTATTTCTAAGG
Found at i:19828548 original size:10 final size:10
Alignment explanation
Indices: 19828522--19828660 Score: 56
Period size: 10 Copynumber: 13.8 Consensus size: 10
19828512 AAAATAGAAT
19828522 AATAAAAA-A
1 AATAAAAATA
* *
19828531 AGTGAAAATA
1 AATAAAAATA
19828541 AATAAAAATA
1 AATAAAAATA
*
19828551 AA-AAAATTA
1 AATAAAAATA
* *
19828560 AAGAAAAGTAA
1 AATAAAAAT-A
*
19828571 AACAAAAATA
1 AATAAAAATA
19828581 AA-AACAAGATA
1 AATAA-AA-ATA
*
19828592 AAGAAAAA-A
1 AATAAAAATA
* *
19828601 TATTAAATGAATTT
1 -AATAAA--AA-TA
**
19828615 AATCTA-ATA
1 AATAAAAATA
19828624 AATAAAAATA
1 AATAAAAATA
*
19828634 AATAAAGATA
1 AATAAAAATA
*
19828644 AA-ACAAATA
1 AATAAAAATA
19828653 AATAAAAA
1 AATAAAAA
19828661 ATTTCAAAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 25
0.68 0.15 0.18
Matches are distributed among these distances:
9 29 0.30
10 45 0.47
11 15 0.16
12 4 0.04
13 3 0.03
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.19
Consensus pattern (10 bp):
AATAAAAATA
Found at i:19828553 original size:22 final size:23
Alignment explanation
Indices: 19828511--19828554 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19828501 TTTATTTAAA
19828511 GAAAATAGAATAATAAAAAAAGT
1 GAAAATAGAATAATAAAAAAAGT
*
19828534 GAAAATA-AATAAAAATAAAAA
1 GAAAATAGAATAATAA-AAAAA
19828555 AATTAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (23 bp):
GAAAATAGAATAATAAAAAAAGT
Found at i:19828593 original size:22 final size:21
Alignment explanation
Indices: 19828535--19828602 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 21
19828525 AAAAAAAGTG
* *
19828535 AAAATAAATAAAAAT-AA-AA
1 AAAATAAAGAAAAGTAAAGAA
*
19828554 AAATTAAAGAAAAGTAAA-ACA
1 AAAATAAAGAAAAGTAAAGA-A
19828575 AAAATAAA-AACAAGATAAAGAA
1 AAAATAAAGAA-AAG-TAAAGAA
19828597 AAAATA
1 AAAATA
19828603 TTAAATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.30
20 5 0.12
21 11 0.28
22 11 0.28
23 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAATAAAGAAAAGTAAAGAA
Found at i:19828760 original size:5 final size:5
Alignment explanation
Indices: 19828750--19828781 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
19828740 GGCTTGGGAA
*
19828750 GCTCG GCTCG GCTCG GCTTG GCTCG GCTCG GC
1 GCTCG GCTCG GCTCG GCTCG GCTCG GCTCG GC
19828782 ACGCGCGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.41, T:0.22
Consensus pattern (5 bp):
GCTCG
Found at i:19831551 original size:18 final size:18
Alignment explanation
Indices: 19831530--19831567 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19831520 AAAATATTAA
19831530 TATTAGAAAACTAAGAGT
1 TATTAGAAAACTAAGAGT
19831548 TATTAGAAAACTAAGAGT
1 TATTAGAAAACTAAGAGT
19831566 TA
1 TA
19831568 CAATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (18 bp):
TATTAGAAAACTAAGAGT
Found at i:19833311 original size:50 final size:50
Alignment explanation
Indices: 19832969--19833312 Score: 183
Period size: 50 Copynumber: 6.9 Consensus size: 50
19832959 AGATATTCGC
** *
19832969 TTCAAGGGTTTTGATG-CTT-ATTCTTGAATTGAATAA-ATTTAAACTTCAC
1 TTCAAGGGTTTTGATGACTTGA-TCTTGAATTGAA-AAGATTTGGACTTCAT
** * * * *
19833018 TTCAAGGGTTTACATGGCTTGATCTTGTATTGAATAA-ATTTGGACTTTAC
1 TTCAAGGGTTTTGATGACTTGATCTTGAATTGAA-AAGATTTGGACTTCAT
*** * * * * * **
19833068 TTCAAATTTTTTTTTTTTAT-AATTGGTCTTAAATTGAATAAG-TTTGGATTTTGT
1 TTC-AA----GGGTTTTGATGACTTGATCTTGAATTGAA-AAGATTTGGACTTCAT
* * * * * *
19833122 TTCAGGGGTCTTGATGATTTGGTCTTGAATT-AAAA-TTTTGGATTTCACT
1 TTCAAGGGTTTTGATGACTTGATCTTGAATTGAAAAGATTTGGACTTCA-T
* * * * *
19833171 TT-AAGGGTCTTTGATGACATGATTTTAAATTGAAGAA-A-TTAGACTTCAC
1 TTCAAGGGT-TTTGATGACTTGATCTTGAATTGAA-AAGATTTGGACTTCAT
* *
19833220 TTCAAGTGTTTTTGATGACTT--TCTTGAATTGAAGAGATTTGGACTTCAT
1 TTCAAG-GGTTTTGATGACTTGATCTTGAATTGAAAAGATTTGGACTTCAT
*
19833269 TTCAAGGGTTTTGATGACTTGATATTGAATTGAAAAGATTTGGA
1 TTCAAGGGTTTTGATGACTTGATCTTGAATTGAAAAGATTTGGA
19833313 TCCAAAATTT
Statistics
Matches: 225, Mismatches: 50, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
47 1 0.00
48 40 0.18
49 57 0.25
50 86 0.38
51 7 0.03
53 1 0.00
54 28 0.12
55 5 0.02
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (50 bp):
TTCAAGGGTTTTGATGACTTGATCTTGAATTGAAAAGATTTGGACTTCAT
Found at i:19833848 original size:36 final size:36
Alignment explanation
Indices: 19833766--19833868 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
19833756 TCTTCCCTGT
* *
19833766 TTGTCTTCTTGATCTTCATATCTTCATTCTCCAAGAG
1 TTGTCTTCTTGATCTTCAAATCTTCATT-TCCAAGAA
*
19833803 TTGTGTTCTTGATCTTCAAATCTTCATTTCCAAGAA
1 TTGTCTTCTTGATCTTCAAATCTTCATTTCCAAGAA
* * * *
19833839 TTGTCTTCTTGACCTTTAGATCTCCATTTC
1 TTGTCTTCTTGATCTTCAAATCTTCATTTC
19833869 TCGCGAATTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 32 0.55
37 26 0.45
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (36 bp):
TTGTCTTCTTGATCTTCAAATCTTCATTTCCAAGAA
Found at i:19835647 original size:17 final size:18
Alignment explanation
Indices: 19835627--19835663 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19835617 TTTTTATTTA
*
19835627 ATAAAAATTTA-AAAAAT
1 ATAAAAATTAATAAAAAT
19835644 ATAAAAATTAATAAAAAT
1 ATAAAAATTAATAAAAAT
19835662 AT
1 AT
19835664 TTAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAAATTAATAAAAAT
Found at i:19841877 original size:21 final size:20
Alignment explanation
Indices: 19841852--19841894 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19841842 ATAAATAAAA
19841852 TTATAAGAAAGATTAAATTTT
1 TTATAAGAAA-ATTAAATTTT
* * *
19841873 TTATATGATAATTTAATTTT
1 TTATAAGAAAATTAAATTTT
19841893 TT
1 TT
19841895 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TTATAAGAAAATTAAATTTT
Found at i:19842630 original size:86 final size:84
Alignment explanation
Indices: 19842466--19842741 Score: 308
Period size: 85 Copynumber: 3.3 Consensus size: 84
19842456 TCAATTAATT
* * * *
19842466 AAAAATTATTTTT-TAAATTCTAAAATTTCAACATAGTTACATTTTTAAAATAAAAAATATATTT
1 AAAAATTATTTTTCAAAATTCTAAAATTTCAACAAAATTACATTTTTAAAAT-AAAAATATATCT
**
19842530 ATGCTGAAAATATATTATAA
65 ATTTTGAAAATATATTATAA
*
19842550 AAAAATTATTTTTCAAAATTCTAAAATTTCAACAAACATTACATTTTGAAAATAAAAATATAGTC
1 AAAAATTATTTTTCAAAATTCTAAAATTTCAACAAA-ATTACATTTTTAAAATAAAAATATA-TC
* *
19842615 TATTTTAAAAATATATTAT-G
64 TATTTTGAAAATATATTATAA
* * * * * * * * *
19842635 AAAAGTTATTTTTTAAAATTTTATAGTTTCAACATAAACTATATTTTTAAGATAAAAATTTAATC
1 AAAAATTATTTTTCAAAATTCTAAAATTTCAACA-AAATTACATTTTTAAAATAAAAATAT-ATC
19842700 TATTTTGAAAATATA-T-TAA
64 TATTTTGAAAATATATTATAA
*
19842719 GAAAATTATTTTTCAAAATTCTA
1 AAAAATTATTTTTCAAAATTCTA
19842742 TAGATTCAAT
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
83 1 0.01
84 33 0.20
85 93 0.58
86 34 0.21
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (84 bp):
AAAAATTATTTTTCAAAATTCTAAAATTTCAACAAAATTACATTTTTAAAATAAAAATATATCTA
TTTTGAAAATATATTATAA
Found at i:19843641 original size:18 final size:16
Alignment explanation
Indices: 19843618--19843723 Score: 100
Period size: 18 Copynumber: 6.7 Consensus size: 16
19843608 AATTTTACTT
19843618 ATAAATAATATATTATTA
1 ATAAAT-ATATA-TATTA
19843636 ATAAATAATATACTATTA
1 ATAAAT-ATATA-TATTA
19843654 AT--ATA-ATATATTA
1 ATAAATATATATATTA
19843667 ATAAATA-ATATA--A
1 ATAAATATATATATTA
*
19843680 ATAAAAATAATATATTA
1 ATAAATAT-ATATATTA
19843697 ATAAATA-ATATTATTA
1 ATAAATATATA-TATTA
19843713 ATAAATATATA
1 ATAAATATATA
19843724 AAGAATAATA
Statistics
Matches: 77, Mismatches: 3, Indels: 17
0.79 0.03 0.18
Matches are distributed among these distances:
13 14 0.18
14 3 0.04
15 17 0.22
16 14 0.18
17 10 0.13
18 19 0.25
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATATATATATTA
Found at i:19843667 original size:13 final size:13
Alignment explanation
Indices: 19843622--19843722 Score: 61
Period size: 15 Copynumber: 7.7 Consensus size: 13
19843612 TTACTTATAA
19843622 ATAATATATT-AT
1 ATAATATATTAAT
*
19843634 -TAATA-AATAAT
1 ATAATATATTAAT
*
19843645 AT-A-CTATTAAT
1 ATAATATATTAAT
19843656 ATAATATATTAAT
1 ATAATATATTAAT
* *
19843669 AAATAATATAAATAAAA
1 --ATAATAT--ATTAAT
19843686 ATAATATATTAAT
1 ATAATATATTAAT
19843699 AAATAATATTATTAAT
1 --ATAATA-TATTAAT
19843715 A-AATATAT
1 ATAATATAT
19843723 AAAGAATAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
10 2 0.03
11 15 0.22
12 5 0.07
13 15 0.22
14 1 0.01
15 20 0.29
16 7 0.10
17 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATATATTAAT
Found at i:19843753 original size:50 final size:45
Alignment explanation
Indices: 19843638--19843737 Score: 128
Period size: 46 Copynumber: 2.1 Consensus size: 45
19843628 TATTATTAAT
* *
19843638 AAATAATATACTATTAATATAATATATTAATAAATAATATAAATAA
1 AAATAATATATTATTAA-ATAATATATTAATAAATAATAAAAATAA
*
19843684 AAATAATATATTAATAAATAATATTATTAATAAATATATAAAGAATAA
1 AAATAATATATTATTAAATAATA-TATTAATAAATA-ATAAA-AATAA
19843732 TAAATA
1 -AAATA
19843738 GTTTTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
45 6 0.13
46 27 0.57
47 4 0.09
48 5 0.11
49 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (45 bp):
AAATAATATATTATTAAATAATATATTAATAAATAATAAAAATAA
Found at i:19843766 original size:16 final size:16
Alignment explanation
Indices: 19843727--19843851 Score: 63
Period size: 16 Copynumber: 7.4 Consensus size: 16
19843717 ATATATAAAG
* *
19843727 AATAATAAATAGTTTT
1 AATATTAAATATTTTT
* *
19843743 ATTTTTAAATATTTTT
1 AATATTAAATATTTTT
* *
19843759 TATATTAACATAATATCTT
1 AATATTAA-AT-AT-TTTT
*
19843778 AATATTAAATGTTATTATT
1 AATATTAAA---TATTTTT
* * *
19843797 AAAAATAATTATTTTTT
1 AATATTAAATA-TTTTT
*
19843814 AATATT-AATAATTTT
1 AATATTAAATATTTTT
*
19843829 AATAATAAATAATTTTT
1 AATATTAAAT-ATTTTT
19843846 AATATT
1 AATATT
19843852 TTAATAGTTA
Statistics
Matches: 79, Mismatches: 21, Indels: 17
0.68 0.18 0.15
Matches are distributed among these distances:
15 9 0.11
16 25 0.32
17 20 0.25
18 3 0.04
19 19 0.24
20 2 0.03
21 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
AATATTAAATATTTTT
Found at i:19843822 original size:17 final size:15
Alignment explanation
Indices: 19843809--19843851 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
19843799 AAATAATTAT
19843809 TTTTTAATATTAATA
1 TTTTTAATATTAATA
* *
19843824 ATTTTAATAATAAATAA
1 TTTTTAAT-ATTAAT-A
19843841 TTTTTAATATT
1 TTTTTAATATT
19843852 TTAATAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTAATATTAATA
Found at i:19845911 original size:11 final size:10
Alignment explanation
Indices: 19845887--19845936 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 10
19845877 GAAGTTTATT
19845887 TAAAGAAAATAA
1 TAAA-AAAA-AA
19845899 TAACAAAAAAA
1 TAA-AAAAAAA
19845910 TAAAATAAAAA
1 TAAAA-AAAAA
19845921 T-AAAAAAAA
1 TAAAAAAAAA
19845930 TAAAAAA
1 TAAAAAA
19845937 TACTAAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 6 0.17
10 10 0.29
11 11 0.31
12 7 0.20
13 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:19845916 original size:19 final size:20
Alignment explanation
Indices: 19845892--19845943 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
19845882 TTATTTAAAG
*
19845892 AAAATAATAA-CAAAAAAAT
1 AAAATAATAATAAAAAAAAT
*
19845911 AAAATAAAAATAAAAAAAAT
1 AAAATAATAATAAAAAAAAT
*
19845931 AAAA-AATACTAAA
1 AAAATAATAATAAA
19845944 CAATTCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAATAATAATAAAAAAAAT
Found at i:19845930 original size:9 final size:9
Alignment explanation
Indices: 19845903--19845936 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
19845893 AAATAATAAC
19845903 AAAAAAATAA
1 AAAAAAAT-A
19845913 AATAAAAATA
1 AA-AAAAATA
19845923 AAAAAAATA
1 AAAAAAATA
19845932 AAAAA
1 AAAAA
19845937 TACTAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.52
10 5 0.22
11 6 0.26
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:19845936 original size:16 final size:16
Alignment explanation
Indices: 19845892--19845938 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
19845882 TTATTTAAAG
*
19845892 AAAATAATAACAAAA-A
1 AAAAAAATAA-AAAATA
*
19845908 AATAAAAT-AAAAATA
1 AAAAAAATAAAAAATA
19845923 AAAAAAATAAAAAATA
1 AAAAAAATAAAAAATA
19845939 CTAAACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 13 0.50
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:19846879 original size:20 final size:20
Alignment explanation
Indices: 19846825--19846886 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
19846815 AATCAAATAA
*
19846825 AAAAATGTTAATAGATAATT
1 AAAAATGTTAATAGATAAAT
**
19846845 AAAAA-AATAATTAGATAAAT
1 AAAAATGTTAA-TAGATAAAT
19846865 AAAAATGTTAATAGATAAAT
1 AAAAATGTTAATAGATAAAT
19846885 AA
1 AA
19846887 TAATAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAATGTTAATAGATAAAT
Found at i:19846890 original size:3 final size:3
Alignment explanation
Indices: 19846882--19846967 Score: 50
Period size: 3 Copynumber: 26.7 Consensus size: 3
19846872 TTAATAGATA
*
19846882 AAT AAT AAT AAT AAT AAT AGAT ATAT AAAC AGAT AAGT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT A-AT A-AT -AAT A-AT AA-T AAT AAT AAT
* * *
19846928 AAA AAT -AT ATT AAT AAAT AGT AAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT -AAT AAT AA
19846968 AAAAATATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
2 4 0.06
3 41 0.61
4 21 0.31
5 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:19846896 original size:20 final size:20
Alignment explanation
Indices: 19846833--19846967 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 20
19846823 AAAAAAATGT
* *
19846833 TAATAGATAATTAA-AAAAA
1 TAATAGATAAATAATAATAA
* **
19846852 TAATTAGATAAATAAAAATGT
1 TAA-TAGATAAATAATAATAA
19846873 TAATAGATAAATAATAATAA
1 TAATAGATAAATAATAATAA
*
19846893 TAATA-ATAGAT-AT-AT-A
1 TAATAGATAAATAATAATAA
* *
19846909 -AACAGATAAGTAATAATAAAA
1 TAATAGATAAATAATAAT--AA
* * * *
19846930 AAATATATTAATAAATAGTAA
1 TAATAGATAAAT-AATAATAA
*
19846951 TAATAAATAAATAATAA
1 TAATAGATAAATAATAA
19846968 AAAAATATAA
Statistics
Matches: 86, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
15 3 0.03
16 5 0.06
17 4 0.05
18 4 0.05
19 8 0.09
20 33 0.38
21 17 0.20
22 7 0.08
23 5 0.06
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.30
Consensus pattern (20 bp):
TAATAGATAAATAATAATAA
Found at i:19846962 original size:29 final size:29
Alignment explanation
Indices: 19846874--19846982 Score: 100
Period size: 29 Copynumber: 3.9 Consensus size: 29
19846864 TAAAAATGTT
* *
19846874 AATAGATAAAT-AATAATAATAAT-AATA
1 AATATATAAATAAATAGTAATAATAAATA
* * * *
19846901 GATATATAAACAGATAAGTAATAATAAAAA
1 AATATATAAATAAAT-AGTAATAATAAATA
*
19846931 AATATATTAATAAATAGTAATAATAAATA
1 AATATATAAATAAATAGTAATAATAAATA
* *
19846960 AATA-ATAAAAAAATA-TAAAAATA
1 AATATATAAATAAATAGTAATAATA
19846983 TAAAAAAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
27 15 0.23
28 11 0.17
29 25 0.38
30 14 0.22
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (29 bp):
AATATATAAATAAATAGTAATAATAAATA
Found at i:19846977 original size:13 final size:13
Alignment explanation
Indices: 19846921--19846977 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 13
19846911 CAGATAAGTA
19846921 ATAATAAAAAAAT
1 ATAATAAAAAAAT
* *
19846934 AT-ATTAATAAAT
1 ATAATAAAAAAAT
19846946 AGTAATAATAAATAA-
1 A-TAATAA-AAA-AAT
19846961 ATAATAAAAAAAT
1 ATAATAAAAAAAT
19846974 ATAA
1 ATAA
19846978 AAATATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
12 11 0.31
13 10 0.29
14 9 0.26
15 3 0.09
16 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:19846987 original size:16 final size:15
Alignment explanation
Indices: 19846949--19847019 Score: 65
Period size: 16 Copynumber: 4.7 Consensus size: 15
19846939 AATAAATAGT
* *
19846949 AATAATAAATA-AAT
1 AATAAAAAATATAAA
19846963 AATAAAAAAATATAAA
1 AAT-AAAAAATATAAA
*
19846979 AATATAAAAAAATAAA
1 AATA-AAAAATATAAA
* *
19846995 AATACAAAATAT-AG
1 AATAAAAAATATAAA
19847009 AATAAAAAATA
1 AATAAAAAATA
19847020 AAATAAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 14 0.30
15 14 0.30
16 19 0.40
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (15 bp):
AATAAAAAATATAAA
Found at i:19846987 original size:18 final size:18
Alignment explanation
Indices: 19846920--19846996 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
19846910 ACAGATAAGT
**
19846920 AATAATAAAAAAATATATT
1 AATAATAAAAAAATA-AAA
* *
19846939 AATAAATAGTAATAATAAATA
1 AAT-AATA-AAAAAATAAA-A
19846960 AATAATAAAAAAATATAAA
1 AATAATAAAAAAATA-AAA
19846979 AAT-ATAAAAAAATAAAA
1 AATAATAAAAAAATAAAA
19846996 A
1 A
19846997 TACAAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
17 4 0.08
18 11 0.23
19 13 0.27
20 11 0.23
21 9 0.19
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (18 bp):
AATAATAAAAAAATAAAA
Found at i:19846993 original size:40 final size:39
Alignment explanation
Indices: 19846920--19847027 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 39
19846910 ACAGATAAGT
** **
19846920 AATAATAAAAAAATATATTAATAAATAGTAATAATAAATA
1 AATAATAAAAAAATATAAAAATAAATAAAAATAA-AAATA
19846960 AATAATAAAAAAATATAAAAATATAA-AAAAATAAAAATA
1 AATAATAAAAAAATATAAAAATA-AATAAAAATAAAAATA
* *
19846999 CAA-AAT-ATAGAATA-AAAAATAAAATAAAA
1 -AATAATAAAAAAATATAAAAAT-AAATAAAA
19847028 CAAACTGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
37 8 0.14
38 11 0.19
39 8 0.14
40 29 0.50
41 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (39 bp):
AATAATAAAAAAATATAAAAATAAATAAAAATAAAAATA
Found at i:19847003 original size:8 final size:8
Alignment explanation
Indices: 19846957--19847019 Score: 60
Period size: 8 Copynumber: 8.1 Consensus size: 8
19846947 GTAATAATAA
19846957 ATAAATAAT
1 ATAAA-AAT
*
19846966 AAAAAAAT
1 ATAAAAAT
19846974 ATAAAAAT
1 ATAAAAAT
*
19846982 ATAAAAAA
1 ATAAAAAT
19846990 ATAAAAAT
1 ATAAAAAT
*
19846998 A-CAAAAT
1 ATAAAAAT
*
19847005 AT-AGAAT
1 ATAAAAAT
19847012 A-AAAAAT
1 ATAAAAAT
19847019 A
1 A
19847020 AAATAAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 16 0.36
8 25 0.56
9 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (8 bp):
ATAAAAAT
Found at i:19847021 original size:7 final size:7
Alignment explanation
Indices: 19846949--19847022 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 7
19846939 AATAAATAGT
*
19846949 AATAATA
1 AATAAAA
*
19846956 AATAAAT
1 AATAAAA
19846963 AATAAAAA
1 AAT-AAAA
19846971 AATATAAA
1 AATA-AAA
19846979 AATATAAA
1 AATA-AAA
*
19846987 AAAATAAA
1 AATA-AAA
*
19846995 AATACAA
1 AATAAAA
* *
19847002 AATATAG
1 AATAAAA
19847009 AATAAAA
1 AATAAAA
19847016 AATAAAA
1 AATAAAA
19847023 TAAAACAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
7 28 0.51
8 27 0.49
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (7 bp):
AATAAAA
Found at i:19847409 original size:41 final size:41
Alignment explanation
Indices: 19847309--19847471 Score: 168
Period size: 41 Copynumber: 3.9 Consensus size: 41
19847299 AAGTAAATTG
* * * ** *
19847309 CTCCTCTAATCAAAGGCTTTATGACTTTGAAAAATAAACAAA
1 CTCCTCTAATCAGAGGCATCACAACTTTGAAAAATAAAC-TA
*
19847351 GCTCCTCTAATCAGAGGC-TCAATAACTTTTG-AAAATAAACTA
1 -CTCCTCTAATCAGAGGCATC-ACAAC-TTTGAAAAATAAACTA
* * * * *
19847393 CTCCTCTAAACAGAGGCATCACAACTTTGAAGAATAGATTG
1 CTCCTCTAATCAGAGGCATCACAACTTTGAAAAATAAACTA
19847434 CTCCTCTAATCAGAGGCATCACAACTTTGAAAAATAAA
1 CTCCTCTAATCAGAGGCATCACAACTTTGAAAAATAAA
19847472 TTGTTTTTTG
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
40 4 0.04
41 62 0.60
42 4 0.04
43 29 0.28
44 4 0.04
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (41 bp):
CTCCTCTAATCAGAGGCATCACAACTTTGAAAAATAAACTA
Found at i:19848507 original size:10 final size:11
Alignment explanation
Indices: 19848503--19848563 Score: 72
Period size: 11 Copynumber: 5.4 Consensus size: 11
19848493 TTTTTTTTTC
19848503 TTTTTTCATTT
1 TTTTTTCATTT
19848514 TTTTTTCA-TT
1 TTTTTTCATTT
19848524 TTTTTTCATTTT
1 TTTTTTCA-TTT
19848536 TTTCATTTCATTT
1 TTT--TTTCATTT
19848549 TTTTTCTC-TTT
1 TTTTT-TCATTT
19848560 TTTT
1 TTTT
19848564 AAAGCATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.22
11 17 0.38
12 7 0.16
13 6 0.13
14 5 0.11
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:19848507 original size:11 final size:11
Alignment explanation
Indices: 19848493--19848563 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
19848483 TTTCATTCAC
*
19848493 TTTTTT-TTTC
1 TTTTTTCTTTT
*
19848503 TTTTTTCATTT
1 TTTTTTCTTTT
*
19848514 TTTTTTC-ATT
1 TTTTTTCTTTT
19848524 TTTTTTCATTTT
1 TTTTTTC-TTTT
19848536 TTTCATTTCATTTT
1 TTT--TTTC-TTTT
*
19848550 TTTTCTCTTTT
1 TTTTTTCTTTT
19848561 TTT
1 TTT
19848564 AAAGCATAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
10 15 0.29
11 16 0.31
12 8 0.16
14 12 0.24
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:19848508 original size:9 final size:9
Alignment explanation
Indices: 19848494--19848563 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
19848484 TTCATTCACT
19848494 TTTTTTTTC
1 TTTTTTTTC
*
19848503 TTTTTTCAT-
1 TTTTTT-TTC
19848512 TTTTTTTTC
1 TTTTTTTTC
19848521 ATTTTTTTTC
1 -TTTTTTTTC
*
19848531 ATTTTTTTC
1 TTTTTTTTC
* **
19848540 ATTTCATT-
1 TTTTTTTTC
*
19848548 TTTTTTCTC
1 TTTTTTTTC
19848557 TTTTTTT
1 TTTTTTT
19848564 AAAGCATAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
8 5 0.11
9 32 0.68
10 10 0.21
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:19848515 original size:19 final size:20
Alignment explanation
Indices: 19848488--19848538 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
19848478 TCCTTTTTCA
*
19848488 TTCACTTTTTTTT-TCTTTT
1 TTCATTTTTTTTTATCTTTT
*
19848507 TTCATTTTTTTTTCATTTTTT
1 TTCATTTTTTTTT-ATCTTTT
19848528 TTCATTTTTTT
1 TTCATTTTTTT
19848539 CATTTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCATTTTTTTTTATCTTTT
Found at i:19848515 original size:30 final size:29
Alignment explanation
Indices: 19848481--19848543 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
19848471 TGAGTCCTCC
19848481 TTTTTCATTCACTTTTTTTTTC-TTTTTTCA
1 TTTTTCATTCA--TTTTTTTTCATTTTTTCA
**
19848511 TTTTTTTTTCATTTTTTTTCATTTTTTTCA
1 TTTTTCATTCATTTTTTTTCA-TTTTTTCA
19848541 TTT
1 TTT
19848544 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.31
30 20 0.69
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTCATTCATTTTTTTTCATTTTTTCA
Found at i:19848517 original size:21 final size:21
Alignment explanation
Indices: 19848488--19848563 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 21
19848478 TCCTTTTTCA
19848488 TTCACTTTTTTTTTC---TTTT
1 TTCA-TTTTTTTTTCATTTTTT
19848507 TTCATTTTTTTTTCATTTTTT
1 TTCATTTTTTTTTCATTTTTT
19848528 TTCATTTTTTTCATTTCATTTTTT
1 TTCA-TTTTTT--TTTCATTTTTT
*
19848552 TTC-TCTTTTTTT
1 TTCATTTTTTTTT
19848564 AAAGCATAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
18 10 0.20
19 4 0.08
20 3 0.06
21 8 0.16
22 11 0.22
24 14 0.28
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (21 bp):
TTCATTTTTTTTTCATTTTTT
Found at i:19859082 original size:58 final size:56
Alignment explanation
Indices: 19859018--19859257 Score: 272
Period size: 58 Copynumber: 4.1 Consensus size: 56
19859008 TACTTTTGTA
* *
19859018 CAAGAAAAATTGATACTTTTAACTTTTTGCT-AAAATATTTTTTAGAAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTT-CTAAAAATATTTTTTAGAAA-TTTATTTT
* *
19859075 CGAAG-AAAATTGATACTTTCAAC-TTTTCTTCGAAAATATTTTTTAGAAAAAAAATTATTTT
1 C-AAGAAAAATTGATACTTTCAACTTTTTC-T-AAAAATATTTTTTAG----AAATTTATTTT
*
19859136 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAATCTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCT-AAAAATATTTTTTAGAAAT-TTATTTT
* *
19859194 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAATTTA-TTT
1 CAAGAAAAATTGATACTTTCAACTTTTTC-TAAAAATATTTTTTAGAAATTTATTTT
*
19859250 AAAGAAAA
1 CAAGAAAA
19859258 TAATAACAAA
Statistics
Matches: 162, Mismatches: 9, Indels: 25
0.83 0.05 0.13
Matches are distributed among these distances:
55 1 0.01
56 15 0.09
57 24 0.15
58 69 0.43
59 1 0.01
60 3 0.02
61 41 0.25
62 8 0.05
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (56 bp):
CAAGAAAAATTGATACTTTCAACTTTTTCTAAAAATATTTTTTAGAAATTTATTTT
Found at i:19859232 original size:119 final size:118
Alignment explanation
Indices: 19859018--19859242 Score: 332
Period size: 119 Copynumber: 1.9 Consensus size: 118
19859008 TACTTTTGTA
*
19859018 CAAGAAAAATTGATACTTTTAACTTTTTGCTAAAATATTTTTTAGAAACTTTAATTTCGAAGAAA
1 CAAGAAAAATTGATACTTTCAACTTTTTGCTAAAATATTTTTTAGAAACTTTAATTTCGAAGAAA
*
19859083 ATTGATACTTTCAACTTTTCTTCGAAAATATTTTTTAGAAAAAAAATTATTTT
66 ATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAAAAAATTATTTT
* *
19859136 CAAGGAAAATTGATACTTTCAACTTTTT-CTCAAAAATATTTTTTAGAAA-TCTTATTTTC-AAG
1 CAAGAAAAATTGATACTTTCAACTTTTTGCT--AAAATATTTTTTAGAAACT-TTAATTTCGAAG
*
19859198 AAAAATTGATACTTTCAACTTTTCCTT-AAAAATATTTTTTTGAAA
63 -AAAATTGATACTTTCAACTTTT-CTTCAAAAATATTTTTTAGAAA
19859243 TTTATTTAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
117 2 0.02
118 30 0.31
119 62 0.64
120 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (118 bp):
CAAGAAAAATTGATACTTTCAACTTTTTGCTAAAATATTTTTTAGAAACTTTAATTTCGAAGAAA
ATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAAAAAATTATTTT
Found at i:19859280 original size:10 final size:9
Alignment explanation
Indices: 19859254--19859331 Score: 84
Period size: 10 Copynumber: 8.2 Consensus size: 9
19859244 TTATTTAAAG
*
19859254 AAAATAATA
1 AAAAAAATA
*
19859263 ACAAAAATA
1 AAAAAAATA
19859272 AAGAAAAATA
1 AA-AAAAATA
*
19859282 AAGAAAATA
1 AAAAAAATA
19859291 AAATAAAATA
1 AAA-AAAATA
*
19859301 ATAAAAATA
1 AAAAAAATA
19859310 AAATAAAATA
1 AAA-AAAATA
19859320 AAATAAAATA
1 AAA-AAAATA
19859330 AA
1 AA
19859332 TACTAAACAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
9 24 0.41
10 35 0.59
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (9 bp):
AAAAAAATA
Found at i:19859288 original size:19 final size:18
Alignment explanation
Indices: 19859259--19859425 Score: 86
Period size: 19 Copynumber: 9.4 Consensus size: 18
19859249 TAAAGAAAAT
19859259 AATAACAAAAATAAAGA-AA
1 AATAA-AAAAATAAA-ATAA
19859278 AATAAAGAAAATAAAATAA
1 AATAAA-AAAATAAAATAA
19859297 AATAATAAAAATAAAATAA
1 AATAA-AAAAATAAAATAA
19859316 AAT---AAAATAAAATAA
1 AATAAAAAAATAAAATAA
* * ** **
19859331 ATACTAAACAATTCTAATTT
1 A-A-TAAAAAAATAAAATAA
*
19859351 AAT-AAATAATAATAAT-A
1 AATAAAAAAATAA-AATAA
*
19859368 AATAAATAAAT-AAAT-A
1 AATAAAAAAATAAAATAA
*
19859384 AATAAAAATAA-GAAATAAA
1 AATAAAAA-AATAAAAT-AA
*
19859403 AATAAATAAAT-AAAT-A
1 AATAAAAAAATAAAATAA
19859419 AATAAAA
1 AATAAAA
19859426 CTTGAGAACG
Statistics
Matches: 116, Mismatches: 17, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
15 13 0.11
16 19 0.16
17 15 0.13
18 17 0.15
19 44 0.38
20 8 0.07
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAAAAAATAAAATAA
Found at i:19859295 original size:5 final size:5
Alignment explanation
Indices: 19859266--19859331 Score: 84
Period size: 5 Copynumber: 13.6 Consensus size: 5
19859256 AATAATAACA
* *
19859266 AAAAT AAAGA- AAAAT -AAAG AAAAT AAAAT AAAAT AATA- AAAAT AAAAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
19859314 AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
19859332 TACTAAACAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 7 0.13
5 45 0.85
6 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:19859368 original size:13 final size:13
Alignment explanation
Indices: 19859350--19859416 Score: 80
Period size: 13 Copynumber: 4.8 Consensus size: 13
19859340 AATTCTAATT
*
19859350 TAATAAATAATAA
1 TAATAAATAAAAA
19859363 TAATAAATAAATAAA
1 TAATAAAT-AA-AAA
19859378 TAAATAAATAAAAA
1 T-AATAAATAAAAA
*
19859392 TAAGAAATAAAAA
1 TAATAAATAAAAA
19859405 TAAATAAATAAA
1 T-AATAAATAAA
19859417 TAAATAAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
13 20 0.43
14 15 0.32
15 5 0.11
16 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (13 bp):
TAATAAATAAAAA
Found at i:19859371 original size:4 final size:4
Alignment explanation
Indices: 19859351--19859424 Score: 86
Period size: 4 Copynumber: 19.5 Consensus size: 4
19859341 ATTCTAATTT
* *
19859351 AATA AAT- AAT- AAT- AATA AATA AATA AATA AATA AATA AAAA TAAGA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA -AATA
19859397 AAT- AA-A AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
19859425 ACTTGAGAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
3 13 0.21
4 47 0.75
5 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:19859591 original size:24 final size:22
Alignment explanation
Indices: 19859563--19859616 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 22
19859553 CAAGTTTGAG
19859563 TGAAAAAAAAAAGAAAAAATGAAA
1 TGAAAAAAAAAAG-AAAAA-GAAA
19859587 TGAAAAAAAAAAGAAAAAGAAA
1 TGAAAAAAAAAAGAAAAAGAAA
*
19859609 AGAAAAAA
1 TGAAAAAA
19859617 TGAATGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 11 0.38
23 5 0.17
24 13 0.45
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (22 bp):
TGAAAAAAAAAAGAAAAAGAAA
Found at i:19859592 original size:12 final size:11
Alignment explanation
Indices: 19859564--19859615 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
19859554 AAGTTTGAGT
*
19859564 GAAAAAAAAAA
1 GAAAAAGAAAA
*
19859575 GAAAAAATGAAAT
1 G-AAAAA-GAAAA
*
19859588 GAAAAAAAAAA
1 GAAAAAGAAAA
19859599 GAAAAAGAAAA
1 GAAAAAGAAAA
19859610 GAAAAA
1 GAAAAA
19859616 ATGAATGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 20 0.59
12 10 0.29
13 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:19859618 original size:30 final size:30
Alignment explanation
Indices: 19859565--19859630 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
19859555 AGTTTGAGTG
*
19859565 AAAAA-AAAAAGAAAAAATGAAATGAAAAA
1 AAAAAGAAAAAGAAAAAATAAAATGAAAAA
**
19859594 AAAAAGAAAAAGAAAAGAA-AAAATGAATGA
1 AAAAAGAAAAAGAAAA-AATAAAATGAAAAA
19859624 AAAAAGA
1 AAAAAGA
19859631 GGACTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 25 0.78
31 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAAATAAAATGAAAAA
Found at i:19860789 original size:85 final size:84
Alignment explanation
Indices: 19860637--19860962 Score: 291
Period size: 85 Copynumber: 4.0 Consensus size: 84
19860627 GTTAAGGAGT
* ** * * * *
19860637 ATTTACCTTTCCAAAGTTGTTGAGCCTCTGTTCAGATGAGCTTTAATTATTTTTCAAAGTCATTG
1 ATTTACCTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTG
19860702 AGCCTCTATTTAGGGGAGCA
66 AGCCTCTATTTA-GGGAGCA
* * *
19860722 ATTTACCTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAATGTCGCTG
1 ATTTACCTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTG
* *
19860787 AGCCTCTGTTTA-GAAG-A
66 AGCCTCTATTTAGGGAGCA
* * * *
19860804 GTTT-TC-TTT--AAGTCATTGAGCCTCTGTTTAGAGGAGC--AATTTATTTTTCAAAGTCGTTA
1 ATTTACCTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTG
*
19860863 AGCCTCTGA-TTAGAGGAGCT
66 AGCCTCT-ATTTAG-GGAGCA
* * * * * * * *
19860883 ATTTA-TTTTTCAAAATCATTGAGCCTCTGATTAGAAGAGC--CATTTA-TTTTCAAGGTCATGG
1 ATTTACCTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTG
*
19860944 AGCCTCTGTTTAGAGGAGC
66 AGCCTCTATTTAG-GGAGC
19860963 TTTGTTTATT
Statistics
Matches: 201, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
76 28 0.14
78 30 0.15
79 3 0.01
80 6 0.03
81 29 0.14
82 34 0.17
83 3 0.01
85 68 0.34
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (84 bp):
ATTTACCTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTG
AGCCTCTATTTAGGGAGCA
Found at i:19860790 original size:43 final size:41
Alignment explanation
Indices: 19860656--19861008 Score: 315
Period size: 41 Copynumber: 8.6 Consensus size: 41
19860646 TCCAAAGTTG
* * *
19860656 TTGAGCCTCTGTTCAGATGAGCTTTAATTATTTTTCAAAGTCA
1 TTGAGCCTCTGTTTAGAGGAGC--TATTTATTTTTCAAAGTCA
* * * * *
19860699 TTGAGCCTCTATTTAGGGGAGCAATTTACCTTTTCAAAGTCG
1 TTGAGCCTCTGTTTAGAGGAGCTATTTA-TTTTTCAAAGTCA
* *
19860741 TTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAATGTCG
1 TTGAGCCTCTGTTTAGAGGAGC--TATTTATTTTTCAAAGTCA
* * *
19860784 CTGAGCCTCTGTTTAGAAGAG---TTT-TCTTT--AAGTCA
1 TTGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCA
* *
19860819 TTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
1 TTGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCA
* * *
19860860 TTAAGCCTCTGATTAGAGGAGCTATTTATTTTTCAAAATCA
1 TTGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCA
* * * *
19860901 TTGAGCCTCTGATTAGAAGAGCCATTTA-TTTTCAAGGTCA
1 TTGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCA
* * * *
19860941 TGGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTTTTAAAGTCG
1 TTGAGCCTCTGTTTAGAGGAGC--TATTTA--TTTTTCAAAGTCA
* **
19860986 TTGAGCCTTTACTTAGAGGAGCT
1 TTGAGCCTCTGTTTAGAGGAGCT
19861009 TTGATCAAAA
Statistics
Matches: 252, Mismatches: 44, Indels: 28
0.78 0.14 0.09
Matches are distributed among these distances:
35 23 0.09
37 4 0.02
38 6 0.02
39 4 0.02
40 29 0.12
41 70 0.28
42 35 0.14
43 49 0.19
44 5 0.02
45 27 0.11
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (41 bp):
TTGAGCCTCTGTTTAGAGGAGCTATTTATTTTTCAAAGTCA
Found at i:19860830 original size:78 final size:76
Alignment explanation
Indices: 19860735--19860932 Score: 216
Period size: 76 Copynumber: 2.5 Consensus size: 76
19860725 TACCTTTTCA
* * * * *
19860735 AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAATGTCGCTGAGCCTCTGTTTAG
1 AAGTCATTGAGCCTCTGTTTAGAGGAGC--AATTTATTTTTCAAAGTCGCTAAGCCTCTGATTAG
19860800 AAGAGTTTTCTTT
64 AAGAGTTTTCTTT
* *
19860813 AAGTCATTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTTAAGCCTCTGATTAGAG
1 AAGTCATTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGCTAAGCCTCTGATTAGAA
*
19860878 GAGCTATTTATTTTT
66 GAG---TTT-TCTTT
* * * *
19860893 CAAAATCATTGAGCCTCTGATTAGAAGAGCCATTTATTTT
1 --AAGTCATTGAGCCTCTGTTTAGAGGAGCAATTTATTTT
19860933 CAAGGTCATG
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
76 34 0.33
78 27 0.26
79 3 0.03
80 4 0.04
82 34 0.33
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (76 bp):
AAGTCATTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGCTAAGCCTCTGATTAGAA
GAGTTTTCTTT
Found at i:19861230 original size:21 final size:20
Alignment explanation
Indices: 19861190--19861264 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 20
19861180 AATGGCCCAT
*
19861190 TTTATTTTTAGTTTTATTATC
1 TTTATTTTTA-TTTTATTATA
19861211 TTTATTTTT-TTATTATTTATA
1 TTTATTTTTATT-TTA-TTATA
* * * *
19861232 TATATTTTATATCTAATAATA
1 TTTATTTT-TATTTTATTATA
*
19861253 TATATTTTTATT
1 TTTATTTTTATT
19861265 AGTTATCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.05
20 6 0.14
21 32 0.73
22 3 0.07
23 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTATTTTTATTTTATTATA
Found at i:19861271 original size:27 final size:26
Alignment explanation
Indices: 19861241--19861424 Score: 104
Period size: 27 Copynumber: 7.3 Consensus size: 26
19861231 ATATATTTTA
* *
19861241 TATCTAATAATATATATTTTTATTAGT
1 TATCTATTAATAT-TATTTTTATTACT
* * *
19861268 TATCCATTAATGTTATTTTTTATTATT
1 TATCTATTAATATTA-TTTTTATTACT
* *
19861295 TATTTATTAATGTATATTTTT-TATACT
1 TATCTATTAATAT-TATTTTTAT-TACT
*
19861322 TATCTATTATTATTATTTTTA-T--T
1 TATCTATTAATATTATTTTTATTACT
* *
19861345 TATCTATCAATATT-TTTTTA-TATT
1 TATCTATTAATATTATTTTTATTACT
* *
19861369 TAT-TGATTAAT-GTATATATTATTA-T
1 TATCT-ATTAATATTAT-TTTTATTACT
* *
19861394 TAT-TATTACTATTATTATTATTA-T
1 TATCTATTAATATTATTTTTATTACT
19861418 TAT-TATT
1 TATCTATT
19861425 TTGGTTGGTT
Statistics
Matches: 129, Mismatches: 17, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
22 7 0.05
23 15 0.12
24 31 0.24
25 13 0.10
26 12 0.09
27 49 0.38
28 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (26 bp):
TATCTATTAATATTATTTTTATTACT
Found at i:19861325 original size:54 final size:52
Alignment explanation
Indices: 19861241--19861397 Score: 128
Period size: 47 Copynumber: 3.0 Consensus size: 52
19861231 ATATATTTTA
*
19861241 TATCTAAT-AATATATATTTTTATTAGTTATCCATTAATGTTATTTTTTATTATT
1 TATCT-ATCAATATAT-TTTTTA-TACTTATCCATTAATGTTATTTTTTATTATT
* * * *
19861295 TATTTATTAATGTATATTTTTTATACTTATCTATT-A--TTATTATTT-TTATT
1 TATCTATCAA--TATATTTTTTATACTTATCCATTAATGTTATTTTTTATTATT
* ** *
19861345 TATCTATCAATAT-TTTTTTATATTTATTGATTAATGTATATATTATTATTATT
1 TATCTATCAATATATTTTTTATACTTATCCATTAATGT-TAT-TTTTTATTATT
19861398 ATTACTATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
47 16 0.19
48 4 0.05
50 14 0.17
51 11 0.13
52 3 0.04
53 8 0.10
54 16 0.19
55 6 0.07
56 5 0.06
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (52 bp):
TATCTATCAATATATTTTTTATACTTATCCATTAATGTTATTTTTTATTATT
Found at i:19861334 original size:3 final size:3
Alignment explanation
Indices: 19861321--19861424 Score: 77
Period size: 3 Copynumber: 32.7 Consensus size: 3
19861311 TTTTTTATAC
* * * *
19861321 TTA TCTA TTA TTA TTA TTT TTA TTTA TCTA TCA ATA TT- TTT TTA -TA
1 TTA T-TA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA
*
19861367 TTTA TTGA TTAA TGTA TATA TTA TTA TTA TTA TTA CTA TTA TTA TTA
1 -TTA TT-A TT-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19861414 TTA TTA TTA TT
1 TTA TTA TTA TT
19861425 TTGGTTGGTT
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
2 4 0.05
3 56 0.68
4 21 0.26
5 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19861335 original size:23 final size:23
Alignment explanation
Indices: 19861308--19861371 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
19861298 TTATTAATGT
* *
19861308 ATATTTTTTATACTTATCTATTA
1 ATATTTTTTATATTTATCTATCA
*
19861331 TTATTATTTT-TATTTATCTATCA
1 ATATT-TTTTATATTTATCTATCA
19861354 ATATTTTTTTATATTTAT
1 ATA-TTTTTTATATTTAT
19861372 TGATTAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
ATATTTTTTATATTTATCTATCA
Found at i:19862199 original size:6 final size:6
Alignment explanation
Indices: 19862190--19862326 Score: 65
Period size: 6 Copynumber: 23.3 Consensus size: 6
19862180 TCTTTCTTAT
* * *
19862190 TTATTA TTATTA TTATTA TTATTA TTATTG TTGTTG TTATTTA TTGATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTA-TTA TT-ATTA
* ** * * * *
19862240 -GATTA GAATTA TTTAGTA TTCTTTA TT-TTA TT-TTA TTTTTA TTTTTA
1 TTATTA TTATTA -TTATTA TT-ATTA TTATTA TTATTA TTATTA TTATTA
* *
19862287 TTTTTA TCT-TTA TTTTTA TT-TTA TT-TTA TT-TTA TT-TTA TT
1 TTATTA T-TATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
19862327 TTTTGATTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
5 35 0.31
6 61 0.54
7 15 0.13
8 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.70
Consensus pattern (6 bp):
TTATTA
Found at i:19862207 original size:12 final size:11
Alignment explanation
Indices: 19862190--19862328 Score: 83
Period size: 12 Copynumber: 12.6 Consensus size: 11
19862180 TCTTTCTTAT
19862190 TTATTATTATTA
1 TTATT-TTATTA
19862202 TTATTATTATTA
1 TTATT-TTATTA
* *
19862214 TTATTGTTGTTG
1 TTATT-TTATTA
19862226 TTA-TTTATTGA
1 TTATTTTATT-A
** **
19862237 TTAGATTAGAA
1 TTATTTTATTA
*
19862248 TTA-TTTAGTA
1 TTATTTTATTA
*
19862258 TT-CTTTATT-
1 TTATTTTATTA
*
19862267 TTATTTTATTT
1 TTATTTTATTA
*
19862278 TTATTTTTATTT
1 TTA-TTTTATTA
*
19862290 TTATCTTTATTT
1 TTAT-TTTATTA
19862302 TTATTTTATT-
1 TTATTTTATTA
19862312 TTATTTTATT-
1 TTATTTTATTA
19862322 TTATTTT
1 TTATTTT
19862329 TTGATTTTCT
Statistics
Matches: 108, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
9 2 0.02
10 39 0.36
11 18 0.17
12 49 0.45
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:19862210 original size:15 final size:15
Alignment explanation
Indices: 19862190--19862326 Score: 65
Period size: 15 Copynumber: 9.3 Consensus size: 15
19862180 TCTTTCTTAT
19862190 TTATTATTATTATTA
1 TTATTATTATTATTA
*
19862205 TTATTATTATTATTG
1 TTATTATTATTATTA
* *
19862220 TTGTTGTTATTTATTGA
1 TTATTATTA-TTATT-A
* **
19862237 TTA-GATTAGAATTA
1 TTATTATTATTATTA
* *
19862251 TTTAGTATTCTTTATT-
1 -TTATTATT-ATTATTA
*
19862267 TTATT-TTATTTTTA
1 TTATTATTATTATTA
* *
19862281 TTTTTATTTTTATCT-
1 TTATTATTATTAT-TA
*
19862296 TTATTTTTATT-TTA
1 TTATTATTATTATTA
19862310 TT-TTATT-TTATT-
1 TTATTATTATTATTA
19862322 TTATT
1 TTATT
19862327 TTTTGATTTT
Statistics
Matches: 88, Mismatches: 23, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
12 4 0.05
13 13 0.15
14 10 0.11
15 44 0.50
16 12 0.14
17 5 0.06
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:19862336 original size:6 final size:5
Alignment explanation
Indices: 19862261--19862328 Score: 91
Period size: 5 Copynumber: 12.6 Consensus size: 5
19862251 TTTAGTATTC
19862261 TTTAT TTTAT TTTATT TTTATT TTTATT TTTAT CTTTATT TTTAT TTTAT
1 TTTAT TTTAT TTTA-T TTTA-T TTTA-T TTTAT -TTTA-T TTTAT TTTAT
19862311 TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
19862329 TTGATTTTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
5 34 0.57
6 25 0.42
7 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:19862395 original size:58 final size:56
Alignment explanation
Indices: 19862332--19862571 Score: 232
Period size: 58 Copynumber: 4.2 Consensus size: 56
19862322 TTATTTTTTG
** *
19862332 ATTTTCTTTAAACAAAATTCCCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTCTTTAAA-AAAATTTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCA
* * * * * *
19862390 ATTTTCCTTGAAAATAAGTTTTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTGTTA
1 ATTTT-CTTTAAAA-AAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCA
* * * *
19862448 ATTTTCCTTAAAAATTAGTTTTCTAAAAAATATTTTTGAGGAAAAGTGGAAAATATCA
1 ATTTTCTTTAAAAA--AATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCA
** * *
19862506 ATTTTTCTCGAAATTAAAA-TTTCAGAAAAATA-TTTTGGGGAAAAGTTGAAAATATCA
1 A-TTTTCTTTAAA--AAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCA
19862563 ATTTTCTTT
1 ATTTTCTTT
19862572 GTACAAAAGC
Statistics
Matches: 152, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
56 7 0.05
57 30 0.20
58 93 0.61
59 20 0.13
61 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (56 bp):
ATTTTCTTTAAAAAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCA
Found at i:19862550 original size:57 final size:58
Alignment explanation
Indices: 19862356--19862568 Score: 270
Period size: 58 Copynumber: 3.7 Consensus size: 58
19862346 AAATTCCCAA
* * *
19862356 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTAGAAATTAAGTTTTCT
* * * *
19862414 AAAAAATATTTTTGAGGAAAAGTTGAAAGTGTTAATTTTCCTTAAAAATT-AGTTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCC-TAGAAATTAAGTTTTCT
* * * **
19862472 AAAAAATATTTTTGAGGAAAAGTGGAAAATATCAATTTTTCTCGAAATTAAAATTTC-
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTAGAAATTAAGTTTTCT
*
19862529 AGAAAAATA-TTTTGGGGAAAAGTTGAAAATATCAATTTTC
1 A-AAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTC
19862569 TTTGTACAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 35 0.26
58 95 0.70
59 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (58 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTAGAAATTAAGTTTTCT
Found at i:19864478 original size:57 final size:57
Alignment explanation
Indices: 19864414--19864794 Score: 391
Period size: 57 Copynumber: 6.7 Consensus size: 57
19864404 TTTTGTGCAG
* *
19864414 GAAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTAGAAATTTTAATTTTGA
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTAGAAAATTTAATTTTAA
* * * **
19864471 GAAAAATTGATACTTTCTACTTTTTCCC-AAAATATCTTTT-GAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAAC-TTTTCCCTAAAATATTTTTTAGAAAATTTAATTTTAA
* * *
19864527 GGAAAATTGATACTTTCAACTTTT-CCTCAAAA-ACTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCT-AAAATA-TTTTTTAGAAAATTTAATTTTAA
* * * ** * **
19864584 GGAAAATTGATATTTTCAACTTTTCCCTAAAAATATTTTTTGGAAACCTTAAATTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTAGAAAATTTAATTTTAA
* ** *
19864642 GGAAAATTGATACTTTCAACTTTT-CCTCAAAA-ACCGTTTTA-AAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCT-AAAATA-TTTTTTAGAAAATTTAATTTTAA
* * * *
19864698 GAAAAATTGATATTTTTAACTTTTCCCTAAAA-ATATTTTTAGAAAGTTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAATAT-TTTTTAGAAAATTTAATTTTAA
* *
19864755 GAAAAATTGATACTTTCAATTTTTCCCAAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTT
19864795 TGGATTTTAT
Statistics
Matches: 271, Mismatches: 41, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
54 2 0.01
55 5 0.02
56 82 0.30
57 126 0.46
58 55 0.20
59 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTAGAAAATTTAATTTTAA
Found at i:19864704 original size:17 final size:18
Alignment explanation
Indices: 19864682--19864716 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19864672 AAACCGTTTT
19864682 AAAAATT-TATTTTTAAG
1 AAAAATTATATTTTTAAG
19864699 AAAAATTGATATTTTTAA
1 AAAAATT-ATATTTTTAA
19864717 CTTTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AAAAATTATATTTTTAAG
Found at i:19864706 original size:171 final size:171
Alignment explanation
Indices: 19864414--19864794 Score: 495
Period size: 171 Copynumber: 2.2 Consensus size: 171
19864404 TTTTGTGCAG
** * *
19864414 GAAAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTAGAAATTTTAATTTTGAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAACCTTAAATTCGAGAAAAAT
* * * * * *
19864478 TGATACTTTCTACTTTTTCCCAAAATATCTTTTGAAACTTTAATTTCGAGGAAAATTGATACTTT
66 TGATACTTTCAACTTTTTCCCAAAATACCTTTTAAAAATTTAATTTCAAGAAAAATTGATACTTT
*
19864543 CAACTTTT-CCTCAAAAACT-TTTTTTGAAAATTTATTTTTAA
131 CAACTTTTCCCT-AAAAA-TATTTTTAGAAAATTTATTTTTAA
* * * *
19864584 GGAAAATTGATATTTTCAACTTTTCCCTAAAAATATTTTTTGGAAACCTTAAATTCGAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAACCTTAAATTCGAGAAAAAT
* * *
19864649 TGATACTTTCAAC-TTTTCCTCAAAA-ACCGTTTTAAAAATTTATTTTTAAGAAAAATTGATATT
66 TGATACTTTCAACTTTTTCC-CAAAATACC-TTTTAAAAATTTAATTTCAAGAAAAATTGATACT
* *
19864712 TTTAACTTTTCCCTAAAAATATTTTTAGAAAGTTTATTTTTAA
129 TTCAACTTTTCCCTAAAAATATTTTTAGAAAATTTATTTTTAA
*
19864755 GAAAAATTGATACTTTCAATTTTTCCC-AAAAATATTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
19864795 TGGATTTTAT
Statistics
Matches: 183, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
170 48 0.26
171 132 0.72
172 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (171 bp):
GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAACCTTAAATTCGAGAAAAAT
TGATACTTTCAACTTTTTCCCAAAATACCTTTTAAAAATTTAATTTCAAGAAAAATTGATACTTT
CAACTTTTCCCTAAAAATATTTTTAGAAAATTTATTTTTAA
Found at i:19864819 original size:5 final size:5
Alignment explanation
Indices: 19864811--19864968 Score: 59
Period size: 5 Copynumber: 31.8 Consensus size: 5
19864801 TTATTTAAAG
*
19864811 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT -AAA- AAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAA-AT
* * * *
19864859 AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAAAT AAAAG AATAT
1 AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT -AAAAT AAAAT AAAAT
* * ** *
19864908 TAAAT AAACCT AATCT AATAAT -AAA- AAAAT -AAAT AAAAT -ATAT AAAA-
1 AAAAT AAA-AT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
19864955 AAAAT GAAAA- AAAA
1 AAAAT -AAAAT AAAA
19864969 CCTGAAATGG
Statistics
Matches: 115, Mismatches: 18, Indels: 41
0.66 0.10 0.24
Matches are distributed among these distances:
3 3 0.03
4 26 0.23
5 55 0.48
6 24 0.21
7 7 0.06
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:19864860 original size:17 final size:17
Alignment explanation
Indices: 19864841--19864901 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
19864831 AATAAAAGTG
19864841 AAAATAAAA-AAATAAA
1 AAAATAAAACAAATAAA
19864857 GAAAAGTAAAACAAA-AATA
1 -AAAA-TAAAACAAATAA-A
* * *
19864876 AAAATAAAATAAAGATA
1 AAAATAAAACAAATAAA
19864893 AAAATAAAA
1 AAAATAAAA
19864902 GAATATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 22 0.58
18 12 0.32
19 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.13
Consensus pattern (17 bp):
AAAATAAAACAAATAAA
Found at i:19864902 original size:40 final size:40
Alignment explanation
Indices: 19864806--19864888 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
19864796 GGATTTTATT
* *
19864806 TAAAGAAAATAAA-ATAA-TAAAACAAAATAAAAGTGAAAA
1 TAAA-AAAATAAAGAAAAGTAAAACAAAATAAAAATGAAAA
19864845 TAAAAAAATAAAGAAAAGTAAAACAAAAATAAAAAT-AAAA
1 TAAAAAAATAAAGAAAAGTAAAAC-AAAATAAAAATGAAAA
19864885 TAAA
1 TAAA
19864889 GATAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 8 0.21
39 7 0.18
40 14 0.36
41 10 0.26
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.14
Consensus pattern (40 bp):
TAAAAAAATAAAGAAAAGTAAAACAAAATAAAAATGAAAA
Found at i:19865855 original size:21 final size:20
Alignment explanation
Indices: 19865825--19865903 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
19865815 CAAATAAATA
19865825 AAATAAAAAATATTAATAGAT
1 AAAT-AAAAATATTAATAGAT
* *
19865846 AATTAGAAAA-A-AAATAAGAT
1 AAATA-AAAATATTAAT-AGAT
19865866 AAATAAAAAATATTACA-AGAT
1 AAAT-AAAAATATTA-ATAGAT
*
19865887 AAATAAAAATAATAATA
1 AAATAAAAATATTAATA
19865904 ACAGATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
19 4 0.09
20 23 0.50
21 17 0.37
22 1 0.02
23 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAAAATATTAATAGAT
Found at i:19865943 original size:25 final size:24
Alignment explanation
Indices: 19865857--19865979 Score: 91
Period size: 26 Copynumber: 5.2 Consensus size: 24
19865847 ATTAGAAAAA
19865857 AAATAAGATAAATAAAA-AATAT-T
1 AAAT-AGATAAATAAAATAATATAT
*
19865880 ACA-AGATAAATAAAAATAATA-AT
1 AAATAGATAAAT-AAAATAATATAT
* * *
19865903 -AACAGATAAAT--CATAATATAA
1 AAATAGATAAATAAAATAATATAT
19865924 AAAT-GAATAAATAATAATAAATATAT
1 AAATAG-ATAAATAA-AAT-AATATAT
*
19865950 AACTAGATAAATAAAATACATATAT
1 AAATAGATAAATAAAATA-ATATAT
19865975 AAATA
1 AAATA
19865980 TTAACAAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
20 6 0.08
21 10 0.13
22 13 0.17
23 15 0.19
24 1 0.01
25 15 0.19
26 17 0.22
27 1 0.01
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATAGATAAATAAAATAATATAT
Found at i:19865973 original size:51 final size:46
Alignment explanation
Indices: 19865862--19865978 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 46
19865852 AAAAAAAATA
* *
19865862 AGATAAATAAAA-AATATTACAA-GATAAATAAAAATAATAATAAC
1 AGATAAATAAAATAATATAAAAATGATAAATAAAAATAATAATAAC
* *
19865906 AGATAAAT--CATAATATAAAAATGAATAAATAATAATAAATATATAAC
1 AGATAAATAAAATAATATAAAAATG-ATAAATAAAAAT-AATA-ATAAC
*
19865953 TAGATAAATAAAATACATATATAAAT
1 -AGATAAATAAAATA-ATATAAAAAT
19865979 ATTAACAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
42 1 0.02
43 8 0.14
44 9 0.16
45 11 0.19
46 4 0.07
47 5 0.09
48 8 0.14
50 3 0.05
51 9 0.16
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (46 bp):
AGATAAATAAAATAATATAAAAATGATAAATAAAAATAATAATAAC
Found at i:19866000 original size:10 final size:9
Alignment explanation
Indices: 19865985--19866017 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
19865975 AAATATTAAC
19865985 AAAAAAGAAG
1 AAAAAAG-AG
19865995 AAAAAAGA-
1 AAAAAAGAG
19866003 AAAAAAGAG
1 AAAAAAGAG
19866012 AAAAAA
1 AAAAAA
19866018 TAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 7 0.32
10 7 0.32
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:19866072 original size:15 final size:15
Alignment explanation
Indices: 19866052--19866129 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 15
19866042 AATACATAGT
19866052 AATAATAAATAAATA
1 AATAATAAATAAATA
*
19866067 AATAATAAATACATA
1 AATAATAAATAAATA
**
19866082 AGATACA-AAGGAAA-A
1 A-ATA-ATAAATAAATA
19866097 AAT-AT--A-AAATA
1 AATAATAAATAAATA
19866108 AA-AATAAATAAATA
1 AATAATAAATAAATA
19866122 AAT-ATAAA
1 AATAATAAA
19866130 ATACAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 19
0.67 0.07 0.26
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 1 0.02
13 1 0.02
14 14 0.29
15 17 0.35
16 7 0.14
17 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.22
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:19866138 original size:18 final size:18
Alignment explanation
Indices: 19866055--19866141 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 18
19866045 ACATAGTAAT
19866055 AATAAATAAATAAATAATA
1 AATAAATAAATAAA-AATA
* **
19866074 AATACATAAGATACAAAGGA
1 AATAAATAA-ATA-AAAATA
*
19866094 AAAAATATAAAATAAAAATA
1 AATAA-AT-AAATAAAAATA
19866114 AATAAATAAATATAAAATA
1 AATAAATAAATA-AAAATA
*
19866133 CA-AAATAAA
1 AATAAATAAA
19866142 AGTAAAATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
18 12 0.22
19 17 0.31
20 16 0.30
21 7 0.13
22 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAATAAATAAAAATA
Found at i:19866443 original size:1 final size:1
Alignment explanation
Indices: 19866439--19866481 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
19866429 ATTTTTTTGC
* * * *
19866439 TTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19866482 AATTTGATCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:19866455 original size:20 final size:20
Alignment explanation
Indices: 19866430--19866473 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
19866420 TCAGAGGTAA
19866430 TTTTTTTGCTTTTTTTGTTT
1 TTTTTTTGCTTTTTTTGTTT
*
19866450 TTTTTTTGTTTTTTTTGTTT
1 TTTTTTTGCTTTTTTTGTTT
19866470 TTTT
1 TTTT
19866474 GTTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTTGTTT
Found at i:19866481 original size:8 final size:9
Alignment explanation
Indices: 19866430--19866481 Score: 70
Period size: 9 Copynumber: 5.7 Consensus size: 9
19866420 TCAGAGGTAA
19866430 TTTTTTTGCT
1 TTTTTTTG-T
*
19866440 TTTTTTGTTT
1 TTTTTT-TGT
19866450 TTTTTTTGT
1 TTTTTTTGT
19866459 TTTTTTTG-
1 TTTTTTTGT
19866467 TTTTTTTGT
1 TTTTTTTGT
19866476 TTTTTT
1 TTTTTT
19866482 AATTTGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
8 8 0.21
9 16 0.42
10 13 0.34
11 1 0.03
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:19866559 original size:43 final size:41
Alignment explanation
Indices: 19866494--19866576 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 41
19866484 TTTGATCAAA
*
19866494 GCTCCTTTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGA-AAA-ATAAATG
* *
19866537 GCTCCTCTAATCAGAGGTTCAACGACTTTGAAAAATAAAT
1 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAAT
19866577 AAACAGAGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 6 0.16
42 3 0.08
43 28 0.76
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAATG
Found at i:19866621 original size:41 final size:41
Alignment explanation
Indices: 19866576--19866654 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
19866566 GAAAAATAAA
*
19866576 TAAACAGAGGCACCACGACTTTAAAAAGTAAATTGCTCCTC
1 TAAACAGAAGCACCACGACTTTAAAAAGTAAATTGCTCCTC
**
19866617 TAAACAGAAGCACCACGACTTTGGAAAGTAAATTGCTC
1 TAAACAGAAGCACCACGACTTTAAAAAGTAAATTGCTC
19866655 ATTAACAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (41 bp):
TAAACAGAAGCACCACGACTTTAAAAAGTAAATTGCTCCTC
Found at i:19866635 original size:73 final size:75
Alignment explanation
Indices: 19866505--19866649 Score: 170
Period size: 73 Copynumber: 2.0 Consensus size: 75
19866495 CTCCTTTAAG
* * * **
19866505 CAGAGGCTCAACGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGTTCAACGACTTTGAAA
1 CAGAGGCACAACGACTTTGAGAAACATAAATGGCTCCTCTAAACAGAAGCACAACGACTTTGAAA
19866570 AATAAATAAA
66 AATAAATAAA
* * * *
19866580 CAGAGGCACCACGACTTT-A-AAA-AGTAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGA
1 CAGAGGCACAACGACTTTGAGAAACA-TAAATGGCTCCTCTAAACAGAAGCACAACGACTTTGAA
*
19866642 AAGTAAAT
65 AAATAAAT
19866650 TGCTCATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
72 1 0.02
73 41 0.69
74 1 0.02
75 16 0.27
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (75 bp):
CAGAGGCACAACGACTTTGAGAAACATAAATGGCTCCTCTAAACAGAAGCACAACGACTTTGAAA
AATAAATAAA
Found at i:19867667 original size:8 final size:8
Alignment explanation
Indices: 19867654--19867699 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
19867644 TTCATTCACT
*
19867654 TTTTTTTC
1 TTTTTTTA
*
19867662 TTTTTTCA
1 TTTTTTTA
19867670 TTTTTTTA
1 TTTTTTTA
19867678 TTTTTTTA
1 TTTTTTTA
19867686 TTTTTTTA
1 TTTTTTTA
19867694 TTTTTT
1 TTTTTT
19867700 CTTCTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:19876605 original size:27 final size:28
Alignment explanation
Indices: 19876546--19876598 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
19876536 TATTATGCTT
19876546 AAAAAAAGAGAAAAAATGAAATGAAAAA
1 AAAAAAAGAGAAAAAATGAAATGAAAAA
*
19876574 AAAAAAA-AGAAAAAGTG-AATGAAAA
1 AAAAAAAGAGAAAAAATGAAATGAAAA
19876599 CGGAAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 9 0.38
28 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (28 bp):
AAAAAAAGAGAAAAAATGAAATGAAAAA
Found at i:19877748 original size:41 final size:41
Alignment explanation
Indices: 19877606--19877886 Score: 287
Period size: 41 Copynumber: 6.7 Consensus size: 41
19877596 TTCACCTTTC
*
19877606 CAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTAA-TTATTTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGC---AATTTATTTTT
* * *
19877649 CAAAGTCGTTGAGCCTCTATTTAGAGGAGCAATTTACCTTTC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTA-TTTTT
*
19877691 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAACTTATTTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTT
* * * *
19877732 CAAAGTCGTTAAGCCTCCGATTAGAGGAGCCATTTATTTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTT
* * *
19877773 CAAAGTCATTGAGCCTCTGATTAGAGGAGCCATTTA-TTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTT
* * * * ***
19877813 CAAGGTCGTGGAGCCTCTATTTAGAGAAGTTTTGTTTATTTTTT
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAG--CAATTTA-TTTTT
* **
19877857 TAAAGTCGTTGAGCCTCTACTTAGAGGAGC
1 CAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
19877887 TTTGATCAAA
Statistics
Matches: 201, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.14
41 75 0.37
42 41 0.20
43 28 0.14
44 28 0.14
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (41 bp):
CAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTT
Found at i:19877767 original size:83 final size:82
Alignment explanation
Indices: 19877599--19877838 Score: 288
Period size: 83 Copynumber: 2.9 Consensus size: 82
19877589 ATGAGTATTC
* *
19877599 ACCTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTAATTATTTTTCAAAGTCGTTGAGCC
1 ACCTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC---AATTATTTTTCAAAGTCGTTAAGCC
*
19877664 TCTATTTAGAGGAGCAATTT
63 TCGATTTAGAGGAGCAATTT
19877684 ACCTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAACTTATTTTTCAAAGTCGTTAAGCCTC
1 ACCTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAA-TTATTTTTCAAAGTCGTTAAGCCT-
*
19877749 CGA-TTAGAGGAGCCATTT
64 CGATTTAGAGGAGCAATTT
* * * * * * **
19877767 A-TTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATT-TATTTTCAAGGTCGTGGAGCCTC
1 ACCTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTAT-TTTTCAAAGTCGTTAAGCCTC
*
19877830 TATTTAGAG
65 GATTTAGAG
19877839 AAGTTTTGTT
Statistics
Matches: 138, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
80 3 0.02
81 25 0.18
82 34 0.25
83 38 0.28
84 2 0.01
85 36 0.26
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (82 bp):
ACCTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTATTTTTCAAAGTCGTTAAGCCTCG
ATTTAGAGGAGCAATTT
Found at i:19878108 original size:3 final size:3
Alignment explanation
Indices: 19878067--19878288 Score: 77
Period size: 3 Copynumber: 71.7 Consensus size: 3
19878057 ATGGCCCATT
* * * *
19878067 TTA TTT TTA TTT TTA TTT TTA TTA TCT- TTA TT- TTT TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * * * *
19878110 TATA TTA -TA TCTA ATA ATA TATA TTT TTA TTA GTTA TCCA TTA ATA
1 T-TA TTA TTA T-TA TTA TTA T-TA TTA TTA TTA -TTA T-TA TTA TTA
* *
19878156 TTA TT- TTT TTA TTTA TTA TTG TATA TT- TT- TTA -TA CTTA TCTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA -TTA T-TA TTA
* * * *
19878201 TTA TTA TTA TTT TTA TTTA TCTA TCA ATA TT- TTT TTA -TA TTTA TTGA
1 TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TT-A
*
19878248 TTAA TGTA TATA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TT-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19878289 TTGGTTGGTT
Statistics
Matches: 166, Mismatches: 29, Indels: 48
0.68 0.12 0.20
Matches are distributed among these distances:
2 19 0.11
3 104 0.63
4 42 0.25
5 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19878115 original size:17 final size:17
Alignment explanation
Indices: 19878082--19878115 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19878072 TTTATTTTTA
* *
19878082 TTTTTATTATCTTTATT
1 TTTTTATTATATATATT
19878099 TTTTTATTATATATATT
1 TTTTTATTATATATATT
19878116 ATATCTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTATATATATT
Found at i:19878205 original size:23 final size:21
Alignment explanation
Indices: 19878149--19878205 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
19878139 TTAGTTATCC
* *
19878149 ATTAATATTATTTTTTTATTT
1 ATTATTATTATTTTTTTACTT
*
19878170 ATTATTGTATATTTTTTATACTT
1 ATTATTAT-TATTTTTT-TACTT
19878193 ATCTATTATTATT
1 AT-TATTATTATT
19878206 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 10 0.34
24 5 0.17
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATTATTATTTTTTTACTT
Found at i:19878234 original size:48 final size:48
Alignment explanation
Indices: 19878130--19878234 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
19878120 CTAATAATAT
* **
19878130 ATATTTTTATTAGTTATCCATTAATATTATTTTTTTATTTATTATTGT
1 ATATTTTTATTACTTATCCATTAATATTATTTTTTTATTTATTATTCA
* *
19878178 ATATTTTT-TATACTTATCTATTATTATTATTATTTTTATTTATCTA-TCA
1 ATATTTTTAT-TACTTATCCATTAATATTATT-TTTTTATTTAT-TATTCA
19878227 ATATTTTT
1 ATATTTTT
19878235 TTATATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 26 0.53
49 20 0.41
50 2 0.04
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (48 bp):
ATATTTTTATTACTTATCCATTAATATTATTTTTTTATTTATTATTCA
Found at i:19879129 original size:6 final size:6
Alignment explanation
Indices: 19879109--19879166 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
19879099 AATTGTTTAG
*
19879109 TATTCTT TA-TTT TATTTT TATTTT TATCTT TATTTT TA-TTT TA-TTT
1 TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
19879155 TA-TTT TATTTT T
1 TATTTT TATTTT T
19879167 TGATTTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
5 19 0.40
6 26 0.55
7 2 0.04
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:19879173 original size:6 final size:5
Alignment explanation
Indices: 19879114--19879165 Score: 68
Period size: 5 Copynumber: 9.6 Consensus size: 5
19879104 TTTAGTATTC
19879114 TTTAT TTTATT TTTATT TTTAT CTTTATT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTA-T TTTA-T TTTAT -TTTA-T TTTAT TTTAT TTTAT TTTAT
19879163 TTT
1 TTT
19879166 TTGATTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 24 0.55
6 19 0.43
7 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:19879342 original size:58 final size:58
Alignment explanation
Indices: 19879192--19879468 Score: 389
Period size: 58 Copynumber: 4.8 Consensus size: 58
19879182 AAAATTTCAA
* *
19879192 AAAAATATATTTTTGAGTAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
1 AAAAAT-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT
*
19879251 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT
1 -AAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT
* *
19879310 AAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAAATTTCCTTGAAAATAAGTTTTCT
1 AAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT
* * * * *
19879368 AAAAATTATTTTTGAGGAAAAGTTAAAAATATCAATTTTTCTCGAAATTAAAG-TTTC-
1 AAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAGTTTTCT
* *
19879425 AGAAAAATA-TTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 A-AAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
19879469 TACAAAAGCA
Statistics
Matches: 196, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
57 31 0.16
58 107 0.55
59 53 0.27
60 5 0.03
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (58 bp):
AAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCT
Found at i:19879547 original size:16 final size:16
Alignment explanation
Indices: 19879522--19879559 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19879512 AAGTTGAATC
19879522 ATTT-TTTTTCATTTT
1 ATTTCTTTTTCATTTT
*
19879537 ATTTCTTTTTCTTTTT
1 ATTTCTTTTTCATTTT
*
19879553 GTTTCTT
1 ATTTCTT
19879560 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTCTTTTTCATTTT
Found at i:19880909 original size:38 final size:38
Alignment explanation
Indices: 19880856--19880931 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
19880846 TGTTTCGTAT
* *
19880856 TCAAAGCAATTACTTCCAAGTTCCATCTAATTCTGCTA
1 TCAAAGCAATAACTTCCAACTTCCATCTAATTCTGCTA
19880894 TCAAAGCAATAACTTCCAACTTCCATCTAATTCTGCTA
1 TCAAAGCAATAACTTCCAACTTCCATCTAATTCTGCTA
19880932 ATGAAGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (38 bp):
TCAAAGCAATAACTTCCAACTTCCATCTAATTCTGCTA
Found at i:19883694 original size:2 final size:2
Alignment explanation
Indices: 19883687--19883730 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
19883677 CAACTCAAAG
* * *
19883687 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT CT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19883729 AT
1 AT
19883731 CGAGTGGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19885853 original size:99 final size:100
Alignment explanation
Indices: 19885739--19885926 Score: 231
Period size: 100 Copynumber: 1.9 Consensus size: 100
19885729 AATTCTCACT
* * *
19885739 AGTTTAAGAACAAAGATCAAGAACACAA-TTAAGAAAAAGAAAACAT-GAAGACAAATGG-G-AA
1 AGTTTAAGAACAAAGATCAAGAACACAACTAAAAAAAAAAAAAACATAG-AGACAAATGGTGTAA
*
19885800 ACATAAGATTTGAACAATCAAAATCTCTAAAAGCGTAA
65 A-A-AAGATTTGAAAAATCAAAATCTCTAAAAGCGTAA
* * * * * *
19885838 AGTTTAAGAATAAAGATTAAGAATATAACTAAAAAAAAAAAAAACCTAGAGATAAATGGTGTAAA
1 AGTTTAAGAACAAAGATCAAGAACACAACTAAAAAAAAAAAAAACATAGAGACAAATGGTGTAAA
19885903 AAAGATTTGAAAAATCAAAATCTC
66 AAAGATTTGAAAAATCAAAATCTC
19885927 CAAAGTTCTA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
99 24 0.32
100 45 0.60
101 3 0.04
102 3 0.04
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.20
Consensus pattern (100 bp):
AGTTTAAGAACAAAGATCAAGAACACAACTAAAAAAAAAAAAAACATAGAGACAAATGGTGTAAA
AAAGATTTGAAAAATCAAAATCTCTAAAAGCGTAA
Found at i:19886249 original size:28 final size:28
Alignment explanation
Indices: 19886214--19886423 Score: 128
Period size: 28 Copynumber: 7.6 Consensus size: 28
19886204 TGAAGATCTA
* *
19886214 AAAAATCCGTAAATTGATATCAAATTCT
1 AAAAATCCCTAAATTGAGATCAAATTCT
* * *
19886242 AAAAATCCCTAAAATAAGATCAAATTTT
1 AAAAATCCCTAAATTGAGATCAAATTCT
* * * * *
19886270 AAAAATCTCTAAATTGGGATTAAGTTCC
1 AAAAATCCCTAAATTGAGATCAAATTCT
* *
19886298 AAGAATCCCTAAATTGGGATCAAATT-T
1 AAAAATCCCTAAATTGAGATCAAATTCT
*
19886325 CAAGAATCCCTAAATTG-GAATCAAATT-T
1 -AAAAATCCCTAAATTGAG-ATCAAATTCT
* * * *
19886353 CAAGAA--CTTAAATT-AGGATAAAATTCC
1 -AAAAATCCCTAAATTGA-GATCAAATTCT
* * *
19886380 AAAAATCACTAAATTGAAACCAAATT-T
1 AAAAATCCCTAAATTGAGATCAAATTCT
* *
19886407 CAAGAATCCTTAAATTG
1 -AAAAATCCCTAAATTG
19886424 GGGCTAAGTT
Statistics
Matches: 142, Mismatches: 31, Indels: 18
0.74 0.16 0.09
Matches are distributed among these distances:
26 18 0.13
27 2 0.01
28 121 0.85
29 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (28 bp):
AAAAATCCCTAAATTGAGATCAAATTCT
Found at i:19886392 original size:54 final size:55
Alignment explanation
Indices: 19886270--19886422 Score: 164
Period size: 54 Copynumber: 2.8 Consensus size: 55
19886260 ATCAAATTTT
* * * * * * * * *
19886270 AAAAATCTCTAAATTGGGATTAAGTTCCAAGAATCCCTAAATTGGGATCAAATTTC
1 AAAAATCACTAAATTGGAATCAAATTTCAAGAA-CCTTAAATTAGGATAAAATTCC
* *
19886326 AAGAATCCCTAAATTGGAATCAAATTTCAAGAA-CTTAAATTAGGATAAAATTCC
1 AAAAATCACTAAATTGGAATCAAATTTCAAGAACCTTAAATTAGGATAAAATTCC
* *
19886380 AAAAATCACTAAATTGAAACCAAATTTCAAGAATCCTTAAATT
1 AAAAATCACTAAATTGGAATCAAATTTCAAGAA-CCTTAAATT
19886423 GGGGCTAAGT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
54 46 0.57
56 35 0.43
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (55 bp):
AAAAATCACTAAATTGGAATCAAATTTCAAGAACCTTAAATTAGGATAAAATTCC
Done.