Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 56 of 187
Found at i:16611673 original size:18 final size:18
Alignment explanation
Indices: 16611625--16611691 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
16611615 TAAAAAAAAT
* *
16611625 ATTTTAATAATTTTTGATA
1 ATTTT-ATAATTGTTAATA
*
16611644 AATTTATAAATTGTTAATA
1 ATTTTAT-AATTGTTAATA
*
16611663 ATTTTATAATTTGATAA-A
1 ATTTTATAA-TTGTTAATA
*
16611681 TTTTTATAATT
1 ATTTTATAATT
16611692 ATATACATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 13 0.32
19 25 0.62
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTTTATAATTGTTAATA
Found at i:16611702 original size:26 final size:27
Alignment explanation
Indices: 16611644--16611696 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
16611634 ATTTTTGATA
*
16611644 AATTT-ATAAATTGTTAATAATTTTAT
1 AATTTGATAAATTGTTAATAATTATAT
*
16611670 AATTTGATAAATT-TTTATAATTATAT
1 AATTTGATAAATTGTTAATAATTATAT
16611696 A
1 A
16611697 CATTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
AATTTGATAAATTGTTAATAATTATAT
Found at i:16617554 original size:31 final size:31
Alignment explanation
Indices: 16617519--16617577 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
16617509 TAGCTCAATG
16617519 ACTTAAATAAAAACTTTCAAATAGTTCAGTA
1 ACTTAAATAAAAACTTTCAAATAGTTCAGTA
* *
16617550 ACTTAAATGAAAACTTTCGAATAGTTCA
1 ACTTAAATAAAAACTTTCAAATAGTTCA
16617578 ATTACCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGTTCAGTA
Found at i:16624914 original size:6 final size:6
Alignment explanation
Indices: 16624903--16624947 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
16624893 TAAGTCCGTA
16624903 TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTA
1 TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTAAAC TTA
16624948 CTGTAATTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAC
Found at i:16631236 original size:27 final size:27
Alignment explanation
Indices: 16631190--16631447 Score: 267
Period size: 27 Copynumber: 9.6 Consensus size: 27
16631180 AGACTTTAGA
*
16631190 CATA-GGTAAAATGATCGAAATACCCT
1 CATAGGGTAAAATGACCGAAATACCCT
* **
16631216 CAGAGGGTAAAATGATTGAAATACCC-
1 CATAGGGTAAAATGACCGAAATACCCT
* *
16631242 CTATAGGGTAAAATAACCGAAATACCCC
1 C-ATAGGGTAAAATGACCGAAATACCCT
* **
16631270 CATAGGGTAAAATAAATGAAATACCCT
1 CATAGGGTAAAATGACCGAAATACCCT
* *
16631297 CATAAGGTAAAATAACCGAAATACCCT
1 CATAGGGTAAAATGACCGAAATACCCT
*
16631324 CATAGGGTAAAATGACCAAAATA-CCT
1 CATAGGGTAAAATGACCGAAATACCCT
**
16631350 CCATAGGGTAAAATGACTTAAATACCC-
1 -CATAGGGTAAAATGACCGAAATACCCT
* * *
16631377 CTTTAGGGTAAAATTACCAAAATA-CCT
1 C-ATAGGGTAAAATGACCGAAATACCCT
*
16631404 CCATAGGGTAAAATTACCGAAATATCCCT
1 -CATAGGGTAAAATGACCGAAATA-CCCT
16631433 -ATAGGGTAAAATGAC
1 CATAGGGTAAAATGAC
16631448 TGTTATACCC
Statistics
Matches: 198, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.05
27 181 0.91
28 4 0.02
29 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (27 bp):
CATAGGGTAAAATGACCGAAATACCCT
Found at i:16631880 original size:29 final size:32
Alignment explanation
Indices: 16631847--16631905 Score: 88
Period size: 29 Copynumber: 1.9 Consensus size: 32
16631837 GATCTGCACT
*
16631847 GATTAATGAT-TT-TATACTGTT-ACTACATC
1 GATTAATGATATTACATACTGTTCACTACATC
16631876 GATTAATGATATTACATACTGTTCACTACA
1 GATTAATGATATTACATACTGTTCACTACA
16631906 AGATTGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 2 0.08
31 8 0.31
32 6 0.23
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (32 bp):
GATTAATGATATTACATACTGTTCACTACATC
Found at i:16631956 original size:33 final size:35
Alignment explanation
Indices: 16631910--16631981 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
16631900 ACTACAAGAT
* ** *
16631910 TGATATCTGTTACTGTTA-TGGGCCAAGGCCCCAC
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCCAC
*
16631944 TGATA-CTATTACTGAAATTGGGCAAAGGCCCTAC
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCCAC
16631978 TGAT
1 TGAT
16631982 TGCTGGCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 9 0.28
34 23 0.72
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (35 bp):
TGATATCTATTACTGAAATTGGGCAAAGGCCCCAC
Found at i:16639234 original size:16 final size:17
Alignment explanation
Indices: 16639204--16639236 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
16639194 TTTTGGATTT
16639204 AATTGAATAGAGTGAAA
1 AATTGAATAGAGTGAAA
16639221 AATTGAAT-GAGTGAAA
1 AATTGAATAGAGTGAAA
16639237 TTTGATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AATTGAATAGAGTGAAA
Found at i:16650241 original size:13 final size:13
Alignment explanation
Indices: 16650220--16650249 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16650210 TATTGTATAA
16650220 TTTTCTCTTTAGT
1 TTTTCTCTTTAGT
*
16650233 TTTTGTCTTTAGT
1 TTTTCTCTTTAGT
16650246 TTTT
1 TTTT
16650250 TTCCCATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (13 bp):
TTTTCTCTTTAGT
Found at i:16651854 original size:30 final size:30
Alignment explanation
Indices: 16651820--16651878 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
16651810 GAGGCATCTT
* *
16651820 TTTTATCAGAGATCGCCACAAAGGCTTTCA
1 TTTTAACAGAGATCACCACAAAGGCTTTCA
* * *
16651850 TTTTAACAGAGTTCACCATAAAGGTTTTC
1 TTTTAACAGAGATCACCACAAAGGCTTTC
16651879 TTACGGAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (30 bp):
TTTTAACAGAGATCACCACAAAGGCTTTCA
Found at i:16652045 original size:29 final size:29
Alignment explanation
Indices: 16651987--16652071 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
16651977 AAGGTATTTC
* *
16651987 TTTAACAGAGATAGCCATAATGACTCACT
1 TTTAACAGAGATAGCCACAAAGACTCACT
* *
16652016 TTTAACTGAGATAGCCACAAAGGCAT-AC-
1 TTTAACAGAGATAGCCACAAAGAC-TCACT
* *
16652044 TTT--CAGAGATAGCCACAGAGGCTCACT
1 TTTAACAGAGATAGCCACAAAGACTCACT
16652071 T
1 T
16652072 ATATGGTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 1 0.02
26 19 0.40
27 1 0.02
28 3 0.06
29 22 0.47
30 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (29 bp):
TTTAACAGAGATAGCCACAAAGACTCACT
Found at i:16653687 original size:2 final size:2
Alignment explanation
Indices: 16653680--16653725 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
16653670 TTGGAGGAGT
16653680 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16653722 AG AG
1 AG AG
16653726 CAACAACAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16654424 original size:45 final size:45
Alignment explanation
Indices: 16654357--16654448 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
16654347 GTCTAGGGAA
* *
16654357 AGAGTTTTGGGCTGAAGTCGTAAATTTAGTAA-ATTTGGTAAACT
1 AGAGTTTTGGGCTGAAGCCGTAAATTTAGCAACATTTGGTAAACT
*
16654401 NAGAGTTTTGGGCTGGAGCCGTAAATTTAGCAAGCTATTTGGTAAACT
1 -AGAGTTTTGGGCTGAAGCCGTAAATTTAGCAA-C-ATTTGGTAAACT
16654449 GATCTCCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 29 0.71
48 12 0.29
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.34
Consensus pattern (45 bp):
AGAGTTTTGGGCTGAAGCCGTAAATTTAGCAACATTTGGTAAACT
Found at i:16662283 original size:13 final size:13
Alignment explanation
Indices: 16662267--16662336 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
16662257 AAAACAAGTG
16662267 AGGAAAAAGAAAA
1 AGGAAAAAGAAAA
*
16662280 AGG-AAAAGAGAA
1 AGGAAAAAGAAAA
*
16662292 AGAGAAAAA-TAAA
1 AG-GAAAAAGAAAA
16662305 AGTGAAAAAGAAGAAA
1 AG-GAAAAAG-A-AAA
* *
16662321 ATGAAAATGAAAA
1 AGGAAAAAGAAAA
16662334 AGG
1 AGG
16662337 CGAAAAGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
12 10 0.23
13 19 0.43
14 5 0.11
15 6 0.14
16 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (13 bp):
AGGAAAAAGAAAA
Found at i:16662305 original size:19 final size:20
Alignment explanation
Indices: 16662269--16662316 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
16662259 AACAAGTGAG
16662269 GAAAAAGAAAAAGGAAAAGA
1 GAAAAAGAAAAAGGAAAAGA
* * *
16662289 GAAAGAGAAAAA-TAAAAGT
1 GAAAAAGAAAAAGGAAAAGA
16662308 GAAAAAGAA
1 GAAAAAGAA
16662317 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (20 bp):
GAAAAAGAAAAAGGAAAAGA
Found at i:16662342 original size:21 final size:22
Alignment explanation
Indices: 16662269--16662335 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
16662259 AACAAGTGAG
* *
16662269 GAAAAAG-A-AAAAGGAAAAGA
1 GAAAAAGAAGAAAATGAAAAGT
*
16662289 GAAAGAG-A-AAAAT-AAAAGT
1 GAAAAAGAAGAAAATGAAAAGT
16662308 GAAAAAGAAGAAAATGAAAA-T
1 GAAAAAGAAGAAAATGAAAAGT
16662329 GAAAAAG
1 GAAAAAG
16662336 GCGAAAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.28
20 12 0.30
21 13 0.32
22 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (22 bp):
GAAAAAGAAGAAAATGAAAAGT
Found at i:16662347 original size:21 final size:21
Alignment explanation
Indices: 16662307--16662347 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16662297 AAAATAAAAG
* *
16662307 TGAAAAAGAAGAAAATGAAAA
1 TGAAAAAGGAGAAAAGGAAAA
*
16662328 TGAAAAAGGCGAAAAGGAAA
1 TGAAAAAGGAGAAAAGGAAA
16662348 GCGAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.07
Consensus pattern (21 bp):
TGAAAAAGGAGAAAAGGAAAA
Found at i:16666550 original size:21 final size:22
Alignment explanation
Indices: 16666505--16666550 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
16666495 AGAGAAAAAT
*
16666505 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
16666527 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
16666548 AAA
1 AAA
16666551 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:16666649 original size:36 final size:33
Alignment explanation
Indices: 16666584--16666650 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
16666574 GTGAATGAAG
*
16666584 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
16666617 TGAGTGAAGAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
16666651 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.31, T:0.12
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:16667739 original size:24 final size:24
Alignment explanation
Indices: 16667707--16667754 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16667697 AGGAATTTGT
16667707 TAGCAAGGCCTTAGATGCGTACAC
1 TAGCAAGGCCTTAGATGCGTACAC
16667731 TAGCAAGGCCTTAGATGCGTACAC
1 TAGCAAGGCCTTAGATGCGTACAC
16667755 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (24 bp):
TAGCAAGGCCTTAGATGCGTACAC
Found at i:16681439 original size:17 final size:18
Alignment explanation
Indices: 16681401--16681441 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
16681391 GAAAAATATT
*
16681401 TATATTAAATTAAATTTA
1 TATATTTAATTAAATTTA
*
16681419 -ATATTTAA-TAATTTTA
1 TATATTTAATTAAATTTA
16681435 TATATTT
1 TATATTT
16681442 TCATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTTAATTAAATTTA
Found at i:16689695 original size:40 final size:40
Alignment explanation
Indices: 16689610--16689739 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
16689600 CAGCGACATG
* * * *
16689610 TATGTGCATTTAGGGGTA-TCAAAGTAAAAATAGGTGTACG
1 TATGTGCATTTAGGGGTACT-AAAGTACAAATAGGGGCACA
* *
16689650 CATGTGCATTTAGGGGTACTAAAGTACAAATAGGGGCACT
1 TATGTGCATTTAGGGGTACTAAAGTACAAATAGGGGCACA
* * * * * * *
16689690 TATGTGTATTCAGAGGTACCAAAGTCCAAATCGAGGCACA
1 TATGTGCATTTAGGGGTACTAAAGTACAAATAGGGGCACA
16689730 TATGTGCATT
1 TATGTGCATT
16689740 CATATATAAC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
40 73 0.99
41 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (40 bp):
TATGTGCATTTAGGGGTACTAAAGTACAAATAGGGGCACA
Found at i:16694525 original size:23 final size:23
Alignment explanation
Indices: 16694480--16694527 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16694470 TGTTACTTGC
* *
16694480 ATGTTTTTATTTTTTTCTGTTAT
1 ATGTATTTATTTTTATCTGTTAT
16694503 ATGTATTTATTTTTATC-GCTTAT
1 ATGTATTTATTTTTATCTG-TTAT
16694526 AT
1 AT
16694528 ATAAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (23 bp):
ATGTATTTATTTTTATCTGTTAT
Found at i:16694772 original size:22 final size:22
Alignment explanation
Indices: 16694747--16694804 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
16694737 GCCATCGCAT
16694747 ACGGCGGTGCCGGCGCCGGAGA
1 ACGGCGGTGCCGGCGCCGGAGA
16694769 ACGGCGGTGCCGGCGCCGGAGA
1 ACGGCGGTGCCGGCGCCGGAGA
16694791 ACGGC-G-GCCGGCGC
1 ACGGCGGTGCCGGCGC
16694805 AGTGGCCGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.22
21 1 0.03
22 27 0.75
ACGTcount: A:0.12, C:0.34, G:0.50, T:0.03
Consensus pattern (22 bp):
ACGGCGGTGCCGGCGCCGGAGA
Found at i:16697532 original size:22 final size:24
Alignment explanation
Indices: 16697498--16697541 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
16697488 GAAATATCCC
*
16697498 TAAAAATGTTATTCTAA-AAATCT
1 TAAAAATGATATTCTAATAAATCT
*
16697521 TAAAAAT-ATATTTTAATAAAT
1 TAAAAATGATATTCTAATAAAT
16697542 AATAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAAATGATATTCTAATAAATCT
Found at i:16698359 original size:20 final size:20
Alignment explanation
Indices: 16698334--16698373 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16698324 TTGAGAGTAA
16698334 AGGGGGAGAAGT-AAAAGTTT
1 AGGGGGAGAA-TAAAAAGTTT
16698354 AGGGGGAGAATAAAAAGTTT
1 AGGGGGAGAATAAAAAGTTT
16698374 TGGGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (20 bp):
AGGGGGAGAATAAAAAGTTT
Found at i:16698384 original size:17 final size:17
Alignment explanation
Indices: 16698337--16698389 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
16698327 AGAGTAAAGG
*
16698337 GGGAGAAGTAAAAGTTTAGG
1 GGGAGAA-TAAAAGTTT--T
16698357 GGGAGAATAAAAAGTTTT
1 GGGAGAAT-AAAAGTTTT
16698375 GGGA-AATAAAAGTTT
1 GGGAGAATAAAAGTTT
16698390 GAAGGAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 8 0.26
17 3 0.10
18 4 0.13
19 1 0.03
20 15 0.48
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (17 bp):
GGGAGAATAAAAGTTTT
Found at i:16701759 original size:14 final size:15
Alignment explanation
Indices: 16701714--16701767 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
16701704 TAGAGACAAA
16701714 AATAAAATTTTAAAAT
1 AATAAAA-TTTAAAAT
* * *
16701730 GATAAAGTCCTAAAAT
1 AATAAAAT-TTAAAAT
16701746 AA-AAAATTTAAAAT
1 AATAAAATTTAAAAT
16701760 AATAAAAT
1 AATAAAAT
16701768 AACGTAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.27
15 10 0.33
16 12 0.40
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (15 bp):
AATAAAATTTAAAAT
Found at i:16702475 original size:9 final size:9
Alignment explanation
Indices: 16702461--16702498 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
16702451 TGGTTAAAAT
16702461 TTAACCGAA
1 TTAACCGAA
16702470 TTAACCGAA
1 TTAACCGAA
*
16702479 TTACCCGAA
1 TTAACCGAA
*
16702488 TTAATCGAA
1 TTAACCGAA
16702497 TT
1 TT
16702499 GAATCACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (9 bp):
TTAACCGAA
Found at i:16702633 original size:18 final size:18
Alignment explanation
Indices: 16702593--16702636 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16702583 AATTTTTATG
**
16702593 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
16702611 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
16702629 CTTGGGTT
1 ATTGGGTT
16702637 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:16704399 original size:40 final size:40
Alignment explanation
Indices: 16704355--16704469 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 40
16704345 CCCTTGATTG
* * *
16704355 CACTTCGGTGTTCCTATTTGCACAACTGTGCCTCTGTAAA
1 CACTTCGGTGTTCCTGTTTGCACAACTATGCCCCTGTAAA
* ** *
16704395 CACTTTGGTGTTCCTGTTTGCACATTTAAGCCCCTGTAAA
1 CACTTCGGTGTTCCTGTTTGCACAACTATGCCCCTGTAAA
*
16704435 CAATTCGGTG-TCCTTGTTTGCACAACTATGCCCCT
1 CACTTCGGTGTTCC-TGTTTGCACAACTATGCCCCT
16704470 AAATGCACTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
39 3 0.05
40 59 0.95
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (40 bp):
CACTTCGGTGTTCCTGTTTGCACAACTATGCCCCTGTAAA
Found at i:16704498 original size:40 final size:40
Alignment explanation
Indices: 16704454--16704538 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
16704444 GTCCTTGTTT
* *
16704454 GCACAACTATGCCCCTAAATGCACTCTGGTGCTCCTGATA
1 GCACAACTATGCCCCTAAATGCACTCCGGTGCCCCTGATA
** * * *
16704494 GCACATTTGTGCCCCTGAATGCACTCCGGTGCCCCTGATT
1 GCACAACTATGCCCCTAAATGCACTCCGGTGCCCCTGATA
16704534 GCACA
1 GCACA
16704539 CTCGTGCTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (40 bp):
GCACAACTATGCCCCTAAATGCACTCCGGTGCCCCTGATA
Found at i:16704517 original size:20 final size:20
Alignment explanation
Indices: 16704463--16704570 Score: 76
Period size: 20 Copynumber: 5.4 Consensus size: 20
16704453 TGCACAACTA
*
16704463 TGCCCCTAAATGCACTCTGG
1 TGCCCCTGAATGCACTCTGG
* *
16704483 TGCTCCTG-ATAGCACAT-TTG
1 TGCCCCTGAAT-GCAC-TCTGG
*
16704503 TGCCCCTGAATGCACTCCGG
1 TGCCCCTGAATGCACTCTGG
* * *
16704523 TGCCCCTGATTGCACACTCG
1 TGCCCCTGAATGCACTCTGG
* * ** *
16704543 TGCTCTTGGTTGCACTTTGG
1 TGCCCCTGAATGCACTCTGG
16704563 TGCCCCTG
1 TGCCCCTG
16704571 TTTTGCATCT
Statistics
Matches: 66, Mismatches: 18, Indels: 8
0.72 0.20 0.09
Matches are distributed among these distances:
19 3 0.05
20 60 0.91
21 3 0.05
ACGTcount: A:0.14, C:0.33, G:0.23, T:0.30
Consensus pattern (20 bp):
TGCCCCTGAATGCACTCTGG
Found at i:16706385 original size:3 final size:3
Alignment explanation
Indices: 16706377--16706545 Score: 123
Period size: 3 Copynumber: 58.0 Consensus size: 3
16706367 CTCCTTCTAT
* *
16706377 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * *
16706425 TTC TTC TTC TTC TTC TTC TTC TCC TCC TCC TCC TCC TCC TCC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * ** * **
16706472 CTC CTC CTC TTC CCC TTC TTC TT- TTC TTC TTT TTC -TC CAC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
16706518 -TC TTA TTC TTC TTT TTC -TC TTG TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16706546 CATTTCCCAA
Statistics
Matches: 139, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
2 10 0.07
3 129 0.93
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:16709783 original size:260 final size:259
Alignment explanation
Indices: 16709233--16709944 Score: 1115
Period size: 260 Copynumber: 2.7 Consensus size: 259
16709223 AAAACAATCT
*
16709233 TATAAGAAATATTACATAGAGCAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
1 TATAAGAAACATTACATAGAGCAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
* * * *
16709298 ATCTAGTGCCTTAAGTGTAGTATATTTGTTTTGTATACTTATATTTTTCAAAAAAAAATAGTTTA
66 ATCTAGTGCC-TAAGTGTAGTATATTTGTTTTGTATACTTATATTTTTTAGAACAAAATGGTTTA
* * * *
16709363 ATAAAAATATCCATTAATGACATTTATATCCCTTG--TATTGTACTCAATGTTTTTACATGCAAA
130 ATAAAAATATCCATAAATTACATTTATATCCTTTGTATATTGTCCTCAATGTTTTTACATGCAAA
*
16709426 AATGAGTAATCAATTATGGATTATCATGTTGGATCTAGTGTCCTAAGTGTAGTATATTTTTTTTG
195 AATGAGTAATCAATTATGGATTATCATGTTGGATCTAGTGTCCTAAGTGTAGTATATTTGTTTTG
*
16709491 TATAAGAAACATTACATAGAACAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
1 TATAAGAAACATTACATAGAGCAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
* * *
16709556 ATCTAGTGTCCTAAGTGTAGTATATTTATTTTTTATACTTATATTTTTTTGAACAAAATGGTTTA
66 ATCTAGTG-CCTAAGTGTAGTATATTTGTTTTGTATACTTATATTTTTTAGAACAAAATGGTTTA
* * * *
16709621 ATAAAAATACCCATCAATTACATTTATATCATTTGTATATTGTCCTCAATGTTTTTGCATGCAAA
130 ATAAAAATATCCATAAATTACATTTATATCCTTTGTATATTGTCCTCAATGTTTTTACATGCAAA
*
16709686 AATGAGTAATCAATTATGGATTATCATGTTGGATCTAGTGTCCTACGTGTAGTATATTTGTTTTG
195 AATGAGTAATCAATTATGGATTATCATGTTGGATCTAGTGTCCTAAGTGTAGTATATTTGTTTTG
* *
16709751 TATAAGAAACATTACATAGAGCAATAAGTCTAAAATGAGTAATCAATTATGGATTATAATGTTGG
1 TATAAGAAACATTACATAGAGCAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
* * **
16709816 ATCTAGTGCCCTAAGTATAGTATATTTGTTTTGTATACTTAT-TTTTTTCGAACAATTTGGTTTA
66 ATCTAGTG-CCTAAGTGTAGTATATTTGTTTTGTATACTTATATTTTTTAGAACAAAATGGTTTA
* * * *
16709880 ATAAAAATATCCATAAATTACATTTATATCCTTTGTATATTGTCTTAAATGTTTTTTCATACAAA
130 ATAAAAATATCCATAAATTACATTTATATCCTTTGTATATTGTCCTCAATGTTTTTACATGCAAA
16709945 GAAAAATGGA
Statistics
Matches: 416, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
258 148 0.36
259 79 0.19
260 189 0.45
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (259 bp):
TATAAGAAACATTACATAGAGCAATGAGTCTAAAATGAGTAATCAATTATGGATTATCATGTTGG
ATCTAGTGCCTAAGTGTAGTATATTTGTTTTGTATACTTATATTTTTTAGAACAAAATGGTTTAA
TAAAAATATCCATAAATTACATTTATATCCTTTGTATATTGTCCTCAATGTTTTTACATGCAAAA
ATGAGTAATCAATTATGGATTATCATGTTGGATCTAGTGTCCTAAGTGTAGTATATTTGTTTTG
Found at i:16717508 original size:7 final size:6
Alignment explanation
Indices: 16717456--16717506 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
16717446 AACAACCTAA
*
16717456 AAAATT AAAA-T GAAATT AAAATTTT AAAA-- AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAA--TT AAAATT AAAATT AAAATT AAAATT
16717503 AAAA
1 AAAA
16717507 ATATTGTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 24 0.63
8 6 0.16
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:16717915 original size:16 final size:17
Alignment explanation
Indices: 16717875--16717914 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
16717865 GAAATTAAAT
*
16717875 AACTAAAATAAATAAAC
1 AACTAAAATAAACAAAC
16717892 AA-TAAAATAAACAAAC
1 AACTAAAATAAACAAAC
16717908 AACTAAA
1 AACTAAA
16717915 TCAATTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (17 bp):
AACTAAAATAAACAAAC
Found at i:16719876 original size:11 final size:11
Alignment explanation
Indices: 16719862--16719891 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
16719852 TTTATTTTTT
16719862 TATTTTTAAAA
1 TATTTTTAAAA
16719873 TATTTTTAAAA
1 TATTTTTAAAA
16719884 TACTTTTT
1 TA-TTTTT
16719892 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:16729840 original size:15 final size:15
Alignment explanation
Indices: 16729807--16729854 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
16729797 AGCTATTGCT
* *
16729807 AGAAAGAGGAGAAGG
1 AGAAGGAGGAGAAGA
*
16729822 AGAAGGAGGAGGAGA
1 AGAAGGAGGAGAAGA
* *
16729837 AGAAGAAGAAGAAGA
1 AGAAGGAGGAGAAGA
16729852 AGA
1 AGA
16729855 GATACATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (15 bp):
AGAAGGAGGAGAAGA
Found at i:16731430 original size:33 final size:33
Alignment explanation
Indices: 16731353--16731441 Score: 151
Period size: 34 Copynumber: 2.7 Consensus size: 33
16731343 TCAATTTACA
*
16731353 CGTTACAAACACCAATATACAAGGCAGAACAGT
1 CGTTATAAACACCAATATACAAGGCAGAACAGT
*
16731386 CGGTTATAAACACCAATATACAAGGCATAACAGT
1 C-GTTATAAACACCAATATACAAGGCAGAACAGT
16731420 CGTTATAAACACCAATATACAA
1 CGTTATAAACACCAATATACAA
16731442 CGATTTTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 22 0.42
34 31 0.58
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.19
Consensus pattern (33 bp):
CGTTATAAACACCAATATACAAGGCAGAACAGT
Found at i:16737837 original size:42 final size:42
Alignment explanation
Indices: 16737778--16737861 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
16737768 AATCAATTTC
16737778 ATTGAAATTAAACAAAAATCAAACTATGGTTTGTATATCAGT
1 ATTGAAATTAAACAAAAATCAAACTATGGTTTGTATATCAGT
16737820 ATTGAAATTAAACAAAAATCAAACTATGGTTTGTATATCAGT
1 ATTGAAATTAAACAAAAATCAAACTATGGTTTGTATATCAGT
16737862 TGTTATTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (42 bp):
ATTGAAATTAAACAAAAATCAAACTATGGTTTGTATATCAGT
Found at i:16741349 original size:24 final size:24
Alignment explanation
Indices: 16741322--16741373 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16741312 TTAGTAAGTC
*
16741322 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16741346 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16741370 AAAT
1 AAAT
16741374 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16743319 original size:24 final size:24
Alignment explanation
Indices: 16743292--16743343 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16743282 TTAGTAAGTC
*
16743292 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16743316 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16743340 AAAT
1 AAAT
16743344 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16743534 original size:16 final size:16
Alignment explanation
Indices: 16743477--16743545 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
16743467 TGTGTCTAAG
16743477 GTAATGGAATAGAGCT
1 GTAATGGAATAGAGCT
* * **
16743493 ATAATGAAATAGAAAT
1 GTAATGGAATAGAGCT
*
16743509 GTAATTGAATAGAGCT
1 GTAATGGAATAGAGCT
* *
16743525 GCAATGGAATAAAGCT
1 GTAATGGAATAGAGCT
16743541 GTAAT
1 GTAAT
16743546 CAGTAATTAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGAGCT
Found at i:16743784 original size:58 final size:58
Alignment explanation
Indices: 16743722--16743845 Score: 169
Period size: 58 Copynumber: 2.1 Consensus size: 58
16743712 TTTTAATAAG
* *
16743722 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAATAAAAA-AATAAATAATTTAACAAAATTCTTAACATA
* * * * *
16743780 ATTATTATTAAATATAATTTAATAAAAAAGTATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAAAAATAAATAATTTAACAAAATTCTTAACATA
16743838 ATTATTAT
1 ATTATTAT
16743846 ATGAATTTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 16 0.28
58 42 0.72
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAAAAATAAATAATTTAACAAAATTCTTAACATA
Found at i:16750022 original size:30 final size:30
Alignment explanation
Indices: 16749986--16750100 Score: 176
Period size: 30 Copynumber: 3.8 Consensus size: 30
16749976 ATCCATATTT
* *
16749986 ATGGAAAATCAAAGATATGTGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
16750016 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
16750046 TTGGAAAGTCAAAGATACGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
16750076 TTGGAAAGTCAAATATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
16750101 GAGATATTGG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:16750057 original size:15 final size:15
Alignment explanation
Indices: 16750009--16750091 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
16749999 GATATGTGTA
*
16750009 TCAAATAATGGAAAG
1 TCAAATATTGGAAAG
* **
16750024 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
16750039 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
* * **
16750054 TCAAAGATACGGGTA-
1 TCAAATAT-TGGAAAG
16750069 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
16750084 TCAAATAT
1 TCAAATAT
16750092 ATGGGTATCG
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
14 7 0.14
15 35 0.71
16 7 0.14
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (15 bp):
TCAAATATTGGAAAG
Found at i:16754707 original size:15 final size:15
Alignment explanation
Indices: 16754687--16754794 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
16754677 TTTATGGAAA
16754687 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
16754702 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
16754716 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
16754732 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
16754746 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
16754762 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
16754776 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
16754792 ATC
1 ATC
16754795 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:16754716 original size:30 final size:30
Alignment explanation
Indices: 16754680--16754794 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
16754670 ATCCATATTT
*
16754680 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
16754710 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
16754740 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
16754770 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
16754795 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:16766714 original size:16 final size:18
Alignment explanation
Indices: 16766685--16766724 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
16766675 TACAAAAACT
16766685 AATTTTTAACTAAAT-AA
1 AATTTTTAACTAAATGAA
16766702 AATTTTTAA-TAAATGAA
1 AATTTTTAACTAAATGAA
16766719 AATTTT
1 AATTTT
16766725 ATTGATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTTTTAACTAAATGAA
Found at i:16767825 original size:20 final size:21
Alignment explanation
Indices: 16767781--16767834 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
16767771 TTGATTTCAT
16767781 ATCATTAATTTATTATATTAC
1 ATCATTAATTTATTATATTAC
16767802 ATCATTAAATATT-TTATA-TA-
1 ATCATT-AAT-TTATTATATTAC
16767822 ATCATTTAATTTA
1 ATCA-TTAATTTA
16767835 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.07
20 7 0.24
21 10 0.34
22 8 0.28
23 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
ATCATTAATTTATTATATTAC
Found at i:16767980 original size:14 final size:15
Alignment explanation
Indices: 16767943--16767980 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
16767933 TATTTATTTT
16767943 AATTTATAATTTAAC
1 AATTTATAATTTAAC
*
16767958 -ATTTATAATTTTAC
1 AATTTATAATTTAAC
16767972 AATTT-TAAT
1 AATTTATAAT
16767981 ATAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTATAATTTAAC
Found at i:16768878 original size:17 final size:18
Alignment explanation
Indices: 16768846--16768881 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
16768836 GGAATTGCAT
16768846 TGCTATCTATTTTACTTG
1 TGCTATCTATTTTACTTG
*
16768864 TGCTATTTA-TTTACTTG
1 TGCTATCTATTTTACTTG
16768881 T
1 T
16768882 AGTTGCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (18 bp):
TGCTATCTATTTTACTTG
Found at i:16776293 original size:61 final size:61
Alignment explanation
Indices: 16776198--16776315 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
16776188 GCAGTACGGT
* * * *
16776198 AGGCCGCGTAACTCACTATTTTAAAATTAAAGTCATACGGGCTAGAGACATGTGTGTGTAC
1 AGGCCGCGCAACTCACTATTTTAAAATTAAAGTCACACGGGCCAGAGACATGGGTGTGTAC
* ** *
16776259 AGGCCGTGCAACTCACTATTTTGGAATTAGAGTCACACGGGCCAGAGACATGGGTGT
1 AGGCCGCGCAACTCACTATTTTAAAATTAAAGTCACACGGGCCAGAGACATGGGTGT
16776316 ATGCTAGGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
AGGCCGCGCAACTCACTATTTTAAAATTAAAGTCACACGGGCCAGAGACATGGGTGTGTAC
Found at i:16778011 original size:16 final size:17
Alignment explanation
Indices: 16777976--16778035 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
16777966 ACTTTAGTTC
*
16777976 AGAACAACTGTAATTTG
1 AGAACAACTCTAATTTG
*
16777993 AGAACAACTCTTA-TTG
1 AGAACAACTCTAATTTG
16778009 AGAAC-A-TCTAAAGTTTG
1 AGAACAACTCT-AA-TTTG
16778026 -GAACAACTCT
1 AGAACAACTCT
16778036 TGTTTAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 3 0.09
15 2 0.06
16 12 0.34
17 15 0.43
18 3 0.09
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (17 bp):
AGAACAACTCTAATTTG
Found at i:16779500 original size:16 final size:17
Alignment explanation
Indices: 16779471--16779503 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16779461 ATTATAATAA
16779471 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
*
16779488 AATAAACTT-TAATATT
1 AATAAAATTCTAATATT
16779504 TTGATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:16783486 original size:18 final size:18
Alignment explanation
Indices: 16783463--16783505 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16783453 ACCCAATCCA
*
16783463 AACCCAAGTAATCAACCC
1 AACCCAAGTAACCAACCC
* *
16783481 AACCCAATTACCCAACCC
1 AACCCAAGTAACCAACCC
16783499 AACCCAA
1 AACCCAA
16783506 TCATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.44, G:0.02, T:0.09
Consensus pattern (18 bp):
AACCCAAGTAACCAACCC
Found at i:16783623 original size:9 final size:9
Alignment explanation
Indices: 16783609--16783684 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
16783599 GTAGTGATTC
16783609 AATTCGGTT
1 AATTCGGTT
*
16783618 AATTCGGGT
1 AATTCGGTT
*
16783627 AATCCGGTT
1 AATTCGGTT
*
16783636 AATTCGTTT
1 AATTCGGTT
16783645 AATTCGGTT
1 AATTCGGTT
*
16783654 AATTCGGGT
1 AATTCGGTT
*
16783663 AATTCGATT
1 AATTCGGTT
16783672 AATTCGGTT
1 AATTCGGTT
16783681 AATT
1 AATT
16783685 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:16783899 original size:30 final size:31
Alignment explanation
Indices: 16783865--16783924 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
16783855 AAACCTTTTA
16783865 TTTTCCCCAAAAAATTTTACTCCC-TCCCAC
1 TTTTCCCCAAAAAATTTTACTCCCTTCCCAC
* * *
16783895 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCAAAAAATTTTACTCCCTTCCCA
16783925 TCCTACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTTCCCCAAAAAATTTTACTCCCTTCCCAC
Found at i:16784206 original size:17 final size:16
Alignment explanation
Indices: 16784182--16784228 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
16784172 CACATTTTAT
16784182 ATTATTTATATTATTG
1 ATTATTTATATTATTG
*
16784198 AATTGTTTAGTCA-TATTG
1 -ATTATTTA-T-ATTATTG
16784216 ATTATTTATATTA
1 ATTATTTATATTA
16784229 AAATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 14 0.56
18 6 0.24
19 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (16 bp):
ATTATTTATATTATTG
Found at i:16784576 original size:5 final size:5
Alignment explanation
Indices: 16784566--16784596 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
16784556 GAACAAATAT
16784566 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
16784597 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:16786628 original size:58 final size:60
Alignment explanation
Indices: 16786566--16786681 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 60
16786556 ATCACTTTAA
* *
16786566 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATC
* *
16786624 TATTAAATTAATAGGATACTTATCTACAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAATATTAA
16786682 GATAATCACA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.39
60 1 0.02
61 30 0.59
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:16799472 original size:31 final size:28
Alignment explanation
Indices: 16799419--16799502 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 28
16799409 TAAATATTTT
**
16799419 TATTTTTTTAATTTTTTTAATTTTAAAA
1 TATTTTTAAAATTTTTTTAATTTTAAAA
16799447 TACTTTTTTAAAATTTTATTTAATTTTAAAA
1 TA--TTTTTAAAATTTT-TTTAATTTTAAAA
*
16799478 TATTTTTAAAATACTTTTTAATTTT
1 TATTTTTAAAAT-TTTTTTAATTTT
16799503 TTTAATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 2 0.04
29 19 0.39
30 13 0.27
31 15 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTTTAAAATTTTTTTAATTTTAAAA
Found at i:16799486 original size:11 final size:12
Alignment explanation
Indices: 16799470--16799498 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
16799460 TTTTATTTAA
16799470 TTTTAAAATA-T
1 TTTTAAAATACT
16799481 TTTTAAAATACT
1 TTTTAAAATACT
16799493 TTTTAA
1 TTTTAA
16799499 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAAAATACT
Found at i:16799489 original size:42 final size:39
Alignment explanation
Indices: 16799439--16799518 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 39
16799429 ATTTTTTTAA
16799439 TTTTAAAATACTTTTTTAAAATTTTATTTAA-TTTTAAAATAT
1 TTTTAAAATAC-TTTTT--AATTTT-TTTAATTTTTAAAATAT
16799481 TTTTAAAATACTTTTTAATTTTTTTAATTTTTAAAATA
1 TTTTAAAATACTTTTTAATTTTTTTAATTTTTAAAATA
16799519 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
38 5 0.14
39 16 0.43
41 5 0.14
42 11 0.30
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (39 bp):
TTTTAAAATACTTTTTAATTTTTTTAATTTTTAAAATAT
Found at i:16801325 original size:41 final size:41
Alignment explanation
Indices: 16801265--16801349 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
16801255 GAGATCTAGC
*
16801265 ATATGTTGTGGATTATCTACATCTTGTGTGAGTAGCATCGA
1 ATATGTTGTGGATTATCTACATCTTGTGTGAGCAGCATCGA
*
16801306 ATATGTTGTGGATTCTCTACATCTTGTGTGAGCAGCATCGA
1 ATATGTTGTGGATTATCTACATCTTGTGTGAGCAGCATCGA
16801347 ATA
1 ATA
16801350 ACACTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (41 bp):
ATATGTTGTGGATTATCTACATCTTGTGTGAGCAGCATCGA
Found at i:16802441 original size:13 final size:14
Alignment explanation
Indices: 16802423--16802451 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16802413 TGTTATGATT
16802423 TGTTTGAA-AGATA
1 TGTTTGAATAGATA
16802436 TGTTTGAATAGATA
1 TGTTTGAATAGATA
16802450 TG
1 TG
16802452 AATGGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (14 bp):
TGTTTGAATAGATA
Found at i:16805294 original size:13 final size:13
Alignment explanation
Indices: 16805276--16805300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16805266 GTTTGGGTAA
16805276 AAATATAGGCTTG
1 AAATATAGGCTTG
16805289 AAATATAGGCTT
1 AAATATAGGCTT
16805301 AGGCAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (13 bp):
AAATATAGGCTTG
Found at i:16805393 original size:17 final size:17
Alignment explanation
Indices: 16805366--16805411 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
16805356 TGGATATAAT
* * *
16805366 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
16805383 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
16805400 AAATATTTTTAA
1 AAATATTTTTAA
16805412 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:16805409 original size:11 final size:11
Alignment explanation
Indices: 16805395--16805458 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
16805385 ATTTTTTTAA
16805395 TTTTAAAATAT
1 TTTTAAAATAT
16805406 TTTTAAAATACT
1 TTTTAAAATA-T
*
16805418 TTTT---TTAT
1 TTTTAAAATAT
*
16805426 TTTT--TA-AT
1 TTTTAAAATAT
16805434 -TTTAAAATAT
1 TTTTAAAATAT
16805444 TTTTAAAATAT
1 TTTTAAAATAT
16805455 TTTT
1 TTTT
16805459 TTTTAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.07
8 7 0.16
9 3 0.07
10 2 0.05
11 24 0.55
12 5 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16805436 original size:38 final size:39
Alignment explanation
Indices: 16805387--16805471 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 39
16805377 TTTTTTAAAT
16805387 TTTTTTAATTTTAAAATATTTTTAAAATA-CTTTTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATCTTTTTTTA
*
16805425 TTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATATCTTTTTTTA
*
16805464 ATTTTTAA
1 TTTTTTAA
16805472 AATAAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 29 0.66
39 15 0.34
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATATTTTTAAAATATCTTTTTTTA
Found at i:16805489 original size:22 final size:21
Alignment explanation
Indices: 16805441--16805496 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
16805431 AATTTTAAAA
* **
16805441 TATTTTTAAAATATTTTTTTT
1 TATTTTTAAAATAATTTTTGG
16805462 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTTGG
16805485 TATTTATTAAAA
1 TATTT-TTAAAA
16805497 ATGGGCCGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 15 0.52
23 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTGG
Found at i:16807273 original size:21 final size:21
Alignment explanation
Indices: 16807249--16807290 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16807239 TTTACCTAAG
* *
16807249 ATATGAATTGGATTGAATTGA
1 ATATAAATTGGATTAAATTGA
*
16807270 ATATAAATTGTATTAAATTGA
1 ATATAAATTGGATTAAATTGA
16807291 TGTTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATAAATTGGATTAAATTGA
Found at i:16807704 original size:24 final size:24
Alignment explanation
Indices: 16807669--16807715 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16807659 AGTTTCCTAT
*
16807669 TTTATGGTTCTT-GCGAGCTTCTCA
1 TTTATGGCTCTTCG-GAGCTTCTCA
16807693 TTTATGGCTCTTCGGAGCTTCTC
1 TTTATGGCTCTTCGGAGCTTCTC
16807716 GATAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (24 bp):
TTTATGGCTCTTCGGAGCTTCTCA
Found at i:16808156 original size:25 final size:25
Alignment explanation
Indices: 16808084--16808148 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
16808074 TACAGCTCTT
* *
16808084 ATGAGCTTTCCGTTACATGGCTCAC
1 ATGAGATTCCCGTTACATGGCTCAC
**
16808109 ATG-GACTTCTTGTTACATGGCTCAC
1 ATGAGA-TTCCCGTTACATGGCTCAC
16808134 ATGAGATTCCCGTTA
1 ATGAGATTCCCGTTA
16808149 TATAGCTCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 1 0.03
25 29 0.91
26 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAGATTCCCGTTACATGGCTCAC
Found at i:16808812 original size:2 final size:2
Alignment explanation
Indices: 16808807--16808844 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16808797 GATATATATA
*
16808807 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16808845 GCTTTATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16811481 original size:13 final size:13
Alignment explanation
Indices: 16811463--16811492 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16811453 TCCAGAAACT
*
16811463 ATGAATTTATTTC
1 ATGAATTTATTTA
16811476 ATGAATTTATTTA
1 ATGAATTTATTTA
16811489 ATGA
1 ATGA
16811493 TGATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTA
Found at i:16817484 original size:27 final size:25
Alignment explanation
Indices: 16817420--16817478 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
16817410 CAGCTTGAAA
* * *
16817420 GAGCGTCCCGTTA-TTTTCTCTCAG
1 GAGCATCCCGATATTTTTCTCTCAC
*
16817444 GAGCATCTCGATATTTTTCTCTCAC
1 GAGCATCCCGATATTTTTCTCTCAC
*
16817469 GAGCTTCCCG
1 GAGCATCCCG
16817479 TTATATGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.15, C:0.31, G:0.19, T:0.36
Consensus pattern (25 bp):
GAGCATCCCGATATTTTTCTCTCAC
Found at i:16817602 original size:24 final size:24
Alignment explanation
Indices: 16817575--16817633 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
16817565 CTCGCTTGAA
**
16817575 CTTCCCGATTACA-GCTCTTATGAG
1 CTTCCCG-TTACAGGCTCACATGAG
16817599 CTTCCCGTTACATGGCTCACATGAG
1 CTTCCCGTTACA-GGCTCACATGAG
16817624 CTTCCCGTTA
1 CTTCCCGTTA
16817634 TATGGCTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 5 0.16
24 7 0.23
25 19 0.61
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (24 bp):
CTTCCCGTTACAGGCTCACATGAG
Found at i:16817622 original size:25 final size:25
Alignment explanation
Indices: 16817594--16817641 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
16817584 TACAGCTCTT
16817594 ATGAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTCAC
*
16817619 ATGAGCTTCCCGTTATATGGCTC
1 ATGAGCTTCCCGTTACATGGCTC
16817642 GAAAGAGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAC
Found at i:16820346 original size:5 final size:5
Alignment explanation
Indices: 16820336--16820367 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
16820326 ATCTAAACAA
16820336 TAATT TAATT TAATT TAATT TAATT TAATT TA
1 TAATT TAATT TAATT TAATT TAATT TAATT TA
16820368 TTAATTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:16834936 original size:19 final size:20
Alignment explanation
Indices: 16834903--16834945 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
16834893 GTTACAAAAT
*
16834903 AATTCAAAATAATTT-TCAAA
1 AATTAAAAATAATTTAT-AAA
16834923 AATTAAAAAT-ATTTATAAA
1 AATTAAAAATAATTTATAAA
16834942 AATT
1 AATT
16834946 CCAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAAAAATAATTTATAAA
Found at i:16834951 original size:20 final size:20
Alignment explanation
Indices: 16834903--16834952 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
16834893 GTTACAAAAT
16834903 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
*
16834923 AATTAAAAAT-ATTTAT-AAA
1 AATTCAAAATAATTT-TCAAA
16834942 AATTCCAAAAT
1 AATT-CAAAAT
16834953 TTATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:16837313 original size:155 final size:155
Alignment explanation
Indices: 16836976--16837405 Score: 580
Period size: 153 Copynumber: 2.8 Consensus size: 155
16836966 GTTGTTCAAG
*
16836976 ATTTTATTCCAAAATTGTTTTATTTCCAAAAACGAGTAAAATAAAATTGTTTTGGGATCA-ATTC
1 ATTTTATTCCAAATTTGTTTTATTTCCAAAAACGAGTAAAATAAAATTGTTTTGGGAT-AGATTC
* * * * * * * *
16837040 CCACCGTTTAACGATTTTA-TTCTAATTTTTTTTATTTTCAAAAACGAGTAAAAT-AAAATTGTT
65 CCGCCGTTCAACGATTTTATTTCAAATTTGTTTTATTTCCAAAAATGAGTAATATAAAAATCGTT
* * *
16837103 TTGGGATTGACTCCTGCCGTTCAACG
130 TTGGGATTGACTCCCGCCATTCAACA
* * *
16837129 TTTTTATTCCAAATTTGTTTTATTTCCAAAAACGAGTAAAATAAAATCGTTTCGGGATAGATTCC
1 ATTTTATTCCAAATTTGTTTTATTTCCAAAAACGAGTAAAATAAAATTGTTTTGGGATAGATTCC
* *
16837194 CGCCGGTCAACAATTTTATTTCAAATTTGTTTTATTTCCAAAAATGAGTAATATAAAAATCGTTT
66 CGCCGTTCAACGATTTTATTTCAAATTTGTTTTATTTCCAAAAATGAGTAATATAAAAATCGTTT
*
16837259 TGGGATTGATTCCCGCCATTCAACA
131 TGGGATTGACTCCCGCCATTCAACA
* * * *
16837284 ATTTTATTCCAAATTTATTTTATTTCCAAAAATGAGTAAAATAAAAATTGTTTTAGGATTGATTC
1 ATTTTATTCCAAATTTGTTTTATTTCCAAAAACGAGTAAAAT-AAAATTGTTTTGGGATAGATTC
* * * *
16837349 CCGCCGTTCAACGATTTCATTCCAAATTTGGTTTATTTCCAAAAATGAGAAAT-TAAA
65 CCGCCGTTCAACGATTTTATTTCAAATTTGTTTTATTTCCAAAAATGAGTAATATAAA
16837406 TTAAAGAAAA
Statistics
Matches: 242, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
152 1 0.00
153 73 0.30
154 30 0.12
155 73 0.30
156 65 0.27
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (155 bp):
ATTTTATTCCAAATTTGTTTTATTTCCAAAAACGAGTAAAATAAAATTGTTTTGGGATAGATTCC
CGCCGTTCAACGATTTTATTTCAAATTTGTTTTATTTCCAAAAATGAGTAATATAAAAATCGTTT
TGGGATTGACTCCCGCCATTCAACA
Found at i:16837397 original size:78 final size:78
Alignment explanation
Indices: 16836933--16837393 Score: 590
Period size: 78 Copynumber: 6.0 Consensus size: 78
16836923 GGAAATTAAA
* * * * ** *
16836933 AGTAAAATAAAAATTATTTCGGAATTGATTCTCGTTGTTCAA-GATTTTATTCCAAAATTGTTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
16836997 ATTTCCAAAAACG
66 ATTTCCAAAAACG
** * * * *
16837010 AGTAAAAT-AAAATTGTTTTGGGATCAATTCCCACCGTTTAACGATTTTATT-CTAATTTTTTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
*
16837073 ATTTTCAAAAACG
66 ATTTCCAAAAACG
* * *
16837086 AGTAAAAT-AAAATTGTTTTGGGATTGACTCCTGCCGTTCAACGTTTTTATTCCAAATTTGTTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
16837150 ATTTCCAAAAACG
66 ATTTCCAAAAACG
* * * * * *
16837163 AGTAAAAT-AAAATCGTTTCGGGATAGATTCCCGCCGGTCAACAATTTTATTTCAAATTTGTTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
*
16837227 ATTTCCAAAAATG
66 ATTTCCAAAAACG
* * * * *
16837240 AGTAATATAAAAATCGTTTTGGGATTGATTCCCGCCATTCAACAATTTTATTCCAAATTTATTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
*
16837305 ATTTCCAAAAATG
66 ATTTCCAAAAACG
* * *
16837318 AGTAAAATAAAAATTGTTTTAGGATTGATTCCCGCCGTTCAACGATTTCATTCCAAATTTGGTTT
1 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
16837383 ATTTCCAAAAA
66 ATTTCCAAAAA
16837394 TGAGAAATTA
Statistics
Matches: 332, Mismatches: 49, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
76 88 0.27
77 113 0.34
78 131 0.39
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (78 bp):
AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
ATTTCCAAAAACG
Found at i:16843173 original size:70 final size:69
Alignment explanation
Indices: 16843057--16843310 Score: 294
Period size: 70 Copynumber: 3.6 Consensus size: 69
16843047 ATTGCGGATA
* * *
16843057 ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAACAAGTTGTCGATTCATTCAACTAGTGC
1 ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAATAATTTGTC-ATTCATTCGACTAGTGC
16843122 TGGGC
65 TGGGC
* ** * * *
16843127 ACAACTATCGTCAGTTATTTGACCAGTGCTGGGCGCAATAATTTGTCAATTCGTTCGACTAGTGC
1 ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAATAATTTGTC-ATTCATTCGACTAGTGC
16843192 TGGGC
65 TGGGC
* * * * *
16843197 ACAACTACCATC-GATTATCCGACTAGCGTTGAGTGCAATAATTTATCAGTTCATTCGACTAGTG
1 ACAACTATCATCAG-TTATCCGACTAGCGCTGGGCGCAATAATTTGTCA-TTCATTCGACTAGTG
*
16843261 TTGGGC
64 CTGGGC
** * *
16843267 ACAACTATCGCCAGTTATCTGACTAGCACTGGGCGCAATAATTT
1 ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAATAATTT
16843311 TTTGACTTGT
Statistics
Matches: 151, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
69 2 0.01
70 148 0.98
71 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (69 bp):
ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAATAATTTGTCATTCATTCGACTAGTGCT
GGGC
Found at i:16843333 original size:140 final size:140
Alignment explanation
Indices: 16843057--16843310 Score: 350
Period size: 140 Copynumber: 1.8 Consensus size: 140
16843047 ATTGCGGATA
* * *
16843057 ACAACTATCATCAGTTATCCGACTAGCGCTGGGCGCAACAAGTTGTCGATTCATTCAACTAGTGC
1 ACAACTACCATCAGTTATCCGACTAGCGCTGAGCGCAACAAGTTATCGATTCATTCAACTAGTGC
* * **
16843122 TGGGCACAACTATCGTCAGTTATTTGACCAGTGCTGGGCGCAATAATTTGTCAATTCGTTCGACT
66 TGGGCACAACTATCGCCAGTTATCTGACCAGCACTGGGCGCAATAATTTGTCAATTCGTTCGACT
16843187 AGTGCTGGGC
131 AGTGCTGGGC
* * * * *
16843197 ACAACTACCATC-GATTATCCGACTAGCGTTGAGTGCAATAATTTATC-AGTTCATTCGACTAGT
1 ACAACTACCATCAG-TTATCCGACTAGCGCTGAGCGCAACAAGTTATCGA-TTCATTCAACTAGT
* *
16843260 GTTGGGCACAACTATCGCCAGTTATCTGACTAGCACTGGGCGCAATAATTT
64 GCTGGGCACAACTATCGCCAGTTATCTGACCAGCACTGGGCGCAATAATTT
16843311 TTTGACTTGT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
139 2 0.02
140 96 0.98
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (140 bp):
ACAACTACCATCAGTTATCCGACTAGCGCTGAGCGCAACAAGTTATCGATTCATTCAACTAGTGC
TGGGCACAACTATCGCCAGTTATCTGACCAGCACTGGGCGCAATAATTTGTCAATTCGTTCGACT
AGTGCTGGGC
Found at i:16858345 original size:27 final size:26
Alignment explanation
Indices: 16858298--16858360 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
16858288 ATAAACCATA
16858298 AACCCTAAA-CTTAACATGAACCTCG
1 AACCCTAAACCTTAACATGAACCTCG
** *
16858323 AACCCTAAACTCTTAATTTGAACCTTG
1 AACCCTAAAC-CTTAACATGAACCTCG
*
16858350 AACCATAAACC
1 AACCCTAAACC
16858361 CTAAACCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.28
26 1 0.03
27 22 0.69
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.24
Consensus pattern (26 bp):
AACCCTAAACCTTAACATGAACCTCG
Found at i:16858419 original size:14 final size:14
Alignment explanation
Indices: 16858400--16858437 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
16858390 AAAGGACAAA
16858400 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
16858414 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
16858428 TTCAAGGTTT
1 TTTAAGGTTT
16858438 GTGTTTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.32, T:0.45
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:16869327 original size:35 final size:35
Alignment explanation
Indices: 16869286--16869444 Score: 201
Period size: 35 Copynumber: 4.5 Consensus size: 35
16869276 CTCTCTGTTT
** * * *
16869286 TGGTGTGTTTCAGTTGGACTAGCTCTTACGAGCAC
1 TGGTGTGTTTTGGATGGATTAGCTCTAACGAGCAC
* * *
16869321 TAGTGTGTTTTGGATGGATTAGCTCTAACGGGCAT
1 TGGTGTGTTTTGGATGGATTAGCTCTAACGAGCAC
*
16869356 TGGAGTGTTTTGGATGGATTAGCTCTAACGAGCAC
1 TGGTGTGTTTTGGATGGATTAGCTCTAACGAGCAC
* *
16869391 TGGTGTGTTTTGGATGGATTAGCTCTTATGAGCATC
1 TGGTGTGTTTTGGATGGATTAGCTCTAACGAGCA-C
*
16869427 TGGTGTGTTTCGGATGGA
1 TGGTGTGTTTTGGATGGA
16869445 ATACCAATGT
Statistics
Matches: 107, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 89 0.83
36 18 0.17
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.36
Consensus pattern (35 bp):
TGGTGTGTTTTGGATGGATTAGCTCTAACGAGCAC
Found at i:16871049 original size:25 final size:26
Alignment explanation
Indices: 16870933--16871049 Score: 82
Period size: 25 Copynumber: 4.6 Consensus size: 26
16870923 CAATTTTCAA
* * *
16870933 GAAGCTTATAAGAGCCGTAT-ATCAG
1 GAAGCTCATAAGAGCCATATAATCGG
*
16870958 GAAGCTC-TAGAGAGTCAT-TAATCGG
1 GAAGCTCATA-AGAGCCATATAATCGG
* *
16870983 GAAGCTCATGATAGAGCC-TTTAATCGA
1 GAAGCTCAT-A-AGAGCCATATAATCGG
*** *
16871010 GAAGCTCCGGAGAGCCACAT-ATCGG
1 GAAGCTCATAAGAGCCATATAATCGG
16871035 GAAGCTCATAAGAGC
1 GAAGCTCATAAGAGC
16871050 TATGGTGTGT
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
24 3 0.04
25 45 0.64
26 3 0.04
27 19 0.27
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (26 bp):
GAAGCTCATAAGAGCCATATAATCGG
Found at i:16871171 original size:24 final size:24
Alignment explanation
Indices: 16871144--16871190 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16871134 ATATTGGGTA
*
16871144 GCTCAAGAGAGCCAATATCGGGAT
1 GCTCAAGAGAGCCAATAACGGGAT
* *
16871168 GCTCATGAGAGCTAATAACGGGA
1 GCTCAAGAGAGCCAATAACGGGA
16871191 CGATCTTACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (24 bp):
GCTCAAGAGAGCCAATAACGGGAT
Found at i:16884681 original size:44 final size:46
Alignment explanation
Indices: 16884631--16884752 Score: 142
Period size: 45 Copynumber: 2.7 Consensus size: 46
16884621 GATCGCATCT
* *
16884631 AGTCTTATCTCCCTGAAGTTGTAGTCGAGTAGACTG-AGAAAGC-A
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGA
* * * * **
16884675 AGTCTTATCCCCCTGATGTTGCAGTGGGGCAGACTGAAGATGGCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGA
*
16884721 A-CCTTATCTCCCTGAAGTTGCAGTGGAGTAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGA
16884753 TTAAAGCCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
44 30 0.48
45 31 0.49
46 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (46 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGA
Found at i:16884996 original size:41 final size:42
Alignment explanation
Indices: 16884846--16885223 Score: 227
Period size: 44 Copynumber: 8.8 Consensus size: 42
16884836 TAGATCACAT
* *
16884846 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-CAGAAGAAA
1 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-G-A-ATA
* * * * * * *
16884890 CCAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGAT-TAAAA
1 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATA
* * * *
16884931 CCACAGATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCGCAT-
1 -C-CAG-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATA
* *
16884975 CCAGTCTTATCTCACTGAAGTTGCAGTGGAGCAGA-CAGAATAAA
1 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-GAAT--A
* * * * * **
16885019 CCAATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAATGA
1 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCGAAT-A
* * * *
16885063 -CAGGTCTTATCTCTCTGAAGTTGCAGTAGAGTAAATCGCAT-
1 CCA-GTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATA
* *
16885104 CCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-CAGAAGATA
1 CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-G-A-ATA
* * * * * *
16885148 GCAAGTCTTAT-TCTCTGAAGTTACAATAGAGCAAATCGTAT-
1 -CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATA
16885189 CCAGTCTTATCTCCCTGAAGTTGCAGTCA-AGCAGA
1 CCAGTCTTATCTCCCTGAAGTTGCAGT-AGAGCAGA
16885224 CTGAAGATAG
Statistics
Matches: 254, Mismatches: 59, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
40 11 0.04
41 79 0.31
42 10 0.04
43 10 0.04
44 130 0.51
45 14 0.06
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
CCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAATA
Found at i:16885020 original size:129 final size:129
Alignment explanation
Indices: 16884723--16885145 Score: 550
Period size: 129 Copynumber: 3.3 Consensus size: 129
16884713 GATGGCGAAC
* * * * *
16884723 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA-AAGCCAA-TAATCCTATCTCCCTGAAGTTGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAG-AAACCAATCCTATCTCCCTGAAGTTGC
* * * * * *
16884786 AGCGGAGCGGATTAAAATGCCA-A-ATCTTATCACTGTGAAGTTCCAG-AAAGTAGATCACATCC
64 AGTGGAGCGGATTAAAA--CCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCC
16884848 AGT
127 AGT
* * *
16884851 CTTATCTCCCTGAAGTTGCAGTAGAGTAGACAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
* *
16884916 TGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAGT
66 TGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCCAGT
* * *
16884980 CTTATCTCACTGAAGTTGCAGTGGAGCAGACAGAATAAACCAATCCTATCTCCCTGATGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
** * * *
16885045 TGGAGCGGATTAAAATGACAGGTCTTATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCCAGT
66 TGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCCAGT
*
16885109 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACAGAAGA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGA
16885146 TAGCAAGTCT
Statistics
Matches: 260, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
126 3 0.01
127 4 0.02
128 87 0.33
129 166 0.64
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
TGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCCAGT
Found at i:16885163 original size:85 final size:85
Alignment explanation
Indices: 16885066--16885251 Score: 264
Period size: 85 Copynumber: 2.2 Consensus size: 85
16885056 AAAATGACAG
* * *
16885066 GTCTTATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGT
1 GTCTTAT-TCTCTGAAGTTACAATAGAGCAAATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGT
**
16885131 GGAGCAGACAGAAGATAGCAA
65 CAAGCAGACAGAAGATAGCAA
* *
16885152 GTCTTATTCTCTGAAGTTACAATAGAGCAAATCGTATCCAGTCTTATCTCCCTGAAGTTGCAGTC
1 GTCTTATTCTCTGAAGTTACAATAGAGCAAATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTC
*
16885217 AAGCAGACTGAAGATAGCAA
66 AAGCAGACAGAAGATAGCAA
* *
16885237 ATTTTATTCTACTGA
1 GTCTTATTCT-CTGA
16885252 GAAACTACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 78 0.88
86 11 0.12
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (85 bp):
GTCTTATTCTCTGAAGTTACAATAGAGCAAATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTC
AAGCAGACAGAAGATAGCAA
Found at i:16885537 original size:17 final size:18
Alignment explanation
Indices: 16885497--16885541 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
16885487 AGTAAACACC
*
16885497 AAAATAAACACAGAAAAA
1 AAAAAAAACACAGAAAAA
16885515 AGAAAAAAACACA-AAAATA
1 A-AAAAAAACACAGAAAA-A
16885534 AAAAAAAA
1 AAAAAAAA
16885542 TTAAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.04
Consensus pattern (18 bp):
AAAAAAAACACAGAAAAA
Found at i:16889117 original size:17 final size:18
Alignment explanation
Indices: 16889086--16889125 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
16889076 AGCAAGCCAT
16889086 AAAG-AAAATAAAAACAA
1 AAAGTAAAATAAAAACAA
*
16889103 AAAGTAAAAT-AAAACTA
1 AAAGTAAAATAAAAACAA
16889120 AAAGTA
1 AAAGTA
16889126 GCTATATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAGTAAAATAAAAACAA
Found at i:16889176 original size:183 final size:173
Alignment explanation
Indices: 16888860--16889207 Score: 536
Period size: 183 Copynumber: 2.0 Consensus size: 173
16888850 AACTTTATAA
*
16888860 AATCAAACTTTGAATATTACTTTTACTAGAATATTTAAAGTTTAGCAAGCCATAAAAAATAAAAA
1 AATCAAACTTTGAATATTACTTTGACTAGAATATTTAAAGTTTAGCAAGCCATAAAAAATAAAAA
* *
16888925 GTAAAATAAAACTTAAAACAGGTATATCACGTCTCTCTCTCTAAAAAGATCATATTTATAGAGTT
66 GTAAAATAAAACTTAAAACAGCTATATCACCTCTCTCTCTCTAAAAAGATCATATTTATAGAGTT
16888990 TATTTGACCTAAAATTAAGGTTATAATACTTGCTTCTTTACAG
131 TATTTGACCTAAAATTAAGGTTATAATACTTGCTTCTTTACAG
16889033 AATCAAACTTTGAATATTACTTTGACTAGAATATTTAAAGTTTAGCAAGCCATAAAGAAAATAAA
1 AATCAAACTTTGAATATTACTTTGACTAGAATATTTAAAGTTTAGCAAGCCAT-AA-AAAAT---
* *
16889098 AACAAAAAGTAAAATAAAAC-TAAAAGTAGCTATATCACATCTCTCTCTCTCTAAAAAGATCCTA
61 ---AAAAAGTAAAATAAAACTTAAAA-CAGCTATATCAC--CTCTCTCTCTCTAAAAAGATCATA
*
16889162 TTTATAGAGTTTATTTGACCTAAAATTAGGGTTATAATACTTGCTT
120 TTTATAGAGTTTATTTGACCTAAAATTAAGGTTATAATACTTGCTT
16889208 AAGCTTAAAT
Statistics
Matches: 158, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
173 52 0.33
174 2 0.01
175 5 0.03
180 5 0.03
181 27 0.17
183 67 0.42
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (173 bp):
AATCAAACTTTGAATATTACTTTGACTAGAATATTTAAAGTTTAGCAAGCCATAAAAAATAAAAA
GTAAAATAAAACTTAAAACAGCTATATCACCTCTCTCTCTCTAAAAAGATCATATTTATAGAGTT
TATTTGACCTAAAATTAAGGTTATAATACTTGCTTCTTTACAG
Found at i:16890114 original size:29 final size:29
Alignment explanation
Indices: 16890082--16890167 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 29
16890072 GACTAAATAT
16890082 TAAAAACTATATTTGGCAAATTAAAAGCA
1 TAAAAACTATATTTGGCAAATTAAAAGCA
* * * **
16890111 T-AAATC-A-ATGT-G--AATTCAAATAA
1 TAAAAACTATATTTGGCAAATTAAAAGCA
16890134 TCAAAAACTATATTTGGCAAATTAAAAGCA
1 T-AAAAACTATATTTGGCAAATTAAAAGCA
16890164 TAAA
1 TAAA
16890168 TCAATGCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
23 9 0.22
25 5 0.12
26 4 0.10
27 4 0.10
28 5 0.12
29 4 0.10
30 9 0.22
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.28
Consensus pattern (29 bp):
TAAAAACTATATTTGGCAAATTAAAAGCA
Found at i:16890145 original size:53 final size:53
Alignment explanation
Indices: 16890083--16890192 Score: 202
Period size: 53 Copynumber: 2.1 Consensus size: 53
16890073 ACTAAATATT
**
16890083 AAAAACTATATTTGGCAAATTAAAAGCATAAATCAATGTGAATTCAAATAATC
1 AAAAACTATATTTGGCAAATTAAAAGCATAAATCAATGCAAATTCAAATAATC
16890136 AAAAACTATATTTGGCAAATTAAAAGCATAAATCAATGCAAATTCAAATAATC
1 AAAAACTATATTTGGCAAATTAAAAGCATAAATCAATGCAAATTCAAATAATC
16890189 AAAA
1 AAAA
16890193 GTAATGGCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (53 bp):
AAAAACTATATTTGGCAAATTAAAAGCATAAATCAATGCAAATTCAAATAATC
Found at i:16891535 original size:25 final size:25
Alignment explanation
Indices: 16891480--16891528 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
16891470 CTTTACTGAA
*
16891480 GATAGTGATACATGCAATTTGTTTT
1 GATAATGATACATGCAATTTGTTTT
16891505 GATAATGATACATGCAATTTGTTT
1 GATAATGATACATGCAATTTGTTT
16891529 CTCTAATTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (25 bp):
GATAATGATACATGCAATTTGTTTT
Found at i:16892978 original size:39 final size:39
Alignment explanation
Indices: 16892935--16893021 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 39
16892925 CAACAAATTT
**
16892935 AACAATACTA-ATAATTAAAATAAAGGTGTAGTATATTAA
1 AACAATACTACATAAAAAAAATAAAGGTGTAGTAT-TTAA
* *
16892974 AACAATATATTACATAAAAAAAATAAAGGTGTAGTATTTAT
1 AAC-A-ATACTACATAAAAAAAATAAAGGTGTAGTATTTAA
16893015 AACAATA
1 AACAATA
16893022 TATTAAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
39 6 0.15
40 2 0.05
41 11 0.27
42 22 0.54
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (39 bp):
AACAATACTACATAAAAAAAATAAAGGTGTAGTATTTAA
Found at i:16893054 original size:22 final size:22
Alignment explanation
Indices: 16893028--16893083 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
16893018 AATATATTAA
16893028 AACAGTATATTACAAATTTTAT
1 AACAGTATATTACAAATTTTAT
* *
16893050 AACAGTACATTTCAAATTTTAT
1 AACAGTATATTACAAATTTTAT
*
16893072 AATAGTATATTA
1 AACAGTATATTA
16893084 AAACAGTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
AACAGTATATTACAAATTTTAT
Found at i:16894780 original size:115 final size:115
Alignment explanation
Indices: 16894655--16894892 Score: 458
Period size: 115 Copynumber: 2.1 Consensus size: 115
16894645 NNNNNNNNNN
* *
16894655 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAATGTAAAAAAAAAAATTTTGGGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAAATTTTAGGTGCT
16894720 GGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTATTTTTTTCT
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTATTTTTTTCT
16894770 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAAATTTTAGGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAAATTTTAGGTGCT
16894835 GGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTATTTTTTTCT
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTATTTTTTTCT
16894885 TTTTTTTT
1 TTTTTTTT
16894893 TCCTTTTTCA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 121 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (115 bp):
TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAGTAAAAAAAAAAATTTTAGGTGCT
GGCCTGTCAATGGCCGGCACCCAACAGTAAATTTTTTTTTATTTTTTTCT
Found at i:16895075 original size:19 final size:17
Alignment explanation
Indices: 16895035--16895079 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
16895025 TATTTTATTG
*
16895035 ATTATTTTTAAACTTAA
1 ATTATTTTTAAAATTAA
16895052 ATTATTTTTATAAATATAA
1 ATTATTTTTA-AAAT-TAA
*
16895071 TTTATTTTT
1 ATTATTTTT
16895080 GGGCTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 3 0.12
19 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTTTTAAAATTAA
Found at i:16900382 original size:3 final size:3
Alignment explanation
Indices: 16900374--16900399 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16900364 CTAAAAAGAA
16900374 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
16900400 AAAGCCATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16908632 original size:36 final size:35
Alignment explanation
Indices: 16908500--16908633 Score: 107
Period size: 36 Copynumber: 3.9 Consensus size: 35
16908490 TACCGGATCT
* **
16908500 TCCCAAGCTCCTAAACGAGATATCAACACTTCTCAA
1 TCCCAAGCTCCTGAACGAGATATC-AGTCTTCTCAA
* * * *
16908536 TCCCAAGCTCCTGCATGCGATATCA--ATTCT---
1 TCCCAAGCTCCTGAACGAGATATCAGTCTTCTCAA
* *
16908566 TCCCAAGCTCCTGAACAAGGTATCAGGTCTTCTCAA
1 TCCCAAGCTCCTGAACGAGATATCA-GTCTTCTCAA
* *
16908602 TCCCAAGATCCTGAATGAGATATCGAGTCTTC
1 TCCCAAGCTCCTGAACGAGATATC-AGTCTTC
16908634 CCAAGCTCTT
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
30 20 0.26
33 8 0.11
35 1 0.01
36 46 0.61
37 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (35 bp):
TCCCAAGCTCCTGAACGAGATATCAGTCTTCTCAA
Found at i:16908667 original size:66 final size:66
Alignment explanation
Indices: 16908497--16908646 Score: 192
Period size: 66 Copynumber: 2.3 Consensus size: 66
16908487 AAATACCGGA
* * *** * * *
16908497 TCTTCCCAAGCTCCTAAACGAGATATCAACACTTCTCAATCCCAAGCTCCTGCATGCGATATCAA
1 TCTTCCCAAGCTCCTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTGAATGAGATATCAA
*
16908562 T
66 G
* *
16908563 TCTTCCCAAGCTCCTGAACAAGGTATCAGGTCTTCTCAATCCCAAGATCCTGAATGAGATATCGA
1 TCTTCCCAAGCTCCTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTGAATGAGATATCAA
16908628 G
66 G
*
16908629 TCTTCCCAAGCTCTTGAA
1 TCTTCCCAAGCTCCTGAA
16908647 TGAGATATTG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (66 bp):
TCTTCCCAAGCTCCTGAACAAGATATCAGGTCTTCTCAATCCCAAGATCCTGAATGAGATATCAA
G
Found at i:16911467 original size:37 final size:38
Alignment explanation
Indices: 16911384--16911941 Score: 353
Period size: 37 Copynumber: 15.2 Consensus size: 38
16911374 TCATTTCACC
* * * * *
16911384 TAATCAATGGATAATGCTTGTTTGAGCA-TGCATTCCGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACT--ATTCAGTA
* *
16911423 TAATCAGTACATATTGCTCATTTGAGC-CTATTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * ** *
16911460 TAATCAGTGGGTATCACTCATTTGAGCAACT-TTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGC-ACTATTCAGTA
* * *
16911498 TAATCAATAGACATTGCTCTTTTGAGCACGT-TT-AGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCAC-TATTCAGTA
* * * *
16911535 TATTCAGTAGATATTGCTCGTTTGAGC-CCATTCAATG
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * *
16911572 TAATCAGTGGGTATTGCTTGTTTGAGCAACT-TTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGC-ACTATTCAGTA
* *
16911610 TAATCAGTAGACATTGCTCTTTTGAGCAC-ATTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * * * *
16911647 GATTCAATAGATATTTCTCGTTTGAGCAC-ATTCAATA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * * *
16911684 TAATCAGTAGACATTGCTCATTTGATCTC-ATTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * ** * *
16911721 TAATTAGTGGATATCACTTGTTTGAGCAACT-TTTAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGC-ACTATTCAGTA
* * *
16911759 TAATTAGTAGACATTGCTCTTTTGAG--C-A-T--GT-
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
*
16911790 T-A--AGTAGATATTGCTCATTTGAGCAC-ATTCAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * * *
16911824 TAATCAGTAGACATTGCTTGTTTGAGC-CCATTTAGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* ** * *
16911861 TAATTAGTAGATATCACTCGTTTCA--ACTCTT-AGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
* * *
16911896 TAATTAGTAGACATTGCTCTTTTGAGCACGT-TT-AGTA
1 TAATCAGTAGATATTGCTCGTTTGAGCAC-TATTCAGTA
*
16911933 TATTCAGTA
1 TAATCAGTA
16911942 TTCCATTTTT
Statistics
Matches: 402, Mismatches: 91, Indels: 54
0.73 0.17 0.10
Matches are distributed among these distances:
28 19 0.05
30 3 0.01
31 2 0.00
32 2 0.00
33 2 0.00
34 2 0.00
35 26 0.06
36 7 0.02
37 229 0.57
38 85 0.21
39 25 0.06
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (38 bp):
TAATCAGTAGATATTGCTCGTTTGAGCACTATTCAGTA
Found at i:16911691 original size:149 final size:148
Alignment explanation
Indices: 16911453--16911938 Score: 512
Period size: 149 Copynumber: 3.3 Consensus size: 148
16911443 TTTGAGCCTA
* ** ** * * * * *
16911453 TTCAGTATAATCAGTGGGTATCACTCATTTGAGCAACTTTCAGTATAATCAATAGACATTGCTCT
1 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGC-AC-TTCAGTAGATTCAATAGATATTGCTCA
* * * * * * * *
16911518 TTTGAGCACGTTTAGTATATTCAGTAGATATTGCTCGTTTGAGCCCATTCAATGTAATCAGTGGG
64 TTTGAGCACATTCAGTATAATCAGTAGACATTGCTCGTTTGAGCCCATTCAGTATAATTAGTGGA
**
16911583 TATTGCTTGTTTGAGCAACT
129 TATCACTTGTTTGAGCAACT
* *
16911603 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACATTCAGTAGATTCAATAGATATTTCTCGT
1 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCAC-TTCAGTAGATTCAATAGATATTGCTCAT
* * * *
16911668 TTGAGCACATTCAATATAATCAGTAGACATTGCTCATTTGATCTCATTCAGTATAATTAGTGGAT
65 TTGAGCACATTCAGTATAATCAGTAGACATTGCTCGTTTGAGCCCATTCAGTATAATTAGTGGAT
16911733 ATCACTTGTTTGAGCAACT
130 ATCACTTGTTTGAGCAACT
* *
16911752 TTTAGTATAATTAGTAGACATTGCTCTTTTGAG-----CA-T-G-TT-AAGTAGATATTGCTCAT
1 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACTTCAGTAGATTCAA-TAGATATTGCTCAT
* * *
16911808 TTGAGCACATTCAGTATAATCAGTAGACATTGCTTGTTTGAGCCCATTTAGTATAATTAGTAGAT
65 TTGAGCACATTCAGTATAATCAGTAGACATTGCTCGTTTGAGCCCATTCAGTATAATTAGTGGAT
*
16911873 ATCACTCGTTT---CAACT
130 ATCACTTGTTTGAGCAACT
* * *
16911889 CTT-AGTATAATTAGTAGACATTGCTCTTTTGAGCACGTTTAGTATATTCA
1 -TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCAC-TTCAGTAGATTCA
16911939 GTATTCCATT
Statistics
Matches: 284, Mismatches: 40, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
137 35 0.12
138 2 0.01
139 2 0.01
140 82 0.29
141 1 0.00
142 1 0.00
143 3 0.01
144 1 0.00
146 2 0.01
147 1 0.00
149 126 0.44
150 28 0.10
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (148 bp):
TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACTTCAGTAGATTCAATAGATATTGCTCATT
TGAGCACATTCAGTATAATCAGTAGACATTGCTCGTTTGAGCCCATTCAGTATAATTAGTGGATA
TCACTTGTTTGAGCAACT
Found at i:16911708 original size:112 final size:109
Alignment explanation
Indices: 16911398--16911941 Score: 430
Period size: 112 Copynumber: 5.0 Consensus size: 109
16911388 CAATGGATAA
** * * * *
16911398 TGCTTGTTTGAGCATGCATTCCGTATAATCAGTACATATTGCTCATTTGAGCCTATTCAGTATAA
1 TGCTTGTTTGAGCA--CATTTAGTATAATTAGTAGATATTGCTCGTTTGAGCC-ATT-AATATAA
* ** ** *
16911463 TCAGTGGGTATCACTCATTTGAGCAACTTTCAGTATAATCAATAGACAT
62 TCAGTAGACATTGCTCATTTGAGC-ACTTTCAGTATAATCAGTAGACAT
* *
16911512 TGCTCT-TTTGAGCACGTTTAGTAT-ATTCAGTAGATATTGCTCGTTTGAGCCCATTCAATGTAA
1 TGCT-TGTTTGAGCACATTTAGTATAATT-AGTAGATATTGCTCGTTTGAG-CCATT-AATATAA
* ** **
16911575 TCAGTGGGTATTGCTTGTTTGAGCAACTTTCAGTATAATCAGTAGACAT
62 TCAGTAGACATTGCTCATTTGAGC-ACTTTCAGTATAATCAGTAGACAT
* * * *
16911624 TGCTCT-TTTGAGCACATTCAGTA-GATTCAATAGATATTTCTCGTTTGAGCACATTCAATATAA
1 TGCT-TGTTTGAGCACATTTAGTATAATT-AGTAGATATTGCTCGTTTGAGC-CATT-AATATAA
* * * * * *
16911687 TCAGTAGACATTGCTCATTTGATCTCATTCAGTATAATTAGTGGATAT
62 TCAGTAGACATTGCTCATTTGAGCACTTTCAGTATAATCAGTAGACAT
** * * * *
16911735 CACTTGTTTGAGCAACTTTTAGTATAATTAGTAGACATTGCTCTTTTGAG-CA-T-GT-T-A--A
1 TGCTTGTTTGAGC-ACATTTAGTATAATTAGTAGATATTGCTCGTTTGAGCCATTAATATAATCA
* *
16911793 GTAGATATTGCTCATTTGAGCACATTCAGTATAATCAGTAGACAT
65 GTAGACATTGCTCATTTGAGCACTTTCAGTATAATCAGTAGACAT
* ** * * * *
16911838 TGCTTGTTTGAGCCCATTTAGTATAATTAGTAGATATCACTCGTTTCAACTC-TTAGTATAATTA
1 TGCTTGTTTGAGCACATTTAGTATAATTAGTAGATATTGCTCGTTTGAGC-CATTAATATAATCA
* *
16911902 GTAGACATTGCTCTTTTGAGCACGTTT-AGTATATTCAGTA
65 GTAGACATTGCTCATTTGAGCAC-TTTCAGTATAATCAGTA
16911942 TTCCATTTTT
Statistics
Matches: 354, Mismatches: 59, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
102 28 0.08
103 51 0.14
104 2 0.01
105 3 0.01
106 2 0.01
107 2 0.01
109 35 0.10
110 5 0.01
111 31 0.09
112 177 0.50
113 5 0.01
114 12 0.03
115 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (109 bp):
TGCTTGTTTGAGCACATTTAGTATAATTAGTAGATATTGCTCGTTTGAGCCATTAATATAATCAG
TAGACATTGCTCATTTGAGCACTTTCAGTATAATCAGTAGACAT
Found at i:16911823 original size:28 final size:28
Alignment explanation
Indices: 16911764--16911823 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16911754 TAGTATAATT
* **
16911764 AGTAGACATTGCTCTTTTGAGCATGTTA
1 AGTAGACATTGCTCATTTGAGCACATTA
* *
16911792 AGTAGATATTGCTCATTTGAGCACATTC
1 AGTAGACATTGCTCATTTGAGCACATTA
16911820 AGTA
1 AGTA
16911824 TAATCAGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (28 bp):
AGTAGACATTGCTCATTTGAGCACATTA
Found at i:16912630 original size:21 final size:20
Alignment explanation
Indices: 16912604--16912643 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16912594 AATAAACACT
*
16912604 AAAAATTTATTTTAAAAATA
1 AAAAAATTATTTTAAAAATA
16912624 AAAAAATTATTTTAAAAATA
1 AAAAAATTATTTTAAAAATA
16912644 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATA
Found at i:16921333 original size:69 final size:69
Alignment explanation
Indices: 16921212--16921350 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
16921202 TACCAACCAA
* *
16921212 CTACAAAATTTGAAAGGTTAGTATATAAAATTGAAATATGCCAACTCAAAAGATGTTAAGTGAAG
1 CTACAAAATTTGAAAGATTAGTATATAAAATTGAAATATGCCAACTCAAAAGATATTAAGTGAAG
16921277 TTGC
66 TTGC
* * *
16921281 CTACAAAATTTGAAAGATTAGTATATAAAATTGAAATGTGTCGACCTC-AAAGATATTAAGTGAA
1 CTACAAAATTTGAAAGATTAGTATATAAAATTGAAATATG-CCAACTCAAAAGATATTAAGTGAA
16921345 GTTGC
65 GTTGC
16921350 C
1 C
16921351 ATTAGAAGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 59 0.92
70 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.29
Consensus pattern (69 bp):
CTACAAAATTTGAAAGATTAGTATATAAAATTGAAATATGCCAACTCAAAAGATATTAAGTGAAG
TTGC
Found at i:16928603 original size:69 final size:68
Alignment explanation
Indices: 16928526--16928669 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 68
16928516 AAGGGGTTCA
* *
16928526 CCTATAGGGGATTTCATACAATAG-TTTGCACATGCAAACA-AGGAGGTTCGCATACATCAAGAG
1 CCTATAGGGGATTTCATACAA-AGTTTTACACATGCAAACATA-G-GGTTCACATACATCAAGAG
16928589 GATTCG
63 GATTCG
* * * * * * *
16928595 CCTATAGGGGTTTTCATGCAAGGTTTTACACATGCAAATATAGGGTTCACATGCATCAAGTGGGT
1 CCTATAGGGGATTTCATACAAAGTTTTACACATGCAAACATAGGGTTCACATACATCAAGAGGAT
16928660 TCG
66 TCG
16928663 CCTATAG
1 CCTATAG
16928670 AAGATTTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
68 29 0.45
69 34 0.53
70 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (68 bp):
CCTATAGGGGATTTCATACAAAGTTTTACACATGCAAACATAGGGTTCACATACATCAAGAGGAT
TCG
Found at i:16928682 original size:68 final size:68
Alignment explanation
Indices: 16928570--16928715 Score: 170
Period size: 68 Copynumber: 2.1 Consensus size: 68
16928560 CAAACAAGGA
* * * *
16928570 GGTTCGCATACATCAAGAGGATTCGCCTATAGGGGTTTTCATGCAAG-GTTTTACACATGCAAAT
1 GGTTCACATACATCAAGAGGATTCGCCTATAGAGATTTTCATGCAAGCG-TTCACACATGCAAAT
*
16928634 ATAG
65 AGAG
* * * *
16928638 GGTTCACATGCATCAAGTGGGTTCGCCTATAGAAGATTTT-ATGCAAGCGTTCGCACATGCAAAT
1 GGTTCACATACATCAAGAGGATTCGCCTATAG-AGATTTTCATGCAAGCGTTCACACATGCAAAT
*
16928702 AGGG
65 AGAG
16928706 GGTTCACATA
1 GGTTCACATA
16928716 AGGGTTCGCA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 59 0.91
69 6 0.09
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (68 bp):
GGTTCACATACATCAAGAGGATTCGCCTATAGAGATTTTCATGCAAGCGTTCACACATGCAAATA
GAG
Found at i:16928778 original size:80 final size:80
Alignment explanation
Indices: 16928636--16928804 Score: 214
Period size: 80 Copynumber: 2.1 Consensus size: 80
16928626 ATGCAAATAT
*
16928636 AGGGTTCACATGCATCAAGTGGGTTCGCCTATAGAAGATTTTATGCAAGCGTTCGCACATGCAAA
1 AGGGTTCACATGCATCAAGTGGGTTCGCCTATAGAAGATTTCATGCAAGCGTTCGCACATGCAAA
* *
16928701 TAGGGGGTTCACATA
66 CAGGAGGTTCACATA
* * * ** * * *
16928716 AGGGTTCGCATGCATCAAG-GGGCTTCTCCTATGGGGGATTTCATGCAAGGGTTCTCATATGCAA
1 AGGGTTCACATGCATCAAGTGGG-TTCGCCTATAGAAGATTTCATGCAAGCGTTCGCACATGCAA
*
16928780 ACAGGAGGTTCGCATA
65 ACAGGAGGTTCACATA
16928796 AGGGTTCAC
1 AGGGTTCAC
16928805 GCACGATCAC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
79 3 0.04
80 72 0.96
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
AGGGTTCACATGCATCAAGTGGGTTCGCCTATAGAAGATTTCATGCAAGCGTTCGCACATGCAAA
CAGGAGGTTCACATA
Found at i:16943091 original size:14 final size:14
Alignment explanation
Indices: 16943031--16943094 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
16943021 TCATAGAAAT
16943031 AATAT-AAATAAAA
1 AATATCAAATAAAA
16943044 TGAATATACATAAT-AAA
1 --AATAT-CA-AATAAAA
* *
16943061 AATAATCACATACAA
1 AAT-ATCAAATAAAA
16943076 AATATCAAATAAAA
1 AATATCAAATAAAA
16943090 AATAT
1 AATAT
16943095 GCCAACATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 16 0.40
15 15 0.38
16 2 0.05
17 4 0.10
18 3 0.08
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (14 bp):
AATATCAAATAAAA
Found at i:16946218 original size:346 final size:345
Alignment explanation
Indices: 16945586--16946277 Score: 1285
Period size: 346 Copynumber: 2.0 Consensus size: 345
16945576 TTAGCATATG
* *
16945586 ATGCTGCTTCCACCCACTTAGTGAAGTAGTCAATAACCACAAAAATGAAACGATGTCCATTAGAA
1 ATGCTGCTTCCACCCACTTAGTGAAGTAGTCAACAACCACAAAAATGAAACGATATCCATTAGAA
* *
16945651 GCCTTCGGTGATATTGGTCCAATGACGTCCATACCCCACATGGAAAAAGGCCACGGAGAAGTCAT
66 GCCTTCGGTGATATTGGTCCAATGACATCCATACCCCACATGGAAAAAGACCACGGAGAAGTCAT
16945716 CACATGAAGAGGAGAAGGAGGCGCGTGTATTTTATCCCCATAAATTTGGCATTTATGGCATTTTT
131 CACATGAAGAGGAGAAGGAGGCGCGTGTATTTTATCCCCATAAATTTGGCATTTATGGCATTTTT
16945781 TGGCATAATTAATGCAATCTCTTTCCATAGTGGACCAGTAATATCTGAATCTCATAATCTGTCTA
196 TGGCATAATTAATGCAATCTCTTTCCATAGTGGACCAGTAATATCTGAATCTCATAATCTGTCTA
* *
16945846 GCCATGGTAAATCCATTAGCGTGCATTCCATAAACACCCTCATGGACTTCTTCTAAAATTTCCTT
261 GCCAGGGTAAAGCCATTAGCGTGCATTCCATAAACACCCTCATGGACTTCTTCTAAAATTTCCTT
16945911 AGCCTCTACAGCGTCCACGC
326 AGCCTCTACAGCGTCCACGC
*
16945931 ATGCTGCTTCCACCCACTTAGTGAAGTAGTCAACAGCCACAAAAAATGAAACGATATCCATTAGA
1 ATGCTGCTTCCACCCACTTAGTGAAGTAGTCAACAACCAC-AAAAATGAAACGATATCCATTAGA
* * *
16945996 AGCCTTCGGTGATATTGGTCCAATGACATTCATTCCCCACATGGAGAAAGACCACGGAGAAGTCA
65 AGCCTTCGGTGATATTGGTCCAATGACATCCATACCCCACATGGAAAAAGACCACGGAGAAGTCA
16946061 TCACATGAAGAGGAGAAGGAGGCGCGTGTATTTTATCCCCATAAATTTGGCATTTATGGCATTTT
130 TCACATGAAGAGGAGAAGGAGGCGCGTGTATTTTATCCCCATAAATTTGGCATTTATGGCATTTT
16946126 TTGGCATAATTAATGCAATCTCTTTCCATAGTGGACCAGTAATATCTGAATCTCATAATCTGTCT
195 TTGGCATAATTAATGCAATCTCTTTCCATAGTGGACCAGTAATATCTGAATCTCATAATCTGTCT
16946191 AGCCAGGGTAAAGCCATTAGCGTGCATTCCATAAACACCCTCATGGACTTCTTCTAAAATTTCCT
260 AGCCAGGGTAAAGCCATTAGCGTGCATTCCATAAACACCCTCATGGACTTCTTCTAAAATTTCCT
16946256 TAGCCTCTACAGCGTCCACGC
325 TAGCCTCTACAGCGTCCACGC
16946277 A
1 A
16946278 CCTCAATAAT
Statistics
Matches: 336, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
345 38 0.11
346 298 0.89
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (345 bp):
ATGCTGCTTCCACCCACTTAGTGAAGTAGTCAACAACCACAAAAATGAAACGATATCCATTAGAA
GCCTTCGGTGATATTGGTCCAATGACATCCATACCCCACATGGAAAAAGACCACGGAGAAGTCAT
CACATGAAGAGGAGAAGGAGGCGCGTGTATTTTATCCCCATAAATTTGGCATTTATGGCATTTTT
TGGCATAATTAATGCAATCTCTTTCCATAGTGGACCAGTAATATCTGAATCTCATAATCTGTCTA
GCCAGGGTAAAGCCATTAGCGTGCATTCCATAAACACCCTCATGGACTTCTTCTAAAATTTCCTT
AGCCTCTACAGCGTCCACGC
Done.