Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 1 of 13
Found at i:1486 original size:2 final size:2
Alignment explanation
Indices: 1479--1510 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1469 TCGTTCATCC
1479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511 TTGAGCTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5352 original size:4 final size:4
Alignment explanation
Indices: 5343--5367 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5333 TTTTATCTAT
5343 GCTG GCTG GCTG GCTG GCTG GCTG G
1 GCTG GCTG GCTG GCTG GCTG GCTG G
5368 TTCTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (4 bp):
GCTG
Found at i:10868 original size:7 final size:7
Alignment explanation
Indices: 10853--10886 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
10843 ATGCCCTGAA
10853 CAAAAAC
1 CAAAAAC
*
10860 CATAAAC
1 CAAAAAC
10867 CAAAAAC
1 CAAAAAC
10874 CAAAAAC
1 CAAAAAC
10881 CAAAAA
1 CAAAAA
10887 ATATGCGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (7 bp):
CAAAAAC
Found at i:42345 original size:2 final size:2
Alignment explanation
Indices: 42333--42365 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42323 TCCATGCAAC
*
42333 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42366 CTCTAAGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42673 original size:2 final size:2
Alignment explanation
Indices: 42668--42710 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42658 TGTGTGTGTG
42668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42710 T
1 T
42711 TTGTGCAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45238 original size:15 final size:15
Alignment explanation
Indices: 45215--45244 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45205 TTCATAATTT
45215 TTTACAATCATATTA
1 TTTACAATCATATTA
*
45230 TTTATAATCATATTA
1 TTTACAATCATATTA
45245 GTAAAGTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTACAATCATATTA
Found at i:47232 original size:19 final size:19
Alignment explanation
Indices: 47208--47265 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
47198 AAGAAAGAAT
47208 TGAAATATATAAATTTTGG
1 TGAAATATATAAATTTTGG
47227 TGAAATATATAAATTTTGG
1 TGAAATATATAAATTTTGG
47246 TGAAATATATAAATTTTGG
1 TGAAATATATAAATTTTGG
47265 T
1 T
47266 TGTCTCTAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (19 bp):
TGAAATATATAAATTTTGG
Found at i:47763 original size:28 final size:28
Alignment explanation
Indices: 47723--47782 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
47713 CAGCATGTAA
47723 CTTTAGGATTATTGTCAATTAATTTAGC
1 CTTTAGGATTATTGTCAATTAATTTAGC
47751 CTTTAGGATTATTGTCAATTAATTTAGC
1 CTTTAGGATTATTGTCAATTAATTTAGC
47779 CTTT
1 CTTT
47783 CTTTTGTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (28 bp):
CTTTAGGATTATTGTCAATTAATTTAGC
Found at i:56996 original size:18 final size:18
Alignment explanation
Indices: 56973--57013 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56963 ATAAATTTCA
56973 TTTAATTTTATTCAAATT
1 TTTAATTTTATTCAAATT
* * *
56991 TTTAATTTTTTTTAATTT
1 TTTAATTTTATTCAAATT
57009 TTTAA
1 TTTAA
57014 ATTTCATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAATTTTATTCAAATT
Found at i:56998 original size:28 final size:26
Alignment explanation
Indices: 56966--57017 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
56956 TAATCTTATA
56966 AATTTCATTTAATTTTATTCAAATTTTT
1 AATTTCATTTAATTTT-TT-AAATTTTT
**
56994 AATTTTTTTTAATTTTTTAAATTT
1 AATTTCATTTAATTTTTTAAATTT
57018 CATCATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 2 0.09
28 14 0.64
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (26 bp):
AATTTCATTTAATTTTTTAAATTTTT
Found at i:57264 original size:15 final size:16
Alignment explanation
Indices: 57244--57274 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57234 TCTGATATGT
57244 TGATTTT-ATTTTTAA
1 TGATTTTAATTTTTAA
57259 TGATTTTAATTTTTAA
1 TGATTTTAATTTTTAA
57275 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TGATTTTAATTTTTAA
Found at i:68717 original size:2 final size:2
Alignment explanation
Indices: 68712--68744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68702 ATAATTAATT
68712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68745 TGCATGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69561 original size:20 final size:20
Alignment explanation
Indices: 69536--69574 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
69526 TCGTGAAGAC
69536 CCTTGAAGTGAAGACTAGTA
1 CCTTGAAGTGAAGACTAGTA
69556 CCTTGAAGTGAAGACTAGT
1 CCTTGAAGTGAAGACTAGT
69575 GTTTGTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
CCTTGAAGTGAAGACTAGTA
Found at i:69675 original size:48 final size:48
Alignment explanation
Indices: 69619--69827 Score: 364
Period size: 48 Copynumber: 4.3 Consensus size: 48
69609 TAAAGACACT
* *
69619 GTGAAGACCCTTGAAGCAAAGACAAGTGTTCGTGATCAAGATCAAGTT
1 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAAGATCAAGTC
*
69667 GTGAAGACCCTTAAAGCGAAGATCAAGTGTTCGTGATCAAGATCAAGTC
1 GTGAAGACCCTTGAAGCGAAGA-CAAGTGTTCGTGATCAAGATCAAGTC
*
69716 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAATATCAAGTC
1 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAAGATCAAGTC
*
69764 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAATATCAAGTC
1 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAAGATCAAGTC
69812 GTGAAGACCCTTGAAG
1 GTGAAGACCCTTGAAG
69828 AGAATATTAA
Statistics
Matches: 155, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 109 0.70
49 46 0.30
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (48 bp):
GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAAGATCAAGTC
Found at i:69725 original size:97 final size:96
Alignment explanation
Indices: 69619--69827 Score: 364
Period size: 97 Copynumber: 2.2 Consensus size: 96
69609 TAAAGACACT
*
69619 GTGAAGACCCTTGAAGCAAAGACAAGTGTTCGTGATCAAGATCAAGTTGTGAAGACCCTTAAAGC
1 GTGAAGACCCTTGAAGCAAAGACAAGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGC
69684 GAAGATCAAGTGTTCGTGATCAAGATCAAGTC
66 GAAGA-CAAGTGTTCGTGATCAAGATCAAGTC
* * *
69716 GTGAAGACCCTTGAAGCGAAGACAAGTGTTCGTGATCAATATCAAGTCGTGAAGACCCTTGAAGC
1 GTGAAGACCCTTGAAGCAAAGACAAGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGC
*
69781 GAAGACAAGTGTTCGTGATCAATATCAAGTC
66 GAAGACAAGTGTTCGTGATCAAGATCAAGTC
69812 GTGAAGACCCTTGAAG
1 GTGAAGACCCTTGAAG
69828 AGAATATTAA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
96 41 0.38
97 66 0.62
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (96 bp):
GTGAAGACCCTTGAAGCAAAGACAAGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTAAAGC
GAAGACAAGTGTTCGTGATCAAGATCAAGTC
Found at i:70136 original size:58 final size:57
Alignment explanation
Indices: 70017--70407 Score: 381
Period size: 58 Copynumber: 7.1 Consensus size: 57
70007 TTGAGCACGA
* * *
70017 ATCAAGATCAAGTCGTGAAGACCCTTGAAGGGAGATATTAAAATTCTTCGTGATCAAG
1 ATCAAG-TCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTCGTGATCAAG
**
70075 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTTATTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTC-TTCGTGATCAAG
**
70133 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAA-ATATTAAAATTCTTCGTGATCAAG
* * * * * * *
70191 ATCAAGTCGTATCGTGAAGACCCTTG-AGCG--A-A-GACAAGTGTTCGTGATC-A-
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTCGTGATCAAG
*
70241 AT--A-TCAAGTCGTGAAGACCCTTGAAGAG-AATATTAAAATTCTTCGTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTCGTGATCAAG
* * * * * *
70294 ATCAAGTCGTGTCATGAAGACCCTTGAAGAG-AAGA-T-CAAGTGTTCGTGATC-A-
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTCGTGATCAAG
* * * *
70346 AT--A-TTAAGTCGTGAAGA-CTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAA-ATATTAAAATTCTTCGTGATCAAG
70400 ATCAAGTC
1 ATCAAGTC
70408 GTGAAGACCC
Statistics
Matches: 271, Mismatches: 42, Indels: 41
0.77 0.12 0.12
Matches are distributed among these distances:
47 17 0.06
48 13 0.05
49 12 0.04
50 6 0.02
51 15 0.06
52 25 0.09
53 5 0.02
54 15 0.06
55 2 0.01
56 26 0.10
57 40 0.15
58 83 0.31
59 12 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (57 bp):
ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTCGTGATCAAG
Found at i:70317 original size:411 final size:406
Alignment explanation
Indices: 69874--70736 Score: 1440
Period size: 411 Copynumber: 2.1 Consensus size: 406
69864 CAAAGTACAA
69874 CGTGATC-AGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATA
1 CGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATA
69938 TTAAGTCGTGAAGACTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGTCGTGAAG
66 TTAAGTCGTGAAGACTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGTCGTGAAG
70003 ACCCTTG-AGCACGAATCAAGATCAAGTCGTGAAGACCCTTGAAG-GGAGATATTAAAATTCTTC
131 ACCCTTGAAG--CGAATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTC
70066 GTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAA-ATATTAAAATTCTTTATTGATC
194 GTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTA-TGATC
*
70130 AAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCA
258 AAGATCAAGTCATATCGTGAAGACCCTTGAAGAGAAGATATTAAAATTC---ATGAT-AAGATCA
* *
70195 AGTCGTATCGTGAAGACCCTTG-AGCGAAG-A-C-AAGTGTTCGTGATCAATATCAAGTCGTGAA
319 A---G--TCGTGAAAACCCTTGAAGCGAAGAATCAAAGT-TT-GTGATCAAGATCAAGTCGTGAA
70256 GACCCTTGAAGA-GA-ATATTAAAATTCTT
377 GACCCTTGAAGAGGAGATATTAAAATTCTT
70284 CGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATA
1 CGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATA
70349 TTAAGTCGTGAAGACTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGTCGTGAAG
66 TTAAGTCGTGAAGACTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGTCGTGAAG
70414 ACCCTTGAAGCGAATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGT
131 ACCCTTGAAGCGAATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGT
70479 GATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
196 GATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
* * * *
70544 ATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAAGTCGTG
261 ATCAAGTCATATCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCATGATAAGATCAAGTCGTG
70609 AAAACCCTTGAAGCGAAGATATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAG
326 AAAACCCTTGAAGCGAAGA-ATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAG
70674 GAGATATTAAAATTCTT
390 GAGATATTAAAATTCTT
* *
70691 CGTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGAT
1 CGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGAT
70737 ATTAAAATTC
Statistics
Matches: 433, Mismatches: 9, Indels: 25
0.93 0.02 0.05
Matches are distributed among these distances:
402 14 0.03
403 7 0.02
404 1 0.00
405 34 0.08
406 5 0.01
407 70 0.16
408 4 0.01
410 40 0.09
411 240 0.55
412 18 0.04
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (406 bp):
CGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATA
TTAAGTCGTGAAGACTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGTCGTGAAG
ACCCTTGAAGCGAATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGT
GATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
ATCAAGTCATATCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCATGATAAGATCAAGTCGTG
AAAACCCTTGAAGCGAAGAATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGG
AGATATTAAAATTCTT
Found at i:70369 original size:48 final size:49
Alignment explanation
Indices: 70202--70423 Score: 207
Period size: 52 Copynumber: 4.4 Consensus size: 49
70192 TCAAGTCGTA
*
70202 TCGTGAAGACCCTTG-AGCGAAGA-CAAGTGTTCGTGATCAATATCAAG
1 TCGTGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATATCAAG
* * * * *
70249 TCGTGAAGACCCTTGAAGAGAATATTAAAATTCTTCGTGATCAAGATCAAG
1 TCGTGAAGACCCTTGAAGAGAAGA-T-CAAGTGTTCGTGATCAATATCAAG
*
70300 TCGTGTCATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATATTAAG
1 TC--G---TGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATATCAAG
* * * * * *
70354 TCGTGAAGA-CTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAG
1 TCGTGAAGACCCTTGAAGAGAAG--A-T-CAAGTGTTCGTGATCAATATCAAG
70406 TCGTGAAGACCCTTGAAG
1 TCGTGAAGACCCTTGAAG
70424 CGAATCAAGA
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
47 15 0.11
48 18 0.13
49 6 0.04
50 1 0.01
51 23 0.16
52 28 0.20
53 8 0.06
54 21 0.15
55 1 0.01
56 20 0.14
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (49 bp):
TCGTGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTGATCAATATCAAG
Found at i:70416 original size:157 final size:156
Alignment explanation
Indices: 70017--70989 Score: 610
Period size: 157 Copynumber: 6.2 Consensus size: 156
70007 TTGAGCACGA
* *
70017 ATCAAGATCAAGTCGTGAAGACCCTTGAAG-GGAGATATTAAAATTCTTCGTGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATC-A-
** *
70081 TCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTTATTGATCAAGATCAAGTCATGTC
64 --A-GTCGTGAAGACCCTTGAAGAG-AATATTAAAA-TC-TTCGTGATCAAGATCAAGTCGTGT-
* * * * **
70146 GTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATG
122 ATGAAGACCCTTGAAGAGAAG--A-T-CAAGTGTTCGTG
* * * * * *
70185 ATCAAGATCAAGTCGTATCGTGAAGACCCTTG-AGCGAAG-----ACAAGTGTTCGTGATCAATA
1 ATCAAGATCAA---G--TCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGA
70244 TCAAGTCGTGAAGACCCTTGAAGAGAATATTAAAATTCTTCGTGATCAAGATCAAGTCGTGTCAT
61 TCAAGTCGTGAAGACCCTTGAAGAGAATATTAAAA-TCTTCGTGATCAAGATCAAGTCGTGT-AT
70309 GAAGACCCTTGAAGAGAAGATCAAGTGTTCGTG
124 GAAGACCCTTGAAGAGAAGATCAAGTGTTCGTG
* * *
70342 ATCAATATTAAGTCGTGAAGA-CTTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAG
* * * * * * *
70406 TCGTGAAGACCCTTGAAGCG-A-ATCAAGATCAAGTCGTG---AAGA-C---CCTTG-AAGAGGA
66 TCGTGAAGACCCTTGAAGAGAATATTAAAATC--TTCGTGATCAAGATCAAGTCGTGTATGA--A
** * ** * **
70461 GA-TATT--A-A-AA-TTCTTCGTGATCAAG
127 GACCCTTGAAGAGAAGATC-AAGTGTTCGTG
* *
70486 ATCAAG-TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAA-
* *
70550 TCGTATCGTGAAGACCCTTGAAGCGAAGATATT-AAA-GTTCGTGAT-AAGATCAAGTCGTG-A-
65 --G--TCGTGAAGACCCTTGAAGAG-A-ATATTAAAATCTTCGTGATCAAGATCAAGTCGTGTAT
*
70610 -AA-ACCCTTGAAGCGAAGATATCAAAGT-TT-GTG
124 GAAGACCCTTGAAGAGAAG--ATC-AAGTGTTCGTG
* *
70642 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATC-A-
** *
70707 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
64 --A-GTCGTGAAGACCCTTGAAGAG-A-ATATTAAAA-TCTTCGTGATCAAGATCAAGTCGTGT-
* * *
70772 GTGAAGACCCTTGAAGAGAAGACCAAGTGTTTGTG
122 ATGAAGACCCTTGAAGAGAAGATCAAGTGTTCGTG
* * *
70807 ATCAAGATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGATATT-AAA--GTTCGTGATCAAGA
1 ATCAAGATCAA---G--TCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGA
* * * * ** * *
70869 TCAAGTCGTGAAAACCCTTAAAGTGAAGA-CCAAGTGTTCGTGATCAAGATCAAGTC--G--TGA
61 TCAAGTCGTGAAGACCCTTGAAGAGAATATTAAAATCTTCGTGATCAAGATCAAGTCGTGTATGA
* *
70929 AGACCCTTGAAGCGAAGATATCAA-CGTTCGTG
126 AGACCCTTGAAGAGAAG--ATCAAGTGTTCGTG
* * *
70961 ATCAAGATCAAGTCATGAAAACTCTTGAA
1 ATCAAGATCAAGTCGTGAAGACCCTTGAA
70990 AACCAAGATC
Statistics
Matches: 648, Mismatches: 93, Indels: 147
0.73 0.10 0.17
Matches are distributed among these distances:
143 14 0.02
144 53 0.08
145 1 0.00
146 1 0.00
147 4 0.01
148 2 0.00
149 45 0.07
150 1 0.00
151 12 0.02
152 20 0.03
153 27 0.04
154 20 0.03
155 15 0.02
156 13 0.02
157 134 0.21
158 28 0.04
159 4 0.01
160 8 0.01
161 57 0.09
162 31 0.05
163 26 0.04
164 5 0.01
165 16 0.02
166 15 0.02
167 16 0.02
168 30 0.05
169 3 0.00
170 26 0.04
171 1 0.00
172 2 0.00
173 18 0.03
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (156 bp):
ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAG
TCGTGAAGACCCTTGAAGAGAATATTAAAATCTTCGTGATCAAGATCAAGTCGTGTATGAAGACC
CTTGAAGAGAAGATCAAGTGTTCGTG
Found at i:70436 original size:33 final size:33
Alignment explanation
Indices: 70394--70456 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
70384 ATTCTTCATG
70394 ATCAAGATCAAGTCGTGAAGACCCTTGAAGCGA
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGCGA
70427 ATCAAGATCAAGTCGTGAAGACCCTTGAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAG
70457 AGGAGATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (33 bp):
ATCAAGATCAAGTCGTGAAGACCCTTGAAGCGA
Found at i:70512 original size:58 final size:58
Alignment explanation
Indices: 70427--70875 Score: 489
Period size: 58 Copynumber: 8.1 Consensus size: 58
70417 CTTGAAGCGA
* *
70427 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAG
1 ATCAAG-TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
**
70486 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
* * * *
70544 ATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGATATT-AAA--GTTCGTGAT-AAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
* * * *
70598 ATC-A---A-GTCGTGAAAACCCTTGAAGCGAAGATA-TCAAAGT-TT-GTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
*
70648 ATC-A---A-GTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
**
70701 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
* * ** *
70759 ATCAAGTCGTATCGTGAAGACCCTTGAAGAGAAG--A-CCAAGTGT-TT-GTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAAT-TCTTCGTGATCAAG
* * * *
70813 ATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGATATT-AAA--GTTCGTGATCAAG
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
70868 ATCAAGTC
1 ATCAAGTC
70876 GTGAAAACCC
Statistics
Matches: 342, Mismatches: 30, Indels: 40
0.83 0.07 0.10
Matches are distributed among these distances:
48 1 0.00
49 33 0.10
50 34 0.10
51 5 0.01
52 2 0.01
53 13 0.04
54 50 0.15
55 28 0.08
56 5 0.01
57 4 0.01
58 161 0.47
59 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (58 bp):
ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCGTGATCAAG
Found at i:70526 original size:353 final size:356
Alignment explanation
Indices: 70075--70768 Score: 1000
Period size: 353 Copynumber: 2.0 Consensus size: 356
70065 CGTGATCAAG
* *
70075 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTTATTGATCAAGATCAAGT
1 ATCAAGTCAAGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTTAGTGATCAAGATCAAGT
70140 CATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATCG
66 CATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATCG
** * *
70205 TGAAGACCCTTG-AGCGAAGACA-AGTGTTCGTGATCAATATCAAGTCGTGAAGACCCTTGAAGA
131 TGAAGACCCTTGAAGCGAAGACATAAAGTTCGTGAT-AAGATCAAGTCGTGAAAACCCTTGAAGA
* *
70268 GAATAT-TAAAATTCTTCGTGATCAAGATCAAGTCGTGTCATGAAGACCCTTGAAGA-GA-AGA-
195 GAAGATATAAAAGT-TT-GTGATCAAGATCAAGTC--G---TGAAGACCCTTGAAGAGGAGAGAT
* * * *
70329 T-CAAGTGTTCGTGATC-A-AT-A-TTAAGTCGTGAAGA-CTTTGAAGAGAAGATATTAAAATTC
253 TAAAAGTCTTCGTGATCAAGATAAGTCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTC
70388 TTCATGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGA
318 TTCATGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGA
* *
70427 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTC-TTCGTGATCAAGATCAA
1 ATCAAG-TCAAGTCGTGAAGACCCTTGAAGA-GAAATATTAAAATTCTTTAGTGATCAAGATCAA
70491 GTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTAT
64 GTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTAT
*
70556 CGTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTGAA
129 CGTGAAGACCCTTGAAGCGAAGACA-TAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTGAA
* * *
70621 GCGAAGATATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAA
193 GAGAAGATATAAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGAGATTAAAA
* * *
70686 TTCTTCGTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTA
258 GTCTTCGTGATCAAGAT-AAGTCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCA
70751 TGATCAAGATCAAGTCGT
322 TGATCAAGATCAAGTCGT
70769 ATCGTGAAGA
Statistics
Matches: 305, Mismatches: 21, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
349 16 0.05
350 2 0.01
351 2 0.01
352 8 0.03
353 129 0.42
354 41 0.13
355 34 0.11
356 15 0.05
357 1 0.00
358 12 0.04
359 45 0.15
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (356 bp):
ATCAAGTCAAGTCGTGAAGACCCTTGAAGAGAAATATTAAAATTCTTTAGTGATCAAGATCAAGT
CATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATCG
TGAAGACCCTTGAAGCGAAGACATAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTGAAGAG
AAGATATAAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGAGATTAAAAGTC
TTCGTGATCAAGATAAGTCAAGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGAT
CAAGATCAAGTCGTGAAGACCCTTGAAGCGA
Found at i:70816 original size:215 final size:216
Alignment explanation
Indices: 70427--70887 Score: 766
Period size: 215 Copynumber: 2.1 Consensus size: 216
70417 CTTGAAGCGA
70427 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
70492 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
66 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
* *
70557 GTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAA-G-TCGTGAAAACCCTTGA
131 GTGAAGACCCTTGAAGAGAAGACA-TAAAGTTCGTGATAAGATCAACGATCGTGAAAACCCTTGA
*
70620 AGCGAAGATATCAAAGTTTGTG
195 AGCGAAGATATCAAAGTTCGTG
70642 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
1 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
70707 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
66 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
** * *
70772 GTGAAGACCCTTGAAGAGAAGACCA-AGTGTTTGTGATCAAGATCAAGTCGTATCGTGAAGACCC
131 GTGAAGACCCTTGAAGAGAAGA-CATAAAGTTCGTGAT-AAGATCAA--CG-ATCGTGAAAACCC
*
70836 TTGAAGCGAAGATATTAAAGTTCGTG
191 TTGAAGCGAAGATATCAAAGTTCGTG
*
70862 ATCAAGATCAAGTCGTGAAAACCCTT
1 ATCAAGATCAAGTCGTGAAGACCCTT
70888 AAAGTGAAGA
Statistics
Matches: 230, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
214 9 0.04
215 159 0.69
216 1 0.00
218 1 0.00
220 60 0.26
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (216 bp):
ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
GTGAAGACCCTTGAAGAGAAGACATAAAGTTCGTGATAAGATCAACGATCGTGAAAACCCTTGAA
GCGAAGATATCAAAGTTCGTG
Found at i:70828 original size:112 final size:103
Alignment explanation
Indices: 70474--70982 Score: 428
Period size: 99 Copynumber: 4.8 Consensus size: 103
70464 ATTAAAATTC
* *
70474 TTCGTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGA
1 TTCGTGATCAAGATCAAGTCGT-TCGTGAAGACCCTTGAAGCGAAGATATTAAAATTC---ATGA
* * * * **
70539 TCAAGATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGA-TATTAAAG
62 TCAAGATCAA---G--TCGTGAAAACCCTTAAAGAGAAGACCA--AGTG
* * * **
70587 TTCGTGAT-AAGATCAA---G-TCGTGAAAACCCTTGAAGCGAAGATATCAAAGTTTGTGATCAA
1 TTCGTGATCAAGATCAAGTCGTTCGTGAAGACCCTTGAAGCGAAGATATTAAAATTCATGATCAA
* * * * *
70647 GATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTA-AAATTC
66 GATCAAGTCGTGAAAACCCTT-AA-A-GAGA-A-GACCAAGTG
* *
70689 TTCGTGATCAAGATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGA
1 TTCGTGATCAAGATCAAGTCGT-TCGTGAAGACCCTTGAAGCGAAGATATTAAAATTC---ATGA
* *
70754 TCAAGATCAAGTCGTATCGTGAAGACCCTTGAAGAGAAGACCAAGTG
62 TCAAGATCAA---G--TCGTGAAAACCCTTAAAGAGAAGACCAAGTG
* * *
70801 TTTGTGATCAAGATCAAGTCGTATCGTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATCA
1 TTCGTGATCAAGATCAAGTCGT-TCGTGAAGACCCTTGAAGCGAAGATATTAAAATTCATGATCA
*
70866 AGATCAAGTCGTGAAAACCCTTAAAGTGAAGACCAAGTG
65 AGATCAAGTCGTGAAAACCCTTAAAGAGAAGACCAAGTG
* ** *
70905 TTCGTGATCAAGATCAA---G-TCGTGAAGACCCTTGAAGCGAAGATATCAACGTTCGTGATCAA
1 TTCGTGATCAAGATCAAGTCGTTCGTGAAGACCCTTGAAGCGAAGATATTAAAATTCATGATCAA
*
70966 GATCAAGTCATGAAAAC
66 GATCAAGTCGTGAAAAC
70983 TCTTGAAAAC
Statistics
Matches: 337, Mismatches: 39, Indels: 54
0.78 0.09 0.13
Matches are distributed among these distances:
99 71 0.21
100 1 0.00
101 3 0.01
102 12 0.04
103 9 0.03
104 59 0.18
106 1 0.00
107 30 0.09
108 30 0.09
109 13 0.04
111 14 0.04
112 65 0.19
113 12 0.04
114 2 0.01
115 1 0.00
116 14 0.04
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (103 bp):
TTCGTGATCAAGATCAAGTCGTTCGTGAAGACCCTTGAAGCGAAGATATTAAAATTCATGATCAA
GATCAAGTCGTGAAAACCCTTAAAGAGAAGACCAAGTG
Found at i:70925 original size:269 final size:267
Alignment explanation
Indices: 70427--70977 Score: 815
Period size: 269 Copynumber: 2.0 Consensus size: 267
70417 CTTGAAGCGA
* * *
70427 ATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAATTCTTCGTGATCAAGATCAAG
1 ATCAAG-TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAG
* *
70492 TCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGTCGTATC
65 TCATATCGTGAAGACCCTTGAAGAGAAGA-A-TAAAAGTCTTTATGATCAAGATCAAGTCGTATC
*
70557 GTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTGAAG
128 GTGAAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTAAAG
*
70622 CGAAGATATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGGAGATATTAAAAT
193 CGAAGA-ATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATA-T-AAA-
70687 TC-TTCGTGATCAAG
254 -CGTTCGTGATCAAG
*
70701 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTTATGATCAAGATCAAGT
1 ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGT
* ** * *
70766 CGTATCGTGAAGACCCTTGAAGAGAAG-A-CCAAGTGTTTGTGATCAAGATCAAGTCGTATCGTG
66 CATATCGTGAAGACCCTTGAAGAGAAGAATAAAAGTCTTTATGATCAAGATCAAGTCGTATCGTG
*
70829 AAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATCAAGATCAAGTCGTGAAAACCCTTAAAGTG
131 AAGACCCTTGAAGCGAAGATATTAAAGTTCGTGAT-AAGATCAAGTCGTGAAAACCCTTAAAGCG
* * *
70894 AAG-A-CCAAGTGTTCGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGCGAAGATATCAACGTT
195 AAGAATCAAAGT-TT-GTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATAAACGTT
70957 CGTGATCAAG
258 CGTGATCAAG
70967 ATCAAGTCATG
1 ATCAAGTCATG
70978 AAAACTCTTG
Statistics
Matches: 256, Mismatches: 17, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
265 1 0.00
266 23 0.09
267 7 0.03
268 4 0.02
269 104 0.41
270 30 0.12
271 1 0.00
273 80 0.31
274 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (267 bp):
ATCAAGTCATGTCGTGAAGACCCTTGAAGAGAAGATATTAAAATTCTTCATGATCAAGATCAAGT
CATATCGTGAAGACCCTTGAAGAGAAGAATAAAAGTCTTTATGATCAAGATCAAGTCGTATCGTG
AAGACCCTTGAAGCGAAGATATTAAAGTTCGTGATAAGATCAAGTCGTGAAAACCCTTAAAGCGA
AGAATCAAAGTTTGTGATCAAGATCAAGTCGTGAAGACCCTTGAAGAGAAGATATAAACGTTCGT
GATCAAG
Found at i:71638 original size:22 final size:23
Alignment explanation
Indices: 71613--71656 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
71603 ACAAATAAAG
71613 TAAAAAAGT-TAAAATTT-TTTAT
1 TAAAAAAGTAT-AAATTTATTTAT
71635 TAAAAAAGTATAAATTTATTTA
1 TAAAAAAGTATAAATTTATTTA
71657 ATTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TAAAAAAGTATAAATTTATTTAT
Found at i:72002 original size:15 final size:15
Alignment explanation
Indices: 71963--72004 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
71953 TTTACAATGC
*
71963 AATGTGATTACAGGT
1 AATGTGATTGCAGGT
* *
71978 AATATAATTGCAGGT
1 AATGTGATTGCAGGT
71993 AATGTGATTGCA
1 AATGTGATTGCA
72005 AGCAATGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAGGT
Found at i:72011 original size:15 final size:15
Alignment explanation
Indices: 71961--72012 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
71951 ACTTTACAAT
*
71961 GCAATGTGATTACAG
1 GCAATGTGATTGCAG
* * *
71976 GTAATATAATTGCAG
1 GCAATGTGATTGCAG
* *
71991 GTAATGTGATTGCAA
1 GCAATGTGATTGCAG
72006 GCAATGT
1 GCAATGT
72013 CATTACAGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (15 bp):
GCAATGTGATTGCAG
Found at i:72273 original size:33 final size:34
Alignment explanation
Indices: 72234--72316 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
72224 ATTTTTAAGG
*
72234 TTATATATTTTATATTCATTT-ATTATTATAATC
1 TTATATATTTTATATTCATTTCATTAATATAATC
* * *
72267 TTATATATTTTATTTTCATTTCTTTAATATAATT
1 TTATATATTTTATATTCATTTCATTAATATAATC
* *
72301 TTTTATATTATATATT
1 TTATATATTTTATATT
72317 TTATTTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 20 0.48
34 22 0.52
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (34 bp):
TTATATATTTTATATTCATTTCATTAATATAATC
Found at i:72308 original size:34 final size:33
Alignment explanation
Indices: 72234--72322 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
72224 ATTTTTAAGG
* *
72234 TTATATATTTTATATTCATTTATTATTATAATC
1 TTATATATTTTATTTTCATTTATTAATATAATC
* *
72267 TTATATATTTTATTTTCATTTCTTTAATATAATT
1 TTATATATTTTATTTTCATTT-ATTAATATAATC
*
72301 TTTTATATTATATATTTT-ATTT
1 TTATATATT-T-TATTTTCATTT
72323 TAATTTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 20 0.42
34 17 0.35
35 5 0.10
36 6 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (33 bp):
TTATATATTTTATTTTCATTTATTAATATAATC
Found at i:72367 original size:35 final size:32
Alignment explanation
Indices: 72304--72369 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
72294 TATAATTTTT
72304 TATATTATATATTTTATTTTAATTTATTTTACC
1 TATATTATATATTTTATTTT-ATTTATTTTACC
72337 TATATTATATAAATTTTAATTTT-TTATATTTTA
1 TATATTATAT--ATTTT-ATTTTATT-TATTTTA
72370 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 12 0.41
36 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
TATATTATATATTTTATTTTATTTATTTTACC
Found at i:72387 original size:33 final size:34
Alignment explanation
Indices: 72350--72424 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
72340 ATTATATAAA
72350 TTTTAATTTTTTATATT-T-TATTTTATTTTAAT-T
1 TTTT-ATTTTTTATATTATATATTTTA-TTTAATAT
72383 TTTTA-TTTTTATATTATATATTTTATTTAATAT
1 TTTTATTTTTTATATTATATATTTTATTTAATAT
72416 TTTTATTTT
1 TTTTATTTT
72425 AATTATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
31 10 0.26
32 8 0.21
33 17 0.45
34 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTTATTTTTTATATTATATATTTTATTTAATAT
Found at i:72391 original size:38 final size:39
Alignment explanation
Indices: 72349--72424 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
72339 TATTATATAA
* *
72349 ATTTTAATTTTTTATATTTTATTT-TATTTTAATTTTTT
1 ATTTTAATATTATATATTTTATTTATATTTTAATTTTTT
* *
72387 ATTTTTATATTATATATTTTATTTAATATTTTTATTTT
1 ATTTTAATATTATATATTTTATTT-ATATTTTAATTTT
72425 AATTATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 21 0.66
40 11 0.34
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (39 bp):
ATTTTAATATTATATATTTTATTTATATTTTAATTTTTT
Found at i:72416 original size:50 final size:54
Alignment explanation
Indices: 72313--72425 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 54
72303 TTATATTATA
*
72313 TATTTTATTTTAATTTATTTTACCTATATTATATAAATTTTAATTTT-TTATATTT
1 TATTTTATTTTAATTTATTTTACCTATATTATAT-AATTTTAATTTTAATAT-TTT
***
72368 TATTTTATTTTAATTT-TTTATTTTTATATTATAT-ATTTT-A-TTTAATATTTT
1 TATTTTATTTTAATTTATTT-TACCTATATTATATAATTTTAATTTTAATATTTT
72419 TATTTTA
1 TATTTTA
72426 ATTATAACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
51 13 0.25
52 4 0.08
53 5 0.10
54 3 0.06
55 27 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (54 bp):
TATTTTATTTTAATTTATTTTACCTATATTATATAATTTTAATTTTAATATTTT
Found at i:80095 original size:20 final size:19
Alignment explanation
Indices: 80054--80117 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
80044 TTATTAATAG
* *
80054 TAGA-TATCTATTTATTAA
1 TAGATTATCTATCTATCAA
*
80072 TAGATTATGTGATCTATCAA
1 TAGATTATCT-ATCTATCAA
* *
80092 TAGAATTTTCTATCTATCGA
1 TAG-ATTATCTATCTATCAA
80112 TAGATT
1 TAGATT
80118 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 21 0.57
21 5 0.14
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (19 bp):
TAGATTATCTATCTATCAA
Found at i:80211 original size:15 final size:14
Alignment explanation
Indices: 80193--80231 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
80183 TTTATATATT
80193 TTAATATTTAAATAA
1 TTAATATTTAAAT-A
*
80208 TTAATATATAAATA
1 TTAATATTTAAATA
80222 TTATATATTT
1 TTA-ATATTT
80232 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATTTAAATA
Found at i:80239 original size:26 final size:24
Alignment explanation
Indices: 80208--80256 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
80198 ATTTAAATAA
80208 TTAAT-ATATAAATATTATATATTTTT
1 TTAATAATAT-AAT-TTAT-TATTTTT
80234 TTAATAATATAATTTATTATTTT
1 TTAATAATATAATTTATTATTTT
80257 AATTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 8 0.36
27 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAATAATATAATTTATTATTTTT
Found at i:80251 original size:21 final size:21
Alignment explanation
Indices: 80218--80259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
80208 TTAATATATA
* *
80218 AATATTATATATTTTTTTAAT
1 AATATAATATATTATTTTAAT
*
80239 AATATAATTTATTATTTTAAT
1 AATATAATATATTATTTTAAT
80260 TATTTAAAGT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATAATATATTATTTTAAT
Found at i:108602 original size:2 final size:2
Alignment explanation
Indices: 108595--108621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
108585 TTCAAAGAAC
108595 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
108622 TAAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:115605 original size:2 final size:2
Alignment explanation
Indices: 115593--115623 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
115583 AACACAAGCA
*
115593 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115624 ATTGGCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:132062 original size:21 final size:22
Alignment explanation
Indices: 132038--132081 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
132028 AATTGATCAA
132038 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* * *
132059 TTTATGTTGTTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
132081 T
1 T
132082 ACTTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:188050 original size:12 final size:12
Alignment explanation
Indices: 188033--188059 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
188023 ACAACTCAGT
188033 GAAGACAGCAAA
1 GAAGACAGCAAA
188045 GAAGACAGCAAA
1 GAAGACAGCAAA
188057 GAA
1 GAA
188060 TGAATCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGACAGCAAA
Found at i:211140 original size:2 final size:2
Alignment explanation
Indices: 211133--211157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
211123 GTCTGTTTAT
211133 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
211158 GCATAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:257866 original size:46 final size:46
Alignment explanation
Indices: 257788--257915 Score: 220
Period size: 46 Copynumber: 2.8 Consensus size: 46
257778 CTTTTGACAG
* * * *
257788 TTTCTATGGAGAAATCTAAATGGAGGTTAGAACCAAGAAGTTACGC
1 TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAAGAAGTTACGC
257834 TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAAGAAGTTACGC
1 TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAAGAAGTTACGC
257880 TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAA
1 TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAA
257916 AAAAGTTGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (46 bp):
TTTCCATGGAGAAATCTGAATGGAGATCAGAACCAAGAAGTTACGC
Found at i:258101 original size:119 final size:118
Alignment explanation
Indices: 257891--258107 Score: 265
Period size: 119 Copynumber: 1.8 Consensus size: 118
257881 TTCCATGGAG
* * *
257891 AAATCTGAATGGAGATCAGAACCAAAAAAGTTGAAAAACCACTAAACGTGTCTAAAAGGGAATAA
1 AAATCTGAATGGAGATCAGAACCAAAAAAGTTGAAAAACCAATAAAAGTGTCTAAAAGGGAAGAA
*
257956 TGATAATAATAAAAAATGGTGGAAGAAGAAGGGTGGTGGAATCAGATGCCATA
66 TGATAATAATAAAAAATGGTGGAAGAACAAGGGTGGTGGAATCAGATGCCATA
** ** * * **
258009 AAATCTGAATGGAGATCAGAATGTAGGAAGGTTGAGAAACCAATAAAAGTGTCTGGAAGGGAAGA
1 AAATCTGAATGGAGATCAGAA-CCAAAAAAGTTGAAAAACCAATAAAAGTGTCTAAAAGGGAAGA
*** *
258074 ATGATAACTAA-AAAGGGTGTTGGAAGAACAAGGG
65 ATGATAA-TAATAAAAAATGGTGGAAGAACAAGGG
258108 AGATTAGATG
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
118 21 0.26
119 57 0.70
120 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.27, T:0.18
Consensus pattern (118 bp):
AAATCTGAATGGAGATCAGAACCAAAAAAGTTGAAAAACCAATAAAAGTGTCTAAAAGGGAAGAA
TGATAATAATAAAAAATGGTGGAAGAACAAGGGTGGTGGAATCAGATGCCATA
Found at i:260911 original size:252 final size:252
Alignment explanation
Indices: 260349--261461 Score: 1169
Period size: 252 Copynumber: 4.4 Consensus size: 252
260339 TTTAAACAGA
* * * * * *
260349 TTAAATCTCACCCATTTATGTCAATTTTTTAACAATGTCTATTCCACCTTTATATATTTTTTACA
1 TTAAATTTCACACATTTACGTCAATATTTTGACAATGTCTATTCTACCTTTATA-ATTTTTTACA
* * * * * * ** *
260414 TTAATTCTCACTATTTTACATCAAGGTTTGTCAACCACTAATTTTCTCTATACTTGGTTTTATAC
65 TTAATTCTTACTACTTTACATCAAGATTTTTCAACTACTAATTTTCTCTATAATTATTTTTATCC
* * * *
260479 TTACTATTATTTATTCATAGATTAAAGTTTGTAAACCGTTACATACTTGAAACTCAAGAATAAAA
130 TTATTATTATTCATTCATAGATTAAAATTTGTAAACCGTTACAAACTTGAAACTCAAGAATAAAA
* * * *
260544 ACTTAAATGCTTAATTTTTTC-AAAATTATATTTATTTGATATAATTGATTTTTTACG
195 ATTTAAATGTTTAATTTTTTCAAAAATTATATTTATTTGACATAATTGACTTTTTACG
* *
260601 TTAAATTTCACACATTTACGTCAGTATTTTGACAATGTCTATTCCACCTTTCATAATTTTTTACA
1 TTAAATTTCACACATTTACGTCAATATTTTGACAATGTCTATTCTACCTTT-ATAATTTTTTACA
* * * * *
260666 TTAATTTTTACTACTTTACATCAAGATTTTTTAACTATTAATTTTTTGTATAATTATTTTTATCA
65 TTAATTCTTACTACTTTACATCAAGATTTTTCAACTACTAATTTTCTCTATAATTATTTTTATC-
* * *
260731 C-TATTATTATTCATTCATAGATTAAAATTTGTAAGCCATTACAAACTTGAAATTCAAGAATAAA
129 CTTATTATTATTCATTCATAGATTAAAATTTGTAAACCGTTACAAACTTGAAACTCAAGAATAAA
*
260795 ATTTTAAATGTTTAATTTTTTCAAAAATTA-AGTTTATTTGACATAATTGACTTTTTACG
194 AATTTAAATGTTTAATTTTTTCAAAAATTATA-TTTATTTGACATAATTGACTTTTTACG
* ** * **
260854 TTAAATTTCACATATTTATATCAATATTTTGACAATGTCTATTCTGCCTTTATAATTTTTTAGGT
1 TTAAATTTCACACATTTACGTCAATATTTTGACAATGTCTATTCTACCTTTATAATTTTTTACAT
* ** ** * *
260919 TAATTTTTACTGTTTTATGTCAA-AGTTTTTCAATTACTAATTTTCTGTATAATTA-TTTTATCC
66 TAATTCTTACTACTTTACATCAAGA-TTTTTCAACTACTAATTTTCTCTATAATTATTTTTATCC
* * *** * * **
260982 TTATTATTATTCATTTATAGATTGAAATTTGTAAGTTGTTA-AATACTTTACACTTGAGAATAAA
130 TTATTATTATTCATTCATAGATTAAAATTTGTAAACCGTTACAA-ACTTGAAACTCAAGAATAAA
* ** * * *
261046 AATTTAAATGTTTAATTTCTAAAAAAATTATATTTATTTGA-AGTAATTAACTTGTTATG
194 AATTTAAATGTTTAATTTTTTCAAAAATTATATTTATTTGACA-TAATTGACTTTTTACG
* * * **
261105 TTAAATTTCATATATTTACGTCAATATTTTGACAA-GCTTTATTCTACCTTTATAATTTTTTATG
1 TTAAATTTCACACATTTACGTCAATATTTTGACAATG-TCTATTCTACCTTTATAATTTTTTACA
* * * * * * * *
261169 TTAATCCTTATTGCTTTA-AGTCAACATTTTTTAACAAGTAATTTT-TACTCTAATTATTTTTAT
65 TTAATTCTTACTACTTTACA-TCAAGATTTTTCAACTACTAATTTTCT-CTATAATTATTTTTAT
* * * * * *
261232 CCTTATTATTTTTTATTTACAGATTAAAATTTGTAAACCGTTACATACTTTAAACTCAAGAAT-A
128 CCTTATTATTATTCATTCATAGATTAAAATTTGTAAACCGTTACAAACTTGAAACTCAAGAATAA
* * *
261296 AAATTTAAATATTTAATTTTTTCAAAAA-T-TATGTATTTAACATAATTGACTTTTTACG
193 AAATTTAAATGTTTAATTTTTTCAAAAATTATATTTATTTGACATAATTGACTTTTTACG
* * * * * *
261354 TTAAATCTCACACATATACATTAATATTTTGACAAT-ACTTATTCTACTTTTATAATTTTTTACA
1 TTAAATTTCACACATTTACGTCAATATTTTGACAATGTC-TATTCTACCTTTATAATTTTTTACA
* *
261418 TTAATTCTTACTACTTTATC-TC-AGAATTTTTCAATTACTGATTT
65 TTAATTCTTACTACTTTA-CATCAAG-ATTTTTCAACTACTAATTT
261462 GTACTATATA
Statistics
Matches: 718, Mismatches: 122, Indels: 45
0.81 0.14 0.05
Matches are distributed among these distances:
248 1 0.00
249 104 0.14
250 8 0.01
251 227 0.32
252 296 0.41
253 82 0.11
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (252 bp):
TTAAATTTCACACATTTACGTCAATATTTTGACAATGTCTATTCTACCTTTATAATTTTTTACAT
TAATTCTTACTACTTTACATCAAGATTTTTCAACTACTAATTTTCTCTATAATTATTTTTATCCT
TATTATTATTCATTCATAGATTAAAATTTGTAAACCGTTACAAACTTGAAACTCAAGAATAAAAA
TTTAAATGTTTAATTTTTTCAAAAATTATATTTATTTGACATAATTGACTTTTTACG
Found at i:262906 original size:18 final size:18
Alignment explanation
Indices: 262864--262906 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
262854 AATAGTCGCA
262864 CAATGCTCTCACCAATGC
1 CAATGCTCTCACCAATGC
*
262882 CAGATGCTC-CACCAGTGAC
1 CA-ATGCTCTCACCAATG-C
262901 CAATGC
1 CAATGC
262907 CACTTTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (18 bp):
CAATGCTCTCACCAATGC
Found at i:272923 original size:18 final size:19
Alignment explanation
Indices: 272887--272925 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
272877 CGACAGCCGC
*
272887 GAAGCAGCAAGAAAGAAGA
1 GAAGCAGCAAGAAAAAAGA
*
272906 GAAGCA-CAGGAAAAAAGA
1 GAAGCAGCAAGAAAAAAGA
272924 GA
1 GA
272926 TGGGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.59, C:0.10, G:0.31, T:0.00
Consensus pattern (19 bp):
GAAGCAGCAAGAAAAAAGA
Found at i:291130 original size:15 final size:12
Alignment explanation
Indices: 291098--291123 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
291088 GACCAATGGA
291098 AGCACAACAAAG
1 AGCACAACAAAG
291110 AGCACAACAAAG
1 AGCACAACAAAG
291122 AG
1 AG
291124 TATCACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.23, G:0.19, T:0.00
Consensus pattern (12 bp):
AGCACAACAAAG
Found at i:297721 original size:215 final size:216
Alignment explanation
Indices: 297471--297897 Score: 559
Period size: 215 Copynumber: 2.0 Consensus size: 216
297461 AATTGAGTAA
* *
297471 ATATATTATATATACATATATTTAATTTATACATAAATATTACTATAAATTATAATAGACTTTAT
1 ATATATTATATATACA-ATATTTAATTTATACATAAATATTACTACAAATTATAATAAACTTTAT
* ** * ** * * *
297536 TTATATGATTATACTAAATAACTTTATTAGTTATCATCTTATTTTTTTTATAACATTGTTTATAA
65 TTATATGATTACACTAAATAACTTTATTAACTATCATATTAGGTTTTATAGAACATTATTTATAA
* * * * * *
297601 TTAGTTATTATTTATACAAATTTTGATATAAAATATTTTAAAATATAATTTGTATCATTAAATAT
130 TTAGTTATTATTTATACAAACTTAGATATAAAACATTATAAAATATAAGTTATATCATTAAATAT
297666 ATATATACATATATATAACGTC
195 ATATATACATATATATAACGTC
* *
297688 ATATATTATATATAC-ATATTTAATTTATACATAAGTATTACTACAACTTATAATAAACTTTATT
1 ATATATTATATATACAATATTTAATTTATACATAAATATTACTACAAATTATAATAAACTTTATT
* * * * *
297752 TATATGATTCCACTTAATAAGTTTATTAACTATCATATTAGGTTTTATAGCATATTATTTATAAT
66 TATATGATTACACTAAATAACTTTATTAACTATCATATTAGGTTTTATAGAACATTATTTATAAT
* ** * * *
297817 TAGTTATTATTTATACAAACTTAGATATTAAACATTATAGCATATAAGTTATATCATTCATTTTA
131 TAGTTATTATTTATACAAACTTAGATATAAAACATTATAAAATATAAGTTATATCATTAAATATA
*
297882 TATATATATATATATA
196 TATATACATATATATA
297898 TATATAATTA
Statistics
Matches: 179, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
215 164 0.92
217 15 0.08
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.47
Consensus pattern (216 bp):
ATATATTATATATACAATATTTAATTTATACATAAATATTACTACAAATTATAATAAACTTTATT
TATATGATTACACTAAATAACTTTATTAACTATCATATTAGGTTTTATAGAACATTATTTATAAT
TAGTTATTATTTATACAAACTTAGATATAAAACATTATAAAATATAAGTTATATCATTAAATATA
TATATACATATATATAACGTC
Found at i:301482 original size:83 final size:83
Alignment explanation
Indices: 301343--301510 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
301333 GCTAATAAAT
*
301343 GAAAAGAAATTGTATCAGATAAGATGACCAACATGAACAGAAAATCTTTTCATCTGTTACAAATG
1 GAAAAGAAATTGTATCAGATAAGATGACCAACAAGAACAGAAAATCTTTTCATCTGTTACAAATG
301408 GTTTAAGAGAAAAGGTAG
66 GTTTAAGAGAAAAGGTAG
*
301426 GAAAAGAAATTGTATCAGGTAAGATGACCAACAAGAACAGAAAATCTTTTCATCTGTTACAAATG
1 GAAAAGAAATTGTATCAGATAAGATGACCAACAAGAACAGAAAATCTTTTCATCTGTTACAAATG
301491 GTTTAAGAGAAAAGGTAG
66 GTTTAAGAGAAAAGGTAG
301509 GA
1 GA
301511 TGATGAAGTG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (83 bp):
GAAAAGAAATTGTATCAGATAAGATGACCAACAAGAACAGAAAATCTTTTCATCTGTTACAAATG
GTTTAAGAGAAAAGGTAG
Found at i:316633 original size:191 final size:191
Alignment explanation
Indices: 316309--316691 Score: 667
Period size: 191 Copynumber: 2.0 Consensus size: 191
316299 TCAGGTCAAC
* *
316309 TAGGGATTGGAGGTGTGCTACGGAATGATTTAGGAAAAGTGAAGCTTATTTTTTCTTAGAAAGTA
1 TAGGGATTGGAGGTGTGCTACGGAATGATTTAGGAAAAGTGAAACTTATTTTCTCTTAGAAAGTA
316374 GGTTAGGATGATGCGAACCTTGCTGAAATTATAGTGATACAAGAGGCCATGATCATCTTCGCAGC
66 GGTTAGGATGATGCGAACCTTGCTGAAATTATAGTGATACAAGAGGCCATGATCATCTTCGCAGC
* *
316439 TTCCTCTTGGGTTAACCTTGCTAGTATTTTTATTGAAAATGACTCCAGGAATACAGTTACT
131 TTCCTCTTGGGTTAACCTTGCTAGTATTATTATTGAAAATGACTCCAGGAATACAATTACT
* * *
316500 TAGGGATTGGAGGTGTGCTACGGAATGATTTGGGAAAGGTGAAACTTGTTTTCTCTTAGAAAGTA
1 TAGGGATTGGAGGTGTGCTACGGAATGATTTAGGAAAAGTGAAACTTATTTTCTCTTAGAAAGTA
* * *
316565 GGTTCGGGTGATGCGAACCTTGCTGAAATTATGGTGATACAAGAGGCCATGATCATCTTCGCAGC
66 GGTTAGGATGATGCGAACCTTGCTGAAATTATAGTGATACAAGAGGCCATGATCATCTTCGCAGC
*
316630 TTCCTCTTGGGTTAACCTTGCTAGTATTATTATTGAAAATGACTCTAGGAATACAATTACT
131 TTCCTCTTGGGTTAACCTTGCTAGTATTATTATTGAAAATGACTCCAGGAATACAATTACT
316691 T
1 T
316692 GGATAATCAA
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
191 181 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (191 bp):
TAGGGATTGGAGGTGTGCTACGGAATGATTTAGGAAAAGTGAAACTTATTTTCTCTTAGAAAGTA
GGTTAGGATGATGCGAACCTTGCTGAAATTATAGTGATACAAGAGGCCATGATCATCTTCGCAGC
TTCCTCTTGGGTTAACCTTGCTAGTATTATTATTGAAAATGACTCCAGGAATACAATTACT
Found at i:318038 original size:74 final size:74
Alignment explanation
Indices: 317936--318077 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 74
317926 ATGAATGAAA
* * * **
317936 TAAATTTTACAAATAATTATGATTAAAAATATTTCAATAAT-GTTCATTTGGTGAATACATATAT
1 TAAATCTTACAAATAATTATAATAAAAAATATTTCAATAATCG-TCATTTAATGAATACATATAT
318000 ATAATAGGTT
65 ATAATAGGTT
* *
318010 TAAATCTTACTAAA-AATTATAATAAAAAATATTTCAATGATCGTCATTTAATGAATACATATTT
1 TAAATCTTAC-AAATAATTATAATAAAAAATATTTCAATAATCGTCATTTAATGAATACATATAT
318074 ATAA
65 ATAA
318078 GTATATGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 55 0.93
75 4 0.07
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (74 bp):
TAAATCTTACAAATAATTATAATAAAAAATATTTCAATAATCGTCATTTAATGAATACATATATA
TAATAGGTT
Found at i:332415 original size:77 final size:77
Alignment explanation
Indices: 332283--332439 Score: 271
Period size: 77 Copynumber: 2.0 Consensus size: 77
332273 CCAACTAGCT
* * *
332283 AGCTTTAGTAAACACATTTAATGATTGTATCAAAAACCCTTTTCTCTTCTTTTTCTTTCTTTTTT
1 AGCTTTAGTAAACACATTTAATGATTGTATCAAAAACCCGTTTCTCTTCTCTTTCTTTCTTTATT
332348 GTTGGTTTTGGA
66 GTTGGTTTTGGA
332360 AGCTTTAGTAAACAC-TTTCAATGATTGTATCAAAAACCCGTTTCTCTTCTCTTTCTTTCTTTAT
1 AGCTTTAGTAAACACATTT-AATGATTGTATCAAAAACCCGTTTCTCTTCTCTTTCTTTCTTTAT
332424 TGTTGGTTTTGGA
65 TGTTGGTTTTGGA
332437 AGC
1 AGC
332440 CATTGAAACT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 3 0.04
77 73 0.96
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (77 bp):
AGCTTTAGTAAACACATTTAATGATTGTATCAAAAACCCGTTTCTCTTCTCTTTCTTTCTTTATT
GTTGGTTTTGGA
Found at i:352644 original size:2 final size:2
Alignment explanation
Indices: 352637--352675 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
352627 AGTGGGGGAA
*
352637 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
352676 ACAGAGAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:371627 original size:16 final size:15
Alignment explanation
Indices: 371594--371633 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
371584 TCATTTATTC
371594 TTTTTTATTTTCAAT
1 TTTTTTATTTTCAAT
371609 TTTTTTAATTTTC--T
1 TTTTTT-ATTTTCAAT
371623 TTTTTT-TTTTC
1 TTTTTTATTTTC
371634 TAGCTGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
14 7 0.29
15 6 0.25
16 6 0.25
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTATTTTCAAT
Found at i:378720 original size:2 final size:2
Alignment explanation
Indices: 378713--378739 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
378703 TCCGTATAAG
378713 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
378740 CACACACTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386961 original size:24 final size:24
Alignment explanation
Indices: 386929--386978 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
386919 ACATTACAAA
*
386929 ACAATCAATTTAATCACTTAAGTG
1 ACAATCAATTCAATCACTTAAGTG
*
386953 ACAATCAATTCAGTCACTTAAGTG
1 ACAATCAATTCAATCACTTAAGTG
386977 AC
1 AC
386979 CATTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (24 bp):
ACAATCAATTCAATCACTTAAGTG
Found at i:403232 original size:2 final size:2
Alignment explanation
Indices: 403225--403250 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
403215 TTCTAAAAGC
403225 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
403251 TTACATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:407709 original size:22 final size:23
Alignment explanation
Indices: 407684--407737 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
407674 ATTTCTACTT
407684 TATTCTATTTTTTA-AAAATAAA
1 TATTCTATTTTTTATAAAATAAA
* *
407706 TATTTTA-TTTTTATAAAATAAT
1 TATTCTATTTTTTATAAAATAAA
407728 TATTCTATTT
1 TATTCTATTT
407738 CATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 19 0.70
23 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTCTATTTTTTATAAAATAAA
Found at i:423572 original size:27 final size:27
Alignment explanation
Indices: 423534--423585 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
423524 TGGAGTAGTC
* *
423534 GCTCCGAGCCCTCAGATTCAGTCCCGT
1 GCTCCAAGCCCTCAGAATCAGTCCCGT
423561 GCTCCAAGCCCTCAGAATCAGTCCC
1 GCTCCAAGCCCTCAGAATCAGTCCC
423586 CCGATGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (27 bp):
GCTCCAAGCCCTCAGAATCAGTCCCGT
Found at i:431806 original size:2 final size:2
Alignment explanation
Indices: 431799--431832 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
431789 GAAATTAGTG
431799 AT AT AT AT GAT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
431833 TCAAATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:432969 original size:19 final size:18
Alignment explanation
Indices: 432932--432974 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
432922 GTGCATGGCA
* *
432932 TTAGGGTTAGGGGATAGG
1 TTAGGGGTAGGGGAGAGG
*
432950 TGTAGGGGTAGGGGGGAGG
1 T-TAGGGGTAGGGGAGAGG
432969 TTAGGG
1 TTAGGG
432975 TTGGAATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.19, C:0.00, G:0.58, T:0.23
Consensus pattern (18 bp):
TTAGGGGTAGGGGAGAGG
Found at i:433760 original size:2 final size:2
Alignment explanation
Indices: 433753--433780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
433743 TATACATCAT
433753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
433781 GAAAGCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:438811 original size:17 final size:17
Alignment explanation
Indices: 438785--438818 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
438775 AATAATCCTT
438785 AAATAGAAACATGTTTA
1 AAATAGAAACATGTTTA
* *
438802 AAATATAAACTTGTTTA
1 AAATAGAAACATGTTTA
438819 TTTGGTTAAA
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:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATAGAAACATGTTTA
Found at i:460225 original size:26 final size:26
Alignment explanation
Indices: 460194--460245 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
460184 TCCTATTATT
460194 TAGTTTGATATAGCAATTATGATTAA
1 TAGTTTGATATAGCAATTATGATTAA
460220 TAGTTTGATATAGCAATTATGATTAA
1 TAGTTTGATATAGCAATTATGATTAA
460246 AAATTGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (26 bp):
TAGTTTGATATAGCAATTATGATTAA
Found at i:466124 original size:22 final size:22
Alignment explanation
Indices: 466096--466144 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
466086 TAATATAATA
466096 ATTATTAGAAATATTAATTCAT
1 ATTATTAGAAATATTAATTCAT
466118 ATTATTAGAAATATTAATTCAT
1 ATTATTAGAAATATTAATTCAT
466140 ATTAT
1 ATTAT
466145 AAATAGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTATTAGAAATATTAATTCAT
Found at i:466148 original size:19 final size:19
Alignment explanation
Indices: 466098--466154 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
466088 ATATAATAAT
*
466098 TATTAGAAATATTAATTCA
1 TATTATAAATATTAATTCA
466117 TATTATTAGAAATATTAATTCA
1 TATTA-T--AAATATTAATTCA
*
466139 TATTATAAATAGTAAT
1 TATTATAAATATTAAT
466155 AAGGATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 14 0.42
21 1 0.03
22 18 0.55
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (19 bp):
TATTATAAATATTAATTCA
Found at i:466167 original size:3 final size:3
Alignment explanation
Indices: 466159--466183 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
466149 AGTAATAAGG
466159 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
466184 AGACCGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:466399 original size:31 final size:30
Alignment explanation
Indices: 466320--466407 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
466310 AATGTGGTAA
*
466320 ATAATAATA-TTTATTTTATTTTATTTACT
1 ATAATAATATTTTATTTTATTATATTTACT
* **
466349 -TAATAATACTATTTCTTTTATTATATTTTGT
1 ATAATAATA-T-TTTATTTTATTATATTTACT
*
466380 ATAATCAATATTTTATTTTA-AATATTTA
1 ATAAT-AATATTTTATTTTATTATATTTA
466408 TATTTTGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 8 0.17
30 6 0.13
31 24 0.51
32 5 0.11
33 4 0.09
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (30 bp):
ATAATAATATTTTATTTTATTATATTTACT
Found at i:466405 original size:14 final size:16
Alignment explanation
Indices: 466386--466419 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
466376 TTGTATAATC
466386 AATATTT-TATTTT-A
1 AATATTTATATTTTGA
466400 AATATTTATATTTTGA
1 AATATTTATATTTTGA
466416 AATA
1 AATA
466420 ATATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATATTTATATTTTGA
Found at i:466433 original size:80 final size:80
Alignment explanation
Indices: 466365--466808 Score: 463
Period size: 80 Copynumber: 5.6 Consensus size: 80
466355 TACTATTTCT
* * * * * *
466365 TTTATTATATTTT-GTATAATCAATATTTTATTTTAAATATTTATATTTTGAAATAATATATAAA
1 TTTATTATATTTTAG-ATAATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAA
*
466429 TAATAAT--ACT-TAA
65 TAATAATAAAATATAA
* * * *
466442 TTTATCATATTTT-G-TAGTCATTATTTTATTGTAAATATTTATAATATG-AATAATATTTCAAT
1 TTTATTATATTTTAGATAATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAAT
*
466504 TATAATAAAATATAA
66 AATAATAAAATATAA
* * *
466519 TTTATTATATTTTAGATAATTATTAATTTAGTTTAAATATTTATAACATGAAATAATATTTCAAT
1 TTTATTATATTTTAGATAATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAAT
*
466584 TATAATAAAATATAA
66 AATAATAAAATATAA
* * * * *
466599 TTTATTATATTTTAGATAATTATTAATATACTTTCAATATTTATAATATGAAATAATATTTCGAT
1 TTTATTATATTTTAGATAATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAAT
** * *
466664 TCTAAGAAAATTTAA
66 AATAATAAAATATAA
* * * * *
466679 TTTAGTATATTTCAGATAAATTATTAATTTATTTTAAATATTTATGATATGAAATTATATTTCAA
1 TTTATTATATTTTAGAT-AATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAA
* * *
466744 TACTAATAAACTCTAA
65 TAATAATAAAATATAA
** * * *
466760 TTTATTATATCGTAGATAA-CTATTAATTTATTTCAAATATGTATTATAT
1 TTTATTATATTTTAGATAATC-ATTAATTTATTTTAAATATTTATAATAT
466809 TTTAAACAAT
Statistics
Matches: 314, Mismatches: 45, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
74 17 0.05
75 29 0.09
76 2 0.01
77 28 0.09
78 1 0.00
79 28 0.09
80 143 0.46
81 66 0.21
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (80 bp):
TTTATTATATTTTAGATAATCATTAATTTATTTTAAATATTTATAATATGAAATAATATTTCAAT
AATAATAAAATATAA
Found at i:466722 original size:161 final size:156
Alignment explanation
Indices: 466391--466795 Score: 494
Period size: 161 Copynumber: 2.6 Consensus size: 156
466381 TAATCAATAT
* * * *
466391 TTTATTTTAAATATTTATATTTTGAAATAATATAT-AA-ATAATAATACTTAATTTATCATATTT
1 TTTATTTTAAATATTTATAATATGAAATAATATTTCAATATAATAA-ACTTAATTTATTATATTT
* * * * *
466454 T-G-TAGTCATTATTTTATTGTAAATATTTATAATATGAATAATATTTCAATTATAATAAAATAT
65 TAGATAATTATTAATTTATT-TCAATATTTATAATATGAATAATATTTCAATTATAAGAAAATAT
* *
466517 AATTTATTATATTTTAGATAATTATTAA
129 AATTTAGTATATTTCAGATAATTATTAA
* * *
466545 TTTAGTTTAAATATTTATAACATGAAATAATATTTCAATTATAATAAAATATAATTTATTATATT
1 TTTATTTTAAATATTTATAATATGAAATAATATTTCAA-TATAATAAACT-TAATTTATTATATT
* * *
466610 TTAGATAATTATTAATATACTTTCAATATTTATAATATGAAATAATATTTCGATTCTAAGAAAAT
64 TTAGATAATTATTAATTTA-TTTCAATATTTATAATATG-AATAATATTTCAATTATAAGAAAAT
*
466675 TTAATTTAGTATATTTCAGATAAATTATTAA
127 ATAATTTAGTATATTTCAGAT-AATTATTAA
* * *
466706 TTTATTTTAAATATTTATGATATGAAATTATATTTCAATACTAATAAACTCTAATTTATTATATC
1 TTTATTTTAAATATTTATAATATGAAATAATATTTCAATA-TAATAAACT-TAATTTATTATATT
* *
466771 GTAGATAACTATTAATTTATTTCAA
64 TTAGATAATTATTAATTTATTTCAA
466796 ATATGTATTA
Statistics
Matches: 213, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
154 30 0.14
155 2 0.01
156 2 0.01
157 22 0.10
158 1 0.00
159 26 0.12
160 50 0.23
161 80 0.38
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (156 bp):
TTTATTTTAAATATTTATAATATGAAATAATATTTCAATATAATAAACTTAATTTATTATATTTT
AGATAATTATTAATTTATTTCAATATTTATAATATGAATAATATTTCAATTATAAGAAAATATAA
TTTAGTATATTTCAGATAATTATTAA
Found at i:466841 original size:119 final size:119
Alignment explanation
Indices: 466697--466927 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 119
466687 ATTTCAGATA
* * * * *
466697 AATTATTAATTTATTTTAAATATTTATGA-TATGAAATTATATTTCAA-TACTAATAAACTCTAA
1 AATTATTAATTTATTATAAACATTTAT-ACTATGAAATAATATTTCAATTA-AAATAAAATCTAA
*
466760 TTTATTATA-TCGTAGATAACTATTAATTT-ATTTCAAATATGTATTATATTTTAAAC
64 TTTATTATAGT-GTAGATAACTATTAATTTAATTT-AAATATGTATGATATTTTAAAC
* *
466816 AATTATTAATTTGTTATAAACATTTATACTATGAAATAATATTTCAATTAAAATAAAATCTATTT
1 AATTATTAATTTATTATAAACATTTATACTATGAAATAATATTTCAATTAAAATAAAATCTAATT
* * * *
466881 TATTTTAGTTTAGATAATTATTAATTTAATTTAAATATTTATGATAT
66 TATTATAGTGTAGATAACTATTAATTTAATTTAAATATGTATGATAT
466928 GAAATTATAT
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
118 1 0.01
119 88 0.92
120 7 0.07
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (119 bp):
AATTATTAATTTATTATAAACATTTATACTATGAAATAATATTTCAATTAAAATAAAATCTAATT
TATTATAGTGTAGATAACTATTAATTTAATTTAAATATGTATGATATTTTAAAC
Found at i:466907 original size:80 final size:77
Alignment explanation
Indices: 466801--467112 Score: 390
Period size: 80 Copynumber: 3.9 Consensus size: 77
466791 TTCAAATATG
* * * *
466801 TATTATATTTTAAACAATTATTAATTTGTTATAAACATTTATACTATGAAATAATATTTCAATTA
1 TATTATA-TTT-AATAATTATTAATTTATTTTAAATATTTATA-TATGAAATAATATTTCAATTA
*
466866 AAATAAAATCTATTT
63 AAATAAAATCTAATT
* * *
466881 TATTTTAGTTTAGATAATTATTAATTTAATTTAAATATTTATGATATGAAATTATATTTCAATTA
1 TATTATA-TTTA-ATAATTATTAATTTATTTTAAATATTTAT-ATATGAAATAATATTTCAATTA
*
466946 TAATAAAATCTAATT
63 AAATAAAATCTAATT
*
466961 TATTATATTTTAATAAATTATTAATTTATTTTAAATATTTATGGTATGAAATAATATTTCAATTA
1 TATTATA-TTTAAT-AATTATTAATTTATTTTAAATATTTAT-ATATGAAATAATATTTCAATTA
*
467026 TAATAAAATCTAATT
63 AAATAAAATCTAATT
* * *
467041 TAATATATTGTAAATAATTATTAATTTATTTTAAATACTTATAAGATGAAATAATATTTCAATTA
1 TATTATATT-T-AATAATTATTAATTTATTTTAAATATTTAT-ATATGAAATAATATTTCAATTA
467106 AAATAAA
63 AAATAAA
467113 TTTATTTTAA
Statistics
Matches: 206, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
79 5 0.02
80 197 0.96
81 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (77 bp):
TATTATATTTAATAATTATTAATTTATTTTAAATATTTATATATGAAATAATATTTCAATTAAAA
TAAAATCTAATT
Found at i:466942 original size:199 final size:200
Alignment explanation
Indices: 466601--466998 Score: 536
Period size: 199 Copynumber: 2.0 Consensus size: 200
466591 AAATATAATT
* * * * * *
466601 TATTATATTTTAGATAATTATTAATATACTTTCAATATTTATAATATGAAATAATATTTCGATTC
1 TATTATATTTTAAACAATTATTAATATACTTTAAACATTTATAATATGAAATAATATTTCAATTA
* * *
466666 TAAGAAAATTTAATTTAGTATATTTCAGATAAATTATTAATTTATTTTAAATATTTATGATATGA
66 AAAGAAAATCTAATTTAGTATATTTCAGATAAATTATTAATTTAATTTAAATATTTATGATATGA
*
466731 AATTATATTTCAA-TACTAATAAACTCTAATTTATTATATCGTAGAT-AACTATTAATTTATTTC
131 AATTATATTTCAATTA-TAATAAAATCTAATTTATTATATCGTA-ATAAACTATTAATTTATTTC
466794 AAATATG
194 AAATATG
** *
466801 TATTATATTTTAAACAATTATTAAT-TTGTTATAAACATTTATACTATGAAATAATATTTCAATT
1 TATTATATTTTAAACAATTATTAATATACTT-TAAACATTTATAATATGAAATAATATTTCAATT
* * * *
466865 AAAATAAAATCTATTTTATTTTAGTTT-AGAT-AATTATTAATTTAATTTAAATATTTATGATAT
65 AAAAGAAAATCTAATTTAGTATA-TTTCAGATAAATTATTAATTTAATTTAAATATTTATGATAT
** * *
466928 GAAATTATATTTCAATTATAATAAAATCTAATTTATTATATTTTAATAAATTATTAATTTATTTT
129 GAAATTATATTTCAATTATAATAAAATCTAATTTATTATATCGTAATAAACTATTAATTTATTTC
466993 AAATAT
194 AAATAT
466999 TTATGGTATG
Statistics
Matches: 173, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
198 2 0.01
199 94 0.54
200 74 0.43
201 3 0.02
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (200 bp):
TATTATATTTTAAACAATTATTAATATACTTTAAACATTTATAATATGAAATAATATTTCAATTA
AAAGAAAATCTAATTTAGTATATTTCAGATAAATTATTAATTTAATTTAAATATTTATGATATGA
AATTATATTTCAATTATAATAAAATCTAATTTATTATATCGTAATAAACTATTAATTTATTTCAA
ATATG
Found at i:466982 original size:160 final size:160
Alignment explanation
Indices: 466801--467112 Score: 448
Period size: 160 Copynumber: 1.9 Consensus size: 160
466791 TTCAAATATG
*
466801 TATTATATTTTAAACAATTATTAATTTGTTATAAACATTTATACTATGAAATAATATTTCAATTA
1 TATTATATTTTAAACAATTATTAATTTATTATAAACATTTATACTATGAAATAATATTTCAATTA
* * * * * * *
466866 AAATAAAATCTATTTTATTTTAGTT-TAGATAATTATTAATTTAATTTAAATATTTATGATATGA
66 AAATAAAATCTAATTTAATATA-TTGTAAATAATTATTAATTTAATTTAAATACTTATAAGATGA
* *
466930 AATTATATTTCAATTATAATAAAATCTAATT
130 AATAATATTTCAATTAAAATAAAATCTAATT
* * **
466961 TATTATATTTTAATA-AATTATTAATTTATTTTAAATATTTATGGTATGAAATAATATTTCAATT
1 TATTATATTTTAA-ACAATTATTAATTTATTATAAACATTTATACTATGAAATAATATTTCAATT
* *
467025 ATAATAAAATCTAATTTAATATATTGTAAATAATTATTAATTTATTTTAAATACTTATAAGATGA
65 AAAATAAAATCTAATTTAATATATTGTAAATAATTATTAATTTAATTTAAATACTTATAAGATGA
467090 AATAATATTTCAATTAAAATAAA
130 AATAATATTTCAATTAAAATAAA
467113 TTTATTTTAA
Statistics
Matches: 134, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
159 2 0.01
160 131 0.98
161 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (160 bp):
TATTATATTTTAAACAATTATTAATTTATTATAAACATTTATACTATGAAATAATATTTCAATTA
AAATAAAATCTAATTTAATATATTGTAAATAATTATTAATTTAATTTAAATACTTATAAGATGAA
ATAATATTTCAATTAAAATAAAATCTAATT
Found at i:467064 original size:21 final size:21
Alignment explanation
Indices: 467040--467082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
467030 AAAATCTAAT
467040 TTAATATATTGTAAATAATTA
1 TTAATATATTGTAAATAATTA
* * *
467061 TTAATTTATTTTAAATACTTA
1 TTAATATATTGTAAATAATTA
467082 T
1 T
467083 AAGATGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATATATTGTAAATAATTA
Found at i:467116 original size:48 final size:48
Alignment explanation
Indices: 467063--467160 Score: 171
Period size: 48 Copynumber: 2.0 Consensus size: 48
467053 AATAATTATT
467063 AATTTATTTTAAATACTTATAAGATGAAAT-AATATTTCAATTAAAATA
1 AATTTATTTTAAATACTTATAAGATG-AATCAATATTTCAATTAAAATA
*
467111 AATTTATTTTAAATATTTATAAGATGAATCAATATTTCAATTAAAATA
1 AATTTATTTTAAATACTTATAAGATGAATCAATATTTCAATTAAAATA
467159 AA
1 AA
467161 ATAAAAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 3 0.06
48 45 0.94
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (48 bp):
AATTTATTTTAAATACTTATAAGATGAATCAATATTTCAATTAAAATA
Found at i:467155 original size:80 final size:80
Alignment explanation
Indices: 466846--467144 Score: 268
Period size: 80 Copynumber: 3.7 Consensus size: 80
466836 CATTTATACT
* * * * * *
466846 ATGAAATAATATTTCAATTAAAATAAAATCTATTTTATTTTAGTT-TAGATAATTATTAATTTA-
1 ATGAAATAATATTTCAATTAAAATAAAATCTAATTTAATATA-TTATAAATAATCAATAATTTAT
* * *
466909 ATTTAAATATTTATGAT
65 A-TTAAATACTTATAAG
* * * * * *
466926 ATGAAATTATATTTCAATTATAATAAAATCTAATTTATTATATT-TTAATAAATTATTAATTTAT
1 ATGAAATAATATTTCAATTAAAATAAAATCTAATTTAATATATTATAAAT-AATCAATAATTTAT
* * *
466990 TTTAAATATTTAT-GG
65 ATTAAATACTTATAAG
* * * *
467005 TATGAAATAATATTTCAATTATAATAAAATCTAATTTAATATATTGTAAATAATTATTAATTTAT
1 -ATGAAATAATATTTCAATTAAAATAAAATCTAATTTAATATATTATAAATAATCAATAATTTAT
*
467070 TTTAAATACTTATAAG
65 ATTAAATACTTATAAG
* *
467086 ATGAAATAATATTTCAATTAAAAT-AAATTTATTTTAA-ATATTTATAAGATGAATCAATA
1 ATGAAATAATATTTCAATTAAAATAAAATCTAATTTAATATA-TTATAA-AT-AATCAATA
467145 TTTCAATTAA
Statistics
Matches: 191, Mismatches: 20, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
78 3 0.02
79 21 0.11
80 156 0.82
81 11 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (80 bp):
ATGAAATAATATTTCAATTAAAATAAAATCTAATTTAATATATTATAAATAATCAATAATTTATA
TTAAATACTTATAAG
Found at i:474939 original size:26 final size:26
Alignment explanation
Indices: 474910--474964 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
474900 GGTTTAATTT
474910 TTTTTAGTT-TAAAAAT-TTTTATAAAA
1 TTTTTA-TTATAAAAATATTTT-TAAAA
474936 TTTTTATTATAAAAATAATTTTTAAAA
1 TTTTTATTATAAAAAT-ATTTTTAAAA
474963 TT
1 TT
474965 AAATTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.08
26 13 0.50
27 7 0.27
28 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTTATTATAAAAATATTTTTAAAA
Found at i:479860 original size:20 final size:20
Alignment explanation
Indices: 479832--479878 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
479822 CGCCGTCTTG
* *
479832 CCCACGCCCTCATGACCGGA
1 CCCATGCCCACATGACCGGA
*
479852 CCCATGCCCACATGACCTGA
1 CCCATGCCCACATGACCGGA
479872 CCCATGC
1 CCCATGC
479879 TTCCAACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.49, G:0.17, T:0.13
Consensus pattern (20 bp):
CCCATGCCCACATGACCGGA
Found at i:480214 original size:16 final size:16
Alignment explanation
Indices: 480195--480282 Score: 67
Period size: 16 Copynumber: 5.6 Consensus size: 16
480185 AATTTTGTGA
480195 TTATAAAAAAAAATAT
1 TTATAAAAAAAAATAT
* **
480211 TTATAAATAATTATA-
1 TTATAAAAAAAAATAT
***
480226 TTA-AAAAGTTAATAT
1 TTATAAAAAAAAATAT
480241 TTATAAAAATAAAAT-T
1 TTATAAAAA-AAAATAT
480257 TTA-AAAAATAAAATAT
1 TTATAAAAA-AAAATAT
480273 ATTATAAAAA
1 -TTATAAAAA
480283 TTTAAAACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.12
15 17 0.30
16 21 0.38
17 6 0.11
18 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
TTATAAAAAAAAATAT
Found at i:480247 original size:17 final size:16
Alignment explanation
Indices: 480195--480284 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 16
480185 AATTTTGTGA
**
480195 TTATAAAAAAAAATAT
1 TTATAAAAATTAATAT
480211 TTATAAATAATT-ATA-
1 TTATAAA-AATTAATAT
*
480226 TTA-AAAAGTTAATAT
1 TTATAAAAATTAATAT
*
480241 TTATAAAAA-TAAAAT
1 TTATAAAAATTAATAT
*
480256 TT-TAAAAAATAAAATAT
1 TTAT-AAAAAT-TAATAT
480273 ATTATAAAAATT
1 -TTATAAAAATT
480285 TAAAACTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
13 3 0.05
14 7 0.12
15 18 0.32
16 14 0.25
17 6 0.11
18 8 0.14
19 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
TTATAAAAATTAATAT
Found at i:513334 original size:114 final size:110
Alignment explanation
Indices: 513170--513384 Score: 279
Period size: 114 Copynumber: 1.9 Consensus size: 110
513160 TGTAGACGAG
* * * *
513170 ATTAAAGGTTCAACAAGTTTTTCGTTTATGAAATGAATACATTTTTAATTAAATTCACTGAGATT
1 ATTAAAAGTTCAACAAGTGTTTCGTTTATGAAATGAATACATTTTCAATTAAATTCACCGAGATT
** *
513235 CT-ATTAGTATTTTATTAGAGTCTATTTATGAAATGGATAGTTTCA
66 -TGACAAGTATTTTATTAGAGTATATTTATGAAATGGATAGTTTCA
** *
513280 ATTAAAAGTTCAACAAGTGTTTCGTATATTTATGAAATGGGTACATTTTCAATTACATTCACCGA
1 ATTAAAAGTTCAACAAGTGTTTCG----TTTATGAAATGAATACATTTTCAATTAAATTCACCGA
*
513345 GATTTGACAAGTATTTTATTGGAGTATATTTATGAAATGG
62 GATTTGACAAGTATTTTATTAGAGTATATTTATGAAATGG
513385 TTATGAGGTT
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
110 22 0.25
113 1 0.01
114 66 0.74
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (110 bp):
ATTAAAAGTTCAACAAGTGTTTCGTTTATGAAATGAATACATTTTCAATTAAATTCACCGAGATT
TGACAAGTATTTTATTAGAGTATATTTATGAAATGGATAGTTTCA
Found at i:516599 original size:125 final size:126
Alignment explanation
Indices: 516363--516614 Score: 382
Period size: 125 Copynumber: 2.0 Consensus size: 126
516353 CAACATTCCA
* *
516363 ATATTAAAAGTTTTTTGATAAATGATAAGGGTAATGCTAATGGTGGTAATTACTGGCAACATGGC
1 ATATTAAAAGTTTTTTGATAAATGATAACGGTAATGCTAATGGTGGTAATTACTGGCAACATAGC
* * * *
516428 AACATTCAGATAGACACATATGATACGTTCGGGTTTGGTTCAAGGTAATGCTAATGGTGGT
66 AACATTCAAACAGACACATATGATACGTTCGGATTTGGTTCAAGGTAATGCTAATGGCGGT
*
516489 ATATTAAAAG-TTTTTGATAAATGAT-ACGGTAAATGCTAATGGTGGTAATTATTGGCAACATAG
1 ATATTAAAAGTTTTTTGATAAATGATAACGGT-AATGCTAATGGTGGTAATTACTGGCAACATAG
* * * *
516552 CGACATTCAAACAGACACATTTGATAGGTTCGGATTTGGTTCGAGGTAATGCTAATGGCGGT
65 CAACATTCAAACAGACACATATGATACGTTCGGATTTGGTTCAAGGTAATGCTAATGGCGGT
516614 A
1 A
516615 AGTAGTGGTG
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 4 0.04
125 100 0.88
126 10 0.09
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (126 bp):
ATATTAAAAGTTTTTTGATAAATGATAACGGTAATGCTAATGGTGGTAATTACTGGCAACATAGC
AACATTCAAACAGACACATATGATACGTTCGGATTTGGTTCAAGGTAATGCTAATGGCGGT
Found at i:519651 original size:18 final size:18
Alignment explanation
Indices: 519628--519676 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
519618 AATACAAATA
*
519628 AATTAAACAATTTTCATC
1 AATTAAAAAATTTTCATC
519646 AATTAAAAAATTTTCATC
1 AATTAAAAAATTTTCATC
519664 AATTAAAAAATTT
1 AATTAAAAAATTT
519677 CTTGATATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAAAAATTTTCATC
Found at i:525640 original size:13 final size:13
Alignment explanation
Indices: 525622--525657 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
525612 AACTCAAAGG
525622 AAAAATAAAAATA
1 AAAAATAAAAATA
525635 AAAAAT-AAAATA
1 AAAAATAAAAATA
525647 AAATAATAAAA
1 AAA-AATAAAA
525658 TACCCCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.43
13 9 0.43
14 3 0.14
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:525646 original size:18 final size:18
Alignment explanation
Indices: 525623--525659 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
525613 ACTCAAAGGA
525623 AAAATAAAAATAA-AAAAT
1 AAAAT-AAAATAATAAAAT
525641 AAAATAAAATAATAAAAT
1 AAAATAAAATAATAAAAT
525659 A
1 A
525660 CCCCAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATAAAATAATAAAAT
Found at i:525658 original size:13 final size:12
Alignment explanation
Indices: 525622--525659 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
525612 AACTCAAAGG
525622 AAAAATAAAAATA
1 AAAAAT-AAAATA
525635 AAAAATAAAATA
1 AAAAATAAAATA
525647 AAATAATAAAATA
1 AAA-AATAAAATA
525660 CCCCAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:557209 original size:20 final size:20
Alignment explanation
Indices: 557169--557212 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
557159 ATCATTATAC
557169 TATTT-TTTAAAAAAATAAA
1 TATTTATTTAAAAAAATAAA
*
557188 TATTTATTTAATAATAATAATA
1 TATTTATTTAA-AAAAATAA-A
557210 TAT
1 TAT
557213 ATTCTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 5 0.24
21 7 0.33
22 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTATTTAAAAAAATAAA
Found at i:558402 original size:2 final size:2
Alignment explanation
Indices: 558395--558429 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
558385 TTAGATCTAG
*
558395 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
558430 AAAGGGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:558502 original size:2 final size:2
Alignment explanation
Indices: 558495--558524 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
558485 TTAACGTTGA
558495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558525 TTATGCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:562663 original size:35 final size:35
Alignment explanation
Indices: 562617--562686 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
562607 GCGATGGATT
562617 TCATTCAAAGCTTAGAAACAAAACACCAACGGTTA
1 TCATTCAAAGCTTAGAAACAAAACACCAACGGTTA
562652 TCATTCAAAGCTTAGAAACAAAACACCAACGGTTA
1 TCATTCAAAGCTTAGAAACAAAACACCAACGGTTA
562687 ACGTTCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (35 bp):
TCATTCAAAGCTTAGAAACAAAACACCAACGGTTA
Found at i:572272 original size:80 final size:80
Alignment explanation
Indices: 572139--572300 Score: 279
Period size: 80 Copynumber: 2.0 Consensus size: 80
572129 TTTACATGAA
* * * *
572139 CATTAAAGTTACCTTGTCTGTTCTATTTCCCTATTTTTTAGAATAACAATTACTATAACTTTTTT
1 CATTAAAGTTACCTTATCTGTTCTATTTCCCTATTCTTTAGAATAACAATTACTACAACTTTTAT
572204 GGACTTTACAGACTG
66 GGACTTTACAGACTG
*
572219 CATTAAAGTTACCTTATCTGTTCTATTTCCCTATTCTTTAGAATAATAATTACTACAACTTTTAT
1 CATTAAAGTTACCTTATCTGTTCTATTTCCCTATTCTTTAGAATAACAATTACTACAACTTTTAT
572284 GGACTTTACAGACTG
66 GGACTTTACAGACTG
572299 CA
1 CA
572301 GCACTAATGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (80 bp):
CATTAAAGTTACCTTATCTGTTCTATTTCCCTATTCTTTAGAATAACAATTACTACAACTTTTAT
GGACTTTACAGACTG
Found at i:606591 original size:15 final size:14
Alignment explanation
Indices: 606571--606618 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
606561 TAGAATATAA
606571 TAATTTTCTTATTTT
1 TAATTTT-TTATTTT
* *
606586 TAATTTTTTGTTAT
1 TAATTTTTTATTTT
*
606600 TATTTTATTTATTTT
1 TAATTT-TTTATTTT
606615 TAAT
1 TAAT
606619 ATGTGAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (14 bp):
TAATTTTTTATTTT
Found at i:612885 original size:18 final size:19
Alignment explanation
Indices: 612844--612889 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
612834 TAATATTCTT
612844 ATTT-TTTTCTATATTATAA
1 ATTTATTTTCTATA-TATAA
*
612863 ATTTATTTTCTATA-ATTA
1 ATTTATTTTCTATATATAA
612881 ATTTATTTT
1 ATTTATTTT
612890 TTTCATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 12 0.48
19 4 0.16
20 9 0.36
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTATTTTCTATATATAA
Found at i:612891 original size:20 final size:21
Alignment explanation
Indices: 612846--612891 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
612836 ATATTCTTAT
612846 TTTTTTCTATATTATAAATTTA
1 TTTTTTCTATA-TATAAATTTA
*
612868 --TTTTCTATA-ATTAATTTA
1 TTTTTTCTATATATAAATTTA
612886 TTTTTT
1 TTTTTT
612892 TCATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTTCTATATATAAATTTA
Found at i:613971 original size:15 final size:15
Alignment explanation
Indices: 613951--613979 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
613941 AATATTATAA
613951 TTAAAATAAAAAATT
1 TTAAAATAAAAAATT
613966 TTAAAATAAAAAAT
1 TTAAAATAAAAAAT
613980 ATAATATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAATAAAAAATT
Found at i:626043 original size:77 final size:77
Alignment explanation
Indices: 625940--626095 Score: 258
Period size: 77 Copynumber: 2.0 Consensus size: 77
625930 AATCGAAATC
* * *
625940 CGAATCCGATCAAGTGATCTTCTGCTAACTACAGGATTCTGAGTCCAAGTAGAAATGTTCAAAAG
1 CGAATCCGATCAAGTGATCCTATGCTAACTACAGGATTCTGAGTCCAACTAGAAATGTTCAAAAG
*
626005 GGAAATCAAAAA
66 GAAAATCAAAAA
* *
626017 CGAATCCGATCAGGTGATCCTATGCTAACTACAGGATTCTGAGTCCAACTAGAAATGTTCAAAAT
1 CGAATCCGATCAAGTGATCCTATGCTAACTACAGGATTCTGAGTCCAACTAGAAATGTTCAAAAG
626082 GAAAATCAAAAA
66 GAAAATCAAAAA
626094 CG
1 CG
626096 TTTCCCCATA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (77 bp):
CGAATCCGATCAAGTGATCCTATGCTAACTACAGGATTCTGAGTCCAACTAGAAATGTTCAAAAG
GAAAATCAAAAA
Found at i:646467 original size:12 final size:12
Alignment explanation
Indices: 646447--646476 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
646437 ATAGTGAAAG
*
646447 AGGGGAAAGGAA
1 AGGGAAAAGGAA
646459 AGGGAAAAGGAA
1 AGGGAAAAGGAA
646471 AGGGAA
1 AGGGAA
646477 GAAGAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AGGGAAAAGGAA
Found at i:646672 original size:27 final size:25
Alignment explanation
Indices: 646634--646683 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
646624 ACTTATTCAT
646634 AAAAAATTAATTA-AAACATATGTGA
1 AAAAAATTAATTACAAA-ATATGTGA
646659 AAAAAATTGAAATTACAAAATATGT
1 AAAAAATT--AATTACAAAATATGT
646684 AGATGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (25 bp):
AAAAAATTAATTACAAAATATGTGA
Found at i:650418 original size:3 final size:3
Alignment explanation
Indices: 650410--650449 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
650400 GTGGGGGAAA
*
650410 TGG TGG TGG TGG TGG TGG TGG TGG T-G TGG TGA T-G TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
650450 GGGAGGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.03, C:0.00, G:0.62, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:665966 original size:17 final size:18
Alignment explanation
Indices: 665944--665978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
665934 GCTTTCTAAT
665944 ATTAC-TTTAACACGGAG
1 ATTACTTTTAACACGGAG
*
665961 ATTACTTTTAATACGGAG
1 ATTACTTTTAACACGGAG
665979 TTATTACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
ATTACTTTTAACACGGAG
Found at i:679261 original size:28 final size:28
Alignment explanation
Indices: 679211--679265 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
679201 TTAATATCCC
*
679211 TTTTTATTAATACGGTACCGTTTTAATT
1 TTTTTATTAATACCGTACCGTTTTAATT
*
679239 TTTTATATTTATACCGTA-CGTTTTAAT
1 TTTT-TATTAATACCGTACCGTTTTAAT
679266 CATGCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (28 bp):
TTTTTATTAATACCGTACCGTTTTAATT
Found at i:679611 original size:80 final size:78
Alignment explanation
Indices: 679466--679612 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 78
679456 ATATTAAACT
**
679466 TTTTTATTAATATCTTTTCTTTAATAATATTGTACAGTTTTAATTTTTTTATTAATATTTTACTT
1 TTTTTATTAATATCTTTTCTTTAATAATATTGTACAGTTTTAATTTTTTTATTAATATCATACTT
679531 TTGTAATCGTCCC
66 TTGTAATCGTCCC
* **
679544 TTTTTATTAATAT-TATTT-TTTATTAATATTGTATTGTTTTAATTTTTTGTTTATTAATATCAT
1 TTTTTATTAATATCT-TTTCTTTAATAATATTGTACAGTTTTAA--TTTT-TTTATTAATATCAT
679607 ACTTTT
62 ACTTTT
679613 TTATTATATT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 22 0.37
78 16 0.27
79 4 0.07
80 18 0.30
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (78 bp):
TTTTTATTAATATCTTTTCTTTAATAATATTGTACAGTTTTAATTTTTTTATTAATATCATACTT
TTGTAATCGTCCC
Found at i:679628 original size:14 final size:15
Alignment explanation
Indices: 679544--679753 Score: 88
Period size: 16 Copynumber: 12.9 Consensus size: 15
679534 TAATCGTCCC
679544 TTTTTATTAATATTAT
1 TTTTTATTAATATT-T
679560 TTTTTATTAATATTGT
1 TTTTTATTAATATT-T
*
679576 ATTGTT-TTAAT-TTT
1 -TTTTTATTAATATTT
679590 TTGTTTATTAATATCATACT
1 TT-TTTATTAATAT--T--T
679610 TTTTTATT-ATATTT
1 TTTTTATTAATATTT
679624 TTTTTATTAATATTGT
1 TTTTTATTAATATT-T
****
679640 ACAATATTAATATTCTT
1 TTTTTATTAATA-T-TT
* *
679657 TTTTTATTGATATCGTACA
1 TTTTTATTAATAT--T--T
*
679676 TTTTTA-TCATAATTT
1 TTTTTATTAAT-ATTT
*
679691 TTTTTATTGATATTGT
1 TTTTTATTAATATT-T
*
679707 TTCTTTATTAATATCGTA
1 TT-TTTATTAATAT--TT
**
679725 TGGTT-TTAATATTT
1 TTTTTATTAATATTT
679739 TTGTTTATTAATATT
1 TT-TTTATTAATATT
679754 GTGCAAATTT
Statistics
Matches: 147, Mismatches: 24, Indels: 46
0.68 0.11 0.21
Matches are distributed among these distances:
13 2 0.01
14 14 0.10
15 23 0.16
16 53 0.36
17 27 0.18
18 10 0.07
19 15 0.10
20 3 0.02
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTTTATTAATATTT
Found at i:679634 original size:33 final size:33
Alignment explanation
Indices: 679544--679703 Score: 132
Period size: 33 Copynumber: 4.8 Consensus size: 33
679534 TAATCGTCCC
*
679544 TTTTTATTAATATTATTTTTTATTAATATTGT--A
1 TTTTTATT-ATATT-TTTTTTATTAATATCGTACA
* * *
679577 TTGTT-TTA-ATTTTTTGTTTATTAATATCATACT
1 TTTTTATTATA-TTTTT-TTTATTAATATCGTACA
*
679610 TTTTTATTATATTTTTTTTATTAATATTGTACA
1 TTTTTATTATATTTTTTTTATTAATATCGTACA
* * * *
679643 ATATTAATAT-TCTTTTTTTATTGATATCGTACA
1 TTTTTATTATAT-TTTTTTTATTAATATCGTACA
* *
679676 TTTTTATCATAATTTTTTTTATTGATAT
1 TTTTTATTAT-ATTTTTTTTATTAATAT
679704 TGTTTCTTTA
Statistics
Matches: 101, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
30 4 0.04
31 15 0.15
32 3 0.03
33 54 0.53
34 23 0.23
35 2 0.02
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (33 bp):
TTTTTATTATATTTTTTTTATTAATATCGTACA
Found at i:679680 original size:66 final size:64
Alignment explanation
Indices: 679544--679706 Score: 191
Period size: 66 Copynumber: 2.5 Consensus size: 64
679534 TAATCGTCCC
*** *
679544 TTTTTATTAATATTATTTTTTATTAATATTGTATTGTTTTAATTTTTTGTTTATTAATATCATAC
1 TTTTTATT-ATATT-TTTTTTATTAATATTGTACAATATTAATTTTTTGTTTATTAATATCATAC
*
679609 T
64 A
* * *
679610 TTTTTATTATATTTTTTTTATTAATATTGTACAATATTAATATTCTTTTTTTATTGATATCGTAC
1 TTTTTATTATATTTTTTTTATTAATATTGTACAATATTAAT-TT-TTTGTTTATTAATATCATAC
679675 A
64 A
* *
679676 TTTTTATCATAATTTTTTTTATTGATATTGT
1 TTTTTATTAT-ATTTTTTTTATTAATATTGT
679707 TTCTTTATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 24 0.29
65 7 0.08
66 34 0.40
67 19 0.23
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (64 bp):
TTTTTATTATATTTTTTTTATTAATATTGTACAATATTAATTTTTTGTTTATTAATATCATACA
Found at i:679732 original size:51 final size:49
Alignment explanation
Indices: 679644--679755 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 49
679634 TATTGTACAA
* * * *
679644 TATTAATATTCTTTTTTTATTGATATCGTACATTTTTATCATAATTTTT-TT
1 TATTAATATTGTTTCTTTATTAATATCGTACAGTTTTA--AT-ATTTTTGTT
* **
679695 TATTGATATTGTTTCTTTATTAATATCGTATGGTTTTAATATTTTTGTT
1 TATTAATATTGTTTCTTTATTAATATCGTACAGTTTTAATATTTTTGTT
679744 TATTAATATTGT
1 TATTAATATTGT
679756 GCAAATTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
48 6 0.12
49 15 0.29
51 31 0.60
ACGTcount: A:0.25, C:0.05, G:0.08, T:0.62
Consensus pattern (49 bp):
TATTAATATTGTTTCTTTATTAATATCGTACAGTTTTAATATTTTTGTT
Found at i:679922 original size:43 final size:43
Alignment explanation
Indices: 679844--679927 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
679834 CAACATGACG
***
679844 TTAAAGCATAAAATATATATAAACTTGGGACTTAAAACTTTTA
1 TTAAAGCATAAAATATATATAAACTCAAGACTTAAAACTTTTA
* * * *
679887 TTAATGCATCAAATATATATAAACTCAAGATTTAAACCTTT
1 TTAAAGCATAAAATATATATAAACTCAAGACTTAAAACTTT
679928 ATTTTTGCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (43 bp):
TTAAAGCATAAAATATATATAAACTCAAGACTTAAAACTTTTA
Found at i:695260 original size:16 final size:16
Alignment explanation
Indices: 695224--695253 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
695214 TGCAACTTTC
695224 CCCAGATTCTTGTTTA
1 CCCAGATTCTTGTTTA
695240 CCCAGA-TCTTGTTT
1 CCCAGATTCTTGTTT
695254 TTCCCAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.27, G:0.13, T:0.43
Consensus pattern (16 bp):
CCCAGATTCTTGTTTA
Found at i:699558 original size:13 final size:13
Alignment explanation
Indices: 699535--699568 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
699525 AAAAAATCTA
699535 TTTTTATAATAATT
1 TTTTTA-AATAATT
699549 TTTTTAAATAATT
1 TTTTTAAATAATT
699562 TTTTTAA
1 TTTTTAA
699569 TCAAACTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTAAATAATT
Found at i:703091 original size:119 final size:119
Alignment explanation
Indices: 702880--703119 Score: 462
Period size: 119 Copynumber: 2.0 Consensus size: 119
702870 AGAAAATTGA
*
702880 ATCAACCCCATTCCCATGGTAAACAAGGGGAGTGATAGCTTGTTAGGATTTAGAAGAAACTTTCC
1 ATCAACCCCATTCCCATGGTAAACAAGGGGAGTGATAGCTTGTTAGGATTTAGAAGAAACTTTAC
702945 ATCAACAAATGACGAAAAGAGGTCAAAGTTTCATTACTAAAAGCTTCACCTGCC
66 ATCAACAAATGACGAAAAGAGGTCAAAGTTTCATTACTAAAAGCTTCACCTGCC
*
702999 ATCAACCCCATTGCCATGGTAAACAAGGGGAGTGATAGCTTGTTAGGATTTAGAAGAAACTTTAC
1 ATCAACCCCATTCCCATGGTAAACAAGGGGAGTGATAGCTTGTTAGGATTTAGAAGAAACTTTAC
703064 ATCAACAAATGACGAAAAGAGGTCAAAGTTTCATTACTAAAAGCTTCACCTGCC
66 ATCAACAAATGACGAAAAGAGGTCAAAGTTTCATTACTAAAAGCTTCACCTGCC
703118 AT
1 AT
703120 GCCATTTTGC
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (119 bp):
ATCAACCCCATTCCCATGGTAAACAAGGGGAGTGATAGCTTGTTAGGATTTAGAAGAAACTTTAC
ATCAACAAATGACGAAAAGAGGTCAAAGTTTCATTACTAAAAGCTTCACCTGCC
Found at i:713293 original size:2 final size:2
Alignment explanation
Indices: 713286--713314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
713276 TGATACATAC
713286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
713315 GAATATTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:713773 original size:21 final size:21
Alignment explanation
Indices: 713742--713792 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
713732 TGAAGAAAGA
* *
713742 AAAAGAGAGACTCGTGTGTTGT
1 AAAA-AGAGACCCGTGTGTTGC
*
713764 AGAAAGAGACCCGTGTGTTGC
1 AAAAAGAGACCCGTGTGTTGC
713785 AAAAAGAG
1 AAAAAGAG
713793 GTCTAGTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (21 bp):
AAAAAGAGACCCGTGTGTTGC
Found at i:715038 original size:3 final size:3
Alignment explanation
Indices: 715030--715060 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
715020 AAACCTACAA
715030 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
715061 GGTCACAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:731439 original size:29 final size:29
Alignment explanation
Indices: 731405--731483 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
731395 AACTATTTAA
731405 AAATTAAAATAAATTTTTATTTTT-TTATG
1 AAATTAAAATAAATTTTTATTTTTATT-TG
* * *
731434 ATATTAAATTAAAATTTTTTATTTTTATTTT
1 AAATTAAAAT-AAA-TTTTTATTTTTATTTG
731465 AAATT-AAATAAATTTTTAT
1 AAATTAAAATAAATTTTTAT
731484 AATTAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 7 0.17
29 11 0.26
30 6 0.14
31 16 0.38
32 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
AAATTAAAATAAATTTTTATTTTTATTTG
Found at i:743084 original size:6 final size:6
Alignment explanation
Indices: 743073--743103 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
743063 AAGAAGCAAG
743073 TCTGGA TCTGGA TCTGGA TCTGGA TCTGGA T
1 TCTGGA TCTGGA TCTGGA TCTGGA TCTGGA T
743104 TGATATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (6 bp):
TCTGGA
Found at i:749787 original size:15 final size:16
Alignment explanation
Indices: 749772--749852 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 16
749762 TAATGTCATT
*
749772 TATTT-TATTTTTATT
1 TATTTATATTTTTATA
*
749787 TATTATAATAATTTTATA
1 TATT-T-ATATTTTTATA
749805 TATTT-TATTTTTAATA
1 TATTTATATTTTT-ATA
749821 TATTTATATTTTT-TA
1 TATTTATATTTTTATA
749836 T-TATTA-ATTTTTATA
1 TAT-TTATATTTTTATA
749851 TA
1 TA
749853 ATATGATCTC
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
14 7 0.13
15 19 0.35
16 9 0.16
17 8 0.15
18 12 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATATTTTTATA
Done.