Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 121 of 210
Found at i:36495073 original size:50 final size:50
Alignment explanation
Indices: 36494994--36495285 Score: 428
Period size: 50 Copynumber: 5.9 Consensus size: 50
36494984 CATTTGGGTA
*
36494994 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * *
36495044 ATGGGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
36495094 AAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
36495144 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * *
36495194 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATTGGCAGTAC-AGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA--CCGAGAT
** *
36495244 AA-ACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
36495286 TGTTATTATC
Statistics
Matches: 220, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
49 35 0.16
50 181 0.82
51 3 0.01
52 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:36499090 original size:17 final size:16
Alignment explanation
Indices: 36499060--36499101 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
36499050 GTATACAATA
36499060 TTTTTTTTCAATTTTT
1 TTTTTTTTCAATTTTT
*
36499076 TTTTCTTTTCGATTTTT
1 TTTT-TTTTCAATTTTT
36499093 TTTATTTTT
1 TTT-TTTTT
36499102 TTTCAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCAATTTTT
Found at i:36499094 original size:20 final size:20
Alignment explanation
Indices: 36499058--36499114 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
36499048 CCGTATACAA
36499058 TATTTTTTTTCAA--TTTTT
1 TATTTTTTTTCAATTTTTTT
* *
36499076 T-TTTCTTTTCGATTTTTTT
1 TATTTTTTTTCAATTTTTTT
36499095 TATTTTTTTTCAATTTTTTT
1 TATTTTTTTTCAATTTTTTT
36499115 GAAACTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.28
18 1 0.03
19 6 0.19
20 16 0.50
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (20 bp):
TATTTTTTTTCAATTTTTTT
Found at i:36501705 original size:21 final size:21
Alignment explanation
Indices: 36501681--36501720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36501671 TCTCTCTCGC
*
36501681 TTTCTTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
**
36501702 TTTCATTTTCTTCTTTTTC
1 TTTCATTTTCGCCTTTTTC
36501721 CCTTGTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:36503468 original size:27 final size:27
Alignment explanation
Indices: 36503438--36503491 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
36503428 TTCAGGGAGA
36503438 TTTGAAAAACAAGATCATGAGAATAGG
1 TTTGAAAAACAAGATCATGAGAATAGG
36503465 TTTGAAAAACAAGATCATGAGAATAGG
1 TTTGAAAAACAAGATCATGAGAATAGG
36503492 CTCCCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (27 bp):
TTTGAAAAACAAGATCATGAGAATAGG
Found at i:36512921 original size:20 final size:20
Alignment explanation
Indices: 36512898--36512944 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36512888 GGGTTGAGGT
36512898 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
36512918 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
36512938 TGAGCTG
1 TGAGCTG
36512945 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:36514432 original size:20 final size:20
Alignment explanation
Indices: 36514407--36514453 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36514397 AGCTCGTTTC
36514407 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * *
36514427 CAGCTCATTCGAGTTCAATT
1 CAGCTCACTCGAGCTCAAGT
36514447 CAGCTCA
1 CAGCTCA
36514454 ACCTCAACCC
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:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:36527896 original size:30 final size:30
Alignment explanation
Indices: 36527860--36527933 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
36527850 CACAAGAGAA
36527860 CAAGAAAATCAAGATTCACTTTCTTATTTT
1 CAAGAAAATCAAGATTCACTTTCTTATTTT
*
36527890 CAAGAAAATCAAGATTCACTTTCTTGTTTT
1 CAAGAAAATCAAGATTCACTTTCTTATTTT
36527920 CAAGAAAATCAAGA
1 CAAGAAAATCAAGA
36527934 AACCGAATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (30 bp):
CAAGAAAATCAAGATTCACTTTCTTATTTT
Found at i:36531871 original size:22 final size:22
Alignment explanation
Indices: 36531828--36531892 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
36531818 CCTTTTTGAA
*
36531828 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
36531851 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
36531873 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
36531893 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:36532609 original size:29 final size:30
Alignment explanation
Indices: 36532559--36532616 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
36532549 ATGAGTGGTA
*
36532559 AAAAAGAGAGAGTGATTCAAAA-GAAAAAG
1 AAAAAGAAAGAGTGATTCAAAATGAAAAAG
*
36532588 AAAAAGAAACGAGTGA-TGAAAATGAAAAA
1 AAAAAGAAA-GAGTGATTCAAAATGAAAAA
36532617 AAGAGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.64, C:0.03, G:0.22, T:0.10
Consensus pattern (30 bp):
AAAAAGAAAGAGTGATTCAAAATGAAAAAG
Found at i:36534237 original size:10 final size:10
Alignment explanation
Indices: 36534222--36534283 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
36534212 TTTGAACCAT
*
36534222 TACCAATTCG
1 TACCAATTCA
*
36534232 TACCAAATACCA
1 TACC-AAT-TCA
*
36534244 TACCATTTCA
1 TACCAATTCA
36534254 TACCAATTTCA
1 TACCAA-TTCA
*
36534265 TACCATTTCA
1 TACCAATTCA
36534275 TACCAATTC
1 TACCAATTC
36534284 CCAAATACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 23 0.55
11 14 0.33
12 5 0.12
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (10 bp):
TACCAATTCA
Found at i:36534248 original size:22 final size:23
Alignment explanation
Indices: 36534217--36534280 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
36534207 ACCTCTTTGA
*
36534217 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCATACCAAAT
*
36534240 ACCA-TACCATTTCATACC-AAT
1 ACCATTACCAATTCATACCAAAT
** *
36534261 TTCA-TACCATTTCATACCAA
1 ACCATTACCAATTCATACCAA
36534281 TTCCCAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 19 0.53
22 13 0.36
23 4 0.11
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.30
Consensus pattern (23 bp):
ACCATTACCAATTCATACCAAAT
Found at i:36534264 original size:11 final size:10
Alignment explanation
Indices: 36534242--36534279 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
36534232 TACCAAATAC
36534242 CATACCATTT
1 CATACCATTT
36534252 CATACCAATTT
1 CATACC-ATTT
36534263 CATACCATTT
1 CATACCATTT
36534273 CATACCA
1 CATACCA
36534280 ATTCCCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (10 bp):
CATACCATTT
Found at i:36534268 original size:21 final size:21
Alignment explanation
Indices: 36534242--36534282 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
36534232 TACCAAATAC
36534242 CATACCATTTCATACCAATTT
1 CATACCATTTCATACCAATTT
36534263 CATACCATTTCATACCAATT
1 CATACCATTTCATACCAATT
36534283 CCCAAATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (21 bp):
CATACCATTTCATACCAATTT
Found at i:36534638 original size:21 final size:20
Alignment explanation
Indices: 36534597--36534642 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
36534587 AAAAAGTTCG
**
36534597 AAAAAAAAATTTTAAAAAAA
1 AAAAAAAAATTCGAAAAAAA
36534617 ACAAAAAAAATTCGAAAGAAAA
1 A-AAAAAAAATTCGAAA-AAAA
36534639 AAAA
1 AAAA
36534643 TTAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAAAAATTCGAAAAAAA
Found at i:36534647 original size:35 final size:36
Alignment explanation
Indices: 36534584--36534653 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
36534574 TAGGTACGTA
**
36534584 AAAAAAAAGTTCGAAAAAAAAATTTTAAAA-AAAAC
1 AAAAAAAAGTTCGAAAAAAAAAAATTAAAAGAAAAC
36534619 AAAAAAAA-TTCGAAAGAAAAAAAATTAAAAGAAAA
1 AAAAAAAAGTTCGAAA-AAAAAAAATTAAAAGAAAA
36534654 AAATTGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
35 20 0.65
36 4 0.13
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.14
Consensus pattern (36 bp):
AAAAAAAAGTTCGAAAAAAAAAAATTAAAAGAAAAC
Found at i:36534658 original size:14 final size:16
Alignment explanation
Indices: 36534614--36534656 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
36534604 AATTTTAAAA
*
36534614 AAAACAAAAAAAATTC
1 AAAAGAAAAAAAATTC
*
36534630 GAAAGAAAAAAAATT-
1 AAAAGAAAAAAAATTC
36534645 AAAAGAAAAAAA
1 AAAAGAAAAAAA
36534657 TTGCATACGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.09
Consensus pattern (16 bp):
AAAAGAAAAAAAATTC
Found at i:36536874 original size:20 final size:20
Alignment explanation
Indices: 36536849--36536893 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
36536839 GCGAAAATAC
*
36536849 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
36536869 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
36536888 AAAAGA
1 AAAAGA
36536894 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:36546510 original size:23 final size:22
Alignment explanation
Indices: 36546458--36546510 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
36546448 TCCTTGTCTT
*
36546458 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
36546480 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
36546503 TTTCTTTT
1 TTTCTTTT
36546511 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:36546524 original size:18 final size:18
Alignment explanation
Indices: 36546503--36546542 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36546493 CTTTCTTCAA
* * *
36546503 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
36546521 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
36546539 TTTC
1 TTTC
36546543 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:36554670 original size:42 final size:42
Alignment explanation
Indices: 36554623--36554705 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
36554613 AATATGTGTG
36554623 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
36554665 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
36554706 CTTTGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.39
Consensus pattern (42 bp):
AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
Found at i:36555989 original size:14 final size:15
Alignment explanation
Indices: 36555953--36555993 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
36555943 GAATATTTAC
36555953 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
36555969 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
36555983 ATAAAAATAAA
1 ATAAAAATAAA
36555994 AATAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:36563418 original size:10 final size:10
Alignment explanation
Indices: 36563403--36563464 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
36563393 TTTGAACCAT
*
36563403 TACCAATTCG
1 TACCAATTCA
*
36563413 TACCAAATACCA
1 TACC-AAT-TCA
*
36563425 TACCATTTCA
1 TACCAATTCA
36563435 TACCAATTCCA
1 TACCAATT-CA
* *
36563446 TACCATTTCG
1 TACCAATTCA
36563456 TACCAATTC
1 TACCAATTC
36563465 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:36563448 original size:21 final size:21
Alignment explanation
Indices: 36563403--36563465 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36563393 TTTGAACCAT
* *
36563403 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
36563425 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
36563446 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
36563466 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:36572985 original size:8 final size:8
Alignment explanation
Indices: 36572972--36573005 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
36572962 GGACTAACTG
36572972 AACAAATA
1 AACAAATA
*
36572980 AACAAACA
1 AACAAATA
36572988 AACAAATA
1 AACAAATA
*
36572996 AACGAATA
1 AACAAATA
36573004 AA
1 AA
36573006 TCGACCACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (8 bp):
AACAAATA
Found at i:36573006 original size:12 final size:12
Alignment explanation
Indices: 36572940--36573006 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
36572930 ACACCACATT
36572940 TAAATAAACAAA
1 TAAATAAACAAA
* *
36572952 TAAATGAAACGGAC
1 TAAAT-AAAC-AAA
* *
36572966 TAACTGAACAAA
1 TAAATAAACAAA
*
36572978 TAAACAAACAAA
1 TAAATAAACAAA
* *
36572990 CAAATAAACGAA
1 TAAATAAACAAA
36573002 TAAAT
1 TAAAT
36573007 CGACCACACC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
12 28 0.70
13 7 0.17
14 5 0.12
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.15
Consensus pattern (12 bp):
TAAATAAACAAA
Found at i:36573288 original size:15 final size:15
Alignment explanation
Indices: 36573257--36573290 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36573247 TTTCTTTATT
*
36573257 AAAAATAAAAGACAA
1 AAAAATAAAAAACAA
*
36573272 AAAAATAAAAAATAA
1 AAAAATAAAAAACAA
36573287 AAAA
1 AAAA
36573291 GGTTAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAATAAAAAACAA
Found at i:36575506 original size:18 final size:18
Alignment explanation
Indices: 36575485--36575564 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
36575475 TTTTTCATCA
*
36575485 TCTTTTTCAATTTCTTTT
1 TCTTTTTCAATTTCTATT
* *
36575503 TCTTTTGCAATTTCTTTT
1 TCTTTTTCAATTTCTATT
**
36575521 TCTTTTTCGTTTTCTATT
1 TCTTTTTCAATTTCTATT
*
36575539 TCTTTTTCACTTTCTATT
1 TCTTTTTCAATTTCTATT
36575557 TCTTTTTC
1 TCTTTTTC
36575565 TTCTTTTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTCTATT
Found at i:36575533 original size:7 final size:6
Alignment explanation
Indices: 36575471--36575566 Score: 75
Period size: 6 Copynumber: 16.0 Consensus size: 6
36575461 TTTTCTTTCG
* ** ** * **
36575471 TTTCTT TTTCAT CATCTT TTTCAA TTTCTT TTTCTT TTGCAA TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* * ** *
36575519 TTTCTT TTTCGT TTTCTA TTTCTT TTTCAC TTTCTA TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
36575567 CTTTTTTGTT
Statistics
Matches: 65, Mismatches: 25, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTCTT
Found at i:36576406 original size:18 final size:18
Alignment explanation
Indices: 36576383--36576425 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
36576373 ATACTTCACT
*
36576383 TTTTTTTTACTCGTACTC
1 TTTTTTTTACTCGAACTC
36576401 TTTTTTTTACTCGAACTC
1 TTTTTTTTACTCGAACTC
36576419 TTTTTTT
1 TTTTTTT
36576426 CTCAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTTTACTCGAACTC
Found at i:36577792 original size:10 final size:10
Alignment explanation
Indices: 36577779--36577822 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
36577769 AGCTCTGACC
36577779 AGCTCAATTG
1 AGCTCAATTG
* *
36577789 AGCTCATTTC
1 AGCTCAATTG
*
36577799 AGCTCAATCG
1 AGCTCAATTG
*
36577809 AGCTCAATTT
1 AGCTCAATTG
36577819 AGCT
1 AGCT
36577823 ACAAATCAGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:36577839 original size:20 final size:19
Alignment explanation
Indices: 36577779--36577839 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
36577769 AGCTCTGACC
*
36577779 AGCTCAATTGAGCTCATTT
1 AGCTCAATCGAGCTCATTT
36577798 CAGCTCAATCGAGCTCAATTT
1 -AGCTCAATCGAGCTC-ATTT
36577819 AGCTACAAATC-AGCTCATTT
1 AGCT-C-AATCGAGCTCATTT
36577839 A
1 A
36577840 TTTTATTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 23 0.62
21 10 0.27
22 4 0.11
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (19 bp):
AGCTCAATCGAGCTCATTT
Found at i:36580546 original size:23 final size:23
Alignment explanation
Indices: 36580514--36580625 Score: 109
Period size: 23 Copynumber: 4.9 Consensus size: 23
36580504 CTTTTTGAAC
* *
36580514 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
*
36580537 TATTACCATTTCG-AGCCAAATCA
1 CATTACCATTTCGTA-CCAAATCA
* * * *
36580560 CCTTACCAATTCATACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36580583 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36580606 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36580626 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
22 1 0.01
23 66 0.97
24 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36580913 original size:16 final size:16
Alignment explanation
Indices: 36580892--36580951 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 16
36580882 ATAGGTACGT
*
36580892 AAAAAAAAGTTCGAAA
1 AAAAAAAAATTCGAAA
* *
36580908 AAAAAATCAAAATCAAAA
1 AAAAAA--AAATTCGAAA
36580926 AAAAAAAAATT-GAAA
1 AAAAAAAAATTCGAAA
*
36580941 AGAAAAAAATT
1 AAAAAAAAATT
36580952 GCATACGGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 13 0.36
16 10 0.28
18 13 0.36
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATTCGAAA
Found at i:36584989 original size:23 final size:23
Alignment explanation
Indices: 36584954--36585065 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
36584944 CGGTTTTGGG
* *
36584954 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36584977 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36585000 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36585023 TTTGGTTCGAATTGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
36585046 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36585066 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:36585016 original size:46 final size:46
Alignment explanation
Indices: 36584954--36585065 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36584944 CGGTTTTGGG
*
36584954 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * * *
36585000 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAATTGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
36585046 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36585066 GTTCAAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:36611625 original size:12 final size:11
Alignment explanation
Indices: 36611598--36611662 Score: 82
Period size: 11 Copynumber: 6.0 Consensus size: 11
36611588 AGACCGTATG
36611598 CAATTTTTTTT
1 CAATTTTTTTT
36611609 C---TTTTTTT
1 CAATTTTTTTT
36611617 CAATTTTTTTT
1 CAATTTTTTTT
36611628 CAATTTTTTTT
1 CAATTTTTTTT
*
36611639 CGATTTTTTTTT
1 C-AATTTTTTTT
36611651 CAAATTTTTTTT
1 C-AATTTTTTTT
36611663 TCCACGAGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
8 8 0.17
11 20 0.43
12 19 0.40
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:36611993 original size:21 final size:21
Alignment explanation
Indices: 36611967--36612029 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36611957 TTGGTATTTG
36611967 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36611988 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
36612009 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36612030 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36613126 original size:10 final size:10
Alignment explanation
Indices: 36613111--36613152 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
36613101 TTTGCAAGTT
36613111 TTGAGCTAAA
1 TTGAGCTAAA
* *
36613121 TTGAGCTGAT
1 TTGAGCTAAA
*
36613131 TTGAGCT-CA
1 TTGAGCTAAA
36613140 TTGAGCTAAA
1 TTGAGCTAAA
36613150 TTG
1 TTG
36613153 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:36623661 original size:15 final size:15
Alignment explanation
Indices: 36623635--36623679 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
36623625 AAAATTAGAG
*
36623635 GAAAAGAAAGAAGAAT
1 GAAAA-AAAGAAAAAT
36623651 GAAAAAAAGAAAAAT
1 GAAAAAAAGAAAAAT
36623666 GACAAAAAAGAAAA
1 GA-AAAAAAGAAAA
36623680 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:36624566 original size:14 final size:15
Alignment explanation
Indices: 36624542--36624570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
36624532 AAAAAATGGG
36624542 TGAATAATGAAAAAA
1 TGAATAATGAAAAAA
36624557 TGAA-AATGAAAAAA
1 TGAATAATGAAAAAA
36624571 GTAAAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
TGAATAATGAAAAAA
Found at i:36626141 original size:129 final size:129
Alignment explanation
Indices: 36625922--36626159 Score: 309
Period size: 129 Copynumber: 1.8 Consensus size: 129
36625912 GAAGACGGTA
* * *
36625922 AATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCCACAAGTCCTTTCTCCCTGAGGTTGAAGT
1 AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGAAGTTGAAGT
* *
36625987 GGAGCAGACTAAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGACAGATGAAAGACGACG
66 GGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGTGGGACAGATGAAAGACGACG
* * * *
36626051 AATCTTATCTTCAAGTGTAAGGAAGTAGATTGAAGCCGATAA-TCCTATCTCCCTGAAGTTGTAG
1 AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCC-ACAAGTCCTATCTCCCTGAAGTTGAAG
** * * * *
36626115 TGGAGTGGATTAAAGTAA-TAGATCTTATCTCTCTGAAGTGGCAGT
65 TGGAGCAGACT-AAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGT
36626160 AGAGTGGATC
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
129 83 0.90
130 9 0.10
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (129 bp):
AATCTTATCTTCAAGTGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGAAGTTGAAGT
GGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTGGCAGTGGGACAGATGAAAGACGACG
Found at i:36630879 original size:20 final size:20
Alignment explanation
Indices: 36630854--36630900 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36630844 AGCTCATTTC
*
36630854 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
36630874 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
36630894 CAGCTCA
1 CAGCTCA
36630901 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:36630903 original size:10 final size:10
Alignment explanation
Indices: 36630844--36630903 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
36630834 AGCTCTGTTT
*
36630844 AGCTCATTTCC
1 AGCTCAATT-C
* *
36630855 AGCTCACTTG
1 AGCTCAATTC
*
36630865 AGCTCAAGTC
1 AGCTCAATTC
36630875 AGCTC-ATTC
1 AGCTCAATTC
*
36630884 GAGATCAATTC
1 -AGCTCAATTC
36630895 AGCTCAATT
1 AGCTCAATT
36630904 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:36632524 original size:12 final size:13
Alignment explanation
Indices: 36632507--36632535 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
36632497 AAAAAAAATC
36632507 AAAATTC-AAAAA
1 AAAATTCGAAAAA
36632519 AAAATTCGAAAAA
1 AAAATTCGAAAAA
36632532 AAAA
1 AAAA
36632536 GAAAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAATTCGAAAAA
Found at i:36632584 original size:27 final size:26
Alignment explanation
Indices: 36632526--36632588 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
36632516 AAAAAAATTC
*
36632526 GAAAAAAAAAGAAAAAAAAGAAGTGA
1 GAAAAAAAAAGAAAAAAAAGAAGTAA
36632552 GCAAAAAAAAAGAGTAAAAAAAGAAG-AA
1 G-AAAAAAAAAGA--AAAAAAAGAAGTAA
36632580 GAAAAAAAA
1 GAAAAAAAA
36632589 GAAGTGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 2 0.06
29 11 0.33
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (26 bp):
GAAAAAAAAAGAAAAAAAAGAAGTAA
Found at i:36632585 original size:15 final size:15
Alignment explanation
Indices: 36632534--36632592 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
36632524 TCGAAAAAAA
36632534 AAGAAAAAAAAGAAG
1 AAGAAAAAAAAGAAG
* *
36632549 TGAGCAAAAAAA-AAG
1 -AAGAAAAAAAAGAAG
*
36632564 -AGTAAAAAAAGAAG
1 AAGAAAAAAAAGAAG
36632578 AAGAAAAAAAAGAAG
1 AAGAAAAAAAAGAAG
36632593 TGAAAAGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 9 0.24
14 3 0.08
15 16 0.43
16 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (15 bp):
AAGAAAAAAAAGAAG
Found at i:36632586 original size:29 final size:27
Alignment explanation
Indices: 36632527--36632588 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
36632517 AAAAAATTCG
*
36632527 AAAAAAAAAGAAAAAAAAGAAGTGAGCA
1 AAAAAAAAAGAAAAAAAAGAAGAGAG-A
*
36632555 AAAAAAAAGAGTAAAAAAAGAAGA-AGA
1 AAAAAAAA-AGAAAAAAAAGAAGAGAGA
36632582 AAAAAAA
1 AAAAAAA
36632589 GAAGTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 8 0.26
28 10 0.32
29 13 0.42
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAAAGAAGAGAGA
Found at i:36633656 original size:15 final size:15
Alignment explanation
Indices: 36633631--36633677 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36633621 AGAAAAGAAT
36633631 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
36633647 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
36633662 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
36633677 A
1 A
36633678 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:36633724 original size:12 final size:12
Alignment explanation
Indices: 36633707--36633782 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
36633697 AGTGAAAAGC
36633707 AAAAAGAGATTG
1 AAAAAGAGATTG
*
36633719 AAAAAGAAATTG
1 AAAAAGAGATTG
*
36633731 --AAAGAGA-AG
1 AAAAAGAGATTG
*
36633740 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
36633755 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
36633767 AAAGAGAGCTTG
1 AAAAAGAGATTG
36633779 AAAA
1 AAAA
36633783 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:36633748 original size:15 final size:15
Alignment explanation
Indices: 36633730--36633763 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36633720 AAAAGAAATT
36633730 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
36633745 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
36633760 GAAA
1 GAAA
36633764 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:36644374 original size:18 final size:18
Alignment explanation
Indices: 36644353--36644387 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36644343 TTTTTCTTTT
36644353 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
36644371 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
36644388 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:36653380 original size:13 final size:12
Alignment explanation
Indices: 36653354--36653401 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
36653344 GAACTAGCTC
36653354 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
36653366 TTTATTTTTCAAA
1 TTTTTTTTTC-AA
36653379 TTTTTTTTTCAA
1 TTTTTTTTTCAA
36653391 TTTTTTTTTCA
1 TTTTTTTTTCA
36653402 CAACTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:36653383 original size:25 final size:25
Alignment explanation
Indices: 36653354--36653401 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
36653344 GAACTAGCTC
36653354 TTTTTTTTTCAATTTATTTTTCAAA
1 TTTTTTTTTCAATTTATTTTTCAAA
*
36653379 TTTTTTTTTCAATTTTTTTTTCA
1 TTTTTTTTTCAATTTATTTTTCA
36653402 CAACTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTTTTTCAATTTATTTTTCAAA
Found at i:36653460 original size:12 final size:12
Alignment explanation
Indices: 36653443--36653496 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
36653433 GGAAACTAGT
36653443 TTTTTTTTCGAA
1 TTTTTTTTCGAA
36653455 TTTTTTTTCGAA
1 TTTTTTTTCGAA
36653467 TTTTTTTT-GAA
1 TTTTTTTTCGAA
* *
36653478 TTTTTTTTCTAG
1 TTTTTTTTCGAA
36653490 TTTTTTT
1 TTTTTTT
36653497 CGAGAAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.28
12 28 0.72
ACGTcount: A:0.13, C:0.06, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:36653470 original size:23 final size:23
Alignment explanation
Indices: 36653444--36653499 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
36653434 GAAACTAGTT
36653444 TTTTTTTCGAATTTTTTTTCGAA
1 TTTTTTTCGAATTTTTTTTCGAA
* * *
36653467 TTTTTTTTGAATTTTTTTTCTAG
1 TTTTTTTCGAATTTTTTTTCGAA
36653490 TTTTTTTCGA
1 TTTTTTTCGA
36653500 GAAACTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTTTTCGAATTTTTTTTCGAA
Found at i:36656922 original size:20 final size:20
Alignment explanation
Indices: 36656899--36656945 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36656889 TAGCTCCAAC
*
36656899 CAGCTTATTTGAGCTCAATT
1 CAGCTTATTCGAGCTCAATT
*
36656919 CAGCTCATTCGAGCTCAATT
1 CAGCTTATTCGAGCTCAATT
*
36656939 TAGCTTA
1 CAGCTTA
36656946 CTTTCAGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
CAGCTTATTCGAGCTCAATT
Found at i:36662797 original size:20 final size:20
Alignment explanation
Indices: 36662769--36662833 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
36662759 TCTTAGTGCA
* *
36662769 AGCTGATTTTAGCTCCAA-TC
1 AGCTCATTTGAGCT-CAATTC
36662789 AGCTCATTTGAGCTCAATTC
1 AGCTCATTTGAGCTCAATTC
* *
36662809 AGCTCATTCGAGCTCAATTT
1 AGCTCATTTGAGCTCAATTC
36662829 AGCTC
1 AGCTC
36662834 GTTAATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 37 0.93
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (20 bp):
AGCTCATTTGAGCTCAATTC
Found at i:36673887 original size:30 final size:30
Alignment explanation
Indices: 36673834--36673892 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
36673824 ACTTTAATAC
* *
36673834 GAGCTGAATTAACTTCCATTTCAGCTCAAT
1 GAGCTGAATTAACTTCAACTTCAGCTCAAT
36673864 GAGCTTGAATTAAC-TCAACTTCAGCTCAA
1 GAGC-TGAATTAACTTCAACTTCAGCTCAA
36673893 ACATTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (30 bp):
GAGCTGAATTAACTTCAACTTCAGCTCAAT
Found at i:36678359 original size:20 final size:20
Alignment explanation
Indices: 36678308--36678361 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
36678298 TAATTCATGT
*
36678308 TTTAATTTAAGACATACTTAA
1 TTTAA-TTAAGACACACTTAA
** * *
36678329 TAAAATCAAGACACATTTAA
1 TTTAATTAAGACACACTTAA
36678349 TTTAATTAAGACA
1 TTTAATTAAGACA
36678362 AGACAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAATTAAGACACACTTAA
Found at i:36680543 original size:18 final size:18
Alignment explanation
Indices: 36680522--36680556 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36680512 TTTTTCTTTT
36680522 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
36680540 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
36680557 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:36681498 original size:17 final size:16
Alignment explanation
Indices: 36681471--36681526 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
36681461 AACACTTCAC
36681471 TTTTTTT-TTCGAATT
1 TTTTTTTATTCGAATT
*
36681486 TTTTTTTACTTCGTACTCT
1 TTTTTTTA-TTCG-AAT-T
*
36681505 TTTTTTTATTCTCAATT
1 TTTTTTTATTC-GAATT
36681522 TTTTT
1 TTTTT
36681527 CGTAATTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 7 0.21
17 10 0.30
18 7 0.21
19 9 0.27
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTTTATTCGAATT
Found at i:36683778 original size:12 final size:12
Alignment explanation
Indices: 36683761--36683785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36683751 CCTTATACAC
36683761 ATTACACATTGA
1 ATTACACATTGA
36683773 ATTACACATTGA
1 ATTACACATTGA
36683785 A
1 A
36683786 ATCATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:36686163 original size:12 final size:12
Alignment explanation
Indices: 36686145--36686178 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
36686135 CTAGCTCTCT
36686145 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
36686158 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
36686171 TTTTTTTT
1 TTTTTTTT
36686179 TCACAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:36686163 original size:14 final size:14
Alignment explanation
Indices: 36686144--36686184 Score: 75
Period size: 13 Copynumber: 3.0 Consensus size: 14
36686134 ACTAGCTCTC
36686144 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
36686158 TTTTTTTTTCA-AA
1 TTTTTTTTTCACAA
36686171 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
36686185 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:36686251 original size:11 final size:12
Alignment explanation
Indices: 36686222--36686254 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
36686212 TGGAAACTAG
36686222 TTTTTTTTCGAA
1 TTTTTTTTCGAA
36686234 -TTTTTTT-GAA
1 TTTTTTTTCGAA
36686244 TTTTTTTTCGA
1 TTTTTTTTCGA
36686255 GAAACTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.16
11 14 0.74
12 2 0.11
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:36688491 original size:19 final size:19
Alignment explanation
Indices: 36688463--36688507 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
36688453 GCGAAAATAC
*
36688463 AAAAGAAAAGAAAAATGAAA
1 AAAAG-AAAGAAAAATCAAA
*
36688483 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAAATCAAA
36688502 AAAAGA
1 AAAAGA
36688508 GAATGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATCAAA
Found at i:36688528 original size:13 final size:15
Alignment explanation
Indices: 36688483--36688548 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
36688473 AAAAATGAAA
* *
36688483 AAAAGAAAGAAAATTC
1 AAAAGAAAGAGAA-TG
36688499 AAAA-AAAGAGAATG
1 AAAAGAAAGAGAATG
36688513 AAAAGAAAG-GAA-G
1 AAAAGAAAGAGAATG
*
36688526 AAAAGAAAAAG-ATG
1 AAAAGAAAGAGAATG
36688540 AAAAAGAAA
1 -AAAAGAAA
36688549 CATTGAGTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 10 0.23
14 10 0.23
15 19 0.44
16 4 0.09
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAAGAAAGAGAATG
Found at i:36693895 original size:22 final size:22
Alignment explanation
Indices: 36693864--36693927 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
36693854 CCTTTTTGAA
*
36693864 CCATTTCCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
* **
36693886 CCATTACCATTTTGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* *
36693908 CCCTTACCGTTTCGTACCAA
1 CCATTACCATTTCGTACCAA
36693928 TTCCCAAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:36695371 original size:18 final size:19
Alignment explanation
Indices: 36695350--36695408 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
36695340 TGAAGGCAAA
36695350 GGAACAAAAAGAAAAGA-T
1 GGAACAAAAAGAAAAGAGT
*
36695368 GGAA-AAAGAAAAAAAGAGT
1 GGAACAAA-AAGAAAAGAGT
36695387 GAGAAAACAAAAAGAAAA-AGT
1 G-G--AACAAAAAGAAAAGAGT
36695408 G
1 G
36695409 AGTTGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 2 0.06
20 1 0.03
21 4 0.12
22 8 0.24
23 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (19 bp):
GGAACAAAAAGAAAAGAGT
Found at i:36695410 original size:21 final size:21
Alignment explanation
Indices: 36695352--36695410 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
36695342 AAGGCAAAGG
36695352 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
*
36695372 AA-AGAAAA-AAAGAGTGAGAA
1 AACA-AAAAGAAAAAGTGAGAA
36695392 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
36695411 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.09
20 19 0.59
21 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:36704818 original size:20 final size:20
Alignment explanation
Indices: 36704795--36704841 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36704785 GGGTTAAAAT
*
36704795 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36704815 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36704835 TGAGCTG
1 TGAGCTG
36704842 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36707500 original size:22 final size:22
Alignment explanation
Indices: 36707469--36707532 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
36707459 CCTTTTTGAA
* *
36707469 CCATTTCCATTTCATACCAAAT
1 CCATTACCATTTCGTACCAAAT
**
36707491 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* *
36707513 CCCTTACCGTTTCGTACCAA
1 CCATTACCATTTCGTACCAA
36707533 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.33, G:0.05, T:0.36
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:36710327 original size:23 final size:23
Alignment explanation
Indices: 36710292--36710403 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36710282 CGGTTTTGGG
* *
36710292 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36710315 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36710338 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
36710361 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
36710384 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36710404 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:36710354 original size:46 final size:46
Alignment explanation
Indices: 36710292--36710403 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
36710282 CGGTTTTGGG
*
36710292 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
36710338 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
36710384 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36710404 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:36715241 original size:20 final size:20
Alignment explanation
Indices: 36715216--36715257 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
36715206 CATGGATGAG
36715216 AAGAAACCATTCTTTAACCA
1 AAGAAACCATTCTTTAACCA
36715236 AAGAAACCATTCTTTAACCA
1 AAGAAACCATTCTTTAACCA
36715256 AA
1 AA
36715258 AGATGGCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (20 bp):
AAGAAACCATTCTTTAACCA
Found at i:36716987 original size:40 final size:40
Alignment explanation
Indices: 36716943--36717025 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
36716933 GCTCAGCATG
36716943 TCCTCAATAATCACATACTTTCAGTAAATGGAAACAGTGT
1 TCCTCAATAATCACATACTTTCAGTAAATGGAAACAGTGT
*
36716983 TCCTCAATAATCACATACTTTCAGTAAATGGAAATAGTGT
1 TCCTCAATAATCACATACTTTCAGTAAATGGAAACAGTGT
36717023 TCC
1 TCC
36717026 AATATTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
TCCTCAATAATCACATACTTTCAGTAAATGGAAACAGTGT
Found at i:36737354 original size:25 final size:25
Alignment explanation
Indices: 36737280--36737354 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
36737270 GAGAGCTTAT
* * * *
36737280 CGATTCTCAGCTCATATGAGCTTAA
1 CGATTCACAGCTCGTATGAGCATAC
* *
36737305 CGATTTACAGCTCGTGA-GAGTATAC
1 CGATTCACAGCTCGT-ATGAGCATAC
*
36737330 CGATTCACAGCTTGTATGAGCATAC
1 CGATTCACAGCTCGTATGAGCATAC
36737355 ATGTACAAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 1 0.03
25 37 0.95
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (25 bp):
CGATTCACAGCTCGTATGAGCATAC
Found at i:36750201 original size:46 final size:46
Alignment explanation
Indices: 36750149--36750239 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
36750139 TAGTGTGGCG
*
36750149 TTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAGT
1 TTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAGT
*
36750195 TTCATCATATACCCAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 TTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
36750240 GTCTTTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 40 0.95
47 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (46 bp):
TTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAGT
Found at i:36751629 original size:27 final size:27
Alignment explanation
Indices: 36751582--36751640 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
36751572 TGAACTCGAG
*
36751582 AAAAGAAAAAAAGATAGTGAGAGTGAGA
1 AAAAGAAAAAAAGATA-TGAGAGTGAAA
* *
36751610 AAAAGAAAAACGAGAT-TGAGATTGAAA
1 AAAAGAAAAA-AAGATATGAGAGTGAAA
36751637 AAAA
1 AAAA
36751641 ATGTGAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 10 0.37
29 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.12
Consensus pattern (27 bp):
AAAAGAAAAAAAGATATGAGAGTGAAA
Found at i:36759571 original size:10 final size:10
Alignment explanation
Indices: 36759556--36759617 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
36759546 TTTGAACCAT
*
36759556 TACCAATTCG
1 TACCAATTCA
*
36759566 TACCAAATACCA
1 TACC-AAT-TCA
*
36759578 TACCATTTCA
1 TACCAATTCA
36759588 TACCAATTCCA
1 TACCAATT-CA
* *
36759599 TACCATTTCG
1 TACCAATTCA
36759609 TACCAATTC
1 TACCAATTC
36759618 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:36759601 original size:21 final size:21
Alignment explanation
Indices: 36759556--36759618 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36759546 TTTGAACCAT
* *
36759556 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
36759578 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
36759599 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
36759619 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:36759935 original size:16 final size:16
Alignment explanation
Indices: 36759914--36759946 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36759904 GTTATTCATC
36759914 CATGAAGAATCAGTAT
1 CATGAAGAATCAGTAT
36759930 CATGAAGAATCAGTAT
1 CATGAAGAATCAGTAT
36759946 C
1 C
36759947 GAAGAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (16 bp):
CATGAAGAATCAGTAT
Found at i:36760117 original size:17 final size:18
Alignment explanation
Indices: 36760095--36760129 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36760085 ATTGAGAGTG
*
36760095 AAAAAG-AATTTGAAAAA
1 AAAAAGAAAATTGAAAAA
36760112 AAAAAGAAAATTGAAAAA
1 AAAAAGAAAATTGAAAAA
36760130 GAGATTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAAAGAAAATTGAAAAA
Found at i:36760147 original size:48 final size:47
Alignment explanation
Indices: 36760046--36760149 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 47
36760036 TGTAATAAAA
* *
36760046 TAAAAAAAGCATGTGAAAAAGAAAAAGAGATCGAAAGAGATTGAGAG
1 TAAAAAAAGAATGTGAAAAAGAAAAAGAAATCGAAAGAGATTGAGAG
* * *
36760093 T-GAAAAAGAATTTGAAAAA-AAAAAGAAAATTGAAAAAGAGATTGAG-G
1 TAAAAAAAGAATGTGAAAAAGAAAAAG-AAATCG--AAAGAGATTGAGAG
36760140 TAAAAAAAGA
1 TAAAAAAAGA
36760150 GAGTAAGCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
45 6 0.13
46 19 0.40
47 3 0.06
48 19 0.40
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.14
Consensus pattern (47 bp):
TAAAAAAAGAATGTGAAAAAGAAAAAGAAATCGAAAGAGATTGAGAG
Found at i:36773987 original size:20 final size:20
Alignment explanation
Indices: 36773952--36774000 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
36773942 ATCATGGTCT
*
36773952 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
36773971 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
36773991 TTGCTTACTT
1 TTGCTTACTT
36774001 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:36774325 original size:50 final size:49
Alignment explanation
Indices: 36774202--36774386 Score: 178
Period size: 50 Copynumber: 3.8 Consensus size: 49
36774192 GATAATAACA
* * * *
36774202 TGCCAAAGCCATGT-CTAGACATGGTCTTACATGGGATGTT-TCCTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CG
* * * *
36774250 TACCAATGCCATATTCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATC-G
* ** ** *
36774300 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATC-G
*
36774350 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
36774387 TCTCATTCCC
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
48 15 0.14
49 24 0.22
50 72 0.65
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCG
Found at i:36776583 original size:23 final size:23
Alignment explanation
Indices: 36776553--36776615 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
36776543 TTTGAACCAT
**
36776553 TACCATTTCGTACCAAATCGTAA
1 TACCATTTCGTACCAAATCACAA
* *
36776576 TACCATTTCGAACCAAATCACAT
1 TACCATTTCGTACCAAATCACAA
*
36776599 TACCATTTCGTAACAAA
1 TACCATTTCGTACCAAA
36776616 CCTAAACCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (23 bp):
TACCATTTCGTACCAAATCACAA
Found at i:36780135 original size:24 final size:23
Alignment explanation
Indices: 36780106--36780161 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
36780096 ACTGATTGAG
* *
36780106 AAAAGAGAGAATGAAATGAAAAA-
1 AAAAGAGAAAAAGAAAT-AAAAAC
36780129 AACAAGAAGAAAAAGAAATAAAAAC
1 AA-AAG-AGAAAAAGAAATAAAAAC
36780154 AAAAGAGA
1 AAAAGAGA
36780162 CTGAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 5 0.18
24 11 0.39
25 12 0.43
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAAAGAAATAAAAAC
Found at i:36780172 original size:33 final size:33
Alignment explanation
Indices: 36780135--36780239 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 33
36780125 AAAAAACAAG
36780135 AAGAAAAAGAAAT-AAAA-ACAAAAGAGACTGAAA
1 AAGAAAAAG-AATGAAAAGA-AAAAGAGACTGAAA
* *
36780168 AAG-AAATGAGTGAAAAGGAAAAAGAGACTGAAA
1 AAGAAAAAGAATGAAAA-GAAAAAGAGACTGAAA
*
36780201 AAGAAACAAG--TGAAAGAGAAAAAGAG-CTTGCAA
1 AAGAAA-AAGAATGAAA-AGAAAAAGAGAC-TGAAA
36780234 AAGAAA
1 AAGAAA
36780240 CGAGTGAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
31 2 0.03
32 9 0.15
33 44 0.72
34 4 0.07
35 2 0.03
ACGTcount: A:0.65, C:0.06, G:0.22, T:0.08
Consensus pattern (33 bp):
AAGAAAAAGAATGAAAAGAAAAAGAGACTGAAA
Found at i:36780183 original size:15 final size:15
Alignment explanation
Indices: 36780148--36780247 Score: 58
Period size: 17 Copynumber: 6.1 Consensus size: 15
36780138 AAAAAGAAAT
*
36780148 AAAAACAAAAGAGACTG
1 AAAAAGAAAAGAG--TG
*
36780165 AAAAAGAAATGAGTG
1 AAAAAGAAAAGAGTG
*
36780180 AAAAGGAAAAAGAGACTG
1 AAAAAG-AAAAGAG--TG
36780198 AAAAAGAAACA-AGTG
1 AAAAAGAAA-AGAGTG
*
36780213 AAAGAGAAAAAGAGCTTG
1 AAAAAG-AAAAGAG--TG
* *
36780231 CAAAAGAAACGAGTG
1 AAAAAGAAAAGAGTG
36780246 AA
1 AA
36780248 GAGAGTGACC
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 18 0.28
16 11 0.17
17 22 0.34
18 14 0.22
ACGTcount: A:0.61, C:0.07, G:0.24, T:0.08
Consensus pattern (15 bp):
AAAAAGAAAAGAGTG
Found at i:36780201 original size:18 final size:18
Alignment explanation
Indices: 36780154--36780239 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
36780144 AAATAAAAAC
36780154 AAAAGAGACTGAAAAAG-
1 AAAAGAGACTGAAAAAGA
* *
36780171 AAATGAG--TGAAAAGGA
1 AAAAGAGACTGAAAAAGA
36780187 AAAAGAGACTGAAAAAGA
1 AAAAGAGACTGAAAAAGA
* *
36780205 AACA-AG--TGAAAGAGA
1 AAAAGAGACTGAAAAAGA
*
36780220 AAAAGAG-CTTGCAAAAGA
1 AAAAGAGAC-TGAAAAAGA
36780238 AA
1 AA
36780240 CGAGTGAAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
15 18 0.33
16 8 0.15
17 8 0.15
18 20 0.37
ACGTcount: A:0.62, C:0.06, G:0.24, T:0.08
Consensus pattern (18 bp):
AAAAGAGACTGAAAAAGA
Found at i:36780240 original size:33 final size:33
Alignment explanation
Indices: 36780154--36780252 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
36780144 AAATAAAAAC
*
36780154 AAAAGAGACTGAAAAAGAAATGAGTGAAA-AGGA
1 AAAAGAGACTGAAAAAGAAACGAGTGAAAGA-GA
*
36780187 AAAAGAGACTGAAAAAGAAACAAGTGAAAGAGA
1 AAAAGAGACTGAAAAAGAAACGAGTGAAAGAGA
*
36780220 AAAAGAG-CTTGCAAAAGAAACGAGTGAAGAGAG
1 AAAAGAGAC-TGAAAAAGAAACGAGTGAA-AGAG
36780253 TGACCAAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 1 0.02
33 53 0.90
34 5 0.08
ACGTcount: A:0.59, C:0.06, G:0.27, T:0.08
Consensus pattern (33 bp):
AAAAGAGACTGAAAAAGAAACGAGTGAAAGAGA
Found at i:36784205 original size:17 final size:15
Alignment explanation
Indices: 36784175--36784208 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
36784165 TATTAAATTG
36784175 AATTTTTTAATTTTT
1 AATTTTTTAATTTTT
36784190 AATTTTTATAAATTTTT
1 AATTTTT-T-AATTTTT
36784207 AA
1 AA
36784209 ATAATTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTTTAATTTTT
Found at i:36794861 original size:23 final size:21
Alignment explanation
Indices: 36794835--36794886 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
36794825 AGACACTTGC
*
36794835 ATTAAACACATTAAAATAAACTT
1 ATTAAACACATT-AAA-AAACTA
* *
36794858 ATTAAACATATTTAAAAACTA
1 ATTAAACACATTAAAAAACTA
36794879 ATTAAACA
1 ATTAAACA
36794887 TATCAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
22 2 0.08
23 11 0.42
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAAACACATTAAAAAACTA
Found at i:36807161 original size:27 final size:26
Alignment explanation
Indices: 36807125--36807175 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
36807115 ACAAGAAATC
36807125 AAAAAAGAAAATGAGAGTGAGAAAAAG
1 AAAAAAGAAAATGAGAGTGA-AAAAAG
* *
36807152 AAAAAAGAAATTGAGATTGAAAAA
1 AAAAAAGAAAATGAGAGTGAAAAA
36807176 GGAAGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.12
Consensus pattern (26 bp):
AAAAAAGAAAATGAGAGTGAAAAAAG
Found at i:36807166 original size:21 final size:19
Alignment explanation
Indices: 36807093--36807167 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
36807083 GAGAAATGAA
36807093 AAAAAGAAATGAAAGAAAAAG
1 AAAAAGAAATG--AGAAAAAG
* *
36807114 AACAAGAAATCA-AAAAAG
1 AAAAAGAAATGAGAAAAAG
* *
36807132 AAAATGAGAGTGAGAAAAAG
1 AAAAAGA-AATGAGAAAAAG
36807152 AAAAAAGAAATTGAGA
1 -AAAAAGAAA-TGAGA
36807168 TTGAAAAAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 11 0.26
19 4 0.10
20 7 0.17
21 20 0.48
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (19 bp):
AAAAAGAAATGAGAAAAAG
Found at i:36817465 original size:52 final size:51
Alignment explanation
Indices: 36817387--36817491 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 51
36817377 GAAAATGATG
36817387 AAATTTTGTGAGGGGGTAAGGGAGAAAGGGTAAGTACAAAAGACAGAGAGAA
1 AAATTTTGTGAGGGGGTAAGGGAGAAAGGGTAAGTAC-AAAGACAGAGAGAA
36817439 AAATTTTGTGAGGGGGTAAGGGAGAAAGGGTAAGTACAAAGACAGAGAGAA
1 AAATTTTGTGAGGGGGTAAGGGAGAAAGGGTAAGTACAAAGACAGAGAGAA
36817490 AA
1 AA
36817492 GAGGCTAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 16 0.30
52 37 0.70
ACGTcount: A:0.45, C:0.04, G:0.36, T:0.15
Consensus pattern (51 bp):
AAATTTTGTGAGGGGGTAAGGGAGAAAGGGTAAGTACAAAGACAGAGAGAA
Found at i:36839074 original size:19 final size:19
Alignment explanation
Indices: 36839047--36839086 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
36839037 GGTCACATAG
*
36839047 CCGTGTGACATAGCTTAGA
1 CCGTCTGACATAGCTTAGA
36839066 CCGTCTGACATAGCTTAGA
1 CCGTCTGACATAGCTTAGA
36839085 CC
1 CC
36839087 ATGTGAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (19 bp):
CCGTCTGACATAGCTTAGA
Found at i:36840509 original size:27 final size:27
Alignment explanation
Indices: 36840470--36841263 Score: 691
Period size: 27 Copynumber: 29.5 Consensus size: 27
36840460 ATTTGTGGGC
*
36840470 AAATGACCGAAATACCCTTGATA-GGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
* *
36840497 AAATGACCAAAATACCC-CTACAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
*
36840524 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
36840551 AAATGATCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
36840578 AAATGACCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** *
36840605 AAATGATCGAAATAATCTCGTAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
36840632 AAATGATCGAAATGCCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * **
36840659 AAATGACCAAAATATCCTCGATTGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* **
36840686 AAATGACCGAAATACCTTTAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
36840713 AAATGATCGAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
36840740 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
36840767 AAATGATCAAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * * *
36840794 AAATAACTGAGAT-GCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** * *
36840820 AAATGACTAAAATATCCTCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
36840847 AAATGACCGAAATACCCTTAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
36840874 AAATGATTGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
*
36840901 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
36840928 AAATGACCGAAATACCC-CTACAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
* * *
36840955 AAATGACTGAAATA-CCTCTACAGAGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
* * *
36840982 AAATGATCGAAATTCCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
36841009 AAATGACCAAAATACCATCGATGAGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
36841036 AAATGATCGAAATACCCCCAAAGGGTG
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** **
36841063 AAATAATTGAAATACTCC-CGAAAAG-A
1 AAATGACCGAAATAC-CCTCGAAGGGTA
*
36841089 GAAATAACCGAAATATCCC-C-ATAGGGTA
1 -AAATGACCGAAATA-CCCTCGA-AGGGTA
* * *
36841117 AGATGACTGAATTACCCTC-ATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
* * *
36841144 AAATAACCGAAATACCC-CGAAAGGTG
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
36841170 AAATGATCAAAATACCC-CGAAGGGTG
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
36841196 AAATGATCGAAATACCC-CCATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
* *
36841223 AAATGACCGAATTACCC-CGATAAGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
*
36841250 AAATGACCAAAATA
1 AAATGACCGAAATA
36841264 GCCCCATATT
Statistics
Matches: 628, Mismatches: 123, Indels: 32
0.80 0.16 0.04
Matches are distributed among these distances:
26 76 0.12
27 540 0.86
28 12 0.02
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:36841493 original size:32 final size:26
Alignment explanation
Indices: 36841430--36841506 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
36841420 TGAAGGAAGT
*
36841430 ATACTGTTACTGGCAGCTTTGTTGCA
1 ATACTGTTACTGGCAGCTTTGCTGCA
*
36841456 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCA
* *
36841482 ATTCTATTACTGGCAGCTTTGCTGC
1 ATACTGTTACTGGCAGCTTTGCTGC
36841507 GATATTGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCA
Found at i:36841663 original size:28 final size:28
Alignment explanation
Indices: 36841618--36841817 Score: 280
Period size: 28 Copynumber: 7.2 Consensus size: 28
36841608 ACGGTACTGA
36841618 TACTGT-TTAGGGCTAAGGCCCACATTGT
1 TACTGTATT-GGGCTAAGGCCCACATTGT
* *
36841646 TACTATATTGGGTTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
36841674 TACTATATTGGGTTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
36841702 TACTGTTTTGGGCTAAGGCCCATATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
36841730 TACTGTATTGGTCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
36841758 T-GTGTATTGGGCTAAGGCCCATATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
36841785 TGCTGTATTGGGCTAAGGCCCACATTG-
1 TACTGTATTGGGCTAAGGCCCACATTGT
36841812 TACTGT
1 TACTGT
36841818 TACTGAATAG
Statistics
Matches: 155, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
27 29 0.19
28 124 0.80
29 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:36844683 original size:647 final size:648
Alignment explanation
Indices: 36843448--36844740 Score: 2471
Period size: 647 Copynumber: 2.0 Consensus size: 648
36843438 TCTTTGATAT
* *
36843448 TTAAATTCATAACTTTGTCACCAATATCACATTTACAAAACGTGTGTTTCATACACATAACTATA
1 TTAAATTCATAACTTTGTCACCAATAACACATTTACAAAACGCGTGTTTCATACACATAACTATA
36843513 AAGTTTTCGCTTGTTTCAATATTGTTACAAAGAACTTTTAAATAGATAATCGTTAATTACTCAAT
66 AAGTTTTCGCTTGTTTCAATATTGTTACAAAGAACTTTTAAATAGATAATCGTTAATTACTCAAT
**
36843578 TTCATTACCTAACATCTCCATATTCATCTAAACATATCATATCCAAATCATTTATGAATTCAACA
131 TTCATTACCTAACATCTCCATATTCATCTAAACATATCATATCCAAATCATTTACAAATTCAACA
36843643 TCAACTTACCTTAAACAAAATAGATAATCAAGAGGATGAATTTCTAATTCCTGATAACCGAATGC
196 TCAACTTACCTTAAACAAAATAGATAATCAAGAGGATGAATTTCTAATTCCTGATAACCGAATGC
36843708 AAGATCACACTGCATTAGTATATAATCGTATATAACATAAATGGTTCTTTTCAAAAGAACCAACC
261 AAGATCACACTGCATTAGTATATAATCGTATATAACATAAATGGTTCTTTTCAAAAGAACCAACC
36843773 AAATTTTATGAATAACCATATGTCAATGTACTTATCAACATTTATACATAAGCATTTCATACTGC
326 AAATTTTATGAATAACCATATGTCAATGTACTTATCAACATTTATACATAAGCATTTCATACTGC
36843838 TATTTATCACATAGTAACAATTTAAATGTTCCATAGAATTGAGCAAGTAAATAAGTTTTAAGTTA
391 TATTTATCACATAGTAACAATTTAAATGTTCCATAGAATTGAGCAAGTAAATAAGTTTTAAGTTA
36843903 ATTAATACATAGCCCGATGAACTATAGTAACTTGAGTCAGATACACAGGTAACTACACCACACCA
456 ATTAATACATAGCCCGATGAACTATAGTAACTTGAGTCAGATACACAGGTAACTACACCACACCA
36843968 GAGGCATAAAAAATGCATAATAGAGGCACTGAAGTGCAATCCCTACAAGCGCGCGTTCTAACCCT
521 GAGGCATAAAAAATGCATAATAGAGGCACTGAAGTGCAATCCCTACAAGCGCGCGTTCTAACCCT
36844033 ATTGGCATGTCAATCGTATCCTAATCGTTTACTACGTTCAAATGGACATTTAAACTGAGTTAA
586 ATTGGCATGTCAATCGTATCCTAATCGTTTACTACGTTCAAATGGACATTTAAACTGAGTTAA
* *
36844096 TTAAATTCATAACTTTGTCACCAATAACACATTTACAAAGCGCGTGTTTCATACATATAACTATA
1 TTAAATTCATAACTTTGTCACCAATAACACATTTACAAAACGCGTGTTTCATACACATAACTATA
36844161 AAGTTTTCGCTTGTTTCAATATTGTTACAAAGAACTTTTAAATAGATAATCGTTAATTACTCAAT
66 AAGTTTTCGCTTGTTTCAATATTGTTACAAAGAACTTTTAAATAGATAATCGTTAATTACTCAAT
*
36844226 TTCATTACCTAACATCTCCATATTCATCTAAACATATCATATCCAAATCATTTACAAATTCAATA
131 TTCATTACCTAACATCTCCATATTCATCTAAACATATCATATCCAAATCATTTACAAATTCAACA
*
36844291 TCAACTTACCTTAAACAAAATAGATAATCAAGAGGATGAATTTTTAATTCCTGATAACCGAATGC
196 TCAACTTACCTTAAACAAAATAGATAATCAAGAGGATGAATTTCTAATTCCTGATAACCGAATGC
36844356 AAGATCACACTGCATTAGT-TATAATCGTATATAACATAAATGGTTCTTTTCAAAAGAACCAACC
261 AAGATCACACTGCATTAGTATATAATCGTATATAACATAAATGGTTCTTTTCAAAAGAACCAACC
*
36844420 AAATTTTATGAATAACCATATGTCAATGTATTTATCAACATTTATACATAAGCATTTCATACTGC
326 AAATTTTATGAATAACCATATGTCAATGTACTTATCAACATTTATACATAAGCATTTCATACTGC
36844485 TATTTATCACATAGTAACAATTTAAATGTTCCATAGAATTGAGCAAGTAAATAAGTTTTAAGTTA
391 TATTTATCACATAGTAACAATTTAAATGTTCCATAGAATTGAGCAAGTAAATAAGTTTTAAGTTA
*
36844550 ATTAATACATAGCCCGATGAACTATAGTAACTTGAGTCGGATACACAGGTAACTACACCACACCA
456 ATTAATACATAGCCCGATGAACTATAGTAACTTGAGTCAGATACACAGGTAACTACACCACACCA
*
36844615 GAGGCATAAAAAATGCATAATAGAGGCACTGAAGTGCAATCCCTACAAGTGCGCGTTCTAACCCT
521 GAGGCATAAAAAATGCATAATAGAGGCACTGAAGTGCAATCCCTACAAGCGCGCGTTCTAACCCT
*
36844680 ATTGGCATGTCAATCGTATCCTAATCGTTTACTACGTTCAAATGGAGATTTAAACTGAGTT
586 ATTGGCATGTCAATCGTATCCTAATCGTTTACTACGTTCAAATGGACATTTAAACTGAGTT
36844741 CGTCACATTA
Statistics
Matches: 633, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
647 362 0.57
648 271 0.43
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (648 bp):
TTAAATTCATAACTTTGTCACCAATAACACATTTACAAAACGCGTGTTTCATACACATAACTATA
AAGTTTTCGCTTGTTTCAATATTGTTACAAAGAACTTTTAAATAGATAATCGTTAATTACTCAAT
TTCATTACCTAACATCTCCATATTCATCTAAACATATCATATCCAAATCATTTACAAATTCAACA
TCAACTTACCTTAAACAAAATAGATAATCAAGAGGATGAATTTCTAATTCCTGATAACCGAATGC
AAGATCACACTGCATTAGTATATAATCGTATATAACATAAATGGTTCTTTTCAAAAGAACCAACC
AAATTTTATGAATAACCATATGTCAATGTACTTATCAACATTTATACATAAGCATTTCATACTGC
TATTTATCACATAGTAACAATTTAAATGTTCCATAGAATTGAGCAAGTAAATAAGTTTTAAGTTA
ATTAATACATAGCCCGATGAACTATAGTAACTTGAGTCAGATACACAGGTAACTACACCACACCA
GAGGCATAAAAAATGCATAATAGAGGCACTGAAGTGCAATCCCTACAAGCGCGCGTTCTAACCCT
ATTGGCATGTCAATCGTATCCTAATCGTTTACTACGTTCAAATGGACATTTAAACTGAGTTAA
Found at i:36847800 original size:13 final size:13
Alignment explanation
Indices: 36847782--36847806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36847772 TTTGAATGTA
36847782 TTATTGTGTGAAT
1 TTATTGTGTGAAT
36847795 TTATTGTGTGAA
1 TTATTGTGTGAA
36847807 GTTCTGGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
TTATTGTGTGAAT
Found at i:36851299 original size:18 final size:19
Alignment explanation
Indices: 36851254--36851302 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
36851244 GAATATTTAC
*
36851254 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
36851274 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
36851292 ATAAAAATAAA
1 ATAAAAATAAA
36851303 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:36855044 original size:18 final size:19
Alignment explanation
Indices: 36854999--36855047 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
36854989 GAATATTTAC
*
36854999 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
36855019 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
36855037 ATAAAAATAAA
1 ATAAAAATAAA
36855048 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:36860535 original size:23 final size:23
Alignment explanation
Indices: 36860503--36860568 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
36860493 CTTTTTGAAC
* *
36860503 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36860526 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36860549 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36860569 CCCAAAACCG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36866580 original size:17 final size:18
Alignment explanation
Indices: 36866552--36866601 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
36866542 TAATAAATAA
*
36866552 AATTATCCAACCCAACCC
1 AATTACCCAACCCAACCC
*
36866570 AATTA-CCAACCTAACCC
1 AATTACCCAACCCAACCC
36866587 AATTACCCAACCCAA
1 AATTACCCAACCCAA
36866602 TAAAACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:36866641 original size:38 final size:39
Alignment explanation
Indices: 36866583--36866660 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
36866573 TACCAACCTA
*
36866583 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
36866622 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
36866660 A
1 A
36866661 ACTCCAAGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 29 0.76
39 9 0.24
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:36866836 original size:37 final size:37
Alignment explanation
Indices: 36866786--36866859 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
36866776 GTTAATTTCC
36866786 AGACTTATGTAATGTTTTTAACTATGTAGTGATTCAA
1 AGACTTATGTAATGTTTTTAACTATGTAGTGATTCAA
*
36866823 AGACTTATGTAATGTTTTTAATTATGTAGTGATTCAA
1 AGACTTATGTAATGTTTTTAACTATGTAGTGATTCAA
36866860 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (37 bp):
AGACTTATGTAATGTTTTTAACTATGTAGTGATTCAA
Found at i:36866872 original size:9 final size:9
Alignment explanation
Indices: 36866858--36866915 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
36866848 GTAGTGATTC
*
36866858 AATTCGGGT
1 AATTCGGTT
*
36866867 AATTCGGGT
1 AATTCGGTT
36866876 AATTCGGTT
1 AATTCGGTT
36866885 AATTCGGTT
1 AATTCGGTT
*
36866894 AATTTGGTT
1 AATTCGGTT
36866903 AATTCGGTT
1 AATTCGGTT
36866912 AATT
1 AATT
36866916 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:36876702 original size:15 final size:16
Alignment explanation
Indices: 36876667--36876705 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
36876657 TTTAAAAATC
*
36876667 AAATTAAAATATTAAT
1 AAATTAATATATTAAT
36876683 AAATTAATAT-TTAAT
1 AAATTAATATATTAAT
*
36876698 TAATTAAT
1 AAATTAAT
36876706 TAATCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTAATATATTAAT
Found at i:36877167 original size:23 final size:23
Alignment explanation
Indices: 36877139--36877182 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36877129 CTTTCTTACT
* *
36877139 GTAGTAATTTTTGGGGTATTATA
1 GTAGTAATTTTCGGGATATTATA
36877162 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
36877183 CACTGTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTATA
Found at i:36877190 original size:22 final size:23
Alignment explanation
Indices: 36877140--36877190 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
36877130 TTTCTTACTG
* * * *
36877140 TAGTAATTTTTGGGGTATTATAG
1 TAGTAATTTTCGGGATATTACAC
36877163 TAGTAATTTTCGGGATATTACAC
1 TAGTAATTTTCGGGATATTACAC
36877186 T-GTAA
1 TAGTAA
36877191 CACCCCAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAC
Found at i:36878933 original size:30 final size:30
Alignment explanation
Indices: 36878899--36878971 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
36878889 AGACTCGATT
36878899 TCTTGATTTTCTTGAAAACAAGAAAGTGGA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGGA
36878929 TCTTGATTTTCTTGAAAACAAGAAAGTGGA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGGA
36878959 TCTTGATTTTCTT
1 TCTTGATTTTCTT
36878972 TTTCCTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGGA
Found at i:36879157 original size:12 final size:12
Alignment explanation
Indices: 36879140--36879169 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
36879130 CCACATACTC
36879140 TCGTGTGCTAGG
1 TCGTGTGCTAGG
36879152 TCGTGTGCTAGG
1 TCGTGTGCTAGG
*
36879164 CCGTGT
1 TCGTGT
36879170 AACTGCCTGA
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:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (12 bp):
TCGTGTGCTAGG
Found at i:36879808 original size:20 final size:20
Alignment explanation
Indices: 36879780--36879824 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
36879770 TTAATGTGTT
*
36879780 TGTCCTAACTGAATTAATTA
1 TGTCTTAACTGAATTAATTA
* *
36879800 TGTCTTAACTTAATTAATTG
1 TGTCTTAACTGAATTAATTA
36879820 TGTCT
1 TGTCT
36879825 AGTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (20 bp):
TGTCTTAACTGAATTAATTA
Found at i:36881157 original size:15 final size:16
Alignment explanation
Indices: 36881137--36881170 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
36881127 TACGAAATTT
36881137 TTAAAAAAA-AGTGAA
1 TTAAAAAAATAGTGAA
*
36881152 TTAAAAAAATCGTGAA
1 TTAAAAAAATAGTGAA
36881168 TTA
1 TTA
36881171 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.26
Consensus pattern (16 bp):
TTAAAAAAATAGTGAA
Found at i:36881160 original size:16 final size:17
Alignment explanation
Indices: 36881138--36881183 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
36881128 ACGAAATTTT
36881138 TAAAAAAAAGTGAATTA
1 TAAAAAAAAGTGAATTA
**
36881155 -AAAAAATCGTGAATTA
1 TAAAAAAAAGTGAATTA
36881171 TTAAAAAAAAGTG
1 -TAAAAAAAAGTG
36881184 TCTGTGTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 14 0.61
18 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (17 bp):
TAAAAAAAAGTGAATTA
Found at i:36890460 original size:20 final size:20
Alignment explanation
Indices: 36890431--36890470 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36890421 TGTCTAGTCC
36890431 TAACTGAATTAATTATGTCT
1 TAACTGAATTAATTATGTCT
* *
36890451 TAACTTAATTAATTGTGTCT
1 TAACTGAATTAATTATGTCT
36890471 AGTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (20 bp):
TAACTGAATTAATTATGTCT
Done.