Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 169 of 276
Found at i:55380213 original size:89 final size:88
Alignment explanation
Indices: 55380019--55380331 Score: 263
Period size: 89 Copynumber: 3.5 Consensus size: 88
55380009 AATTTTGTAG
* * * * * *
55380019 CTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATC-TACTCCATTGC
1 CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAA-CATGCTCCACTGC
* * * * *
55380083 AACTTTAGGGAGATAAAATTTGTTA
64 AACTTCAGGAAGACAAGATTTGTGA
* * ** * * * * * *
55380108 TTTTTAACCTGTTCCACTACAACTTCAAGGAGATAAGGTTTGTAGCTTTAATATGCTCTACTGCT
1 -CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAACATGCTCCACTGCA
*
55380173 GCTTCA-GAGAGACAAGATTTGCT-A
65 ACTTCAGGA-AGACAAGATTTG-TGA
* * * ** *
55380197 TTTTCAATCTACTCCACTGCAAATTCAGGGAGATAATATTTGTTATTTTTAACCTGCTCCACTGC
1 CTTT-AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAACATGCTCCACTGC
* * *
55380262 AACTTCAGGAAGATAAGGTTTGTGG
64 AACTTCAGGAAGACAAGATTTGTGA
55380287 CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
1 CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
55380332 CTGTAGCTTT
Statistics
Matches: 172, Mismatches: 44, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
88 7 0.04
89 95 0.55
90 68 0.40
91 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (88 bp):
CTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAACATGCTCCACTGCAA
CTTCAGGAAGACAAGATTTGTGA
Found at i:55380252 original size:134 final size:134
Alignment explanation
Indices: 55380012--55380327 Score: 481
Period size: 134 Copynumber: 2.4 Consensus size: 134
55380002 GTAGCTAAAT
55380012 TTTGTAGCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTC
1 TTTGTAGCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTC
* * * *
55380077 CATTGCAACTTTAGGGAGATAAAATTTGTTATTTTTAACCTGTTCCACTACAACTTCAAGG-AGA
66 CACTGCAAATTCAGGGAGATAAAATTTGTTATTTTTAACCTGCTCCACTACAACTTC-AGGAAGA
55380141 TAAGG
130 TAAGG
* * ** * *
55380146 TTTGTAGCTTTAATATGCTCTACTGCTGCTTCAGAGAGACAAGATTTGCTATTTTCAATCTACTC
1 TTTGTAGCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTC
* *
55380211 CACTGCAAATTCAGGGAGATAATATTTGTTATTTTTAACCTGCTCCACTGCAACTTCAGGAAGAT
66 CACTGCAAATTCAGGGAGATAAAATTTGTTATTTTTAACCTGCTCCACTACAACTTCAGGAAGAT
55380276 AAGG
131 AAGG
* * *
55380280 TTTGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG
1 TTTGTAGCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTG
55380328 TAGCCTGTAG
Statistics
Matches: 161, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
133 3 0.02
134 158 0.98
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (134 bp):
TTTGTAGCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACTC
CACTGCAAATTCAGGGAGATAAAATTTGTTATTTTTAACCTGCTCCACTACAACTTCAGGAAGAT
AAGG
Found at i:55380603 original size:47 final size:43
Alignment explanation
Indices: 55380517--55380653 Score: 116
Period size: 47 Copynumber: 3.1 Consensus size: 43
55380507 AGAGGTATGG
* * * * *
55380517 GATTTGT-AATTCAATCTACTCTACTGCAACTTCACGGAGATAA
1 GATTTGTGACTTCAACCTGCTCCACTGCAATTTCA-GGAGATAA
* * *
55380560 GATTTGTTATTTTTTTAACCTGCTCCACTGCAATTTCAGGGAGATAA
1 GATTTGTGA---CTTCAACCTGCTCCACTGCAATTTCA-GGAGATAA
* *
55380607 GGTTTGTGACTTCAATCTGCTCCACTGCAACTTT-AGGAGATAA
1 GATTTGTGACTTCAACCTGCTCCACTGCAA-TTTCAGGAGATAA
55380650 GATT
1 GATT
55380654 CGCCATAATG
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
43 18 0.24
44 20 0.26
45 3 0.04
47 35 0.46
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (43 bp):
GATTTGTGACTTCAACCTGCTCCACTGCAATTTCAGGAGATAA
Found at i:55388472 original size:20 final size:20
Alignment explanation
Indices: 55388447--55388518 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 20
55388437 CCCGAAATCT
55388447 GTGCT-AACTGAAGCACATAA
1 GTGCTAAACTGAAGC-CATAA
* **
55388467 GTGCTAAACGGAAGCCCGAA
1 GTGCTAAACTGAAGCCATAA
*
55388487 G-GCT-AACTGAAGCTCATCA
1 GTGCTAAACTGAAGC-CATAA
* *
55388506 GAGCTGAACTGAA
1 GTGCTAAACTGAA
55388519 ACCCCAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 8 0.20
19 6 0.15
20 12 0.29
21 15 0.37
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (20 bp):
GTGCTAAACTGAAGCCATAA
Found at i:55407218 original size:19 final size:19
Alignment explanation
Indices: 55407181--55407218 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55407171 AAATGACTAT
*
55407181 ATAAGTAGAATGATAAATA
1 ATAAGTAGAATGAAAAATA
55407200 ATAAGTA-AATGAAAGAATA
1 ATAAGTAGAATGAAA-AATA
55407219 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
ATAAGTAGAATGAAAAATA
Found at i:55407497 original size:13 final size:14
Alignment explanation
Indices: 55407475--55407503 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55407465 ACATAAATAT
55407475 AAATAGATAATAAA
1 AAATAGATAATAAA
55407489 AAATA-ATAATAAA
1 AAATAGATAATAAA
55407502 AA
1 AA
55407504 CAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAGATAATAAA
Found at i:55407509 original size:30 final size:33
Alignment explanation
Indices: 55407451--55407514 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 33
55407441 TTAAATATGT
* * *
55407451 ATAAAAGAAGTAATACATAAATATAAATAGATA
1 ATAAAAGAAGTAATACATAAAAACAAATAAATA
55407484 ATAAAA-AA-TAATA-ATAAAAACAAATAAATA
1 ATAAAAGAAGTAATACATAAAAACAAATAAATA
55407514 A
1 A
55407515 ATGCTTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.54
31 5 0.18
32 2 0.07
33 6 0.21
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (33 bp):
ATAAAAGAAGTAATACATAAAAACAAATAAATA
Found at i:55407602 original size:14 final size:14
Alignment explanation
Indices: 55407583--55407612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55407573 AAATAAATAC
55407583 AATAATACATAAAA
1 AATAATACATAAAA
*
55407597 AATAATATATAAAA
1 AATAATACATAAAA
55407611 AA
1 AA
55407613 AATCTACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATACATAAAA
Found at i:55410309 original size:31 final size:31
Alignment explanation
Indices: 55410273--55410332 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
55410263 TATTTTATTG
* *
55410273 TTAATTTTGTTATTATTTTAAAGATATTTTT
1 TTAATTTTGTTACTATTTTAAAGACATTTTT
*
55410304 TTAATTTTGTTACTATTTTAGAGACATTT
1 TTAATTTTGTTACTATTTTAAAGACATTT
55410333 GCTTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.60
Consensus pattern (31 bp):
TTAATTTTGTTACTATTTTAAAGACATTTTT
Found at i:55410522 original size:19 final size:18
Alignment explanation
Indices: 55410500--55410540 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
55410490 TAAAAACAAA
*
55410500 TATTGGTTTTATTTTTTGT
1 TATTGATTTTATTTTTT-T
55410519 TATTGATTTTATTTTTTT
1 TATTGATTTTATTTTTTT
55410537 TATT
1 TATT
55410541 TGCGGTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (18 bp):
TATTGATTTTATTTTTTT
Found at i:55419793 original size:8 final size:8
Alignment explanation
Indices: 55419780--55419807 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55419770 AATTATGTAT
55419780 ATTTTGTG
1 ATTTTGTG
55419788 ATTTTGTG
1 ATTTTGTG
55419796 ATTTTGTG
1 ATTTTGTG
55419804 ATTT
1 ATTT
55419808 AGGGACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64
Consensus pattern (8 bp):
ATTTTGTG
Found at i:55425426 original size:28 final size:28
Alignment explanation
Indices: 55425393--55425447 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
55425383 TGAGTATTTA
*
55425393 AATGTATAT-ATTTAATTGAATTGAATTG
1 AATGTATATGATTTAA-TAAATTGAATTG
*
55425421 AATGTATATGATTTGATAAATTGAATT
1 AATGTATATGATTTAATAAATTGAATT
55425448 ATTGATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (28 bp):
AATGTATATGATTTAATAAATTGAATTG
Found at i:55425672 original size:23 final size:24
Alignment explanation
Indices: 55425621--55425676 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
55425611 TCAGCTCGTA
* *
55425621 AGAGCTTACTGATTTCAGCTCATT
1 AGAGCTTACCGATTTCAGCTCAAT
* *
55425645 GGAGCTTACCG-TTTCAGCTTAAT
1 AGAGCTTACCGATTTCAGCTCAAT
55425668 AGAGCTTAC
1 AGAGCTTAC
55425677 TGCTCATTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (24 bp):
AGAGCTTACCGATTTCAGCTCAAT
Found at i:55425880 original size:20 final size:20
Alignment explanation
Indices: 55425857--55425947 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
55425847 GTGTTTATAT
55425857 GGATGAATTACTGTTAATAC
1 GGATGAATTACTGTTAATAC
*
55425877 GGATGAATTACTGTTATTAC
1 GGATGAATTACTGTTAATAC
* * * * *
55425897 TGATAAACTACTATTTATAC
1 GGATGAATTACTGTTAATAC
* *
55425917 GGATGAACTACTGGTT-ATAT
1 GGATGAATTACT-GTTAATAC
*
55425937 GAATGAATTAC
1 GGATGAATTAC
55425948 AATTTATACG
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 55 0.96
21 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
GGATGAATTACTGTTAATAC
Found at i:55425953 original size:40 final size:38
Alignment explanation
Indices: 55425851--55425957 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 38
55425841 AGATATGTGT
* * *
55425851 TTATATGGATGAATTACTGTTAATACGGATGAATTACTG
1 TTATAT-GATGAATTACTATTTATACGGATGAACTACTG
* *
55425890 TTATTACTGATAAACTACTATTTATACGGATGAACTACTGG
1 TTA-TA-TGATGAATTACTATTTATACGGATGAACTACT-G
*
55425931 TTATATGAATGAATTACAATTTATACG
1 TTATATG-ATGAATTACTATTTATACG
55425958 AATAGAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 5 0.09
40 46 0.82
41 5 0.09
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (38 bp):
TTATATGATGAATTACTATTTATACGGATGAACTACTG
Found at i:55428316 original size:13 final size:14
Alignment explanation
Indices: 55428300--55428341 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
55428290 TTTCAATTTT
55428300 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
55428313 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
55428328 ATTTTAAATAATAT
1 ATTTT-AATAATAT
55428342 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:55428326 original size:16 final size:16
Alignment explanation
Indices: 55428304--55428340 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
55428294 AATTTTATTT
55428304 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
55428321 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
55428336 TAATA
1 TAATA
55428341 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:55428393 original size:15 final size:15
Alignment explanation
Indices: 55428373--55428429 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
55428363 ATTCAATATT
55428373 AATATTTTAATAATA
1 AATATTTTAATAATA
*
55428388 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
55428407 AATATATTAATAATA
1 AATATTTTAATAATA
*
55428422 AATGTTTT
1 AATATTTT
55428430 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:55428905 original size:14 final size:13
Alignment explanation
Indices: 55428886--55428924 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
55428876 CTAGAAAAGT
55428886 AAATCATTTTCCAG
1 AAATCATTTTCC-G
55428900 AAATCATTTTCCG
1 AAATCATTTTCCG
55428913 AAAGTCATTTTC
1 AAA-TCATTTTC
55428925 AGTGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:55432803 original size:2 final size:2
Alignment explanation
Indices: 55432796--55432849 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
55432786 TTTCTTATAA
* * *
55432796 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AT GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
55432838 AC AA AC AC AC AC
1 AC AC AC AC AC AC
55432850 TCTAAAGCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.44, G:0.02, T:0.04
Consensus pattern (2 bp):
AC
Found at i:55437032 original size:9 final size:10
Alignment explanation
Indices: 55437009--55437038 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
55436999 TTCACATCTT
55437009 TCTCTCAAGC
1 TCTCTCAAGC
55437019 TCTCTCAA-C
1 TCTCTCAAGC
55437028 TCTCTCAAGC
1 TCTCTCAAGC
55437038 T
1 T
55437039 TTTTATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.20, C:0.40, G:0.07, T:0.33
Consensus pattern (10 bp):
TCTCTCAAGC
Found at i:55442140 original size:13 final size:13
Alignment explanation
Indices: 55442122--55442147 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55442112 GTGGTCACAC
55442122 GGTCGTGTGGTCA
1 GGTCGTGTGGTCA
55442135 GGTCGTGTGGTCA
1 GGTCGTGTGGTCA
55442148 ATAACAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.46, T:0.31
Consensus pattern (13 bp):
GGTCGTGTGGTCA
Found at i:55446239 original size:36 final size:36
Alignment explanation
Indices: 55446189--55446354 Score: 226
Period size: 36 Copynumber: 4.6 Consensus size: 36
55446179 GTACATCAAC
* * * *
55446189 AATCCAACCAAAACACACCAGATGCTCATTAGAGCT
1 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
55446225 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
1 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
* * *
55446261 CATCCATCTGAAACACACCAAATGCTTATAAGAGCT
1 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
**
55446297 AATCCATCCGAAACACACC-AATGGCTCCGAAGAGCT
1 AATCCATCCGAAACACACCAAAT-GCTCATAAGAGCT
*
55446333 AATCCAACCGAAACACACCAAA
1 AATCCATCCGAAACACACCAAA
55446355 ACAGAAAGTA
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 3 0.03
36 110 0.96
37 2 0.02
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.16
Consensus pattern (36 bp):
AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
Found at i:55448710 original size:17 final size:18
Alignment explanation
Indices: 55448678--55448718 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
55448668 GGAACAGTTG
55448678 ATAA-CAATTTATATTCA
1 ATAATCAATTTATATTCA
*
55448695 ATAATCAATTTA-ATTCC
1 ATAATCAATTTATATTCA
55448712 ATAATCA
1 ATAATCA
55448719 TAAGTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATCAATTTATATTCA
Found at i:55448932 original size:19 final size:19
Alignment explanation
Indices: 55448882--55448932 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
55448872 GGCTGTTTGT
* **
55448882 CCAGGCCGTGTGACAGAGC
1 CCAGCCCGTGTGGTAGAGC
55448901 CCAGCCCGTGTGGTAGAGC
1 CCAGCCCGTGTGGTAGAGC
* *
55448920 CTAGCCCTTGTGG
1 CCAGCCCGTGTGG
55448933 CTCTAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (19 bp):
CCAGCCCGTGTGGTAGAGC
Found at i:55449892 original size:37 final size:37
Alignment explanation
Indices: 55449851--55449941 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 37
55449841 CAGTATATTT
* *
55449851 GTAGATTTTACTCGTTTGAGCTCCATTCAGTATAACA
1 GTAGATTTTACTCGTTTAAGCTCCACTCAGTATAACA
* * *
55449888 GTAGAATTTT-CTCATTTAAGCTTCACTCAGTATAATA
1 GTAG-ATTTTACTCGTTTAAGCTCCACTCAGTATAACA
* *
55449925 GTAAAATTTACTCGTTT
1 GTAGATTTTACTCGTTT
55449942 TAGTAGAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 4 0.09
37 35 0.80
38 5 0.11
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (37 bp):
GTAGATTTTACTCGTTTAAGCTCCACTCAGTATAACA
Found at i:55450010 original size:15 final size:14
Alignment explanation
Indices: 55449990--55450040 Score: 61
Period size: 13 Copynumber: 3.7 Consensus size: 14
55449980 TTAGTATATA
55449990 AATATTCAATAAGAG
1 AATATT-AATAAGAG
55450005 AATATTAATAA-AG
1 AATATTAATAAGAG
*
55450018 AATATTAA-CAGAG
1 AATATTAATAAGAG
*
55450031 AATATAAATA
1 AATATTAATA
55450041 CTATTAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 19 0.61
14 5 0.16
15 6 0.19
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (14 bp):
AATATTAATAAGAG
Found at i:55450064 original size:34 final size:34
Alignment explanation
Indices: 55450021--55450089 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
55450011 AATAAAGAAT
55450021 ATTAACAGAGAATATAAATACTATTAGAAGCATA
1 ATTAACAGAGAATATAAATACTATTAGAAGCATA
* *
55450055 ATTAGCAGAGAATATAAATACTATTAGAAGTATA
1 ATTAACAGAGAATATAAATACTATTAGAAGCATA
55450089 A
1 A
55450090 ATAAATGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (34 bp):
ATTAACAGAGAATATAAATACTATTAGAAGCATA
Found at i:55450083 original size:17 final size:18
Alignment explanation
Indices: 55450029--55450092 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
55450019 ATATTAACAG
55450029 AGAA-TATAAATACTATT
1 AGAAGTATAAATACTATT
* * *
55450046 AGAAGCATAATTAGC-A-G
1 AGAAGTATAAATA-CTATT
55450063 AGAA-TATAAATACTATT
1 AGAAGTATAAATACTATT
55450080 AGAAGTATAAATA
1 AGAAGTATAAATA
55450093 AATGTACGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
15 1 0.03
16 7 0.19
17 12 0.33
18 15 0.42
19 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (18 bp):
AGAAGTATAAATACTATT
Found at i:55452061 original size:19 final size:19
Alignment explanation
Indices: 55452026--55452063 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55452016 AAGAAACACT
**
55452026 AGAAATAAAAATCAACAAA
1 AGAAATAAAAAAAAACAAA
55452045 AGAAATAAAAAAAAACAAA
1 AGAAATAAAAAAAAACAAA
55452064 TCCTGGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (19 bp):
AGAAATAAAAAAAAACAAA
Found at i:55456511 original size:18 final size:18
Alignment explanation
Indices: 55456488--55456524 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55456478 ATGAAGCTGG
* *
55456488 TTTATCTCATTTTTCCAC
1 TTTATCTAATTTATCCAC
55456506 TTTATCTAATTTATCCAC
1 TTTATCTAATTTATCCAC
55456524 T
1 T
55456525 GCGTCGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATCTAATTTATCCAC
Found at i:55465035 original size:43 final size:43
Alignment explanation
Indices: 55464964--55465124 Score: 277
Period size: 43 Copynumber: 3.7 Consensus size: 43
55464954 TAAAAAAAAT
*
55464964 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
*
55465007 GCCGCTAAAAGTCATGGCCTTTAACGGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
*
55465050 GCCGTTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
* *
55465093 GCCGCTAAAAGTCACGGCTTTTAGCGGCGTTT
1 GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTT
55465125 TTCTGGCAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 111 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGTTGGAAAAGC
Found at i:55465299 original size:18 final size:18
Alignment explanation
Indices: 55465276--55465312 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
55465266 CAACCAACCT
55465276 CTGCCTCCCTCGCTGCTG
1 CTGCCTCCCTCGCTGCTG
*
55465294 CTGCCTCCCTCTCTGCTG
1 CTGCCTCCCTCGCTGCTG
55465312 C
1 C
55465313 CTCCGCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.51, G:0.19, T:0.30
Consensus pattern (18 bp):
CTGCCTCCCTCGCTGCTG
Found at i:55465309 original size:15 final size:16
Alignment explanation
Indices: 55465276--55465321 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
55465266 CAACCAACCT
55465276 CTGCCTCCCTCGCTGCTG
1 CTGCCTCCCT--CTGCTG
55465294 CTGCCTCCCTCT-CTG
1 CTGCCTCCCTCTGCTG
55465309 CTGCCTCCGCTCT
1 CTGCCTCC-CTCT
55465322 AAGTTGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.41
16 6 0.22
18 10 0.37
ACGTcount: A:0.00, C:0.52, G:0.17, T:0.30
Consensus pattern (16 bp):
CTGCCTCCCTCTGCTG
Found at i:55465755 original size:13 final size:14
Alignment explanation
Indices: 55465730--55465758 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55465720 TGATGAATTG
55465730 AATTAAACAATTAT
1 AATTAAACAATTAT
55465744 AATTAAAC-ATTAT
1 AATTAAACAATTAT
55465757 AA
1 AA
55465759 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:55467538 original size:114 final size:114
Alignment explanation
Indices: 55467208--55467540 Score: 406
Period size: 114 Copynumber: 2.9 Consensus size: 114
55467198 AAAACGACGA
* * * * *
55467208 CGTTTTCATATGAACAGAATAA-CATTTAGTGGCGTTTTATCACC-AAGCGCCGCTAAAGGCGAA
1 CGTTTTGATATAAACAAAATAACCA-TTAGTGGCG-TTTAT-ACCTTAGCGCCGCTAAA-TC-AA
** * * * * *
55467271 A-CTATTCCGGCGTTTTACCCTAAAACGCCACTAATAGTCGAATAAAACTACAT
61 ACCTATTGTGGCGTTTTAACCTAAAACGCCACTAAAAATCCAATAAAACTACAC
*
55467324 CGTTTTGATATAAACAAATTAACCATTAGTGGCGTTTATACCTTAGCGCCGCTAAATCAAACCTA
1 CGTTTTGATATAAACAAAATAACCATTAGTGGCGTTTATACCTTAGCGCCGCTAAATCAAACCTA
* *
55467389 TTGTGGCGTTTGAACCAAAAACGCCACTAAAAATCC-ATAAAAACTACAC
66 TTGTGGCGTTTTAACCTAAAACGCCACTAAAAATCCAAT-AAAACTACAC
* * *
55467438 CGTTTTGATCTAAACAAAATAACCCTTAGTGGCGTTTATAACCTT-GCGCCGCTAAATCAACCCT
1 CGTTTTGATATAAACAAAATAACCATTAGTGGCGTTTAT-ACCTTAGCGCCGCTAAATCAAACCT
55467502 ATTGTGGCGTTTTAACCTAAAACGCCACTAAAAATCCAA
65 ATTGTGGCGTTTTAACCTAAAACGCCACTAAAAATCCAA
55467541 AGAAAACGGT
Statistics
Matches: 190, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
113 5 0.03
114 133 0.70
115 23 0.12
116 27 0.14
117 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (114 bp):
CGTTTTGATATAAACAAAATAACCATTAGTGGCGTTTATACCTTAGCGCCGCTAAATCAAACCTA
TTGTGGCGTTTTAACCTAAAACGCCACTAAAAATCCAATAAAACTACAC
Found at i:55468433 original size:16 final size:17
Alignment explanation
Indices: 55468412--55468444 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
55468402 AAAGGTTATA
55468412 GTTTAGTG-TTTAGGGG
1 GTTTAGTGTTTTAGGGG
55468428 GTTTAGTGTTTTAGGGG
1 GTTTAGTGTTTTAGGGG
55468445 TTATAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (17 bp):
GTTTAGTGTTTTAGGGG
Found at i:55468445 original size:16 final size:16
Alignment explanation
Indices: 55468412--55468491 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
55468402 AAAGGTTATA
55468412 GTTTAGTG-TTTAGGGG
1 GTTTAGTGTTTTA-GGG
55468428 GTTTAGTGTTTTAGGG
1 GTTTAGTGTTTTAGGG
* *
55468444 G-TTA-TAG-ATTA-GT
1 GTTTAGT-GTTTTAGGG
*
55468457 GTTTA-TGTTTTTTGGG
1 GTTTAGTG-TTTTAGGG
*
55468473 GTTTAGGGTTTTAGGG
1 GTTTAGTGTTTTAGGG
55468489 GTT
1 GTT
55468492 AAATGACTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 3 0.06
14 8 0.16
15 6 0.12
16 28 0.56
17 5 0.10
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (16 bp):
GTTTAGTGTTTTAGGG
Found at i:55468633 original size:41 final size:41
Alignment explanation
Indices: 55468498--55468636 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
55468488 GGTTAAATGA
*
55468498 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGG
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* ** * *
55468539 TTTTTAGTAGCGTTTTA-CACAAAGCGCCGCTAATTCTTTGG
1 CTTTTAGCGGCGTTTTACCA-AAAGCGCCGCTAATGCTCTGG
* * *
55468580 TTTTTAGTGGCGTTTTACCAAAAGCGCCACTAATGCTCTGG
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
*
55468621 CTTTTAACGGCGTTTT
1 CTTTTAGCGGCGTTTT
55468637 TGGTAAAACG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.02
41 79 0.95
42 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (41 bp):
CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
Found at i:55468649 original size:41 final size:41
Alignment explanation
Indices: 55468599--55468689 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
55468589 GCGTTTTACC
*
55468599 AAAAGCGCCACTAATGCTCTGGCTTTTAACGGCGTTTT-TGGT
1 AAAA-CGCCACTAATGCTATGGCTTTTAACGGCGTTTTCT-GT
* ** **
55468641 AAAACGCCACTATTGCTATGTTTTTTGGCGGCGTTTTCTGT
1 AAAACGCCACTAATGCTATGGCTTTTAACGGCGTTTTCTGT
55468682 AAAACGCC
1 AAAACGCC
55468690 GCTATTTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (41 bp):
AAAACGCCACTAATGCTATGGCTTTTAACGGCGTTTTCTGT
Found at i:55468666 original size:82 final size:82
Alignment explanation
Indices: 55468499--55468677 Score: 198
Period size: 82 Copynumber: 2.2 Consensus size: 82
55468489 GTTAAATGAC
* * ** *
55468499 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGGTTTTTAGTAGCGTTTTACACAAAGC
1 TTTTAGCGGCGTTTTACCAAAAACGCCACTAATGCTCTGGCTTTTAACAGCGTTTTACACAAAAC
* *
55468564 GCCGCTAATTCTTTGGT
66 GCCACTAATTCTATGGT
* * * ****
55468581 TTTTAGTGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGCTTTTAACGGCGTTTTTGGTAAAAC
1 TTTTAGCGGCGTTTTACCAAAAACGCCACTAATGCTCTGGCTTTTAACAGCGTTTTACACAAAAC
*
55468646 GCCACT-ATTGCTATGTT
66 GCCACTAATT-CTATGGT
*
55468663 TTTTGGCGGCGTTTT
1 TTTTAGCGGCGTTTT
55468678 CTGTAAAACG
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 3 0.04
82 76 0.96
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCACTAATGCTCTGGCTTTTAACAGCGTTTTACACAAAAC
GCCACTAATTCTATGGT
Found at i:55468695 original size:41 final size:41
Alignment explanation
Indices: 55468622--55468740 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
55468612 ATGCTCTGGC
* * **
55468622 TTTTAACGGCGTTTT-TGGTAAAACGCCACTATTGCTATGTT
1 TTTTAGCGGCGTTTTCT-GTAAAACGCCGCTATTGCTATAAT
* *
55468663 TTTTGGCGGCGTTTTCTGTAAAACGCCGCTATTTCTATAAT
1 TTTTAGCGGCGTTTTCTGTAAAACGCCGCTATTGCTATAAT
* * *
55468704 TTTTAGCGTCGTTTTAACT-AAAAACGCTGCTATTGCT
1 TTTTAGCGGCGTTTT--CTGTAAAACGCCGCTATTGCT
55468741 TTGCGTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 46 0.72
42 16 0.25
43 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTCTGTAAAACGCCGCTATTGCTATAAT
Found at i:55469741 original size:19 final size:19
Alignment explanation
Indices: 55469701--55469742 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
55469691 AATTTTGTAA
**
55469701 TAATTAAAAGATTTTTTGT
1 TAATTAAAAGATTTTTCAT
55469720 TAATTAAAAGATTTTTCAT
1 TAATTAAAAGATTTTTCAT
55469739 TAAT
1 TAAT
55469743 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (19 bp):
TAATTAAAAGATTTTTCAT
Found at i:55472180 original size:26 final size:26
Alignment explanation
Indices: 55472149--55472200 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
55472139 GCAAAATATG
55472149 TATTTCTACTATTTAATTATTGAATT
1 TATTTCTACTATTTAATTATTGAATT
*
55472175 TATTTCTATTATTTAATTATTGAATT
1 TATTTCTACTATTTAATTATTGAATT
55472201 AAATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (26 bp):
TATTTCTACTATTTAATTATTGAATT
Found at i:55472659 original size:19 final size:20
Alignment explanation
Indices: 55472623--55472665 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
55472613 ACTCAACTCG
*
55472623 AATTAAAAAAAATTAAATAA
1 AATTAAAAAAAATAAAATAA
*
55472643 AATT-AAAATAATAAAATAA
1 AATTAAAAAAAATAAAATAA
55472662 AATT
1 AATT
55472666 TATCAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AATTAAAAAAAATAAAATAA
Found at i:55476971 original size:36 final size:36
Alignment explanation
Indices: 55476924--55476996 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
55476914 AAGATTGGGA
55476924 TAGAATCCCTTACATTTTTGGAACGTATTCAAGGTG
1 TAGAATCCCTTACATTTTTGGAACGTATTCAAGGTG
*
55476960 TAGAATCCCTTACATTTTTGGAACGTATTTAAGGTG
1 TAGAATCCCTTACATTTTTGGAACGTATTCAAGGTG
55476996 T
1 T
55476997 TTATTTTGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (36 bp):
TAGAATCCCTTACATTTTTGGAACGTATTCAAGGTG
Found at i:55477630 original size:20 final size:18
Alignment explanation
Indices: 55477580--55477631 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
55477570 CTATAAGATA
55477580 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
55477597 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
55477617 AATATTAAATTAATA
1 AATATTAAATTAATA
55477632 AAAGACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:55488467 original size:121 final size:121
Alignment explanation
Indices: 55488320--55488563 Score: 434
Period size: 121 Copynumber: 2.0 Consensus size: 121
55488310 CATCAGCCAC
*
55488320 TAACACATATCCCAAGATGGTTTAATTTCCATTTTGGACCTTTGGTTAATTGCAATTTAAATCCC
1 TAACACATATCCCAAGATGGTTTAATTTCCATTTTGGACCTTTGGTTAATTACAATTTAAATCCC
* * *
55488385 TAAATCTTTGGCTAATTAAAAACCTATAACGATAAAGTTTTACAATTTAGTCCTTG
66 TAAATCTTTGGCCAATTAAAAACCTATAACAATAAAGTTTTACAATTTAGTCCATG
*
55488441 TAACACATATCCCAATATGGTTTAATTTCCATTTTGGACCTTTGGTTAATTACAATTTAAATCCC
1 TAACACATATCCCAAGATGGTTTAATTTCCATTTTGGACCTTTGGTTAATTACAATTTAAATCCC
*
55488506 TAAATCTTTGGCCAATTAAAAACCTATAGCAATAAAGTTTTACAATTTAGTCCATG
66 TAAATCTTTGGCCAATTAAAAACCTATAACAATAAAGTTTTACAATTTAGTCCATG
55488562 TA
1 TA
55488564 CCTTAATTAA
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (121 bp):
TAACACATATCCCAAGATGGTTTAATTTCCATTTTGGACCTTTGGTTAATTACAATTTAAATCCC
TAAATCTTTGGCCAATTAAAAACCTATAACAATAAAGTTTTACAATTTAGTCCATG
Found at i:55489985 original size:20 final size:20
Alignment explanation
Indices: 55489960--55490007 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
55489950 TTATTATATT
*
55489960 ATGCGGGGCAAGCGGGGATG
1 ATGCGGGGCAAGCGAGGATG
*
55489980 ATGCGGGGCAAGTGAGGATG
1 ATGCGGGGCAAGCGAGGATG
55490000 ATGCGGGG
1 ATGCGGGG
55490008 ATGGGGCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.54, T:0.12
Consensus pattern (20 bp):
ATGCGGGGCAAGCGAGGATG
Found at i:55497133 original size:117 final size:118
Alignment explanation
Indices: 55496971--55497205 Score: 319
Period size: 117 Copynumber: 2.0 Consensus size: 118
55496961 CACCCGCTAA
* *
55496971 AAAGAATACAAAGATAATAAAGAGGCATATAAAAATTCAATACCATAAACAAGTCATGGCCAGAT
1 AAAGAATACAAAGATAATAAAGAGGCATATAAAAATTCAATACCATAAACAAGACATGACCAGAT
** * * * *
55497036 TTGAATCTTGAAATTTCTTTTTACAGCCTATCTAG-CCAAGAATAATTAGCAG
66 TTGAATCCAGAAATTTCTGTTTACAGCCTAACTAGTCCAAAAATAACTAGCAG
* * * * * * *
55497088 AAAGAGTACAGAGATAATAATGATGCATGTAAAAATTCAATACCATACACAAGACATGACTAGAT
1 AAAGAATACAAAGATAATAAAGAGGCATATAAAAATTCAATACCATAAACAAGACATGACCAGAT
*
55497153 TTGAATCCAGAAATTTCTGTTTACAGCCTAAGTAGTCCAAAAATAACTAGCAG
66 TTGAATCCAGAAATTTCTGTTTACAGCCTAACTAGTCCAAAAATAACTAGCAG
55497206 TGCACAGTGA
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
117 86 0.85
118 15 0.15
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (118 bp):
AAAGAATACAAAGATAATAAAGAGGCATATAAAAATTCAATACCATAAACAAGACATGACCAGAT
TTGAATCCAGAAATTTCTGTTTACAGCCTAACTAGTCCAAAAATAACTAGCAG
Found at i:55497289 original size:27 final size:27
Alignment explanation
Indices: 55497259--55497312 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
55497249 TTCTTAAAGA
*
55497259 AAATTTATTTTTGACATGAAATGAGTT
1 AAATTTATTTTTAACATGAAATGAGTT
*
55497286 AAATTTATTTTTAACATGAATTGAGTT
1 AAATTTATTTTTAACATGAAATGAGTT
55497313 CTGTTCTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (27 bp):
AAATTTATTTTTAACATGAAATGAGTT
Found at i:55499546 original size:141 final size:141
Alignment explanation
Indices: 55499290--55499575 Score: 554
Period size: 141 Copynumber: 2.0 Consensus size: 141
55499280 TAATAACACA
55499290 AGGAACCAGAAAATTCTGATGCAATATGCTTAAGATATTATAGAATGAATATCTTACAACATTGA
1 AGGAACCAGAAAATTCTGATGCAATATGCTTAAGATATTATAGAATGAATATCTTACAACATTGA
*
55499355 TCATAAAAGATGAGTTCCAGAAAGAAATGCCGAGAGTGCAAGAAAGCAGGTAGGGAAGGATGCTC
66 TCATAAAAGATGAGTTCCAGAAAGAAATGCCGAGAGTGCAAGAAAACAGGTAGGGAAGGATGCTC
55499420 CCCAAATTGAT
131 CCCAAATTGAT
55499431 AGGAACCAGAAAATTCTGATGCAATATGCTTAAGATATTATAGAATGAATATCTTACAACATTGA
1 AGGAACCAGAAAATTCTGATGCAATATGCTTAAGATATTATAGAATGAATATCTTACAACATTGA
*
55499496 TCATAAAAGATGAGTTCCAGAAAGAAATGCCGAGAGTGCAAGAAAACAGGTATGGAAGGATGCTC
66 TCATAAAAGATGAGTTCCAGAAAGAAATGCCGAGAGTGCAAGAAAACAGGTAGGGAAGGATGCTC
55499561 CCCAAATTGAT
131 CCCAAATTGAT
55499572 AGGA
1 AGGA
55499576 GTTCAAAGCA
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 143 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (141 bp):
AGGAACCAGAAAATTCTGATGCAATATGCTTAAGATATTATAGAATGAATATCTTACAACATTGA
TCATAAAAGATGAGTTCCAGAAAGAAATGCCGAGAGTGCAAGAAAACAGGTAGGGAAGGATGCTC
CCCAAATTGAT
Found at i:55514857 original size:20 final size:21
Alignment explanation
Indices: 55514824--55514863 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55514814 AAGCATGGCT
55514824 GAAAACTGGCTT-CCACTAAG
1 GAAAACTGGCTTCCCACTAAG
* *
55514844 GAAAATTGGGTTCCCACTAA
1 GAAAACTGGCTTCCCACTAA
55514864 TTGAGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GAAAACTGGCTTCCCACTAAG
Found at i:55515435 original size:10 final size:10
Alignment explanation
Indices: 55515420--55515444 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55515410 TATCATCAAA
55515420 ATTTTGATAT
1 ATTTTGATAT
55515430 ATTTTGATAT
1 ATTTTGATAT
55515440 ATTTT
1 ATTTT
55515445 AAATGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTTGATAT
Found at i:55526603 original size:30 final size:30
Alignment explanation
Indices: 55526567--55526626 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
55526557 CCCTGTCACA
55526567 ACAACTCAACATGCTCCAAGCCCATAGAGT
1 ACAACTCAACATGCTCCAAGCCCATAGAGT
*
55526597 ACAACTCAACATGCTCCAAGCTCATAGAGT
1 ACAACTCAACATGCTCCAAGCCCATAGAGT
55526627 CTGCAATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (30 bp):
ACAACTCAACATGCTCCAAGCCCATAGAGT
Found at i:55529057 original size:7 final size:7
Alignment explanation
Indices: 55529048--55529215 Score: 110
Period size: 7 Copynumber: 24.0 Consensus size: 7
55529038 TTCTTTTTAA
*
55529048 CTCAATA
1 CTCAATT
55529055 CTCAATT
1 CTCAATT
* *
55529062 TTCAATC
1 CTCAATT
55529069 CTCAATT
1 CTCAATT
*
55529076 TTCAATT
1 CTCAATT
55529083 CTCAATT
1 CTCAATT
55529090 CTCAATT
1 CTCAATT
*
55529097 CTTAATT
1 CTCAATT
* * *
55529104 TTTAATC
1 CTCAATT
55529111 CTCAATT
1 CTCAATT
*
55529118 TTCAATT
1 CTCAATT
*
55529125 CTCAATC
1 CTCAATT
*
55529132 CACAATT
1 CTCAATT
*
55529139 TTCAATT
1 CTCAATT
55529146 -TCCAATT
1 CT-CAATT
55529153 -TCCAATT
1 CT-CAATT
55529160 -TCCAATT
1 CT-CAATT
* *
55529167 TTCAGTT
1 CTCAATT
55529174 CTCAA-T
1 CTCAATT
55529180 CGTCAATT
1 C-TCAATT
* *
55529188 GTCAATC
1 CTCAATT
55529195 CTCAATT
1 CTCAATT
*
55529202 CTAAATT
1 CTCAATT
*
55529209 CTGAATT
1 CTCAATT
55529216 ATTCTTTAAT
Statistics
Matches: 128, Mismatches: 29, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
6 3 0.02
7 123 0.96
8 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.43
Consensus pattern (7 bp):
CTCAATT
Found at i:55529072 original size:14 final size:14
Alignment explanation
Indices: 55529049--55529215 Score: 122
Period size: 14 Copynumber: 11.9 Consensus size: 14
55529039 TCTTTTTAAC
*
55529049 TCAATACTCAATTT
1 TCAATTCTCAATTT
*
55529063 TCAATCCTCAATTT
1 TCAATTCTCAATTT
*
55529077 TCAATTCTCAATTC
1 TCAATTCTCAATTT
*
55529091 TCAATTCTTAATTT
1 TCAATTCTCAATTT
* *
55529105 TTAATCCTCAATTT
1 TCAATTCTCAATTT
**
55529119 TCAATTCTCAATCC
1 TCAATTCTCAATTT
* *
55529133 ACAATTTTCAATTT
1 TCAATTCTCAATTT
*
55529147 CCAATT-TCCAATTT
1 TCAATTCT-CAATTT
* * * *
55529161 CCAATTTTCAGTTC
1 TCAATTCTCAATTT
*
55529175 TCAA-TCGTCAATTG
1 TCAATTC-TCAATTT
* *
55529189 TCAATCCTCAATTC
1 TCAATTCTCAATTT
* *
55529203 TAAATTCTGAATT
1 TCAATTCTCAATT
55529216 ATTCTTTAAT
Statistics
Matches: 121, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
13 2 0.02
14 117 0.97
15 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.02, T:0.44
Consensus pattern (14 bp):
TCAATTCTCAATTT
Found at i:55529072 original size:21 final size:21
Alignment explanation
Indices: 55529056--55529201 Score: 143
Period size: 21 Copynumber: 7.0 Consensus size: 21
55529046 AACTCAATAC
55529056 TCAATTTTCAATCCTCAATTT
1 TCAATTTTCAATCCTCAATTT
* *
55529077 TCAATTCTCAATTCTCAATTCT
1 TCAATTTTCAATCCTCAATT-T
*
55529099 T-AATTTTTAATCCTCAATTT
1 TCAATTTTCAATCCTCAATTT
* *
55529119 TCAATTCTCAATCCACAATTT
1 TCAATTTTCAATCCTCAATTT
* *
55529140 TCAATTTCCAAT-TTCCAATTT
1 TCAATTTTCAATCCT-CAATTT
* * * **
55529161 CCAATTTTCAGTTCTCAATCG
1 TCAATTTTCAATCCTCAATTT
*
55529182 TCAATTGTCAATCCTCAATT
1 TCAATTTTCAATCCTCAATT
55529202 CTAAATTCTG
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.02
21 93 0.95
22 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.45
Consensus pattern (21 bp):
TCAATTTTCAATCCTCAATTT
Found at i:55530926 original size:42 final size:42
Alignment explanation
Indices: 55530868--55531032 Score: 156
Period size: 42 Copynumber: 3.9 Consensus size: 42
55530858 ACATTAGGGT
55530868 TATGAG-TTTACGTGTAAGACCATATCTGGGATATGGCATC-A
1 TATGAGATTT-CGTGTAAGACCATATCTGGGATATGGCATCGA
* * *
55530909 TTATGAGATTTCGTGTAAGAACATGTCTGGGACATGGCATCGA
1 -TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGA
* * * * *
55530952 TATGAGA-ATCGTGCAAGACCATAGCTGGGCTATTGGTATCGA
1 TATGAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGA
** * * * *
55530994 TATGAGATCCCATATAAGACTATATCTAGGATATGGCAT
1 TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCAT
55531033 GGTGTGATTC
Statistics
Matches: 98, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 18 0.18
42 60 0.61
43 20 0.20
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
TATGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:55533425 original size:33 final size:33
Alignment explanation
Indices: 55533383--55533449 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
55533373 AATTGTATAA
* *
55533383 GATTGACTTGCGAGGGAGACTTGAGGAAGATTG
1 GATTGACTTGCGAGAGAGACTCGAGGAAGATTG
55533416 GATTGACTTGCGAGAGAGACTCGAGGAAGATTG
1 GATTGACTTGCGAGAGAGACTCGAGGAAGATTG
55533449 G
1 G
55533450 CCAACATTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.39, T:0.22
Consensus pattern (33 bp):
GATTGACTTGCGAGAGAGACTCGAGGAAGATTG
Found at i:55534225 original size:25 final size:25
Alignment explanation
Indices: 55534186--55534258 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
55534176 TATTTGTAAT
*
55534186 TTTCCCGAATTGTATACTTTATTTT-
1 TTTCCC-AAATGTATACTTTATTTTA
*
55534211 TCTTCCCAAATGTATACTTTGTTTTA
1 T-TTCCCAAATGTATACTTTATTTTA
* *
55534237 TATCCCAAATGTACAC-TTATTT
1 TTTCCCAAATGTATACTTTATTT
55534259 ACATTCTACG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 5 0.12
25 30 0.73
26 6 0.15
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (25 bp):
TTTCCCAAATGTATACTTTATTTTA
Found at i:55540674 original size:19 final size:19
Alignment explanation
Indices: 55540650--55540695 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
55540640 TGAGCCTATG
55540650 AGCTTACTAAGCTTTCATA
1 AGCTTACTAAGCTTTCATA
*
55540669 AGCTTACTAAGCTTTGATA
1 AGCTTACTAAGCTTTCATA
55540688 AGCTTACT
1 AGCTTACT
55540696 TTTATGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (19 bp):
AGCTTACTAAGCTTTCATA
Found at i:55541901 original size:10 final size:10
Alignment explanation
Indices: 55541882--55541931 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
55541872 TTAAATTCTA
55541882 AAAGATAAAT
1 AAAGATAAAT
55541892 ACAA-ATAAAT
1 A-AAGATAAAT
*
55541902 AAAGATAATT
1 AAAGATAAAT
55541912 AAAGATAAAT
1 AAAGATAAAT
55541922 GAAA-ATAAAT
1 -AAAGATAAAT
55541932 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:55542784 original size:97 final size:97
Alignment explanation
Indices: 55542615--55542802 Score: 281
Period size: 97 Copynumber: 1.9 Consensus size: 97
55542605 ATTTTATTTA
* *
55542615 TTTATTTTTACTTAGAAATATATTGAACCTTTTGACGCGAAGAAAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAGAAACATATTGAACCTTTTGACGCGAAGAAAGATGACAACCAAGCACCCCA
*
55542680 CCCCGGTTACTCAGCCTAACATATTCCTAATT
66 CCCCGGTTACTCAGCCCAACATATTCCTAATT
* *
55542712 TTTATTTTT-CTTA-AGAACATATTGAACCTTTTTGACGCGAAGAGAGATGACAACCAAGCACCT
1 TTTATTTTTACTTAGA-AACATATTGAACC-TTTTGACGCGAAGAAAGATGACAACCAAGCACCC
* *
55542775 CACCTCGGTTACTTAGCCCAACATATTC
64 CACCCCGGTTACTCAGCCCAACATATTC
55542803 TTAAAAATTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 1 0.01
96 16 0.20
97 65 0.79
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (97 bp):
TTTATTTTTACTTAGAAACATATTGAACCTTTTGACGCGAAGAAAGATGACAACCAAGCACCCCA
CCCCGGTTACTCAGCCCAACATATTCCTAATT
Found at i:55543528 original size:10 final size:9
Alignment explanation
Indices: 55543513--55543577 Score: 78
Period size: 10 Copynumber: 6.8 Consensus size: 9
55543503 ATCAACATCC
55543513 AAATAAAATA
1 AAAT-AAATA
55543523 AAAT-AATA
1 AAATAAATA
55543531 AAATAAAATA
1 AAAT-AAATA
55543541 AGAATAAATA
1 A-AATAAATA
55543551 AGAATAAATA
1 A-AATAAATA
55543561 AAATAAATAA
1 AAATAAAT-A
55543571 AAATAAA
1 AAATAAA
55543578 AATTGGGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.16
9 7 0.14
10 33 0.65
11 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:55543548 original size:29 final size:30
Alignment explanation
Indices: 55543513--55543578 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
55543503 ATCAACATCC
55543513 AAATAAAATAA-AAT-AATAAAATAAAATAA
1 AAATAAAATAAGAATAAATAAAAT-AAATAA
*
55543542 GAAT-AAATAAGAATAAATAAAATAAATAA
1 AAATAAAATAAGAATAAATAAAATAAATAA
55543571 AAATAAAA
1 AAATAAAA
55543579 ATTGGGTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 15 0.47
30 11 0.34
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (30 bp):
AAATAAAATAAGAATAAATAAAATAAATAA
Found at i:55543556 original size:6 final size:5
Alignment explanation
Indices: 55543513--55543578 Score: 70
Period size: 5 Copynumber: 13.6 Consensus size: 5
55543503 ATCAACATCC
55543513 AAATA AAATA AAAT- -AATA AAATA AAATA AGAAT- AAATA AGAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA A-AATA AAATA A-AATA AAATA
55543561 AAAT- AAATAA AAATA AAA
1 AAATA AAAT-A AAATA AAA
55543579 ATTGGGTTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 30 0.57
6 10 0.19
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:55543565 original size:19 final size:18
Alignment explanation
Indices: 55543513--55543577 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 18
55543503 ATCAACATCC
55543513 AAATAAAATAAAAT-AATA
1 AAAT-AAATAAAATAAATA
55543531 AAATAAAATAAGAATAAATA
1 AAAT-AAATAA-AATAAATA
55543551 AGAATAAATAAAATAAATAA
1 A-AATAAATAAAATAAAT-A
55543571 AAATAAA
1 AAATAAA
55543578 AATTGGGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.26
19 16 0.37
20 13 0.30
21 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATAAATAAAATAAATA
Found at i:55547201 original size:11 final size:11
Alignment explanation
Indices: 55547187--55547239 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
55547177 AGATAAATAT
55547187 TATTTTATTAA
1 TATTTTATTAA
*
55547198 TATTTTAATAA
1 TATTTTATTAA
* * *
55547209 GATATT-TTAT
1 TATTTTATTAA
*
55547219 TATTTTATTAT
1 TATTTTATTAA
55547230 TATTTTATTA
1 TATTTTATTA
55547240 GTATATAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 6 0.18
11 28 0.82
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55547659 original size:21 final size:21
Alignment explanation
Indices: 55547629--55547711 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 21
55547619 TTGATATGTT
55547629 AGTGAAGAGAAAATAAGAGAA
1 AGTGAAGAGAAAATAAGAGAA
* * *
55547650 AGTGATGAGAAATAGTGTAGAAAAAGATT
1 AGTGAAGAGAAA-A---T---AAGAGA-A
55547679 AGTGAAGAGAAAATAAGAGAA
1 AGTGAAGAGAAAATAAGAGAA
*
55547700 AGTGATGAGAAA
1 AGTGAAGAGAAA
55547712 TAGTGTAGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
21 22 0.47
22 6 0.13
25 2 0.04
28 6 0.13
29 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (21 bp):
AGTGAAGAGAAAATAAGAGAA
Found at i:55547702 original size:50 final size:50
Alignment explanation
Indices: 55547627--55547726 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
55547617 TCTTGATATG
55547627 TTAGTGAAGAGAAAATAAGAGAAAGTGATGAGAAATAGTGTAGAAAAAGA
1 TTAGTGAAGAGAAAATAAGAGAAAGTGATGAGAAATAGTGTAGAAAAAGA
55547677 TTAGTGAAGAGAAAATAAGAGAAAGTGATGAGAAATAGTGTAGAAAAAGA
1 TTAGTGAAGAGAAAATAAGAGAAAGTGATGAGAAATAGTGTAGAAAAAGA
55547727 AAATAAGGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (50 bp):
TTAGTGAAGAGAAAATAAGAGAAAGTGATGAGAAATAGTGTAGAAAAAGA
Found at i:55552121 original size:10 final size:10
Alignment explanation
Indices: 55552106--55552139 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
55552096 CTAAATACAA
55552106 ATAATTAAAG
1 ATAATTAAAG
55552116 ATAATTAAAG
1 ATAATTAAAG
* *
55552126 ATAAATAAAA
1 ATAATTAAAG
55552136 ATAA
1 ATAA
55552140 ATCCTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
ATAATTAAAG
Found at i:55555667 original size:31 final size:31
Alignment explanation
Indices: 55555614--55555675 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
55555604 TTTGATGAAG
*
55555614 CATTGTAATCATCCATTTGATTAATAAAGTA
1 CATTATAATCATCCATTTGATTAATAAAGTA
* *
55555645 CATTATAATTATCCCTTTGATTAATAAAGTA
1 CATTATAATCATCCATTTGATTAATAAAGTA
55555676 TATTCTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (31 bp):
CATTATAATCATCCATTTGATTAATAAAGTA
Found at i:55556764 original size:24 final size:25
Alignment explanation
Indices: 55556732--55556780 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
55556722 GCGTTTGAAT
*
55556732 CAAAAACGCTAC-AAAGGTAAAGCA
1 CAAAAACGCTACAAAAAGTAAAGCA
*
55556756 CAAAAACGCTGCAAAAAGTAAAGCA
1 CAAAAACGCTACAAAAAGTAAAGCA
55556781 ATAGCGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.55, C:0.20, G:0.16, T:0.08
Consensus pattern (25 bp):
CAAAAACGCTACAAAAAGTAAAGCA
Found at i:55556835 original size:41 final size:40
Alignment explanation
Indices: 55556766--55556854 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
55556756 CAAAAACGCT
*
55556766 GCAAAAAGTAAAGCAATAGCGACTTTTTTTTCATAAACACC
1 GCAAAAAGTAAAGCAATAACGACTTTTTTTT-ATAAACACC
* * *
55556807 GCAAAAGGTAAAGCAATAACG-GTATTTTTTTATAAACGCC
1 GCAAAAAGTAAAGCAATAACGACT-TTTTTTTATAAACACC
55556847 GCTAAAAA
1 GC-AAAAA
55556855 TTTTTCCCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 11 0.27
41 30 0.73
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (40 bp):
GCAAAAAGTAAAGCAATAACGACTTTTTTTTATAAACACC
Found at i:55556857 original size:24 final size:23
Alignment explanation
Indices: 55556830--55556886 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
55556820 CAATAACGGT
55556830 ATTTTTTTATAAACGCCGCTAAAA
1 ATTTTTTTATAAACGCCG-TAAAA
** *
55556854 ATTTTTCCCATAAACGCCGTAAAT
1 ATTTTT-TTATAAACGCCGTAAAA
*
55556878 ATCTTTTTA
1 ATTTTTTTA
55556887 CTTTTATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.04
24 15 0.58
25 10 0.38
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (23 bp):
ATTTTTTTATAAACGCCGTAAAA
Found at i:55557940 original size:73 final size:73
Alignment explanation
Indices: 55557820--55557967 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
55557810 TTAATTGATT
* *
55557820 TTACTTTAGATAAGATCTCTTTAAGGGTTACCATCTATGTGATTGCTGGTCGAAGTTTCTCTTGA
1 TTACTTTAGATAAAATCTCTTTAAGGGTTACCATCTATGTGACTGCTGGTCGAAGTTTCTCTTGA
55557885 AAAGCACA
66 AAAGCACA
* *
55557893 TTACTTTAGATAAAATCTCTTTAAGGGTTGCCATCTATGTGACTGCTGGTTGAAGTTTCTCTTGA
1 TTACTTTAGATAAAATCTCTTTAAGGGTTACCATCTATGTGACTGCTGGTCGAAGTTTCTCTTGA
55557958 AAAGCACA
66 AAAGCACA
55557966 TT
1 TT
55557968 GATATTTTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (73 bp):
TTACTTTAGATAAAATCTCTTTAAGGGTTACCATCTATGTGACTGCTGGTCGAAGTTTCTCTTGA
AAAGCACA
Found at i:55560849 original size:35 final size:35
Alignment explanation
Indices: 55560781--55560846 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
55560771 TAATTGTGTT
55560781 ATTAATTTATTATTTTAAATTGTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTGTAAATTTAAATTC
* *
55560816 ATTAATTT-TTATATTT-AGTTTTAAATTTAAA
1 ATTAATTTATTAT-TTTAAATTGTAAATTTAAA
55560847 ATTTCATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTGTAAATTTAAATTC
Found at i:55561050 original size:43 final size:43
Alignment explanation
Indices: 55560983--55561083 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 43
55560973 ATAATTTTTT
* * * * * *
55560983 TAAAGGTCAAGTTCTTTTAGCGGCATTTGTAGGAGAAGCGCCGC
1 TAAAGGTCATGTTCTATTAGCGGCATTTGCA-GAAAAACGACGC
55561027 TAAAGGTCATGTTC-ATTAGCGGCATTTGCAGAAAAACGACGC
1 TAAAGGTCATGTTCTATTAGCGGCATTTGCAGAAAAACGACGC
*
55561069 TAAAAGTCATGTTCT
1 TAAAGGTCATGTTCT
55561084 TCGAAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 22 0.45
43 14 0.29
44 13 0.27
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TAAAGGTCATGTTCTATTAGCGGCATTTGCAGAAAAACGACGC
Found at i:55561673 original size:41 final size:41
Alignment explanation
Indices: 55561628--55561871 Score: 276
Period size: 41 Copynumber: 6.0 Consensus size: 41
55561618 TTATAAAACA
* *
55561628 CAGAGCAATAGCGGCGTTTTTTGGTAAAACGCCGCTAAAAA-
1 CAGAGCATTAGCGGCG-TTTTCGGTAAAACGCCGCTAAAAAT
* * * * *
55561669 CAGAGCAATAGCGGCATTTTTGGTAAAGCGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAAAT
*
55561710 CAGAGCATTAGCGGCGTTTTCGGTAAAACGCTGCTAAAAAT
1 CAGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAAAT
* * * * * *
55561751 CAAAGCATTAGCTGTGCTTTCGGTAAAATGTCGCTAAAAAT
1 CAGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAAAT
* * * *
55561792 CAGAGCATTAGTGGCGCTTTCTGTAAAATGCCGCTAAAAA-
1 CAGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAAAT
* *
55561832 CTAGAGCATTAGCGGCGCTTTCAGTAAAACGCCGCTAAAA
1 C-AGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAA
55561872 GTCATATAAC
Statistics
Matches: 177, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 24 0.14
41 153 0.86
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGTTTTCGGTAAAACGCCGCTAAAAAT
Found at i:55561840 original size:123 final size:122
Alignment explanation
Indices: 55561650--55561871 Score: 311
Period size: 123 Copynumber: 1.8 Consensus size: 122
55561640 GGCGTTTTTT
* *
55561650 GGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTTTGGTAAAGCGCCGCTAAAAACCAGAG
1 GGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTCTGGTAAAACGCCGCTAAAAACCAGAG
* * *
55561715 CATTAGCGGCGTTTTCGGTAAAACGCTGCTAAAAATCAAAGCATTAGCTGTGCTTTC
66 CATTAGCGGCGCTTTCAGTAAAACGCCGCTAAAAATCAAAGCATTAGCTGTGCTTTC
* * * * * * *
55561772 GGTAAAATGTCGCTAAAAATCAGAGCATTAGTGGCGCTTTCT-GTAAAATGCCGCTAAAAACTAG
1 GGTAAAACGCCGCTAAAAA-CAGAGCAATAGCGGC-ATTTCTGGTAAAACGCCGCTAAAAACCAG
55561836 AGCATTAGCGGCGCTTTCAGTAAAACGCCGCTAAAA
64 AGCATTAGCGGCGCTTTCAGTAAAACGCCGCTAAAA
55561872 GTCATATAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
122 17 0.20
123 65 0.76
124 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (122 bp):
GGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTCTGGTAAAACGCCGCTAAAAACCAGAG
CATTAGCGGCGCTTTCAGTAAAACGCCGCTAAAAATCAAAGCATTAGCTGTGCTTTC
Found at i:55561975 original size:16 final size:16
Alignment explanation
Indices: 55561930--55561975 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
55561920 TCTATATAAC
*
55561930 CCCTAAAACACT-AAAT
1 CCCT-AAACACTAAAAA
55561946 CCCTAAAC-CTTAAAAA
1 CCCTAAACAC-TAAAAA
55561962 CCCTAAACACTAAA
1 CCCTAAACACTAAA
55561976 CTATAACCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.04
15 5 0.19
16 19 0.73
17 1 0.04
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (16 bp):
CCCTAAACACTAAAAA
Found at i:55562217 original size:28 final size:28
Alignment explanation
Indices: 55562186--55562240 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
55562176 TATGGATTAT
* *
55562186 GGGTTTAGGGATTATGGTTTAAGGGTTG
1 GGGTTTAAGGATTATGGGTTAAGGGTTG
* *
55562214 GGGTTTAAGGTTTATGGGTTATGGGTT
1 GGGTTTAAGGATTATGGGTTAAGGGTT
55562241 ATGGGTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (28 bp):
GGGTTTAAGGATTATGGGTTAAGGGTTG
Found at i:55562235 original size:7 final size:7
Alignment explanation
Indices: 55562175--55562253 Score: 54
Period size: 7 Copynumber: 11.1 Consensus size: 7
55562165 ATTTTAACTT
*
55562175 TTATGGA
1 TTATGGG
55562182 TTATGGG
1 TTATGGG
55562189 TT-TAGGG
1 TTAT-GGG
*
55562196 ATTATGGT
1 -TTATGGG
*
55562204 TTAAGGG
1 TTATGGG
*
55562211 TT-GGGG
1 TTATGGG
* *
55562217 TTTAAGGT
1 -TTATGGG
55562225 TTATGGG
1 TTATGGG
55562232 TTATGGG
1 TTATGGG
55562239 TTATGGG
1 TTATGGG
*
55562246 TTAGGGG
1 TTATGGG
55562253 T
1 T
55562254 CTAGGATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
6 4 0.07
7 46 0.81
8 6 0.11
9 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.42
Consensus pattern (7 bp):
TTATGGG
Found at i:55562253 original size:14 final size:14
Alignment explanation
Indices: 55562182--55562253 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
55562172 CTTTTATGGA
*
55562182 TTATGGGTTTAGGG
1 TTATGGGTTAAGGG
*
55562196 ATTATGGTTTAAGGG
1 -TTATGGGTTAAGGG
* *
55562211 TT-GGGGTTTAAGGT
1 TTATGGG-TTAAGGG
*
55562225 TTATGGGTTATGGG
1 TTATGGGTTAAGGG
*
55562239 TTATGGGTTAGGGG
1 TTATGGGTTAAGGG
55562253 T
1 T
55562254 CTAGGATTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.04
14 29 0.63
15 15 0.33
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (14 bp):
TTATGGGTTAAGGG
Found at i:55562280 original size:20 final size:21
Alignment explanation
Indices: 55562255--55562306 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
55562245 GTTAGGGGTC
55562255 TAGGATTAAGAGTTTAT-GTT
1 TAGGATTAAGAGTTTATGGTT
* *
55562275 TAGGATTTAGGGTTTATGGTT
1 TAGGATTAAGAGTTTATGGTT
55562296 TAGTGATTAAG
1 TAG-GATTAAG
55562307 GATTAGGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 15 0.56
21 6 0.22
22 6 0.22
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (21 bp):
TAGGATTAAGAGTTTATGGTT
Found at i:55562298 original size:14 final size:14
Alignment explanation
Indices: 55562182--55562297 Score: 51
Period size: 14 Copynumber: 8.2 Consensus size: 14
55562172 CTTTTATGGA
*
55562182 TTATGGGTTTAGGGA
1 TTAT-GGTTTAGGGT
55562197 TTATGGTTTAAGGG-
1 TTATGGTTT-AGGGT
** *
55562211 TTGGGGTTTAAGGT
1 TTATGGTTTAGGGT
*
55562225 TTATGGGTTATGGG-
1 TTATGGTTTA-GGGT
*
55562239 TTATGGGTTAGGGGT
1 TTATGGTTTA-GGGT
* * *
55562254 CTA-GGATTAAGAGT
1 TTATGG-TTTAGGGT
*
55562268 TTAT-GTTTAGGAT
1 TTATGGTTTAGGGT
* *
55562281 TTAGGGTTTATGGT
1 TTATGGTTTAGGGT
55562295 TTA
1 TTA
55562298 GTGATTAAGG
Statistics
Matches: 75, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
13 11 0.15
14 50 0.67
15 14 0.19
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.43
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:55563275 original size:60 final size:59
Alignment explanation
Indices: 55563152--55563286 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 59
55563142 AAGTTAACTA
* *
55563152 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATACTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATACTG
*
55563213 GGCCTAGCCCATGA-CAGTATCAATCTGGGCCATAGCCCTATTACA-AGTC-GAG-ATACATTG
1 GGCCTAGCCCAT-ATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAGTATAC--TG
*
55563273 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
55563287 TAACACAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
58 4 0.06
59 5 0.08
60 45 0.70
61 10 0.16
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (59 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATACTG
Found at i:55565368 original size:21 final size:22
Alignment explanation
Indices: 55565313--55565380 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
55565303 AGTTTATGGA
55565313 TTATGGTTTAAGGGTT-GGGGT
1 TTATGGTTTAAGGGTTAGGGGT
*
55565334 TTAAGGTTTAAGGGTTAGGGG-
1 TTATGGTTTAAGGGTTAGGGGT
**
55565355 TTATGTGTTT-AGGGTTAACGGT
1 TTATG-GTTTAAGGGTTAGGGGT
55565377 TTAT
1 TTAT
55565381 ATTTTAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 28 0.70
22 12 0.30
ACGTcount: A:0.19, C:0.01, G:0.37, T:0.43
Consensus pattern (22 bp):
TTATGGTTTAAGGGTTAGGGGT
Found at i:55565727 original size:19 final size:20
Alignment explanation
Indices: 55565689--55565732 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
55565679 ATTAGATTTA
* *
55565689 AAAAATATTGATAAATAAAT
1 AAAAACATTGATAAACAAAT
55565709 AAAAACATTGAT-AACAAAT
1 AAAAACATTGATAAACAAAT
55565728 AAAAA
1 AAAAA
55565733 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAACATTGATAAACAAAT
Found at i:55570861 original size:22 final size:20
Alignment explanation
Indices: 55570817--55570872 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
55570807 AAAGTTCAAA
55570817 AATTAAACATAATATAATATTT
1 AATTAAA-ATAA-ATAATATTT
*
55570839 AATGTAGAAATAAATATTATTT
1 AAT-TA-AAATAAATAATATTT
55570861 AATTAAAATAAA
1 AATTAAAATAAA
55570873 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 7 0.23
21 2 0.06
22 14 0.45
23 6 0.19
24 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTAAAATAAATAATATTT
Found at i:55570910 original size:61 final size:61
Alignment explanation
Indices: 55570845--55570967 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
55570835 ATTTAATGTA
* *
55570845 GAAATAAATATTATTTAATTAAAATAAAATAAATTTTTTAAAGGTTATGCTTTTTAGCGGC
1 GAAATAAATATTATTTAATTAAAATAAAATAAATGTTTTAAAGGTTATGATTTTTAGCGGC
55570906 GAAATAAATATTATTTAATTAAAATAAAATAAATGTTTTAAAGGTTATGATTTTTAGCGGC
1 GAAATAAATATTATTTAATTAAAATAAAATAAATGTTTTAAAGGTTATGATTTTTAGCGGC
55570967 G
1 G
55570968 TTTGTGAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (61 bp):
GAAATAAATATTATTTAATTAAAATAAAATAAATGTTTTAAAGGTTATGATTTTTAGCGGC
Found at i:55571010 original size:43 final size:43
Alignment explanation
Indices: 55570944--55571108 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
55570934 ATAAATGTTT
*
55570944 TAAAGGTTATGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
1 TAAAGGTTAAGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
* *
55570987 TAAAGGTTAAGATTTTTAACGGCGTTTGTGAGAAAAGTGTCGC
1 TAAAGGTTAAGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
* * * * *
55571030 TAAAGGTCATA-ATTTTTAGCGGCATTTGCGAGAAAAGCGCCGT
1 TAAAGGTTA-AGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
* * * * * *
55571073 TAAAGGTCATGGTCTTTAGCGGCGCTTGTGAAAAAA
1 TAAAGGTTAAGATTTTTAGCGGCGTTTGTGAGAAAA
55571109 AGCCTTTAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
43 102 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (43 bp):
TAAAGGTTAAGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
Found at i:55571096 original size:86 final size:86
Alignment explanation
Indices: 55570944--55571108 Score: 213
Period size: 86 Copynumber: 1.9 Consensus size: 86
55570934 ATAAATGTTT
* * * * * * *
55570944 TAAAGGTTATGATTTTTAGCGGCGTTTGTGAGAAAAGTGCCGCTAAAGGTTAAGATTTTTAACGG
1 TAAAGGTCATAATTTTTAGCGGCATTTGCGAGAAAAGCGCCGCTAAAGGTCAAGATCTTTAACGG
* *
55571009 CGTTTGTGAGAAAAGTGTCGC
66 CGCTTGTGAAAAAAGTGTCGC
* * * *
55571030 TAAAGGTCATAATTTTTAGCGGCATTTGCGAGAAAAGCGCCGTTAAAGGTCATGGTCTTTAGCGG
1 TAAAGGTCATAATTTTTAGCGGCATTTGCGAGAAAAGCGCCGCTAAAGGTCAAGATCTTTAACGG
55571095 CGCTTGTGAAAAAA
66 CGCTTGTGAAAAAA
55571109 AGCCTTTAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (86 bp):
TAAAGGTCATAATTTTTAGCGGCATTTGCGAGAAAAGCGCCGCTAAAGGTCAAGATCTTTAACGG
CGCTTGTGAAAAAAGTGTCGC
Found at i:55577096 original size:26 final size:26
Alignment explanation
Indices: 55577039--55577119 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
55577029 ATTCTGAAAT
* *
55577039 TGAAATGTCATTTTGA-CTTGA-TAA
1 TGAAATGTCATTTTAATTTTGATTAA
55577063 TGAAATGTCATTTTAATTTTGATTAA
1 TGAAATGTCATTTTAATTTTGATTAA
*
55577089 TCG-AATGTCATTTGAGATTTTGATT-A
1 T-GAAATGTCATTTTA-ATTTTGATTAA
55577115 TGAAA
1 TGAAA
55577120 GCTTATTCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
24 15 0.31
25 5 0.10
26 19 0.39
27 10 0.20
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.44
Consensus pattern (26 bp):
TGAAATGTCATTTTAATTTTGATTAA
Found at i:55580302 original size:213 final size:213
Alignment explanation
Indices: 55579931--55580357 Score: 836
Period size: 213 Copynumber: 2.0 Consensus size: 213
55579921 TCATTAACAC
55579931 TCCACATTATACATTTCAAGTCTAAATTTCACCTCAGGTCCAAATGACTGTTTTGCCCCTAACTT
1 TCCACATTATACATTTCAAGTCTAAATTTCACCTCAGGTCCAAATGACTGTTTTGCCCCTAACTT
55579996 TTCACATTTTTACGATTTAGTCCCTAGGCTCGTATAATGAAACGCATGCAATTTCTACCTTACTC
66 TTCACATTTTTACGATTTAGTCCCTAGGCTCGTATAATGAAACGCATGCAATTTCTACCTTACTC
* *
55580061 AAGCTTAGCTGAACACTTTTCGCTCTTATGGTAGCCCACATTTTCCATTATTTTCACATTTCTAC
131 AAGCTTAGCCGAACACTTTTCCCTCTTATGGTAGCCCACATTTTCCATTATTTTCACATTTCTAC
55580126 CACACATTTTACAACTTT
196 CACACATTTTACAACTTT
55580144 TCCACATTATACATTTCAAGTCTAAATTTCACCTCAGGTCCAAATGACTGTTTTGCCCCTAACTT
1 TCCACATTATACATTTCAAGTCTAAATTTCACCTCAGGTCCAAATGACTGTTTTGCCCCTAACTT
55580209 TTCACATTTTTACGATTTAGTCCCTAGGCTCGTATAATGAAACGCATGCAATTTCTACCTTACTC
66 TTCACATTTTTACGATTTAGTCCCTAGGCTCGTATAATGAAACGCATGCAATTTCTACCTTACTC
55580274 AAGCTTAGCCGAACACTTTTCCCTCTTATGGTAGCCCACATTTTCCATTATTTTCACATTTCTAC
131 AAGCTTAGCCGAACACTTTTCCCTCTTATGGTAGCCCACATTTTCCATTATTTTCACATTTCTAC
55580339 CACACATTTTACAACTTT
196 CACACATTTTACAACTTT
55580357 T
1 T
55580358 GCAAAAAGGT
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 212 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (213 bp):
TCCACATTATACATTTCAAGTCTAAATTTCACCTCAGGTCCAAATGACTGTTTTGCCCCTAACTT
TTCACATTTTTACGATTTAGTCCCTAGGCTCGTATAATGAAACGCATGCAATTTCTACCTTACTC
AAGCTTAGCCGAACACTTTTCCCTCTTATGGTAGCCCACATTTTCCATTATTTTCACATTTCTAC
CACACATTTTACAACTTT
Found at i:55594533 original size:12 final size:12
Alignment explanation
Indices: 55594499--55594533 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
55594489 ATTGGATAAA
55594499 TAAATAAAATAT
1 TAAATAAAATAT
* *
55594511 TAAACAGAATAT
1 TAAATAAAATAT
55594523 TAAATAAAATA
1 TAAATAAAATA
55594534 GTTTTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:55595753 original size:16 final size:16
Alignment explanation
Indices: 55595719--55595752 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
55595709 AAATGGGCTA
55595719 TTTATTATTATTTGGT
1 TTTATTATTATTTGGT
55595735 TTTATTATT-TTTGGT
1 TTTATTATTATTTGGT
55595750 TTT
1 TTT
55595753 TGTATGGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (16 bp):
TTTATTATTATTTGGT
Found at i:55596003 original size:44 final size:44
Alignment explanation
Indices: 55595949--55596206 Score: 195
Period size: 44 Copynumber: 5.8 Consensus size: 44
55595939 TTGTCGCTTC
* * **
55595949 AATCTGCTCCACTGCAACTTCATGGAGATAAGA-TCTGTAGTTTT
1 AATCTACTCCACTGCAACTTCAAGGAGATAAGATTC-GTAGCATT
** * *
55595993 AAT-TCACTCCACTATAACTTCAAGAAGATAAGATTCGTGGCATT
1 AATCT-ACTCCACTGCAACTTCAAGGAGATAAGATTCGTAGCATT
* *
55596037 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGT--CATTT
1 AATCTACTCCACTGCAACTTCAAGGAGATAAGATTCGTAGCA-TT
* * * * * *
55596080 ACAATTTTCTCCACTGCAACTTCAGGGAGTTGAGATTCGTAAC-TT
1 --AATCTACTCCACTGCAACTTCAAGGAGATAAGATTCGTAGCATT
* * * * * * *
55596125 CAACCTGCTCCACTGCAACTTC-AGTAAGACAAGGTTCGTGGCTTT
1 -AATCTACTCCACTGCAACTTCAAG-GAGATAAGATTCGTAGCATT
*
55596170 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTCG
1 AATCTACTCCACTGCAACTTCAAGGAGATAAGATTCG
55596207 CTATGATAAC
Statistics
Matches: 169, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 120 0.71
45 42 0.25
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTACTCCACTGCAACTTCAAGGAGATAAGATTCGTAGCATT
Found at i:55608574 original size:14 final size:14
Alignment explanation
Indices: 55608555--55608597 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
55608545 GATGCAAATG
55608555 ATAATATAAGAACA
1 ATAATATAAGAACA
* * *
55608569 ATAATAAAAAAATA
1 ATAATATAAGAACA
55608583 ATAATATAAGTAACA
1 ATAATATAAG-AACA
55608598 GCAACAACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
ATAATATAAGAACA
Found at i:55608630 original size:3 final size:3
Alignment explanation
Indices: 55608618--55608654 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
55608608 CAACAACAAC
* *
55608618 AAT AAC AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55608655 GAAAATCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:55610101 original size:15 final size:16
Alignment explanation
Indices: 55610071--55610103 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
55610061 AAATGGACTA
55610071 TTTATTATTATTTGGT
1 TTTATTATTATTTGGT
55610087 TTTATTATT-TTTGGT
1 TTTATTATTATTTGGT
55610102 TT
1 TT
55610104 CTGTATGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (16 bp):
TTTATTATTATTTGGT
Found at i:55613634 original size:16 final size:18
Alignment explanation
Indices: 55613603--55613635 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
55613593 CAAGAAAACA
55613603 TAAAATATATTAATAGAG
1 TAAAATATATTAATAGAG
55613621 TAAAATA-A-TAATAGA
1 TAAAATATATTAATAGA
55613636 TAATTAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (18 bp):
TAAAATATATTAATAGAG
Found at i:55614837 original size:15 final size:14
Alignment explanation
Indices: 55614817--55614858 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
55614807 ACTATTGTAA
55614817 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
55614831 GGGTTTAAGGATTAT
1 -GGTTTATGGATTAT
55614846 GGTTTATGGATTA
1 GGTTTATGGATTA
55614859 AAGGTTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:55614839 original size:22 final size:22
Alignment explanation
Indices: 55614814--55614864 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
55614804 GTTACTATTG
*
55614814 TAAGGTTTATGGATTATGGGTT
1 TAAGGTTTATGGATTATGGATT
* *
55614836 TAAGGATTATGGTTTATGGATT
1 TAAGGTTTATGGATTATGGATT
*
55614858 AAAGGTT
1 TAAGGTT
55614865 AGGGTTTAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.43
Consensus pattern (22 bp):
TAAGGTTTATGGATTATGGATT
Found at i:55614864 original size:15 final size:15
Alignment explanation
Indices: 55614815--55614864 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
55614805 TTACTATTGT
55614815 AAGGTTTATGGATTA
1 AAGGTTTATGGATTA
** *
55614830 TGGGTTTAAGGATT-
1 AAGGTTTATGGATTA
*
55614844 ATGGTTTATGGATTA
1 AAGGTTTATGGATTA
55614859 AAGGTT
1 AAGGTT
55614865 AGGGTTTAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (15 bp):
AAGGTTTATGGATTA
Found at i:55614870 original size:21 final size:22
Alignment explanation
Indices: 55614827--55614872 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55614817 GGTTTATGGA
* * *
55614827 TTATGGGTTTAAGGATTATGGT
1 TTATGGATTAAAGGATTAGGGT
55614849 TTATGGATTAAAGG-TTAGGGT
1 TTATGGATTAAAGGATTAGGGT
55614870 TTA
1 TTA
55614873 AGTTTTAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.43
Consensus pattern (22 bp):
TTATGGATTAAAGGATTAGGGT
Found at i:55614891 original size:22 final size:21
Alignment explanation
Indices: 55614861--55614959 Score: 74
Period size: 22 Copynumber: 4.6 Consensus size: 21
55614851 ATGGATTAAA
*
55614861 GGTTAGGGTTTAAGTTTTAAGG
1 GGTTAGGGTTTAAGATTT-AGG
*
55614883 GGTTGGGGTTTAAGATTTAGG
1 GGTTAGGGTTTAAGATTTAGG
* *
55614904 GGTTAAGGG-TTAATGGTTTATG
1 GGTT-AGGGTTTAA-GATTTAGG
** * * *
55614926 TTTTATGGTTTAAGGTCTAGG
1 GGTTAGGGTTTAAGATTTAGG
55614947 GGTTAGGGATTTA
1 GGTTAGGG-TTTA
55614960 GGGTTTAGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
21 25 0.42
22 35 0.58
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.41
Consensus pattern (21 bp):
GGTTAGGGTTTAAGATTTAGG
Found at i:55618151 original size:27 final size:26
Alignment explanation
Indices: 55618113--55618198 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 26
55618103 NNNNNNNNNN
*
55618113 TATCTGATCTGGTGGCTCTGCCACATA
1 TATCTGTTCTGGTGGCTCTGCCACA-A
55618140 TATCTGTTCTGGTGGCTCTGCCACAA
1 TATCTGTTCTGGTGGCTCTGCCACAA
* *
55618166 TATCTGTATCTGGTGACT-TCGTCACAA
1 TATCTGT-TCTGGTGGCTCT-GCCACAA
55618193 TATCTG
1 TATCTG
55618199 GCAGCCTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
26 9 0.17
27 45 0.83
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (26 bp):
TATCTGTTCTGGTGGCTCTGCCACAA
Found at i:55631747 original size:34 final size:34
Alignment explanation
Indices: 55631704--55631771 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
55631694 CTACTCTTTT
* *
55631704 TTATTCGAGATTAATTTACTTATTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
*
55631738 TTATTCGAGATGAATTTACTTGGTTGTTAAGAAC
1 TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
55631772 ACATAAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (34 bp):
TTATTCGAGATGAATTTACTTAGTTGTTAAGAAC
Found at i:55636726 original size:13 final size:13
Alignment explanation
Indices: 55636699--55636775 Score: 82
Period size: 13 Copynumber: 5.9 Consensus size: 13
55636689 ACACTTAAAT
*
55636699 TTTTCTAAAGCAC
1 TTTTCAAAAGCAC
* *
55636712 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
55636725 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* * * *
55636738 TTTTCCACAGTAT
1 TTTTCAAAAGCAC
55636751 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
55636764 TTTTCAAAAGCA
1 TTTTCAAAAGCA
55636776 ATGAAGAACT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:55636735 original size:26 final size:26
Alignment explanation
Indices: 55636705--55636773 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
55636695 AAATTTTTCT
*
55636705 AAAGCACTTCTCAAAAGTACTTCTCA
1 AAAGCACTTTTCAAAAGTACTTCTCA
* * * *
55636731 AAAGCACTTTTCCACAGTATTTTTCA
1 AAAGCACTTTTCAAAAGTACTTCTCA
55636757 AAAGCACTTTTCAAAAG
1 AAAGCACTTTTCAAAAG
55636774 CAATGAAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAGCACTTTTCAAAAGTACTTCTCA
Found at i:55639394 original size:21 final size:21
Alignment explanation
Indices: 55639368--55639410 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
55639358 TTGAAGGATT
*
55639368 TGTAAATCTTTTTAAACATGC
1 TGTAAATCTTCTTAAACATGC
55639389 TGTAAATCTTCTTAAACATGC
1 TGTAAATCTTCTTAAACATGC
55639410 T
1 T
55639411 TTCATCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (21 bp):
TGTAAATCTTCTTAAACATGC
Found at i:55641913 original size:23 final size:22
Alignment explanation
Indices: 55641861--55641913 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55641851 TCCACGTCTT
*
55641861 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55641883 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55641906 TTTCTTTT
1 TTTCTTTT
55641914 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55647305 original size:18 final size:17
Alignment explanation
Indices: 55647282--55647326 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
55647272 AAAATCCTAG
*
55647282 TTTTTCCTTTCTTTTTCT
1 TTTTTCCTTT-TTCTTCT
55647300 TTTTTCCCTTTTTCTTCT
1 TTTTT-CCTTTTTCTTCT
55647318 TTCTTTCCT
1 TT-TTTCCT
55647327 CTGTTTCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTCCTTTTTCTTCT
Found at i:55651104 original size:14 final size:14
Alignment explanation
Indices: 55651093--55651124 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55651083 GGTGAAAAGC
55651093 AAAA-AAAAA-AAA
1 AAAAGAAAAAGAAA
55651105 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
55651119 AAAAGA
1 AAAAGA
55651125 TTGGTAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 5 0.28
14 9 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:55651108 original size:18 final size:18
Alignment explanation
Indices: 55651087--55651122 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
55651077 AATATTGGTG
55651087 AAAAGCAAAAA-AAAAAAA
1 AAAAG-AAAAAGAAAAAAA
55651105 AAAAGAAAAAGAAAAAAA
1 AAAAGAAAAAGAAAAAAA
55651123 GATTGGTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAAA
Found at i:55652683 original size:29 final size:29
Alignment explanation
Indices: 55652646--55652703 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
55652636 AAGATGCATA
55652646 TACACAACTCTCTAAAATATGTGTTATAG
1 TACACAACTCTCTAAAATATGTGTTATAG
55652675 TACACAACTCTCTAAAATATGTGTTATAG
1 TACACAACTCTCTAAAATATGTGTTATAG
55652704 GATGAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (29 bp):
TACACAACTCTCTAAAATATGTGTTATAG
Found at i:55656385 original size:72 final size:72
Alignment explanation
Indices: 55656268--55656411 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
55656258 CTCTTCCGGT
55656268 AACCAAGCATCAGTCCAATTGGATAGTACTTAGCTTTCAATACTCAAGCAAACAAACATTCTGAT
1 AACCAAGCATCAGTCCAATTGGATAGTACTTAGCTTTCAATACTCAAGCAAACAAACATTCTGAT
55656333 TTCATCA
66 TTCATCA
55656340 AACCAAGCATCAGTCCAATTGGATAGTACTTAGCTTTCAATACTCAAGCAAACAAACATTCTGAT
1 AACCAAGCATCAGTCCAATTGGATAGTACTTAGCTTTCAATACTCAAGCAAACAAACATTCTGAT
55656405 TTCATCA
66 TTCATCA
55656412 TTAGCCTCCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.28
Consensus pattern (72 bp):
AACCAAGCATCAGTCCAATTGGATAGTACTTAGCTTTCAATACTCAAGCAAACAAACATTCTGAT
TTCATCA
Found at i:55657433 original size:24 final size:25
Alignment explanation
Indices: 55657366--55657442 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 25
55657356 TCTTTTTAAG
* *
55657366 TTATTTATTTATTTACTTCTTAAGTT
1 TTATTTATTTGTTTA-TTATTAAGTT
* *
55657392 TT-TTTATTTGTCCT-TTATTTA-TT
1 TTATTTATTTGT-TTATTATTAAGTT
*
55657415 TTATTTATTTGTTTATTATT-GGTT
1 TTATTTATTTGTTTATTATTAAGTT
55657439 TTAT
1 TTAT
55657443 AAAATTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
23 5 0.12
24 25 0.61
25 8 0.20
26 3 0.07
ACGTcount: A:0.18, C:0.05, G:0.06, T:0.70
Consensus pattern (25 bp):
TTATTTATTTGTTTATTATTAAGTT
Done.