Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 368 of 410
Found at i:112744369 original size:8 final size:8
Alignment explanation
Indices: 112744280--112744338 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 8
112744270 TGATTACATA
112744280 AAAATATT
1 AAAATATT
112744288 AAAAATATT
1 -AAAATATT
112744297 AAAAATATATT
1 --AAA-ATATT
112744308 AAAATATT
1 AAAATATT
112744316 AAAA-A-T
1 AAAATATT
112744322 ACAAATATT
1 A-AAATATT
112744331 AAAA-ATT
1 AAAATATT
112744338 A
1 A
112744339 TAAAAAATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 2 0.04
7 8 0.18
8 13 0.29
9 13 0.29
10 4 0.09
11 5 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAATATT
Found at i:112744371 original size:43 final size:43
Alignment explanation
Indices: 112744281--112744364 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
112744271 GATTACATAA
* *
112744281 AAATATTAAAAATATTAAAAATATATTAAAATATTAAAAATAC
1 AAATATTAAAAATATTAAAAATATAGTAAAATATCAAAAATAC
*
112744324 AAATATTAAAAAT-TATAAAAA-AT-GTAAAATCTCATAAAATA
1 AAATATTAAAAATAT-TAAAAATATAGTAAAATATCA-AAAATA
112744365 TTAAATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.22
42 9 0.25
43 19 0.53
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (43 bp):
AAATATTAAAAATATTAAAAATATAGTAAAATATCAAAAATAC
Found at i:112746099 original size:16 final size:18
Alignment explanation
Indices: 112746078--112746115 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
112746068 GAATGTACAT
112746078 TATAAT-ATCATA-ATTA
1 TATAATAATCATATATTA
*
112746094 TATAATAATTATATATTA
1 TATAATAATCATATATTA
112746112 TATA
1 TATA
112746116 TTCGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATAATCATATATTA
Found at i:112749028 original size:34 final size:33
Alignment explanation
Indices: 112748980--112749113 Score: 87
Period size: 34 Copynumber: 3.9 Consensus size: 33
112748970 AAGAGAAAAG
*
112748980 AAAAATAATTAATAATATCATATAATATATATTAA
1 AAAAAT-ATAAATAATAT-ATATAATATATATTAA
*
112749015 AAAAATGA-AAATAAAAAGTATATAATA-ATATTAA
1 AAAAAT-ATAAAT-AATA-TATATAATATATATTAA
* * **
112749049 AAGAATATACATAATATATAT-ATAATATACAAA
1 AAAAATATAAATAATATATATAAT-ATATATTAA
* *
112749082 ACAAAATATACGCATAATATAT-TAAAATATAT
1 A-AAAATATA--AATAATATATATAATATATAT
112749114 CCATAATGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
31 2 0.03
32 6 0.08
33 10 0.13
34 25 0.32
35 24 0.30
36 12 0.15
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (33 bp):
AAAAATATAAATAATATATATAATATATATTAA
Found at i:112749062 original size:20 final size:19
Alignment explanation
Indices: 112748999--112749065 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
112748989 TAATAATATC
112748999 ATATAATATATATTAAAA-A
1 ATATAATA-ATATTAAAAGA
*
112749018 A-ATGAA-AATA--AAAAGT
1 ATAT-AATAATATTAAAAGA
112749034 ATATAATAATATTAAAAGA
1 ATATAATAATATTAAAAGA
112749053 ATATACATAATAT
1 ATATA-ATAATAT
112749066 ATATATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 4 0.10
16 3 0.08
17 9 0.23
18 3 0.08
19 13 0.33
20 7 0.18
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (19 bp):
ATATAATAATATTAAAAGA
Found at i:112749108 original size:21 final size:22
Alignment explanation
Indices: 112749084--112749136 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
112749074 TATACAAAAC
*
112749084 AAAATATACGCATAATATA-TT
1 AAAATATACGCATAATATACAT
*
112749105 AAAATATATC-CATAATGTACAT
1 AAAATATA-CGCATAATATACAT
112749127 AAAATATACG
1 AAAATATACG
112749137 TATATACGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (22 bp):
AAAATATACGCATAATATACAT
Found at i:112749230 original size:2 final size:2
Alignment explanation
Indices: 112749225--112749261 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
112749215 CATCAAATGA
112749225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112749262 CATACAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112750880 original size:21 final size:21
Alignment explanation
Indices: 112750854--112750965 Score: 66
Period size: 21 Copynumber: 5.3 Consensus size: 21
112750844 AAGACATGTG
112750854 ACTTCAATCAATTCTACTGAA
1 ACTTCAATCAATTCTACTGAA
** * *
112750875 ACTTCAAGGAGA-TCTGCTGTA
1 ACTTCAATCA-ATTCTACTGAA
* * *
112750896 GCTTCGATTAATTCTACTGAA
1 ACTTCAATCAATTCTACTGAA
* * * *
112750917 ACTTCAA-GAAGATCTGCTGTA
1 ACTTCAATCAA-TTCTACTGAA
* * *
112750938 GCTTCGATCAATTCCACTGAA
1 ACTTCAATCAATTCTACTGAA
112750959 ACTTCAA
1 ACTTCAA
112750966 GGAGATCTGT
Statistics
Matches: 62, Mismatches: 25, Indels: 8
0.65 0.26 0.08
Matches are distributed among these distances:
20 3 0.05
21 56 0.90
22 3 0.05
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (21 bp):
ACTTCAATCAATTCTACTGAA
Found at i:112750910 original size:42 final size:42
Alignment explanation
Indices: 112750855--112750974 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
112750845 AGACATGTGA
*
112750855 CTTCAATCAATTCTACTGAAACTTCAAGGAGATCTGCTGTAG
1 CTTCGATCAATTCTACTGAAACTTCAAGGAGATCTGCTGTAG
* *
112750897 CTTCGATTAATTCTACTGAAACTTCAAGAAGATCTGCTGTAG
1 CTTCGATCAATTCTACTGAAACTTCAAGGAGATCTGCTGTAG
*
112750939 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTG
1 CTTCGATCAATTCTACTGAAACTTCAAGGAGATCTG
112750975 TTGTGCCTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (42 bp):
CTTCGATCAATTCTACTGAAACTTCAAGGAGATCTGCTGTAG
Found at i:112751136 original size:42 final size:42
Alignment explanation
Indices: 112751075--112751225 Score: 131
Period size: 43 Copynumber: 3.5 Consensus size: 42
112751065 CATCATTGAT
* * *
112751075 CTGTTTCCCTACTGTTTAGGGGTTTAGATCTGTAAACTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTTAGATCTGTAAACTCAGC
* * * * **
112751117 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAATTTGGC
1 CTGTTACCCTACTGCTTAGGGGTTT-AGATCTGTAAACTCAGC
* * * * * *
112751160 TTGTTACCCTATTGCTTAGGGTGATAATATCTATAAACTTCAGC
1 CTGTTACCCTACTGCTTAGGG-GTTTAGATCTGTAAAC-TCAGC
*
112751204 TTGTTACCCTACTGCTTAGGGG
1 CTGTTACCCTACTGCTTAGGGG
112751226 GTTAAAGCTT
Statistics
Matches: 84, Mismatches: 22, Indels: 5
0.76 0.20 0.05
Matches are distributed among these distances:
42 23 0.27
43 36 0.43
44 25 0.30
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (42 bp):
CTGTTACCCTACTGCTTAGGGGTTTAGATCTGTAAACTCAGC
Found at i:112751557 original size:44 final size:44
Alignment explanation
Indices: 112751507--112751626 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 44
112751497 CTGTACATTT
* *
112751507 AGTCTGCTCCACTGCGACTTCAAGGAGATGAGACTTGTAACTTC
1 AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
* * * *
112751551 AGTCTGCTCCACTAC-ACTTCAGGGAGATAAGGCTAGTGACTTC
1 AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
* * * * * *
112751594 AATCTGCTTCGCTGAGACTTCAAGAAGACAAGA
1 AGTCTGCTCCACTGCGACTTCAAGGAGATAAGA
112751627 TTCGCTGGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
43 33 0.55
44 27 0.45
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (44 bp):
AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
Found at i:112751790 original size:44 final size:45
Alignment explanation
Indices: 112751686--112751844 Score: 155
Period size: 44 Copynumber: 3.6 Consensus size: 45
112751676 TAATTCTCGG
* * ***
112751686 CCTATTACCCTACTGCTTAAGGGGTT-AAGGTCTA-TAAATTTGG
1 CCTATTACCCTACTGCTTAGGGGGTTAAAGATCTAGTAAATTCAA
* * * **
112751729 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTC-AGTATCTTCAA
1 CCTATTACCCTACTGCTTAGGGGGTTAAAGATCTAGTAAATTCAA
* * *
112751773 TCTATTTCCCTACTGCTTAGGGGGTT-AAGATCTTGTAAATTCAA
1 CCTATTACCCTACTGCTTAGGGGGTTAAAGATCTAGTAAATTCAA
* *
112751817 CCTGTTACCCTACTGCTTAGGGGTTTAA
1 CCTATTACCCTACTGCTTAGGGGGTTAA
112751845 GGCTTGGTGA
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 29 0.32
44 61 0.67
45 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (45 bp):
CCTATTACCCTACTGCTTAGGGGGTTAAAGATCTAGTAAATTCAA
Found at i:112758469 original size:39 final size:39
Alignment explanation
Indices: 112758415--112758616 Score: 332
Period size: 39 Copynumber: 5.2 Consensus size: 39
112758405 TGTGTATGAA
* *
112758415 TGTGCGAATTGTGATATCCGGGCTAAGCCCAAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
112758454 TGTGCGAGTTGTGATATCTGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
112758493 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
112758532 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
112758571 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
112758611 TGTGCG
1 TGTGCG
112758617 GGTTACCATA
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 137 0.89
40 17 0.11
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:112758547 original size:78 final size:78
Alignment explanation
Indices: 112758415--112758647 Score: 340
Period size: 78 Copynumber: 3.0 Consensus size: 78
112758405 TGTGTATGAA
* * * *
112758415 TGTGCGAATTGTGATATCCGGGCTAAGCCCAAAGGCAATTGTGCGAGTTGTGATATCTGGGCTAA
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
112758480 GCCCGAAGGCAAT
66 GCCCGAAGGCAAT
*
112758493 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
112758558 GCCCGAAGGCAAT
66 GCCCGAAGGCAAT
* * * ** *
112758571 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTA
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTA
*
112758636 TGTCCCGAAGGC
65 AG-CCCGAAGGC
112758648 GTTTGAACGA
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
78 98 0.70
79 33 0.24
80 9 0.06
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (78 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
GCCCGAAGGCAAT
Found at i:112766501 original size:39 final size:39
Alignment explanation
Indices: 112766447--112766648 Score: 332
Period size: 39 Copynumber: 5.2 Consensus size: 39
112766437 TGTGTATGAA
* * *
112766447 TGTGCGAATTGTGATATCCGGGCTAAGCTCGAAGACAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
112766486 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
112766525 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
112766564 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
112766603 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
112766643 TGTGCG
1 TGTGCG
112766649 GGTTACCATA
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 138 0.89
40 17 0.11
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:112766579 original size:78 final size:78
Alignment explanation
Indices: 112766447--112766679 Score: 340
Period size: 78 Copynumber: 3.0 Consensus size: 78
112766437 TGTGTATGAA
* * * *
112766447 TGTGCGAATTGTGATATCCGGGCTAAGCTCGAAGACAATTGTGCGAGTTGTGATATCCGGGCTAA
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
112766512 GCCCGAAGGCAAT
66 GCCCGAAGGCAAT
*
112766525 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
112766590 GCCCGAAGGCAAT
66 GCCCGAAGGCAAT
* * * ** *
112766603 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTA
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTA
*
112766668 TGTCCCGAAGGC
65 AG-CCCGAAGGC
112766680 GTTTGAACGA
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
78 98 0.70
79 33 0.24
80 9 0.06
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (78 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
GCCCGAAGGCAAT
Found at i:112766715 original size:79 final size:79
Alignment explanation
Indices: 112766476--112766717 Score: 206
Period size: 78 Copynumber: 3.1 Consensus size: 79
112766466 GGGCTAAGCT
* *** * **
112766476 CGAAGACAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA-TGAT
1 CGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGCAATTGAACGAG-TAGTGAT
* *
112766540 ATCCGGGCT-AA-GCC
65 ATCC-GGATAAACTCC
** * ** *
112766554 CGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATA
1 CGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATA
* * *
112766619 TCCGGGTTAAGTCC
66 TCCGGATAAACTCC
* * * **
112766633 CGAAGGCATTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-A
1 CGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGA
112766697 TATCCGGATAAACT-C
64 TATCCGGATAAACTCC
112766712 CGAAGG
1 CGAAGG
112766718 TATGTGATTC
Statistics
Matches: 140, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
77 4 0.03
78 65 0.46
79 40 0.29
80 30 0.21
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (79 bp):
CGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATA
TCCGGATAAACTCC
Found at i:112774810 original size:37 final size:37
Alignment explanation
Indices: 112774760--112774833 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
112774750 CAGTAAGTTA
112774760 GGGCACGATTATCTCGGATTACCGGATACGGAATATC
1 GGGCACGATTATCTCGGATTACCGGATACGGAATATC
112774797 GGGCACGATTATCTCGGATTACCGGATACGGAATATC
1 GGGCACGATTATCTCGGATTACCGGATACGGAATATC
112774834 ACTTTTATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (37 bp):
GGGCACGATTATCTCGGATTACCGGATACGGAATATC
Found at i:112775784 original size:34 final size:32
Alignment explanation
Indices: 112775737--112775871 Score: 96
Period size: 34 Copynumber: 3.9 Consensus size: 32
112775727 AAGAGAAAAG
112775737 AAAAATAAT-TAATAATATCATATAATATATATT
1 AAAAA-AATATAATAATAT-ATATAATATATATT
*
112775770 AAAAAAATGATAATAAAAAGTATATAATA-ATATT
1 AAAAAAAT-ATAAT-AATA-TATATAATATATATT
* **
112775804 AAAAGAATATACATAATATATAT-ATAATATACA
1 AAAAAAATATA-ATAATATATATAAT-ATATATT
*
112775837 AAACAAAATATACGCATAATATATTAAAATATATA
1 AAA-AAAATATA---ATAATATA-TATAATATATA
112775872 CATAATGTAC
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
31 2 0.02
32 9 0.11
33 17 0.20
34 25 0.30
35 11 0.13
36 10 0.12
37 7 0.08
38 2 0.02
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (32 bp):
AAAAAAATATAATAATATATATAATATATATT
Found at i:112775801 original size:17 final size:19
Alignment explanation
Indices: 112775779--112775823 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
112775769 TAAAAAAATG
*
112775779 ATAATA-AAAAGTATATA-
1 ATAATATAAAAGAATATAC
112775796 ATAATATTAAAAGAATATAC
1 ATAATA-TAAAAGAATATAC
112775816 ATAATATA
1 ATAATATA
112775824 TATATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
ATAATATAAAAGAATATAC
Found at i:112775819 original size:20 final size:19
Alignment explanation
Indices: 112775756--112775822 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 19
112775746 TAATAATATC
112775756 ATATAATATATATTAAAA-A
1 ATATAATA-ATATTAAAAGA
* *
112775775 A-ATGATAATA--AAAAGT
1 ATATAATAATATTAAAAGA
112775791 ATATAATAATATTAAAAGA
1 ATATAATAATATTAAAAGA
112775810 ATATACATAATAT
1 ATATA-ATAATAT
112775823 ATATATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.10
16 1 0.03
17 11 0.28
18 5 0.13
19 11 0.28
20 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (19 bp):
ATATAATAATATTAAAAGA
Found at i:112775865 original size:21 final size:22
Alignment explanation
Indices: 112775841--112775893 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
112775831 TATACAAAAC
*
112775841 AAAATATACGCATAATATA-TT
1 AAAATATACGCATAATATACAT
** *
112775862 AAAATATATACATAATGTACAT
1 AAAATATACGCATAATATACAT
112775884 AAAATATACG
1 AAAATATACG
112775894 TATATACGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (22 bp):
AAAATATACGCATAATATACAT
Found at i:112777310 original size:14 final size:12
Alignment explanation
Indices: 112777277--112777301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112777267 TTGGGTTAGT
112777277 GTTTTGGGCTAA
1 GTTTTGGGCTAA
112777289 GTTTTGGGCTAA
1 GTTTTGGGCTAA
112777301 G
1 G
112777302 AGTTTTGGGT
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:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:112780616 original size:11 final size:11
Alignment explanation
Indices: 112780595--112780632 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
112780585 AATTTAGTGA
*
112780595 AAGAAAGAGAG
1 AAGAAAAAGAG
*
112780606 AAGAAGAAGAG
1 AAGAAAAAGAG
112780617 AAGAAAAAGA-
1 AAGAAAAAGAG
112780627 AAGAAA
1 AAGAAA
112780633 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:112780634 original size:14 final size:14
Alignment explanation
Indices: 112780594--112780636 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
112780584 GAATTTAGTG
*
112780594 AAAGAAAGAGAGAA
1 AAAGAAAGAAAGAA
*
112780608 GAAG-AAGAGAAGAA
1 AAAGAAAGA-AAGAA
112780622 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
112780636 A
1 A
112780637 GAAAAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.67
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:112781129 original size:17 final size:17
Alignment explanation
Indices: 112781107--112781140 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
112781097 TTATCGACCG
112781107 ATTGGTCCGACAAACCA
1 ATTGGTCCGACAAACCA
* *
112781124 ATTGGTCTGACGAACCA
1 ATTGGTCCGACAAACCA
112781141 GTAGCTTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (17 bp):
ATTGGTCCGACAAACCA
Found at i:112782432 original size:8 final size:7
Alignment explanation
Indices: 112782405--112782429 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
112782395 TATTGAAGGG
112782405 AAAACCA
1 AAAACCA
112782412 AAAACCA
1 AAAACCA
112782419 AAAACCA
1 AAAACCA
112782426 AAAA
1 AAAA
112782430 ACCTCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACCA
Found at i:112789365 original size:2 final size:2
Alignment explanation
Indices: 112789358--112789502 Score: 185
Period size: 2 Copynumber: 75.5 Consensus size: 2
112789348 CATAGTTTTG
* * *
112789358 TC TC TC TC -C CC TC TC TC CC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
112789399 -C T- TC TC TC TC TC -C CC CC TC TC -C CC T- TC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
112789436 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
112789478 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
112789503 GTGTGTGTGC
Statistics
Matches: 128, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
1 6 0.05
2 122 0.95
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:112793987 original size:29 final size:29
Alignment explanation
Indices: 112793955--112794012 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
112793945 AAAATTTAAA
112793955 AGCCTATTATTTTCAATCAATAACATTAT
1 AGCCTATTATTTTCAATCAATAACATTAT
112793984 AGCCTATTATTTTCAATCAATAACATTAT
1 AGCCTATTATTTTCAATCAATAACATTAT
112794013 GGACTAACTA
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:0.03, T:0.41
Consensus pattern (29 bp):
AGCCTATTATTTTCAATCAATAACATTAT
Found at i:112794364 original size:2 final size:2
Alignment explanation
Indices: 112794357--112794397 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
112794347 CAAAATTACA
112794357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112794398 CGAATTAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112795146 original size:30 final size:30
Alignment explanation
Indices: 112795110--112795176 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
112795100 CTAAAATGAC
*
112795110 TATTATATAAAAAGGTCTTTTAAGGTCTTA
1 TATTATATAAAAAGCTCTTTTAAGGTCTTA
112795140 TATTATATAAAAAGCTCTTTTAAGGTCTTA
1 TATTATATAAAAAGCTCTTTTAAGGTCTTA
112795170 TATTATA
1 TATTATA
112795177 CATATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (30 bp):
TATTATATAAAAAGCTCTTTTAAGGTCTTA
Found at i:112804546 original size:9 final size:9
Alignment explanation
Indices: 112804525--112804582 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
112804515 ACAATAATTA
112804525 ATAT-ATAT
1 ATATAATAT
112804533 ATATAATAT
1 ATATAATAT
* *
112804542 GTATAATAA
1 ATATAATAT
*
112804551 AAATAATA-
1 ATATAATAT
112804559 ATATACATAAT
1 ATATA-AT-AT
112804570 ATATAA-AT
1 ATATAATAT
112804578 ATATA
1 ATATA
112804583 CGTATATAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 15 0.37
9 19 0.46
10 2 0.05
11 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
ATATAATAT
Found at i:112804548 original size:34 final size:31
Alignment explanation
Indices: 112804490--112804571 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 31
112804480 AGATATATGC
112804490 ATATATGATATAATACATGAATAATACAATAATTAAT
1 ATATAT-ATATAAT--ATGAATAATA-AA-AA-TAAT
*
112804527 ATATATATATAATATGTATAATAAAAATAAT
1 ATATATATATAATATGAATAATAAAAATAAT
*
112804558 A-ATATACATAATAT
1 ATATATATATAATAT
112804572 ATAAATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 12 0.28
31 5 0.12
32 2 0.05
33 2 0.05
34 9 0.21
36 7 0.16
37 6 0.14
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (31 bp):
ATATATATATAATATGAATAATAAAAATAAT
Found at i:112804755 original size:3 final size:3
Alignment explanation
Indices: 112804747--112804806 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
112804737 ACTAACATAT
112804747 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
112804792 ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA A
112804807 CAAGAATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:112805313 original size:16 final size:16
Alignment explanation
Indices: 112805268--112805314 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
112805258 AGAAAAAAAA
*
112805268 AGAAAAAAGAGAGGGG
1 AGAAAGAAGAGAGGGG
*
112805284 AGAAAGGAGAGAGGGG
1 AGAAAGAAGAGAGGGG
*
112805300 AGAAAGAAGGGAGGG
1 AGAAAGAAGAGAGGG
112805315 AATCCGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (16 bp):
AGAAAGAAGAGAGGGG
Found at i:112805555 original size:35 final size:35
Alignment explanation
Indices: 112805509--112805581 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
112805499 ATAAAAAAAA
112805509 ATCACCTTTTGGTCTTTTTAGCTTCTGATTTGTTG
1 ATCACCTTTTGGTCTTTTTAGCTTCTGATTTGTTG
112805544 ATCACCTTTTGGTCTTTTTAGCTTCTGATTTGTTG
1 ATCACCTTTTGGTCTTTTTAGCTTCTGATTTGTTG
112805579 ATC
1 ATC
112805582 TTTGATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.12, C:0.18, G:0.16, T:0.53
Consensus pattern (35 bp):
ATCACCTTTTGGTCTTTTTAGCTTCTGATTTGTTG
Found at i:112807732 original size:26 final size:26
Alignment explanation
Indices: 112807659--112807741 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
112807649 AAACAATTTG
* *
112807659 AAATAAAATAATATATAAAGTAAATTTC
1 AAAT-AAATAATATATAAAATAAA-TTA
* *
112807687 AAATAAATAATATGTTAAATAAATTA
1 AAATAAATAATATATAAAATAAATTA
* *
112807713 AAATAAATAATATACAAAATAAAATA
1 AAATAAATAATATATAAAATAAATTA
112807739 AAA
1 AAA
112807742 AGGACCCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 27 0.57
27 16 0.34
28 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAAATAATATATAAAATAAATTA
Found at i:112807998 original size:30 final size:28
Alignment explanation
Indices: 112807964--112808049 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 28
112807954 TAACTAGATA
112807964 ACATATGAAAAGAAATTTAAAATGAATAAT
1 ACATAT-AAAA-AAATTTAAAATGAATAAT
* * *
112807994 ACATATATAATAGTTTAAAATGAAT-A-
1 ACATATAAAAAAATTTAAAATGAATAAT
* *
112808020 ACGTATAAAAATATTTTAAAAT-AAGTAAT
1 ACATATAAAAA-AATTTAAAATGAA-TAAT
112808049 A
1 A
112808050 TGTATAATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
26 10 0.22
27 11 0.24
28 14 0.31
29 4 0.09
30 6 0.13
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (28 bp):
ACATATAAAAAAATTTAAAATGAATAAT
Found at i:112808040 original size:27 final size:28
Alignment explanation
Indices: 112807979--112808093 Score: 100
Period size: 27 Copynumber: 4.3 Consensus size: 28
112807969 TGAAAAGAAA
*
112807979 TTTAAAATGAATAATACATATATAATAG
1 TTTAAAATGAATAATACATATAAAATAG
* *
112808007 TTTAAAATGAAT-A-ACGTATAAAAATAT
1 TTTAAAATGAATAATACATAT-AAAATAG
* *
112808034 TTTAAAAT-AAGTAAT--ATGTATAATAG
1 TTTAAAATGAA-TAATACATATAAAATAG
* *
112808060 -TTAAAATGAATAATATATGTAAAATA-
1 TTTAAAATGAATAATACATATAAAATAG
112808086 TTTAAAAT
1 TTTAAAAT
112808094 CTGTAATATC
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
25 11 0.15
26 14 0.20
27 33 0.46
28 13 0.18
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (28 bp):
TTTAAAATGAATAATACATATAAAATAG
Found at i:112808090 original size:52 final size:53
Alignment explanation
Indices: 112807999--112808102 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 53
112807989 ATAATACATA
*
112807999 TATAATAGTTTAAAATGAATAACGTATAAAAATATTTTAAAATAAGTAATATG
1 TATAATAGTTTAAAATGAATAACATATAAAAATATTTTAAAATAAGTAATATG
* * **
112808052 TATAATAG-TTAAAATGAATAATATATGTAAAATA-TTTAAAATCTGTAATAT
1 TATAATAGTTTAAAATGAATAACATAT-AAAAATATTTTAAAATAAGTAATAT
112808103 CTTAAAGTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 31 0.69
53 14 0.31
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (53 bp):
TATAATAGTTTAAAATGAATAACATATAAAAATATTTTAAAATAAGTAATATG
Found at i:112809356 original size:18 final size:18
Alignment explanation
Indices: 112809333--112809373 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
112809323 TACTTTTCTC
112809333 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
112809351 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
112809369 TTTCT
1 TTTCT
112809374 TTTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:112809388 original size:19 final size:20
Alignment explanation
Indices: 112809364--112809411 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
112809354 CTATTCATAA
*
112809364 TTCAATTTCTTT-TTCTCAT
1 TTCAATTTCTTTATTCACAT
**
112809383 TTCAATGCCTTTAATTCACAT
1 TTCAATTTCTTT-ATTCACAT
112809404 TTCAATTT
1 TTCAATTT
112809412 TTCATTCTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (20 bp):
TTCAATTTCTTTATTCACAT
Found at i:112809544 original size:39 final size:40
Alignment explanation
Indices: 112809501--112809612 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
112809491 TCAAATACTT
*
112809501 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
112809540 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
112809579 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
112809613 CTCGAGGTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.33
39 20 0.35
40 1 0.02
41 17 0.30
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:112810819 original size:23 final size:24
Alignment explanation
Indices: 112810763--112810821 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
112810753 AAATTAATTA
*
112810763 TTTTATTACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
112810787 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
112810811 TTTTATTACAA
1 TTTTATTACAA
112810822 TTGTCATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.31
24 2 0.06
25 18 0.56
26 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:112812784 original size:137 final size:136
Alignment explanation
Indices: 112812620--112812963 Score: 420
Period size: 137 Copynumber: 2.5 Consensus size: 136
112812610 CTTTGACCTG
** *** *
112812620 TTCCACTGCAACTTCAGGGAAATAAGATCCACTATCTTCAGTCTATTTCACTACTACTTCAGGAA
1 TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
* * * * *
112812685 GATAAGGTTTGCTATGATCTGCTCTACTGTAACTTCATAGAGATAAGATCTGTAATTTATAGCTT
66 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAA-TTATAGCTT
112812750 CAATCTA
130 CAATCTA
* * ** * *
112812757 TTCCACTGCAACTTCAGGGAAATAAGATTTGTTATCTTCAGTCGGCCCCACTGCAACTTCAGGGA
1 TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
*
112812822 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTTATTATAGCTTC
66 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAATTATAGCTTC
*
112812887 AATCTG
131 AATCTA
* * * * * * *
112812893 TTCCCCCTACAACTTCAGTGAAATAAGATCTGCTATCTTCAGTCTGCTCCATTGCAACTTCAAGG
1 TT-CCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTC-AGG
112812958 -AGATAA
64 AAGATAA
112812964 GACTTGTCAT
Statistics
Matches: 178, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
136 17 0.10
137 158 0.89
138 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (136 bp):
TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAATTATAGCTTC
AATCTA
Found at i:112814665 original size:41 final size:41
Alignment explanation
Indices: 112814591--112814758 Score: 200
Period size: 41 Copynumber: 4.1 Consensus size: 41
112814581 CAAAAATTGT
* *
112814591 AAAACACATAGCAATAGCGGCG-TTTT-ACCAAAAACGCCACTA
1 AAAAC-CAGAGCAATAGCGGCGCTTTTGA--AAAAACGCCGCTA
*
112814633 AAAA-CAGAGCAATAGCTGCG-TTTTAGTAAAAAACGCCGCTA
1 AAAACCAGAGCAATAGCGGCGCTTTT-G-AAAAAACGCCGCTA
* *
112814674 AAAACCAGAGCATTAGCGGCGCTTTTGAAAAAATGCCGCTA
1 AAAACCAGAGCAATAGCGGCGCTTTTGAAAAAACGCCGCTA
* *
112814715 AAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCTA
1 AAAACCAGAGCAATAGCGGCGCTTTTGAAAAAACGCCGCTA
112814756 AAA
1 AAA
112814759 GTCATATAAC
Statistics
Matches: 113, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
40 18 0.16
41 71 0.63
42 19 0.17
43 5 0.04
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
AAAACCAGAGCAATAGCGGCGCTTTTGAAAAAACGCCGCTA
Found at i:112814943 original size:14 final size:14
Alignment explanation
Indices: 112814920--112814993 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
112814910 TATTATTATA
112814920 GTTTATGGTTTAGG
1 GTTTATGGTTTAGG
* *
112814934 GTTTAAGGTTTATGA
1 GTTTATGGTTTA-GG
*
112814949 GTTAACTATGGTTTAAG
1 GTT---TATGGTTTAGG
* *
112814966 ATATATGGTTTAGG
1 GTTTATGGTTTAGG
*
112814980 GTTTAAGGTTTAGG
1 GTTTATGGTTTAGG
112814994 AGTTAACTAG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
14 32 0.71
15 4 0.09
17 1 0.02
18 8 0.18
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (14 bp):
GTTTATGGTTTAGG
Found at i:112822474 original size:41 final size:45
Alignment explanation
Indices: 112822415--112822499 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 45
112822405 ATAGTGTTAG
112822415 AAATATACTATATATAGT-AT-TTGAAA-TATATACATAA-AATAA
1 AAATATACTATATATAGTAATGTT-AAAGTATATACATAATAATAA
112822457 AAATATA-TATA-ACTAGTAATGTTAAAGTATATACATAATAATA
1 AAATATACTATATA-TAGTAATGTTAAAGTATATACATAATAATA
112822500 TATATATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
40 1 0.03
41 8 0.21
42 12 0.32
43 13 0.34
44 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (45 bp):
AAATATACTATATATAGTAATGTTAAAGTATATACATAATAATAA
Found at i:112822560 original size:24 final size:23
Alignment explanation
Indices: 112822512--112822582 Score: 63
Period size: 26 Copynumber: 2.9 Consensus size: 23
112822502 TATATAAAAA
*
112822512 ATAAATAT-TGAAAAATGTATGTAC
1 ATAAATATATGAAAAA--TATATAC
112822536 ATAACATATATGAAAAATATATAC
1 ATAA-ATATATGAAAAATATATAC
*
112822560 ATTATATAATATGTAAAAATATA
1 A-TAAAT-ATATG-AAAAATATA
112822583 ATATAGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 13 0.32
25 11 0.28
26 16 0.40
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (23 bp):
ATAAATATATGAAAAATATATAC
Found at i:112823055 original size:12 final size:13
Alignment explanation
Indices: 112823040--112823242 Score: 70
Period size: 12 Copynumber: 15.8 Consensus size: 13
112823030 ATACTAGTAC
*
112823040 TAATAATAT-TAT
1 TAATAATATATAA
112823052 TAATAA-ATATAA
1 TAATAATATATAA
112823064 TAATAATA-ATAA
1 TAATAATATATAA
* * *
112823076 TATGTTAATA-ACAG
1 TA--ATAATATATAA
* *
112823090 CAAGAATATATAA
1 TAATAATATATAA
**
112823103 -AATAATAATATGG
1 TAATAAT-ATATAA
112823116 TAA-AATA-ATAA
1 TAATAATATATAA
*
112823127 TAATAATGTATTAA
1 TAATAATATA-TAA
*
112823141 TAAGAATGATAATAA
1 TAATAAT-AT-ATAA
* *
112823156 TAA-AATAAGATTA
1 TAATAAT-ATATAA
*
112823169 TAATAATAGTATCA
1 TAATAATA-TATAA
* *
112823183 TAA-AAAATAGACA
1 TAATAATATATA-A
* * * *
112823196 TGA-AAGAAATAG
1 TAATAATATATAA
112823208 TAATAATA-ATAA
1 TAATAATATATAA
112823220 TAATAATATA-AA
1 TAATAATATATAA
112823232 TAATAATATAT
1 TAATAATATAT
112823243 GTATGCAAAT
Statistics
Matches: 140, Mismatches: 33, Indels: 35
0.67 0.16 0.17
Matches are distributed among these distances:
11 7 0.05
12 60 0.43
13 33 0.24
14 32 0.23
15 7 0.05
16 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:112823066 original size:3 final size:3
Alignment explanation
Indices: 112823040--112823239 Score: 61
Period size: 3 Copynumber: 69.7 Consensus size: 3
112823030 ATACTAGTAC
* * **
112823040 TAA TAA TAT TAT TAA TAA -ATA TAA TAA TAA TAA TAA T-A TGT TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * * * **
112823084 TAA CAG CAA GAA TATA TAA -AA TAA TAA T-A TGG TAA -AA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
112823127 TAA TAA T-G TAT TAA TAA GAA TGA TAA TAA TAA -AA TAA -GA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
112823172 TAA TAG T-A TCA TAA -AA -AA TAGA -CA TGAA -AGA -AA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TA-A TAA TAA TAA TAA
112823214 TAA TAA TAA TAA T-A TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TA
112823240 TATGTATGCA
Statistics
Matches: 148, Mismatches: 30, Indels: 38
0.69 0.14 0.18
Matches are distributed among these distances:
2 23 0.16
3 117 0.79
4 8 0.05
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:112823173 original size:19 final size:20
Alignment explanation
Indices: 112823139--112823176 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
112823129 ATAATGTATT
112823139 AATAAGAATGATAATAATAA
1 AATAAGAATGATAATAATAA
*
112823159 AATAAG-ATTATAATAATA
1 AATAAGAATGATAATAATA
112823177 GTATCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AATAAGAATGATAATAATAA
Found at i:112829091 original size:26 final size:26
Alignment explanation
Indices: 112829045--112829097 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
112829035 TCAAACATGC
*
112829045 ATTTAGGTCAATTTAACCCTATGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* *
112829071 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAAC-CCTAGGGGT
112829097 A
1 A
112829098 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:112830599 original size:26 final size:26
Alignment explanation
Indices: 112830570--112830678 Score: 209
Period size: 26 Copynumber: 4.2 Consensus size: 26
112830560 AATAAATTCC
112830570 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
112830596 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
*
112830622 TATCATGAAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
112830648 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
112830674 TATCA
1 TATCA
112830679 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:112841014 original size:19 final size:20
Alignment explanation
Indices: 112840972--112841019 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
112840962 AATGAATAAC
*
112840972 CTAAAATAATAAAAAAGAAG
1 CTAAAAAAATAAAAAAGAAG
112840992 --AAAAAAATAAAAAA-AAG
1 CTAAAAAAATAAAAAAGAAG
112841009 CTAAAAAAATA
1 CTAAAAAAATA
112841020 TTTGAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 13 0.52
19 9 0.36
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (20 bp):
CTAAAAAAATAAAAAAGAAG
Found at i:112841257 original size:17 final size:17
Alignment explanation
Indices: 112841232--112841265 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
112841222 CATAGATGAA
*
112841232 AATATGATAGTAATAAT
1 AATACGATAGTAATAAT
112841249 AATACGATAGTAATAAT
1 AATACGATAGTAATAAT
112841266 GATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (17 bp):
AATACGATAGTAATAAT
Found at i:112841349 original size:3 final size:3
Alignment explanation
Indices: 112841343--112841415 Score: 121
Period size: 3 Copynumber: 24.0 Consensus size: 3
112841333 TTAATAGTAG
112841343 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
112841391 TAA TAA TAA T-A TACA TGAA TAA TAA
1 TAA TAA TAA TAA TA-A T-AA TAA TAA
112841416 CAGTAACAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 60 0.90
4 4 0.06
5 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:112841639 original size:3 final size:3
Alignment explanation
Indices: 112841631--112841671 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
112841621 TAGTACTAAG
*
112841631 ATA ATA ATA ATA ATG ATA A-A A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
112841672 CGACAATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:112847227 original size:22 final size:22
Alignment explanation
Indices: 112847183--112847227 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
112847173 TACAGCGCTA
* *
112847183 TTTTAAGTTCTTCTATCTTCTC
1 TTTTAAGTTCTTCGATCTGCTC
112847205 TTTTAA-TTCTTCGATTCTGCTC
1 TTTTAAGTTCTTCGA-TCTGCTC
112847227 T
1 T
112847228 GACTAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAGTTCTTCGATCTGCTC
Found at i:112851121 original size:3 final size:3
Alignment explanation
Indices: 112851107--112851174 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
112851097 TAAAGATTGT
*
112851107 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TACA TGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA
* * *
112851153 TAA TAA CAA TAA CAA TTA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
112851175 GACACAACAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 4 0.07
5 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:112851318 original size:18 final size:18
Alignment explanation
Indices: 112851262--112851319 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
112851252 TAATAAGGAC
112851262 AATAATAAATAACAATTAAT
1 AATAATAAAT-A-AATTAAT
* * *
112851282 AATACTACATTAATTAAT
1 AATAATAAATAAATTAAT
*
112851300 AATAATAAATAAATAAAT
1 AATAATAAATAAATTAAT
112851318 AA
1 AA
112851320 ATAAACATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 23 0.74
20 8 0.26
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAATAAATAAATTAAT
Found at i:112851395 original size:3 final size:3
Alignment explanation
Indices: 112851387--112851529 Score: 132
Period size: 3 Copynumber: 48.0 Consensus size: 3
112851377 TAGTACTAAG
112851387 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
112851435 ATA ATA ATA CATT A-A ATT ATA ATA GTA A-A GTA ATA ATA ATA GTG
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
112851479 ATA ATC ATA AT- ATA TTA GACA ATA ATA GTA A-A ATA ATA AGCA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA
112851524 ATA ATA
1 ATA ATA
112851530 TATTAAATTA
Statistics
Matches: 111, Mismatches: 22, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
2 6 0.05
3 100 0.90
4 5 0.05
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:112851489 original size:47 final size:47
Alignment explanation
Indices: 112851388--112851529 Score: 125
Period size: 47 Copynumber: 3.1 Consensus size: 47
112851378 AGTACTAAGA
* *
112851388 TAATAATAATAATA-A-T-AATAATAATAATAATAAT-A--ATAATAA
1 TAATAATAATAATACATTAAACAATAATAGTAA-AATAATAATAATAA
** * *
112851430 TAATAATAATAATACATTAAATTATAATAGTAAAGTAATAATAATAG
1 TAATAATAATAATACATTAAACAATAATAGTAAAATAATAATAATAA
* * * * *
112851477 TGATAATCATAATATATTAGACAATAATAGTAAAATAATAAGCAATAA
1 TAATAATAATAATACATTAAACAATAATAGTAAAATAATAA-TAATAA
112851525 TAATA
1 TAATA
112851530 TATTAAATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
42 14 0.18
43 1 0.01
44 3 0.04
45 13 0.16
47 40 0.51
48 8 0.10
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (47 bp):
TAATAATAATAATACATTAAACAATAATAGTAAAATAATAATAATAA
Found at i:112852090 original size:9 final size:10
Alignment explanation
Indices: 112852074--112852114 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
112852064 TCAAAAAAGG
112852074 TATATTTTTT
1 TATATTTTTT
112852084 TAT-TTTTTT
1 TATATTTTTT
112852093 TATATTTTTT
1 TATATTTTTT
* *
112852103 GATATATTTT
1 TATATTTTTT
112852113 TA
1 TA
112852115 ATATATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (10 bp):
TATATTTTTT
Found at i:112852112 original size:21 final size:19
Alignment explanation
Indices: 112852074--112852114 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
112852064 TCAAAAAAGG
*
112852074 TATATTTTTTTATTTTTTT
1 TATATTTTTTTATATTTTT
*
112852093 TATATTTTTTGATATATTTT
1 TATATTTTTTTATAT-TTTT
112852113 TA
1 TA
112852115 ATATATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TATATTTTTTTATATTTTT
Found at i:112852577 original size:15 final size:16
Alignment explanation
Indices: 112852557--112852598 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
112852547 AGGGTTAAAA
112852557 GGGTTTTGGGCT-GTT
1 GGGTTTTGGGCTAGTT
*
112852572 GGGTTTTGGGATAGTT
1 GGGTTTTGGGCTAGTT
*
112852588 AGGTTTTGGGC
1 GGGTTTTGGGC
112852599 AGGGTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.07, C:0.05, G:0.45, T:0.43
Consensus pattern (16 bp):
GGGTTTTGGGCTAGTT
Found at i:112853624 original size:27 final size:26
Alignment explanation
Indices: 112853594--112853644 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
112853584 AATGTAAATC
* *
112853594 ATGTATATATATATATACAAAATAATA
1 ATGTATAAAAATATATA-AAAATAATA
*
112853621 ATGTATAAAAATATTTAAAAATAA
1 ATGTATAAAAATATATAAAAATAA
112853645 CCATGATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
ATGTATAAAAATATATAAAAATAATA
Found at i:112853790 original size:17 final size:17
Alignment explanation
Indices: 112853770--112853820 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
112853760 GAATAATATA
112853770 GAATAATTTAAAATAAT
1 GAATAATTTAAAATAAT
* *
112853787 GAATAGTATAAAAATGAAT
1 GAATAAT-TTAAAAT-AAT
*
112853806 -AATAACTTAAAATAA
1 GAATAATTTAAAATAA
112853821 ATAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 2 0.07
17 12 0.44
18 10 0.37
19 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (17 bp):
GAATAATTTAAAATAAT
Found at i:112856143 original size:19 final size:20
Alignment explanation
Indices: 112856121--112856170 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
112856111 GGTCTTTTCG
* *
112856121 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGAA
112856140 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
112856160 TGAAATG-AATG
1 TGAAATGTAATG
112856171 TGAAAAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:112860441 original size:52 final size:53
Alignment explanation
Indices: 112860348--112860450 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
112860338 TAATACATAA
*
112860348 ATAATAGTTTAAAATGAATAACGTATAAAAATATTTCAAAATAAGTAATATGT
1 ATAATAGTTTAAAATGAATAACATATAAAAATATTTCAAAATAAGTAATATGT
* * **
112860401 ATAATAG-TTAAAATGAATAATATATGTAAAATATTT-AAAATCTGTAATAT
1 ATAATAGTTTAAAATGAATAACATAT-AAAAATATTTCAAAATAAGTAATAT
112860451 CTTAAAGTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
52 28 0.64
53 16 0.36
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (53 bp):
ATAATAGTTTAAAATGAATAACATATAAAAATATTTCAAAATAAGTAATATGT
Found at i:112863370 original size:5 final size:5
Alignment explanation
Indices: 112863360--112863391 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
112863350 GTACATGTGA
112863360 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
112863392 GAACATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:112863385 original size:9 final size:9
Alignment explanation
Indices: 112863361--112863391 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
112863351 TACATGTGAA
112863361 AAATAAAAT
1 AAATAAAAT
112863370 AAAATAAAAT
1 -AAATAAAAT
112863380 AAATAAAAT
1 AAATAAAAT
112863389 AAA
1 AAA
112863392 GAACATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:112881445 original size:20 final size:20
Alignment explanation
Indices: 112881417--112881462 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
112881407 CAAGCCTTGG
*
112881417 TTGTAAATAAAAGGACCAAA
1 TTGTGAATAAAAGGACCAAA
112881437 TTGTGAATAAAAGGACCAAA
1 TTGTGAATAAAAGGACCAAA
112881457 TTGTGA
1 TTGTGA
112881463 GAATTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGTGAATAAAAGGACCAAA
Found at i:112886013 original size:20 final size:22
Alignment explanation
Indices: 112885982--112886023 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
112885972 TGAAAATAGT
112885982 TAAATGTTGTGTTAAT-TTTAC
1 TAAATGTTGTGTTAATGTTTAC
112886003 TAAAT-TTGTGTTAATGTTTAC
1 TAAATGTTGTGTTAATGTTTAC
112886024 AGTCAATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (22 bp):
TAAATGTTGTGTTAATGTTTAC
Found at i:112886820 original size:5 final size:5
Alignment explanation
Indices: 112886810--112886844 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
112886800 CCAATTAGTA
112886810 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
112886845 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:112897240 original size:13 final size:13
Alignment explanation
Indices: 112897219--112897258 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
112897209 AGTAATCAAA
* *
112897219 CACGAGCGTGTGC
1 CACGGGCGTGTCC
112897232 CACGGGCGTGTCC
1 CACGGGCGTGTCC
112897245 CACGGGCGTGTCC
1 CACGGGCGTGTCC
112897258 C
1 C
112897259 TACCGAGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.10, C:0.38, G:0.38, T:0.15
Consensus pattern (13 bp):
CACGGGCGTGTCC
Found at i:112907086 original size:15 final size:18
Alignment explanation
Indices: 112907051--112907089 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
112907041 TAAAGAAAAT
112907051 AAAGAAAGAAATAATGTA
1 AAAGAAAGAAATAATGTA
112907069 AAAGAAA-AAA-AA-GTA
1 AAAGAAAGAAATAATGTA
112907084 AAAGAA
1 AAAGAA
112907090 TTATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 2 0.10
17 3 0.14
18 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAGAAAGAAATAATGTA
Found at i:112924405 original size:2 final size:2
Alignment explanation
Indices: 112924398--112924429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
112924388 AAATGTATCG
112924398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112924430 GTTATTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112928609 original size:3 final size:3
Alignment explanation
Indices: 112928601--112928644 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
112928591 TTCCAAAAGT
112928601 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
112928645 GTTTAATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:112928718 original size:30 final size:30
Alignment explanation
Indices: 112928684--112928755 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
112928674 CTTAAGAAAA
* * * *
112928684 AATTTCAAAAACTTTTA-TAAATTTACTTGG
1 AATTT-AAAAAATTTTAGAAAATTTAATTAG
*
112928714 AATTTTTAAAAATTTTAGAAAATTTAATTAG
1 AA-TTTAAAAAATTTTAGAAAATTTAATTAG
112928745 AATTTAAAAAA
1 AATTTAAAAAA
112928756 ATTTCATGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTTAAAAAATTTTAGAAAATTTAATTAG
Found at i:112929070 original size:53 final size:51
Alignment explanation
Indices: 112928983--112929083 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 51
112928973 ATGGTTAACT
112928983 TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
1 TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
112929034 TTTTTAAAGAAATTATAAAAAATTAT-AAAATAATTATTTAACTTATCAAC
1 TTTTTAAAG-AA--ATAAAAAATTATAAAAATAATTATTTAACTTATCAAC
112929084 TTCGCCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
51 9 0.19
52 2 0.04
53 24 0.51
54 12 0.26
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (51 bp):
TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
Found at i:112940322 original size:2 final size:2
Alignment explanation
Indices: 112940315--112940342 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
112940305 TTTCATTCAG
112940315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112940343 AAGTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112942186 original size:22 final size:20
Alignment explanation
Indices: 112942150--112942190 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
112942140 AGTGAATAAA
112942150 GGAGAAGGAAAAGAAAGAAG
1 GGAGAAGGAAAAGAAAGAAG
112942170 GGAGAAAGGAAAAAGAAAGAA
1 GGAG-AAGG-AAAAGAAAGAA
112942191 AATCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GGAGAAGGAAAAGAAAGAAG
Found at i:112942917 original size:31 final size:31
Alignment explanation
Indices: 112942859--112942917 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
112942849 ATTATCATCC
* *
112942859 TTATAATCAATCAATTTTATACGTTTATACT
1 TTATAATCAATCAATTTTACACATTTATACT
*
112942890 TTATAATCATTCAAATTTT-CACATTTAT
1 TTATAATCAATC-AATTTTACACATTTAT
112942918 GCCCTGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.49
Consensus pattern (31 bp):
TTATAATCAATCAATTTTACACATTTATACT
Found at i:112952094 original size:5 final size:5
Alignment explanation
Indices: 112952084--112952108 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
112952074 GCATACATAG
112952084 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
112952109 AGAACAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:112963151 original size:40 final size:40
Alignment explanation
Indices: 112963081--112963178 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
112963071 CCGTCTCCGT
*
112963081 CCAACCCAACACACC-A-TATGGGGATAAAATCAACCCAC
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
* *
112963119 CCAACCCTACACACCAAGTATGGGGATAAAATCGACCCAT
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
*
112963159 CCAGCCCTACACACCAAGTA
1 CCAACCCTACACACCAAGTA
112963179 GTATTGTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 14 0.26
39 1 0.02
40 39 0.72
ACGTcount: A:0.39, C:0.37, G:0.12, T:0.12
Consensus pattern (40 bp):
CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
Found at i:112970292 original size:22 final size:22
Alignment explanation
Indices: 112970261--112970315 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
112970251 TTTCACGATT
112970261 CACACGGCCT-AGCCATTGAGCC
1 CACACGGCCTGA-CCATTGAGCC
*
112970283 CATACGGCCTGACCATTGAGCC
1 CACACGGCCTGACCATTGAGCC
112970305 CACACGGCCTG
1 CACACGGCCTG
112970316 GTAATCACGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.22, C:0.40, G:0.24, T:0.15
Consensus pattern (22 bp):
CACACGGCCTGACCATTGAGCC
Found at i:112978761 original size:6 final size:6
Alignment explanation
Indices: 112978750--112978841 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
112978740 AATCCTCCTA
* * * *
112978750 TTTTAT TTTTAT TCTTAT TATTA- -TTTAT TCTTAT TTTT-G TTTTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
** * * *
112978794 TTTTA- TTTTA- TTTTAT TCCTAT TTTTCT TTTGAT TTTTAT TTTCAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
112978840 TT
1 TT
112978842 CAATTTTCTT
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
4 3 0.04
5 19 0.28
6 45 0.67
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:112978778 original size:16 final size:16
Alignment explanation
Indices: 112978752--112978816 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
112978742 TCCTCCTATT
112978752 TTATT-TTTATTCTTA
1 TTATTATTTATTCTTA
112978767 TTATTATTTATTCTTA
1 TTATTATTTATTCTTA
* *
112978783 TTTTTGTTTTATT-TTA
1 TTATT-ATTTATTCTTA
*
112978799 TT-TTATTTTATTCCTA
1 TTATTA-TTTATTCTTA
112978815 TT
1 TT
112978817 TTTCTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.31
16 23 0.55
17 6 0.14
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (16 bp):
TTATTATTTATTCTTA
Found at i:112978817 original size:16 final size:16
Alignment explanation
Indices: 112978748--112978841 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 16
112978738 TGAATCCTCC
112978748 TATTTTATTTTTATTCT
1 TATTTTA-TTTTATTCT
112978765 TATTATTA-TTTATTCT
1 TATT-TTATTTTATTCT
*
112978781 TATTTTTGTTTTATT-T
1 TA-TTTTATTTTATTCT
*
112978797 TATTTTATTTTATTCC
1 TATTTTATTTTATTCT
* *
112978813 TATTTTTCTTTTGATTTT
1 TA-TTTTATTTT-ATTCT
112978831 TATTTTCATTT
1 TATTTT-ATTT
112978842 CAATTTTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
15 11 0.17
16 17 0.27
17 24 0.38
18 11 0.17
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (16 bp):
TATTTTATTTTATTCT
Found at i:112978832 original size:39 final size:43
Alignment explanation
Indices: 112978748--112978841 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 43
112978738 TGAATCCTCC
* **
112978748 TATTTTATTTTTATTCTTATTATTATTTATTCTTATTTTTGTTT
1 TATTTTA-TTTTATTCTTATTACTATTTATTCTTATTGATGTTT
*
112978792 TATTTTATTTTATT-TTATTCCTATTT-TTCTT-TTGAT-TTT
1 TATTTTATTTTATTCTTATTACTATTTATTCTTATTGATGTTT
112978831 TATTTTCATTT
1 TATTTT-ATTT
112978842 CAATTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 9 0.20
40 7 0.16
41 5 0.11
42 10 0.22
43 7 0.16
44 7 0.16
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (43 bp):
TATTTTATTTTATTCTTATTACTATTTATTCTTATTGATGTTT
Found at i:112982168 original size:22 final size:22
Alignment explanation
Indices: 112982129--112982187 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
112982119 GTTTTAAGAA
*
112982129 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
112982150 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
112982172 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
112982188 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:112982204 original size:26 final size:24
Alignment explanation
Indices: 112982158--112982217 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
112982148 ATTTGTTTTA
*
112982158 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
112982182 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
112982208 TTTTTTATTT
1 ATATTTATTT
112982218 AATAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:112987089 original size:27 final size:27
Alignment explanation
Indices: 112987052--112987105 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
112987042 GCACTTCGAG
112987052 CTCCTCAACATAGAAGCCCAATCATCC
1 CTCCTCAACATAGAAGCCCAATCATCC
112987079 CTCCTCAACATAGAAGCCCAATCATCC
1 CTCCTCAACATAGAAGCCCAATCATCC
112987106 TCTCTTACTC
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:0.33, C:0.41, G:0.07, T:0.19
Consensus pattern (27 bp):
CTCCTCAACATAGAAGCCCAATCATCC
Found at i:112989340 original size:12 final size:12
Alignment explanation
Indices: 112989325--112989349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112989315 TTTTATGGAT
112989325 GATTTTTCCTTA
1 GATTTTTCCTTA
112989337 GATTTTTCCTTA
1 GATTTTTCCTTA
112989349 G
1 G
112989350 GTGAGCATGG
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:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (12 bp):
GATTTTTCCTTA
Found at i:112991572 original size:237 final size:238
Alignment explanation
Indices: 112991112--112991574 Score: 730
Period size: 237 Copynumber: 1.9 Consensus size: 238
112991102 TTACTCACAA
* * * *
112991112 ATCCATAAATGTCTAGCAGTGGTCACCATCGAATCCTCTGCCACACCGATCCATCTACTGCTGAG
1 ATCCATAAATGTCCAACAGTGGTCACCATCGAACCCTCTACCACACCGATCCATCTACTGCTGAG
*
112991177 GATTACCTGACATAAAATAAATAAAGGGGTAAGTTTTTGCAAACTCAGTGTGTACATCCCCACAA
66 GATTACCTGACATAAAATAAATAAAGGGGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAA
* * * * * **
112991242 ATAGCATGCATACAAATAAATAACAGAATATAGATATTCGTCCTTAGCCTTACAAATATCACATG
131 ACAGCATGCATAAAAATAAATAACAAAATACAGATATCCAACCTTAGCCTTACAAATATCACATG
*
112991307 CAGATCAGATCAGATATCAGAAAACAGAAATGAGAAATCATTC
196 CAGATCAAATCAGATATCAGAAAACAGAAATGAGAAATCATTC
* *
112991350 ATCCATAAATGTCCAACAGTGGTCACCATCGAGCCCTCTACCATACCGATCCATCTACTGCTGAG
1 ATCCATAAATGTCCAACAGTGGTCACCATCGAACCCTCTACCACACCGATCCATCTACTGCTGAG
* *
112991415 GATTATCTGACATAAAATAAATAAAGGGGTGAG-TTTTCCAAACTCAGTGTGTACATCCCCACAA
66 GATTACCTGACATAAAATAAATAAAGGGGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAA
* * *
112991479 ACAGCATGCATAAAAATAGATAACAAAATACAGATATCCAACCTTAGCCTTACAGATATCGCATG
131 ACAGCATGCATAAAAATAAATAACAAAATACAGATATCCAACCTTAGCCTTACAAATATCACATG
*
112991544 CAGATCAAATCAGATATCAGAGAACAGAAAT
196 CAGATCAAATCAGATATCAGAAAACAGAAAT
112991575 CATGCCCACC
Statistics
Matches: 204, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
237 114 0.56
238 90 0.44
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (238 bp):
ATCCATAAATGTCCAACAGTGGTCACCATCGAACCCTCTACCACACCGATCCATCTACTGCTGAG
GATTACCTGACATAAAATAAATAAAGGGGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAA
ACAGCATGCATAAAAATAAATAACAAAATACAGATATCCAACCTTAGCCTTACAAATATCACATG
CAGATCAAATCAGATATCAGAAAACAGAAATGAGAAATCATTC
Found at i:112991656 original size:38 final size:38
Alignment explanation
Indices: 112991614--112991704 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 38
112991604 GTCTAACACA
*
112991614 ACACACCATGTGGGGATAAAATCGACCCACCCAGCTCT
1 ACACACCATGTGGGGATAAAATCGACCCACCCAGCCCT
* *
112991652 ACACACCAAGTATGGGGATAAAATCGACCCATCCAGCCCT
1 ACACACC-A-TGTGGGGATAAAATCGACCCACCCAGCCCT
*
112991692 ACACACCAAGTGG
1 ACACACCATGTGG
112991705 TACTGTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 10 0.22
39 2 0.04
40 34 0.74
ACGTcount: A:0.34, C:0.33, G:0.19, T:0.14
Consensus pattern (38 bp):
ACACACCATGTGGGGATAAAATCGACCCACCCAGCCCT
Found at i:112991671 original size:40 final size:40
Alignment explanation
Indices: 112991624--112991702 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
112991614 ACACACCATG
*
112991624 TGGGGATAAAATCGACCCACCCAGCTCTACACACCAAGTA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
*
112991664 TGGGGATAAAATCGACCCATCCAGCCCTACACACCAAGT
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
112991703 GGTACTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.34, C:0.33, G:0.18, T:0.15
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
Found at i:112993133 original size:20 final size:20
Alignment explanation
Indices: 112993110--112993165 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
112993100 TAAATATAAG
*
112993110 AAAATAAAAATAAAACAACT
1 AAAATAAAAATAAAAAAACT
112993130 AAAATAAAAAATAAAAAAACT
1 AAAAT-AAAAATAAAAAAACT
* *
112993151 AACATAAAACTAAAA
1 AAAATAAAAATAAAA
112993166 TTAGTGGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAATAAAAATAAAAAAACT
Found at i:112993147 original size:14 final size:13
Alignment explanation
Indices: 112993096--112993146 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
112993086 GATAATGAAT
*
112993096 AAAATAAATATAA
1 AAAATAAAAATAA
112993109 GAAAATAAAAATAA
1 -AAAATAAAAATAA
112993123 AACAACT-AAAATAA
1 AA-AA-TAAAAATAA
112993137 AAAATAAAAA
1 AAAATAAAAA
112993147 AACTAACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 23 0.70
15 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:112996851 original size:30 final size:30
Alignment explanation
Indices: 112996815--112996871 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
112996805 ATGACCATGA
* *
112996815 CACACGGGGATGTGGTTTGCCCGTGTGCCT
1 CACACGGGCATGTGGTTTACCCGTGTGCCT
*
112996845 CACACGGGCATGTGGTTTACCTGTGTG
1 CACACGGGCATGTGGTTTACCCGTGTG
112996872 GTTGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.35, T:0.28
Consensus pattern (30 bp):
CACACGGGCATGTGGTTTACCCGTGTGCCT
Found at i:112997469 original size:47 final size:44
Alignment explanation
Indices: 112997353--112997470 Score: 111
Period size: 47 Copynumber: 2.7 Consensus size: 44
112997343 ATAATGAAAT
* * *
112997353 AACAATAATAATAATCA-AAACAG-TAAAACAAATAAAAAATAA
1 AACAATAATAATAATGATAAACAGATAAAACAAAGAAAAAAAAA
* *
112997395 AA-AATAATAATAA-GATAATGATA-ATAAAACTAAGAAAAATAAAA
1 AACAATAATAATAATGATAA--ACAGATAAAACAAAGAAAAA-AAAA
112997439 CAACCAATAATAATAATGATAAACAGATAAAA
1 -AA-CAATAATAATAATGATAAACAGATAAAA
112997471 AAGCACTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
40 1 0.02
41 13 0.22
42 2 0.03
43 15 0.25
44 3 0.05
45 2 0.03
46 2 0.03
47 17 0.28
48 5 0.08
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.19
Consensus pattern (44 bp):
AACAATAATAATAATGATAAACAGATAAAACAAAGAAAAAAAAA
Found at i:112999590 original size:20 final size:20
Alignment explanation
Indices: 112999567--112999605 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
112999557 ATGAATTTAT
112999567 CAACTTTAATAAGTACATAC
1 CAACTTTAATAAGTACATAC
112999587 CAACTTTAATAAGTACATA
1 CAACTTTAATAAGTACATA
112999606 GCCATAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
CAACTTTAATAAGTACATAC
Found at i:113003829 original size:14 final size:14
Alignment explanation
Indices: 113003810--113003836 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
113003800 TTCATTTGAT
113003810 CTCATCCATCATCC
1 CTCATCCATCATCC
113003824 CTCATCCATCATC
1 CTCATCCATCATC
113003837 ATTCTCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.48, G:0.00, T:0.30
Consensus pattern (14 bp):
CTCATCCATCATCC
Found at i:113007475 original size:36 final size:36
Alignment explanation
Indices: 113007435--113007506 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
113007425 ATTCCATTTG
*
113007435 CATCATACATAATTTATATAATATTTCAAATAACTA
1 CATCATACATAATTTATATAACATTTCAAATAACTA
*
113007471 CATCATACATAATTTATATCACATTTCAAATAACTA
1 CATCATACATAATTTATATAACATTTCAAATAACTA
113007507 TCTTACCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (36 bp):
CATCATACATAATTTATATAACATTTCAAATAACTA
Found at i:113008510 original size:6 final size:6
Alignment explanation
Indices: 113008499--113008530 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
113008489 TTCTAAAATC
113008499 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
113008531 GTTATAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:113008825 original size:13 final size:13
Alignment explanation
Indices: 113008807--113008831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
113008797 ACACAAACGA
113008807 TAAAATTTTCACC
1 TAAAATTTTCACC
113008820 TAAAATTTTCAC
1 TAAAATTTTCAC
113008832 ACATATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATTTTCACC
Found at i:113027916 original size:38 final size:38
Alignment explanation
Indices: 113027868--113027945 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
113027858 ATTACTTACA
*
113027868 AACAACCATATAATAATCATTTAGGAATTTAATTTATC
1 AACAACCATATAATAATCATTTAGAAATTTAATTTATC
*
113027906 AACAACCATATAATAATCGTTTAGAAATTTAATTTATC
1 AACAACCATATAATAATCATTTAGAAATTTAATTTATC
113027944 AA
1 AA
113027946 ATAGCCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (38 bp):
AACAACCATATAATAATCATTTAGAAATTTAATTTATC
Found at i:113029125 original size:8 final size:7
Alignment explanation
Indices: 113029097--113029140 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
113029087 TCCCTGTGAG
113029097 TTTTTCT
1 TTTTTCT
113029104 TTTTTC-
1 TTTTTCT
113029110 -TTTTCT
1 TTTTTCT
113029116 TTTTTCCT
1 TTTTT-CT
113029124 TTTTT-T
1 TTTTTCT
113029130 TTTTT-T
1 TTTTTCT
113029136 TTTTT
1 TTTTT
113029141 TTAAGGGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.15
6 12 0.35
7 10 0.29
8 7 0.21
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTCT
Found at i:113034480 original size:28 final size:28
Alignment explanation
Indices: 113034439--113034494 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
113034429 AGTTCATGTT
*
113034439 CATAGTCTCGTGATTACCTTTAGCACAG
1 CATAGTCTCATGATTACCTTTAGCACAG
113034467 CATAGTCTCATGATTACCTTTAGCACAG
1 CATAGTCTCATGATTACCTTTAGCACAG
113034495 ATGAATAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (28 bp):
CATAGTCTCATGATTACCTTTAGCACAG
Found at i:113036807 original size:21 final size:18
Alignment explanation
Indices: 113036777--113036822 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
113036767 ATTTGTCTTT
*
113036777 TTTTAATTTAATATTTTTGAG
1 TTTTATTTTAA-ATTTTT--G
113036798 TTTTATTTTAAATTTTTG
1 TTTTATTTTAAATTTTTG
113036816 TTTTATT
1 TTTTATT
113036823 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTATTTTAAATTTTTG
Found at i:113036812 original size:20 final size:21
Alignment explanation
Indices: 113036777--113036815 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
113036767 ATTTGTCTTT
113036777 TTTTAATTTAATATTTTTGAG
1 TTTTAATTTAATATTTTTGAG
*
113036798 TTTTATTTTAA-ATTTTTG
1 TTTTAATTTAATATTTTTG
113036816 TTTTATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTTAATTTAATATTTTTGAG
Found at i:113039679 original size:12 final size:13
Alignment explanation
Indices: 113039656--113039681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113039646 AAAATTTTAA
113039656 AATTTTTAAAAAT
1 AATTTTTAAAAAT
113039669 AATTTTTAAAAAT
1 AATTTTTAAAAAT
113039682 GTTATAAATT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:113041438 original size:22 final size:22
Alignment explanation
Indices: 113041412--113041453 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
113041402 AACGAATCTA
**
113041412 GTTAATGGCCGACAGATCAAAT
1 GTTAATGGAAGACAGATCAAAT
113041434 GTTAATGGAAGACAGATCAA
1 GTTAATGGAAGACAGATCAA
113041454 CAAAAGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (22 bp):
GTTAATGGAAGACAGATCAAAT
Found at i:113041808 original size:22 final size:23
Alignment explanation
Indices: 113041764--113041809 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
113041754 AAAATATTTC
113041764 AATTATTATTAAATTAAATTATA
1 AATTATTATTAAATTAAATTATA
*
113041787 AATTA-TATTACATTCAAA-TATA
1 AATTATTATTAAATT-AAATTATA
113041809 A
1 A
113041810 TTTTGTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTATTATTAAATTAAATTATA
Found at i:113042556 original size:19 final size:20
Alignment explanation
Indices: 113042534--113042581 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
113042524 TTAGACATCC
113042534 TTAAATTATTATCTTT-ATT
1 TTAAATTATTATCTTTAATT
113042553 TTAAATTA--ATCTTTAAATT
1 TTAAATTATTATCTTT-AATT
*
113042572 TTAAAATATT
1 TTAAATTATT
113042582 TTAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.25
19 18 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTATTATCTTTAATT
Found at i:113042597 original size:28 final size:30
Alignment explanation
Indices: 113042549--113042604 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
113042539 TTATTATCTT
*
113042549 TATTTTAAATTAATCTTTAAATT-TTAAAA
1 TATTTTAAATTAATCTCTAAATTATTAAAA
113042578 TATTTT-AATTATATC-CTAAATTATTAA
1 TATTTTAAATTA-ATCTCTAAATTATTAA
113042605 TATTATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTAAATTAATCTCTAAATTATTAAAA
Found at i:113048106 original size:48 final size:47
Alignment explanation
Indices: 113047994--113048136 Score: 178
Period size: 48 Copynumber: 3.0 Consensus size: 47
113047984 ACGGATGAAG
*
113047994 TAGTCGGTAGTTTATCTACACGACCAGTGGTTCATCCACAACGCATTT
1 TAGTCGGTAG-TTATCTACACGACCAGTGGTTCATCCACAACGTATTT
** * * * *
113048042 TAGTCGACAGTCTATCTGCACAACTAGTGGTTCATCCACAATGTATTT
1 TAGTCGGTAGT-TATCTACACGACCAGTGGTTCATCCACAACGTATTT
* *
113048090 TAGTTGGTAGCTTATCTACATGACCAGTGGTTCATCCACAACGTATT
1 TAGTCGGTAG-TTATCTACACGACCAGTGGTTCATCCACAACGTATT
113048137 AGTAGTTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
47 1 0.01
48 76 0.97
49 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (47 bp):
TAGTCGGTAGTTATCTACACGACCAGTGGTTCATCCACAACGTATTT
Found at i:113048636 original size:17 final size:15
Alignment explanation
Indices: 113048598--113048638 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
113048588 TATTAAGAAG
*
113048598 TATTTTAGATTTTTT
1 TATTTGAGATTTTTT
113048613 TATTTGAGATTTTTGT
1 TATTTGAGATTTTT-T
113048629 TAATTTGAGA
1 T-ATTTGAGA
113048639 ATTGTATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (15 bp):
TATTTGAGATTTTTT
Found at i:113049123 original size:14 final size:14
Alignment explanation
Indices: 113049093--113049137 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
113049083 ACTCACCATT
*
113049093 TGTTTGCCAGTAAAA
1 TGTTTTCCAG-AAAA
113049108 TGTTTTCCAGAAAA
1 TGTTTTCCAGAAAA
* *
113049122 TGCTTTCTAGAAAA
1 TGTTTTCCAGAAAA
113049136 TG
1 TG
113049138 ATTTACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (14 bp):
TGTTTTCCAGAAAA
Done.