Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 4 of 259
Found at i:1002690 original size:16 final size:16
Alignment explanation
Indices: 1002669--1002736 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
1002659 TTTGGTTCGC
1002669 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1002685 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
1002701 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
1002717 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
1002733 TGTA
1 TGTA
1002737 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1002783 original size:45 final size:44
Alignment explanation
Indices: 1002717--1002807 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 44
1002707 GGATTAGAGG
* * *
1002717 TGTATTGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
1002762 TGTAATGGAATAAAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGAAATCATGTGTTTGGTTGAA
1002806 TG
1 TG
1002808 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 1 0.03
44 18 0.45
45 21 0.52
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAAAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:1002989 original size:16 final size:16
Alignment explanation
Indices: 1002952--1002993 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1002942 TTAATCATAT
*
1002952 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1002968 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1002983 TTAAAATATAT
1 TTAAAATATAT
1002994 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1003000 original size:14 final size:15
Alignment explanation
Indices: 1002961--1003002 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1002951 TTTAAACATA
*
1002961 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1002976 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1002990 A-TATAATTTAATA
1 ATTATAATTAAATA
1003003 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1003052 original size:61 final size:61
Alignment explanation
Indices: 1002987--1003174 Score: 215
Period size: 61 Copynumber: 3.1 Consensus size: 61
1002977 TTATAATTAA
1002987 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
1003048 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATATTAAAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCAAATCAT
1003107 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1003168 AATATAT
1 AATATAT
1003175 GATACTATAA
Statistics
Matches: 97, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 1 0.01
59 32 0.33
60 24 0.25
61 39 0.40
62 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:1003105 original size:120 final size:120
Alignment explanation
Indices: 1002955--1003184 Score: 451
Period size: 120 Copynumber: 1.9 Consensus size: 120
1002945 ATCATATTTA
*
1002955 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTAAAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1003020 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
1003075 AACATAATTATTATTAAATATATTAAAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTAAAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1003140 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
1003185 TTTACTCAAA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTAAAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:1003173 original size:59 final size:59
Alignment explanation
Indices: 1002990--1003173 Score: 180
Period size: 59 Copynumber: 3.1 Consensus size: 59
1002980 TAATTAAAAT
1002990 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * * * *
1003049 ATAT-ATGATACTATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATATTAAAATTAAAA
1 ATATAAT-TTA--ATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCAAA-TCATA
1003109 TATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 -ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1003169 ATATA
1 ATATA
1003174 TGATACTATA
Statistics
Matches: 93, Mismatches: 20, Indels: 24
0.68 0.15 0.18
Matches are distributed among these distances:
58 2 0.02
59 32 0.34
60 30 0.32
61 27 0.29
62 2 0.02
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
Found at i:1014514 original size:12 final size:12
Alignment explanation
Indices: 1014494--1014527 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1014484 GTTCTTGTAC
*
1014494 ATTAGATTAAAG
1 ATTAAATTAAAG
1014506 ATTAAATTAAAG
1 ATTAAATTAAAG
*
1014518 AGTAAATTAA
1 ATTAAATTAA
1014528 TCTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (12 bp):
ATTAAATTAAAG
Found at i:1027400 original size:38 final size:38
Alignment explanation
Indices: 1027321--1027404 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
1027311 TTATGCTGGA
* * * *
1027321 ATTATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGT
1 ATTATATCCGGGTTAAATCCCGCAAGCCTAGTACTGAT
* *
1027359 ATTATATCCGGGTTAAATCCCGCAAGCCTAGTGCTTAT
1 ATTATATCCGGGTTAAATCCCGCAAGCCTAGTACTGAT
1027397 ATTATATC
1 ATTATATC
1027405 TGAGTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (38 bp):
ATTATATCCGGGTTAAATCCCGCAAGCCTAGTACTGAT
Found at i:1028878 original size:21 final size:22
Alignment explanation
Indices: 1028853--1028894 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1028843 AAGATACATT
*
1028853 TTTCA-ATTTTTGAGTACCTCA
1 TTTCACATTTTGGAGTACCTCA
1028874 TTTCATCATTTTGGAGTACCT
1 TTTCA-CATTTTGGAGTACCT
1028895 TGCTGATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (22 bp):
TTTCACATTTTGGAGTACCTCA
Found at i:1032653 original size:46 final size:46
Alignment explanation
Indices: 1032593--1032703 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 46
1032583 TGTGAATTGG
* *
1032593 GACCACAAACTCCCCTTGCAAGCACACATTGGCATGTGCGAGCTGA
1 GACCGCAAGCTCCCCTTGCAAGCACACATTGGCATGTGCGAGCTGA
* *** * *
1032639 GACCGTAAGCTCCCCTTATGAGCACTCCTTGGCATGTGCGAGCTGA
1 GACCGCAAGCTCCCCTTGCAAGCACACATTGGCATGTGCGAGCTGA
*
1032685 GACCGCGAGCTCCCCTTGC
1 GACCGCAAGCTCCCCTTGC
1032704 TGACTTCTCA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (46 bp):
GACCGCAAGCTCCCCTTGCAAGCACACATTGGCATGTGCGAGCTGA
Found at i:1037477 original size:14 final size:14
Alignment explanation
Indices: 1037458--1037484 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1037448 GACTTTTTTT
1037458 TTTTTTATAAACAC
1 TTTTTTATAAACAC
1037472 TTTTTTATAAACA
1 TTTTTTATAAACA
1037485 TTCTAACATA
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:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTTTATAAACAC
Found at i:1039342 original size:29 final size:28
Alignment explanation
Indices: 1039287--1039360 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
1039277 TTTTTATTTG
* * *
1039287 ATTTTATAT-ATTATATATCATATTTAA
1 ATTTAATATAATTATATATAAAATTTAA
*
1039314 ATTTGATATAATTATATATAAAACTTTAA
1 ATTTAATATAATTATATATAAAA-TTTAA
*
1039343 TTTTAAT-TAAATTATATA
1 ATTTAATAT-AATTATATA
1039361 CATATTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 8 0.21
28 12 0.31
29 19 0.49
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTAATATAATTATATATAAAATTTAA
Found at i:1041790 original size:21 final size:22
Alignment explanation
Indices: 1041764--1041810 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1041754 CTCTGCTCAA
*
1041764 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1041785 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1041807 ACTC
1 ACTC
1041811 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1048919 original size:42 final size:42
Alignment explanation
Indices: 1048806--1048929 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 42
1048796 AGTACCGTAC
* *
1048806 CAATGTCATATCTCAGATATGGTCTTACATGTAATCTCGTAT
1 CAATGTCATATCTCAGATATGGTCTTACACGTAATCTCATAT
* * *
1048848 CAATGCCAATAGCCCA-ATTATGGTCTTACACG-AAGTCTCATAT
1 CAATGTC-ATATCTCAGA-TATGGTCTTACACGTAA-TCTCATAT
* *
1048891 CGATGTCATATCTCAGATATGGTCTTACATGTAATCTCA
1 CAATGTCATATCTCAGATATGGTCTTACACGTAATCTCA
1048930 GTAACCCTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
42 33 0.49
43 34 0.51
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (42 bp):
CAATGTCATATCTCAGATATGGTCTTACACGTAATCTCATAT
Found at i:1050745 original size:32 final size:32
Alignment explanation
Indices: 1050709--1050769 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1050699 TCATAAACTT
* *
1050709 ATAAATTGATTACTTGAATTTAATAACTCGTG
1 ATAAATTAATTAATTGAATTTAATAACTCGTG
* *
1050741 ATAAATTAATTAATTTAATTTGATAACTC
1 ATAAATTAATTAATTGAATTTAATAACTC
1050770 ATATTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCGTG
Found at i:1058139 original size:18 final size:18
Alignment explanation
Indices: 1058118--1058162 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1058108 CATTCTTCTC
1058118 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
1058136 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
1058154 CCCTTTCCC
1 CCCTTTCCC
1058163 GTTTCGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CCCTTTCCCCTTCTCCTT
Found at i:1059337 original size:35 final size:34
Alignment explanation
Indices: 1059298--1059363 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1059288 CAAACACCAG
*
1059298 AAAACATTTTCCAGTAAGTCATTTTACAGAAATAT
1 AAAACATTTTCCAG-AAATCATTTTACAGAAATAT
* *
1059333 AAAACATTTTCCAGAAATTATTTTACGGAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAA
1059364 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAATAT
Found at i:1060390 original size:22 final size:22
Alignment explanation
Indices: 1060347--1060391 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1060337 AATTCATGAG
**
1060347 AGGTTAAGCAAAATTATTTTTA
1 AGGTTAAGCAAAATTAGCTTTA
1060369 AGGTTAAGCAAAATTAGCTTTA
1 AGGTTAAGCAAAATTAGCTTTA
1060391 A
1 A
1060392 AATTATAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGTTAAGCAAAATTAGCTTTA
Found at i:1061026 original size:35 final size:33
Alignment explanation
Indices: 1060978--1061043 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
1060968 AAAAATACTA
1060978 AAAAAATAAAAAAAAACAACACAAAATGGAAATAC
1 AAAAAATAAAAAAAAACAACA-AAAAT-GAAATAC
** * *
1061013 AAAAAATCCAAAAAATCAAGAAAAATGAAAT
1 AAAAAATAAAAAAAAACAACAAAAATGAAAT
1061044 CTTTGAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 5 0.19
34 5 0.19
35 17 0.63
ACGTcount: A:0.73, C:0.11, G:0.06, T:0.11
Consensus pattern (33 bp):
AAAAAATAAAAAAAAACAACAAAAATGAAATAC
Found at i:1062974 original size:25 final size:26
Alignment explanation
Indices: 1062932--1062980 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1062922 ATTATTATTA
*
1062932 AAAGTAAAGTAAATAG-AAAGAAAAT
1 AAAGTAAAGTAAAAAGAAAAGAAAAT
1062957 AAAGTAAAG-AACAAAGAAAAGAAA
1 AAAGTAAAGTAA-AAAGAAAAGAAA
1062981 CAGAATAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 12 0.57
26 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAGTAAAGTAAAAAGAAAAGAAAAT
Found at i:1063681 original size:21 final size:21
Alignment explanation
Indices: 1063642--1063681 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1063632 TTAAATTTGG
*
1063642 AAAATCATTATAAATTGTACA
1 AAAATCATTATAAAGTGTACA
* *
1063663 AAAATTATTATGAAGTGTA
1 AAAATCATTATAAAGTGTA
1063682 ATTTATATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAATCATTATAAAGTGTACA
Found at i:1064695 original size:23 final size:23
Alignment explanation
Indices: 1064665--1064737 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 23
1064655 GCTTTATCGA
* *
1064665 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
1064688 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
1064709 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
1064731 T-AGGCAC
1 TCAGGCAC
1064738 TTTATGTACT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 26 0.58
22 1 0.02
23 18 0.40
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:1064712 original size:21 final size:21
Alignment explanation
Indices: 1064677--1064737 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
1064667 AGGCACTTTA
1064677 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1064700 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
1064721 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
1064738 TTTATGTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.75
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1066003 original size:23 final size:23
Alignment explanation
Indices: 1065972--1066016 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1065962 TATAACATTA
*
1065972 CAAGTAATGAGTGACATCTTAGT
1 CAAGCAATGAGTGACATCTTAGT
*
1065995 CAAGCAATGAGTGACATTTTAG
1 CAAGCAATGAGTGACATCTTAG
1066017 CAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (23 bp):
CAAGCAATGAGTGACATCTTAGT
Found at i:1070616 original size:28 final size:27
Alignment explanation
Indices: 1070563--1070616 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1070553 ATATATACAA
* *
1070563 TATAAAAATATATAAAAGAATTAGTAT
1 TATAAAAATATATAAAAAAATGAGTAT
1070590 TATAAAAA-ATATAAAATAAAGTGAGTA
1 TATAAAAATATATAAAA-AAA-TGAGTA
1070617 ATTGTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 10 0.43
28 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (27 bp):
TATAAAAATATATAAAAAAATGAGTAT
Found at i:1070753 original size:16 final size:15
Alignment explanation
Indices: 1070723--1070771 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
1070713 AACATAAATA
*
1070723 ATATAATA-GATGAT
1 ATATAATATAATGAT
*
1070737 ATATGATATACATGAT
1 ATATAATATA-ATGAT
1070753 ATATAATATAAT-AT
1 ATATAATATAATGAT
1070767 ATATA
1 ATATA
1070772 CATGCATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 14 0.47
15 2 0.07
16 14 0.47
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (15 bp):
ATATAATATAATGAT
Found at i:1070791 original size:25 final size:25
Alignment explanation
Indices: 1070735--1070791 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
1070725 ATAATAGATG
* *
1070735 ATATATGATATACATGATATATAAT
1 ATATATGATATACATGATAGAAAAT
1070760 ATAATAT-ATATACATGCATAGAAAAT
1 AT-ATATGATATACATG-ATAGAAAAT
1070786 ATATAT
1 ATATAT
1070792 TTGAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (25 bp):
ATATATGATATACATGATAGAAAAT
Found at i:1071165 original size:22 final size:21
Alignment explanation
Indices: 1071139--1071181 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1071129 AAATTAAATC
1071139 TCAAGATTACAAGATCATATCT
1 TCAAGATTAC-AGATCATATCT
* *
1071161 TCAAGATTGCATATCATATCT
1 TCAAGATTACAGATCATATCT
1071182 AAGATTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
TCAAGATTACAGATCATATCT
Found at i:1071187 original size:19 final size:19
Alignment explanation
Indices: 1071152--1071211 Score: 88
Period size: 17 Copynumber: 3.2 Consensus size: 19
1071142 AGATTACAAG
1071152 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
1071173 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
1071190 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1071209 ATC
1 ATC
1071212 CTTAAAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.46
19 11 0.30
20 1 0.03
21 8 0.22
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:1071666 original size:43 final size:43
Alignment explanation
Indices: 1071568--1071669 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
1071558 GCGATATCTA
**
1071568 CTATCTTTGATCTGCT-CCCGTTAATACAGAGACGCCAAATTG
1 CTATCTTCAATCTGCTCCCCGTTAATACAGAGACGCCAAATTG
* * *
1071610 TTATTTTCGATCTGCTCCCCGTCTAATACA-AGACGCCAAATTTG
1 CTATCTTCAATCTGCTCCCCGT-TAATACAGAGACGCCAAA-TTG
1071654 CT-TCTTCAATCTGCTC
1 CTATCTTCAATCTGCTC
1071670 TTGCAAACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.25
43 27 0.53
44 11 0.22
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (43 bp):
CTATCTTCAATCTGCTCCCCGTTAATACAGAGACGCCAAATTG
Found at i:1072098 original size:42 final size:42
Alignment explanation
Indices: 1072016--1072124 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 42
1072006 ACAGGTGAAA
* * *
1072016 GCCAAATCAGCTATGTCTTTGATCTGCTCTCGCCAATACAGAGAT
1 GCCAAATCTGCTA--TCTTCGAT-TGCTCTCGACAATACAGAGAT
1072061 GCCAAATCTG-TATCTTCGATTGCTCTCTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATTGCTCTC-GACAATACAGAGAT
1072103 GCCAAATCTGCTATCTTC-ATTG
1 GCCAAATCTGCTATCTTCGATTG
1072125 TTCCCTATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
41 7 0.12
42 34 0.58
43 7 0.12
44 2 0.03
45 9 0.15
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (42 bp):
GCCAAATCTGCTATCTTCGATTGCTCTCGACAATACAGAGAT
Found at i:1072318 original size:79 final size:84
Alignment explanation
Indices: 1072107--1072396 Score: 336
Period size: 85 Copynumber: 3.5 Consensus size: 84
1072097 AGAGATGCCA
* * *
1072107 AATCTGCTATCTTC-AT-TGTTCCCTATAAACACA-GGATGCCATGCTGAAATCCTCGATCTGCT
1 AATCTTCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCATACTGAAATCTTC-ATCTGC-
*
1072169 TCGCTGTAAGCACA-GA-GTGC
64 TCACTGTAAGCACAGGATGT-C
*
1072189 AGATCTT-TATCTTCGATCTGTTCCCTATAAACACAGGGATGTCATACTG-AATC-T-ATCT-C-
1 A-ATCTTCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCATACTGAAATCTTCATCTGCT
1072248 CACT-TAAGCACAGGATGTC
65 CACTGTAAGCACAGGATGTC
*
1072267 AATCTTCTATCTTCGATCTTGTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGC
1 AATCTTCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCATACTGAAATCTTC-ATCTGC
* *
1072332 TTCGCTGTAAG-ACAGAATGTC
64 -TCACTGTAAGCACAGGATGTC
* *
1072353 AATCTGCTATCTTCGATCTGTTCCCTATAAACACAAGGATGCCA
1 AATCTTCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCA
1072397 AATCTTGTTT
Statistics
Matches: 182, Mismatches: 10, Indels: 29
0.82 0.05 0.13
Matches are distributed among these distances:
77 13 0.07
78 18 0.10
79 31 0.17
80 5 0.03
81 5 0.03
82 8 0.04
83 11 0.06
84 22 0.12
85 36 0.20
86 29 0.16
87 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (84 bp):
AATCTTCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCATACTGAAATCTTCATCTGCTC
ACTGTAAGCACAGGATGTC
Found at i:1073321 original size:18 final size:19
Alignment explanation
Indices: 1073293--1073335 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1073283 TCTATTTTTT
1073293 TTTTTTA-TTT-TTTTTCC
1 TTTTTTATTTTCTTTTTCC
*
1073310 TCTTTTTCTTTTCTTTTTCC
1 T-TTTTTATTTTCTTTTTCC
1073330 TTTTTT
1 TTTTTT
1073336 TTGAAACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 5 0.23
19 8 0.36
20 8 0.36
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTATTTTCTTTTTCC
Found at i:1079793 original size:16 final size:16
Alignment explanation
Indices: 1079772--1079802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1079762 AATATAATAG
1079772 ATGATATACAATATAC
1 ATGATATACAATATAC
*
1079788 ATGATATATAATATA
1 ATGATATACAATATA
1079803 ATATATATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
ATGATATACAATATAC
Found at i:1080230 original size:19 final size:19
Alignment explanation
Indices: 1080182--1080293 Score: 138
Period size: 19 Copynumber: 5.8 Consensus size: 19
1080172 AAATTAAATC
* *
1080182 TCTAAGATTACAAGATCATA
1 TCTAAGATTGC-ATATCATA
1080202 TCTTCAAGATTGCATATCATA
1 TC-T-AAGATTGCATATCATA
* *
1080223 TCCAAGATTGCATGTCATA
1 TCTAAGATTGCATATCATA
1080242 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
1080259 TCTAAGATTGCATATCGTA
1 TCTAAGATTGCATATCATA
1080278 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1080294 CTTAAAGATT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
17 16 0.20
19 46 0.57
20 2 0.02
21 10 0.12
22 7 0.09
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1080259 original size:36 final size:37
Alignment explanation
Indices: 1080196--1080293 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 37
1080186 AGATTACAAG
1080196 ATCATATCTTCAAGATTGCATATCATATCCAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCCAAGATTGCAT
* *
1080236 GTCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCCAAGATTGCAT
*
1080272 ATCGTATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
1080294 CTTAAAGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
36 33 0.63
38 11 0.21
39 1 0.02
40 7 0.13
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCCAAGATTGCAT
Found at i:1080293 original size:14 final size:15
Alignment explanation
Indices: 1080235--1080274 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
1080225 CAAGATTGCA
1080235 TGTCATATCTAAGAT
1 TGTCATATCTAAGAT
1080250 TGTATCATATCTAAGAT
1 TG--TCATATCTAAGAT
1080267 TG-CATATC
1 TGTCATATC
1080275 GTATCTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
17 15 0.65
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (15 bp):
TGTCATATCTAAGAT
Found at i:1080303 original size:17 final size:19
Alignment explanation
Indices: 1080207--1080303 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 19
1080197 TCATATCTTC
* *
1080207 AAGATTGCATATCATATCC
1 AAGATTGCATATCCTATCA
* * *
1080226 AAGATTGCATGTCATATCT
1 AAGATTGCATATCCTATCA
* *
1080245 AAGATTG--TATCATATCT
1 AAGATTGCATATCCTATCA
* *
1080262 AAGATTGCATATCGTATCT
1 AAGATTGCATATCCTATCA
1080281 AAGATTGCATATCCT-T-A
1 AAGATTGCATATCCTATCA
1080298 AAGATT
1 AAGATT
1080304 ATATTTCCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
17 22 0.31
18 1 0.01
19 47 0.67
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCCTATCA
Found at i:1081183 original size:44 final size:44
Alignment explanation
Indices: 1081108--1081215 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
1081098 ACAGGTGAAA
* * *
1081108 GCCAAATCAGCTATGTCTTCGATCTGCTCTCTGCCAATACAGAGAT
1 GCCAAATCTGCTA--TCTTCGATCTGATCTCTGACAATACAGAGAT
* *
1081154 GCCAAATCTGCTATCTTCGATGTGATCTCTGACAATATAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGATCTCTGACAATACAGAGAT
1081198 GCCAAATCTGCTATCTTC
1 GCCAAATCTGCTATCTTC
1081216 AACTTGTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 45 0.79
46 12 0.21
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATCTGATCTCTGACAATACAGAGAT
Found at i:1081240 original size:44 final size:44
Alignment explanation
Indices: 1081146--1081470 Score: 265
Period size: 44 Copynumber: 7.4 Consensus size: 44
1081136 CTCTGCCAAT
* * * * *
1081146 ACAGAGATGCCAAATCTGCTATCTTCGATGTGATCTCTGA-CAAT
1 ACAGAGATGCCAAATCTGCTATCTTCGATCTGTTCCCT-ATAAAC
* *
1081190 ATAGAGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGAGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * * *
1081234 ACAGAGATGCC--ATGCTGAAATCCTCGATCTGCTTCGCTGTAAGC
1 ACAGAGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* **
1081278 ACA-AGAGTGCCAGATCTATTATCTTCGATCTGTTCCCTATAAAC
1 ACAGAGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
1081322 ACAGGGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGAGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
* ** * * *
1081366 ACAGGGATGCC--ATGCTGAAATCTTCGATCTGCTTCGCTGTAAGC
1 ACAGAGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
*
1081410 ACAG-GAATGTCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
1 ACAGAG-ATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
1081454 ACA-AGGATGCCAAATCT
1 ACAGA-GATGCCAAATCT
1081471 TGTTTCTTTG
Statistics
Matches: 223, Mismatches: 40, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
42 4 0.02
43 29 0.13
44 155 0.70
45 31 0.14
46 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
ACAGAGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
Found at i:1081333 original size:132 final size:132
Alignment explanation
Indices: 1081195--1081470 Score: 471
Period size: 132 Copynumber: 2.1 Consensus size: 132
1081185 ACAATATAGA
1081195 GATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGAGATGCCATGCTGAAATCCTCG
1 GATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGAGATGCCATGCTGAAATCCTCG
* * *
1081260 ATCTGCTTCGCTGTAAGCACAAGAGTGCCAGATCTATTATCTTCGATCTGTTCCCTATAAACACA
66 ATCTGCTTCGCTGTAAGCACAAGAATGCCAAATCTACTATCTTCGATCTGTTCCCTATAAACACA
*
1081325 GG
131 AG
* *
1081327 GATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCG
1 GATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGAGATGCCATGCTGAAATCCTCG
* * *
1081392 ATCTGCTTCGCTGTAAGCACAGGAATGTCAAATCTGCTATCTTCGATCTGTTCCCTATAAACACA
66 ATCTGCTTCGCTGTAAGCACAAGAATGCCAAATCTACTATCTTCGATCTGTTCCCTATAAACACA
1081457 AG
131 AG
1081459 GATGCCAAATCT
1 GATGCCAAATCT
1081471 TGTTTCTTTG
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (132 bp):
GATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGAGATGCCATGCTGAAATCCTCG
ATCTGCTTCGCTGTAAGCACAAGAATGCCAAATCTACTATCTTCGATCTGTTCCCTATAAACACA
AG
Found at i:1088898 original size:16 final size:15
Alignment explanation
Indices: 1088857--1088908 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 15
1088847 TGAAACATAA
1088857 ATAATATAATAGATGAT
1 ATAATATAAT-GAT-AT
1088874 ATACGATATACATGATAT
1 ATA--ATATA-ATGATAT
1088892 ATAATATAAT-ATAT
1 ATAATATAATGATAT
1088906 ATA
1 ATA
1088909 CATGCATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 5 0.16
17 3 0.09
18 5 0.16
19 8 0.25
20 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (15 bp):
ATAATATAATGATAT
Found at i:1089306 original size:22 final size:21
Alignment explanation
Indices: 1089276--1089341 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
1089266 TACAAATTAA
1089276 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
1089298 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
1089319 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
1089338 ATCT
1 ATCT
1089342 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:1089328 original size:19 final size:19
Alignment explanation
Indices: 1089293--1089387 Score: 158
Period size: 19 Copynumber: 5.0 Consensus size: 19
1089283 AGATTACAAG
1089293 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
1089314 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1089333 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
1089350 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1089369 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1089388 TTCCTTAAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.24
19 46 0.64
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:1089335 original size:14 final size:15
Alignment explanation
Indices: 1089315--1089371 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
1089305 AGATTGCATA
1089315 TCATATCTAAGATTG
1 TCATATCTAAGATTG
1089330 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
1089349 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
1089366 -CATATC
1 TCATATC
1089372 ATATCTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:1089357 original size:36 final size:37
Alignment explanation
Indices: 1089293--1089384 Score: 150
Period size: 36 Copynumber: 2.4 Consensus size: 37
1089283 AGATTACAAG
1089293 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
1089333 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
1089369 ATCATATCTAAGATTG
1 ATCATATCTAAGATTG
1089385 CATTTCCTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
36 36 0.69
38 7 0.13
39 1 0.02
40 8 0.15
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:1106092 original size:17 final size:17
Alignment explanation
Indices: 1106065--1106108 Score: 79
Period size: 17 Copynumber: 2.5 Consensus size: 17
1106055 CCATTCTTCC
1106065 CCCTTTCCCCTTCTCCTT
1 CCCTTT-CCCTTCTCCTT
1106083 CCCTTTCCCTTCTCCTT
1 CCCTTTCCCTTCTCCTT
1106100 CCCTTTCCC
1 CCCTTTCCC
1106109 GTTTCGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (17 bp):
CCCTTTCCCTTCTCCTT
Found at i:1108277 original size:20 final size:20
Alignment explanation
Indices: 1108237--1108277 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1108227 AATTCATGAG
*
1108237 AGGTTAAGCAAAATTATTTA
1 AGGTTAAGCAAAATTACTTA
1108257 AGGTTAAGC-AAATTAGCTTA
1 AGGTTAAGCAAAATTA-CTTA
1108277 A
1 A
1108278 AATATAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (20 bp):
AGGTTAAGCAAAATTACTTA
Found at i:1108891 original size:34 final size:33
Alignment explanation
Indices: 1108838--1108908 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
1108828 ATATTAATAA
*
1108838 AAATACTAAAAATAAAAAAAA-CAACACAAAATGG
1 AAATACAAAAAATAAAAAAAATCAACA-AAAAT-G
** *
1108872 AAATACAAAAAATCCAAAAAATCAAGAAAAATG
1 AAATACAAAAAATAAAAAAAATCAACAAAAATG
1108905 AAAT
1 AAAT
1108909 CTTTGAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 5 0.16
34 23 0.72
35 4 0.12
ACGTcount: A:0.70, C:0.11, G:0.06, T:0.13
Consensus pattern (33 bp):
AAATACAAAAAATAAAAAAAATCAACAAAAATG
Found at i:1110831 original size:25 final size:26
Alignment explanation
Indices: 1110789--1110837 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1110779 ATTATTATTA
*
1110789 AAAGTAAAGTAAATAG-AAAGAAAAT
1 AAAGTAAAGTAAAAAGAAAAGAAAAT
1110814 AAAGTAAAG-AACAAAGAAAAGAAA
1 AAAGTAAAGTAA-AAAGAAAAGAAA
1110838 CAGAATAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 12 0.57
26 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAGTAAAGTAAAAAGAAAAGAAAAT
Found at i:1111540 original size:21 final size:21
Alignment explanation
Indices: 1111501--1111540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1111491 TTAAATTTGG
*
1111501 AAAATCATTATAAATTGTACA
1 AAAATCATTATAAAGTGTACA
* *
1111522 AAAATTATTATGAAGTGTA
1 AAAATCATTATAAAGTGTA
1111541 ATTTATATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAATCATTATAAAGTGTACA
Found at i:1112551 original size:23 final size:23
Alignment explanation
Indices: 1112521--1112593 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 23
1112511 GCTTTATCGA
* *
1112521 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
1112544 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
1112565 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
1112587 T-AGGCAC
1 TCAGGCAC
1112594 TTTATGTACT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 26 0.58
22 1 0.02
23 18 0.40
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:1112568 original size:21 final size:21
Alignment explanation
Indices: 1112533--1112593 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
1112523 AGGCACTTTA
1112533 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1112556 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
1112577 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
1112594 TTTATGTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.75
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1113871 original size:23 final size:23
Alignment explanation
Indices: 1113840--1113884 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1113830 TATAACATTA
*
1113840 CAAGTAATGAGTGACATCTTAGT
1 CAAGCAATGAGTGACATCTTAGT
*
1113863 CAAGCAATGAGTGACATTTTAG
1 CAAGCAATGAGTGACATCTTAG
1113885 CAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (23 bp):
CAAGCAATGAGTGACATCTTAGT
Found at i:1118666 original size:16 final size:15
Alignment explanation
Indices: 1118636--1118684 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
1118626 AACATAAATA
*
1118636 ATATAATA-GATGAT
1 ATATAATATAATGAT
*
1118650 ATATGATATACATGAT
1 ATATAATATA-ATGAT
1118666 ATATAATATAAT-AT
1 ATATAATATAATGAT
1118680 ATATA
1 ATATA
1118685 CATGCATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 14 0.47
15 2 0.07
16 14 0.47
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (15 bp):
ATATAATATAATGAT
Found at i:1118704 original size:25 final size:25
Alignment explanation
Indices: 1118648--1118704 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
1118638 ATAATAGATG
* *
1118648 ATATATGATATACATGATATATAAT
1 ATATATGATATACATGATAGAAAAT
1118673 ATAATAT-ATATACATGCATAGAAAAT
1 AT-ATATGATATACATG-ATAGAAAAT
1118699 ATATAT
1 ATATAT
1118705 TTGAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (25 bp):
ATATATGATATACATGATAGAAAAT
Found at i:1119082 original size:22 final size:21
Alignment explanation
Indices: 1119052--1119098 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1119042 TACAAATTAA
1119052 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
1119074 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
1119095 ATCT
1 ATCT
1119099 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:1119104 original size:19 final size:19
Alignment explanation
Indices: 1119069--1119128 Score: 88
Period size: 17 Copynumber: 3.2 Consensus size: 19
1119059 AGATTACAAG
1119069 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
1119090 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
1119107 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1119126 ATC
1 ATC
1119129 CTTAAAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.46
19 11 0.30
20 1 0.03
21 8 0.22
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:1120015 original size:44 final size:44
Alignment explanation
Indices: 1119944--1120057 Score: 165
Period size: 44 Copynumber: 2.5 Consensus size: 44
1119934 ACACGTGAAA
* * *
1119944 GCCAAATCAGCTATGTCTTTGATCTGCTCTCCGCCAATACAGAGAT
1 GCCAAATCTGCTA--TCTTCGATCTGCTCTCCGACAATACAGAGAT
* *
1119990 GCCAAATCTGGTATCTTCGATCTGCTCTCTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCCGACAATACAGAGAT
1120034 GCCAAATCTGCTATCTTCGATCTG
1 GCCAAATCTGCTATCTTCGATCTG
1120058 TTCCCTATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
44 51 0.82
46 11 0.18
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATCTGCTCTCCGACAATACAGAGAT
Found at i:1120161 original size:44 final size:44
Alignment explanation
Indices: 1119995--1120430 Score: 359
Period size: 44 Copynumber: 9.9 Consensus size: 44
1119985 GAGATGCCAA
* * * * * * * *
1119995 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGTCAG
* *
1120039 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGAAG-C-C
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAG
** * * ** *
1120081 ATGCTGAAATCCTCGATCTGCTTCGCTGCAAGCACA-GGAGTGTCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGA-TGTCAG
* * *
1120127 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAG
* *
1120171 ATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATGTCAT
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGTCAG
** * * * * *
1120215 A-CTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAG
1 ATCTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGATGTCAG
* *
1120259 ATCTTCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAG
* *
1120303 ATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATG-C-C
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGTCAG
** * * * * *
1120345 ATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACATGAATGTCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGATGTCAG
*
1120391 ATCTGCTATCTTCGATCTGTTTCCTATAAACACAGGGATG
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATG
1120431 CCAAATCTTG
Statistics
Matches: 307, Mismatches: 68, Indels: 34
0.75 0.17 0.08
Matches are distributed among these distances:
42 4 0.01
43 45 0.15
44 207 0.67
45 47 0.15
46 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAG
Found at i:1120173 original size:132 final size:132
Alignment explanation
Indices: 1119995--1120438 Score: 669
Period size: 132 Copynumber: 3.4 Consensus size: 132
1119985 GAGATGCCAA
* * * * * * *
1119995 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCAAATCTGCTATCTTCGA-TCTG
1 ATCTGTTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGCCAAATCTGCTATCTTCAACT-TG
* * * *
1120058 TTCCCTATAAACACAGGGAAGCCATGCTGAAATCCTCGATCTGCTTCGCTGCAAGCACAGGAGTG
64 TTCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATG
1120123 TCAG
129 TCAG
1120127 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* * * *
1120192 CCCTATAAACACAGGGATGTCATACTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGTC
1120257 AG
131 AG
*
1120259 ATCT-TCTATCTTCGATCTGTTCCCTATAAACACAGGGATGTCAAATCTGCTATCTTCAACTTGT
1 ATCTGT-TATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGT
*
1120323 TCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACATGAATGT
65 TCCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGT
1120388 CAG
130 CAG
* *
1120391 ATCTGCTATCTTCGATCTGTTTCCTATAAACACAGGGATGCCAAATCT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
1120439 TGTTTCTTTG
Statistics
Matches: 284, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
131 2 0.01
132 281 0.99
133 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGTC
AG
Found at i:1121350 original size:11 final size:11
Alignment explanation
Indices: 1121329--1121370 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
1121319 CCTCTCCATT
1121329 TTTTCTTTTTTC
1 TTTT-TTTTTTC
1121341 TTTTTTTTTTC
1 TTTTTTTTTTC
1121352 TCTTTTTCTTTTC
1 T-TTTTT-TTTTC
1121365 TTTTTT
1 TTTTTT
1121371 CCTTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.29
12 14 0.50
13 6 0.21
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1121350 original size:13 final size:13
Alignment explanation
Indices: 1121327--1121376 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1121317 GGCCTCTCCA
1121327 TTTTTTCTTTT-T
1 TTTTTTCTTTTCT
*
1121339 TCTTTTTTTTTTCT
1 T-TTTTTCTTTTCT
*
1121353 CTTTTTCTTTTCT
1 TTTTTTCTTTTCT
*
1121366 TTTTTCCTTTT
1 TTTTTTCTTTT
1121377 TTTGAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 1 0.03
13 29 0.94
14 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:1121357 original size:19 final size:20
Alignment explanation
Indices: 1121327--1121377 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
1121317 GGCCTCTCCA
1121327 TTTTTTCT-TTTTTCTTTT-
1 TTTTTTCTCTTTTTCTTTTC
1121345 TTTTTTCTCTTTTTCTTTTC
1 TTTTTTCTCTTTTTCTTTTC
1121365 TTTTTTC-CTTTTT
1 TTTTTTCTCTTTTT
1121378 TTGAAATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.26
19 16 0.52
20 7 0.23
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTCTCTTTTTCTTTTC
Found at i:1127728 original size:29 final size:28
Alignment explanation
Indices: 1127673--1127728 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1127663 GATATACACA
* *
1127673 ATATAAAAATATATAAAAGAATTAGTAT
1 ATATAAAAATATATAAAAAAATGAGTAT
1127701 ATATAAAAA-ATATAAAATAAAGTGAGTA
1 ATATAAAAATATATAAAA-AAA-TGAGTA
1127729 ATTGTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 11 0.46
29 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (28 bp):
ATATAAAAATATATAAAAAAATGAGTAT
Found at i:1128283 original size:22 final size:21
Alignment explanation
Indices: 1128253--1128318 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
1128243 TACAAATTAA
1128253 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
1128275 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
1128296 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
1128315 ATCT
1 ATCT
1128319 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:1128305 original size:19 final size:19
Alignment explanation
Indices: 1128270--1128348 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
1128260 AGATTACAAG
1128270 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
1128291 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1128310 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
1128327 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
1128346 ATC
1 ATC
1128349 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
20 1 0.02
21 8 0.14
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:1128312 original size:14 final size:15
Alignment explanation
Indices: 1128292--1128348 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
1128282 AGATTGCATA
1128292 TCATATCTAAGATTG
1 TCATATCTAAGATTG
1128307 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
1128326 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
1128343 -CATATC
1 TCATATC
1128349 CTTAAAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:1128334 original size:36 final size:39
Alignment explanation
Indices: 1128270--1128348 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 39
1128260 AGATTACAAG
1128270 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTG-ATATCATATCTAAGATTGCAT
1128310 ATCATATC-T-AAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
1128346 ATC
1 ATC
1128349 CTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
39 1 0.03
40 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (39 bp):
ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
Found at i:1129656 original size:43 final size:43
Alignment explanation
Indices: 1129595--1129680 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
1129585 CTTTAGAATG
*
1129595 TAAGTTGTTGTCTTTAGAGGCACTAACCAAATAAGCACTTTTA
1 TAAGTTGTTGTCTTTAGAGGCACTAACAAAATAAGCACTTTTA
*
1129638 TAAGTTGTTGTCTTTAGAGGCACTAACAAAATGAGCACTTTTA
1 TAAGTTGTTGTCTTTAGAGGCACTAACAAAATAAGCACTTTTA
1129681 GACTTATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (43 bp):
TAAGTTGTTGTCTTTAGAGGCACTAACAAAATAAGCACTTTTA
Found at i:1145542 original size:15 final size:16
Alignment explanation
Indices: 1145516--1145548 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1145506 CTGGAACTGT
*
1145516 TTATGACATTCATTTA
1 TTATGACATTCATGTA
1145532 TTATG-CATTCATGTA
1 TTATGACATTCATGTA
1145547 TT
1 TT
1145549 TCTATGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (16 bp):
TTATGACATTCATGTA
Found at i:1149188 original size:17 final size:17
Alignment explanation
Indices: 1149162--1149219 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
1149152 AGTGGTAAAA
*
1149162 GAAGATGAAAAGAAGAT
1 GAAGAAGAAAAGAAGAT
1149179 GAAGAAGAAAAGAAGCAT
1 GAAGAAGAAAAGAAG-AT
*
1149197 -AAGGAG-AAA-AAGAT
1 GAAGAAGAAAAGAAGAT
1149211 GAAG-AGAAA
1 GAAGAAGAAA
1149220 GATGAGAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 4 0.11
15 8 0.22
16 3 0.08
17 19 0.53
18 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07
Consensus pattern (17 bp):
GAAGAAGAAAAGAAGAT
Found at i:1149193 original size:11 final size:11
Alignment explanation
Indices: 1149158--1149187 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1149148 AAGAAGTGGT
1149158 AAAAGAAGATG
1 AAAAGAAGATG
1149169 AAAAGAAGATG
1 AAAAGAAGATG
1149180 AAGAAGAA
1 AA-AAGAA
1149188 AAGAAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (11 bp):
AAAAGAAGATG
Found at i:1149229 original size:29 final size:31
Alignment explanation
Indices: 1149168--1149236 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
1149158 AAAAGAAGAT
*
1149168 GAAAAGAAGATGAAGAAGAAAAGAAGCATAAG
1 GAAAA-AAGATGAAGAAGAAAAGAAGCAGAAG
*
1149200 GAGAAAAAGATGAAG-AG-AAAGATG-AGAAG
1 GA-AAAAAGATGAAGAAGAAAAGAAGCAGAAG
1149229 GAAAAAAG
1 GAAAAAAG
1149237 TAAAACCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 6 0.18
29 6 0.18
30 6 0.18
31 2 0.06
32 11 0.32
33 3 0.09
ACGTcount: A:0.62, C:0.01, G:0.30, T:0.06
Consensus pattern (31 bp):
GAAAAAAGATGAAGAAGAAAAGAAGCAGAAG
Found at i:1150788 original size:10 final size:10
Alignment explanation
Indices: 1150773--1150806 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1150763 CACATTTCAT
1150773 AAAAAATTTA
1 AAAAAATTTA
*
1150783 AAAAAATTCA
1 AAAAAATTTA
*
1150793 ACAAAATTTA
1 AAAAAATTTA
1150803 AAAA
1 AAAA
1150807 CTTTCATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:1150821 original size:20 final size:20
Alignment explanation
Indices: 1150766--1150821 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1150756 CCATGTACAC
1150766 ATTTCATAAAAAATTTAAAAA
1 ATTTCAT-AAAAATTTAAAAA
*
1150787 AATTCA-ACAAAATTTAAAAA
1 ATTTCATA-AAAATTTAAAAA
* *
1150807 CTTTCATAAAGATTT
1 ATTTCATAAAAATTT
1150822 TTAGAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.76
21 6 0.21
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (20 bp):
ATTTCATAAAAATTTAAAAA
Found at i:1151332 original size:12 final size:12
Alignment explanation
Indices: 1151315--1151367 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
1151305 TAAAAACATA
1151315 AAAACAAATATT
1 AAAACAAATATT
1151327 AAAACAAATA--
1 AAAACAAATATT
1151337 AAAA-ATAATATT
1 AAAACA-AATATT
* *
1151349 AAAACAATTCTT
1 AAAACAAATATT
1151361 AAAACAA
1 AAAACAA
1151368 TACACAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 1 0.03
10 8 0.23
12 25 0.71
13 1 0.03
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAACAAATATT
Found at i:1151340 original size:22 final size:22
Alignment explanation
Indices: 1151304--1151355 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1151294 TAAAATACGT
*
1151304 TTAAAA-ACATAAAAACA-AATA
1 TTAAAACAAATAAAAA-ATAATA
1151325 TTAAAACAAATAAAAAATAATA
1 TTAAAACAAATAAAAAATAATA
1151347 TTAAAACAA
1 TTAAAACAA
1151356 TTCTTAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (22 bp):
TTAAAACAAATAAAAAATAATA
Found at i:1153252 original size:45 final size:45
Alignment explanation
Indices: 1153188--1153277 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
1153178 GATTGAGAAT
* *
1153188 GTGGTTTACCGAGTCTCTA-GCTCCGATCCTATAAGTATTTTTGTA
1 GTGGTTCACCGAGTCTCTAGGAT-CGATCCTATAAGTATTTTTGTA
*
1153233 GTGGTTCACCGAGTCTCTAGGATCGATCCTGTAAGTATTTTTGTA
1 GTGGTTCACCGAGTCTCTAGGATCGATCCTATAAGTATTTTTGTA
1153278 CTTAGTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (45 bp):
GTGGTTCACCGAGTCTCTAGGATCGATCCTATAAGTATTTTTGTA
Found at i:1165498 original size:29 final size:29
Alignment explanation
Indices: 1165442--1165536 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
1165432 ATCTCAAAAT
1165442 TATACATGAACTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAATTTAA--TGCAATTG
*
1165473 TATACATGAACTTTAATTTAATGCAATTA
1 TATACATGAACTTTAATTTAATGCAATTG
* * * * *
1165502 TACACGTGAAATTCTAATTGTGATTCAATTG
1 TATACATGAACTT-TAATT-TAATGCAATTG
1165533 TATA
1 TATA
1165537 GTAGAAGATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.31
30 5 0.09
31 32 0.59
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAATGCAATTG
Found at i:1165769 original size:31 final size:29
Alignment explanation
Indices: 1165704--1165773 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1165694 AAATCAAAAT
* *
1165704 TTCATGTACAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
* * *
1165733 CTCATGTATACAATTGCACATTAAACCATAG
1 TTCATGTATAAAATTGCACA--AAACCAAAG
1165764 TTCATGTATA
1 TTCATGTATA
1165774 GTTTTGGGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Found at i:1167261 original size:46 final size:44
Alignment explanation
Indices: 1167157--1167264 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1167147 TGTCTTTGAC
** * * *
1167157 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1167201 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1167247 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1167265 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1171731 original size:27 final size:27
Alignment explanation
Indices: 1171707--1171761 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1171697 TTAATGTCAG
1171707 TACAACTTTATGAGAAAACGGTGTCTA
1 TACAACTTTATGAGAAAACGGTGTCTA
1171734 TACAACTTTATGAGAAAACGGTGTCTA
1 TACAACTTTATGAGAAAACGGTGTCTA
1171761 T
1 T
1171762 CTCTTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (27 bp):
TACAACTTTATGAGAAAACGGTGTCTA
Found at i:1172469 original size:19 final size:20
Alignment explanation
Indices: 1172447--1172503 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
1172437 AAATTGCAAA
1172447 AAAAAATT-AAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
1172466 AAAAAGTTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
1172486 -AAAAATTCTAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
1172504 GTAACACCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 21 0.64
20 6 0.18
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:1172478 original size:20 final size:20
Alignment explanation
Indices: 1172454--1172499 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1172444 AAAAAAAAAT
1172454 TAAAATAATTT-TAAAAAGTTC
1 TAAAAT-ATTTATAAAAA-TTC
1172475 -AAAATATTTATAAAAATTC
1 TAAAATATTTATAAAAATTC
1172494 TAAAAT
1 TAAAAT
1172500 TTATGTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATATTTATAAAAATTC
Found at i:1174193 original size:11 final size:10
Alignment explanation
Indices: 1174148--1174214 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 10
1174138 TTATGTTTTT
1174148 TAAAAAATTA
1 TAAAAAATTA
*
1174158 TAAAAGAAAT-
1 TAAAA-AATTA
*
1174168 TAAAAAATTCT
1 TAAAAAATT-A
1174179 TAAAAAATATA
1 TAAAAAAT-TA
*
1174190 TAAAAAAGT-
1 TAAAAAATTA
*
1174199 T-AAAAATTT
1 TAAAAAATTA
1174208 TAAAAAA
1 TAAAAAA
1174215 ATAAAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 6 0.13
9 5 0.11
10 16 0.35
11 18 0.39
12 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1174217 original size:30 final size:31
Alignment explanation
Indices: 1174145--1174214 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1174135 AAATTATGTT
1174145 TTTTAAAAAAT-TATAAAAGAAATTAAAAAA
1 TTTTAAAAAATATATAAAAGAAATTAAAAAA
*
1174175 TTCTTAAAAAATATATAAAA-AAGTT-AAAAA
1 TT-TTAAAAAATATATAAAAGAAATTAAAAAA
1174205 TTTTAAAAAA
1 TTTTAAAAAA
1174215 ATAAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.22
30 9 0.24
31 13 0.35
32 7 0.19
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (31 bp):
TTTTAAAAAATATATAAAAGAAATTAAAAAA
Found at i:1174628 original size:14 final size:15
Alignment explanation
Indices: 1174602--1174634 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1174592 TAAAAAAGTG
1174602 TTAATAAAGATAATA
1 TTAATAAAGATAATA
*
1174617 TTAATAAA-ATAATT
1 TTAATAAAGATAATA
1174631 TTAA
1 TTAA
1174635 ATTTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TTAATAAAGATAATA
Found at i:1175553 original size:15 final size:17
Alignment explanation
Indices: 1175532--1175576 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1175522 TATTTTTCTG
1175532 AATTTTTTAT-ATTTAT
1 AATTTTTTATAATTTAT
1175548 -A-TTTTTATAATTTAT
1 AATTTTTTATAATTTAT
*
1175563 AATTTTTTAAAATT
1 AATTTTTTATAATT
1175577 GATATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 7 0.28
16 1 0.04
17 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTTTATAATTTAT
Found at i:1175559 original size:24 final size:27
Alignment explanation
Indices: 1175510--1175560 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1175500 CTTTTTTTAC
*
1175510 TTTATTATTATATATTTTTCTGAATTT
1 TTTATTATTATATATTTTTATGAATTT
1175537 TTTA-TATT-TATATTTTTAT-AATTT
1 TTTATTATTATATATTTTTATGAATTT
1175561 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 4 0.17
27 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTATTATTATATATTTTTATGAATTT
Found at i:1177281 original size:15 final size:15
Alignment explanation
Indices: 1177254--1177293 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1177244 GATGTTAAGT
1177254 CAAGGAGGTATGCTTC
1 CAAGGA-GTATGCTTC
1177270 CAAGGAGTATGCTTC
1 CAAGGAGTATGCTTC
*
1177285 CAAAGAGTA
1 CAAGGAGTA
1177294 AGTGGGGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (15 bp):
CAAGGAGTATGCTTC
Found at i:1179719 original size:17 final size:16
Alignment explanation
Indices: 1179690--1179766 Score: 60
Period size: 17 Copynumber: 5.0 Consensus size: 16
1179680 TTTTTTTCAG
1179690 TTTAAATTATAATTAT
1 TTTAAATTATAATTAT
1179706 TTTAAATGTATAATTA-
1 TTTAAAT-TATAATTAT
*
1179722 -TCACAATT-T--TTA-
1 TTTA-AATTATAATTAT
1179734 -TTAAATTATAATTATT
1 TTTAAATTATAATTA-T
1179750 TTTAAATGTATAATTAT
1 TTTAAAT-TATAATTAT
1179767 CACAACATCA
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
11 4 0.08
12 6 0.12
14 4 0.08
15 3 0.06
16 10 0.20
17 15 0.30
18 8 0.16
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAAATTATAATTAT
Found at i:1182968 original size:21 final size:22
Alignment explanation
Indices: 1182939--1182985 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1182929 CAGAAGGAGT
*
1182939 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
1182961 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
1182982 GAGT
1 GAGT
1182986 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:1185414 original size:21 final size:22
Alignment explanation
Indices: 1185385--1185425 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1185375 ATTTTAAAAA
1185385 ATTACAAAATGATCATTGAACT
1 ATTACAAAATGATCATTGAACT
**
1185407 ATTA-AAAATTTTCATTGAA
1 ATTACAAAATGATCATTGAA
1185426 AGCTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTACAAAATGATCATTGAACT
Found at i:1187601 original size:47 final size:47
Alignment explanation
Indices: 1187456--1187757 Score: 453
Period size: 47 Copynumber: 6.4 Consensus size: 47
1187446 CCCTTCGGGA
* * * * * * *
1187456 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1187503 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1187549 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1187596 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1187643 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1187690 CTTATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1187737 CTTATCACACATATACACTTT
1 CTTATCACATATATACACTTT
1187758 TAGGCCTTAT
Statistics
Matches: 236, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 39 0.17
47 197 0.83
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1187761 original size:26 final size:26
Alignment explanation
Indices: 1187731--1187783 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1187721 ACATTGGCTA
1187731 TTAGGCCTTATCACACATATACACTT
1 TTAGGCCTTATCACACATATACACTT
1187757 TTAGGCCTTATCACACATATACACTT
1 TTAGGCCTTATCACACATATACACTT
1187783 T
1 T
1187784 CACATTCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (26 bp):
TTAGGCCTTATCACACATATACACTT
Found at i:1187768 original size:73 final size:73
Alignment explanation
Indices: 1187684--1187830 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 73
1187674 ACATCGGCTA
* * *
1187684 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGCCTTATCACACAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACAT
1187749 ATACACTT
66 ATACACTT
*
1187757 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACAT
1187822 ATACACTT
66 ATACACTT
1187830 T
1 T
1187831 CACATTCATC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (73 bp):
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACAT
ATACACTT
Found at i:1187769 original size:120 final size:120
Alignment explanation
Indices: 1187637--1187877 Score: 432
Period size: 120 Copynumber: 2.0 Consensus size: 120
1187627 ACATCGGCTA
*
1187637 TTAGGCCTTATCAC-CTATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATA
1 TTAGGCCTTATCACAC-ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
1187701 TATACACTTTCACATTCATCACATTGGCTATTAGGCCTTATCACAC-ATATACACTT
65 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC-CTATATACACTT
1187757 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1187822 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTT
66 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTT
1187877 T
1 T
1187878 CACATTCATC
Statistics
Matches: 117, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
119 1 0.01
120 115 0.98
121 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (120 bp):
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTT
Found at i:1187809 original size:47 final size:47
Alignment explanation
Indices: 1187757--1187954 Score: 344
Period size: 47 Copynumber: 4.2 Consensus size: 47
1187747 ATATACACTT
1187757 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
* *
1187804 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTA
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
*
1187851 TTAGGCCTTATCAC-CTATATACACTTTCACATTCATCACATCGGCTA
1 TTAGGCCTTATCACAC-ATATACACTTTCACATTCATCACATCGGCCA
*
1187898 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
1187945 TTAGGCCTTA
1 TTAGGCCTTA
1187955 CTATCATTTC
Statistics
Matches: 144, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
47 144 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCA
Found at i:1187872 original size:167 final size:167
Alignment explanation
Indices: 1187590--1187924 Score: 616
Period size: 167 Copynumber: 2.0 Consensus size: 167
1187580 ACATCGGCCA
* * *
1187590 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1187655 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCAT
66 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCAT
*
1187720 CACATTGGCTATTAGGCCTTATCACACATATACACTT
131 CACATCGGCTATTAGGCCTTATCACACATATACACTT
1187757 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
*
1187822 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
66 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCAT
*
1187887 CACATCGGCTATTAGGCCTTATCACATATATACACTT
131 CACATCGGCTATTAGGCCTTATCACACATATACACTT
1187924 T
1 T
1187925 CACATTCATC
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 162 1.00
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (167 bp):
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCAT
CACATCGGCTATTAGGCCTTATCACACATATACACTT
Found at i:1187912 original size:214 final size:214
Alignment explanation
Indices: 1187543--1187954 Score: 806
Period size: 214 Copynumber: 1.9 Consensus size: 214
1187533 ACATCGGCCA
1187543 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1187608 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
66 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
* *
1187673 CACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGCC
131 CACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1187738 TTATCACACATATACACTT
196 TTATCACACATATACACTT
1187757 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1187822 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
66 ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
1187887 CACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
131 CACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1187952 TTA
196 TTA
1187955 CTATCATTTC
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 196 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (214 bp):
TTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACCTATATACACTTTCACATTCAT
CACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
TTATCACACATATACACTT
Found at i:1199240 original size:54 final size:54
Alignment explanation
Indices: 1199176--1199283 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
1199166 TCAAGGATAT
*
1199176 AAGTTCCGAAACATATGCTTTATGTGTTGGAACCTTAGTTGACAATAGCTAAAC
1 AAGTTCCGAAACATATGCTTTATGTGTCGGAACCTTAGTTGACAATAGCTAAAC
1199230 AAGTTCCGAAACATATGCTTTATGTGTCGGAACCTTAGTTGACAATAGCTAAAC
1 AAGTTCCGAAACATATGCTTTATGTGTCGGAACCTTAGTTGACAATAGCTAAAC
1199284 GCCTACAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (54 bp):
AAGTTCCGAAACATATGCTTTATGTGTCGGAACCTTAGTTGACAATAGCTAAAC
Found at i:1200173 original size:29 final size:28
Alignment explanation
Indices: 1200111--1200173 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
1200101 TGTATATTCA
* *
1200111 AAATTTAGTCCTTCTACTTTTATTTCAAG
1 AAATTTAGTCCCTCTACTTTGATTT-AAG
*
1200140 TAATTTAGTCCCTCTACTTTCGGATTT-AG
1 AAATTTAGTCCCTCTACTTT--GATTTAAG
1200169 AAATT
1 AAATT
1200174 CAAGTCCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 24 0.86
31 4 0.14
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (28 bp):
AAATTTAGTCCCTCTACTTTGATTTAAG
Found at i:1206313 original size:14 final size:14
Alignment explanation
Indices: 1206294--1206341 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1206284 TCAGTGATTT
1206294 AAATAAAAACTTTC
1 AAATAAAAACTTTC
*
1206308 AAATAATTTAA-TTT-
1 AAATAA--AAACTTTC
1206322 AAATAAAAACTTTC
1 AAATAAAAACTTTC
1206336 AAATAA
1 AAATAA
1206342 TTTAATGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 3 0.11
14 18 0.64
15 3 0.11
16 2 0.07
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAACTTTC
Found at i:1206330 original size:28 final size:28
Alignment explanation
Indices: 1206290--1206347 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1206280 TAGTTCAGTG
1206290 ATTTAAATAAAAACTTTCAAATAATTTA
1 ATTTAAATAAAAACTTTCAAATAATTTA
1206318 ATTTAAATAAAAACTTTCAAATAATTTA
1 ATTTAAATAAAAACTTTCAAATAATTTA
1206346 AT
1 AT
1206348 GATTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTTAAATAAAAACTTTCAAATAATTTA
Found at i:1213152 original size:105 final size:105
Alignment explanation
Indices: 1212925--1213231 Score: 508
Period size: 105 Copynumber: 2.9 Consensus size: 105
1212915 CTTAACAAGT
* *
1212925 TAGACATAGAACCCATATGAGTAGAGTCGCCGCTAATAATTTGAGTTAGGTTGGTTAGTCGCTTA
1 TAGACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCG-TTA
*
1212990 TTGCCTAAAGTCTCAAAAACAAATTAAGATATTCCTTAAGC
65 TTGCCTAAAGTCTCAAAAATAAATTAAGATATTCCTTAAGC
*
1213031 TAGACATAGAATCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGTTAT
1 TAGACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGTTAT
1213096 TGCCTAAAGTCTCAAAAATAAATTAAGATATTCCTTAAGC
66 TGCCTAAAGTCTCAAAAATAAATTAAGATATTCCTTAAGC
* *
1213136 TAGACATAGAACCCATATGAGTAGAGTTGCCACTAATCATTTAAGTTAGGTTGGTTAGTTAC-TT
1 TAGACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAG-T-CGTT
*
1213200 ATTGCCTAAAGTCTCAAAACTAAAATTAAGAT
64 ATTGCCTAAAGTCTCAAAAAT-AAATTAAGAT
1213232 GTATCTAAGG
Statistics
Matches: 190, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
105 98 0.52
106 81 0.43
107 11 0.06
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (105 bp):
TAGACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGTTAT
TGCCTAAAGTCTCAAAAATAAATTAAGATATTCCTTAAGC
Found at i:1229505 original size:126 final size:126
Alignment explanation
Indices: 1229194--1229942 Score: 995
Period size: 126 Copynumber: 5.8 Consensus size: 126
1229184 ATTTTGATGT
* * * * * *
1229194 TTTCTG-TTCTCAGAAATCGACTCATATTGCGAGAAGTGAGTTGAGCATTTTAATTTCTATTTTT
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
* * *
1229258 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC--GAGACACATGGAGGTATTTTCA
66 CAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGATACAC-T-GAGGTAATTTCA
* * * * *
1229319 GTTTTTATGTTTCAAAAATCAACTTATATTGCGAGATGTGAGTTGAGCCTTTTAATTTCTGTTTT
1 -TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTT
* * *
1229384 TCAAAAATCAACTTATATTGCGAAAGGTGAGTTGAGCCTCAGGATACGCTGAGTTAATTTCA
65 TCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGATACACTGAGGTAATTTCA
1229446 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
* *
1229511 CAAAAATCAACTTATATTGCGAAAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAATTTCA
66 CAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGATACACTGAGGTAATTTCA
*
1229572 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTT
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
* * * * *
1229637 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGACACATTGAGGTATTTTCA
66 CAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAG-GATACACTGAGGTAATTTCA
* * *
1229698 GTTTTTATTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTT
1 -TTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTT
* *
1229763 TTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGATACACTGAGGTAATTTCAAT
64 TTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGATACACTGAGG-----T-AA-
1229828 TTCTGTCTTTAA
122 -T-T-TC----A
1229840 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
*
1229905 CAAAAATCAACTCATATTGC-AAGAAGTGAGTTGAGCCT
66 CAAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCCT
1229943 TTTAATTTCT
Statistics
Matches: 556, Mismatches: 45, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
125 1 0.00
126 240 0.43
127 107 0.19
128 99 0.18
129 6 0.01
133 1 0.00
134 1 0.00
136 1 0.00
137 1 0.00
138 2 0.00
139 1 0.00
140 85 0.15
141 10 0.02
142 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (126 bp):
TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTT
CAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGATACACTGAGGTAATTTCA
Found at i:1229511 original size:54 final size:54
Alignment explanation
Indices: 1229445--1229548 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
1229435 AGTTAATTTC
*
1229445 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTTTA
*
1229499 ATTTCTGTTTTTCAAAAATCAACTTATATTGCGAAAGGTGAGTTGAGCCT
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT
1229549 CAGGATACGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (54 bp):
ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTTTA
Found at i:1229651 original size:54 final size:54
Alignment explanation
Indices: 1229571--1229802 Score: 214
Period size: 54 Copynumber: 3.9 Consensus size: 54
1229561 AGGTAATTTC
*
1229571 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
* *
1229625 ATTTCTATTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACATTGA
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT---------TTTA
*
1229688 GGTATTT-TCAGTTTTTATTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTTT
1 ---ATTTCT--G---TT---TTT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1229752 A
54 A
* *
1229753 ATTTCTGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1229803 CAGGATACAC
Statistics
Matches: 149, Mismatches: 7, Indels: 44
0.75 0.04 0.22
Matches are distributed among these distances:
54 85 0.57
55 3 0.02
58 2 0.01
61 1 0.01
62 4 0.03
63 4 0.03
65 4 0.03
66 4 0.03
70 2 0.01
73 3 0.02
74 37 0.25
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (54 bp):
ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
Found at i:1229901 original size:54 final size:54
Alignment explanation
Indices: 1229835--1229996 Score: 306
Period size: 54 Copynumber: 3.0 Consensus size: 54
1229825 AATTTCTGTC
*
1229835 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
*
1229889 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCT
1 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1229943 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1229997 CGAGACACAT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (54 bp):
TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
Found at i:1234091 original size:131 final size:131
Alignment explanation
Indices: 1233887--1234158 Score: 472
Period size: 131 Copynumber: 2.1 Consensus size: 131
1233877 GATCATGACA
* * * *
1233887 AATATGTGTGTTATATGATATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAGAAATGTTTA
1 AATATGTTTGCTATATGACATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTA
* *
1233952 GAAATGTTATGGGATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTTATATCAAG
66 GAAATGTTATGGAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTCATATCAAG
1234017 T
131 T
1234018 AATATGTTTGCTATATGACATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTA
1 AATATGTTTGCTATATGACATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTA
*
1234083 GAAATGTTATGGAATGATTGGAGATAGTTTGGACTTAATTTTTGGTGATTTGGACTCATATCAAG
66 GAAATGTTATGGAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTCATATCAAG
1234148 T
131 T
*
1234149 AATCTGTTTG
1 AATATGTTTG
1234159 TGGGTTGCAA
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (131 bp):
AATATGTTTGCTATATGACATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTA
GAAATGTTATGGAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTCATATCAAG
T
Found at i:1237984 original size:16 final size:16
Alignment explanation
Indices: 1237963--1237993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1237953 TTTACTATTA
*
1237963 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
1237979 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
1237994 GTGTGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:1239090 original size:13 final size:13
Alignment explanation
Indices: 1239072--1239097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1239062 AGAATTGTTC
1239072 AATTAAAGAATTT
1 AATTAAAGAATTT
1239085 AATTAAAGAATTT
1 AATTAAAGAATTT
1239098 TCTTGAAATA
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:0.08, T:0.38
Consensus pattern (13 bp):
AATTAAAGAATTT
Found at i:1239672 original size:62 final size:58
Alignment explanation
Indices: 1239586--1239718 Score: 160
Period size: 62 Copynumber: 2.2 Consensus size: 58
1239576 TCCAAAAATA
* *
1239586 ATATTATTTTAAT-AGTCTAATATTAAATTAAATTTAATGTTTATCTTGTAGATAAACATT
1 ATATTATTTTAATAAGTCTAATATTAAATTAAATCTAATATTTATC-T-TA-ATAAACATT
* * * *
1239646 CTATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
1 ATATTATTTTAATAAG-TCTAATATTAAATTAAATCTAATATTTATCTTAATAAACATT
*
1239705 ATATTAATTTAATA
1 ATATTATTTTAATA
1239719 TTAAAGTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 20 0.32
60 14 0.22
61 3 0.05
62 26 0.41
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTATTTTAATAAGTCTAATATTAAATTAAATCTAATATTTATCTTAATAAACATT
Found at i:1240601 original size:17 final size:17
Alignment explanation
Indices: 1240579--1240616 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1240569 TAGGACTATT
1240579 ACATAATAATCCAAGAA
1 ACATAATAATCCAAGAA
1240596 ACATAATAATCCAAGAA
1 ACATAATAATCCAAGAA
1240613 ACAT
1 ACAT
1240617 TTTGTAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (17 bp):
ACATAATAATCCAAGAA
Found at i:1241868 original size:40 final size:40
Alignment explanation
Indices: 1241807--1242222 Score: 417
Period size: 40 Copynumber: 10.7 Consensus size: 40
1241797 AGGCACTCAA
* ** * *
1241807 GTGCATTCAAGGGTATTGAAGTACAAATAGGAGTACGTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* * * *
1241847 GTGCATTTTA-AGGTACCGAAGT--ATA-AGGAGCATGTAT
1 GTGCA-TTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
*
1241884 GTGCATTCAGGGGTACCAAAGTACAAACA--AG--C-TA-
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* **
1241918 -TGCATTCAGCGGTATTGAAGTACAAACAGGAGCACGTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* * * *
1241957 GTGCATTCAGGGGTTCCAAAGTACAAATAGGAGCACGCAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* *
1241997 GTGCGTTCAAGGGTACCGAAGTACAAACAGGAGCACGTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* * * * *
1242037 GTGTATTTAGGGGTACTGAAGTACAAACAGGAGCACTTTT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
* * *
1242077 TTGCATTCAGGGGTATCGAAGTACAAACAGGAGCATGTAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
1242117 GTGCATTCAGGTGGTACCGAAGTACAAA-AGGAGCACGTAT
1 GTGCATTCAGG-GGTACCGAAGTACAAACAGGAGCACGTAT
* * * * *
1242157 ATGCGTTCAAGGGTACCGAAGTACAAATAGGAGCACATAT
1 GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
*
1242197 GTGCATTCGGGGGTACC-AGAGTACAA
1 GTGCATTCAGGGGTACCGA-AGTACAA
1242223 TCATAAGCAC
Statistics
Matches: 306, Mismatches: 55, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
33 24 0.08
35 4 0.01
36 3 0.01
37 26 0.08
38 6 0.02
39 19 0.06
40 206 0.67
41 18 0.06
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (40 bp):
GTGCATTCAGGGGTACCGAAGTACAAACAGGAGCACGTAT
Found at i:1246665 original size:95 final size:95
Alignment explanation
Indices: 1246502--1246690 Score: 342
Period size: 95 Copynumber: 2.0 Consensus size: 95
1246492 AATCTTGACC
* *
1246502 AAACAAATATATTTAGTGTCTTATCTCAATTTGGATATCTCTCAAGACATAAAGCGAATGCTAAA
1 AAACAAATATATTTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAA
1246567 AAACTCAAATAATCTTCTAGACTAATACAA
66 AAACTCAAATAATCTTCTAGACTAATACAA
*
1246597 AAACAAATATATTTAGTGTATTATCTCAATTTGGATATTTCTCAAGACATAAAGAGAATGCTAAA
1 AAACAAATATATTTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAA
*
1246662 AAACTCAAATAATCTTCTGGACTAATACA
66 AAACTCAAATAATCTTCTAGACTAATACA
1246691 GAGAAGTCAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (95 bp):
AAACAAATATATTTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAA
AAACTCAAATAATCTTCTAGACTAATACAA
Found at i:1247327 original size:28 final size:28
Alignment explanation
Indices: 1247294--1247350 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1247284 TTTTTACCAG
1247294 GATAATTATTGTAAATCCTAAAGGATAA
1 GATAATTATTGTAAATCCTAAAGGATAA
1247322 GATAATTATTGTAAATCCTAAAGGATAA
1 GATAATTATTGTAAATCCTAAAGGATAA
1247350 G
1 G
1247351 GATGCATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (28 bp):
GATAATTATTGTAAATCCTAAAGGATAA
Found at i:1252617 original size:22 final size:22
Alignment explanation
Indices: 1252589--1252633 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1252579 GCTCTTACTG
1252589 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
1252611 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
1252633 T
1 T
1252634 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Done.