Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 31 of 141
Found at i:10327537 original size:137 final size:138
Alignment explanation
Indices: 10327287--10327555 Score: 350
Period size: 137 Copynumber: 2.0 Consensus size: 138
10327277 AAAATGGGCT
* * * * *
10327287 TGCTCACACAAGCTAATGGTCAGAATGTAAGCTACACGATGCTGCTCACACAAGCTGATGAGTAT
1 TGCTCACACAAGCTAACGGCCAAAATGTAAGCTACACGATGCTACTCACACAAGCTGACGAGTAT
* * * * *
10327352 CTGCAACTAATGTCAGACCTCAGCCCTCGGTAGGACATTCAGGACCAGCACCCGAAACATGGTAA
66 CTGCAACTAATGTCAGAACTCAGCCATCGGTAAGACATTAAGGACCAGCACCCAAAACATGGTAA
10327417 CCTGAGTC
131 CCTGAGTC
* *
10327425 TGCTCACACAAGCTGACGGCCAAAATGT-AGCTACACGGTG-TCACTCACACAAGCTGACGAGTA
1 TGCTCACACAAGCTAACGGCCAAAATGTAAGCTACACGATGCT-ACTCACACAAGCTGACGAGTA
*
10327488 T-TCGTAAC-ATATGTCAGAACTCAGCCATCGGTAAGACATTTAAGG-CCAGCACCCAAAACATG
65 TCT-GCAACTA-ATGTCAGAACTCAGCCATCGGTAAGACA-TTAAGGACCAGCACCCAAAACATG
10327550 GTAACC
127 GTAACC
10327556 CAAATGACAT
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
136 3 0.03
137 82 0.72
138 29 0.25
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (138 bp):
TGCTCACACAAGCTAACGGCCAAAATGTAAGCTACACGATGCTACTCACACAAGCTGACGAGTAT
CTGCAACTAATGTCAGAACTCAGCCATCGGTAAGACATTAAGGACCAGCACCCAAAACATGGTAA
CCTGAGTC
Found at i:10332141 original size:10 final size:10
Alignment explanation
Indices: 10332117--10332157 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
10332107 GCATATATCC
10332117 AATCACATATT
1 AATCACAT-TT
10332128 AATCACATTT
1 AATCACATTT
*
10332138 AATCACATTC
1 AATCACATTT
*
10332148 AGTCACATTT
1 AATCACATTT
10332158 TATGATAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (10 bp):
AATCACATTT
Found at i:10335900 original size:43 final size:43
Alignment explanation
Indices: 10335850--10336163 Score: 411
Period size: 43 Copynumber: 7.3 Consensus size: 43
10335840 TTTTATAAAT
*
10335850 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
10335893 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
** *
10335936 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACAAAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-CCCAC
* * * *
10335980 AAACACCGCTAAAGACCAAGACCTTTAGTGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
10336023 AAACGTCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
** * *
10336066 AAATTCCGCTAAAGA-TATTGAGCTTTAG-GGCGCTTTTTCCCAC
1 AAACGCCGCTAAAGACCA-TGACCTTTAGCGGCGC-TTTTCCCAC
* *
10336109 AAACGCCGCTATAGA--ATAGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTAAAGACCAT-GACCTTTAGCGGCGCTTTTCCCAC
10336151 AAACGCCGCTAAA
1 AAACGCCGCTAAA
10336164 AATATATCTT
Statistics
Matches: 236, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.00
42 35 0.15
43 164 0.69
44 36 0.15
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:10336061 original size:130 final size:130
Alignment explanation
Indices: 10335828--10336163 Score: 428
Period size: 130 Copynumber: 2.6 Consensus size: 130
10335818 GCGTCGCTAA
* * * * * *
10335828 CTTTAGCGACGTTTTTATAAATAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAAC
1 CTTTAGCGGCGCTTTTACAAAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
10335893 AAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-TGA
66 AAACGCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CATTGA
10335957 C
130 C
* * *
10335958 CTTTAGCGGCGCTTTTACAAAAAAACACCGCTAAAGACCAAGACCTTTAGTGGTGCTTTTCCCAC
1 CTTTAGCGGCGCTTTTACAAAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * ** * *
10336023 AAACGTCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCACAAATTCCGCTAAAGATATTGAG
66 AAACGCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACATTGAC
* ** * * *
10336088 CTTTAG-GGCGCTTTTTCCCACAAACGCCGCTATAGA--ATAGACCTTTAGCGGCGCTTTTCACA
1 CTTTAGCGGCGCTTTTACAAAAAAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCCA
10336150 CAAACGCCGCTAAA
65 CAAACGCCGCTAAA
10336164 AATATATCTT
Statistics
Matches: 178, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
127 1 0.01
128 34 0.19
129 25 0.14
130 118 0.66
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (130 bp):
CTTTAGCGGCGCTTTTACAAAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
AAACGCCGCTAAAGACCAGAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACATTGAC
Found at i:10336500 original size:43 final size:43
Alignment explanation
Indices: 10336434--10336524 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
10336424 ACATATGCAA
* * * *
10336434 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
10336477 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
10336520 -GTAAT
1 GGTAAT
10336525 GAACTTAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:10339863 original size:58 final size:61
Alignment explanation
Indices: 10339752--10339866 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
10339742 AGTGATTATC
* * *
10339752 TTAATATTAAATTCAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATGGAT
1 TTAATATTAAATTCAATCTAATATTAATCTTGTAGATAAGTATTATATTAATTTAATGGAT
* *
10339813 TTAATATTAAATTTAATCTAGTATTAATC-T-T-GATAAGTATTATATTAATTTAAT
1 TTAATATTAAATTCAATCTAATATTAATCTTGTAGATAAGTATTATATTAATTTAAT
10339867 ATTAAAGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 22 0.45
59 1 0.02
60 1 0.02
61 25 0.51
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (61 bp):
TTAATATTAAATTCAATCTAATATTAATCTTGTAGATAAGTATTATATTAATTTAATGGAT
Found at i:10342067 original size:18 final size:19
Alignment explanation
Indices: 10342044--10342083 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
10342034 TCTTTAAATT
*
10342044 AATTAATG-GTTTGAAAAA
1 AATTAATGAATTTGAAAAA
10342062 AATTAATGATATTTGAAAAA
1 AATTAATGA-ATTTGAAAAA
10342082 AA
1 AA
10342084 ATATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (19 bp):
AATTAATGAATTTGAAAAA
Found at i:10345004 original size:59 final size:59
Alignment explanation
Indices: 10344912--10345035 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 59
10344902 ATTGATTTAT
* * *
10344912 TTTTGAATATTTTTGTACAATTTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTATTTCATTTAATAAAATAGAAGTTA
* * *
10344971 TTTTGAATATGTTTT-TACAAATTATTTTTATATTATTTTATTTAATAAATTAGGAGTTA
1 TTTTGAATAT-TTTTGTACAAATTATTTTTATATTATTTCATTTAATAAAATAGAAGTTA
10345030 TTTTGA
1 TTTTGA
10345036 TGTGGACATA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 54 0.93
60 4 0.07
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTATTTCATTTAATAAAATAGAAGTTA
Found at i:10348345 original size:29 final size:29
Alignment explanation
Indices: 10348313--10348392 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
10348303 AAATCCATTT
* *
10348313 CGTCAAAATAATTTTTTCAAAACACATCA
1 CGTCAAATTTATTTTTTCAAAACACATCA
* * *
10348342 CGTCAAATTTATTTTTTCATATCACATCT
1 CGTCAAATTTATTTTTTCAAAACACATCA
*
10348371 TGTCAAATTTATTTCTTTCAAA
1 CGTCAAATTTATTT-TTTCAAA
10348393 TCAATACTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 37 0.86
30 6 0.14
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (29 bp):
CGTCAAATTTATTTTTTCAAAACACATCA
Found at i:10360325 original size:125 final size:122
Alignment explanation
Indices: 10360113--10360461 Score: 477
Period size: 125 Copynumber: 2.8 Consensus size: 122
10360103 TAATTTCGAG
* ** *
10360113 TTGAAGTTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGGTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
10360178 AAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAAT--TT-TTTT
*
10360238 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * * *
10360303 AAATTGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTATGTCATGTAAGAAATTTTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATTTTTTT
* * * *
10360360 TTTACGTTTCTGAGCAAGTAATATAAAATCGCTTCTACCAGGATGCTATTT-ATGAAGAACTTGT
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGA-GAAGAATTTGT
**
10360424 GAAATCGCGCCCTCGTGGACGCAATTTTGCTACAGTAG
65 GAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
10360462 CATGTTTGGG
Statistics
Matches: 198, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
121 1 0.01
122 91 0.46
123 3 0.02
124 1 0.01
125 102 0.52
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (122 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATTTTTTT
Found at i:10368389 original size:51 final size:51
Alignment explanation
Indices: 10368334--10368456 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
10368324 TATTTTAAAA
* * *
10368334 AAGGAAATTGAGAAGAAATTGAAATTATATATGGATTTGAGAGAATTTTTG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
* *
10368385 AAGGAAATTAAGAGGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
* *
10368436 AAGGAAATCGAG-AGGAATTGA
1 AAGGAAATTGAGAAGAAATTGA
10368457 GAGGAAATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
50 7 0.11
51 56 0.89
ACGTcount: A:0.46, C:0.01, G:0.25, T:0.28
Consensus pattern (51 bp):
AAGGAAATTGAGAAGAAATTGAAATTAAATATAGATTTGAGAGAATTTTGG
Found at i:10369007 original size:26 final size:26
Alignment explanation
Indices: 10368964--10369052 Score: 105
Period size: 25 Copynumber: 3.5 Consensus size: 26
10368954 AAACTTAGAG
*
10368964 TAATATATATAA-AC-TAAAACTGTT
1 TAATATAAATAATACATAAAACTGTT
* *
10368988 TAATATAAATAATACATAAAAATCTT
1 TAATATAAATAATACATAAAACTGTT
*
10369014 TAAAATAAATAATA-ATAAAACTGTT
1 TAATATAAATAATACATAAAACTGTT
10369039 TAA-ATGAAATAATA
1 TAATAT-AAATAATA
10369053 TAAAAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
24 13 0.23
25 22 0.39
26 21 0.38
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (26 bp):
TAATATAAATAATACATAAAACTGTT
Found at i:10369040 original size:25 final size:25
Alignment explanation
Indices: 10368978--10369057 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 25
10368968 ATATATAAAC
*
10368978 TAAAACTGTTTAATATAAATAATACA
1 TAAAACTGTTTAAAATAAATAATA-A
* *
10369004 TAAAAATCTTTAAAATAAATAATAA
1 TAAAACTGTTTAAAATAAATAATAA
10369029 TAAAACTGTTT-AAATGAAATAAT-A
1 TAAAACTGTTTAAAAT-AAATAATAA
10369053 TAAAA
1 TAAAA
10369058 AAAATCTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 10 0.21
25 17 0.35
26 21 0.44
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAACTGTTTAAAATAAATAATAA
Found at i:10369103 original size:17 final size:16
Alignment explanation
Indices: 10369081--10369131 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
10369071 TTTAAAAAGT
10369081 AAATAAAAATGAAATCA
1 AAATAAAAATGAAA-CA
*
10369098 AAATAAACATGAAA-A
1 AAATAAAAATGAAACA
*
10369113 CTAATAAAAAT-AAACA
1 -AAATAAAAATGAAACA
10369129 AAA
1 AAA
10369132 GCAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (16 bp):
AAATAAAAATGAAACA
Found at i:10370530 original size:13 final size:13
Alignment explanation
Indices: 10370512--10370545 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
10370502 ATATAATTAT
10370512 TAATAATATTTAA
1 TAATAATATTTAA
10370525 TAATAAT-TTTAA
1 TAATAATATTTAA
10370537 T-ATAATATT
1 TAATAATATT
10370546 ATTATTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:10370965 original size:27 final size:27
Alignment explanation
Indices: 10370886--10370973 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
10370876 ATAAAAAATC
*
10370886 AAAACTCATAG-TCCTT-TGTTATTCA
1 AAAACTCATAGTTCTTTATGTTATTCA
*
10370911 AAAAC-CATAGTCCTTGATCTTATGTTATTCA
1 AAAACTCATAG---TT-CT-TTATGTTATTCA
10370942 AAAACTCATAGTTCTTTATGTTATTCA
1 AAAACTCATAGTTCTTTATGTTATTCA
10370969 AAAAC
1 AAAAC
10370974 ATGAAGAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
27 17 0.33
28 2 0.04
29 2 0.04
30 2 0.04
31 14 0.27
32 5 0.10
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (27 bp):
AAAACTCATAGTTCTTTATGTTATTCA
Found at i:10391179 original size:23 final size:21
Alignment explanation
Indices: 10391127--10391184 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
10391117 TAAATTTAGG
* *
10391127 TTTAAATCTTTTTATTTAAAC
1 TTTAAATTTTTTTATTTAAAA
*
10391148 TTGATAATTATTTTTATATTAAAA
1 TTTA-AATT-TTTTTAT-TTAAAA
10391172 TTTAAATTTTTTT
1 TTTAAATTTTTTT
10391185 CGTTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.10
22 8 0.27
23 11 0.37
24 8 0.27
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAATTTTTTTATTTAAAA
Found at i:10391313 original size:118 final size:119
Alignment explanation
Indices: 10391178--10391415 Score: 460
Period size: 118 Copynumber: 2.0 Consensus size: 119
10391168 AAAATTTAAA
10391178 TTTTTTTCGTTTAAATTAATTTTTAATATTTTCTTAAAAACCCTTAAAATTTAGGTTCTAATATA
1 TTTTTTTCG-TTAAATTAATTTTTAATATTTTCTTAAAAACCCTTAAAATTTAGGTTCTAATATA
10391243 CAAAAATATTATGAAGTAAAAAAAATAAATTAATTCCCAATATAAAAGCTGTTGC
65 CAAAAATATTATGAAGTAAAAAAAATAAATTAATTCCCAATATAAAAGCTGTTGC
10391298 TTTTTTTCG-TAAATTAATTTTTAATATTTTCTTAAAAACCCTTAAAATTTAGGTTCTAATATAC
1 TTTTTTTCGTTAAATTAATTTTTAATATTTTCTTAAAAACCCTTAAAATTTAGGTTCTAATATAC
10391362 AAAAATATTATGAAGTAAAAAAAATAAATTAATTCCCAATATAAAAGCTGTTGC
66 AAAAATATTATGAAGTAAAAAAAATAAATTAATTCCCAATATAAAAGCTGTTGC
10391416 GAAATCCAGG
Statistics
Matches: 118, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
118 109 0.92
120 9 0.08
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (119 bp):
TTTTTTTCGTTAAATTAATTTTTAATATTTTCTTAAAAACCCTTAAAATTTAGGTTCTAATATAC
AAAAATATTATGAAGTAAAAAAAATAAATTAATTCCCAATATAAAAGCTGTTGC
Found at i:10393506 original size:17 final size:17
Alignment explanation
Indices: 10393486--10393518 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10393476 CTCAAGTTAA
10393486 TAAATTAAT-TTCTCAAT
1 TAAA-TAATCTTCTCAAT
10393503 TAAATAATCTTCTCAA
1 TAAATAATCTTCTCAA
10393519 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAATCTTCTCAAT
Found at i:10400404 original size:53 final size:53
Alignment explanation
Indices: 10400303--10400466 Score: 161
Period size: 53 Copynumber: 3.1 Consensus size: 53
10400293 TTTATAAATA
* * * * * * *
10400303 GGAAATAAGACCGTATCGTGAAAGATTGTAA-TGGTGGGTTATGTCATCATAT
1 GGAAAGAAGACCATATCATGTAAGACTGTAACTAGTGGGTTATGGCATCATAT
* ** *
10400355 GGAAAGAATACGTTA-CTATGTAAGACTGTAACTAGTTGGTTATGGCATCATAT
1 GGAAAGAAGACCATATC-ATGTAAGACTGTAACTAGTGGGTTATGGCATCATAT
* * * *
10400408 GGAAAGAAGACCATATCGTGTAAGATTGTAATTGGTGGGTTATGGCATCATAT
1 GGAAAGAAGACCATATCATGTAAGACTGTAACTAGTGGGTTATGGCATCATAT
10400461 AGGAAA
1 -GGAAA
10400467 AATTAAGGTT
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
51 1 0.01
52 22 0.24
53 61 0.68
54 6 0.07
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (53 bp):
GGAAAGAAGACCATATCATGTAAGACTGTAACTAGTGGGTTATGGCATCATAT
Found at i:10400646 original size:29 final size:29
Alignment explanation
Indices: 10400613--10400762 Score: 105
Period size: 29 Copynumber: 5.3 Consensus size: 29
10400603 AAAGGACATT
10400613 CTTTGTGGCAAAACTCTGGAAAGGTAAGC
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGC
* * * *
10400642 ATTTGTGGC-GAACT-TGTTAAAGG-ACATC
1 CTTTGTGGCAAAACTCTG-GAAAGGTA-AGC
* * *
10400670 CTTTATGGAAAAACTCTAGAAAGGTAAGC
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGC
* * *
10400699 CTTT-TTGC-AAAC-CTGTTAAAGGAAAGC
1 CTTTGTGGCAAAACTCTG-GAAAGGTAAGC
* * * *
10400726 GTTTGTGGAAAAACTCTAGAAAGGTAAAC
1 CTTTGTGGCAAAACTCTGGAAAGGTAAGC
10400755 CTTTGTGG
1 CTTTGTGG
10400763 TGAACCTATT
Statistics
Matches: 88, Mismatches: 24, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
26 2 0.02
27 19 0.22
28 21 0.24
29 42 0.48
30 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (29 bp):
CTTTGTGGCAAAACTCTGGAAAGGTAAGC
Found at i:10400667 original size:57 final size:57
Alignment explanation
Indices: 10400599--10400877 Score: 253
Period size: 57 Copynumber: 4.9 Consensus size: 57
10400589 TGGCAATCTT
** * * * *
10400599 TGTTAAAGGACATTCTTTGTGGCAAAACTCTGGAAAGGTAAGCATTTGTGGCGAACT
1 TGTTAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACC
* * * *
10400656 TGTTAAAGGACATCCTTTATGGAAAAACTCTAGAAAGGTAAGCCTTT-TTGCAAACC
1 TGTTAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACC
* * *
10400712 TGTTAAAGGA-AAGCGTTTGTGGAAAAACTCTAGAAAGGTAAACCTTTGTGGTGAACC
1 TGTTAAAGGACAA-CCTTTGTGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACC
* * * * ** * *
10400769 TATTAAAGGACAACCTTTGTGGCAAATCT-TTGAAAGAAAACACCTTTGTGGCGATCTC
1 TGTTAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAA-GCCTTTGTGGCGAAC-C
* * * * *
10400827 TGTCAAAGGA-AAGCCTCTGTGG-AAAACTCTAGATAGGAAAGCCTTTATGGC
1 TGTTAAAGGACAA-CCTTTGTGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGC
10400878 AATCTCCGTA
Statistics
Matches: 182, Mismatches: 33, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
55 1 0.01
56 55 0.30
57 99 0.54
58 27 0.15
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (57 bp):
TGTTAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAGCCTTTGTGGCGAACC
Found at i:10400815 original size:113 final size:114
Alignment explanation
Indices: 10400574--10400877 Score: 283
Period size: 113 Copynumber: 2.7 Consensus size: 114
10400564 ATTACTAGGA
* * * * * ** *
10400574 AAAGAAAAACCTTTATGGCAATCTTTGTTAAAGGACATTCTTTGTGGCAAAACTCTGGAAAGGTA
1 AAAGAAAAACCTTTGTGGCAAACTCTGTCAAAGGAAAGCCTTTGTGG-AAAACTCTAGAAAGGTA
* * * * *
10400639 AGCATTTGTGGCGAACTTGTTAAAGGACATCCTTTATGGAAAAACTCTAG
65 AACCTTTGTGGCGAACCTATTAAAGGACAACCTTTATGGAAAAACTCTAG
** * * * *
10400689 AAAGGTAAGCCTTT-TTGCAAAC-CTGTTAAAGGAAAGCGTTTGTGGAAAAACTCTAGAAAGGTA
1 AAAGAAAAACCTTTGTGGCAAACTCTGTCAAAGGAAAGCCTTTGTGG-AAAACTCTAGAAAGGTA
* * * * *
10400752 AACCTTTGTGGTGAACCTATTAAAGGACAACCTTTGTGGCAAATCT-TTG
65 AACCTTTGTGGCGAACCTATTAAAGGACAACCTTTATGGAAAAACTCTAG
* * * *
10400801 AAAGAAAACACCTTTGTGGCGATCTCTGTCAAAGGAAAGCCTCTGTGGAAAACTCTAGATAGG-A
1 AAAGAAAA-ACCTTTGTGGCAAACTCTGTCAAAGGAAAGCCTTTGTGGAAAACTCTAGAAAGGTA
*
10400865 AAGCCTTTATGGC
65 AA-CCTTTGTGGC
10400878 AATCTCCGTA
Statistics
Matches: 151, Mismatches: 34, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
112 8 0.05
113 79 0.52
114 33 0.22
115 31 0.21
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (114 bp):
AAAGAAAAACCTTTGTGGCAAACTCTGTCAAAGGAAAGCCTTTGTGGAAAACTCTAGAAAGGTAA
ACCTTTGTGGCGAACCTATTAAAGGACAACCTTTATGGAAAAACTCTAG
Found at i:10403125 original size:35 final size:35
Alignment explanation
Indices: 10403079--10403149 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
10403069 ATAAACAAAG
10403079 TGTAACTCATAATATTTACACAAACCAACTTTACT
1 TGTAACTCATAATATTTACACAAACCAACTTTACT
10403114 TGTAACTCATAATATTTACACAAACCAACTTTACT
1 TGTAACTCATAATATTTACACAAACCAACTTTACT
10403149 T
1 T
10403150 AAAACCATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (35 bp):
TGTAACTCATAATATTTACACAAACCAACTTTACT
Found at i:10403623 original size:42 final size:43
Alignment explanation
Indices: 10403548--10403682 Score: 134
Period size: 42 Copynumber: 3.2 Consensus size: 43
10403538 GAAGCCCGAA
* * * * *
10403548 GGTTGAAC-AGAAGCACATAAGTGCTAAATAGAAACCCATAAG
1 GGTTAAACGAGAAGCTCATAAGAGCTGAACAGAAACCCATAAG
*
10403590 GGTTAAACGA-AAGCTCATAAGAGCTGAACAGAAACTCATAAG
1 GGTTAAACGAGAAGCTCATAAGAGCTGAACAGAAACCCATAAG
* * * *
10403632 GGTTAAA-AAGAAGTTCAAAAGAGCTGAACA-AATACCCATTAG
1 GGTTAAACGAGAAGCTCATAAGAGCTGAACAGAA-ACCCATAAG
*
10403674 GGTTGAACG
1 GGTTAAACG
10403683 GAAACTTATA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.04
42 72 0.95
43 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (43 bp):
GGTTAAACGAGAAGCTCATAAGAGCTGAACAGAAACCCATAAG
Found at i:10403643 original size:21 final size:21
Alignment explanation
Indices: 10403563--10403643 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
10403553 AACAGAAGCA
* * *
10403563 CATAAGTGCTAAATAGAAACC
1 CATAAGGGCTAAAAAGAAACT
* *
10403584 CATAAGGG-TTAAACGAAAGCT
1 CATAAGGGCTAAAAAGAAA-CT
* * *
10403605 CATAAGAGCTGAACAGAAACT
1 CATAAGGGCTAAAAAGAAACT
*
10403626 CATAAGGGTTAAAAAGAA
1 CATAAGGGCTAAAAAGAA
10403644 GTTCAAAAGA
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 7 0.16
21 31 0.69
22 7 0.16
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (21 bp):
CATAAGGGCTAAAAAGAAACT
Found at i:10413142 original size:17 final size:17
Alignment explanation
Indices: 10413120--10413155 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10413110 GTTCTTTTTA
10413120 AAGATGTATGGAGATTT
1 AAGATGTATGGAGATTT
*
10413137 AAGATGTATGGAGGTTT
1 AAGATGTATGGAGATTT
10413154 AA
1 AA
10413156 CACTTGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (17 bp):
AAGATGTATGGAGATTT
Found at i:10423646 original size:17 final size:18
Alignment explanation
Indices: 10423624--10423687 Score: 82
Period size: 17 Copynumber: 3.7 Consensus size: 18
10423614 TTCAACCAAA
10423624 ATTTTAT-TTTGATGAGT
1 ATTTTATATTTGATGAGT
*
10423641 ATTTTATATTTGA-GTA-A
1 ATTTTATATTTGATG-AGT
10423658 ATTTTAT-TTTGATGAGT
1 ATTTTATATTTGATGAGT
10423675 ATTTTATATTTGA
1 ATTTTATATTTGA
10423688 GTTGTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.15
17 23 0.57
18 11 0.28
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (18 bp):
ATTTTATATTTGATGAGT
Found at i:10423660 original size:34 final size:34
Alignment explanation
Indices: 10423622--10423689 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
10423612 ACTTCAACCA
10423622 AAATTTTATTTTGATGAGTATTTTATATTTGAGT
1 AAATTTTATTTTGATGAGTATTTTATATTTGAGT
10423656 AAATTTTATTTTGATGAGTATTTTATATTTGAGT
1 AAATTTTATTTTGATGAGTATTTTATATTTGAGT
10423690 TGTATTTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (34 bp):
AAATTTTATTTTGATGAGTATTTTATATTTGAGT
Found at i:10423694 original size:18 final size:18
Alignment explanation
Indices: 10423639--10423696 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
10423629 ATTTTGATGA
10423639 GTATTTTATATTTGAG-T
1 GTATTTTATATTTGAGTT
** *
10423656 AAATTTTAT-TTTGA-TGA
1 GTATTTTATATTTGAGT-T
10423673 GTATTTTATATTTGAGTT
1 GTATTTTATATTTGAGTT
10423691 GTATTT
1 GTATTT
10423697 AACCTCAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.16
17 14 0.45
18 11 0.35
19 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.59
Consensus pattern (18 bp):
GTATTTTATATTTGAGTT
Found at i:10426439 original size:4 final size:4
Alignment explanation
Indices: 10426432--10426535 Score: 208
Period size: 4 Copynumber: 26.0 Consensus size: 4
10426422 CTATTTCATT
10426432 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
10426480 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
10426528 CATA CATA
1 CATA CATA
10426536 TATCAAATTG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 100 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:10426802 original size:9 final size:9
Alignment explanation
Indices: 10426785--10426821 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
10426775 TGAGTTTTCG
10426785 AATTCGAAT
1 AATTCGAAT
*
10426794 AACTCGAAT
1 AATTCGAAT
10426803 AATTCGAAT
1 AATTCGAAT
10426812 AATTCGAAT
1 AATTCGAAT
10426821 A
1 A
10426822 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:10430388 original size:45 final size:45
Alignment explanation
Indices: 10430324--10430410 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
10430314 AACAGATACT
* * *
10430324 CGGTGGATTCAGCATATAGCAACCACCTTATTAATCAATGATATC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
10430369 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
10430411 GTTCGATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
Found at i:10437043 original size:17 final size:16
Alignment explanation
Indices: 10437021--10437066 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
10437011 TAAATGTTTT
10437021 ATTTACCATTTAATTCC
1 ATTTACCATTTAATT-C
10437038 ATTTACC-TTT-ATTC
1 ATTTACCATTTAATTC
*
10437052 ATTAAGCCATTTAAT
1 ATTTA-CCATTTAAT
10437067 CACTCAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
16 6 0.24
17 9 0.36
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTTACCATTTAATTC
Found at i:10450928 original size:73 final size:73
Alignment explanation
Indices: 10450809--10450963 Score: 276
Period size: 73 Copynumber: 2.1 Consensus size: 73
10450799 AAGGTGGGTG
10450809 GATGGTTTGCTATTTTGGGAAGGATATTAGCTTGATTCATGCTTGATTCAAGGGAGAAGGGTTCA
1 GATGGTTTGCTATTTTGGGAAGGATATTAGCTTGATTCATGCTTGATTCAAGGGAGAAGGGTT-A
10450874 -AGGGAATA
65 GAGGGAATA
*
10450882 GATGGTTTGCTATTTTGGGAAGGATATTAGGTTGATTCATGCTTGATTCAAGGGAGAAGGGTTAG
1 GATGGTTTGCTATTTTGGGAAGGATATTAGCTTGATTCATGCTTGATTCAAGGGAGAAGGGTTAG
*
10450947 AGGGAATG
66 AGGGAATA
10450955 GATGGTTTG
1 GATGGTTTG
10450964 GGATTCATTC
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
72 1 0.01
73 78 0.99
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (73 bp):
GATGGTTTGCTATTTTGGGAAGGATATTAGCTTGATTCATGCTTGATTCAAGGGAGAAGGGTTAG
AGGGAATA
Found at i:10476014 original size:64 final size:64
Alignment explanation
Indices: 10475945--10476213 Score: 405
Period size: 64 Copynumber: 4.2 Consensus size: 64
10475935 AATATACATC
10475945 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
1 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
*
10476009 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTTAAATGTATATATATACTTATATT
1 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
* * *
10476073 GCCGAAATGAATTGTATAGGTATACACCTATTTCCGAATTGAAATGTATATATATACTTATATT
1 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
* * * * * * * *
10476137 GCCAAAATGAATTGTATAGGTATGCACCTATTACCGAATTGAATTATATATGTATACTTATA-T
1 ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
*
10476200 AGTCGAATTGAATT
1 A-CCGAATTGAATT
10476214 TTATTTGTAT
Statistics
Matches: 189, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
63 1 0.01
64 188 0.99
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (64 bp):
ACCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATGTATATATATACTTATATT
Found at i:10476207 original size:32 final size:32
Alignment explanation
Indices: 10475946--10476234 Score: 247
Period size: 32 Copynumber: 9.0 Consensus size: 32
10475936 ATATACATCA
* ***
10475946 CCGAATTGAATTGTATAGGTATACACCTATTG
1 CCGAATTGAATTGTATATGTATACTTATATTG
* * *
10475978 CCGAATTGAAATGTATATATATACTTATATTA
1 CCGAATTGAATTGTATATGTATACTTATATTG
* ***
10476010 CCGAATTGAATTGTATAGGTATACACCTATTG
1 CCGAATTGAATTGTATATGTATACTTATATTG
* * *
10476042 CCGAATTTAAATGTATATATATACTTATATTG
1 CCGAATTGAATTGTATATGTATACTTATATTG
* * *** *
10476074 CCGAAATGAATTGTATAGGTATACACCTATTT
1 CCGAATTGAATTGTATATGTATACTTATATTG
* *
10476106 CCGAATTGAAATGTATATATATACTTATATTG
1 CCGAATTGAATTGTATATGTATACTTATATTG
* * * * *** *
10476138 CCAAAATGAATTGTATAGGTATGCACCTATTA
1 CCGAATTGAATTGTATATGTATACTTATATTG
* *
10476170 CCGAATTGAATTATATATGTATACTTATATAG
1 CCGAATTGAATTGTATATGTATACTTATATTG
* * *
10476202 TCGAATTGAATTTTATTTGTATA-TATATATTG
1 CCGAATTGAATTGTATATGTATACT-TATATTG
10476234 C
1 C
10476235 TGATTTGATT
Statistics
Matches: 193, Mismatches: 63, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
31 1 0.01
32 192 0.99
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (32 bp):
CCGAATTGAATTGTATATGTATACTTATATTG
Found at i:10477226 original size:16 final size:17
Alignment explanation
Indices: 10477205--10477237 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10477195 TTGAGCAAGT
*
10477205 AAAATG-TGTTTGGTTA
1 AAAATGTTGTTTAGTTA
10477221 AAAATGTTGTTTAGTTA
1 AAAATGTTGTTTAGTTA
10477238 CGAAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (17 bp):
AAAATGTTGTTTAGTTA
Found at i:10479230 original size:29 final size:29
Alignment explanation
Indices: 10479197--10479258 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
10479187 TATCACAAAA
10479197 ATAAAAG-CCCAAAA-AAAATCATAAAGTCC
1 ATAAAAGTCCCAAAATAAAAT-AT-AAGTCC
*
10479226 ATAAAAGTCCCAAAATAAAATGTAAGTCC
1 ATAAAAGTCCCAAAATAAAATATAAGTCC
10479255 ATAA
1 ATAA
10479259 TCAAGAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 17 0.57
30 8 0.27
31 5 0.17
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (29 bp):
ATAAAAGTCCCAAAATAAAATATAAGTCC
Found at i:10479652 original size:51 final size:49
Alignment explanation
Indices: 10479583--10479723 Score: 142
Period size: 49 Copynumber: 2.8 Consensus size: 49
10479573 GAAACACCTG
* * * * * *
10479583 TTGTGGATAAGCCACCACTGAATTGTAGATAAATTGCCATTGATAACACTT
1 TTGTGGACAAGCTACCACTGAATTGTAGATAAACTACCACTAATAA-A-TT
* *
10479634 TTGTGGACAAGCTACCACTG-ATATGCAGATATACTACCACTAATAAATT
1 TTGTGGACAAGCTACCACTGAAT-TGTAGATAAACTACCACTAATAAATT
* *
10479683 TTGTGGACAAG-TCACCACTGATTTGTAGATATACTACCACT
1 TTGTGGACAAGCT-ACCACTGAATTGTAGATAAACTACCACT
10479724 GCTTCCACCT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
48 1 0.01
49 37 0.48
50 4 0.05
51 35 0.45
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (49 bp):
TTGTGGACAAGCTACCACTGAATTGTAGATAAACTACCACTAATAAATT
Found at i:10485522 original size:15 final size:15
Alignment explanation
Indices: 10485484--10485528 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10485474 TATTTGATAA
10485484 ATTGAAAAATTAAGT
1 ATTGAAAAATTAAGT
**
10485499 ACTAAAAAAATTAAGT
1 A-TTGAAAAATTAAGT
*
10485515 ATTGAAAAACTAAG
1 ATTGAAAAATTAAG
10485529 GTCTTGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (15 bp):
ATTGAAAAATTAAGT
Found at i:10485522 original size:16 final size:16
Alignment explanation
Indices: 10485484--10485523 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
10485474 TATTTGATAA
10485484 ATTG-AAAAATTAAGT
1 ATTGAAAAAATTAAGT
* *
10485499 ACTAAAAAAATTAAGT
1 ATTGAAAAAATTAAGT
10485515 ATTGAAAAA
1 ATTGAAAAA
10485524 CTAAGGTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (16 bp):
ATTGAAAAAATTAAGT
Found at i:10485732 original size:26 final size:27
Alignment explanation
Indices: 10485703--10485754 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
10485693 TTAAAGAGAA
* * *
10485703 TAATTTTATTTTATTTTATT-TTTATT
1 TAATTTAATATTATATTATTCTTTATT
10485729 TAATTTAATATTATATTATTCTTTAT
1 TAATTTAATATTATATTATTCTTTAT
10485755 CAAACTGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TAATTTAATATTATATTATTCTTTATT
Found at i:10490391 original size:14 final size:14
Alignment explanation
Indices: 10490372--10490400 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10490362 GATAAATCCA
10490372 AATCATATCCACAT
1 AATCATATCCACAT
10490386 AATCATATCCACAT
1 AATCATATCCACAT
10490400 A
1 A
10490401 CCCATATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCATATCCACAT
Found at i:10490406 original size:14 final size:14
Alignment explanation
Indices: 10490375--10490408 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10490365 AAATCCAAAT
*
10490375 CATATCCACATAAT
1 CATATCCACATAAC
*
10490389 CATATCCACATACC
1 CATATCCACATAAC
10490403 CATATC
1 CATATC
10490409 TGAATATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (14 bp):
CATATCCACATAAC
Found at i:10492428 original size:25 final size:26
Alignment explanation
Indices: 10492400--10492449 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
10492390 TAGGTAGATA
*
10492400 ATTATTGTT-ATTAAATTTTAATAAG
1 ATTATTGTTAAATAAATTTTAATAAG
*
10492425 ATTATTGTTAAATATATTTTAATAA
1 ATTATTGTTAAATAAATTTTAATAA
10492450 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
ATTATTGTTAAATAAATTTTAATAAG
Found at i:10492456 original size:6 final size:6
Alignment explanation
Indices: 10492445--10492474 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
10492435 AATATATTTT
10492445 AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
10492475 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:10494962 original size:13 final size:12
Alignment explanation
Indices: 10494940--10494977 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
10494930 CCTAATATAA
10494940 TTAATTATAATAT
1 TTAA-TATAATAT
10494953 TTAATAATAAT-T
1 TTAAT-ATAATAT
10494965 TTAATATAATAT
1 TTAATATAATAT
10494977 T
1 T
10494978 ATTATTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.22
12 9 0.39
13 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATATAATAT
Found at i:10495806 original size:31 final size:31
Alignment explanation
Indices: 10495768--10495847 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
10495758 CATGGTTGAT
*
10495768 TTAGCAGCAAAAATCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
10495799 TTAGCAGCAAAAACCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
* *
10495830 TTAACTGCAAAAACCAAT
1 TTAGCAGCAAAAACCAAT
10495848 TAAAATCCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (31 bp):
TTAGCAGCAAAAACCAATAGAAGGTACCATC
Found at i:10497427 original size:7 final size:7
Alignment explanation
Indices: 10497417--10497459 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
10497407 AAACTAAATA
10497417 CTAAACC
1 CTAAACC
10497424 CTAAACC
1 CTAAACC
*
10497431 TTAAACC
1 CTAAACC
*
10497438 CTAAATC
1 CTAAACC
*
10497445 CTAAATC
1 CTAAACC
*
10497452 CAAAACC
1 CTAAACC
10497459 C
1 C
10497460 AGAACCATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:10497441 original size:21 final size:20
Alignment explanation
Indices: 10497391--10497449 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
10497381 AAAAGTAATT
10497391 AACCCTAAAGCCCGTAAAACTA
1 AACCCTAAA-CCC-TAAAACTA
** *
10497413 AATACTAAACCCTAAACCTTA
1 AACCCTAAACCCTAAAAC-TA
*
10497434 AACCCTAAATCCTAAA
1 AACCCTAAACCCTAAA
10497450 TCCAAAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.17
21 18 0.60
22 7 0.23
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (20 bp):
AACCCTAAACCCTAAAACTA
Found at i:10497449 original size:14 final size:14
Alignment explanation
Indices: 10497410--10497449 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
10497400 GCCCGTAAAA
*
10497410 CTAAATACTAAACC
1 CTAAATCCTAAACC
10497424 CTAAA-CCTTAAACC
1 CTAAATCC-TAAACC
10497438 CTAAATCCTAAA
1 CTAAATCCTAAA
10497450 TCCAAAACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAATCCTAAACC
Found at i:10497991 original size:12 final size:13
Alignment explanation
Indices: 10497964--10497995 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
10497954 AAAGAAGTCG
10497964 TTTTGCTTAAATT
1 TTTTGCTTAAATT
10497977 TTTTGCTTAAATT
1 TTTTGCTTAAATT
10497990 TTTTGC
1 TTTTGC
10497996 GGCATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (13 bp):
TTTTGCTTAAATT
Found at i:10498358 original size:152 final size:152
Alignment explanation
Indices: 10498042--10498330 Score: 339
Period size: 152 Copynumber: 1.9 Consensus size: 152
10498032 GTTTTCACCT
* * *
10498042 TAGCGCCGCTAAAGCCCAATATACTGTGGCATTTTTTAAAAAGCGCCACTAAACCAATAAAAGAA
1 TAGCGCCGCTAAAGCCCAATATACTGCGGCATTTTTTAAAAAGCACCACTAAAACAATAAAAG-A
* * ** * *
10498107 AAAAAAAACGGAGTCGTTTTGCACAATTTTTTTGCGGCGTTTTATAAGAATCGCCGCTAATTCCT
65 AAAAAAAACGAAGCCGTTTTGCACAAAGTCTTTGCGGCGTTTTATAAGAATCGCCGCTAATTCAT
10498172 GATCTATACTAGCGTTTCTAATA
130 GATCTATACTAGCGTTTCTAATA
* * * * * ** *
10498195 AAGCGCAGCTAAATCCCGATCTTTTGCGGCATTTTTTTAATAAGCACCACTAAAACAATAAAAG-
1 TAGCGCCGCTAAAGCCCAATATACTGCGGCA-TTTTTTAAAAAGCACCACTAAAACAATAAAAGA
* * * * *
10498259 GAGAAAAACGAAGCCGTTTTGCACAAAGTCTTTGCGGCGTTTTA-CAGGATGCGTCGCTAATTCA
65 AAAAAAAACGAAGCCGTTTTGCACAAAGTCTTTGCGGCGTTTTATAAGAAT-CGCCGCTAATTCA
10498323 TGATCTAT
129 TGATCTAT
10498331 TGCGGCGTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
151 4 0.04
152 56 0.50
153 23 0.21
154 29 0.26
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (152 bp):
TAGCGCCGCTAAAGCCCAATATACTGCGGCATTTTTTAAAAAGCACCACTAAAACAATAAAAGAA
AAAAAAACGAAGCCGTTTTGCACAAAGTCTTTGCGGCGTTTTATAAGAATCGCCGCTAATTCATG
ATCTATACTAGCGTTTCTAATA
Found at i:10498645 original size:29 final size:30
Alignment explanation
Indices: 10498613--10498682 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
10498603 ATTAAATATT
10498613 ATTAATAATTATATTAGT-AATGTTATTAA
1 ATTAATAATTATATTAGTAAATGTTATTAA
* * * *
10498642 ATT-ATATATTATTTTATTAAATTTTATTTA
1 ATTAATA-ATTATATTAGTAAATGTTATTAA
10498672 A-TAATAATTAT
1 ATTAATAATTAT
10498683 GGTAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 3 0.09
29 18 0.53
30 13 0.38
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
ATTAATAATTATATTAGTAAATGTTATTAA
Found at i:10498765 original size:25 final size:26
Alignment explanation
Indices: 10498714--10498765 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
10498704 TTATTTTTAT
*
10498714 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATATATAACAATAA
*
10498740 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATTAAAATATATATAACAATAA
10498765 T
1 T
10498766 CATCTACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATTAAAATATATATAACAATAA
Found at i:10498907 original size:44 final size:44
Alignment explanation
Indices: 10498838--10499063 Score: 144
Period size: 44 Copynumber: 5.1 Consensus size: 44
10498828 TACGACATCT
* * *
10498838 ATTCCATTCAACCAAACACAAGAATTCTATTACAACTCTATTTC
1 ATTCCATTCAACCAAATACAAGAATTCTATTACAGCTCTATTCC
* *
10498882 ATTCCATTCAACCAAATA-ATTGAATTACTGATTACAGCTCTATCCC
1 ATTCCATTCAACCAAATACA-AGAATT-CT-ATTACAGCTCTATTCC
* ** * * * * *
10498928 ATTACAATTCTATTCAATTA-GAGCCCTATTCCATTACA--AC-A-T-C
1 ATT-CCATTC-AACCAAATACAAG---AATTCTATTACAGCTCTATTCC
* * *
10498971 ATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTCC
1 ATTCCATTCAACCAAATACAAGAATTCTATTACAGCTCTATTCC
*
10499015 ATTCCATTCAACCAAATA-ATTGAATTACTTATTACAGCTCTATTCC
1 ATTCCATTCAACCAAATACA-AGAATT-C-TATTACAGCTCTATTCC
10499061 ATT
1 ATT
10499064 ACAGTTCTAT
Statistics
Matches: 136, Mismatches: 29, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
39 9 0.07
41 6 0.04
42 8 0.06
43 7 0.05
44 44 0.32
45 4 0.03
46 36 0.26
47 6 0.04
48 12 0.09
49 1 0.01
50 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (44 bp):
ATTCCATTCAACCAAATACAAGAATTCTATTACAGCTCTATTCC
Found at i:10498933 original size:16 final size:16
Alignment explanation
Indices: 10498912--10498978 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
10498902 TGAATTACTG
*
10498912 ATTACAGCTCTATCCC
1 ATTACAGCTCTATTCC
** *
10498928 ATTACAATTCTATTCA
1 ATTACAGCTCTATTCC
* *
10498944 ATTAGAGCCCTATTCC
1 ATTACAGCTCTATTCC
*
10498960 ATTACAACATC-ATTCC
1 ATTACAGC-TCTATTCC
10498976 ATT
1 ATT
10498979 CAACCAAACA
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
16 37 0.97
17 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:10499066 original size:16 final size:16
Alignment explanation
Indices: 10499045--10499100 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
10499035 TGAATTACTT
10499045 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* **
10499061 ATTACAGTTCTATTTA
1 ATTACAGCTCTATTCC
*
10499077 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
10499093 ATTACAGC
1 ATTACAGC
10499101 AAACCAAATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:10499080 original size:133 final size:134
Alignment explanation
Indices: 10498826--10499098 Score: 431
Period size: 133 Copynumber: 2.0 Consensus size: 134
10498816 TTCTTATACT
* * *
10498826 ATTACGACATCTATTCCATTCAACCAAACACAAGAATTCTATTACAACTCTATTTCATTCCATTC
1 ATTACAACATCTATTCCATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCCATTC
* *
10498891 AACCAAATAATTGAATTACTGATTACAGCTCTATCCCATTACAATTCTATTCAATTAGAGCCCTA
66 AACCAAATAATTGAATTACTGATTACAGCTCTATCCCATTACAATTCTATTCAATTACAACCCTA
10498956 TTCC
131 TTCC
**
10498960 ATTACAACATC-ATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTCCATTC
1 ATTACAACATCTATTCCATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCCATTC
* * * * *
10499024 AACCAAATAATTGAATTACTTATTACAGCTCTATTCCATTACAGTTCTATTTAATTACAACTCTA
66 AACCAAATAATTGAATTACTGATTACAGCTCTATCCCATTACAATTCTATTCAATTACAACCCTA
10499089 TTCC
131 TTCC
10499093 ATTACA
1 ATTACA
10499099 GCAAACCAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
133 117 0.92
134 10 0.08
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (134 bp):
ATTACAACATCTATTCCATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCCATTC
AACCAAATAATTGAATTACTGATTACAGCTCTATCCCATTACAATTCTATTCAATTACAACCCTA
TTCC
Found at i:10508865 original size:29 final size:30
Alignment explanation
Indices: 10508833--10508890 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
10508823 TTAACTTTTT
10508833 TATAT-ATCTTTTAGAATTTTTA-AAATATA
1 TATATAAT-TTTTAGAATTTTTATAAATATA
*
10508862 TATATAATTTTTGGAATTTTTATAAATAT
1 TATATAATTTTTAGAATTTTTATAAATAT
10508891 CTTGAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
TATATAATTTTTAGAATTTTTATAAATATA
Found at i:10508899 original size:19 final size:19
Alignment explanation
Indices: 10508875--10508939 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
10508865 ATAATTTTTG
*
10508875 GAATTTTTATAAA-TATCTT
1 GAATTTTTAAAAATTAT-TT
*
10508894 GAA-TTTCAAAAATTATTTT
1 GAATTTTTAAAAATTA-TTT
*
10508913 AAATTTTTAAAAATTATTT
1 GAATTTTTAAAAATTATTT
10508932 GAATTTTT
1 GAATTTTT
10508940 TTTGTAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.18
19 19 0.50
20 12 0.32
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (19 bp):
GAATTTTTAAAAATTATTT
Found at i:10508940 original size:20 final size:20
Alignment explanation
Indices: 10508867--10508939 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 20
10508857 ATATATATAT
* *
10508867 AATT-TTTGGAATTTTTATA
1 AATTATTTGAAATTTTTAAA
*
10508886 AA-TATCTTG-AA-TTTCAAA
1 AATTAT-TTGAAATTTTTAAA
*
10508904 AATTATTTTAAATTTTTAAA
1 AATTATTTGAAATTTTTAAA
10508924 AATTATTTG-AATTTTT
1 AATTATTTGAAATTTTT
10508940 TTTGTAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 10 0.23
19 17 0.39
20 17 0.39
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTATTTGAAATTTTTAAA
Found at i:10509755 original size:23 final size:23
Alignment explanation
Indices: 10509708--10509756 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10509698 CCTCCTCTTT
* * **
10509708 TTTTTTTATTTTAAAATTTTTAA
1 TTTTTATATTTCAAAATTTAAAA
10509731 TTTTTATATTTCAAAATTTAAAA
1 TTTTTATATTTCAAAATTTAAAA
10509754 TTT
1 TTT
10509757 AATTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTATATTTCAAAATTTAAAA
Found at i:10510476 original size:39 final size:39
Alignment explanation
Indices: 10510395--10510490 Score: 94
Period size: 39 Copynumber: 2.5 Consensus size: 39
10510385 ATAATTATTG
* * *
10510395 CTAAAATTCCTATT-GAAAACC--TTTTGTAACCAAATA
1 CTAAAATTCTTATTGGAAACCCATTTTTATAACCAAATA
*
10510431 CTAAAATTACTT-TTGGAAACCCATTTTTATAATCAAATA
1 CTAAAATT-CTTATTGGAAACCCATTTTTATAACCAAATA
*
10510470 -TCAAAATTTTTATTGGAAACC
1 CT-AAAATTCTTATTGGAAACC
10510491 TAACTTTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
36 10 0.20
37 8 0.16
38 3 0.06
39 28 0.57
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (39 bp):
CTAAAATTCTTATTGGAAACCCATTTTTATAACCAAATA
Found at i:10511834 original size:55 final size:56
Alignment explanation
Indices: 10511730--10511837 Score: 182
Period size: 55 Copynumber: 1.9 Consensus size: 56
10511720 ATTACTTAGA
*
10511730 AATCAAATTGCTAAAAGATAATATATCATAATAATATCATATAATATCTCATTATG
1 AATCAAATTGCTAAAAGATAATATACCATAATAATATCATATAATATCTCATTATG
* *
10511786 AATCAAATTGCTAAGAGATAATAT-CCATAATAATATCCTATAATATCTCATT
1 AATCAAATTGCTAAAAGATAATATACCATAATAATATCATATAATATCTCATT
10511838 TTTTGTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 26 0.53
56 23 0.47
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (56 bp):
AATCAAATTGCTAAAAGATAATATACCATAATAATATCATATAATATCTCATTATG
Found at i:10515223 original size:36 final size:36
Alignment explanation
Indices: 10515173--10515299 Score: 116
Period size: 36 Copynumber: 3.5 Consensus size: 36
10515163 GTACATCGAC
* * * * *
10515173 AATCCAACCAAAACACACTAGATGCTCATAAGAGTT
1 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
*
10515209 TATCCATCCGAAACACACCAAATGCTCATAAGAGCT
1 AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
* * *
10515245 AATCTATTCGAAACACACC-AATGGCTTC-GAAGAGCT
1 AATCCATCCGAAACACACCAAAT-GC-TCATAAGAGCT
*
10515281 AGTCCAAT-CGAAACACACC
1 AATCC-ATCCGAAACACACC
10515300 GAAACAGAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
35 3 0.04
36 69 0.91
37 4 0.05
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (36 bp):
AATCCATCCGAAACACACCAAATGCTCATAAGAGCT
Found at i:10516264 original size:21 final size:21
Alignment explanation
Indices: 10516238--10516279 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10516228 TGATAGAAAG
10516238 CCTATTATTGTCCATAAAAAA
1 CCTATTATTGTCCATAAAAAA
10516259 CCTATTATTGTCCATAAAAAA
1 CCTATTATTGTCCATAAAAAA
10516280 TAAACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
CCTATTATTGTCCATAAAAAA
Found at i:10524384 original size:36 final size:36
Alignment explanation
Indices: 10524344--10524413 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
10524334 GTACATCGAC
*
10524344 AATCCAACCAAAACACACCAGATGCTCATAAGAGCT
1 AATCCAACCAAAACACACCAAATGCTCATAAGAGCT
* * * *
10524380 AATCCATCCGAAACGCACCAAATGCTTATAAGAG
1 AATCCAACCAAAACACACCAAATGCTCATAAGAG
10524414 TACATCGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.43, C:0.29, G:0.13, T:0.16
Consensus pattern (36 bp):
AATCCAACCAAAACACACCAAATGCTCATAAGAGCT
Found at i:10526373 original size:16 final size:16
Alignment explanation
Indices: 10526352--10526382 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10526342 ATTTGACAAT
10526352 AAAAATTAAAAGTATG
1 AAAAATTAAAAGTATG
10526368 AAAAATTAAAAGTAT
1 AAAAATTAAAAGTAT
10526383 CTCCTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAAATTAAAAGTATG
Found at i:10541628 original size:17 final size:19
Alignment explanation
Indices: 10541587--10541625 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
10541577 CACAACGAGG
10541587 AATTGAAGTAGATAGAGCAA
1 AATTGAAGTAGATAGAG-AA
10541607 AATTGAAGTA-ATAGAGAA
1 AATTGAAGTAGATAGAGAA
10541625 A
1 A
10541626 TTGCCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 6 0.32
20 10 0.53
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.21
Consensus pattern (19 bp):
AATTGAAGTAGATAGAGAA
Found at i:10551496 original size:14 final size:14
Alignment explanation
Indices: 10551473--10551508 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
10551463 AATACCATTC
10551473 AAAAAAAAG-AAGA
1 AAAAAAAAGAAAGA
10551486 AAAAGAAAAGAAAGA
1 AAAA-AAAAGAAAGA
10551501 AAAAAAAA
1 AAAAAAAA
10551509 ACCATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:10551507 original size:18 final size:18
Alignment explanation
Indices: 10551473--10551507 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10551463 AATACCATTC
*
10551473 AAAAAAAAGAAGAAAAAG
1 AAAAAAAAGAAAAAAAAG
*
10551491 AAAAGAAAGAAAAAAAA
1 AAAAAAAAGAAAAAAAA
10551508 AACCATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAG
Found at i:10551509 original size:15 final size:14
Alignment explanation
Indices: 10551473--10551509 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
10551463 AATACCATTC
10551473 AAAAAAAAGAAGAA
1 AAAAAAAAGAAGAA
*
10551487 AAAGAAAAGAAAGAA
1 AAAAAAAAG-AAGAA
10551502 AAAAAAAA
1 AAAAAAAA
10551510 CCATAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAGAA
Found at i:10558782 original size:17 final size:17
Alignment explanation
Indices: 10558760--10558792 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10558750 ATAGAAAGTC
10558760 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
10558777 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
10558793 AAATCTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:10578698 original size:51 final size:52
Alignment explanation
Indices: 10578638--10578746 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 52
10578628 ACATTTTTAT
* *
10578638 TTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATT-TCATTTCTCTA
1 TTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCA
* * *
10578689 TTTTCATTTTGGAGAAAACCATAATCATTTTCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCA
10578741 TTTTCA
1 TTTTCA
10578747 CCAGTTCTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
51 36 0.69
52 16 0.31
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.45
Consensus pattern (52 bp):
TTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCTCATTTCTCCA
Found at i:10583033 original size:26 final size:27
Alignment explanation
Indices: 10582991--10583045 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
10582981 TGTGCCATAG
10582991 AGGCTTCTTTATCATAGATCCCCACAA
1 AGGCTTCTTTATCATAGATCCCCACAA
* *
10583018 AGGCTT-TTTTTCATAGATCGCCACAA
1 AGGCTTCTTTATCATAGATCCCCACAA
10583044 AG
1 AG
10583046 ACTACCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (27 bp):
AGGCTTCTTTATCATAGATCCCCACAA
Found at i:10584979 original size:73 final size:74
Alignment explanation
Indices: 10584859--10585005 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
10584849 TGGAAAACTC
10584859 ACTAGTGTGCTACGAGGAAGCAAAAAATAAGGTGTGGGTCCTAAACTCATAAAATTCTTTGAAAA
1 ACTAGTGTGCTACGAGGAAGCAAAAAATAAGGTGTGGGTCCTAAACTCATAAAATTCTTTGAAAA
10584924 TTTTAAATA
66 TTTTAAATA
10584933 ACTAGTGTGC-ACGAGGAAGCAAAAAATAAGGTGTGGGTCCTAAACTCATAAAATTCTTTGAAAA
1 ACTAGTGTGCTACGAGGAAGCAAAAAATAAGGTGTGGGTCCTAAACTCATAAAATTCTTTGAAAA
10584997 TTTTAAATA
66 TTTTAAATA
10585006 TCAGGTTATA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.86
74 10 0.14
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (74 bp):
ACTAGTGTGCTACGAGGAAGCAAAAAATAAGGTGTGGGTCCTAAACTCATAAAATTCTTTGAAAA
TTTTAAATA
Found at i:10602175 original size:16 final size:17
Alignment explanation
Indices: 10602136--10602174 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
10602126 GTTAATTAAG
*
10602136 TAAAAAGGTCTAAATCA
1 TAAAAAGGACTAAATCA
*
10602153 TAAAAAGGACTAAATCG
1 TAAAAAGGACTAAATCA
10602170 TAAAA
1 TAAAA
10602175 GTGTAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (17 bp):
TAAAAAGGACTAAATCA
Found at i:10602318 original size:22 final size:21
Alignment explanation
Indices: 10602289--10602333 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
10602279 CATGGATAGG
*
10602289 TTTTAATG-TAATTATGGTAAT
1 TTTTAATGTTAATTA-AGTAAT
10602310 TTTTAAATGTTAATTAAGTAAT
1 TTTT-AATGTTAATTAAGTAAT
10602332 TT
1 TT
10602334 GATAATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 11 0.52
23 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
TTTTAATGTTAATTAAGTAAT
Found at i:10602355 original size:16 final size:16
Alignment explanation
Indices: 10602312--10602358 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
10602302 ATGGTAATTT
10602312 TTAAATGTTAATTAAG
1 TTAAATGTTAATTAAG
* *
10602328 -TAATTTGATAATTAAG
1 TTAA-ATGTTAATTAAG
10602344 TTAAATGTTAATTAA
1 TTAAATGTTAATTAA
10602359 ATAAAAGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (16 bp):
TTAAATGTTAATTAAG
Found at i:10607365 original size:17 final size:18
Alignment explanation
Indices: 10607343--10607376 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10607333 TTTGGGCCGA
10607343 GTGGG-CCACAAGGGCAT
1 GTGGGCCCACAAGGGCAT
*
10607360 GTGGGCCCACATGGGCA
1 GTGGGCCCACAAGGGCA
10607377 GACCACATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.26, G:0.41, T:0.12
Consensus pattern (18 bp):
GTGGGCCCACAAGGGCAT
Found at i:10611400 original size:16 final size:16
Alignment explanation
Indices: 10611357--10611403 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
10611347 ATGGTAATTT
*
10611357 TTAAAGGTTAATTAAG
1 TTAAATGTTAATTAAG
* *
10611373 -TAATTTGATAATTAAG
1 TTAA-ATGTTAATTAAG
10611389 TTAAATGTTAATTAA
1 TTAAATGTTAATTAA
10611404 ATAAAAGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
TTAAATGTTAATTAAG
Found at i:10617452 original size:2 final size:2
Alignment explanation
Indices: 10617445--10617480 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10617435 CGAAGGGTTC
10617445 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10617481 ATTTGATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10624392 original size:18 final size:17
Alignment explanation
Indices: 10624364--10624398 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10624354 ATTATTAAGA
*
10624364 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
10624381 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
10624399 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:10624653 original size:16 final size:16
Alignment explanation
Indices: 10624632--10624685 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
10624622 TTGATTTGCT
10624632 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
10624648 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
10624664 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
10624680 AATACA
1 ATTACA
10624686 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:10625517 original size:80 final size:80
Alignment explanation
Indices: 10625246--10625485 Score: 480
Period size: 80 Copynumber: 3.0 Consensus size: 80
10625236 TTATGAATGG
10625246 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
1 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
10625311 TGATATAATAACATT
66 TGATATAATAACATT
10625326 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
1 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
10625391 TGATATAATAACATT
66 TGATATAATAACATT
10625406 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
1 TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
10625471 TGATATAATAACATT
66 TGATATAATAACATT
10625486 ATATTTGTGA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 160 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (80 bp):
TTAAGTTGTATGATATCGAATGCTCGGTTTAGATGATTATTCTCTTGAATTGGTTTAGATTGGCA
TGATATAATAACATT
Found at i:10627267 original size:8 final size:8
Alignment explanation
Indices: 10627254--10627278 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10627244 ATATAATTGA
10627254 TTTATATT
1 TTTATATT
10627262 TTTATATT
1 TTTATATT
10627270 TTTATATT
1 TTTATATT
10627278 T
1 T
10627279 GAAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTATATT
Found at i:10631068 original size:24 final size:24
Alignment explanation
Indices: 10631041--10631092 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
10631031 TTAGTAAGTC
*
10631041 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
10631065 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
10631089 AAAT
1 AAAT
10631093 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:10638751 original size:10 final size:10
Alignment explanation
Indices: 10638734--10638778 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
10638724 AATTTAATTC
10638734 TTTTCTTTTA
1 TTTTCTTTTA
*
10638744 TGTTCTTTTAA
1 TTTTCTTTT-A
10638755 TTTTCTTTT-
1 TTTTCTTTTA
10638764 TTTTCTTTTA
1 TTTTCTTTTA
10638774 TTTTC
1 TTTTC
10638779 CATTCTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 9 0.29
10 13 0.42
11 9 0.29
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:10638771 original size:20 final size:20
Alignment explanation
Indices: 10638734--10638778 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
10638724 AATTTAATTC
10638734 TTTTCTTTTATGTTCTTTTAA
1 TTTTCTTTTATGTTCTTTT-A
*
10638755 TTTTCTTTT-TTTTCTTTTA
1 TTTTCTTTTATGTTCTTTTA
10638774 TTTTC
1 TTTTC
10638779 CATTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTATGTTCTTTTA
Found at i:10638787 original size:20 final size:20
Alignment explanation
Indices: 10638746--10638789 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10638736 TTCTTTTATG
* *
10638746 TTCTTTTAATTTTCTTTTTT
1 TTCTTTTAATTTTCATTCTT
10638766 TTCTTTT-ATTTTCCATTCTT
1 TTCTTTTAATTTT-CATTCTT
10638786 TTCT
1 TTCT
10638790 ACTTCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (20 bp):
TTCTTTTAATTTTCATTCTT
Found at i:10639384 original size:23 final size:23
Alignment explanation
Indices: 10639358--10639401 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
10639348 AATCGTTACC
*
10639358 CTAAGCAGAAA-ATATATTAAAAA
1 CTAAGCA-AAAGAAATATTAAAAA
*
10639381 CTAATCAAAAGAAATATTAAA
1 CTAAGCAAAAGAAATATTAAA
10639402 CAGAACGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (23 bp):
CTAAGCAAAAGAAATATTAAAAA
Found at i:10644028 original size:25 final size:25
Alignment explanation
Indices: 10643996--10644045 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10643986 CGACATCAAA
10643996 ATATCAAAACAACTATCGAGATGAT
1 ATATCAAAACAACTATCGAGATGAT
10644021 ATATCAAAACAACTATCGAGATGAT
1 ATATCAAAACAACTATCGAGATGAT
10644046 GAACGGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
ATATCAAAACAACTATCGAGATGAT
Found at i:10644535 original size:44 final size:45
Alignment explanation
Indices: 10644432--10644553 Score: 165
Period size: 44 Copynumber: 2.7 Consensus size: 45
10644422 TCGTATCAGA
*
10644432 TTTAATGACATAGTATCTTTCAACTATGGTCTTACACATTTCTGG
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTGG
* * * * **
10644477 TTTAGTGTCGCAGTATCTTTCAACCATGGTCTTATTCA-TTCTGG
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTGG
*
10644521 TTTAATGCCACAGTATCTTTCAACTATGGTCTT
1 TTTAATGACACAGTATCTTTCAACTATGGTCTT
10644554 TCTCATTTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 35 0.53
45 31 0.47
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.43
Consensus pattern (45 bp):
TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTGG
Found at i:10644560 original size:44 final size:44
Alignment explanation
Indices: 10644432--10644605 Score: 163
Period size: 45 Copynumber: 3.9 Consensus size: 44
10644422 TCGTATCAGA
* * *
10644432 TTTAATGACATAGTATCTTTCAACTATGGTCTTACACATTTCTGG
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTTCTCA-TTCTGG
* * * *
10644477 TTTAGTGTCGCAGTATCTTTCAACCATGGTCTTAT-TCATTCTGG
1 TTTAATGACACAGTATCTTTCAACTATGGTCTT-TCTCATTCTGG
* *
10644521 TTTAATGCCACAGTATCTTTCAACTATGGTCTTTCTCATTTTGCG
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTTCTCATTCTG-G
** * * * *
10644566 TAAAATGGCA-TGATATCTTTCAATTATAGTCTTTCTCATT
1 TTTAATGACACAG-TATCTTTCAACTATGGTCTTTCTCATT
10644606 TCTCAATCCA
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
43 1 0.01
44 43 0.40
45 63 0.59
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.44
Consensus pattern (44 bp):
TTTAATGACACAGTATCTTTCAACTATGGTCTTTCTCATTCTGG
Found at i:10644605 original size:89 final size:88
Alignment explanation
Indices: 10644432--10644598 Score: 194
Period size: 89 Copynumber: 1.9 Consensus size: 88
10644422 TCGTATCAGA
* ** *
10644432 TTTAATGACATAGTATCTTTCAACTATGGTCTTACACATTTCTGGTTTAGTGTCGCAGTATCTTT
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTGGTAAAATG-CGCAGTATCTTT
*
10644497 CAACCATGGTCTTATTCATTCTGG
65 CAACCATAGTCTTATTCATTCTGG
* * *
10644521 TTTAATGCCACAGTATCTTTCAACTATGGTCTTTCTCATTT-TGCGTAAAATG-GCATGATATCT
1 TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTG-GTAAAATGCGCA-G-TATCT
**
10644584 TTCAATTATAGTCTT
63 TTCAACCATAGTCTT
10644599 TCTCATTTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
87 3 0.05
88 3 0.05
89 59 0.91
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (88 bp):
TTTAATGACACAGTATCTTTCAACTATGGTCTTACACATTTCTGGTAAAATGCGCAGTATCTTTC
AACCATAGTCTTATTCATTCTGG
Found at i:10661020 original size:19 final size:20
Alignment explanation
Indices: 10660973--10661020 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
10660963 ACCGATGTAA
*
10660973 AATTAAAATAGTTTTATATC
1 AATTAATATAGTTTTATATC
* * *
10660993 ATTTCATATATTTTTATA-C
1 AATTAATATAGTTTTATATC
10661012 AATTAATAT
1 AATTAATAT
10661021 TTTAATGCTC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTAATATAGTTTTATATC
Found at i:10662408 original size:31 final size:31
Alignment explanation
Indices: 10662373--10662513 Score: 85
Period size: 31 Copynumber: 4.6 Consensus size: 31
10662363 AACTAGATTT
*
10662373 AAGGGTTTATTTAAATAAGTCAATATAGCTC
1 AAGGGTTTATTTAAATAAGACAATATAGCTC
* * * *
10662404 AAGGGTTTATCTAGATATAA-AAAAAATA-CTAT
1 AAGGGTTTATTTA-A-ATAAGACAATATAGCT-C
* * *
10662436 AAGGGTTTATTTAAATAGGCCATTATAGC-C
1 AAGGGTTTATTTAAATAAGACAATATAGCTC
** * * *
10662466 TAAGGGTTTATTTAGGTAAAAAAATATTG-T-
1 -AAGGGTTTATTTAAATAAGACAATATAGCTC
*
10662496 AAGGGCTTATTTAAATAA
1 AAGGGTTTATTTAAATAA
10662514 CTTAGTTTGA
Statistics
Matches: 80, Mismatches: 23, Indels: 16
0.67 0.19 0.13
Matches are distributed among these distances:
29 15 0.19
30 3 0.04
31 39 0.49
32 19 0.24
33 4 0.05
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (31 bp):
AAGGGTTTATTTAAATAAGACAATATAGCTC
Found at i:10662471 original size:63 final size:60
Alignment explanation
Indices: 10662372--10662513 Score: 169
Period size: 63 Copynumber: 2.3 Consensus size: 60
10662362 CAACTAGATT
*
10662372 TAAGGGTTTATTTAAATAAGTCAATATAGCTCAAGGGTTTATCTAGATATAAAAAAAATACTA
1 TAAGGGTTTATTTAAATAAGCCAATATAGCTCAAGGGTTTATCTAG--AT-AAAAAAATACTA
* * * * * *
10662435 TAAGGGTTTATTTAAATAGGCCATTATAGC-CTAAGGGTTTATTTAGGTAAAAAAATATTG
1 TAAGGGTTTATTTAAATAAGCCAATATAGCTC-AAGGGTTTATCTAGATAAAAAAATACTA
*
10662495 TAAGGGCTTATTTAAATAA
1 TAAGGGTTTATTTAAATAA
10662514 CTTAGTTTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 27 0.39
61 1 0.01
62 1 0.01
63 40 0.58
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (60 bp):
TAAGGGTTTATTTAAATAAGCCAATATAGCTCAAGGGTTTATCTAGATAAAAAAATACTA
Found at i:10669778 original size:15 final size:15
Alignment explanation
Indices: 10669760--10669791 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10669750 TTTTTTGTAT
*
10669760 TATTTTAATATTAAA
1 TATTTTAAAATTAAA
10669775 TATTTTAAAATTAAA
1 TATTTTAAAATTAAA
10669790 TA
1 TA
10669792 ACATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATTAAA
Found at i:10672760 original size:3 final size:3
Alignment explanation
Indices: 10672747--10672796 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
10672737 TTTACCAAAA
*
10672747 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
10672792 AAG AA
1 AAG AA
10672797 ATAGCAGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10685871 original size:17 final size:17
Alignment explanation
Indices: 10685851--10685890 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
10685841 AGAAGAGTGT
* *
10685851 ACCAAACCTTGGAGTTC
1 ACCAAACCCTAGAGTTC
10685868 ACCAAACCCTAGAGTTC
1 ACCAAACCCTAGAGTTC
*
10685885 GCCAAA
1 ACCAAA
10685891 TGGCAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (17 bp):
ACCAAACCCTAGAGTTC
Found at i:10685987 original size:15 final size:15
Alignment explanation
Indices: 10685967--10685998 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10685957 CATTTAATGG
10685967 ATAATTCACCAATCT
1 ATAATTCACCAATCT
10685982 ATAATTCACCAATCT
1 ATAATTCACCAATCT
10685997 AT
1 AT
10685999 CACTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATTCACCAATCT
Found at i:10707124 original size:70 final size:70
Alignment explanation
Indices: 10707036--10707178 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
10707026 TGATCTCTCG
10707036 GCACAACAGAAACTAGAGTGTTCCACCACTGATATGCTAAATCTTTCAATTAGGATAGAACACAT
1 GCACAACAGAAACTAGAGTGTTCCACCACTGATATGCTAAATCTTTCAATTAGGATAGAACACAT
10707101 TTCAC
66 TTCAC
*
10707106 GCACAACAGAAACTAGAGTGTTCCACCACTGATATGCTGAATCTTTCAATTAGGATAGAACACAT
1 GCACAACAGAAACTAGAGTGTTCCACCACTGATATGCTAAATCTTTCAATTAGGATAGAACACAT
10707171 TTCAC
66 TTCAC
10707176 GCA
1 GCA
10707179 TTCAATCGGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (70 bp):
GCACAACAGAAACTAGAGTGTTCCACCACTGATATGCTAAATCTTTCAATTAGGATAGAACACAT
TTCAC
Found at i:10714908 original size:157 final size:157
Alignment explanation
Indices: 10714622--10714931 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 157
10714612 ATAAGAATAT
*
10714622 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
10714687 AAATATGATTAAATTATTTATTATTCATATTAATAATCTTATCAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
10714752 TAATAATTTACCAAAACAAATTTCTGG
131 TAATAATTTACCAAAACAAATTTCTGG
* *
10714779 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
10714844 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
*
10714909 TAATCATTTACCAAAACAAATTT
131 TAATAATTTACCAAAACAAATTT
10714932 ATGCTAAGGG
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTCTGG
Found at i:10715086 original size:16 final size:16
Alignment explanation
Indices: 10715061--10715112 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
10715051 GATTTGCTAT
10715061 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
10715077 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
10715093 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10715109 TACA
1 TACA
10715113 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:10717335 original size:14 final size:14
Alignment explanation
Indices: 10717316--10717345 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10717306 GCAAAAATTA
10717316 AAAGAAAGAAAAAG
1 AAAGAAAGAAAAAG
*
10717330 AAAGAAAGAATAAG
1 AAAGAAAGAAAAAG
10717344 AA
1 AA
10717346 GAGACCGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAAAG
Found at i:10723416 original size:6 final size:6
Alignment explanation
Indices: 10723405--10723439 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
10723395 GCAAATGTAT
*
10723405 CATTTC CATTTC CATTTC CATTTC CATTTC TATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
10723440 TTGAAACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
CATTTC
Found at i:10730322 original size:113 final size:113
Alignment explanation
Indices: 10730124--10730350 Score: 411
Period size: 113 Copynumber: 2.0 Consensus size: 113
10730114 ACTTTCAAGA
* *
10730124 GGGGATAAATAGTGATAAGATTGTAAACAGTGGAAGACCAAGTTTAGTATTGCATTGCATATCTC
1 GGGGATAAATAGTAATAAGATTATAAACAGTGGAAGACCAAGTTTAGTATTGCATTGCATATCTC
10730189 ATCACTCAGTTGTTCAAAATAGTAATATGGAAAATATTAAATTAGCAT
66 ATCACTCAGTTGTTCAAAATAGTAATATGGAAAATATTAAATTAGCAT
*
10730237 GGGGATAAATAGTAATAGTGA-TATAAACAGTGGAAGACCAAGTTTAGTATTGCATTGCATATCT
1 GGGGATAAATAGTAATA-AGATTATAAACAGTGGAAGACCAAGTTTAGTATTGCATTGCATATCT
10730301 CATCACTCAGTTGTTCAAAATAGTAATATGGAAAATATTAAATTAGCAT
65 CATCACTCAGTTGTTCAAAATAGTAATATGGAAAATATTAAATTAGCAT
10730350 G
1 G
10730351 TTCTACTCTC
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
113 108 0.98
114 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (113 bp):
GGGGATAAATAGTAATAAGATTATAAACAGTGGAAGACCAAGTTTAGTATTGCATTGCATATCTC
ATCACTCAGTTGTTCAAAATAGTAATATGGAAAATATTAAATTAGCAT
Found at i:10733790 original size:6 final size:6
Alignment explanation
Indices: 10733779--10733813 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
10733769 GCAAATGTAT
*
10733779 CATTTC CATTTC CATTTC CATTTC CATTTC TATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
10733814 TTGAAACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
CATTTC
Found at i:10737345 original size:22 final size:22
Alignment explanation
Indices: 10737320--10737367 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
10737310 AAAGGTGTTT
10737320 AGGGTGGTG-ATTTAGAGAGTTA
1 AGGGTGGTGAATTTA-AGAGTTA
*
10737342 AGGGTTGTGAATTTAAGAGTTA
1 AGGGTGGTGAATTTAAGAGTTA
10737364 AGGG
1 AGGG
10737368 AGATGCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (22 bp):
AGGGTGGTGAATTTAAGAGTTA
Found at i:10742060 original size:10 final size:10
Alignment explanation
Indices: 10742041--10742087 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
10742031 AAATCTGTCG
10742041 AAAA-TAATC
1 AAAATTAATC
10742050 AAAATTAATC
1 AAAATTAATC
*
10742060 AAAATTTAATAT
1 AAAA-TTAAT-C
*
10742072 AAAATTAATT
1 AAAATTAATC
10742082 AAAATT
1 AAAATT
10742088 CAACATGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.12
10 16 0.47
11 10 0.29
12 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATC
Found at i:10744063 original size:22 final size:23
Alignment explanation
Indices: 10744033--10744104 Score: 56
Period size: 25 Copynumber: 3.0 Consensus size: 23
10744023 CAAATCTATC
*
10744033 AAAAATAA-TAAAAAATAATTAT
1 AAAATTAAGTAAAAAATAATTAT
* * *
10744055 AAAATTAATTAAAATTAAAAATTTT
1 AAAATTAAGTAAAA--AATAATTAT
*
10744080 AATAATTTAAGTATAAAATAATTAT
1 AA-AA-TTAAGTAAAAAATAATTAT
10744105 TTTATAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
22 7 0.18
23 5 0.13
25 16 0.42
26 2 0.05
27 8 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
AAAATTAAGTAAAAAATAATTAT
Found at i:10748762 original size:290 final size:290
Alignment explanation
Indices: 10748242--10749116 Score: 1388
Period size: 290 Copynumber: 3.0 Consensus size: 290
10748232 TGGATAAACT
10748242 CGGTGAATCTTAAACGGACAGGACCAATGTGATTTTAACTTACCTAGAAAGAACCTTAATCTGGA
1 CGGTGAATCTTAAACGGACAGGACCAATGTGATTTTAACTTACCTAGAAAGAACCTTAATCTGGA
10748307 ATTGAAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATC
66 ATTGAAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATC
10748372 TCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCA
131 TCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCA
10748437 TTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCA
196 TTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCA
10748502 GTAAGCTTTGTACTCTAACACCAAGGGCAG
261 GTAAGCTTTGTACTCTAACACCAAGGGCAG
10748532 CGGTGAATCTTAAACGGACAGGACCAATGTGATTTTAACTTACCTAGAAAGAACCTTAATCTGGA
1 CGGTGAATCTTAAACGGACAGGACCAATGTGATTTTAACTTACCTAGAAAGAACCTTAATCTGGA
10748597 ATTGAAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATC
66 ATTGAAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATC
10748662 TCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCA
131 TCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCA
10748727 TTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCA
196 TTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCA
10748792 GTAAGCTTTGTACTCTAACACCAAGGGCA-
261 GTAAGCTTTGTACTCTAACACCAAGGGCAG
* * * ** * * * ** * * * ***
10748821 -GATGATAGGCTT--TCCCA-AAGACTAACCTAT-AGGTTGACATCCCTA-AAAGTGTCTGGT-A
1 CGGTGA-A-TCTTAAACGGACAGGACCAA--TGTGATTTTAACTTACCTAGAAAGAACCT--TAA
* ** * *
10748879 TGTTGTCCTATCGGCCCATGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGC
60 T-CTG--GAAT-TG---AAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGC
10748944 TTGTCATGCCATCTCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAA
118 TTGTCATGCCATCTCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAA
10749009 TTCTTCTAACTCATTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTT
183 TTCTTCTAACTCATTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTT
10749074 GTTGGAGAGCCCAGTAAGCTTTGTACTCTAACACCAAGGGCAG
248 GTTGGAGAGCCCAGTAAGCTTTGTACTCTAACACCAAGGGCAG
10749117 ATGATAGGCT
Statistics
Matches: 550, Mismatches: 21, Indels: 22
0.93 0.04 0.04
Matches are distributed among these distances:
287 12 0.02
288 18 0.03
289 6 0.01
290 292 0.53
291 2 0.00
292 1 0.00
295 219 0.40
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (290 bp):
CGGTGAATCTTAAACGGACAGGACCAATGTGATTTTAACTTACCTAGAAAGAACCTTAATCTGGA
ATTGAAGAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATC
TCTTAAGTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCA
TTGAGTTCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCA
GTAAGCTTTGTACTCTAACACCAAGGGCAG
Found at i:10749133 original size:295 final size:295
Alignment explanation
Indices: 10748313--10749192 Score: 1408
Period size: 295 Copynumber: 3.0 Consensus size: 295
10748303 TGGAATTGAA
10748313 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
1 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
10748378 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
66 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
10748443 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
131 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
* * * ** * * * ** *
10748508 TTTGTACTCTAACACCAAGGGCAGCGGTGA-A-TCTTAAACGGACAGGACCAA--TGTGATTTTA
196 TTTGTACTCTAACACCAAGGGCA--GATGATAGGCTT--TCCCA-AAGACTAACCTAT-AGGTTG
* * *** * ** * *
10748569 ACTTACCTAGAAAGAACCT--TAAT-CTG--GAAT-TG---AA
255 ACATCCCTA-AAAGTGTCTGGT-ATGTTGTCCTATCGGCCCAT
10748603 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
1 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
10748668 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
66 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
10748733 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
131 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
10748798 TTTGTACTCTAACACCAAGGGCAGATGATAGGCTTTCCCAAAGACTAACCTATAGGTTGACATCC
196 TTTGTACTCTAACACCAAGGGCAGATGATAGGCTTTCCCAAAGACTAACCTATAGGTTGACATCC
10748863 CTAAAAGTGTCTGGTATGTTGTCCTATCGGCCCAT
261 CTAAAAGTGTCTGGTATGTTGTCCTATCGGCCCAT
10748898 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
1 GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
10748963 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
66 GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
10749028 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
131 TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
10749093 TTTGTACTCTAACACCAAGGGCAGATGATAGGCTTTCCCAAAGACTAACCTATAGGTTGACATCC
196 TTTGTACTCTAACACCAAGGGCAGATGATAGGCTTTCCCAAAGACTAACCTATAGGTTGACATCC
10749158 CTAAAAGTGTCTGGTATGTTGTCCTATCGGCCCAT
261 CTAAAAGTGTCTGGTATGTTGTCCTATCGGCCCAT
10749193 AAAGCATCAC
Statistics
Matches: 556, Mismatches: 21, Indels: 21
0.93 0.04 0.04
Matches are distributed among these distances:
287 12 0.02
288 18 0.03
289 6 0.01
290 221 0.40
291 2 0.00
292 1 0.00
295 296 0.53
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (295 bp):
GAAAAAGACTTGCTGACCTGCTTTAAATTCTTGAACCCAAATGTGCTTGTCATGCCATCTCTTAA
GTCTTTCCTTGAGTAATTTGGCATTCTAGTATGAGAACATTTGAAATTCTTCTAACTCATTGAGT
TCGAGCATCTGTTTCTCTTTAGCAAGCTTAAAATCCAAGTTGAGTTGTTGGAGAGCCCAGTAAGC
TTTGTACTCTAACACCAAGGGCAGATGATAGGCTTTCCCAAAGACTAACCTATAGGTTGACATCC
CTAAAAGTGTCTGGTATGTTGTCCTATCGGCCCAT
Found at i:10754283 original size:22 final size:22
Alignment explanation
Indices: 10754240--10754304 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
10754230 TGCCAGTAGT
*
10754240 CAGAATAGCTA-AGAGCCGTAAA
1 CAGAATAGCTACA-AGCCATAAA
* * *
10754262 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTACAAGCCATAAA
*
10754284 CAGAATGGCTACAAGCCATAA
1 CAGAATAGCTACAAGCCATAA
10754305 GTACAGTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (22 bp):
CAGAATAGCTACAAGCCATAAA
Found at i:10754364 original size:32 final size:32
Alignment explanation
Indices: 10754296--10754594 Score: 275
Period size: 32 Copynumber: 9.4 Consensus size: 32
10754286 GAATGGCTAC
* * * *
10754296 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* *
10754327 AAGCCATCAGTAGCAGTGATATGACCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * * *
10754359 CAGCCATCAGTAACGGTAACATGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* **
10754391 AAGCTATCAGTAGTAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * * *
10754423 TAGTCATCAGTAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
*
10754455 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * *
10754487 CAA-CCATCAATAACAGTGAAATGATCAGCACA
1 -AAGCCATCAGTAACAGTGATATGATCGGCACA
* *
10754519 CAA-CCATC-GATAACGGTAATATGATCGGCACA
1 -AAGCCATCAG-TAACAGTGATATGATCGGCACA
* **
10754551 AAGCCATCAGTAACGGT-ACTATGATTTGCACA
1 AAGCCATCAGTAACAGTGA-TATGATCGGCACA
10754583 AAGCCATCAGTA
1 AAGCCATCAGTA
10754595 GCATCGTAAC
Statistics
Matches: 216, Mismatches: 46, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
31 13 0.06
32 200 0.93
33 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTGATATGATCGGCACA
Found at i:10754420 original size:64 final size:64
Alignment explanation
Indices: 10754316--10754597 Score: 356
Period size: 64 Copynumber: 4.4 Consensus size: 64
10754306 TACAGTAATG
*
10754316 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGTAACGGTAACA
1 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACA
* * * *
10754380 TGATTGGCACAAAGCTATCAGTAGTAGTGATATGATCGGCACATAGTCATCAGTAACGGTAACA
1 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACA
* * * *
10754444 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAACCATCAATAACAGTGAA-A
1 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGT-AACA
** * * * *
10754508 TGATCAGCACACAA-CCATC-GATAACGGTAATATGATCGGCACAAAGCCATCAGTAACGGT-AC
1 TGATTGGCACA-AAGCCATCAG-TAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAAC
10754570 TA
64 -A
*
10754572 TGATTTGCACAAAGCCATCAGTAGCA
1 TGATTGGCACAAAGCCATCAGTAGCA
10754598 TCGTAACAAA
Statistics
Matches: 186, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 177 0.95
65 5 0.03
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (64 bp):
TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACA
Found at i:10754796 original size:24 final size:23
Alignment explanation
Indices: 10754765--10754847 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
10754755 GCCATACTCA
10754765 AAATCAGTCATTCAAATCACAGAC
1 AAATCAGTCATTCAAA-CACAGAC
*
10754789 AAATCAGTCATCCCAAACACAGAC
1 AAATCAGTCAT-TCAAACACAGAC
* * *
10754813 AAATCAGTCATTTAACCATAGAC
1 AAATCAGTCATTCAAACACAGAC
* *
10754836 AAAACAATCATT
1 AAATCAGTCATT
10754848 TGACCTCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 18 0.35
24 29 0.57
25 4 0.08
ACGTcount: A:0.47, C:0.25, G:0.07, T:0.20
Consensus pattern (23 bp):
AAATCAGTCATTCAAACACAGAC
Done.