Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 28 of 145
Found at i:9038984 original size:9 final size:9
Alignment explanation
Indices: 9038966--9039019 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
9038956 CCTTTTAAGC
9038966 TTTA-TTTT
1 TTTATTTTT
9038974 TTTATTTTTT
1 TTTA-TTTTT
9038984 TTTATTTTT
1 TTTATTTTT
9038993 TTTATTTTT
1 TTTATTTTT
*
9039002 ATTATTTTGT
1 TTTATTTT-T
9039012 TTT-TTTTT
1 TTTATTTTT
9039020 AAAACAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 5 0.12
9 25 0.61
10 11 0.27
ACGTcount: A:0.11, C:0.00, G:0.02, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:9040639 original size:16 final size:16
Alignment explanation
Indices: 9040602--9040641 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9040592 TTGATAAAAT
* *
9040602 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
9040618 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
9040634 TAAAATTA
1 TAAAATTA
9040642 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:9040970 original size:20 final size:19
Alignment explanation
Indices: 9040911--9040966 Score: 94
Period size: 20 Copynumber: 2.9 Consensus size: 19
9040901 TCTGTCGGGG
*
9040911 AAATGAAATTGAAAACTAA
1 AAATAAAATTGAAAACTAA
9040930 AAATAAAATTGAAAACATAA
1 AAATAAAATTGAAAAC-TAA
9040950 AAATAAAATTGAAAACT
1 AAATAAAATTGAAAACT
9040967 TAAACTGCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.21
Consensus pattern (19 bp):
AAATAAAATTGAAAACTAA
Found at i:9046119 original size:149 final size:149
Alignment explanation
Indices: 9045849--9046146 Score: 578
Period size: 149 Copynumber: 2.0 Consensus size: 149
9045839 TGTTAAGTAT
9045849 AGTAGAACAAGTCGAGAAACGGATCTTACCCTACACAAAAAAATCATTGGGATACATGACTTCTC
1 AGTAGAACAAGTCGAGAAACGGATCTTACCCTACACAAAAAAATCATTGGGATACATGACTTCTC
*
9045914 CTTATGTGGGGCATGAAGGTCATTTGGTCGATCTCGCCAAAAAAGTCTGACGGTCATCGATTCGT
66 CTTATGTGGGGCATGAAGGTCATTTGGTCAATCTCGCCAAAAAAGTCTGACGGTCATCGATTCGT
9045979 CTTTGTGGTCGTCAATTAC
131 CTTTGTGGTCGTCAATTAC
9045998 AGTAGAACAAGTCGAGAAACGGATCTTACCCTACACAAAAAAATCATTGGGATACATGACTTCTC
1 AGTAGAACAAGTCGAGAAACGGATCTTACCCTACACAAAAAAATCATTGGGATACATGACTTCTC
*
9046063 CTTATGTGGGGCATGAAGGTCATTTGGTCAATCTCGCCAAAAAAGTCTTACGGTCATCGATTCGT
66 CTTATGTGGGGCATGAAGGTCATTTGGTCAATCTCGCCAAAAAAGTCTGACGGTCATCGATTCGT
9046128 CTTTGTGGTCGTCAATTAC
131 CTTTGTGGTCGTCAATTAC
9046147 TTTACTAAAT
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (149 bp):
AGTAGAACAAGTCGAGAAACGGATCTTACCCTACACAAAAAAATCATTGGGATACATGACTTCTC
CTTATGTGGGGCATGAAGGTCATTTGGTCAATCTCGCCAAAAAAGTCTGACGGTCATCGATTCGT
CTTTGTGGTCGTCAATTAC
Found at i:9047853 original size:86 final size:88
Alignment explanation
Indices: 9047743--9047967 Score: 283
Period size: 86 Copynumber: 2.6 Consensus size: 88
9047733 TGAAGATTGT
* *
9047743 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTATTTCCTTGAGCAGCA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTATCTCCCTGAGCAGCA
* *
9047808 GTGGAATAGGTT-GAA-AATTAC
66 GCGGAATAGGTTAAAATAATTAC
* * * *
9047829 AGATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGTCCCCAGCCTTATCTCCCTGAGTAGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC-TATCTCCCTGAGCAGC
* *
9047894 AGCGGAGTAGGTTAAAAATAATTGC
65 AGCGGAATAGGTT-AAAATAATTAC
* * * * *
9047919 AAATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCT
9047968 CGCCTCCCTT
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
86 45 0.38
87 24 0.21
89 3 0.03
90 45 0.38
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (88 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTATCTCCCTGAGCAGCA
GCGGAATAGGTTAAAATAATTAC
Found at i:9047967 original size:90 final size:87
Alignment explanation
Indices: 9047745--9047967 Score: 277
Period size: 90 Copynumber: 2.5 Consensus size: 87
9047735 AAGATTGTAG
* *
9047745 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC-TATTTCCTTGAGCAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGAGCAGCAG
* * *
9047809 TGGAATAGGTTGAAAATTACAG
66 CGGAATAGGTTAAAAATTACAA
* * * *
9047831 ATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGTCCCCAGCCTTATCTCCCTGAGTAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGAGCAGCAG
* *
9047896 CGGAGTAGGTTAAAAATAATTGCAA
66 CGGAATAGGTT--AAA-AATTACAA
* * * *
9047921 ATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCT
9047968 CGCCTCCCTT
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
86 43 0.37
87 24 0.21
89 2 0.02
90 46 0.40
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (87 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCCTTATCTCCCTGAGCAGCAG
CGGAATAGGTTAAAAATTACAA
Found at i:9047992 original size:90 final size:90
Alignment explanation
Indices: 9047831--9047999 Score: 196
Period size: 90 Copynumber: 1.9 Consensus size: 90
9047821 AAAATTACAG
* * * * *
9047831 ATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGTCCCCAGCCTTATCTCCCTGAGTAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGACACCAGCCTCACCTCCCTGAGTAGCAA
* *
9047896 CGGAGTAGGTTAAAAATAATTGCAA
66 CAGAGTAGGCTAAAAATAATTGCAA
* * ** * * *
9047921 ATCTTATCTCCTTAAGCAGTAGTGGAGTAGATCGAAGACACTAGCCTCGCCTCCCTTG-GTGGCA
1 ATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGACACCAGCCTCACCTCCC-TGAGTAGCA
9047985 ACAGAGTAGGCTAAA
65 ACAGAGTAGGCTAAA
9048000 GATGACAGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
90 62 0.97
91 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (90 bp):
ATCTTATCTCCCTAAGCAGTAGTAGAACAGATCGAAGACACCAGCCTCACCTCCCTGAGTAGCAA
CAGAGTAGGCTAAAAATAATTGCAA
Found at i:9048234 original size:44 final size:43
Alignment explanation
Indices: 9048122--9048251 Score: 109
Period size: 44 Copynumber: 3.0 Consensus size: 43
9048112 GCAGTAGCGG
* ** * *
9048122 AGCAGACCGAAGATACCAGCCTTGCC-TCTCTGGGTCGTAGTGG
1 AGCAGATCGAAGATACCAGCCTTGCCTTC-CTGGACCGCAGTGA
* * * * *
9048165 AGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGA
1 AGCAGATCGAAGATACCAG-CCTTGCCTTCCTGGACCG-CAGTGA
* * *
9048210 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGTCAGCAGTG
1 AGCAGATCGAAGATACCAGCCTTGCCTTCCTGGACCGCAGTG
9048252 GAATAGACTG
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
43 20 0.30
44 24 0.36
45 22 0.33
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.22
Consensus pattern (43 bp):
AGCAGATCGAAGATACCAGCCTTGCCTTCCTGGACCGCAGTGA
Found at i:9048292 original size:44 final size:44
Alignment explanation
Indices: 9048235--9048521 Score: 266
Period size: 44 Copynumber: 6.7 Consensus size: 44
9048225 CCAGCCTTGC
* * *
9048235 CTCCCTGGTCAGCAGTGGAATAGACTGAAGATTGAGAATTCTAT
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTAT
9048279 CTCCCTGGGCAGCAGTGGAATAGATT--A-A---AGAAT-CTCAT
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCT-AT
* ** * * * *
9048317 CTCCTTGGATAGCAGTGGAATAGGTTAAAGATTGTGAATCCTAC
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTAT
* * * * *
9048361 CTCCCTGGTCAGCAGTGGAATAGGTTGAAAACTGAGAATTCTAT
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTAT
*
9048405 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG-GTCCTAT
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTG-AGAATCCTAT
* * * * * *
9048449 CTCCCTGGTCAGTAGTGGAATAGGTTGAAGATCGTGAACCCTAT
1 CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTAT
* * * *
9048493 CTCCTTGAGCAGCAGTGGAGTAGGTTGAA
1 CTCCCTGGGCAGCAGTGGAATAGATTGAA
9048522 AATAGCAGAT
Statistics
Matches: 198, Mismatches: 35, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
37 2 0.01
38 29 0.15
40 1 0.01
41 2 0.01
42 1 0.01
43 1 0.01
44 158 0.80
45 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (44 bp):
CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTAT
Found at i:9048906 original size:44 final size:43
Alignment explanation
Indices: 9048834--9048944 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 43
9048824 GAAGATTGAG
* *
9048834 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAACCAAT
1 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAACC-AT
* * *
9048878 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAACCAT
1 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAACCAT
*
9048921 AGATCTTATCTCTCTAAAGTTGCA
1 A-ATCTTATCTCCCTAAAGTTGCA
9048945 GAGAGCAGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 3 0.05
44 55 0.95
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAACCAT
Found at i:9049322 original size:44 final size:43
Alignment explanation
Indices: 9049254--9049550 Score: 239
Period size: 44 Copynumber: 6.8 Consensus size: 43
9049244 CAAACGTACG
* *
9049254 AATCTTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAACCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-AT
* * *
9049298 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCAT
* *
9049342 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAA-AT--CAT
* * **
9049388 AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-AT
* * * * *
9049432 AATCCTATCTCCCTGAAGGTGTAGTGGAGCGGATTAAAATCTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAT
* * * *
9049475 GAATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCACATC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAT
* * *
9049516 AGTCTTATCTCCCTGAAGTTGCAGAGGAGTAGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
9049551 GAAGCACTAG
Statistics
Matches: 202, Mismatches: 36, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
40 22 0.11
41 7 0.03
42 7 0.03
43 12 0.06
44 114 0.56
45 7 0.03
46 30 0.15
47 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAT
Found at i:9049494 original size:134 final size:132
Alignment explanation
Indices: 9049254--9049507 Score: 343
Period size: 134 Copynumber: 1.9 Consensus size: 132
9049244 CAAACGTACG
* * *
9049254 AATCTTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCCAAAGTTGCAGTGGAGAAGATTAAAACCGATAATCCTATCTCCCTGAAGGTG
*
9049319 CAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAAGAT
66 CAGTGGAGCAGACTAAG-AAGCAAGTCTTATCCTCCTGAAGTTGCAGAGA-GCAGACTGAAAGAT
9049384 GGCA
129 GGCA
* *
9049388 AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTAAAGCCGATAATCCTATCTCCCTGAAGGTG
1 AATCTTATCTCCCCAAAGTTGCAGTGGAGAAGATTAAAACCGATAATCCTATCTCCCTGAAGGTG
* * * *
9049453 TAGTGGAGCGGATTAA-AATCTTGAA-TCTTAT-CTCTCTGAAGTTGCAGAGAGCAGA
66 CAGTGGAGCAGACTAAGAAGC---AAGTCTTATCCTC-CTGAAGTTGCAGAGAGCAGA
9049508 TCACATCTAG
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
132 3 0.03
133 8 0.08
134 93 0.88
135 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (132 bp):
AATCTTATCTCCCCAAAGTTGCAGTGGAGAAGATTAAAACCGATAATCCTATCTCCCTGAAGGTG
CAGTGGAGCAGACTAAGAAGCAAGTCTTATCCTCCTGAAGTTGCAGAGAGCAGACTGAAAGATGG
CA
Found at i:9050833 original size:18 final size:17
Alignment explanation
Indices: 9050809--9050857 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
9050799 TTATTTTTTC
9050809 ATTTTATTATTATTATT
1 ATTTTATTATTATTATT
* *
9050826 ATTTTTATGATTTTTATT
1 A-TTTTATTATTATTATT
*
9050844 ATTTTGTTATTATT
1 ATTTTATTATTATT
9050858 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
ATTTTATTATTATTATT
Found at i:9065214 original size:21 final size:21
Alignment explanation
Indices: 9065190--9065302 Score: 72
Period size: 21 Copynumber: 5.3 Consensus size: 21
9065180 TTGCTCATAT
9065190 TCATATCATATTTTCCACATC
1 TCATATCATATTTTCCACATC
* * *
9065211 TCATATGTATCTTTTGCCA-ATA
1 TCATAT-CATATTTT-CCACATC
*
9065233 TCAATTTCATA-TTTCCACATC
1 TC-ATATCATATTTTCCACATC
* * *
9065254 TCATATGTATCTTTTGCCA-ATA
1 TCATAT-CATATTTT-CCACATC
*
9065276 TCAATTTCATA-TTTCCACATC
1 TC-ATATCATATTTTCCACATC
9065297 TCATAT
1 TCATAT
9065303 GTATCTTTCG
Statistics
Matches: 67, Mismatches: 16, Indels: 19
0.66 0.16 0.19
Matches are distributed among these distances:
20 12 0.18
21 22 0.33
22 21 0.31
23 12 0.18
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (21 bp):
TCATATCATATTTTCCACATC
Found at i:9065256 original size:43 final size:43
Alignment explanation
Indices: 9065195--9065338 Score: 270
Period size: 43 Copynumber: 3.3 Consensus size: 43
9065185 CATATTCATA
9065195 TCATATTTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
1 TCATA-TTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
9065239 TCATATTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
1 TCATATTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
*
9065282 TCATATTTCCACATCTCATATGTATCTTTCGCCAATATCAATT
1 TCATATTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
9065325 TCATATTTCCACAT
1 TCATATTTCCACAT
9065339 TTCTCCATCT
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
43 94 0.95
44 5 0.05
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (43 bp):
TCATATTTCCACATCTCATATGTATCTTTTGCCAATATCAATT
Found at i:9070315 original size:22 final size:24
Alignment explanation
Indices: 9070260--9070315 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
9070250 TTTCATAAGT
9070260 TTAAT-AAAAAATAAATACGATAATA
1 TTAATCAAAAAATAAATAC-AT-ATA
9070285 TT-ATACAAAAAATAAATAC-T-TA
1 TTAAT-CAAAAAATAAATACATATA
9070307 TTAATCAAA
1 TTAATCAAA
9070316 TTTAAACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
22 8 0.29
23 2 0.07
24 3 0.11
25 2 0.07
26 13 0.46
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAATCAAAAAATAAATACATATA
Found at i:9071862 original size:1 final size:1
Alignment explanation
Indices: 9071856--9071932 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
9071846 TAATGAAGAC
* **** * * ***
9071856 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAGGGGATAATAAAAAAAGTTAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9071921 AAAAAAAAAAAA
1 AAAAAAAAAAAA
9071933 TAGTAGAAGG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (1 bp):
A
Found at i:9080263 original size:22 final size:22
Alignment explanation
Indices: 9080235--9080311 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
9080225 TTTCTTTTAA
9080235 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
9080257 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
9080281 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
9080303 TTAGGAGAT
1 TTAGGAGAT
9080312 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:9080280 original size:46 final size:46
Alignment explanation
Indices: 9080230--9080324 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
9080220 TCTATTTTCT
9080230 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
9080276 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
9080322 TTT
1 TTT
9080325 CTATCTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:9083661 original size:3 final size:3
Alignment explanation
Indices: 9083653--9083686 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9083643 GAATAGCACG
9083653 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9083687 TTGGTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9086576 original size:40 final size:41
Alignment explanation
Indices: 9086435--9086578 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 41
9086425 TAAGGCCCAA
* * *
9086435 ACTGATTCTGTGATGGGCTAAGGCCTTACTGCATATTTGAA
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
* *
9086476 ACTGATTCTGTGATGGGCTAAAGCCCTACTGCATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
*
9086517 ATTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
1 ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
*
9086558 ACT-ATACTGAGATGGGCTAAG
1 ACTGATACTGTGATGGGCTAAG
9086579 ACCTAAACTG
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 17 0.18
41 78 0.82
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (41 bp):
ACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGAT
Found at i:9089956 original size:12 final size:12
Alignment explanation
Indices: 9089939--9089969 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9089929 TTCTAGTTTT
9089939 CACACGGCCTAA
1 CACACGGCCTAA
*
9089951 CACACGGCCTGA
1 CACACGGCCTAA
9089963 CACACGG
1 CACACGG
9089970 GCATGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.42, G:0.23, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAA
Found at i:9098864 original size:67 final size:67
Alignment explanation
Indices: 9098791--9098916 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 67
9098781 ACTTCACATG
*
9098791 TGTAACCCCATGTTTTACGTCCTGGTGGACTACTCA-T-GTGGTCATAGTCGAGCTATGGTCATA
1 TGTAACCCCATGTTTAACGTCCTGGTGGACT-C-CATTGGTGGTCATAGTCGAGCTATGGTCATA
9098854 CACA
64 CACA
* * * *
9098858 TGTAACCCCATGTTTAATGTCTTGGTGGACTCCATTGGTTGTCATATTCGAGCTATGGT
1 TGTAACCCCATGTTTAACGTCCTGGTGGACTCCATTGGTGGTCATAGTCGAGCTATGGT
9098917 TTTAGACCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 2 0.04
66 2 0.04
67 48 0.92
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (67 bp):
TGTAACCCCATGTTTAACGTCCTGGTGGACTCCATTGGTGGTCATAGTCGAGCTATGGTCATACA
CA
Found at i:9100745 original size:14 final size:13
Alignment explanation
Indices: 9100710--9100751 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
9100700 TGCATTCAAT
9100710 TAAAT-AATATAATA
1 TAAATAAAT-TAA-A
9100724 TAAATAAATTAAA
1 TAAATAAATTAAA
9100737 TAAATTAAATTAAA
1 TAAA-TAAATTAAA
9100751 T
1 T
9100752 TCTAAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 18 0.69
15 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATAAATTAAA
Found at i:9106324 original size:21 final size:21
Alignment explanation
Indices: 9106300--9106339 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9106290 ACGATGTTGG
* *
9106300 AATAAATTTATAAATAAAATT
1 AATAAACTAATAAATAAAATT
*
9106321 AATATACTAATAAATAAAA
1 AATAAACTAATAAATAAAA
9106340 CTCTATAGTA
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:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAACTAATAAATAAAATT
Found at i:9116061 original size:698 final size:698
Alignment explanation
Indices: 9114725--9116120 Score: 2792
Period size: 698 Copynumber: 2.0 Consensus size: 698
9114715 CAAAAAACGA
9114725 GGCCCGTTTTGAAAACGGGTCGGGCTTCAGGTAAAAATTTTTTGACCCAGCCCCGGCTCAGCCCG
1 GGCCCGTTTTGAAAACGGGTCGGGCTTCAGGTAAAAATTTTTTGACCCAGCCCCGGCTCAGCCCG
9114790 AATTATATATTATATATATATATATTTTTAATAAAATATATATTTAATATGGGTCGGGCCGGGCT
66 AATTATATATTATATATATATATATTTTTAATAAAATATATATTTAATATGGGTCGGGCCGGGCT
9114855 CGGGCTTAGCAATTTTCTTTCAAGCCGGGCTTGGACAAATTTTTAGGCCCATATTTTAGGCTGGG
131 CGGGCTTAGCAATTTTCTTTCAAGCCGGGCTTGGACAAATTTTTAGGCCCATATTTTAGGCTGGG
9114920 CCTGGGCCTAGAAAACGGGCCTAAGATTTTGTCTGGGTCTGACCCGAACCCAGCCCAGCCCGACC
196 CCTGGGCCTAGAAAACGGGCCTAAGATTTTGTCTGGGTCTGACCCGAACCCAGCCCAGCCCGACC
9114985 CATGATCACCTCTAGACTCAATTGTAAAGAGGTTAAAATATGAGGGGCAAATGTGTAATTTTGAA
261 CATGATCACCTCTAGACTCAATTGTAAAGAGGTTAAAATATGAGGGGCAAATGTGTAATTTTGAA
9115050 AAGTATGAATTTGGACTAAATTGAATAGTATGAATATTAAATGGATTAAATTTGATTATTTAAAT
326 AAGTATGAATTTGGACTAAATTGAATAGTATGAATATTAAATGGATTAAATTTGATTATTTAAAT
9115115 CAAGATAAACCTCGTACAGATCTAGATCGAGGAAAAGCTAAATCTTCAGATCAGTTGATCTTATT
391 CAAGATAAACCTCGTACAGATCTAGATCGAGGAAAAGCTAAATCTTCAGATCAGTTGATCTTATT
9115180 TCGAAATCTTTATAATCGAGGTAAGTTTATATGTTTAAATAATGTTTTAATGTTATTTTGATATA
456 TCGAAATCTTTATAATCGAGGTAAGTTTATATGTTTAAATAATGTTTTAATGTTATTTTGATATA
9115245 TATGTTATAGTGCTATTTATCATGTAAGTGAACGATGGAAATCCAACGACGTTTCGATGATTATC
521 TATGTTATAGTGCTATTTATCATGTAAGTGAACGATGGAAATCCAACGACGTTTCGATGATTATC
9115310 AAACCCGGTTTGAACCTTAGGAATATATAGGATACAAATGACAAGTCATTTGAGTTATCATGTTT
586 AAACCCGGTTTGAACCTTAGGAATATATAGGATACAAATGACAAGTCATTTGAGTTATCATGTTT
9115375 CGAGTGCTAGTCCTGAATGTCCTACTGATGGCTGAGTCCCGTTATTTG
651 CGAGTGCTAGTCCTGAATGTCCTACTGATGGCTGAGTCCCGTTATTTG
9115423 GGCCCGTTTTGAAAACGGGTCGGGCTTCAGGTAAAAATTTTTTGACCCAGCCCCGGCTCAGCCCG
1 GGCCCGTTTTGAAAACGGGTCGGGCTTCAGGTAAAAATTTTTTGACCCAGCCCCGGCTCAGCCCG
9115488 AATTATATATTATATATATATATATTTTTAATAAAATATATATTTAATATGGGTCGGGCCGGGCT
66 AATTATATATTATATATATATATATTTTTAATAAAATATATATTTAATATGGGTCGGGCCGGGCT
9115553 CGGGCTTAGCAATTTTCTTTCAAGCCGGGCTTGGACAAATTTTTAGGCCCATATTTTAGGCTGGG
131 CGGGCTTAGCAATTTTCTTTCAAGCCGGGCTTGGACAAATTTTTAGGCCCATATTTTAGGCTGGG
9115618 CCTGGGCCTAGAAAACGGGCCTAAGATTTTGTCTGGGTCTGACCCGAACCCAGCCCAGCCCGACC
196 CCTGGGCCTAGAAAACGGGCCTAAGATTTTGTCTGGGTCTGACCCGAACCCAGCCCAGCCCGACC
9115683 CATGATCACCTCTAGACTCAATTGTAAAGAGGTTAAAATATGAGGGGCAAATGTGTAATTTTGAA
261 CATGATCACCTCTAGACTCAATTGTAAAGAGGTTAAAATATGAGGGGCAAATGTGTAATTTTGAA
9115748 AAGTATGAATTTGGACTAAATTGAATAGTATGAATATTAAATGGATTAAATTTGATTATTTAAAT
326 AAGTATGAATTTGGACTAAATTGAATAGTATGAATATTAAATGGATTAAATTTGATTATTTAAAT
9115813 CAAGATAAACCTCGTACAGATCTAGATCGAGGAAAAGCTAAATCTTCAGATCAGTTGATCTTATT
391 CAAGATAAACCTCGTACAGATCTAGATCGAGGAAAAGCTAAATCTTCAGATCAGTTGATCTTATT
9115878 TCGAAATCTTTATAATCGAGGTAAGTTTATATGTTTAAATAATGTTTTAATGTTATTTTGATATA
456 TCGAAATCTTTATAATCGAGGTAAGTTTATATGTTTAAATAATGTTTTAATGTTATTTTGATATA
9115943 TATGTTATAGTGCTATTTATCATGTAAGTGAACGATGGAAATCCAACGACGTTTCGATGATTATC
521 TATGTTATAGTGCTATTTATCATGTAAGTGAACGATGGAAATCCAACGACGTTTCGATGATTATC
9116008 AAACCCGGTTTGAACCTTAGGAATATATAGGATACAAATGACAAGTCATTTGAGTTATCATGTTT
586 AAACCCGGTTTGAACCTTAGGAATATATAGGATACAAATGACAAGTCATTTGAGTTATCATGTTT
9116073 CGAGTGCTAGTCCTGAATGTCCTACTGATGGCTGAGTCCCGTTATTTG
651 CGAGTGCTAGTCCTGAATGTCCTACTGATGGCTGAGTCCCGTTATTTG
9116121 TTGCGGATAC
Statistics
Matches: 698, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
698 698 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (698 bp):
GGCCCGTTTTGAAAACGGGTCGGGCTTCAGGTAAAAATTTTTTGACCCAGCCCCGGCTCAGCCCG
AATTATATATTATATATATATATATTTTTAATAAAATATATATTTAATATGGGTCGGGCCGGGCT
CGGGCTTAGCAATTTTCTTTCAAGCCGGGCTTGGACAAATTTTTAGGCCCATATTTTAGGCTGGG
CCTGGGCCTAGAAAACGGGCCTAAGATTTTGTCTGGGTCTGACCCGAACCCAGCCCAGCCCGACC
CATGATCACCTCTAGACTCAATTGTAAAGAGGTTAAAATATGAGGGGCAAATGTGTAATTTTGAA
AAGTATGAATTTGGACTAAATTGAATAGTATGAATATTAAATGGATTAAATTTGATTATTTAAAT
CAAGATAAACCTCGTACAGATCTAGATCGAGGAAAAGCTAAATCTTCAGATCAGTTGATCTTATT
TCGAAATCTTTATAATCGAGGTAAGTTTATATGTTTAAATAATGTTTTAATGTTATTTTGATATA
TATGTTATAGTGCTATTTATCATGTAAGTGAACGATGGAAATCCAACGACGTTTCGATGATTATC
AAACCCGGTTTGAACCTTAGGAATATATAGGATACAAATGACAAGTCATTTGAGTTATCATGTTT
CGAGTGCTAGTCCTGAATGTCCTACTGATGGCTGAGTCCCGTTATTTG
Found at i:9120630 original size:7 final size:7
Alignment explanation
Indices: 9120618--9120652 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
9120608 AGTGACAAAA
9120618 GCACATT
1 GCACATT
9120625 GCACATT
1 GCACATT
9120632 GCACATT
1 GCACATT
9120639 GCACATT
1 GCACATT
9120646 GCACATT
1 GCACATT
9120653 CCTTCCTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
GCACATT
Found at i:9124235 original size:114 final size:113
Alignment explanation
Indices: 9124051--9124311 Score: 267
Period size: 114 Copynumber: 2.3 Consensus size: 113
9124041 TACCGACATT
* * * * *
9124051 TTATCATAAACGCCGCAAAAACTGCTAAGAAAACGGAGCCGTTTTAGGTTTAGGTTTTAGGAAAG
1 TTATCATAAGCGCCGC-AAAACTGTTAAGAAAACGGAGCCGTTTTACGTTTAGCTTTTAAGAAAG
* * * * *
9124116 TTAGTGGCGATTA-CTGGAAAATGCCGCAACGGTCAAGAATTAGCGGCGC
65 ATAGTGGCGATTATC-GAAAAATGCCACAACAGCCAAGAATTAGCGGCGC
* ** * *
9124165 TCTATCATAAGCGCCACAAAACTGTTAAGAAAACGTTGCCGTTTTACGTTTATCTTTTCAAG-AC
1 T-TATCATAAGCGCCGCAAAACTGTTAAGAAAACGGAGCCGTTTTACGTTTAGCTTTT-AAGAAA
* * *
9124229 GATAGTGGCGATTATCGAAAAATGCCACAATAGCCAAGATTTGGCGGCGC
64 GATAGTGGCGATTATCGAAAAATGCCACAACAGCCAAGAATTAGCGGCGC
* *
9124279 TTTTGACA-AAGCGCCGTAAAACTGTTAAGAAAA
1 TTAT--CATAAGCGCCGCAAAACTGTTAAGAAAA
9124312 TGTAGTCGTT
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
113 2 0.02
114 101 0.83
115 18 0.15
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (113 bp):
TTATCATAAGCGCCGCAAAACTGTTAAGAAAACGGAGCCGTTTTACGTTTAGCTTTTAAGAAAGA
TAGTGGCGATTATCGAAAAATGCCACAACAGCCAAGAATTAGCGGCGC
Found at i:9125128 original size:15 final size:15
Alignment explanation
Indices: 9125104--9125183 Score: 84
Period size: 15 Copynumber: 5.7 Consensus size: 15
9125094 GGGTTGGTGT
9125104 TTAA-GGTTTAAGGG
1 TTAAGGGTTTAAGGG
9125118 TTAAGGGTTTAAGGG
1 TTAAGGGTTTAAGGG
9125133 TTAAGGGTTTAA---
1 TTAAGGGTTTAAGGG
9125145 TTAAGGG-TTAAGGG
1 TTAAGGGTTTAAGGG
*
9125159 TT--GGGGTTAAGGG
1 TTAAGGGTTTAAGGG
*
9125172 TTTAGGGGTTTA
1 -TTAAGGGTTTA
9125184 TAGTTAATGT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
11 4 0.07
12 10 0.18
13 7 0.12
14 8 0.14
15 22 0.39
16 6 0.11
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (15 bp):
TTAAGGGTTTAAGGG
Found at i:9125154 original size:34 final size:32
Alignment explanation
Indices: 9125111--9125175 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
9125101 TGTTTAAGGT
9125111 TTAAGGGTTAAGGGTTTAAGGGTTAAGGGTTTAA
1 TTAAGGGTTAAGGG-TT-AGGGTTAAGGGTTTAA
*
9125145 TTAAGGGTTAAGGGTTGGGGTTAAGGGTTTA
1 TTAAGGGTTAAGGGTTAGGGTTAAGGGTTTA
9125176 GGGGTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 2 0.07
34 14 0.47
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (32 bp):
TTAAGGGTTAAGGGTTAGGGTTAAGGGTTTAA
Found at i:9125155 original size:7 final size:7
Alignment explanation
Indices: 9125104--9125178 Score: 77
Period size: 7 Copynumber: 11.0 Consensus size: 7
9125094 GGGTTGGTGT
*
9125104 TTAAGGT
1 TTAAGGG
9125111 TTAAGGG
1 TTAAGGG
9125118 TTAAGGG
1 TTAAGGG
9125125 TTTAAGGG
1 -TTAAGGG
9125133 TTAAGGG
1 TTAAGGG
9125140 TTTAA---
1 -TTAAGGG
9125145 TTAAGGG
1 TTAAGGG
9125152 TTAAGGG
1 TTAAGGG
*
9125159 TT-GGGG
1 TTAAGGG
9125165 TTAAGGG
1 TTAAGGG
*
9125172 TTTAGGG
1 TTAAGGG
9125179 GTTTATAGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 4 0.07
6 5 0.09
7 38 0.66
8 11 0.19
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (7 bp):
TTAAGGG
Found at i:9125167 original size:13 final size:13
Alignment explanation
Indices: 9125149--9125173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9125139 GTTTAATTAA
9125149 GGGTTAAGGGTTG
1 GGGTTAAGGGTTG
9125162 GGGTTAAGGGTT
1 GGGTTAAGGGTT
9125174 TAGGGGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (13 bp):
GGGTTAAGGGTTG
Found at i:9125367 original size:13 final size:14
Alignment explanation
Indices: 9125349--9125411 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
9125339 GGATTATGGT
9125349 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
*
9125362 TTAAGGGTTCATGGG
1 TTAAGGGTT-AGGGG
*
9125377 TTTAGGGTTAGGGG
1 TTAAGGGTTAGGGG
* *
9125391 TTAGGGGTTATGGG
1 TTAAGGGTTAGGGG
*
9125405 TTTAGGG
1 TTAAGGG
9125412 GTTTATAGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
13 9 0.22
14 20 0.50
15 11 0.28
ACGTcount: A:0.16, C:0.02, G:0.48, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:9125383 original size:15 final size:14
Alignment explanation
Indices: 9125342--9125411 Score: 65
Period size: 15 Copynumber: 5.0 Consensus size: 14
9125332 GGCTTATGGA
9125342 TTAT-GGTTTAAGGG
1 TTATGGGTTT-AGGG
* *
9125356 TT-GGGGTTAAGGG
1 TTATGGGTTTAGGG
9125369 TTCATGGGTTTAGGG
1 TT-ATGGGTTTAGGG
*
9125384 TTA-GGGGTTAGGGG
1 TTATGGGTTTA-GGG
9125398 TTATGGGTTTAGGG
1 TTATGGGTTTAGGG
9125412 GTTTATAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 12 0.27
14 16 0.36
15 17 0.38
ACGTcount: A:0.16, C:0.01, G:0.46, T:0.37
Consensus pattern (14 bp):
TTATGGGTTTAGGG
Found at i:9125384 original size:28 final size:28
Alignment explanation
Indices: 9125324--9125411 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
9125314 TAAGGGATAT
* * *
9125324 GGGTTAGAGGCTTATGGATTAT-GGTTTAA
1 GGGTTAG-GGGTTAAGGGTTATGGGTTT-A
9125353 GGGTT-GGGGTTAAGGGTTCATGGGTTTA
1 GGGTTAGGGGTTAAGGGTT-ATGGGTTTA
*
9125381 GGGTTAGGGGTTAGGGGTTATGGGTTTA
1 GGGTTAGGGGTTAAGGGTTATGGGTTTA
9125409 GGG
1 GGG
9125412 GTTTATAGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.17
28 21 0.40
29 22 0.42
ACGTcount: A:0.17, C:0.02, G:0.45, T:0.35
Consensus pattern (28 bp):
GGGTTAGGGGTTAAGGGTTATGGGTTTA
Found at i:9125412 original size:15 final size:15
Alignment explanation
Indices: 9125366--9125414 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
9125356 TTGGGGTTAA
9125366 GGGTTCATGGGTTTA-
1 GGGTT-ATGGGTTTAG
*
9125381 GGGTTA-GGGGTTAG
1 GGGTTATGGGTTTAG
9125395 GGGTTATGGGTTTAG
1 GGGTTATGGGTTTAG
9125410 GGGTT
1 GGGTT
9125415 TATAGTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 7 0.23
15 17 0.57
ACGTcount: A:0.12, C:0.02, G:0.49, T:0.37
Consensus pattern (15 bp):
GGGTTATGGGTTTAG
Found at i:9125416 original size:8 final size:7
Alignment explanation
Indices: 9125353--9125414 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
9125343 TATGGTTTAA
9125353 GGGTT-G
1 GGGTTAG
*
9125359 GGGTTAA
1 GGGTTAG
9125366 GGGTTCATG
1 GGGTT-A-G
*
9125375 GGTTTA-
1 GGGTTAG
9125381 GGGTTAG
1 GGGTTAG
9125388 GGGTTAG
1 GGGTTAG
9125395 GGGTTATG
1 GGGTTA-G
*
9125403 GGTTTAG
1 GGGTTAG
9125410 GGGTT
1 GGGTT
9125415 TATAGTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 10 0.22
7 23 0.51
8 8 0.18
9 4 0.09
ACGTcount: A:0.13, C:0.02, G:0.50, T:0.35
Consensus pattern (7 bp):
GGGTTAG
Found at i:9126178 original size:7 final size:7
Alignment explanation
Indices: 9126166--9126193 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
9126156 AAACATCTTA
9126166 TTTTATG
1 TTTTATG
9126173 TTTTATG
1 TTTTATG
9126180 TTTTATG
1 TTTTATG
9126187 TTTTATG
1 TTTTATG
9126194 CTGTCCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (7 bp):
TTTTATG
Found at i:9126262 original size:31 final size:32
Alignment explanation
Indices: 9126226--9126294 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
9126216 TTCTTTTTAA
*
9126226 ATGTTATGTACTGTTCGAAGG-TATTAT-TTTT
1 ATGTTATGAACTGTT-GAAGGATATTATCTTTT
*
9126257 ATGTTATGAACTGTTGAAGGATTTTATCTTTT
1 ATGTTATGAACTGTTGAAGGATATTATCTTTT
9126289 -TGTTAT
1 ATGTTAT
9126295 TATGAAGCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 5 0.15
31 25 0.74
32 4 0.12
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (32 bp):
ATGTTATGAACTGTTGAAGGATATTATCTTTT
Found at i:9130040 original size:33 final size:33
Alignment explanation
Indices: 9129995--9130074 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
9129985 GTAGAGGCTG
*
9129995 CAGTGA-AGGAAGCAGAGGCTGCAGCGAGAGAAA
1 CAGTGAGA-GAAGCAGAAGCTGCAGCGAGAGAAA
* *
9130028 CAGTGAGAGAAGCAGAAGCTGCAGCTAGAGAAG
1 CAGTGAGAGAAGCAGAAGCTGCAGCGAGAGAAA
*
9130061 CAGCGAGAGAAGCA
1 CAGTGAGAGAAGCA
9130075 AAGGTTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.38, T:0.06
Consensus pattern (33 bp):
CAGTGAGAGAAGCAGAAGCTGCAGCGAGAGAAA
Found at i:9130069 original size:12 final size:12
Alignment explanation
Indices: 9130015--9130074 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
9130005 AGCAGAGGCT
9130015 GCAGCGAGAGAA
1 GCAGCGAGAGAA
* *
9130027 ACAGTGAGAGAA
1 GCAGCGAGAGAA
**
9130039 GCA--GA-AGCT
1 GCAGCGAGAGAA
*
9130048 GCAGCTAGAGAA
1 GCAGCGAGAGAA
9130060 GCAGCGAGAGAA
1 GCAGCGAGAGAA
9130072 GCA
1 GCA
9130075 AAGGTTCAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
9 5 0.14
10 2 0.06
11 1 0.03
12 28 0.78
ACGTcount: A:0.42, C:0.17, G:0.37, T:0.05
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:9131903 original size:44 final size:43
Alignment explanation
Indices: 9131855--9131949 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 43
9131845 ACCAAAAGCA
** * * *
9131855 CCGCTAAAGATCATGGCCTTTAGCGGCGCTTTTATCACAAAATG
1 CCGCTAAAGATCATAACCTTTAGCGGCGATTCTATCAC-AAACG
*
9131899 CCGCTAAAGATCATAACCTTTAGCGGCGATTCTATTACAAACG
1 CCGCTAAAGATCATAACCTTTAGCGGCGATTCTATCACAAACG
9131942 CCGCTAAA
1 CCGCTAAA
9131950 TCATGACTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 12 0.27
44 33 0.73
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
CCGCTAAAGATCATAACCTTTAGCGGCGATTCTATCACAAACG
Found at i:9134517 original size:46 final size:46
Alignment explanation
Indices: 9134450--9134632 Score: 312
Period size: 46 Copynumber: 4.0 Consensus size: 46
9134440 TGACAAAGTG
* *
9134450 TGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGTTC
1 TGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTTC
*
9134496 TGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGTTC
1 TGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTTC
* *
9134542 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTTC
*
9134588 TGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTT
1 TGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTT
9134633 ATAGCAATGT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 132 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACTGAGTTC
Found at i:9139102 original size:118 final size:113
Alignment explanation
Indices: 9138846--9139199 Score: 469
Period size: 114 Copynumber: 3.1 Consensus size: 113
9138836 CAAATTATTT
* * * *
9138846 TAAATCCTTGAGCATTAGCGACACTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA-
* * * *
9138911 GGCGCCGTTGGGCTTA-GTTTTTTATGCGGCGCTTTCCCAAAAACGACGC
65 TG-GCCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* *
9138960 TAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
* ** *
9139025 GGCATCATTACGCTTAGGTTTTTTTTTTTGCGGCGCTTTCTCAAAAACGCCAC
66 GGC--CGTTGGGCTTAGG---TTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
9139078 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
1 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
* *
9139143 AGTGCCGTTGGGCTTAGG-TTTTTTTGCGGTGCTTTTTCAAAAACGCCGC
66 -G-GCCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
9139192 TAAATCCC
1 TAAATCCC
9139200 CGAAAGCTCA
Statistics
Matches: 212, Mismatches: 20, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
112 2 0.01
113 1 0.00
114 104 0.49
115 1 0.00
118 101 0.48
119 1 0.00
120 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (113 bp):
TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAT
GGCCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
Found at i:9139225 original size:73 final size:73
Alignment explanation
Indices: 9139095--9139269 Score: 280
Period size: 73 Copynumber: 2.4 Consensus size: 73
9139085 CTGAGCATTA
* *
9139095 GCGGCGCTTTCTT-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATAGTGCCGTTGGGCTTA
1 GCGGCGCTTT-TTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGCCGTTGGGCTTA
9139159 GGTTTTTTT
65 GGTTTTTTT
* *
9139168 GCGGTGCTTTTTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGCCGTTGGGCTTAG
9139233 GTTTTTTT
66 GTTTTTTT
* *
9139241 ACGGCGCTTTCTCAAAAACGCCGCTAAAT
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAT
9139270 TCCTAATCAT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 2 0.02
73 92 0.98
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGCCGTTGGGCTTAG
GTTTTTTT
Found at i:9142311 original size:15 final size:15
Alignment explanation
Indices: 9142291--9142322 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9142281 ACCCCTAGAC
9142291 TATCTAGTGTCTCGA
1 TATCTAGTGTCTCGA
9142306 TATCTAGTGTCTCGA
1 TATCTAGTGTCTCGA
9142321 TA
1 TA
9142323 CCCCACTCGT
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (15 bp):
TATCTAGTGTCTCGA
Found at i:9142770 original size:59 final size:59
Alignment explanation
Indices: 9142699--9142936 Score: 467
Period size: 59 Copynumber: 4.0 Consensus size: 59
9142689 GACTTTCGAG
9142699 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
1 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
9142758 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
1 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
9142817 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
1 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
*
9142876 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTTGCTGTAGCTACA
1 ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
9142935 AT
1 AT
9142937 GAAAGGCTGG
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 178 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (59 bp):
ATACATTCAGTCCAGTAGTAAGGGCTGTCACCATACGTACAGTTCTGGCTGTAGCTACA
Found at i:9148661 original size:156 final size:157
Alignment explanation
Indices: 9148483--9148796 Score: 621
Period size: 156 Copynumber: 2.0 Consensus size: 157
9148473 TTTCTTAAGA
9148483 ATGAAGTAGTAGAAGACTATTATATTTACTTCAATAATTTATTTATAAGTATATTAATTATAATT
1 ATGAAGTAGTAGAAGACTATTATATTTACTTCAATAATTTATTTATAAGTATATTAATTATAATT
9148548 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
66 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
9148613 CTATAAAAAAAAATTTTAACATCAATT
131 CTATAAAAAAAAATTTTAACATCAATT
9148640 ATGAAGTAGT-GAAGACTATTATATTTACTTCAATAATTTATTTATAAGTATATTAATTATAATT
1 ATGAAGTAGTAGAAGACTATTATATTTACTTCAATAATTTATTTATAAGTATATTAATTATAATT
9148704 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
66 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
9148769 CTATAAAAAAAAATTTTAACATCAATT
131 CTATAAAAAAAAATTTTAACATCAATT
9148796 A
1 A
9148797 AGATACGAGG
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 147 0.94
157 10 0.06
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (157 bp):
ATGAAGTAGTAGAAGACTATTATATTTACTTCAATAATTTATTTATAAGTATATTAATTATAATT
AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
CTATAAAAAAAAATTTTAACATCAATT
Found at i:9148782 original size:74 final size:74
Alignment explanation
Indices: 9148548--9148783 Score: 205
Period size: 74 Copynumber: 3.1 Consensus size: 74
9148538 AATTATAATT
9148548 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
1 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
9148613 CTATAAAAA
66 CTATAAAAA
* * * ** ** * *
9148622 AAAATTTTAACATCAATTATGAAGTAGTGAAGACTATTAT-AT-TTACTTCAATAATTTATTTA-
1 AAAATTAT-ATATGAAAAATG-AG-A-TGATTA-TA-TATGATCTT--TTGAATAA---AATTAC
**
9148684 TAAGT-ATATTAAT-TAT-AATT
55 T--GTCAT-TTAATCTATAAAAA
9148704 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
1 AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
9148769 CTATAAAAA
66 CTATAAAAA
9148778 AAAATT
1 AAAATT
9148784 TTAACATCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
72 7 0.06
73 9 0.08
74 16 0.13
75 8 0.07
76 12 0.10
77 5 0.04
78 12 0.10
79 5 0.04
80 12 0.10
81 8 0.07
82 10 0.08
83 9 0.08
84 7 0.06
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (74 bp):
AAAATTATATATGAAAAATGAGATGATTATATATGATCTTTTGAATAAAATTACTGTCATTTAAT
CTATAAAAA
Found at i:9148845 original size:3 final size:3
Alignment explanation
Indices: 9148837--9148866 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9148827 CAGCAATTTT
9148837 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
9148867 TCACCAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:9153559 original size:16 final size:16
Alignment explanation
Indices: 9153540--9153570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9153530 AAAAAAACAC
*
9153540 AAAAGAAAAAGGAAAA
1 AAAAGAAAAAAGAAAA
9153556 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
9153571 GGCAGAGTTG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAA
Found at i:9154040 original size:29 final size:30
Alignment explanation
Indices: 9153971--9154047 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
9153961 ATAATAGGAA
* * *
9153971 AATTACTCAAATAATATAAATAAAATTATT
1 AATTACTGAAATAATATGAATAAAATAATT
* * *
9154001 ATTTATTGAAATAATATGGATAAAA-AATT
1 AATTACTGAAATAATATGAATAAAATAATT
*
9154030 AATTACTGAAATGATATG
1 AATTACTGAAATAATATG
9154048 TTTTTTTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTACTGAAATAATATGAATAAAATAATT
Found at i:9159971 original size:19 final size:18
Alignment explanation
Indices: 9159947--9159992 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
9159937 ATTTATCAAG
9159947 ATAAATATTAGATTAAATT
1 ATAAATATTAGATTAAA-T
9159966 ATAAATATTAGATTAAAT
1 ATAAATATTAGATTAAAT
9159984 AT-AATATTA
1 ATAAATATTA
9159993 AATCTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 17 0.63
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
ATAAATATTAGATTAAAT
Found at i:9160119 original size:17 final size:17
Alignment explanation
Indices: 9160034--9160124 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
9160024 CAAGATAAAC
9160034 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
*
9160051 ATTAAGA-TAATCAGTTTATT
1 ATTAA-ATTAA--A-TTTAAT
* **
9160071 ATTAGATT-AATAAAAT
1 ATTAAATTAAATTTAAT
*
9160087 ATT--ATTAAGA-TAAAT
1 ATTAAATTAA-ATTTAAT
9160102 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
9160119 ATTAAA
1 ATTAAA
9160125 ATATTAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 3 0.05
15 8 0.14
16 8 0.14
17 24 0.42
18 1 0.02
19 3 0.05
20 10 0.18
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:9162043 original size:18 final size:18
Alignment explanation
Indices: 9162020--9162064 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
9162010 CACTGTTAAC
9162020 AATATAACACA-AGACACA
1 AATATAACACAGA-ACACA
9162038 AATATAACACAGAACACA
1 AATATAACACAGAACACA
9162056 AAT-TAACAC
1 AATATAACAC
9162065 GGTGTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.23
18 19 0.73
19 1 0.04
ACGTcount: A:0.60, C:0.22, G:0.04, T:0.13
Consensus pattern (18 bp):
AATATAACACAGAACACA
Found at i:9164195 original size:39 final size:40
Alignment explanation
Indices: 9164136--9164217 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 40
9164126 ATTTTGCTGG
9164136 TTATTAATTTTTTTATGAGGTTTATGAGTTATAAATATGC
1 TTATTAATTTTTTTATGAGGTTTATGAGTTATAAATATGC
9164176 TTATTAA-TTTTTTATGAGGTTTATGAGTTATAAATATGC
1 TTATTAATTTTTTTATGAGGTTTATGAGTTATAAATATGC
9164215 TTA
1 TTA
9164218 GGTTTATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 35 0.83
40 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.52
Consensus pattern (40 bp):
TTATTAATTTTTTTATGAGGTTTATGAGTTATAAATATGC
Found at i:9167766 original size:27 final size:27
Alignment explanation
Indices: 9167728--9167798 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
9167718 TGTACATATA
9167728 TGCTCACACGAGCTGTGAAAATAGGCT
1 TGCTCACACGAGCTGTGAAAATAGGCT
*
9167755 TGCTCACACGAGCTGTGAAAATGGGCT
1 TGCTCACACGAGCTGTGAAAATAGGCT
9167782 TGCTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
9167799 GAGTATTCGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (27 bp):
TGCTCACACGAGCTGTGAAAATAGGCT
Found at i:9174505 original size:25 final size:25
Alignment explanation
Indices: 9174488--9174580 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
9174478 CTCATTCGAG
* * *
9174488 CATATAAACGGGAAGCTCTTCTAAGC
1 CATAT-AACGGGAAGCTCATGTGAGC
* *
9174514 CATGTAACGGGAAGCTTATGTGAGC
1 CATATAACGGGAAGCTCATGTGAGC
* * * *
9174539 TATGTAACAGGAAGCTTATGTGAGC
1 CATATAACGGGAAGCTCATGTGAGC
9174564 CATATAACGGGAAGCTC
1 CATATAACGGGAAGCTC
9174581 TTGCAAGCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
25 52 0.93
26 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (25 bp):
CATATAACGGGAAGCTCATGTGAGC
Found at i:9174758 original size:24 final size:24
Alignment explanation
Indices: 9174707--9174782 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
9174697 TAACGGGAAA
9174707 CTCATGAGAGCCATATATC-AGGAAG
1 CTCATGAGAGCCA-ATATCGA-GAAG
* *
9174732 CTCAAGAGAGCCAATATCGAGATG
1 CTCATGAGAGCCAATATCGAGAAG
* * *
9174756 CTCATGAGAGCTAATAACGAGACG
1 CTCATGAGAGCCAATATCGAGAAG
9174780 CTC
1 CTC
9174783 TTGCAAGCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 31 0.70
25 13 0.30
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (24 bp):
CTCATGAGAGCCAATATCGAGAAG
Found at i:9185228 original size:75 final size:75
Alignment explanation
Indices: 9185142--9185334 Score: 217
Period size: 75 Copynumber: 2.6 Consensus size: 75
9185132 TCATACACAT
* * ** * * **
9185142 TTATATAAAAGTCATACCTAAATTTAACGCAAGAACATATTCAAATATATTTATATTTCTGAACC
1 TTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAACC
9185207 TCATATAAAC
66 TCATATAAAC
* * * **
9185217 TTATATAAAAGTCATACCTAAACTCAAAACAATAACATATACAATTATATTTGCATTTCCAAATT
1 TTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAACC
9185282 TCATATAAAC
66 TCATATAAAC
* * * *
9185292 TTACATAAAAATCATACCCAAACTTCAATACAAG-ACATATACA
1 TTATATAAAAGTCATACCTAAAC-TCAAAACAAGAACATATACA
9185335 TGTAAATATA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
75 91 0.92
76 8 0.08
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (75 bp):
TTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAACC
TCATATAAAC
Found at i:9191198 original size:23 final size:23
Alignment explanation
Indices: 9191170--9191220 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
9191160 AATGTTAAGT
*
9191170 AAATATATTATATTATTAT-ATA
1 AAATATATTATAGTATTATAATA
9191192 ATAATATATTATAGTATTATAATA
1 A-AATATATTATAGTATTATAATA
9191216 AAATA
1 AAATA
9191221 AATAAGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.04
23 21 0.81
24 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATATTATAGTATTATAATA
Found at i:9191213 original size:18 final size:18
Alignment explanation
Indices: 9191173--9191215 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9191163 GTTAAGTAAA
*
9191173 TATATTATATTATTATAT
1 TATAATATATTATTATAT
*
9191191 AATAATATATTA-TAGTAT
1 TATAATATATTATTA-TAT
9191209 TATAATA
1 TATAATA
9191216 AAATAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATAATATATTATTATAT
Found at i:9191589 original size:28 final size:27
Alignment explanation
Indices: 9191537--9191591 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
9191527 AATTGTAGAA
*
9191537 TAAATTGTAAATTTTGAGTAATAGGGAC
1 TAAATTGTAAAATTTGAG-AATAGGGAC
9191565 TAAATTGTGAAAATTTGA-AATTAGGGA
1 TAAATTGT-AAAATTTGAGAA-TAGGGA
9191592 TTTAAGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 14 0.58
29 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (27 bp):
TAAATTGTAAAATTTGAGAATAGGGAC
Found at i:9191603 original size:18 final size:18
Alignment explanation
Indices: 9191580--9191614 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9191570 TGTGAAAATT
*
9191580 TGAAATTAGGGATTTAAG
1 TGAAATTAGGGAGTTAAG
9191598 TGAAATTAGGGAGTTAA
1 TGAAATTAGGGAGTTAA
9191615 ATCTAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAAATTAGGGAGTTAAG
Found at i:9211407 original size:31 final size:31
Alignment explanation
Indices: 9211369--9211431 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
9211359 TAGCAAAAAG
9211369 ACTTACTAAGGAAGGAAATAAAGAAATTGAC
1 ACTTACTAAGGAAGGAAATAAAGAAATTGAC
*
9211400 ACTTACTAAGGAAGGAAATAAAGAATTTGAC
1 ACTTACTAAGGAAGGAAATAAAGAAATTGAC
9211431 A
1 A
9211432 TACTTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.21
Consensus pattern (31 bp):
ACTTACTAAGGAAGGAAATAAAGAAATTGAC
Found at i:9215481 original size:5 final size:5
Alignment explanation
Indices: 9215471--9215501 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
9215461 CACCCAAACA
9215471 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT C
1 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT C
9215502 TCATCCCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CCAAT
Found at i:9217236 original size:7 final size:7
Alignment explanation
Indices: 9217224--9217252 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
9217214 TCGCATGCAA
9217224 TTGGTAC
1 TTGGTAC
9217231 TTGGTAC
1 TTGGTAC
9217238 TTGGTAC
1 TTGGTAC
9217245 TTGGTAC
1 TTGGTAC
9217252 T
1 T
9217253 CAGATCAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (7 bp):
TTGGTAC
Found at i:9220967 original size:38 final size:38
Alignment explanation
Indices: 9220908--9220986 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
9220898 ACTTGTTCAA
* *
9220908 CATGCCTACTGTTATTGTTGAA-CTAAATACATGTTAAG
1 CATGCCTACTATTATTGTTGAACCT-AATACAGGTTAAG
9220946 CATGCCTACTATTAATT-TTGAACCTAATACAGGTTAAG
1 CATGCCTACTATT-ATTGTTGAACCTAATACAGGTTAAG
9220984 CAT
1 CAT
9220987 ATCTAATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 32 0.86
39 5 0.14
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (38 bp):
CATGCCTACTATTATTGTTGAACCTAATACAGGTTAAG
Found at i:9225835 original size:36 final size:34
Alignment explanation
Indices: 9225770--9225836 Score: 80
Period size: 36 Copynumber: 1.9 Consensus size: 34
9225760 TGATAACTTA
* * *
9225770 ATATATATATGTTATAATAAATAACATGAAATGC
1 ATATATATATATAATAATAAATAAAATGAAATGC
*
9225804 ATATATATTATATAATAATGAATTAAAATGAAA
1 ATATATA-TATATAATAAT-AAATAAAATGAAA
9225837 ACAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 7 0.26
35 9 0.33
36 11 0.41
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (34 bp):
ATATATATATATAATAATAAATAAAATGAAATGC
Found at i:9226593 original size:19 final size:19
Alignment explanation
Indices: 9226532--9226594 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
9226522 AGAAGGATGA
*
9226532 GAAAT-GGATATGAGAT-TG
1 GAAATGGGATATGA-ATATT
*
9226550 GAAATGGAATATGAA-ATGAT
1 GAAATGGGATATGAATAT--T
9226570 GAAATGGGATATGAATATT
1 GAAATGGGATATGAATATT
9226589 GAAATG
1 GAAATG
9226595 AATTCATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.19
19 14 0.38
20 14 0.38
21 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (19 bp):
GAAATGGGATATGAATATT
Found at i:9232217 original size:50 final size:52
Alignment explanation
Indices: 9232144--9232279 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 52
9232134 GATGGTCATG
* * *
9232144 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATAGGCCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATAGTATAGACCACA
* * * * *
9232194 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATAGTATAGACCACA
*
9232245 TGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
9232280 AACATCATTG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 4 0.05
50 33 0.45
51 36 0.49
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (52 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATAGTATAGACCACA
Found at i:9232332 original size:45 final size:45
Alignment explanation
Indices: 9232276--9232370 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
9232266 TACTATGTGA
* *
9232276 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
9232321 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
9232366 ACCGA
1 ACCGA
9232371 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:9238655 original size:24 final size:25
Alignment explanation
Indices: 9238628--9238678 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
9238618 TTAGTAAGTC
*
9238628 AAATAAACTATACT-AATAAATGCT
1 AAATAAACTATACTAAATAAATACT
* *
9238652 AAATATATTATACTAAATAAATACT
1 AAATAAACTATACTAAATAAATACT
9238677 AA
1 AA
9238679 TCTTCTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (25 bp):
AAATAAACTATACTAAATAAATACT
Found at i:9238864 original size:2 final size:2
Alignment explanation
Indices: 9238857--9238897 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9238847 TTTCATTTGT
9238857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9238898 CCANNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9240350 original size:3 final size:3
Alignment explanation
Indices: 9240342--9240407 Score: 68
Period size: 3 Copynumber: 22.3 Consensus size: 3
9240332 ATATATAGGT
9240342 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATGA A-A ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
*
9240387 AT- ATCA ATA CTA ATA A-A ATA A
1 ATA AT-A ATA ATA ATA ATA ATA A
9240408 ACTAAAAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
2 8 0.15
3 39 0.72
4 7 0.13
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9240364 original size:18 final size:18
Alignment explanation
Indices: 9240341--9240390 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
9240331 TATATATAGG
9240341 TATAATAATAATATATAA
1 TATAATAATAATATATAA
9240359 TATAATAATAATA-ATAA
1 TATAATAATAATATATAA
*
9240376 TGAAAATAATAATAT
1 T-ATAATAATAATAT
9240391 CAATACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TATAATAATAATATATAA
Found at i:9241023 original size:17 final size:17
Alignment explanation
Indices: 9241001--9241033 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9240991 TTGTTTTAAG
9241001 AAATAAAAGAAAAACAA
1 AAATAAAAGAAAAACAA
*
9241018 AAATAAAATAAAAACA
1 AAATAAAAGAAAAACA
9241034 GTAAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (17 bp):
AAATAAAAGAAAAACAA
Found at i:9241861 original size:44 final size:43
Alignment explanation
Indices: 9241811--9242266 Score: 209
Period size: 44 Copynumber: 10.5 Consensus size: 43
9241801 GATCTATTCT
* **
9241811 CTGCAACTTTAGAGAGATAAGATCTGCGGTTTCAATCCACTCCA
1 CTGCAACTTCAGAGAGATAAGATCTG-GGTTTCAATCTGCTCCA
* * * **
9241855 CTGCAACCTCAGGGAGATAGGAT-TGGTGTCTTTTATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTGG-GT-TTCAATCTGCTCCA
* * * * * *
9241899 CTGCAACTTCAGGGAGATAAGA-CT-GGATGCGATCTACT-CT
1 CTGCAACTTCAGAGAGATAAGATCTGGGTTTCAATCTGCTCCA
* * * *
9241939 CTGTAACTTCAGAGAGATAAAATCTGTGGTTTTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTG-GGTTTCAATCTGCTCCA
* * * * *
9241983 CAGCAACTTTA-AGGAGATAGGATTATCGGCTTT-AATCTGCTCCA
1 CTGCAACTTCAGA-GAGATAAGA-TCT-GGGTTTCAATCTGCTCCA
* * * ** *
9242027 CTGCAATTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGAGAGATAAGATCTG-GGT-TTCAATCTGCTC-CA
* * * *
9242072 CTGCAACTTCAG-GAGGATAAGA-CTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGATCTGGGTT--TCAATCTGCTCCA
* * * * * * * *
9242116 CTGCAACTTCAGGGAGATAATA-CT-AGATGCGATCTACT-CT
1 CTGCAACTTCAGAGAGATAAGATCTGGGTTTCAATCTGCTCCA
*** * *
9242156 CTGCAACTTCAGAGAGATAAGATCCAAAGTTTTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGAT-CTGGGTTTCAATCTGCTCCA
* * * *
9242200 CTGCAACTTCAGGGAGATAGGATTATTGGCTTT-AATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGA-T-CTGGGTTTCAATCTGCTCCA
* *
9242244 CTGCTACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGAGAGATAAGAT
9242267 TCGCCATTGC
Statistics
Matches: 307, Mismatches: 80, Indels: 51
0.70 0.18 0.12
Matches are distributed among these distances:
40 41 0.13
41 14 0.05
42 5 0.02
43 28 0.09
44 179 0.58
45 39 0.13
46 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (43 bp):
CTGCAACTTCAGAGAGATAAGATCTGGGTTTCAATCTGCTCCA
Found at i:9241970 original size:128 final size:128
Alignment explanation
Indices: 9241800--9242048 Score: 347
Period size: 128 Copynumber: 1.9 Consensus size: 128
9241790 GAATTTGATA
* * * *
9241800 CGATCTATTCTCTGCAACTTTAGAGAGATAAGATCTGCGGTTTCAATCCACTCCACTGCAACCTC
1 CGATCTACTCTCTGCAACTTCAGAGAGATAAAATCTGCGGTTTCAATCCACTCCACAGCAACCTC
* * * *
9241865 AGGGAGATAGGATTGGT-GTCTTTTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATG
66 AAGGAGATAGGATT-ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATG
* * * * * *
9241928 CGATCTACTCTCTGTAACTTCAGAGAGATAAAATCTGTGGTTTTAATCCGCTCCACAGCAACTTT
1 CGATCTACTCTCTGCAACTTCAGAGAGATAAAATCTGCGGTTTCAATCCACTCCACAGCAACCTC
*
9241993 AAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAATTTCAGGGAGATAAGA
66 AAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
9242049 TTTGCCATCT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
127 1 0.01
128 104 0.99
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (128 bp):
CGATCTACTCTCTGCAACTTCAGAGAGATAAAATCTGCGGTTTCAATCCACTCCACAGCAACCTC
AAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATG
Found at i:9242678 original size:44 final size:44
Alignment explanation
Indices: 9242615--9242824 Score: 271
Period size: 44 Copynumber: 4.8 Consensus size: 44
9242605 ATCTGCTATT
* * *
9242615 TTCAACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTTACGATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTTACAATC
* **
9242659 TTCAACCTATTCTACTGCTGACCAGGGAGATAGGACCTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATC
* * *
9242703 TTCAATCTATTCCACTGCTGCCCAGGGAGATA-GAATTATCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTTA-CAATC
* *
9242747 TTCAACCTATTCCACTGCTGACCAGGGAGATAAGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATC
* *
9242791 TTTAACCTATTCCACTGCTGACCAGGAAGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
9242825 GCTAGGGTCA
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
43 4 0.03
44 136 0.94
45 5 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATC
Found at i:9242983 original size:45 final size:45
Alignment explanation
Indices: 9242928--9243068 Score: 114
Period size: 45 Copynumber: 3.2 Consensus size: 45
9242918 TGTCTTCGAT
*
9242928 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGC
*** * * * * *
9242973 CTGCTCCGCTG--GAACCCAGGGAGGCAAG-GCTG-T-CTTTGA-T
1 CTGCTCCGCTGTCG-GTGCAGGAAGGCAAGATCTGCTATTTTTAGC
* * * *
9243013 CTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTACTATTTTTAGC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGC
9243058 CTGCTCCGCTG
1 CTGCTCCGCTG
9243069 CAACCCAGGG
Statistics
Matches: 66, Mismatches: 23, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
40 9 0.14
41 14 0.21
42 4 0.06
43 5 0.08
44 15 0.23
45 19 0.29
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (45 bp):
CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGC
Found at i:9242998 original size:44 final size:44
Alignment explanation
Indices: 9242945--9243085 Score: 103
Period size: 44 Copynumber: 3.3 Consensus size: 44
9242935 GCTGTCGGTG
9242945 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGGAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGGAACC
* * * * * * * ***
9242989 CAGGGAGGCAAG-GCTG-T-CTTTGA-TCTGCTTCGTTGTCG-GTG
1 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTG--GAACC
* * *
9243030 CAAGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGGAACC
*
9243074 CAGGGAGGCAAG
1 CAGGAAGGCAAG
9243086 GCTGGTGTCT
Statistics
Matches: 65, Mismatches: 25, Indels: 14
0.62 0.24 0.13
Matches are distributed among these distances:
40 9 0.14
41 14 0.22
42 4 0.06
43 4 0.06
44 25 0.38
45 9 0.14
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGGAACC
Found at i:9243133 original size:173 final size:173
Alignment explanation
Indices: 9242837--9243177 Score: 540
Period size: 173 Copynumber: 2.0 Consensus size: 173
9242827 TAGGGTCATC
* * *
9242837 GATCTGCTTCGCAGTCAGTGCAGCAAGGCAAGATCTACTATTTTTAGCCTACTTCGCTGTAACCT
1 GATCTGCTTCGCAGTCAGTGCAGCAAGGCAAGATCTACTATTTTTAGCCTACTCCGCTGCAACCC
* *
9242902 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
66 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATT
* * *
9242967 TTTAGCCTGCTCCGCTGGAACCCAGGGAGGCAAGGCTGTCTTT
131 TTTAGCCTGATCCGCTGCAACCCAAGGAGGCAAGGCTGTCTTT
** * *
9243010 GATCTGCTTCGTTGTCGGTGCAAG-AAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAACC
1 GATCTGCTTCGCAGTCAGTGC-AGCAAGGCAAGATCTACTATTTTTAGCCTACTCCGCTGCAACC
*
9243074 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGTAAGATCTACTAT
65 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTAT
*
9243139 TTTTAGCCTGATCTGCTGCAACCCAAGGAGGCAAGGCTG
130 TTTTAGCCTGATCCGCTGCAACCCAAGGAGGCAAGGCTG
9243178 GTGTCTTTGA
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
173 151 0.99
174 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (173 bp):
GATCTGCTTCGCAGTCAGTGCAGCAAGGCAAGATCTACTATTTTTAGCCTACTCCGCTGCAACCC
AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATT
TTTAGCCTGATCCGCTGCAACCCAAGGAGGCAAGGCTGTCTTT
Found at i:9243198 original size:88 final size:88
Alignment explanation
Indices: 9242835--9243184 Score: 510
Period size: 88 Copynumber: 4.0 Consensus size: 88
9242825 GCTAGGGTCA
* * * *
9242835 TCGATCTGCTTCGCAGTCAGTGCAGCAAGGCAAGATCTACTATTTTTAGCCT-ACTTCGCTGTAA
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGA-TCCGCTGCAA
*
9242899 CCTAGGGAGGCAAGGCTGGTGTCT
65 CCCAGGGAGGCAAGGCTGGTGTCT
* * * *
9242923 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGGAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGATCCGCTGCAAC
9242988 CCAGGGAGGCAAGGC---TGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * * * *
9243008 TTGATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTACTATTTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGATCCGCTGCAAC
9243073 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
9243096 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGTAAGATCTACTATTTTTAGCCTGATCTGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGATCCGCTGCAAC
*
9243161 CCAAGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
9243184 T
1 T
9243185 TGATACAGCT
Statistics
Matches: 237, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
85 80 0.34
88 157 0.66
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTACTATTTTTAGCCTGATCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:9245824 original size:21 final size:22
Alignment explanation
Indices: 9245799--9245849 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
9245789 AATTGTATAG
*
9245799 AAATAACATAA-ATAAATAAAT
1 AAATAACATAATAAAAATAAAT
9245820 AAATAACA-AATAAAAATAAAT
1 AAATAACATAATAAAAATAAAT
* *
9245841 CAATGACAT
1 AAATAACAT
9245850 GCAAAGCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.22
Consensus pattern (22 bp):
AAATAACATAATAAAAATAAAT
Found at i:9252405 original size:20 final size:20
Alignment explanation
Indices: 9252381--9252449 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
9252371 AGTTTATTTG
*
9252381 CAATACTGATGGCTTGTCCG
1 CAATACTGATGGCTTGTCCA
* * * *
9252401 CAATACTGATAGTTTATCTA
1 CAATACTGATGGCTTGTCCA
*
9252421 CAATATTGATGGCTTGTCCA
1 CAATACTGATGGCTTGTCCA
*
9252441 TAATACTGA
1 CAATACTGA
9252450 CAGTTTATCT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (20 bp):
CAATACTGATGGCTTGTCCA
Found at i:9252477 original size:40 final size:41
Alignment explanation
Indices: 9252367--9252482 Score: 139
Period size: 40 Copynumber: 2.9 Consensus size: 41
9252357 GAGGAAGATT
* *
9252367 TGACAGTTTATTTGCAATAC-TGATGGCTTGTCCGCAATAC
1 TGACAGTTTATCTGCAATACTTGATGGCTTGTCCACAATAC
* * *
9252407 TGATAGTTTATCTACAATA-TTGATGGCTTGTCCATAATAC
1 TGACAGTTTATCTGCAATACTTGATGGCTTGTCCACAATAC
* **
9252447 TGACAGTTTATCTGTAATACTTG-TAACTTGTCCACA
1 TGACAGTTTATCTGCAATACTTGATGGCTTGTCCACA
9252483 TATTTTTGGC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 60 0.95
41 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (41 bp):
TGACAGTTTATCTGCAATACTTGATGGCTTGTCCACAATAC
Found at i:9252547 original size:43 final size:43
Alignment explanation
Indices: 9252462--9252568 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
9252452 GTTTATCTGT
* * *
9252462 AATACTTGTAACTTGTCCACATATTTTTGGCAGCTTGACTACA
1 AATACTAGTGACTTGTCCACATATTTGTGGCAGCTTGACTACA
* * *
9252505 AATATTGGTGGCTTGTCCACATATTTGTGGCAG-TAT-ATCTACA
1 AATACTAGTGACTTGTCCACATATTTGTGGCAGCT-TGA-CTACA
*
9252548 ATTACTAGTGACTTGTCCACA
1 AATACTAGTGACTTGTCCACA
9252569 AATTGGTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 2 0.04
43 51 0.96
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (43 bp):
AATACTAGTGACTTGTCCACATATTTGTGGCAGCTTGACTACA
Found at i:9254992 original size:7 final size:7
Alignment explanation
Indices: 9254980--9255004 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9254970 TCTCAATTTG
9254980 ATTTCAA
1 ATTTCAA
9254987 ATTTCAA
1 ATTTCAA
9254994 ATTTCAA
1 ATTTCAA
9255001 ATTT
1 ATTT
9255005 ATTTCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTCAA
Found at i:9255017 original size:18 final size:19
Alignment explanation
Indices: 9254987--9255023 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
9254977 TTGATTTCAA
9254987 ATTTCAAATTTCAA-ATTT
1 ATTTCAAATTTCAACATTT
9255005 ATTTCAACA-TTCAACATTT
1 ATTTCAA-ATTTCAACATTT
9255024 TCACATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTCAAATTTCAACATTT
Found at i:9255017 original size:25 final size:27
Alignment explanation
Indices: 9254974--9255023 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
9254964 AGCTCATCTC
9254974 AATTTGATTTCAAATTTCAA-ATTTCA
1 AATTTGATTTCAAATTTCAACATTTCA
9255000 AATTT-ATTTCAACA-TTCAACATTT
1 AATTTGATTTCAA-ATTTCAACATTT
9255024 TCACATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTTGATTTCAAATTTCAACATTTCA
Found at i:9266836 original size:46 final size:46
Alignment explanation
Indices: 9266769--9266863 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
9266759 CAAAATCGTG
*
9266769 ATGTAAACCACGGATCTCTATCCGAAATGATGGAGACTGGTACTCC
1 ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
*
9266815 ATGTAAACCGCGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
1 ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
9266861 ATG
1 ATG
9266864 CAATCTGACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (46 bp):
ATGTAAACCACGGATCTCTATCCAAAATGATGGAGACTGGTACTCC
Found at i:9270817 original size:8 final size:8
Alignment explanation
Indices: 9270804--9270829 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9270794 AGACTTATAG
9270804 ATCAAACA
1 ATCAAACA
9270812 ATCAAACA
1 ATCAAACA
9270820 ATCAAACA
1 ATCAAACA
9270828 AT
1 AT
9270830 TCGAATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCAAACA
Found at i:9279812 original size:21 final size:21
Alignment explanation
Indices: 9279772--9279814 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9279762 TTATACATCC
9279772 TAAATTTCATATTATAATATA
1 TAAATTTCATATTATAATATA
9279793 TAAATTTCATATTATAATATA
1 TAAATTTCATATTATAATATA
9279814 T
1 T
9279815 CTAAGCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTTCATATTATAATATA
Found at i:9284315 original size:14 final size:13
Alignment explanation
Indices: 9284281--9284319 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9284271 ATTTTTGGTG
9284281 AAATTAAA-TTTT
1 AAATTAAAGTTTT
*
9284293 AATTTAAAGTTTT
1 AAATTAAAGTTTT
9284306 AAATTAAAAGTTTT
1 AAATT-AAAGTTTT
9284320 TATGGTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 7 0.30
13 8 0.35
14 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (13 bp):
AAATTAAAGTTTT
Found at i:9286111 original size:20 final size:20
Alignment explanation
Indices: 9286067--9286116 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9286057 TAAAAAAGGA
*
9286067 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
*
9286087 ATATCAATACCTTAAGAAA-
1 ATATCGATACCTTAAGAAAT
9286106 AGTATCGATAC
1 A-TATCGATAC
9286117 TGGATCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:9290459 original size:17 final size:18
Alignment explanation
Indices: 9290425--9290464 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
9290415 TTTACAATTA
9290425 TTTTAAATTCTAACATAT
1 TTTTAAATTCTAACATAT
* *
9290443 TTTTAAA-TCTTATATAT
1 TTTTAAATTCTAACATAT
9290460 TTTTA
1 TTTTA
9290465 TTACTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAATTCTAACATAT
Found at i:9295813 original size:52 final size:51
Alignment explanation
Indices: 9295754--9295989 Score: 166
Period size: 52 Copynumber: 4.7 Consensus size: 51
9295744 AGATCAAAAC
* *
9295754 TTTATTTTAAAAATTTAAACTTTGTCCTTTAAAAAGACTAAAAACACATATT
1 TTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAGACTAAAAACACATA-T
* * *
9295806 TTTATTTTAAAAATCTAAACTTTCTCTTTTTAAAA-A--AAAATCAC-TAT
1 TTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAGACTAAAAACACATAT
* * * * * * * * *
9295853 TTT-TCTTAAAAATCAAAACTTTAT--TTCGAAATAG-TTGAAAAAGATCAAAAC
1 TTTATTTTAAAAATCTAAACTTTCTCCTT-TAAAAAGACT-AAAAACA-C-ATAT
* * * * * * *
9295904 TTTGTTTTAAGAATTTAAA-TTTTTCCTTTAATATGACTAAAAAAACATAT
1 TTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAGACTAAAAACACATAT
9295954 TTTATTTTAAAAATCTAAACTTTCTCCTTTTAAAAA
1 TTTATTTTAAAAATCTAAACTTTCTCC-TTTAAAAA
9295990 AAATCAAAAT
Statistics
Matches: 136, Mismatches: 34, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 18 0.13
47 4 0.03
48 7 0.05
49 8 0.06
50 18 0.13
51 16 0.12
52 57 0.42
53 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (51 bp):
TTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAGACTAAAAACACATAT
Found at i:9295844 original size:150 final size:148
Alignment explanation
Indices: 9295690--9295992 Score: 455
Period size: 149 Copynumber: 2.0 Consensus size: 148
9295680 AGTTTTCTTT
* *
9295690 AAAAAAATCTCTACTTTTCTTAAAAATCAAAA-AAAAATTCGAGATAGTTGAAAAAGATCAAAAC
1 AAAAAAATCACTACTTTTCTTAAAAATCAAAACAAAAATTCGAAATAGTTGAAAAAGATCAAAAC
*
9295754 TTTATTTTAAAAATTTAAACTTTGTCCTTTAAAAAGACTAAAAACACATATTTTTATTTTAAAAA
66 TTTATTTTAAAAATTTAAA-TTTGTCCTTTAAAAAGACTAAAAAAACATA-TTTTATTTTAAAAA
*
9295819 TCTAAACTTTCTCTTTTTAA
129 TCTAAACTTTCTCCTTTTAA
* *** *
9295839 AAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAAC
1 AAAAAAATCACTACTTTTCTTAAAAATCAAAACAAAAATTCGAAATAGTTGAAAAAGATCAAAAC
* * * * *
9295904 TTTGTTTTAAGAATTTAAATTTTTCCTTTAATATGACTAAAAAAACATATTTTATTTTAAAAATC
66 TTTATTTTAAAAATTTAAATTTGTCCTTTAAAAAGACTAAAAAAACATATTTTATTTTAAAAATC
9295969 TAAACTTTCTCCTTTTAA
131 TAAACTTTCTCCTTTTAA
9295987 AAAAAA
1 AAAAAA
9295993 TCAAAATTTT
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
148 39 0.28
149 56 0.40
150 44 0.32
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.38
Consensus pattern (148 bp):
AAAAAAATCACTACTTTTCTTAAAAATCAAAACAAAAATTCGAAATAGTTGAAAAAGATCAAAAC
TTTATTTTAAAAATTTAAATTTGTCCTTTAAAAAGACTAAAAAAACATATTTTATTTTAAAAATC
TAAACTTTCTCCTTTTAA
Found at i:9295877 original size:24 final size:23
Alignment explanation
Indices: 9295810--9295878 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
9295800 CATATTTTTA
* * *
9295810 TTTTAAAAATCTAAACTTTCTCT
1 TTTTAAAAATCAAAACTTTATTT
**
9295833 TTTTAAAAA--AAAATCACTATTT
1 TTTTAAAAATCAAAA-CTTTATTT
9295855 TTCTTAAAAATCAAAACTTTATTT
1 TT-TTAAAAATCAAAACTTTATTT
9295879 CGAAATAGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 3 0.09
22 6 0.17
23 16 0.46
24 6 0.17
25 4 0.11
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTTAAAAATCAAAACTTTATTT
Found at i:9296218 original size:3 final size:3
Alignment explanation
Indices: 9296210--9296235 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9296200 ACTAGAATGC
9296210 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
9296236 TTTTTTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:9296356 original size:3 final size:3
Alignment explanation
Indices: 9296348--9296458 Score: 114
Period size: 3 Copynumber: 36.7 Consensus size: 3
9296338 GTAAAAAATG
*
9296348 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * ** *
9296396 ATA ATA TTTC ATA ATA GTA GTA ATA GTA GTA GTA GCA GTA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9296442 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
9296459 TTGGGCCCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 94 0.99
4 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9296946 original size:42 final size:42
Alignment explanation
Indices: 9296894--9297199 Score: 352
Period size: 42 Copynumber: 7.3 Consensus size: 42
9296884 CTTCATATAC
* *
9296894 AATGCAATGAAAAGTAAATGAACCTCCACACCTGAGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
* *
9296936 AATGTAATGAAAAGTAGATGGACCTCCACACCT-AGACCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAG-CCTCTA
* * * * *
9296978 AATGTAATGAAAAGTCAATGGAACTCCACACATCTGGGCCTTTA
1 AATGCAATGAAAAGTAAATGGACCTCCACAC--CTGAGCCTCTA
*
9297022 AATGCAATGAAAAGTAAATGGAACTCCACACCT-AGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGA-GCCTCTA
* *
9297064 AATGTAAT-AAAACGTAAATGGACCTCTAC-CCT-AGGCCTCTA
1 AATGCAATGAAAA-GTAAATGGACCTCCACACCTGA-GCCTCTA
* * *
9297105 AATGCAATGAAAAGTAAATGGACCTCTACGCCCGAGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
** * *
9297147 AATGCAATGAAAAGTAAATGGAGTTCCACACTTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
9297189 AATGCAATGAA
1 AATGCAATGAA
9297200 TGTTTCCCTT
Statistics
Matches: 230, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
41 41 0.18
42 151 0.66
43 1 0.00
44 36 0.16
45 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTA
Found at i:9297641 original size:22 final size:21
Alignment explanation
Indices: 9297613--9297654 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
9297603 TTTTTTGTTT
* *
9297613 CCTTTTTGTTTTATTGTTTTTC
1 CCTTTTTCTTTT-TTCTTTTTC
9297635 CCTTTTTCTTTTTTCTTTTT
1 CCTTTTTCTTTTTTCTTTTT
9297655 TTCTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (21 bp):
CCTTTTTCTTTTTTCTTTTTC
Found at i:9298225 original size:34 final size:35
Alignment explanation
Indices: 9298187--9298252 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
9298177 CTTTTCTTCA
9298187 TTCTTACTC-CTTTCTAT-TTCCTTTCTTTTTTTGT
1 TTCTTACTCGCTTTCTATATTCC-TTCTTTTTTTGT
* *
9298221 TTCTTATTCGCTTTCTCTATTCCTTCTTTTTT
1 TTCTTACTCGCTTTCTATATTCCTTCTTTTTT
9298253 CTTTTTTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 16 0.57
36 4 0.14
ACGTcount: A:0.06, C:0.24, G:0.03, T:0.67
Consensus pattern (35 bp):
TTCTTACTCGCTTTCTATATTCCTTCTTTTTTTGT
Found at i:9315719 original size:2 final size:2
Alignment explanation
Indices: 9315714--9315740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9315704 CTTATATATA
9315714 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
9315741 TTGCATGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:9320770 original size:45 final size:43
Alignment explanation
Indices: 9320705--9321017 Score: 321
Period size: 45 Copynumber: 7.2 Consensus size: 43
9320695 ATTAGAACGA
*
9320705 ATATCCATT-AATATAAAGGTGGTTGCTAAGTGCTGATTCCACC
1 ATATCC-TTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
* * * *
9320748 GGGTATCCATGAATATAAAGGTGGTTGCTAAATGTTGATTCCACTGG
1 --ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCAC--C
* *
9320795 ATATCCATGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACC
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
* * * * * *
9320838 GTATCTTTGATTATAAAAGG-GGCTGCTATGTGCTGATTCC-CC
1 ATATCCTTGAATAT-AAAGGTGGTTGCTAAGTGTTGATTCCACC
*
9320880 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACC
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
* * * * * *
9320923 GTATCTTTGATTATAAAAGG-GGCTGCTATGTGCTGATTCC-CC
1 ATATCCTTGAATAT-AAAGGTGGTTGCTAAGTGTTGATTCCACC
*
9320965 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACC
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
* *
9321008 GTATCTTTGA
1 ATATCCTTGA
9321018 TTAGAGAGTG
Statistics
Matches: 219, Mismatches: 40, Indels: 20
0.78 0.14 0.07
Matches are distributed among these distances:
41 10 0.05
42 58 0.26
43 65 0.30
44 11 0.05
45 75 0.34
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (43 bp):
ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCCACC
Found at i:9320909 original size:85 final size:85
Alignment explanation
Indices: 9320705--9321020 Score: 456
Period size: 85 Copynumber: 3.7 Consensus size: 85
9320695 ATTAGAACGA
* * ** *
9320705 ATATCCATT-AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGGGTATCCATGAATAT-AAAG
1 ATATCC-TTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACC--GTATCTTTGATTATAAAAG
* ** * *
9320768 GTGGTTGCTAAATGTTGATTCCACTGG
63 G-GGCTGCTATGTGCTGATTCC-C--C
*
9320795 ATATCCATGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTATAAAAGGGG
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTATAAAAGGGG
9320860 CTGCTATGTGCTGATTCCCC
66 CTGCTATGTGCTGATTCCCC
9320880 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTATAAAAGGGG
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTATAAAAGGGG
9320945 CTGCTATGTGCTGATTCCCC
66 CTGCTATGTGCTGATTCCCC
9320965 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTA
1 ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTA
9321021 GAGAGTGACT
Statistics
Matches: 212, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
85 140 0.66
87 1 0.00
88 27 0.13
89 6 0.03
90 38 0.18
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (85 bp):
ATATCCTTGAATATAAAGGTGGTTGCTAAGTGTTGATTCGACCGTATCTTTGATTATAAAAGGGG
CTGCTATGTGCTGATTCCCC
Found at i:9325288 original size:3 final size:3
Alignment explanation
Indices: 9325280--9325318 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
9325270 TATTTGTAAA
* * *
9325280 AAT AAT AAT AAT AGT ACT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9325319 TTGGGTCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9329895 original size:46 final size:46
Alignment explanation
Indices: 9329828--9329920 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
9329818 GTGGAGCAAG
*
9329828 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTGGTTGGTT
1 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
9329874 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
1 TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
9329920 T
1 T
9329921 TCATTTTCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.18, C:0.06, G:0.46, T:0.29
Consensus pattern (46 bp):
TGGGGGTAGAGTGAGAGCGAGTTGGAGCAGGTATGCTTAGTTGGTT
Found at i:9330736 original size:2 final size:2
Alignment explanation
Indices: 9330729--9330757 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9330719 ACATAATCTA
9330729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9330758 AGCTTTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9338042 original size:18 final size:18
Alignment explanation
Indices: 9338011--9338045 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9338001 TTATTTTATT
9338011 TAAATTTAATTATAAAAA
1 TAAATTTAATTATAAAAA
9338029 TAAATATTAA-TATAAAA
1 TAAAT-TTAATTATAAAA
9338046 TTATATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATTTAATTATAAAAA
Found at i:9341388 original size:13 final size:13
Alignment explanation
Indices: 9341372--9341397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9341362 AAATGCAAGG
9341372 ATAAAAGTACATA
1 ATAAAAGTACATA
9341385 ATAAAAGTACATA
1 ATAAAAGTACATA
9341398 CTTGAATTCT
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
ATAAAAGTACATA
Found at i:9344139 original size:19 final size:17
Alignment explanation
Indices: 9344115--9344149 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
9344105 GATTCGATAA
9344115 TTATCAAGTCAAGCTCAAG
1 TTATCAA-TCAAG-TCAAG
9344134 TTATCAATCAAGTCAA
1 TTATCAATCAAGTCAA
9344150 ATTCGAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (17 bp):
TTATCAATCAAGTCAAG
Found at i:9361277 original size:26 final size:25
Alignment explanation
Indices: 9361241--9361289 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
9361231 TAAAATATAT
*
9361241 TCTTATGGCACGTTTTTTCTATTTAC
1 TCTTATGGCACG-TTGTTCTATTTAC
*
9361267 TCTTGTGGCACGTTGTTCTATTT
1 TCTTATGGCACGTTGTTCTATTT
9361290 TTTTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.12, C:0.18, G:0.16, T:0.53
Consensus pattern (25 bp):
TCTTATGGCACGTTGTTCTATTTAC
Found at i:9364756 original size:23 final size:23
Alignment explanation
Indices: 9364730--9364776 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
9364720 TATTTTAGTT
9364730 TAAT-TAAAATTATAAAATAAATA
1 TAATATAAAATTATAAAA-AAATA
* *
9364753 TAATATTAAATTATTAAAAAATA
1 TAATATAAAATTATAAAAAAATA
9364776 T
1 T
9364777 TAGGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATATAAAATTATAAAAAAATA
Found at i:9374507 original size:11 final size:12
Alignment explanation
Indices: 9374487--9374521 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
9374477 ATGTTATAAT
9374487 ATTAATATTTTA
1 ATTAATATTTTA
*
9374499 ATT-ATATTTTT
1 ATTAATATTTTA
9374510 ATTAATATTTTA
1 ATTAATATTTTA
9374522 TTGTGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTAATATTTTA
Found at i:9377542 original size:13 final size:13
Alignment explanation
Indices: 9377520--9377583 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
9377510 TTTGGCAATA
*
9377520 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
9377533 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* * *
9377546 AC-GTGGAAAATTG
1 -CTTTTGAAAAGTG
*
9377559 CTTTTGAGAAA-TA
1 CTTTTGA-AAAGTG
9377572 CTTTTGAAAAGT
1 CTTTTGAAAAGT
9377584 TTAGTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
12 4 0.10
13 32 0.80
14 4 0.10
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:9377580 original size:26 final size:25
Alignment explanation
Indices: 9377516--9377583 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
9377506 CTAGTTTGGC
*
9377516 AATACTTTTAAAAAGTGCTTTTGAA
1 AATACTTTTGAAAAGTGCTTTTGAA
* * *
9377541 AAGTGAC-GTGGAAAATTGCTTTTGAGA
1 AA-T-ACTTTTGAAAAGTGCTTTTGA-A
9377568 AATACTTTTGAAAAGT
1 AATACTTTTGAAAAGT
9377584 TTAGTTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
25 4 0.12
26 23 0.72
27 5 0.16
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (25 bp):
AATACTTTTGAAAAGTGCTTTTGAA
Found at i:9378564 original size:15 final size:15
Alignment explanation
Indices: 9378544--9378605 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
9378534 TGTTTAATTA
*
9378544 TAATTAATTTTTAAT
1 TAATTAAATTTTAAT
*
9378559 TAATTAAAGTTTAAT
1 TAATTAAATTTTAAT
* * *
9378574 TAAATAAATTATGAT
1 TAATTAAATTTTAAT
*
9378589 TAATTAGA-TTTAAT
1 TAATTAAATTTTAAT
9378603 TAA
1 TAA
9378606 AAGTATATAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
14 7 0.19
15 30 0.81
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
TAATTAAATTTTAAT
Done.