Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 10 of 17
Found at i:1255667 original size:2 final size:2
Alignment explanation
Indices: 1255633--1255657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1255623 ACATTAATGT
1255633 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 T
1255658 TAATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1257786 original size:36 final size:36
Alignment explanation
Indices: 1257717--1257805 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
1257707 AATTATAAAG
*
1257717 AATCAAATTATT--GAGATTATGATCCTATAATCGT
1 AATCAAAATATTAGGAGATTATGATCCTATAATCGT
* * * * *
1257751 AAGT-AGAATGTTAGGAGATTATGATTCTGTGATCGT
1 AA-TCAAAATATTAGGAGATTATGATCCTATAATCGT
1257787 AATCAAAATATTAGGAGAT
1 AATCAAAATATTAGGAGAT
1257806 CCTTCATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
34 7 0.16
35 2 0.05
36 34 0.79
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (36 bp):
AATCAAAATATTAGGAGATTATGATCCTATAATCGT
Found at i:1261184 original size:21 final size:21
Alignment explanation
Indices: 1261158--1261210 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1261148 TTTATATTAA
1261158 TGTATTAATACCTCGGGTGTG
1 TGTATTAATACCTCGGGTGTG
1261179 TGTATTAATACCTCGGGTGTG
1 TGTATTAATACCTCGGGTGTG
1261200 TGTATTAATAC
1 TGTATTAATAC
1261211 AATGCTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.40
Consensus pattern (21 bp):
TGTATTAATACCTCGGGTGTG
Found at i:1261276 original size:21 final size:20
Alignment explanation
Indices: 1261252--1261321 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1261242 CCTTTATTTA
1261252 TATTGATATAATTAAGCAATG
1 TATTGATATAATTAA-CAATG
* *
1261273 TATTGATA-CATTTACAATTG
1 TATTGATATAATTAACAA-TG
* *
1261293 TATCGATATAATTAATATATG
1 TATTGATATAATTAACA-ATG
1261314 TATTGATA
1 TATTGATA
1261322 CATGGCTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.08
20 13 0.33
21 22 0.56
22 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (20 bp):
TATTGATATAATTAACAATG
Found at i:1262817 original size:15 final size:15
Alignment explanation
Indices: 1262799--1262834 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1262789 TTCCCCTTTA
*
1262799 ATCATCTCCCTTTTG
1 ATCATCTACCTTTTG
*
1262814 ATCATCTATCTTTTG
1 ATCATCTACCTTTTG
1262829 ATCATC
1 ATCATC
1262835 AGTAAAGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (15 bp):
ATCATCTACCTTTTG
Found at i:1265552 original size:51 final size:51
Alignment explanation
Indices: 1265486--1265639 Score: 245
Period size: 51 Copynumber: 3.0 Consensus size: 51
1265476 CTGTTATTTT
* * *
1265486 CAAGGAGATACTCCAATCCTGATTTTATTTCTAAAACACTGATTTTCCACCA
1 CAAGG-GATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCA
*
1265538 CAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCACCA
1 CAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCA
* *
1265589 CAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCA
1 CAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCA
1265640 TTGGAGATTG
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 90 0.95
52 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (51 bp):
CAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCA
Found at i:1265795 original size:157 final size:157
Alignment explanation
Indices: 1265592--1266121 Score: 471
Period size: 157 Copynumber: 3.3 Consensus size: 157
1265582 TTCACCACAA
*
1265592 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATTGGAGAT-TGTCTAAC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATCGGAGATAT-TC-AAC
** * * *
1265656 CTTATTATTTTCGAGGAGATACTCTAACCCCAATTTTATTTCTAAAATATC-GATTTTCCACCAT
64 CCCATTATTTTCGAGGAGATACTCTAACCCCAATTTTATTTCTAAAACACCAAATTTT-CACCAT
1265720 CGA-GGATACTCCAACCCCGCTCTTTTCGAG
128 -GAGGGATACTCCAACCCCGCTCTTTTCGAG
* * * *
1265750 GGGATACTCCAACCCTGGTTTTA-TTCTAAAACATTTATTTTTCACCATCGGGGATACTTCAACC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATCGGAGATA-TTCAACC
* * * *
1265814 CCGTTATTTTTGAGGAGATACTCTAACCCCCATTTTATTTCTAAAACACCAAATTTTCACCATTA
65 CCATTATTTTCGAGGAGATACTCTAACCCCAATTTTATTTCTAAAACACCAAATTTTCACCATGA
* *
1265879 GGGATACTCCAACCCCGTTATTTAT-GAG
130 GGGATACTCCAACCCCGCTCTTT-TCGAG
* * * * * *
1265907 GAGATA-TCCAACCTCGATTTTATTTCTAAATTTCTAAAATACTTATTTTCCACCATCGGGGATA
1 GGGATACTCCAACCCCGATTTTATTTCT-AA-----AACAT--TAATTTTTCACCATCGGAGATA
* * ** * ** * * *
1265971 CTCCAACCTCATTATTTTTAAGGGGATACTC-AACCTTAATTTTATTTTTAAAACACTAATTTTT
58 -TTCAACCCCATTATTTTCGAGGAGATACTCTAACCCCAATTTTATTTCTAAAACACCAAATTTT
* * * * * * *
1266035 CACTATTAGGGATACTCTAACTCCGTTATTTTTGAG
122 CACCATGAGGGATACTCCAACCCCGCTCTTTTCGAG
* * * ** *
1266071 GGGATACTCCAACCCCGATTTTGTTTCCAAAATATCGACTTTTCACCATCG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATCG
1266122 AGGATACTCT
Statistics
Matches: 311, Mismatches: 45, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
156 14 0.05
157 126 0.41
158 31 0.10
159 5 0.02
163 5 0.02
164 65 0.21
165 65 0.21
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (157 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATCGGAGATATTCAACCC
CATTATTTTCGAGGAGATACTCTAACCCCAATTTTATTTCTAAAACACCAAATTTTCACCATGAG
GGATACTCCAACCCCGCTCTTTTCGAG
Found at i:1265813 original size:78 final size:79
Alignment explanation
Indices: 1265594--1266130 Score: 445
Period size: 79 Copynumber: 6.7 Consensus size: 79
1265584 CACCACAAGG
* * * ** * **
1265594 GATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTTCACCATTGGAGATTGTCTAACCTT
1 GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCC
*
1265659 ATTATTTTCGAGGA
66 GTTATTTTCGAGGA
* * * * * *
1265673 GATACTCTAACCCCAATTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCC
* * *
1265738 GCTCTTTTCGAGGG
66 GTTATTTTCGAGGA
* * ** *
1265752 GATACTCCAACCCTGGTTTTA-TTCTAAAACATTTATTTTTCACCATCGGGGATACTTCAACCCC
1 GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCC
*
1265816 GTTATTTTTGAGGA
66 GTTATTTTCGAGGA
* * * * **
1265830 GATACTCTAACCCCCATTTTATTTCTAAAACACCAAATTTTCACCATTAGGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCC
1265895 GTTATTTAT-GAGGA
66 GTTATTT-TCGAGGA
* * * *
1265909 GATA-TCCAACCTCGATTTTATTTCTAAATTTCTAAAATACTTATTTTCCACCATCGGGGATACT
1 GATACTCCAACCCCGATTTTATTTCT-AA-----AACAT-C-AATTTTTCACCATCGGGGATACT
* * ** *
1265973 CCAACCTCATTATTTTTAAGGG
58 CCAACCCCGTTATTTTCGAGGA
*** * * ** * *
1265995 GATACT-CAACCTTAATTTTATTTTTAAAACA-CTAATTTTTCACTATTAGGGATACTCTAACTC
1 GATACTCCAACCCCGATTTTATTTCTAAAACATC-AATTTTTCACCATCGGGGATACTCCAACCC
* *
1266058 CGTTATTTTTGAGGG
65 CGTTATTTTCGAGGA
* * * * * *
1266073 GATACTCCAACCCCGATTTTGTTTCCAAAATATCGACTTTTCACCATCGAGGATACTC
1 GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTC
1266131 TAAACCCACT
Statistics
Matches: 360, Mismatches: 84, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
78 125 0.35
79 168 0.47
80 5 0.01
84 3 0.01
85 4 0.01
86 54 0.15
87 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
GATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCC
GTTATTTTCGAGGA
Found at i:1266005 original size:86 final size:85
Alignment explanation
Indices: 1265866--1266022 Score: 199
Period size: 86 Copynumber: 1.8 Consensus size: 85
1265856 AAAACACCAA
* * * *
1265866 ATTTTCACCATTAGGGATACTCCAACCCCGTTATTTATGAGGAGATATCCAACCTCGATTTTATT
1 ATTTTCACCATCAGGGATACTCCAACCCCATTATTTATAAGGAGATATCCAACCTCAATTTTATT
1265931 TCTAAATTTCTAAAATACTT
66 TCTAAATTTCTAAAATACTT
* * * * *
1265951 ATTTTCCACCATCGGGGATACTCCAACCTCATTATTTTTAAGGGGATA-CTCAACCTTAATTTTA
1 ATTTT-CACCATCAGGGATACTCCAACCCCATTATTTATAAGGAGATATC-CAACCTCAATTTTA
*
1266015 TTTTTAAA
64 TTTCTAAA
1266023 ACACTAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 6 0.10
86 54 0.90
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (85 bp):
ATTTTCACCATCAGGGATACTCCAACCCCATTATTTATAAGGAGATATCCAACCTCAATTTTATT
TCTAAATTTCTAAAATACTT
Found at i:1266129 original size:243 final size:243
Alignment explanation
Indices: 1265693--1266130 Score: 560
Period size: 243 Copynumber: 1.8 Consensus size: 243
1265683 CCCCAATTTT
* * *
1265693 ATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGCTCTTTTCGAGGGGATACT
1 ATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCACTATTTTCAAGGGGATACT
** * * *
1265758 CCAACCCTGGTTTTATTCTAAAACATTTATTTTTCACCATCGGGGATACTTCAACCCCGTTATTT
66 CCAACCCTAATTTTATTCTAAAACACTAATTTTTCACCATCAGGGATACTTCAACCCCGTTATTT
* * *
1265823 TTGAGGAGATACTCTAACCCCCATTTTATTTCTAAAACACCAAATTTTCACCATTAGGGATACTC
131 TTGAGGAGATACTCCAACCCCCATTTTATTTCCAAAACACCAAATTTTCACCATGAGGGATACTC
1265888 CAACCCCGTTATTTATGAGGAGATATCCAACCTCGATTTTATTTCTAA
196 CAACCCCGTTATTTATGAGGAGATATCCAACCTCGATTTTATTTCTAA
* * * * *
1265936 ATTTCTAAAATA-CTTATTTTCCACCATCGGGGATACTCCAACCTCATTATTTTTAAGGGGATAC
1 ATTTCTAAAATATC-GATTTTCCACCATCGAGGATACTCCAACCCCACTATTTTCAAGGGGATAC
* * * * *
1266000 T-CAACCTTAATTTTATTTTTAAAACACTAATTTTTCACTATTAGGGATAC-TCTAACTCCGTTA
65 TCCAACCCTAATTTTA-TTCTAAAACACTAATTTTTCACCATCAGGGATACTTC-AACCCCGTTA
* * * * * * *
1266063 TTTTTGAGGGGATACTCCAACCCCGATTTTGTTTCCAAAATATCGACTTTTCACCATCGA-GGAT
128 TTTTTGAGGAGATACTCCAACCCCCATTTTATTTCCAAAACACCAAATTTTCACCAT-GAGGGAT
1266127 ACTC
192 ACTC
1266131 TAAACCCACT
Statistics
Matches: 163, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
242 14 0.09
243 148 0.91
244 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (243 bp):
ATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCACTATTTTCAAGGGGATACT
CCAACCCTAATTTTATTCTAAAACACTAATTTTTCACCATCAGGGATACTTCAACCCCGTTATTT
TTGAGGAGATACTCCAACCCCCATTTTATTTCCAAAACACCAAATTTTCACCATGAGGGATACTC
CAACCCCGTTATTTATGAGGAGATATCCAACCTCGATTTTATTTCTAA
Found at i:1267919 original size:17 final size:17
Alignment explanation
Indices: 1267897--1267930 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1267887 CCATGATGCC
1267897 TAAAGATAATAATATGA
1 TAAAGATAATAATATGA
1267914 TAAAGATAATAATATGA
1 TAAAGATAATAATATGA
1267931 CCAAAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAGATAATAATATGA
Found at i:1268196 original size:4 final size:4
Alignment explanation
Indices: 1268187--1268212 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1268177 ATTGAGGTGC
1268187 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1268213 TGTTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1279454 original size:61 final size:61
Alignment explanation
Indices: 1279357--1279673 Score: 415
Period size: 61 Copynumber: 5.2 Consensus size: 61
1279347 TTATCCTGTT
* * * *
1279357 AGTCCTTC-AAGAGTAGGATGCCTTCTCCTTTTAAAGCCTACACAGGTTGGTGGCACCTTTC
1 AGTCC-TCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1279418 AGTCCTCAAAGAGTAGAACGCCTTCTCCTTTCAAAGCCCACACAAATTGGTGGCACCTTTC
1 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
1279479 AGTCCTCAAAGAGCAGGACGTCTTCTCCTTTCAAAGCTCACACAAGTTGGTGGAACCTTTT
1 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
1279540 AGTCCTCAAAGAGTAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTAGCACTTTTC
1 AGTCCTCAAAGAGTAGGACGCC-TTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
1279602 AGTCCTCAAAAAGTAGGAC-AC-TCTCCTTTCAAAGCCCATACAAGTTGATGGCACCTTTC
1 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
1279661 AATCCTCAAAGAG
1 AGTCCTCAAAGAG
1279674 CAAGATGCCT
Statistics
Matches: 222, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
59 43 0.19
60 2 0.01
61 127 0.57
62 50 0.23
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (61 bp):
AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:1280025 original size:33 final size:33
Alignment explanation
Indices: 1279988--1280087 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1279978 TTCAACGATT
*** *
1279988 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1280021 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1280054 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1280087 T
1 T
1280088 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTTTTTTGTATCGATACAA
Found at i:1280026 original size:13 final size:13
Alignment explanation
Indices: 1280008--1280065 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1279998 CATAAAATGT
1280008 TGTATCGATACAA
1 TGTATCGATACAA
1280021 TGTATCGATACATA
1 TGTATCGATACA-A
1280035 TTTTTTTGTATCGATACAA
1 ------TGTATCGATACAA
1280054 TGTATCGATACA
1 TGTATCGATACA
1280066 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
14 1 0.03
19 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1280046 original size:20 final size:19
Alignment explanation
Indices: 1280021--1280089 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1280011 ATCGATACAA
1280021 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
1280041 TGTATCGATACAA------
1 TGTATCGATACAATTTTTT
1280054 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
1280074 TGTATCGATACAATTT
1 TGTATCGATACAATTT
1280090 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.29
14 1 0.02
19 5 0.12
20 24 0.57
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (19 bp):
TGTATCGATACAATTTTTT
Found at i:1280146 original size:13 final size:13
Alignment explanation
Indices: 1280128--1280152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1280118 ATTACTCAAA
1280128 TGTATCGATACAT
1 TGTATCGATACAT
1280141 TGTATCGATACA
1 TGTATCGATACA
1280153 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1280217 original size:52 final size:52
Alignment explanation
Indices: 1280161--1280285 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1280151 CACTGATCTT
* *
1280161 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
*
1280213 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
*
1280265 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1280286 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
Found at i:1284835 original size:10 final size:9
Alignment explanation
Indices: 1284818--1284855 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
1284808 CCTAATCTTC
1284818 ACAAAAAAA
1 ACAAAAAAA
1284827 ACAAAAAAA
1 ACAAAAAAA
1284836 ACAAAAAAA
1 ACAAAAAAA
1284845 A-AAAGAAAA
1 ACAAA-AAAA
1284854 AC
1 AC
1284856 CCCTTTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 3 0.11
9 24 0.89
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:1285992 original size:31 final size:31
Alignment explanation
Indices: 1285802--1285978 Score: 268
Period size: 31 Copynumber: 5.7 Consensus size: 31
1285792 AAAAAAAAAA
*
1285802 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1285833 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1285864 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
*
1285895 AAAGTCCATGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
* *
1285926 AAAGTCCACGACGCAGTGGC-ATCCTTCT-CTTT
1 AAAGTCCACGACTCAGTGGCAAT-C-TCTGC-TC
*
1285958 AAAGTCCATGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1285979 TTTTTTCTTT
Statistics
Matches: 135, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
30 2 0.01
31 111 0.82
32 22 0.16
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:1286090 original size:29 final size:30
Alignment explanation
Indices: 1286023--1286109 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
1286013 TGTTCCTTTT
* *
1286023 AAGTCCACAAATCAGTGGCACCCTTTTTCCG
1 AAGTCCACAAATCAGTGGCACTC-TTTTCCA
* * *
1286054 AAGCCCACAAGTCGGTGGCA-TCTTTTCCA
1 AAGTCCACAAATCAGTGGCACTCTTTTCCA
* *
1286083 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAAATCAGTGGCACTCTTTT
1286110 TCTTTTGTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 23 0.49
30 7 0.15
31 17 0.36
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.26
Consensus pattern (30 bp):
AAGTCCACAAATCAGTGGCACTCTTTTCCA
Found at i:1286192 original size:30 final size:30
Alignment explanation
Indices: 1286146--1286224 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1286136 CACTCTTTTC
* *
1286146 AGCCCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAGTCAGTGGCACACTGTTCAAA
* * * *
1286176 AGCCCATAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCACACTGTTCAAA
1286206 AGCCCACAAGTCAGTGGCA
1 AGCCCACAAGTCAGTGGCA
1286225 ACCTTTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (30 bp):
AGCCCACAAGTCAGTGGCACACTGTTCAAA
Found at i:1286244 original size:30 final size:33
Alignment explanation
Indices: 1286210--1286295 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
1286200 TTCAAAAGCC
*
1286210 CACAAGTCAGTGGCAACC-TT-T-TAAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
*
1286240 CACAAGTTGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
*
1286273 CACAAGTCGGTGGCAACCCTTCT
1 CACAAGTCGGTGGCAACCATTCT
1286296 AAGCCCAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 16 0.33
31 2 0.04
32 1 0.02
33 30 0.61
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCATTCTCTAAAGCCCA
Found at i:1286359 original size:49 final size:49
Alignment explanation
Indices: 1286295--1286941 Score: 837
Period size: 49 Copynumber: 13.7 Consensus size: 49
1286285 GCAACCCTTC
* * * * *
1286295 TAAGCCCAATATAGCTGGCCTTGAATCAGCATAGTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1286344 TAAGTCCAATGTAGCTGGCCTTGACTCCGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1286393 TAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286442 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1286485 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1286534 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1286577 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-TTATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTT
*
1286626 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1286675 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286723 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286772 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286820 TAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGG------CATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286863 TAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1286906 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1286942 ACATCCTTTT
Statistics
Matches: 539, Mismatches: 41, Indels: 42
0.87 0.07 0.07
Matches are distributed among these distances:
43 156 0.29
45 2 0.00
47 2 0.00
48 91 0.17
49 285 0.53
50 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1286517 original size:92 final size:92
Alignment explanation
Indices: 1286387--1286950 Score: 734
Period size: 92 Copynumber: 6.1 Consensus size: 92
1286377 TTGGCACCTT
* *
1286387 CACCATTAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAA
1 CACCTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAA
*
1286451 TGTAGCTGGCCTTGAATCAGCATATTGG
65 TGTAGCTGGCCTTGAATCAGCACATTGG
* *
1286479 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
1286544 GTAGCTGGCCTTGAATCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
* *
1286571 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-TTATCATCTTTAAGTCCAA
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT-TCATCTTTAAGTCCAA
*
1286635 TGTAGCTGGCCTTGACTCAGCACATTGG
65 TGTAGCTGGCCTTGAATCAGCACATTGG
* *
1286663 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAG
1 CA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAG
*
1286727 TCCAATGTAGCTGGCCTTGACTCAGCACATTGG
60 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * *
1286760 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAG
1 CA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAG
*
1286824 TCCAATGTAGTTGGCCTTGAATCAGCACATTGG
60 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
1286857 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--CTTTAAGTTCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
*
1286916 GTAGCTGGCCTTGAATCAGCACATTGA
66 GTAGCTGGCCTTGAATCAGCACATTGG
1286943 CATCCTTT
1 CA-CCTTT
1286951 TTCATCATCT
Statistics
Matches: 442, Mismatches: 20, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
86 39 0.09
87 4 0.01
88 1 0.00
91 42 0.10
92 174 0.39
93 2 0.00
96 1 0.00
97 140 0.32
98 39 0.09
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGG
Found at i:1287851 original size:33 final size:33
Alignment explanation
Indices: 1287814--1287880 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1287804 TTCAACGATT
1287814 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1287847 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1287880 T
1 T
1287881 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1287852 original size:13 final size:13
Alignment explanation
Indices: 1287834--1287858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287824 CATAAAATGT
1287834 TGTATCGATACAA
1 TGTATCGATACAA
1287847 TGTATCGATACA
1 TGTATCGATACA
1287859 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1287939 original size:13 final size:13
Alignment explanation
Indices: 1287921--1287945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287911 ATTACTCAAA
1287921 TGTATCGATACAT
1 TGTATCGATACAT
1287934 TGTATCGATACA
1 TGTATCGATACA
1287946 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1288010 original size:52 final size:52
Alignment explanation
Indices: 1287954--1288078 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1287944 CACTGATCTT
* *
1287954 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
*
1288006 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
*
1288058 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1288079 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAAATTGCCCAGATGTATCGATACACTATAAAA
Found at i:1291297 original size:61 final size:60
Alignment explanation
Indices: 1291146--1291395 Score: 258
Period size: 61 Copynumber: 4.1 Consensus size: 60
1291136 GTTACGACAC
* * *
1291146 CTTTTCTTTTCAAAGCCCACACAAGTTGG-GGGAACTTCTAGTCCTCAAAGAGTAGGA-CA
1 CTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATCA
* * * * *
1291205 CTTTCCTTTTGAAGCCTACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGC-
1 CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGAT-CA
* * *
1291265 CTTTTCTTTTCAAAGCCCGCACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCGGGA-CA
1 CTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATCA
* *
1291325 CTTTCTTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGA-C
1 ----C--TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATC
1291389 A
60 A
*
1291390 CCTTTC
1 CTTTTC
1291396 ACCTTTTCTA
Statistics
Matches: 162, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
58 16 0.10
59 39 0.24
60 9 0.06
61 44 0.27
64 1 0.01
65 44 0.27
66 9 0.06
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (60 bp):
CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATCA
Found at i:1291378 original size:65 final size:67
Alignment explanation
Indices: 1291216--1291395 Score: 205
Period size: 65 Copynumber: 2.8 Consensus size: 67
1291206 TTTCCTTTTG
* * * * * *
1291216 AAGCCTACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGG--A---TGC-CTTTTCTTTT
1 AAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTCTTTTTTCTTTT
1291275 CA
66 CA
* * * *
1291277 AAGCCCGCACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCGGGACA-CTTTCTTTTTTCTTTT
1 AAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTCTTTTTTCTTTT
1291341 -A
66 CA
*
1291342 AAGCCCACATAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTC
1 AAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTC
1291396 ACCTTTTCTA
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
61 41 0.40
63 1 0.01
65 46 0.45
66 14 0.14
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (67 bp):
AAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTCTTTTTTCTTTT
CA
Found at i:1291394 original size:126 final size:119
Alignment explanation
Indices: 1291141--1291394 Score: 319
Period size: 126 Copynumber: 2.1 Consensus size: 119
1291131 CGCACGTTAC
* *
1291141 GACACCTTTTCTTTTCAAAGCCCACACAAGTTGGGGGAACTTCTAGTCCTCAAAGAGTAGGACAC
1 GACACCTTTTCTTTTCAAAGCCCACACAAGTTGGGGCAACTTCTAGTCCTCAAAGAGCAGGACAC
* * * * *
1291206 TTTCCTTTTGAAGCCTACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAG
66 TTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAG
** * * * *
1291260 GATGCCTTTTCTTTTCAAAGCCCGCACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCGGGACA
1 GACACCTTTTCTTTTCAAAGCCCACACAAGTTGG-GGCAACTTCTAGTCCTCAAAGAGCAGGACA
*
1291325 CTTTCTTTTTTCTTTTAAAGCCCACATAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAG
65 CTTTC------CTTTTAAAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAG
1291386 GACACCTTT
1 GACACCTTT
1291395 CACCTTTTCT
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 31 0.28
120 30 0.27
126 51 0.46
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (119 bp):
GACACCTTTTCTTTTCAAAGCCCACACAAGTTGGGGCAACTTCTAGTCCTCAAAGAGCAGGACAC
TTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCTAGTCCTCAAAGAGCAG
Found at i:1291432 original size:69 final size:65
Alignment explanation
Indices: 1291233--1291433 Score: 178
Period size: 65 Copynumber: 3.1 Consensus size: 65
1291223 CACAAGTTGG
* * * ** * *
1291233 TGGCACCTTTTAGTCCTCAAAGAGTAGG--A---TGCCTTTTCTTTTCAAAGCCCGCACAAGTTG
1 TGGCACCTTCTAGTCCTCAAAGAGCAGGACACTTTCCCTTTTCTTTT-AAAGCCCAAATAAGATG
*
1291293 G
65 A
* * ** * * *
1291294 TGGCACCTTTTAGTCCTCAAAGAGCGGGACACTTTCTTTTTTCTTTTAAAGCCCACATAAGCTGG
1 TGGCACCTTCTAGTCCTCAAAGAGCAGGACACTTTCCCTTTTCTTTTAAAGCCCAAATAAGATGA
*
1291359 TGGCACCTTCTAGTCCTCAAAGAGCAGGACACCTTTCACCTTTTCTATCTTAAAGCTCAAATAAG
1 TGGCACCTTCTAGTCCTCAAAGAGCAGGACA-CTTTC-CCTTTTCT-T-TTAAAGCCCAAATAAG
1291424 ATGA
62 ATGA
1291428 TGGCAC
1 TGGCAC
1291434 ATATCTACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
61 26 0.23
63 1 0.01
65 44 0.38
66 15 0.13
67 6 0.05
68 1 0.01
69 22 0.19
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (65 bp):
TGGCACCTTCTAGTCCTCAAAGAGCAGGACACTTTCCCTTTTCTTTTAAAGCCCAAATAAGATGA
Found at i:1296640 original size:21 final size:21
Alignment explanation
Indices: 1296612--1296688 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
1296602 AAAATTTCCA
1296612 AATGTATCGATACATTTATAG
1 AATGTATCGATACATTTATAG
* *
1296633 AATATATCGATACATTTGT-G
1 AATGTATCGATACATTTATAG
*
1296653 AAATGTATCGATACATTCTACA-
1 -AATGTATCGATACATT-TATAG
1296675 AATGTATCGATACA
1 AATGTATCGATACA
1296689 GGGTCCCAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTATAG
Found at i:1296748 original size:19 final size:19
Alignment explanation
Indices: 1296724--1296791 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1296714 AATTCAACGA
1296724 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1296743 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1296758 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1296775 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1296792 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1296762 original size:32 final size:32
Alignment explanation
Indices: 1296726--1296788 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1296716 TTCAACGATT
*
1296726 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1296758 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1296789 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1296763 original size:13 final size:13
Alignment explanation
Indices: 1296745--1296769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1296735 ACATAAGTTT
1296745 TGTATCGATACAA
1 TGTATCGATACAA
1296758 TGTATCGATACA
1 TGTATCGATACA
1296770 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1296849 original size:13 final size:13
Alignment explanation
Indices: 1296831--1296856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1296821 CATTTTTCTA
1296831 TGTATCGATACAT
1 TGTATCGATACAT
1296844 TGTATCGATACAT
1 TGTATCGATACAT
1296857 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1296853 original size:33 final size:33
Alignment explanation
Indices: 1296811--1296877 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1296801 GCCAAGGAAA
***
1296811 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
1296844 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
1296877 T
1 T
1296878 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:1299331 original size:54 final size:51
Alignment explanation
Indices: 1299215--1299338 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 51
1299205 CAATTCTCCG
* * * *
1299215 CAATCAGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
* * *
1299266 TAATTGGGGATACTCTAACTCCGATTTTATTTTCAAAAAAACACAAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAACACAAATTTTCT-A
*
1299320 CAATCGGGGATACTACAAC
1 CAATCGGGGATACTCCAAC
1299339 CCCGTTAATC
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
51 28 0.48
53 1 0.02
54 29 0.50
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
Found at i:1299390 original size:28 final size:27
Alignment explanation
Indices: 1299325--1299396 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1299315 TTTCACAATC
* **
1299325 GGGGATACTACAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
1299352 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
1299380 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1299397 TGCTTTATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:1299498 original size:52 final size:52
Alignment explanation
Indices: 1299380--1299602 Score: 215
Period size: 52 Copynumber: 4.3 Consensus size: 52
1299370 TTATTTCCGA
* * * * * *
1299380 GGGGATACTCCAACCCCTG-CTTTA-TTCTTAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCC-GATTTTATTTC-TAAAACACTAATTTTTTCACAATC
*
1299431 GGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTTCACAATC
* * * *
1299483 GGGGATACTCTAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT--TAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT--TTCACAATC
* * *
1299535 GGGGATACTCCAGCTCCGATTTTATTTCCAAAA-ACATCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACAC-T-AATTTTTTCACAATC
*
1299588 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1299603 TCGTTATTTC
Statistics
Matches: 141, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
50 1 0.01
51 33 0.23
52 83 0.59
53 22 0.16
54 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTTCACAATC
Found at i:1299613 original size:31 final size:28
Alignment explanation
Indices: 1299585--1299661 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
1299575 TTTTTTCACA
*
1299585 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
1299613 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
1299641 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
1299662 GCTCTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:1299704 original size:264 final size:263
Alignment explanation
Indices: 1299235--1299712 Score: 744
Period size: 264 Copynumber: 1.8 Consensus size: 263
1299225 TATTCCATCT
* * *
1299235 CCGATTTTATTTTCAAAACACTAATTTTCTATAATTGGGGATACTCTAACTCCGATTTTATTTTC
1 CCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTTC
*
1299300 AAAAAAACACAAATTTTTCACAATCGGGGATACTACAACCCCGTTAATCATCGGGGATACTCCAA
66 AAAAAAACACAAATTTTTCACAATCGAGGATACTACAACCCCGTTAATCATCGGGGATACTCCAA
** * * **
1299365 CCCCGTTATTTCCGAGGGGATACTCCAACCCCTGCTTTATTCTTAAAATATTGATTTCTCATAAT
131 CCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTCCCAAAATATTGATTTCTCATAAT
1299430 CGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTTCACAATCGGGGATACTCTA
196 CGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTTCACAATCGGGGATACTCTA
1299495 ACC
261 ACC
* * *
1299498 CCGATTTTATTTTTAAAACACCAATTTTCCTTTAATCGGGGATACTCCAGCTCCGATTTTA-TTT
1 CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACTCCGATTTTATTTT
* * * * *
1299562 C-CAAAAACATCAATTTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTC
65 CAAAAAAACA-CAAATTTTTCACAATCGAGGATACTACAACCCCGTTA-ATCATCGGGGATACTC
1299626 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTCCCAAAATATTGATTTCTCAT
128 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTCCCAAAATATTGATTTCTCAT
*
1299691 AATTGGGGATACTCCAACCCCG
193 AATCGGGGATACTCCAACCCCG
1299713 TTATTTTCGA
Statistics
Matches: 193, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
262 7 0.04
263 63 0.33
264 123 0.64
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
CCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTTC
AAAAAAACACAAATTTTTCACAATCGAGGATACTACAACCCCGTTAATCATCGGGGATACTCCAA
CCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTCCCAAAATATTGATTTCTCATAAT
CGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTTCACAATCGGGGATACTCTA
ACC
Found at i:1301144 original size:20 final size:20
Alignment explanation
Indices: 1301116--1301162 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1301106 TGCCCCGTTA
1301116 CGACCTGGGTGTGCCGGTCG
1 CGACCTGGGTGTGCCGGTCG
*
1301136 CGACTTGGGTGTGCCGGTCG
1 CGACCTGGGTGTGCCGGTCG
*
1301156 TGACCTG
1 CGACCTG
1301163 AAGAGGCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.06, C:0.28, G:0.43, T:0.23
Consensus pattern (20 bp):
CGACCTGGGTGTGCCGGTCG
Found at i:1301632 original size:14 final size:14
Alignment explanation
Indices: 1301602--1301642 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
1301592 AAGTAACCTA
*
1301602 TGTATTGATAA-AT
1 TGTATCGATAACAT
1301615 TGTATCGATAACAT
1 TGTATCGATAACAT
1301629 TGTATCGAT-ACAT
1 TGTATCGATAACAT
1301642 T
1 T
1301643 TGGGTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (14 bp):
TGTATCGATAACAT
Found at i:1308543 original size:157 final size:158
Alignment explanation
Indices: 1308258--1309100 Score: 858
Period size: 157 Copynumber: 5.4 Consensus size: 158
1308248 TAAAATACTG
* ** *
1308258 ATTTTCCACCATCGGGGATACTCCAACCCCA-TTATTTTTTAGGGAATACTTCAACCCCGATTTT
1 ATTTTTCACCATCGGGGATACTCCAA-CCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTT
** * * * *
1308322 ATTTCTAAAACATGGATTTTCCACCATCGGGGATACTCAAACCCTGTTA-TTTCTGAGGGAATAC
65 ATTTCTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATAC
* *
1308386 TCTAACCCTAATTTTATTTCTAAAACACCG
129 TCCAACCCTAATTTTATTTCTAAAACACCA
* * * * *
1308416 ATTTTCCACCATC-TGGAAACTCTAACCCAGTTATTTTCGAGGGGATACTTCAACCCTGATTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTTA
** * *
1308480 TTTCTAAAACACCGATTTTTCACCATTAGGGATACTCCAACCCCGTTATTTCCCAGGGGATACTC
66 TTTCTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTC
* *
1308545 TAA-CCTCAATTTTATTTCTAAAACATCA
131 CAACCCT-AATTTTATTTCTAAAACACCA
* *
1308573 ATTTTTCACCATCAGGGATACTCCAA--C--TT-TTATC-AGGGGATACTTCAACCCCGATTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTTA
** * *
1308632 TTTCTAAAACAATGATTTTTCACCATCGAGGATACTCAAACCCCGTTATTTTCGAGGGGATACTC
66 TTTCTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTC
* *
1308697 CAACCCTAGTTTTATTTCTAAAACATCA
131 CAACCCTAATTTTATTTCTAAAACACCA
* * * * ** *
1308725 ATTTTTCA--A-C--CGATACTCCAACCCCGTTATTTCCAAAAGGATAC-TCTAACCCCAATTTT
1 ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTC-AACCCCGATTTT
* * * * **
1308784 ATTTCTAAAACACTGATTTTTCACTATCGGGGATACTCCAATCCTGTTATTTTCGAGATGATACT
65 ATTTCTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACT
* * **
1308849 CCAACCCTTATTTTATTTATAAAACACTG
130 CCAACCCTAATTTTATTTCTAAAACACCA
* * * * * * *
1308878 ATTTTTCACCATCGAGGATACTCTAACCCTGTTATTTT-TAGGAGATACTCCAACCTCGATTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTTA
* * * * *
1308942 TTTCTAAAACATC-AATTTTCTATCATCGGGGATACTCCAACCTCGTTATTTTCGAGGAGATACT
66 TTTCTAAAACACCGATTTTTC-ACCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACT
* * * * * *
1309006 CCAACCTTGATTTTGTTTCCAAAATATCA
130 CCAACCCTAATTTTATTTCTAAAACACCA
* * * * * * *
1309035 ATTTTTCACTATCGGGGATACTCTAACCCCGTTGTTTTCGAAGGGATACTCCAACCCCGTTTTTA
1 ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTTA
1309100 T
66 T
1309101 CTCCAAAATA
Statistics
Matches: 571, Mismatches: 94, Indels: 40
0.81 0.13 0.06
Matches are distributed among these distances:
147 10 0.02
149 2 0.00
150 1 0.00
151 2 0.00
152 116 0.20
153 113 0.20
154 2 0.00
155 1 0.00
156 15 0.03
157 242 0.42
158 67 0.12
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (158 bp):
ATTTTTCACCATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTTCAACCCCGATTTTA
TTTCTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTC
CAACCCTAATTTTATTTCTAAAACACCA
Found at i:1309111 original size:79 final size:79
Alignment explanation
Indices: 1308257--1309100 Score: 782
Period size: 79 Copynumber: 10.8 Consensus size: 79
1308247 CTAAAATACT
* * ** *
1308257 GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTT-TTAGGGAATACTTCAACCCCGATTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCGATTT
*
1308321 TATTTCTAAAACATG
65 TATTTCTAAAACATC
* * * * **
1308336 GATTTTCCACCATCGGGGATACTCAAACCCTGTTA-TTTCTG-AGGGAATACTCTAACCCTAATT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTC-GAAGGG-ATACTCCAACCCCGATT
*
1308399 TTATTTCTAAAACACC
64 TTATTTCTAAAACATC
* * * * * * * *
1308415 GATTTTCCACCATC-TGGAAACTCTAACCCAGTTATTTTCGAGGGGATACTTCAACCCTGATTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
*
1308479 ATTTCTAAAACACC
66 ATTTCTAAAACATC
** * * * * * *
1308493 GATTTTTCACCATTAGGGATACTCCAACCCCGTTATTTCCCAGGGGATACTCTAACCTCAATTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
1308558 ATTTCTAAAACATC
66 ATTTCTAAAACATC
* * * * *
1308572 AATTTTTCACCATCAGGGATACTCCAA---C-TT-TTATC-AGGGGATACTTCAACCCCGATTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
1308631 ATTTCTAAAACAAT-
66 ATTTCTAAAAC-ATC
* * * *
1308645 GATTTTTCACCATCGAGGATACTCAAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCTAGTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGA-TTT
1308709 TATTTCTAAAACATC
65 TATTTCTAAAACATC
* * * * * * *
1308724 AATTTTTCA--A-C--CGATACTCCAACCCCGTTATTTCCAAAAGGATACTCTAACCCCAATTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
1308784 ATTTCTAAAACA-C
66 ATTTCTAAAACATC
* * * * **
1308797 TGATTTTTCACTATCGGGGATACTCCAATCCTGTTATTTTCG-AGATGATACTCCAACCCTTATT
1 -GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAG-GGATACTCCAACCCCGATT
*
1308861 TTATTTATAAAACA-C
64 TTATTTCTAAAACATC
* * * * *
1308876 TGATTTTTCACCATCGAGGATACTCTAACCCTGTTATTTT--TAGGAGATACTCCAACCTCGATT
1 -GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGG-GATACTCCAACCCCGATT
1308939 TTATTTCTAAAACATC
64 TTATTTCTAAAACATC
* * * **
1308955 -AATTTTCTATCATCGGGGATACTCCAACCTCGTTATTTTCG-AGGAGATACTCCAACCTTGATT
1 GATTTTTC-ACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGG-GATACTCCAACCCCGATT
* * *
1309018 TTGTTTCCAAAATATC
64 TTATTTCTAAAACATC
* * * * *
1309034 AATTTTTCACTATCGGGGATACTCTAACCCCGTTGTTTTCGAAGGGATACTCCAACCCCGTTTTT
1 GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
1309099 AT
66 AT
1309101 CTCCAAAATA
Statistics
Matches: 638, Mismatches: 97, Indels: 60
0.80 0.12 0.08
Matches are distributed among these distances:
73 55 0.09
74 61 0.10
75 6 0.01
76 4 0.01
77 10 0.02
78 129 0.20
79 364 0.57
80 9 0.01
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
GATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTT
ATTTCTAAAACATC
Found at i:1314941 original size:70 final size:70
Alignment explanation
Indices: 1314828--1314969 Score: 221
Period size: 70 Copynumber: 2.0 Consensus size: 70
1314818 CAGATTTAGT
* * *
1314828 TGATTAGCTTTGTTTTTGGATACATCTAATACTAGTCTTGAAAAAATTGAACCAAATCGATCGAT
1 TGATTAGCTTTATTTTTGGATACATCTAATACTAGTCTTGAAAAAACTGAACCAAATCAATCGAT
1314893 TCAAC
66 TCAAC
* * *
1314898 TGATTAGCTTTATTTTTGGATACATCTAATACTAGTTTTGAAAAAACTGAACCAGATCAATCGGT
1 TGATTAGCTTTATTTTTGGATACATCTAATACTAGTCTTGAAAAAACTGAACCAAATCAATCGAT
*
1314963 TTAAC
66 TCAAC
1314968 TG
1 TG
1314970 GTTGGTTTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (70 bp):
TGATTAGCTTTATTTTTGGATACATCTAATACTAGTCTTGAAAAAACTGAACCAAATCAATCGAT
TCAAC
Found at i:1315152 original size:23 final size:23
Alignment explanation
Indices: 1315109--1315152 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1315099 AATTAAATCC
* *
1315109 AAATTTAAACTCAATTTTAACCT
1 AAATTTAAACTCAAATATAACCT
1315132 AAATTTAAAC-CAAAATATAAC
1 AAATTTAAACTC-AAATATAAC
1315153 AAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATTTAAACTCAAATATAACCT
Found at i:1315321 original size:11 final size:12
Alignment explanation
Indices: 1315297--1315321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1315287 ATTTTTTTAC
1315297 TTCTTTATTTTT
1 TTCTTTATTTTT
1315309 TTCTTTATTTTT
1 TTCTTTATTTTT
1315321 T
1 T
1315322 AAATTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTATTTTT
Found at i:1315322 original size:19 final size:21
Alignment explanation
Indices: 1315300--1315349 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
1315290 TTTTTACTTC
*
1315300 TTTATTTTTTTCTTTA-T-TT
1 TTTATTTTTTTCTTAATTATT
**
1315319 TTTAAATTTTTCTTAATTATT
1 TTTATTTTTTTCTTAATTATT
1315340 TTTATTTTTT
1 TTTATTTTTT
1315350 AATTATTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 13 0.54
20 1 0.04
21 10 0.42
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTTTTTCTTAATTATT
Found at i:1316234 original size:28 final size:28
Alignment explanation
Indices: 1316194--1316250 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1316184 CGTATATAAC
1316194 TACGTATACTTATGTTTTTGCTTTATTT
1 TACGTATACTTATGTTTTTGCTTTATTT
* *
1316222 TACGTGTACTTATGTTTTTGCTTTCTTT
1 TACGTATACTTATGTTTTTGCTTTATTT
1316250 T
1 T
1316251 CTTTTTGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (28 bp):
TACGTATACTTATGTTTTTGCTTTATTT
Found at i:1319524 original size:21 final size:21
Alignment explanation
Indices: 1319483--1319525 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1319473 TTAAAAAATT
* *
1319483 AATAAATTCTAATATTTTAAA
1 AATAAATTCTAACATTATAAA
1319504 AATAAATT-TAACACTTATAAA
1 AATAAATTCTAACA-TTATAAA
1319525 A
1 A
1319526 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAAATTCTAACATTATAAA
Found at i:1319922 original size:15 final size:15
Alignment explanation
Indices: 1319902--1319948 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1319892 GTGTTTCAAT
1319902 ATTTAAATTAAATAA
1 ATTTAAATTAAATAA
*
1319917 ATTTAAAATTTAA-AA
1 ATTT-AAATTAAATAA
* *
1319932 ATTAAAAATAAATAA
1 ATTTAAATTAAATAA
1319947 AT
1 AT
1319949 AAATAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.23
15 13 0.50
16 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTAAATTAAATAA
Found at i:1321395 original size:21 final size:22
Alignment explanation
Indices: 1321369--1321420 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1321359 TTAAAAATTT
1321369 ATATTATTAATTA-TAATAATA
1 ATATTATTAATTATTAATAATA
*
1321390 ATATTATT-ATTATTAATATTA
1 ATATTATTAATTATTAATAATA
1321411 ATATTATTAA
1 ATATTATTAA
1321421 CATTGTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTATTAATTATTAATAATA
Found at i:1321408 original size:15 final size:15
Alignment explanation
Indices: 1321369--1321420 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1321359 TTAAAAATTT
1321369 ATATTATTAAT-TATA
1 ATATTATTAATAT-TA
1321384 ATA--A-TAATATTA
1 ATATTATTAATATTA
*
1321396 TTATTATTAATATTA
1 ATATTATTAATATTA
1321411 ATATTATTAA
1 ATATTATTAA
1321421 CATTGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 8 0.26
13 2 0.06
14 1 0.03
15 20 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTAATATTA
Found at i:1321649 original size:18 final size:17
Alignment explanation
Indices: 1321619--1321666 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1321609 TTGACTGGAT
1321619 TAAATTTTAAATATTAA
1 TAAATTTTAAATATTAA
*
1321636 TAAATTTTTTAATATTATTA
1 TAAA-TTTTAAATATTA--A
*
1321656 TAAATTATAAA
1 TAAATTTTAAA
1321667 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 5 0.20
20 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTTAAATATTAA
Found at i:1321661 original size:20 final size:18
Alignment explanation
Indices: 1321619--1321652 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1321609 TTGACTGGAT
1321619 TAAA-TTTTAAATATTAA
1 TAAATTTTTAAATATTAA
*
1321636 TAAATTTTTTAATATTA
1 TAAATTTTTAAATATTA
1321653 TTATAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTTTAAATATTAA
Found at i:1323349 original size:27 final size:28
Alignment explanation
Indices: 1323312--1323368 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1323302 TAAAATAAAA
*
1323312 TTAAATAAAA-TTTAT-GATTGAATTAAT
1 TTAAATAAAATTTTATAG-TTAAATTAAT
*
1323339 TTAAATTAAATTTTATAGTTAAATTAAT
1 TTAAATAAAATTTTATAGTTAAATTAAT
1323367 TT
1 TT
1323369 GATTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 16 0.62
29 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (28 bp):
TTAAATAAAATTTTATAGTTAAATTAAT
Found at i:1323864 original size:27 final size:24
Alignment explanation
Indices: 1323801--1323872 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
1323791 TAGTATTTAT
*
1323801 AAAATTTTTAATTA-ATTTAAAAC
1 AAAAATTTTAATTATATTTAAAAC
*
1323824 AAAAATATTT-ATTATTATATTATAAC
1 AAAAAT-TTTAATTA-TAT-TTAAAAC
1323850 AATAAATTTTAATTATATTTAAA
1 AA-AAATTTTAATTATATTTAAA
1323873 TAGTTATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 9 0.22
24 3 0.08
25 6 0.15
26 14 0.35
27 8 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAAATTTTAATTATATTTAAAAC
Found at i:1324573 original size:22 final size:20
Alignment explanation
Indices: 1324538--1324586 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
1324528 ATAAATTTTG
**
1324538 ATAAAAATTTTTATTAAAATAT
1 ATAAAAATAATTA-TAAAAT-T
1324560 ATAAAAATAATTATAAAATT
1 ATAAAAATAATTATAAAATT
*
1324580 TTAAAAA
1 ATAAAAA
1324587 GTGTATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAATAATTATAAAATT
Found at i:1325196 original size:18 final size:19
Alignment explanation
Indices: 1325173--1325211 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1325163 AATTTTTGAA
*
1325173 ATATTA-AAAAATTAATTT
1 ATATTATAAAAAATAATTT
1325191 ATATTATTAAAAAATAATTT
1 ATATTA-TAAAAAATAATTT
1325211 A
1 A
1325212 AATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTATAAAAAATAATTT
Found at i:1325627 original size:18 final size:18
Alignment explanation
Indices: 1325600--1325634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1325590 TACTCCTTTT
* *
1325600 AATATTTTATATTAATAA
1 AATATATTATACTAATAA
1325618 AATATATTATACTAATA
1 AATATATTATACTAATA
1325635 TTATTATTTT
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTATACTAATAA
Found at i:1373530 original size:52 final size:52
Alignment explanation
Indices: 1373450--1373578 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1373440 CGAAATAATG
* *
1373450 AAATTTGCCTGCATGTATCAATAGATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1373502 AAATTTGCCTGCATGTATCGATCCATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1373554 AAATTTTCCTGAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1373579 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1373589 original size:52 final size:52
Alignment explanation
Indices: 1373450--1373598 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 52
1373440 CGAAATAATG
* * * **
1373450 AAATTTGCCTGCATGTATCAATAGATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* * **
1373502 AAATTTGCCTGCATGTATCGATCCATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* *
1373554 AAATTTTCCTGAATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGAATGTATCGATACATAACAT-AGTGTATCGATACA
1373599 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:1373605 original size:13 final size:13
Alignment explanation
Indices: 1373587--1373611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1373577 CAAAGATCAG
1373587 TGTATCGATACAA
1 TGTATCGATACAA
1373600 TGTATCGATACA
1 TGTATCGATACA
1373612 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1373720 original size:19 final size:19
Alignment explanation
Indices: 1373663--1373760 Score: 101
Period size: 19 Copynumber: 5.7 Consensus size: 19
1373653 AGCGATATAT
*
1373663 TGTATCGATACAAAAACTTA
1 TGTATCGATAC-AACACTTA
1373683 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1373696 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1373715 TGTATCGATAC-A-A--T-
1 TGTATCGATACAACACTTA
1373729 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1373748 TGTATCGATACAA
1 TGTATCGATACAA
1373761 ATCGTTGAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
13 9 0.14
14 12 0.18
15 2 0.03
16 6 0.09
17 1 0.02
18 3 0.05
19 24 0.36
20 9 0.14
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1373760 original size:33 final size:33
Alignment explanation
Indices: 1373661--1373760 Score: 175
Period size: 33 Copynumber: 3.0 Consensus size: 33
1373651 GTAGCGATAT
*
1373661 ATTGTATCGATACAAAAACTTATGTATCGATAC-
1 ATTGTATCGATAC-AACACTTATGTATCGATACA
1373694 ATTGTATCGATACAACACTTATGTATCGATACA
1 ATTGTATCGATACAACACTTATGTATCGATACA
1373727 ATTGTATCGATACAACACTTATGTATCGATACA
1 ATTGTATCGATACAACACTTATGTATCGATACA
1373760 A
1 A
1373761 ATCGTTGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
32 18 0.28
33 47 0.72
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTATGTATCGATACA
Found at i:1378627 original size:13 final size:13
Alignment explanation
Indices: 1378609--1378638 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1378599 TTTGGAGGCT
1378609 TAAATAAAGAAAG
1 TAAATAAAGAAAG
*
1378622 TAAATAAAGAAAT
1 TAAATAAAGAAAG
1378635 TAAA
1 TAAA
1378639 AATAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
TAAATAAAGAAAG
Found at i:1378770 original size:13 final size:13
Alignment explanation
Indices: 1378750--1378800 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1378740 GAAAAACTTG
1378750 AAAGAAAAAGAGAGA
1 AAAG-AAAAGAGA-A
*
1378765 AAA-AAAAAAGAA
1 AAAGAAAAGAGAA
1378777 AGAAGAAAAGAGAA
1 A-AAGAAAAGAGAA
1378791 AAAGAAAAGA
1 AAAGAAAAGA
1378801 TTCAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 2 0.06
13 18 0.56
14 9 0.28
15 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAGAA
Found at i:1378777 original size:25 final size:25
Alignment explanation
Indices: 1378749--1378800 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1378739 AGAAAAACTT
1378749 GAAAGAA-AAAGAGAGAAAAAAAAAA
1 GAAAGAAGAAA-AGAGAAAAAAAAAA
*
1378774 GAAAGAAGAAAAGAGAAAAAGAAAA
1 GAAAGAAGAAAAGAGAAAAAAAAAA
1378799 GA
1 GA
1378801 TTCAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
GAAAGAAGAAAAGAGAAAAAAAAAA
Found at i:1378794 original size:20 final size:19
Alignment explanation
Indices: 1378756--1378797 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1378746 CTTGAAAGAA
1378756 AAAGAGAGAAAAAAAAAAG
1 AAAGAGAGAAAAAAAAAAG
1378775 AAAGA-AGAAAAGAGAAAAAG
1 AAAGAGAGAAAA-A-AAAAAG
1378795 AAA
1 AAA
1378798 AGATTCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAGAGAGAAAAAAAAAAG
Found at i:1379164 original size:136 final size:135
Alignment explanation
Indices: 1378919--1379171 Score: 368
Period size: 136 Copynumber: 1.9 Consensus size: 135
1378909 TGAAAGCTTA
* *
1378919 ATGATCCTAGGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTGGTGGCC
1 ATGATCCTAAGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTAGTGGCC
* * * *
1378984 AAGCAACAGCTAAAATCCAGTTTATTTAATTTCTTGTTAGTTATTTAGTTTATATGTAATTAAAG
66 AAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATATGTAATTAAAG
1379049 GTTTG
131 GTTTG
* *
1379054 ATGATCCTAAGTCATTAACTTAGGTGATAGCTTGATCTTAATGGTTTTCTAA-TCATTTTAGTGG
1 ATGATCCTAAGTCATTAACTTAGGTG-TAGCTTGAGCTTAATGGTTTCCTAACT-ATTTTAGTGG
*
1379118 CCAAACAAGAGCTAAAATCC-CTTCCATTTAATTT-TTGTTAGTTTATTTAATTTA
64 CCAAACAACAGCTAAAATCCACTT-CATTTAATTTCTTGTTAG-TTATTTAATTTA
1379172 AGGCAACACT
Statistics
Matches: 105, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
135 35 0.33
136 70 0.67
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (135 bp):
ATGATCCTAAGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTAGTGGCC
AAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATATGTAATTAAAG
GTTTG
Found at i:1379191 original size:136 final size:136
Alignment explanation
Indices: 1378911--1379226 Score: 353
Period size: 136 Copynumber: 2.3 Consensus size: 136
1378901 TGTTTTCATG
* *
1378911 AAAG-CTTAATGATCCTAGGTCATTAACTTAGGTG-TAGCTTGAGCTTAATGGTTTCCTAACTAT
1 AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACTAT
* * * * * *
1378974 TTTGGTGGCCAAGCAACAGCTAAAATCCAGTTTATTTAATTTCTTGTTAGTTATTTAGTTTATAT
66 TTTAGTGGCCAAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATAG
* *
1379039 GTAATT
131 GAAACT
** * *
1379045 AAAGGTTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGATCTTAATGGTTTTCTAA-TCA
1 AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACT-A
*
1379109 TTTTAGTGGCCAAACAAGAGCTAAAATCC-CTTCCATTTAATTT-TTGTTAGTTTATTTAATTTA
65 TTTTAGTGGCCAAACAACAGCTAAAATCCACTT-CATTTAATTTCTTGTTAG-TTATTTAATTTA
1379172 -AGGCAACACT
128 TAGG-AA-ACT
* * *
1379182 -AAGACTTGATGGTCCTAAGT--TTAATATTAGATGATAGCTTGAGCT
1 AAAGACTTGATGATCCTAAGTCATTAA-CTTAGGTGATAGCTTGAGCT
1379227 AGGTTTCCCA
Statistics
Matches: 154, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
134 8 0.05
135 56 0.36
136 88 0.57
137 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (136 bp):
AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACTAT
TTTAGTGGCCAAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATAG
GAAACT
Found at i:1379550 original size:8 final size:8
Alignment explanation
Indices: 1379537--1379776 Score: 75
Period size: 8 Copynumber: 28.4 Consensus size: 8
1379527 TTTTTTATTC
1379537 AAAAAATT
1 AAAAAATT
1379545 AAAAAA--
1 AAAAAATT
*
1379551 AGAAAATCT
1 AAAAAAT-T
1379560 AAAAAA-T
1 AAAAAATT
*
1379567 AAAAATTTT
1 AAAAA-ATT
1379576 AAAAAATT
1 AAAAAATT
**
1379584 TTAAAA-T
1 AAAAAATT
1379591 ATAAAAA-T
1 A-AAAAATT
1379599 -AAAAATT
1 AAAAAATT
*
1379606 CAAAAATT
1 AAAAAATT
1379614 ATAAAAATT
1 A-AAAAATT
* *
1379623 CTATAAATT
1 -AAAAAATT
1379632 CAAAAGAATT
1 -AAAA-AATT
*
1379642 AAAAAGTTTTT
1 AAAAA---ATT
**
1379653 AAAATTTT
1 AAAAAATT
1379661 AAAAAATT
1 AAAAAATT
1379669 ATTAAAAATCT
1 A--AAAAAT-T
* *
1379680 TAAAATTT
1 AAAAAATT
*
1379688 AAAAAAAT
1 AAAAAATT
1379696 ATAAAAA-T
1 A-AAAAATT
1379704 AAAAAATAT
1 AAAAAAT-T
*
1379713 CAAAAATTT
1 -AAAAAATT
*
1379722 AAAAAACT
1 AAAAAATT
1379730 AAAAATATAT
1 AAAAA-AT-T
1379740 AATTAAATATGT
1 AA--AAA-AT-T
*
1379752 AGAAAA-T
1 AAAAAATT
1379759 -AAAAATT
1 AAAAAATT
1379766 AAAAAATT
1 AAAAAATT
1379774 AAA
1 AAA
1379777 TTTGAAAAAT
Statistics
Matches: 176, Mismatches: 29, Indels: 54
0.68 0.11 0.21
Matches are distributed among these distances:
6 14 0.08
7 15 0.09
8 65 0.37
9 45 0.26
10 22 0.12
11 7 0.04
12 8 0.05
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:1379578 original size:9 final size:9
Alignment explanation
Indices: 1379566--1379703 Score: 60
Period size: 9 Copynumber: 15.8 Consensus size: 9
1379556 ATCTAAAAAA
1379566 TAAAAATTT
1 TAAAAATTT
1379575 TAAAAAATTT
1 T-AAAAATTT
*
1379585 T-AAAA-TA
1 TAAAAATTT
1379592 TAAAAA---
1 TAAAAATTT
1379598 TAAAAA-TT
1 TAAAAATTT
* *
1379606 CAAAAATTA
1 TAAAAATTT
*
1379615 TAAAAATTC
1 TAAAAATTT
*
1379624 TATAAA-TT
1 TAAAAATTT
* *
1379632 CAAAAGA-AT
1 TAAAA-ATTT
1379641 TAAAAAGTTT
1 TAAAAA-TTT
*
1379651 TTAAAATTT
1 TAAAAATTT
1379660 TAAAAAATTAT
1 T-AAAAATT-T
*
1379671 TAAAAATCT
1 TAAAAATTT
1379680 T-AAAATTT
1 TAAAAATTT
* * *
1379688 AAAAAAATA
1 TAAAAATTT
1379697 TAAAAAT
1 TAAAAAT
1379704 AAAAAATATC
Statistics
Matches: 97, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
6 6 0.06
7 2 0.02
8 24 0.25
9 36 0.37
10 27 0.28
11 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (9 bp):
TAAAAATTT
Found at i:1379605 original size:22 final size:23
Alignment explanation
Indices: 1379577--1379621 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1379567 AAAAATTTTA
**
1379577 AAAAATTTTAAAA-TATAAAAAT
1 AAAAATTCAAAAATTATAAAAAT
1379599 AAAAATTCAAAAATTATAAAAAT
1 AAAAATTCAAAAATTATAAAAAT
1379622 TCTATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATTCAAAAATTATAAAAAT
Found at i:1379683 original size:28 final size:26
Alignment explanation
Indices: 1379586--1379703 Score: 84
Period size: 27 Copynumber: 4.5 Consensus size: 26
1379576 AAAAAATTTT
* *
1379586 AAAATATAAAAA---TAAAAATTCAA
1 AAAATATAAAAATCTTAAAATTTAAA
* *
1379609 AAATTATAAAAAT-TCTATAAATTCAAA
1 AAAATATAAAAATCT-TA-AAATTTAAA
* *
1379636 AGAAT-TAAAAAGTTTTTAAAATTTTAAA
1 AAAATATAAAAA--TCTTAAAA-TTTAAA
*
1379664 AAATTATTAAAAATCTTAAAATTTAAA
1 AAAATA-TAAAAATCTTAAAATTTAAA
1379691 AAAATATAAAAAT
1 AAAATATAAAAAT
1379704 AAAAAATATC
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
23 11 0.15
26 15 0.20
27 23 0.31
28 18 0.24
29 1 0.01
30 6 0.08
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATATAAAAATCTTAAAATTTAAA
Found at i:1379707 original size:15 final size:16
Alignment explanation
Indices: 1379689--1379719 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1379679 TTAAAATTTA
1379689 AAAAAATAT-AAAAAT
1 AAAAAATATCAAAAAT
1379704 AAAAAATATCAAAAAT
1 AAAAAATATCAAAAAT
1379720 TTAAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAATATCAAAAAT
Found at i:1379733 original size:42 final size:43
Alignment explanation
Indices: 1379660--1379741 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
1379650 TTTAAAATTT
* **
1379660 TAAAAAATTATTAAAAATCTTAAAATTTAAAAAAATATAAAAA
1 TAAAAAATTATCAAAAATCTTAAAAACTAAAAAAATATAAAAA
*
1379703 TAAAAAA-TATCAAAAAT-TTAAAAAACTAAAAATATATAA
1 TAAAAAATTATCAAAAATCTT-AAAAACTAAAAAAATATAA
1379742 TTAAATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.06
42 25 0.74
43 7 0.21
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (43 bp):
TAAAAAATTATCAAAAATCTTAAAAACTAAAAAAATATAAAAA
Found at i:1380194 original size:13 final size:15
Alignment explanation
Indices: 1380165--1380200 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
1380155 TTCTGCCCAT
1380165 TTTCCTCTTTCTTCC
1 TTTCCTCTTTCTTCC
1380180 TTTCC-CTTT-TTCC
1 TTTCCTCTTTCTTCC
1380193 TTTCCTCT
1 TTTCCTCT
1380201 ATCTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCCTCTTTCTTCC
Found at i:1380319 original size:28 final size:28
Alignment explanation
Indices: 1380264--1380325 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1380254 TGTTTTTAAG
*
1380264 TTTTTT-AAATTTTAAGTTTTTGATATA
1 TTTTTTAAAATTTAAAGTTTTTGATATA
1380291 TATTTTTAAAATTTAAAAGTTTTT-A-ATA
1 T-TTTTTAAAATTT-AAAGTTTTTGATATA
1380319 TTTTTTA
1 TTTTTTA
1380326 GATATTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 7 0.23
28 9 0.29
29 7 0.23
30 8 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTTAAAATTTAAAGTTTTTGATATA
Found at i:1380332 original size:28 final size:30
Alignment explanation
Indices: 1380264--1380325 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1380254 TGTTTTTAAG
* *
1380264 TTTTTTAAATTT-TAAGTTTTTGATATATA
1 TTTTTAAAATTTAAAAGTTTTTGATATATA
1380293 TTTTTAAAATTTAAAAGTTTTT-A-ATAT-
1 TTTTTAAAATTTAAAAGTTTTTGATATATA
1380320 TTTTTA
1 TTTTTA
1380326 GATATTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.20
28 4 0.13
29 12 0.40
30 8 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTTAAAATTTAAAAGTTTTTGATATATA
Found at i:1380422 original size:13 final size:14
Alignment explanation
Indices: 1380404--1380440 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
1380394 AAAAATATTC
1380404 TTATATTTTTAA-T
1 TTATATTTTTAATT
1380417 TTATA-TTTTAATTT
1 TTATATTTTTAA-TT
1380431 TTATATTTTT
1 TTATATTTTT
1380441 TGCAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 5 0.24
14 6 0.29
15 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATATTTTTAATT
Found at i:1380711 original size:30 final size:30
Alignment explanation
Indices: 1380670--1380766 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
1380660 TTTATTGTAG
* *
1380670 TTTATTTTTTTAAAATTTAAATTTATGCAT
1 TTTACTTTTTTAAAATTTAAATTTATGCAA
* *
1380700 TTTACTTTTTTACAATTTAAATTCATGCAA
1 TTTACTTTTTTAAAATTTAAATTTATGCAA
* ** *
1380730 TTT--TTTCTT-GCATTTAGAATTTATGCAC
1 TTTACTTTTTTAAAATTTA-AATTTATGCAA
1380758 TTTACTTTT
1 TTTACTTTT
1380767 GTTGCAAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.09
28 17 0.31
30 32 0.59
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTACTTTTTTAAAATTTAAATTTATGCAA
Found at i:1380881 original size:2 final size:2
Alignment explanation
Indices: 1380874--1380909 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1380864 GACATACTTT
1380874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1380910 GATAGATAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1380914 original size:4 final size:4
Alignment explanation
Indices: 1380907--1380945 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
1380897 ATATATATAT
1380907 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1380946 CAACTACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:1390435 original size:32 final size:32
Alignment explanation
Indices: 1390394--1390457 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1390384 GCTTGGATAC
1390394 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
1 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
* *
1390426 ATTCTCAGCAGCTGATTTGGAAACTAATGGCA
1 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
1390458 CCCCTTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (32 bp):
ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
Found at i:1394900 original size:8 final size:8
Alignment explanation
Indices: 1394883--1394956 Score: 51
Period size: 8 Copynumber: 8.5 Consensus size: 8
1394873 TATTTATTTG
1394883 TATTTATA
1 TATTTATA
*
1394891 TATTTTTA
1 TATTTATA
*
1394899 TATATAATTA
1 TAT-TTA-TA
1394909 TATTTA-A
1 TATTTATA
*
1394916 AATATTATA
1 TAT-TTATA
1394925 TATTTATA
1 TATTTATA
1394933 TAGATTTTAATA
1 T--A-TTT-ATA
1394945 TATTTATA
1 TATTTATA
1394953 TATT
1 TATT
1394957 CGTATCATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
7 3 0.06
8 26 0.50
9 9 0.17
10 7 0.13
11 3 0.06
12 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (8 bp):
TATTTATA
Found at i:1398364 original size:13 final size:13
Alignment explanation
Indices: 1398346--1398371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1398336 TACAGCAAGT
1398346 ATGTATCGATACA
1 ATGTATCGATACA
1398359 ATGTATCGATACA
1 ATGTATCGATACA
1398372 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1400571 original size:21 final size:21
Alignment explanation
Indices: 1400538--1400582 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1400528 TTGCAAGTTG
*
1400538 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1400560 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1400580 AAA
1 AAA
1400583 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1402406 original size:15 final size:15
Alignment explanation
Indices: 1402386--1402416 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1402376 TAAAAATGTC
*
1402386 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1402401 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1402416 C
1 C
1402417 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1404503 original size:13 final size:13
Alignment explanation
Indices: 1404485--1404510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1404475 ACATTTTTCT
1404485 TTGTATCGATACA
1 TTGTATCGATACA
1404498 TTGTATCGATACA
1 TTGTATCGATACA
1404511 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1406411 original size:93 final size:93
Alignment explanation
Indices: 1406308--1406494 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
1406298 ATAAATTTTT
1406308 GATATGAATTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGGGAGAATGCG
1 GATATGAATTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGGGAGAATGCG
*
1406373 TAAATTGCTACAATTACTTTGTTAAGGG
66 TAAATTGCTACAATTACTTTATTAAGGG
1406401 GATATGAATTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGGGAGAATGCG
1 GATATGAATTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGGGAGAATGCG
1406466 TAAATTGCTACAATTACTTTATTAAGGG
66 TAAATTGCTACAATTACTTTATTAAGGG
1406494 G
1 G
1406495 GAGAATGTAC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.28
Consensus pattern (93 bp):
GATATGAATTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGGGAGAATGCG
TAAATTGCTACAATTACTTTATTAAGGG
Found at i:1406432 original size:21 final size:21
Alignment explanation
Indices: 1406384--1406449 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
1406374 AAATTGCTAC
*
1406384 AATTACTTTG-TTAAGGGGATATG
1 AATTAC-TTGATTAAGGGG-GA-G
1406407 AATTACTTGATTAAGGGGGAG
1 AATTACTTGATTAAGGGGGAG
* *
1406428 AATTA-TTAATAAACGGGGGAG
1 AATTACTTGATTAA-GGGGGAG
1406449 A
1 A
1406450 TAAAGGGGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.16
21 14 0.37
22 4 0.11
23 14 0.37
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (21 bp):
AATTACTTGATTAAGGGGGAG
Found at i:1407173 original size:13 final size:13
Alignment explanation
Indices: 1407155--1407180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1407145 TACAGCAAGT
1407155 ATGTATCGATACA
1 ATGTATCGATACA
1407168 ATGTATCGATACA
1 ATGTATCGATACA
1407181 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1409021 original size:13 final size:13
Alignment explanation
Indices: 1409003--1409034 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1408993 TTGTTTTCAA
1409003 CCACCTTGCTCAG
1 CCACCTTGCTCAG
1409016 CCACCTTGCTCAG
1 CCACCTTGCTCAG
1409029 CCACCT
1 CCACCT
1409035 CTGTCGGTAG
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:0.16, C:0.50, G:0.12, T:0.22
Consensus pattern (13 bp):
CCACCTTGCTCAG
Found at i:1412184 original size:1 final size:1
Alignment explanation
Indices: 1412178--1412276 Score: 81
Period size: 1 Copynumber: 99.0 Consensus size: 1
1412168 AAATCTTCAC
* * * ** * * *
1412178 TTTTTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * *
1412243 TTTCCTTTTTTTTGTTTTGTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1412277 CCAATTGCCA
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:1412222 original size:36 final size:36
Alignment explanation
Indices: 1412181--1412277 Score: 134
Period size: 31 Copynumber: 2.8 Consensus size: 36
1412171 TCTTCACTTT
1412181 TTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCC
1412217 TTTTTTTTG---TTTTG--TTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCC
1412248 TTTTTTTTGTTTTGTTT-TTTTTTCTTTTTC
1 TTTTTTTTGTTTT-TTTGTTTTTT-TTTTTC
1412278 CAATTGCCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
31 26 0.48
33 5 0.09
34 1 0.02
35 3 0.06
36 13 0.24
37 6 0.11
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (36 bp):
TTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCC
Found at i:1412235 original size:31 final size:31
Alignment explanation
Indices: 1412200--1412278 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
1412190 TTTTTTTGTT
1412200 TTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG
1 TTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG
1412231 TTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG
1 TTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG
1412262 TTTTTTTTTCTTTTTCC
1 TTTTTTTTTCTTTTTCC
1412279 AATTGCCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (31 bp):
TTTTTTTTTCTTTTTCCTTTTTTTTGTTTTG
Found at i:1412255 original size:41 final size:40
Alignment explanation
Indices: 1412178--1412276 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 40
1412168 AAATCTTCAC
*
1412178 TTTTTTTTTTTGTTTTTTTGTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTGTTTTTTTGTTTTTTTCTTTCTTTTTCCT
**
1412218 TTTTTTTGTTTTGTTTTTTT-TTCTTTTTCCTTT-TTTTTGTT
1 TTTTTTT-TTTTGTTTTTTTGTT-TTTTT-CTTTCTTTTTCCT
*
1412259 TTGTTTTTTTTTCTTTTT
1 TT-TTTTTTTTTGTTTTT
1412277 CCAATTGCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
40 9 0.18
41 34 0.67
42 8 0.16
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (40 bp):
TTTTTTTTTTTGTTTTTTTGTTTTTTTCTTTCTTTTTCCT
Found at i:1412269 original size:15 final size:15
Alignment explanation
Indices: 1412178--1412275 Score: 91
Period size: 15 Copynumber: 6.8 Consensus size: 15
1412168 AAATCTTCAC
1412178 TTTTTTT-TTTTG--
1 TTTTTTTGTTTTGTT
1412190 TTTTTTTGTTTT-TT
1 TTTTTTTGTTTTGTT
* **
1412204 TTTTTCT-TTTTCCT
1 TTTTTTTGTTTTGTT
1412218 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
*
1412233 TTTTTTTCTTTT-TCCT
1 TTTTTTTGTTTTGT--T
1412249 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
*
1412264 TTTTTTTCTTTT
1 TTTTTTTGTTTT
1412276 TCCAATTGCC
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
12 7 0.10
13 8 0.11
14 14 0.20
15 28 0.40
16 12 0.17
17 1 0.01
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (15 bp):
TTTTTTTGTTTTGTT
Found at i:1425855 original size:52 final size:52
Alignment explanation
Indices: 1425784--1425909 Score: 162
Period size: 52 Copynumber: 2.4 Consensus size: 52
1425774 ATCGATACAT
* * * * *
1425784 TGAAGAATATATCAATACATTTGGGTCAAAAACCCATAAGGTATCAATATAA
1 TGAAAAATGTATCAATACATTTGGATAAAAAACCCAGAAGGTATCAATATAA
* * *
1425836 TGAAAAATGTATCGATACATTTGGATAAAAAACCCAGAATGTATCGATATAA
1 TGAAAAATGTATCAATACATTTGGATAAAAAACCCAGAAGGTATCAATATAA
* *
1425888 TAAAAAATGTATCAATAAATTT
1 TGAAAAATGTATCAATACATTT
1425910 TCTTTTCAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.29
Consensus pattern (52 bp):
TGAAAAATGTATCAATACATTTGGATAAAAAACCCAGAAGGTATCAATATAA
Found at i:1426015 original size:21 final size:20
Alignment explanation
Indices: 1425952--1426018 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1425942 GGACAATATT
1425952 GATACATTCACTTATGTATC
1 GATACATTCACTTATGTATC
*
1425972 GATATATTCACTTATGTATC
1 GATACATTCACTTATGTATC
* * *
1425992 GATACATTAACTTCTTGTAAC
1 GATACATTCACTT-ATGTATC
1426013 GATACA
1 GATACA
1426019 AATTGTAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 30 0.73
21 11 0.27
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (20 bp):
GATACATTCACTTATGTATC
Found at i:1429657 original size:146 final size:153
Alignment explanation
Indices: 1429474--1430061 Score: 507
Period size: 166 Copynumber: 3.7 Consensus size: 153
1429464 TTTCTTTGCT
*
1429474 CGTAAATTTTTTTGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
1 CGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
*
1429539 TAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGCTTAT-AAAATTTT-C-AA
66 TAATTCATACTAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTATGAAAATTTTCCTAA
1429601 ATTAC-GGGG-TT-T-TTTTC-TC
131 ATT-CTGGGGTTTATATTTTCTTC
* * *
1429620 CGTAAATTTTTTCGAGG-GGATTTTTCTTAGTTGTTAATTTTTAAAATTTATCAAATATTATTAT
1 CGTAAATTTTTTCG-GGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTAT
* * ** * **
1429684 TTAATTCATACTATATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTCCTT
65 TTAATTCATACTAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTATGAAAATTTTCC-T
**** *
1429749 GAAATTCTTTTTTTTCAGAAAATGAAATTTTCTATTT
129 -AAATTCTGGGGTTT------AT---ATTTTC--TTC
1429786 CGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
1 CGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
* * **
1429851 TAATTCATAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTGTGAATTTTTTCCTTG
66 TAATTCATACTAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTATGAAAATTTTCC-T-
*** *
1429916 AAATTCT-TTTTTTCAAAAAACAAAGTTTTCTACTC
129 AAATTCTGGGGTTT--------ATA-TTTTCT--TC
* * * *
1429951 CGTAAATTTTTTTGGGAGGAATTTTT-TTAGTTTTTATTTTTTAAAATTCATCAAATATCATTAT
1 CGTAAATTTTTTCGGGAGG-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTAT
* * * * * *
1430015 TT-ATATCACAATAAATTAGTTTTAAAAACTTCCTTTATTTTCTTGAG
65 TTAAT-TCATACTAAATTAGTTTTAAAAAATTCATTCATTTTCATGAG
1430062 TTTTTGGATT
Statistics
Matches: 373, Mismatches: 39, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
146 103 0.28
147 8 0.02
148 1 0.00
150 1 0.00
151 5 0.01
152 2 0.01
159 1 0.00
163 6 0.02
164 3 0.01
165 106 0.28
166 133 0.36
167 4 0.01
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (153 bp):
CGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
TAATTCATACTAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTATGAAAATTTTCCTAA
ATTCTGGGGTTTATATTTTCTTC
Found at i:1430030 original size:165 final size:165
Alignment explanation
Indices: 1429617--1430228 Score: 736
Period size: 166 Copynumber: 3.7 Consensus size: 165
1429607 GGGTTTTTTT
* * *
1429617 CTCCGTAAATTTTTTCGAGG-GGATTTTTCTTAGTTGTTAATTTTTAAAATTTATCAAATATTAT
1 CTCCGTAAATTTTTTCG-GGAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCAT
* * * * *
1429681 TATTTAATTCATACTATATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTC
65 TATTTAATTCACAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTC
* **
1429746 CTTGAAATTCTTTTTTTTCAGAAAATGAAATTTTCTA
130 CTTGAAATTCATTTTTTTCA-AAAAACAAATTTTCTA
* * * *
1429783 TTTCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATT
1 CTCCGTAAATTTTTTCGGGAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCATT
* *
1429848 ATTTAATTCATAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTGTGAATTTTTTCC
66 ATTTAATTCACAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCC
1429913 TTGAAATTC-TTTTTTTCAAAAAACAAAGTTTTCTA
131 TTGAAATTCATTTTTTTCAAAAAACAAA-TTTTCTA
* *
1429948 CTCCGTAAATTTTTTTGGGAGGAATTTTT-TTAGTTTTTATTTTTTAAAATTCATCAAATATCAT
1 CTCCGTAAATTTTTTCGGGAGG-ATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCAT
* * * * * *
1430012 TATTT-ATATCACAATAAATTAGTTTTAAAAACTTCCTTTATTTTCTTGAGTTTTTGGATTTTTT
65 TATTTAAT-TCACAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTT
* * * * *
1430076 TCTTTAAATTCCATTATTTTT-GAAAAACAGATTTTTCTG
129 CCTTGAAATT-CATT-TTTTTCAAAAAACA-AATTTTCTA
* * *
1430115 CTCTGTAAATTTTTTCAGGAGGATTTTTCTTGGTTTTT-ATATTTTAAAATTCATCAAATATCAT
1 CTCCGTAAATTTTTTCGGGAGGATTTTTCTTAGTTTTTAAT-TTTTAAAATTCATCAAATATCAT
* * * *
1430179 TATTT-ATTC-CATATTAAATTATTTTTCAAAAAGTAATTCATTTTCATGAG
65 TATTTAATTCACA-A-TAAATTAGTTTTAAAAAATTCATTCATTTTCATGAG
1430229 GTTTAGATTT
Statistics
Matches: 390, Mismatches: 44, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
164 9 0.02
165 132 0.34
166 143 0.37
167 100 0.26
168 6 0.02
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.50
Consensus pattern (165 bp):
CTCCGTAAATTTTTTCGGGAGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCATT
ATTTAATTCACAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCC
TTGAAATTCATTTTTTTCAAAAAACAAATTTTCTA
Found at i:1430243 original size:332 final size:331
Alignment explanation
Indices: 1429617--1430228 Score: 810
Period size: 331 Copynumber: 1.8 Consensus size: 331
1429607 GGGTTTTTTT
* *
1429617 CTCCGTAAATTTTTTCGAGGGGATTTTTCTTAGTTGTTAATTTTTAAAATTTATCAAATATTATT
1 CTCCGTAAATTTTTTCGAGGGGATTTTTCTTAGTTGTTAATTTTTAAAATTCATCAAATATCATT
* * *
1429682 ATTTAATTCATACTATATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTCC
66 ATTTAATTCACAATAAATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTCC
* * * *
1429747 TTGAAATTCTTTTTTTTCAGAAAATGAAATTTTCTATTTCGTAAATTTTTTCGGGAGGATTTTTC
131 TTGAAATTCTTATTTTTCAGAAAAAGAAATTTTCTATCTCGTAAATTTTTTCAGGAGGATTTTTC
*
1429812 TTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATAATAAATTAGTTTTAAAA
196 TTGGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAATAAATTAGTTTTAAAA
* *
1429877 AATTCATTCATTTTCATGAGCTTGTGAATTTTTTCCTTGAAATTCTTTTTTTCAAAAAACAAAGT
261 AAGTAATTCATTTTCATGAGCTTGTGAATTTTTTCCTTGAAATTCTTTTTTTCAAAAAACAAAGT
1429942 TTTCTA
326 TTTCTA
* * *
1429948 CTCCGTAAATTTTTTTG-GGAGGAATTTTT-TTAGTTTTTATTTTTTAAAATTCATCAAATATCA
1 CTCCGTAAATTTTTTCGAGG-GG-ATTTTTCTTAGTTGTTAATTTTTAAAATTCATCAAATATCA
* * * * * *
1430011 TTATTT-ATATCACAATAAATTAGTTTTAAAAACTTCCTTTATTTTCTTGAGTTTT-TGGATTTT
64 TTATTTAAT-TCACAATAAATCAGTTTTAAAAAATTCATTCATTTTCATGA-TTTTGTGAATTTT
* * * * *
1430074 TTTCTTTAAATTCCATTATTTTT--GAAAAACAGATTTTTCT-GCTCTGTAAATTTTTTCAGGAG
127 TTCCTTGAAATT-C-TTATTTTTCAGAAAAAGA-AATTTTCTATCTC-GTAAATTTTTTCAGGAG
*
1430136 GATTTTTCTTGGTTTTT-ATATTTTAAAATTCATCAAATATCATTATTT-ATTCCATATTAAATT
188 GATTTTTCTTGGTTTTTAAT-TTTTAAAATTCATCAAATATCATTATTTAATT-CATAATAAATT
* *
1430199 ATTTTTCAAAAAGTAATTCATTTTCATGAG
251 AGTTTTAAAAAAGTAATTCATTTTCATGAG
1430229 GTTTAGATTT
Statistics
Matches: 242, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
330 4 0.02
331 117 0.48
332 114 0.47
333 7 0.03
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.50
Consensus pattern (331 bp):
CTCCGTAAATTTTTTCGAGGGGATTTTTCTTAGTTGTTAATTTTTAAAATTCATCAAATATCATT
ATTTAATTCACAATAAATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTCC
TTGAAATTCTTATTTTTCAGAAAAAGAAATTTTCTATCTCGTAAATTTTTTCAGGAGGATTTTTC
TTGGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAATAAATTAGTTTTAAAA
AAGTAATTCATTTTCATGAGCTTGTGAATTTTTTCCTTGAAATTCTTTTTTTCAAAAAACAAAGT
TTTCTA
Found at i:1430329 original size:167 final size:164
Alignment explanation
Indices: 1429617--1430331 Score: 725
Period size: 167 Copynumber: 4.3 Consensus size: 164
1429607 GGGTTTTTTT
* * * *
1429617 CTCCGTAAATTTTTTCGAGG-GGATTTTTCTTAGTTGTTAATTTTTAAAATTTATCAAATATTAT
1 CTCCGTAAATTTTTTCG-GGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCAT
* * *
1429681 TATTTAATTCATACTATATCAGTTTTAAAAAATTCATTCATTTTCATGATTTTGTGAATTTTTTC
65 TATTTAATTCATA-TAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTT-TGAATTTTTTC
* * * *
1429746 CTTGAAATTCTTTTTTTTCAGAAAATGAAATTTTCTA
128 CTTGAAATTCCTTTTTTTCAAAAAACGAGATTTTCTA
* * *
1429783 TTTCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATT
1 CTCCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATT
*
1429848 ATTTAATTCATAATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGCTTGTGAATTTTTTCC
66 ATTTAATTCAT-ATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAG-TTTTGAATTTTTTCC
*
1429913 TTGAAATT-CTTTTTTTCAAAAAAC-AAAGTTTTCTA
129 TTGAAATTCCTTTTTTTCAAAAAACGAGA-TTTTCTA
* * *
1429948 CTCCGTAAATTTTTTTGGGAGGAATTTTT-TTAGTTTTTATTTTTTAAAATTCATCAAATATCAT
1 CTCCGTAAATTTTTTCGGGAGG-ATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCAT
* * * * * *
1430012 TATTT-ATATCACAATAAATTAGTTTTAAAAACTTCCTTTATTTTCTTGAGTTTTTGGATTTTTT
65 TATTTAAT-TCA-TATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAG-TTTTGAATTTTTT
* * * *
1430076 TCTTTAAATTCCATTATTTTT-GAAAAAC-AGATTTTTCTG
127 CCTTGAAATTCC-TT-TTTTTCAAAAAACGAGA-TTTTCTA
* *
1430115 CTCTGTAAATTTTTTCAGGAGGATTTTTCTTGGTTTTT-ATATTTTAAAATTCATCAAATATCAT
1 CTCCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAAT-TTTTAAAATTCATCAAATATCAT
* * * * * *
1430179 TATTT-ATTCCATATTAAATTATTTTTCAAAAAGTAATTCATTTTCATGAGGTTTAGATTTTTTT
65 TATTTAATT-CATA-TAAATTAGTTTTAAAAAATTCATTCATTTTCATGA-GTTTTGAATTTTTT
* * * **
1430243 CTTTAAAATCTCCCTTTTCCCAAAAAATCGAGA-TTTCTA
127 CCTTGAAAT-TCCTTTTTTTCAAAAAA-CGAGATTTTCTA
* * * * **
1430282 TTCCATAAATGTTTTCGGG-GTGA-TTTTCTTTGGTCTAAAATTTTTAAAAT
1 CTCCGTAAATTTTTTCGGGAG-GATTTTTC-TTGGTTTTTAATTTTTAAAAT
1430332 GCATATAATA
Statistics
Matches: 462, Mismatches: 65, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
164 5 0.01
165 133 0.29
166 146 0.32
167 163 0.35
168 12 0.03
169 3 0.01
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (164 bp):
CTCCGTAAATTTTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATCATT
ATTTAATTCATATAAATTAGTTTTAAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTCCTT
GAAATTCCTTTTTTTCAAAAAACGAGATTTTCTA
Found at i:1436952 original size:19 final size:19
Alignment explanation
Indices: 1436917--1436973 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
1436907 AAAAAATAAT
*
1436917 AAAAAAATAAAATGAAAA-A
1 AAAAAAATCAAA-GAAAACA
1436936 ATGAAAAAA-CAAAGAAAACA
1 A--AAAAAATCAAAGAAAACA
1436956 AAAAAAATCAAAGAAAAC
1 AAAAAAATCAAAGAAAAC
1436974 CCGAAAAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 6 0.18
19 16 0.48
20 5 0.15
21 6 0.18
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAAATCAAAGAAAACA
Found at i:1438403 original size:43 final size:43
Alignment explanation
Indices: 1438228--1438511 Score: 165
Period size: 44 Copynumber: 6.7 Consensus size: 43
1438218 TTCCCTTCTG
* * * * *
1438228 TTTGACGTATGGTTACCATCCTGGTCAAGCTCTTCTCATTTTAGG
1 TTTGACGTATGGTTACCACCCTAGTCAA-TTCTTTTCATTTT-GA
* * *** * * * * *
1438273 TCTGGCGTATGGTTGTTACCCTGGTCAAATTTTTTTTTATTCTAA
1 TTTGACGTATGGTTACCACCCTAGTC-AA-TTCTTTTCATTTTGA
* * * * * *
1438318 TTTGACATATGGTTACCACCGTGGTCAAATCGTTTCCTTTTTG-
1 TTTGACGTATGGTTACCACCCTAGTCAATTC-TTTTCATTTTGA
* *
1438361 TCTGACGTATGGTTACCACCTTAGTCAGATTCTTTTCATTTTGA
1 TTTGACGTATGGTTACCACCCTAGTCA-ATTCTTTTCATTTTGA
* * *
1438405 TTTGACGTATAGTTTCCACCTTAGTCAATT-TTTT--TTTCT--
1 TTTGACGTATGGTTACCACCCTAGTCAATTCTTTTCATTT-TGA
*
1438444 TTT---G-ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGA
1 TTTGACGTATGGTTACCACCCTAGTC-AATTCTTTTCATTTTGA
* *
1438484 TTTGATGTATGGTTATCACCCTAGTCAA
1 TTTGACGTATGGTTACCACCCTAGTCAA
1438512 ATCTGCCTTC
Statistics
Matches: 181, Mismatches: 43, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
35 15 0.08
36 5 0.03
37 4 0.02
38 1 0.01
39 5 0.03
40 6 0.03
41 1 0.01
42 4 0.02
43 39 0.22
44 52 0.29
45 39 0.22
46 10 0.06
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (43 bp):
TTTGACGTATGGTTACCACCCTAGTCAATTCTTTTCATTTTGA
Found at i:1438523 original size:79 final size:79
Alignment explanation
Indices: 1438369--1438523 Score: 195
Period size: 79 Copynumber: 2.0 Consensus size: 79
1438359 TGTCTGACGT
* * * * *
1438369 ATGGTTACCACCTTAGTCAGATTCTTTTCATTTTGATTTGACGTATAGTTTCCACCTTAGTCAAT
1 ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACGTATAGTTTCCACCCTAGTCAAA
* ***
1438434 TTTTTTTTCTTTTG
66 TCTGCCTTCTTTTG
* *
1438448 ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGATGTATGGTTAT-CACCCTAGTCAA
1 ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACGTATAGTT-TCCACCCTAGTCAA
1438512 ATCTGCCTTCTT
65 ATCTGCCTTCTT
1438524 CCTATTTGAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 63 0.98
80 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (79 bp):
ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGACGTATAGTTTCCACCCTAGTCAAA
TCTGCCTTCTTTTG
Found at i:1438531 original size:44 final size:44
Alignment explanation
Indices: 1438448--1438549 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
1438438 TTTTCTTTTG
* * **
1438448 ATGGTTACCACCCTAGTCAAATTCTTTTCATTCTGATTTGATGT
1 ATGGTTATCACCCTAGTCAAATTCTCTTCATTCTGATTTGACAT
1438492 ATGGTTATCACCCTAGTCAAA-TCTGCCTTC-TTCCT-ATTTGACAT
1 ATGGTTATCACCCTAGTCAAATTCT--CTTCATT-CTGATTTGACAT
*
1438536 ATGGTTGTCACCCT
1 ATGGTTATCACCCT
1438550 GATCAAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.06
44 42 0.84
45 5 0.10
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (44 bp):
ATGGTTATCACCCTAGTCAAATTCTCTTCATTCTGATTTGACAT
Found at i:1439951 original size:166 final size:166
Alignment explanation
Indices: 1439744--1440064 Score: 509
Period size: 167 Copynumber: 1.9 Consensus size: 166
1439734 TATTTAAATT
* *
1439744 ACGGAGCTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTATTAA-CTTTAAAATTC
1 ACGGAGCTTTCTACTCCGTAAATTTTTTCGAGAGAATTTTTCTTGATTATTAATCTTTAAAATTC
*
1439808 ATCAAATATTATTATTTAATTCATACTAAATCATTTTTCAAAAATTCATTAATTTTCATGAGTTT
66 ATCAAATATTATTATTTAATTCATACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTT
1439873 GTGAATTTTTTTCCTTGAAATTTTCTTTTTTGGAAAA
131 GTGAA-TTTTTTCCTTGAAATTTTCTTTTTTGGAAAA
* * * * * *
1439910 ACGGAGTTTTCTACTTCGTAAATTTTTTTGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAATTC
1 ACGGAGCTTTCTACTCCGTAAATTTTTTCGAGAGAATTTTTCTTGATTATTAATCTTTAAAATTC
* *
1439975 ATCAAATATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTT
66 ATCAAATATTATTATTTAATTCATACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTT
* *
1440040 GTGAATTTTTTCCTTGGAGTTTTCT
131 GTGAATTTTTTCCTTGAAATTTTCT
1440065 ATTTCGTAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
166 64 0.45
167 77 0.55
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (166 bp):
ACGGAGCTTTCTACTCCGTAAATTTTTTCGAGAGAATTTTTCTTGATTATTAATCTTTAAAATTC
ATCAAATATTATTATTTAATTCATACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTT
GTGAATTTTTTCCTTGAAATTTTCTTTTTTGGAAAA
Found at i:1440060 original size:143 final size:143
Alignment explanation
Indices: 1439912--1440194 Score: 496
Period size: 143 Copynumber: 2.0 Consensus size: 143
1439902 TTGGAAAAAC
*
1439912 GGAGTTTTCTACTTCGTAAATTTTTTTGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
1 GGAGTTTTCTACTTCGTAAATTTTTTCGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
1439977 CAAATATTATTATTTAATTCAT-ACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTG
66 CAAATATTATTATTTAATTCATGA-TAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTG
1440041 TGAATTTTTTCCTT
130 TGAATTTTTTCCTT
* *
1440055 GGAGTTTTCTATTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
1 GGAGTTTTCTACTTCGTAAATTTTTTCGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
* * *
1440120 CAAATATTTTTATTTAATTTATGATAAATTAGTTTTCAAAAATTCATTCATTTTGATGAGTTTGT
66 CAAATATTATTATTTAATTCATGATAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGT
1440185 GAATTTTTTC
131 GAATTTTTTC
1440195 TTGAAATTCT
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
143 132 0.99
144 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (143 bp):
GGAGTTTTCTACTTCGTAAATTTTTTCGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
CAAATATTATTATTTAATTCATGATAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGT
GAATTTTTTCCTT
Found at i:1440250 original size:167 final size:167
Alignment explanation
Indices: 1440059--1440882 Score: 880
Period size: 167 Copynumber: 4.9 Consensus size: 167
1440049 TTCCTTGGAG
* *
1440059 TTTTCTATTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTGTTAATTTTTAAAATTCATCAAA
1 TTTTCTACTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
* * *
1440124 TATTTTTATTTAATTTATGA-TAAATTAGTTTTCAAAAATTCATTCATTTTGATGAGTTTGTGAA
66 TATTATTATTTAATTCAT-ACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAA
*
1440188 TTTTTTCTTGAAATTCTCTTTTTTTCTAAAAAATGAAA
130 TTTTTTCTTGAAATTCTCCTTTTTTCTAAAAAATGAAA
* * * * *
1440226 TTTTTTACTTCGTAAATTTTTTCGAGGGGATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAA
1 TTTTCTACTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
* * * * *
1440291 TATTACTGTTTAATTTATACTAAATTAATTTTTAAAAATTCATTCATTTTCATGAGTTTGTGAAT
66 TATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAAT
* * * *
1440356 TTTTTCCTTGAAATTTTCTTTTTTTTTTCAAAAAACGAAA
131 TTTTT-CTTGAAATTCTC-CTTTTTTCT-AAAAAATGAAA
* * * ** *
1440396 TTTTCTATTTCGTAAA-TTTTTC-AGGGGAGATTTTTCTAGGTTTTTAAGATTCAAAATTCATCA
1 TTTTCTACTTCGTAAATTTTTTCGA-GAG-GATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
*
1440459 AATATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGTGA
64 AATATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTGA
* *
1440524 ATTTTTTCTTGAAATTCT-CTTTTTTCCAAAAAATGAAG
129 ATTTTTTCTTGAAATTCTCCTTTTTTCTAAAAAATGAAA
* * * * * *
1440562 TTTTCTACTCCTTAAATTTTTTTG-GAGGGATTTTTCTTGATTTTTATTTTTTTAAAATTGATCA
1 TTTTCTACTTCGTAAATTTTTTCGAGA-GGATTTTTCTTGGTTTTTA-ATTTTTAAAATTCATCA
* * * * * * *
1440626 AATATCATTATTT-ATGTCATAGTAAATTAGTTTTAAAAAATTCCTTCATTTTCTTGAATTTTTG
64 AATATTATTATTTAAT-TCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTG
* ** * * * * *
1440690 GATTTTTTCGTTTTAATT-TCCCTATTTCTTAAAAATGGAG
128 AATTTTTTC-TTGAAATTCTCCTTTTTTCTAAAAAATGAAA
* * *
1440730 TTTTGTA-TTCCGTAAATTTTTT-TAGGAGGATTTTTCTTGGTTTTTAATTTTTGAAATTCATCA
1 TTTTCTACTT-CGTAAATTTTTTCGA-GAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * * * * * *
1440793 AATATCATTATTT-ATTCCATATTAAATCATTTTTCAAAAAGTAATTCATTTTCATTAGTTT-TG
64 AATATTATTATTTAATT-CATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGT-
*
1440856 GATTTTTTTCTTTGAAA-TCTCCTTTTT
127 GAATTTTTTC-TTGAAATTCTCCTTTTT
1440883 CCCGAAAAAT
Statistics
Matches: 550, Mismatches: 88, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
166 45 0.08
167 290 0.53
168 68 0.12
169 29 0.05
170 118 0.21
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (167 bp):
TTTTCTACTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
TATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAAT
TTTTTCTTGAAATTCTCCTTTTTTCTAAAAAATGAAA
Found at i:1440330 original size:310 final size:309
Alignment explanation
Indices: 1439746--1440374 Score: 913
Period size: 310 Copynumber: 2.0 Consensus size: 309
1439736 TTTAAATTAC
* *
1439746 GGAGCTTTCTACTCCGTAAATTTTTTCGAGGGGATTTTTCTTGATTATTAACTTTAAAATTCATC
1 GGAGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTTGATTATTAACTTTAAAATTCATC
*
1439811 AAATATTATTATTTAATTCATACTAAATCATTTTTCAAAAATTCATTAATTTTCATGAGTTTGTG
66 AAATATTATTATTTAATTCATACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTTGTG
* * * * *
1439876 AATTTTTTTCCTTGAAATTTTCTTTTTTGGAAAAACGGAGTTTTCTACTTCGTAAATTTTTTTGA
131 AATTTTTTTCCTTGAAATTCTCTTTTTTGAAAAAACGAAATTTTCTACTTCGTAAATTTTTTCGA
* * *
1439941 GAGAATTTTTCTTGGTTGTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATACTAAAT
196 GAGAATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAATATTACTATTTAATTCATACTAAAT
*
1440006 TAGTTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTT
261 TAATTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTT
* * * * *
1440055 GGAGTTTTCTATTTCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTGTTAATTTTTAAAATTCAT
1 GGAGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTTGATTATTAA-CTTTAAAATTCAT
* * * * *
1440120 CAAATATTTTTATTTAATTTATGA-TAAATTAGTTTTCAAAAATTCATTCATTTTGATGAGTTTG
65 CAAATATTATTATTTAATTCAT-ACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTTG
* * *
1440184 TGAA-TTTTTT-CTTGAAATTCTCTTTTTTTCTAAAAAATGAAATTTTTTACTTCGTAAATTTTT
129 TGAATTTTTTTCCTTGAAATTCTC-TTTTTT-GAAAAAACGAAATTTTCTACTTCGTAAATTTTT
* * * *
1440247 TCGAGGGGATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAATATTACTGTTTAATTTATACT
192 TCGAGAGAATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAATATTACTATTTAATTCATACT
*
1440312 AAATTAATTTTTAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTT
257 AAATTAATTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTT
* *
1440365 GAAATTTTCT
1 GGAGTTTTCT
1440375 TTTTTTTTTC
Statistics
Matches: 284, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
308 11 0.04
309 57 0.20
310 215 0.76
311 1 0.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (309 bp):
GGAGTTTTCTACTCCGTAAATTTTTTCGAGAGGATTTTTCTTGATTATTAACTTTAAAATTCATC
AAATATTATTATTTAATTCATACTAAATCAGTTTTCAAAAATTCATTAATTTTCATGAGTTTGTG
AATTTTTTTCCTTGAAATTCTCTTTTTTGAAAAAACGAAATTTTCTACTTCGTAAATTTTTTCGA
GAGAATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAATATTACTATTTAATTCATACTAAAT
TAATTTTCAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTT
Found at i:1440676 original size:337 final size:333
Alignment explanation
Indices: 1440059--1440884 Score: 950
Period size: 337 Copynumber: 2.5 Consensus size: 333
1440049 TTCCTTGGAG
*
1440059 TTTTCTATTTCGTAAATTTTTTC--GAGAGGATTTTTCTTGGTTGTTAATTTTTAAAATTCATCA
1 TTTTCTATTTCGTAAATTTTTTCAGGAGA-GATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * * *
1440122 AATATTTTTATTTAATTTATGATAAATTAGTTTTCAAAAATTCATTCATTTTGATGAGTTTGTGA
65 AATATTATTATTTAATTCAT-ATAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGTGA
* * *
1440187 ATTTTTTCTTGAAATTCTCTTTTTTTCTAAAAAATGAAATTTTTTACTTCGTAAATTTTTTCGAG
129 ATTTTTTCTTGAAATTCTC-TTTTTTCCAAAAAATGAAATTTTCTACTCCGTAAATTTTTTCGAG
* * * *
1440252 GGGATTTTTCTTGGTTGTTAATTTTTAAAACTCATAAAATATTACTGTTTAATTTATACTAAATT
193 GGGATTTTTCTTGATTGTTAATTTTTAAAACTCATAAAATATCACTATTTAATTCATACTAAATT
* * ** * *
1440317 AATTTTTAAAAATTCATTCATTTTCATGAGTTTGTGAATTTTTTCCTTGAAATTTTCTTTTTTTT
258 AATTTTAAAAAATTCATTCATTTTCATGAATTTGTGAATTTTTTCCTTGAAA-TTTCCCTATTTC
1440382 TTCAAAAAACGAAA
322 TT--AAAAACGAAA
* * ** *
1440396 TTTTCTATTTCGTAAA-TTTTTCAGGGGAGATTTTTCTAGGTTTTTAAGATTCAAAATTCATCAA
1 TTTTCTATTTCGTAAATTTTTTCAGGAGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
1440460 ATATTATTATTTAATTCATACTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGTGAA
66 ATATTATTATTTAATTCATA-TAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGTGAA
* * *
1440525 TTTTTTCTTGAAATTCTCTTTTTTCCAAAAAATGAAGTTTTCTACTCCTTAAATTTTTTTG-GAG
130 TTTTTTCTTGAAATTCTCTTTTTTCCAAAAAATGAAATTTTCTACTCCGTAAATTTTTTCGAG-G
* * * * * * *
1440589 GGATTTTTCTTGATTTTTATTTTTTTAAAATTGATCAAATATCATTATTT-ATGTCATAGTAAAT
194 GGATTTTTCTTGATTGTTA-ATTTTTAAAACTCATAAAATATCACTATTTAAT-TCATACTAAAT
* * * * * * **
1440653 TAGTTTTAAAAAATTCCTTCATTTTCTTGAATTTTTGGATTTTTTCGTTTTAATTTCCCTATTTC
257 TAATTTTAAAAAATTCATTCATTTTCATGAATTTGTGAATTTTTTCCTTGAAATTTCCCTATTTC
* * *
1440718 TTAAAAATGGAG
322 TTAAAAACGAAA
* * * *
1440730 TTTTGTATTCCGTAAATTTTTTTAGGAG-GATTTTTCTTGGTTTTTAATTTTTGAAATTCATCAA
1 TTTTCTATTTCGTAAATTTTTTCAGGAGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
* * * * * * *
1440794 ATATCATTATTT-ATTCCATATTAAATCATTTTTCAAAAAGTAATTCATTTTCATTA-GTTTTGG
66 ATATTATTATTTAATT-CATA-TAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGT-G
* *
1440857 ATTTTTTTCTTTGAAA-TCTCCTTTTTCC
128 AATTTTTTC-TTGAAATTCTCTTTTTTCC
1440885 CGAAAAATTG
Statistics
Matches: 416, Mismatches: 63, Indels: 23
0.83 0.13 0.05
Matches are distributed among these distances:
333 7 0.02
334 117 0.28
335 16 0.04
336 74 0.18
337 199 0.48
338 3 0.01
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (333 bp):
TTTTCTATTTCGTAAATTTTTTCAGGAGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
ATATTATTATTTAATTCATATAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGGTTGTGAAT
TTTTTCTTGAAATTCTCTTTTTTCCAAAAAATGAAATTTTCTACTCCGTAAATTTTTTCGAGGGG
ATTTTTCTTGATTGTTAATTTTTAAAACTCATAAAATATCACTATTTAATTCATACTAAATTAAT
TTTAAAAAATTCATTCATTTTCATGAATTTGTGAATTTTTTCCTTGAAATTTCCCTATTTCTTAA
AAACGAAA
Found at i:1441487 original size:13 final size:13
Alignment explanation
Indices: 1441469--1441499 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1441459 AAGAAAAGAG
1441469 AGAAAAGAGAGAA
1 AGAAAAGAGAGAA
1441482 AGAAAAGAGAGAA
1 AGAAAAGAGAGAA
1441495 A-AAAA
1 AGAAAA
1441500 TAGAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGAAAAGAGAGAA
Found at i:1441504 original size:10 final size:10
Alignment explanation
Indices: 1441491--1441527 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
1441481 AAGAAAAGAG
1441491 AGAAAAAAAT
1 AGAAAAAAAT
*
1441501 AGAAGAAAAT
1 AGAAAAAAAT
1441511 AGAAAAAAAT
1 AGAAAAAAAT
1441521 AGAAAAA
1 AGAAAAA
1441528 CCCAAGCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (10 bp):
AGAAAAAAAT
Done.