Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 12 of 279
Found at i:3862716 original size:28 final size:28
Alignment explanation
Indices: 3862679--3862732 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
3862669 CTTTTCAAAT
3862679 TTTGATAATTTACTTGTAATTATGTAAA
1 TTTGATAATTTACTTGTAATTATGTAAA
*
3862707 TTTGATAATTTACTTGTATTTATGTA
1 TTTGATAATTTACTTGTAATTATGTA
3862733 TATCTGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (28 bp):
TTTGATAATTTACTTGTAATTATGTAAA
Found at i:3867775 original size:16 final size:16
Alignment explanation
Indices: 3867754--3867802 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
3867744 TGTAATGCCA
3867754 CAAAAATCCCGAAATC
1 CAAAAATCCCGAAATC
**
3867770 CAAAAATCTTGAAATC
1 CAAAAATCCCGAAATC
3867786 CAAAAATCCCGAAATC
1 CAAAAATCCCGAAATC
3867802 C
1 C
3867803 CCAATTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.16
Consensus pattern (16 bp):
CAAAAATCCCGAAATC
Found at i:3869092 original size:27 final size:27
Alignment explanation
Indices: 3869044--3869202 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
3869034 GCAAGGCTGC
* *
3869044 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
3869071 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
3869097 CAGATATATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
3869124 CAGATAATTGTGGCATAGCCACCA-AGA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
3869151 CAGATATATGTGGCAGAGCCAACAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
3869178 TAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
3869203 GACACTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 11 0.10
27 95 0.85
28 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:3869144 original size:54 final size:55
Alignment explanation
Indices: 3869065--3869206 Score: 213
Period size: 54 Copynumber: 2.6 Consensus size: 55
3869055 ACGAAGTCAC
*
3869065 CAGATACAGAT-ATTGTGGCAGAGCCACCAGA-ACAGATATATGTGGCAGAGCC-A
1 CAGAT-CAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGCCAA
3869118 CTAGATCAGATAATTGTGGCATAGCCACCA-AGACAGATATATGTGGCAGAGCCAA
1 C-AGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGCCAA
*
3869173 CAGATTAGATAATTGTGGCATAGCCACCAG-GACA
1 CAGATCAGATAATTGTGGCATAGCCACCAGAGACA
3869207 CTTCCTCCAT
Statistics
Matches: 82, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
53 7 0.09
54 73 0.89
55 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (55 bp):
CAGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGCCAA
Found at i:3870831 original size:26 final size:26
Alignment explanation
Indices: 3870800--3870907 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3870790 TGAAATGCCC
*
3870800 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
3870826 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
3870852 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
3870878 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3870904 ATCA
1 ATCA
3870908 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:3875772 original size:27 final size:27
Alignment explanation
Indices: 3875725--3875880 Score: 149
Period size: 27 Copynumber: 5.8 Consensus size: 27
3875715 CGAGGCTGCC
* * *
3875725 AGATATTGTGACGAAGTCACCAGATAT
1 AGATATTGTGGCAAAGCCACCAGATAT
*
3875752 AGATATTGTGGCAAAGCCACCAGA-AC
1 AGATATTGTGGCAAAGCCACCAGATAT
*
3875778 AGATATATGTGGCAGAGCCACCAGAT-T
1 AGATAT-TGTGGCAAAGCCACCAGATAT
* * *
3875805 AGATAATTGTGGCATAGCCACCA-AGAC
1 AGAT-ATTGTGGCAAAGCCACCAGATAT
* *
3875832 AGATATATGTGGTAGAGCCACCAGAT-T
1 AGATAT-TGTGGCAAAGCCACCAGATAT
*
3875859 AGATAATTGTGGCATAGCCACC
1 AGAT-ATTGTGGCAAAGCCACC
3875881 TGGACGCTTC
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
26 10 0.09
27 92 0.86
28 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (27 bp):
AGATATTGTGGCAAAGCCACCAGATAT
Found at i:3875814 original size:54 final size:54
Alignment explanation
Indices: 3875742--3875880 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 54
3875732 GTGACGAAGT
*
3875742 CACCAGATATAGAT-ATTGTGGCAAAGCCACC-AGAACAGATATATGTGGCAGAGC
1 CACCAGAT-TAGATAATTGTGGCATAGCCACCAAG-ACAGATATATGTGGCAGAGC
*
3875796 CACCAGATTAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGTAGAGC
1 CACCAGATTAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGC
3875850 CACCAGATTAGATAATTGTGGCATAGCCACC
1 CACCAGATTAGATAATTGTGGCATAGCCACC
3875881 TGGACGCTTC
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
53 5 0.06
54 74 0.91
55 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (54 bp):
CACCAGATTAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGC
Found at i:3878478 original size:39 final size:39
Alignment explanation
Indices: 3878389--3878637 Score: 358
Period size: 39 Copynumber: 6.4 Consensus size: 39
3878379 ATAAAGCATG
* * *
3878389 CGGGACTTTAAGCCCGGATGTAATACCAGCAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
3878429 CAGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
3878468 CGGGACTTAGCCCGTG-TCTAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCG-GATATAACACCAGCACGAATGCCTT
* * *
3878507 CCGGACTTAGCCCAGATATAACACTAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
3878546 CAGGACTTAGCCCGAATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
3878585 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
3878624 CGGGAATTAGCCCG
1 CGGGACTTAGCCCG
3878638 AATAGATATC
Statistics
Matches: 189, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
38 21 0.11
39 162 0.86
40 6 0.03
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:3886558 original size:39 final size:39
Alignment explanation
Indices: 3886472--3886687 Score: 317
Period size: 39 Copynumber: 5.5 Consensus size: 39
3886462 ACAAAGCATG
* * * *
3886472 CGGGACTTTAAGCCCGGATGTAATACCAACAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
** *
3886512 CAAGACTTAGCCCGGATATAACACCATCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
3886551 CGGGACTTAGCCCGGGTATAACACCGGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
3886590 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
3886629 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
3886668 CGGGAATTAGCCCGGATATA
1 CGGGACTTAGCCCGGATATA
3886688 TATCTCACAC
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 19 0.12
39 138 0.86
40 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:3889246 original size:26 final size:26
Alignment explanation
Indices: 3889215--3889374 Score: 284
Period size: 26 Copynumber: 6.2 Consensus size: 26
3889205 TGAAATTCCC
*
3889215 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
3889241 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
3889267 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3889293 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
3889319 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
3889345 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3889371 ATCA
1 ATCA
3889375 ATTTGTACCA
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 127 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:3890504 original size:8 final size:8
Alignment explanation
Indices: 3890479--3890524 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
3890469 ATGTATCGGC
3890479 AAAAGCCG
1 AAAAGCCG
* *
3890487 AAATGTCG
1 AAAAGCCG
3890495 AAAAGCCG
1 AAAAGCCG
3890503 AAAAGCC-
1 AAAAGCCG
3890510 AAAATGCCG
1 AAAA-GCCG
3890519 AAAAGC
1 AAAAGC
3890525 TAAAAGTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 4 0.12
8 24 0.75
9 4 0.12
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:3890514 original size:24 final size:24
Alignment explanation
Indices: 3890479--3890524 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3890469 ATGTATCGGC
* *
3890479 AAAAGCCGAAATGTCGAAAAGCCG
1 AAAAGCCAAAATGCCGAAAAGCCG
3890503 AAAAGCCAAAATGCCGAAAAGC
1 AAAAGCCAAAATGCCGAAAAGC
3890525 TAAAAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.07
Consensus pattern (24 bp):
AAAAGCCAAAATGCCGAAAAGCCG
Found at i:3890518 original size:16 final size:15
Alignment explanation
Indices: 3890478--3890530 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
3890468 TATGTATCGG
*
3890478 CAAAAGCCGAAATGTC
1 CAAAAGCCGAAAAG-C
*
3890494 GAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
3890509 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
*
3890525 TAAAAG
1 CAAAAG
3890531 TTTGGCTACG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 6 0.19
16 26 0.81
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.08
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:3890797 original size:29 final size:28
Alignment explanation
Indices: 3890740--3890854 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
3890730 GTAAGCATTG
* * * *
3890740 ATATGAATGTGACTGGTCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
3890768 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
3890797 ATATACAGGTGATTTGGGCCTAATGGACC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
3890826 ATATGAATATGATTGGGCTTAGTGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
3890854 A
1 A
3890855 GATACAAGTA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
28 25 0.35
29 47 0.65
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:3896210 original size:46 final size:46
Alignment explanation
Indices: 3896087--3896294 Score: 151
Period size: 46 Copynumber: 4.5 Consensus size: 46
3896077 GCGGATGACG
* * *
3896087 TGTCCCAAACATGGTCTTACACTGACA--CATCTCGTA-GCTGATGCA
1 TGTCCCAGACAT-GTCTTACACTAACACTCATCTCG-AGGCCGATGCA
* ** * *
3896132 TG-CCTAAGACATGTCTTACACTGTC-TTACGTCTCGAGGCCGATGCA
1 TGTCC-CAGACATGTCTTACACTAACACT-CATCTCGAGGCCGATGCA
* * *
3896178 TGTCCCAGACATGTCTTACACTAACACTCGTCTCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTAACACTCATCTCGAGGCCGATG-CA
* * * *
3896225 TGTCCCAGACATAGTCTTACAC-AAGCTCTCATAAT-GTGGCCGATGTA
1 TGTCCCAGACAT-GTCTTACACTAA-CACTCAT-CTCGAGGCCGATGCA
*
3896272 TGTCCTAGACATGTCTTACACTA
1 TGTCCCAGACATGTCTTACACTA
3896295 GTTCACAATA
Statistics
Matches: 132, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
44 14 0.11
45 8 0.06
46 56 0.42
47 32 0.24
48 21 0.16
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
TGTCCCAGACATGTCTTACACTAACACTCATCTCGAGGCCGATGCA
Found at i:3897810 original size:46 final size:46
Alignment explanation
Indices: 3897760--3897932 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
3897750 TGGTTGAGCA
3897760 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3897806 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
3897851 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3897899 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3897933 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3897916 original size:93 final size:93
Alignment explanation
Indices: 3897757--3897927 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
3897747 GGATGGTTGA
* *
3897757 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3897822 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
3897850 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3897915 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3897928 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3899959 original size:41 final size:41
Alignment explanation
Indices: 3899902--3899984 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
3899892 TTCGGTGGAG
*
3899902 AAAGAAGATGAAAAAGGGATGATATCATATTTCTTTTATTT
1 AAAGAAGATGAAAAAGGGATGATATCATATTTCCTTTATTT
3899943 AAAGAAGATGAAAAAGGGATGATATCATATTTCCTTTATTT
1 AAAGAAGATGAAAAAGGGATGATATCATATTTCCTTTATTT
3899984 A
1 A
3899985 CTCCTATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (41 bp):
AAAGAAGATGAAAAAGGGATGATATCATATTTCCTTTATTT
Found at i:3906110 original size:46 final size:46
Alignment explanation
Indices: 3906043--3906260 Score: 359
Period size: 46 Copynumber: 4.7 Consensus size: 46
3906033 AACCCGCCCC
*
3906043 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCA
*
3906089 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCA
*
3906135 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
*
3906181 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
*
3906227 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
3906261 TGCTCAACCA
Statistics
Matches: 169, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
45 2 0.01
46 167 0.99
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
Found at i:3911947 original size:204 final size:204
Alignment explanation
Indices: 3911542--3911949 Score: 676
Period size: 204 Copynumber: 2.0 Consensus size: 204
3911532 TAAGCAAAAT
3911542 TGAAGGCATGAAGTATAAATTATGAAAATTGAAATAATTAAAAGAACCTTTTACCCACTTCATTT
1 TGAAGGCATGAAGTATAAATTATGAAAATTGAAATAATTAAAAGAACCTTTTACCCACTTCATTT
3911607 TAGGTGAATGTTTATACTTTATTACATTAAAAACAAATTTTTAAATAATCACGAGATTTAGATGA
66 TAGGTGAATGTTTATACTTTATTACATTAAAAACAAATTTTTAAATAATCACGAGATTTAGATGA
* * ** * * *** * *
3911672 GATGATAAGAATCTTTTTTACCTTAATCAGTTATTGAGGGTTTGACCTTTGTCTTGGGTATGGAA
131 GAAGATAAGAATCTTTTTTACCTTAATCAGTGATCAAGAGTTCGACCTTCACCTTGAGTATGAAA
3911737 CAGCTTTAA
196 CAGCTTTAA
3911746 TGAAGGCATGAAGTATAAATTATGAAAATTGAAATAATTAAAAGAACCTTTTACCCACTTCATTT
1 TGAAGGCATGAAGTATAAATTATGAAAATTGAAATAATTAAAAGAACCTTTTACCCACTTCATTT
3911811 TAGGTGAATGTTTATACTTTATTACATTAAAAACAAATTTTTAAATAATCACGAGATTTAGATGA
66 TAGGTGAATGTTTATACTTTATTACATTAAAAACAAATTTTTAAATAATCACGAGATTTAGATGA
*
3911876 GAAGATAATAATCTTTTTTACCTTAATCAGTGATCAAGAGTTCGATCC-TCACCTTGAGTAT-AA
131 GAAGATAAGAATCTTTTTTACCTTAATCAGTGATCAAGAGTTCGA-CCTTCACCTTGAGTATGAA
3911939 AGCAGCTTTAA
195 A-CAGCTTTAA
3911950 AACTCACGAT
Statistics
Matches: 190, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
203 2 0.01
204 186 0.98
205 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (204 bp):
TGAAGGCATGAAGTATAAATTATGAAAATTGAAATAATTAAAAGAACCTTTTACCCACTTCATTT
TAGGTGAATGTTTATACTTTATTACATTAAAAACAAATTTTTAAATAATCACGAGATTTAGATGA
GAAGATAAGAATCTTTTTTACCTTAATCAGTGATCAAGAGTTCGACCTTCACCTTGAGTATGAAA
CAGCTTTAA
Found at i:3912141 original size:60 final size:60
Alignment explanation
Indices: 3912067--3912191 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
3912057 ACCAAGTAAT
* *
3912067 GATATTTTCATCGTATTTATTTTGTTATTTTATATAAAATATATACACTCTGACTTTCAA
1 GATATTTTCATCGTATTTATTTTGTTATTTTATACAAAATATATACACTCTGACGTTCAA
* *
3912127 GATATTTTTATCGTATTTGTTTTGTTATTTTATACAAAATATATACACTCTGACGTTCAA
1 GATATTTTCATCGTATTTATTTTGTTATTTTATACAAAATATATACACTCTGACGTTCAA
*
3912187 TATAT
1 GATAT
3912192 ATATTTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (60 bp):
GATATTTTCATCGTATTTATTTTGTTATTTTATACAAAATATATACACTCTGACGTTCAA
Found at i:3912907 original size:20 final size:20
Alignment explanation
Indices: 3912882--3912921 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3912872 ACATGAACTG
3912882 ATTATTTAACTAGTAAACGA
1 ATTATTTAACTAGTAAACGA
3912902 ATTATTTAACTAGTAAACGA
1 ATTATTTAACTAGTAAACGA
3912922 CGTAGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
ATTATTTAACTAGTAAACGA
Found at i:3916165 original size:93 final size:93
Alignment explanation
Indices: 3916006--3916191 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
3915996 ACCGACCATT
3916006 AACAAGTAGGATATGGAAATGTCAACTCGGGAGTAGTCATGCTTGCCAACGGCGAAGAAGAAGGC
1 AACAAGTAGGATATGGAAATGTCAACTCGGGAGTAGTCATGCTTGCCAACGGCGAAGAAGAAGGC
3916071 AAGCAGTGTGCAAGTGATCAAGGATAAG
66 AAGCAGTGTGCAAGTGATCAAGGATAAG
3916099 AACAAGTAGGATATGGAAATGTCAACTCGGGAGTAGTCATGCTTGCCAACGGCGAAGAAGAAGGC
1 AACAAGTAGGATATGGAAATGTCAACTCGGGAGTAGTCATGCTTGCCAACGGCGAAGAAGAAGGC
*
3916164 AAGCAGTGTGCAAGTGATGAAGGATAAG
66 AAGCAGTGTGCAAGTGATCAAGGATAAG
3916192 CAAATGAAGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.37, C:0.15, G:0.32, T:0.17
Consensus pattern (93 bp):
AACAAGTAGGATATGGAAATGTCAACTCGGGAGTAGTCATGCTTGCCAACGGCGAAGAAGAAGGC
AAGCAGTGTGCAAGTGATCAAGGATAAG
Found at i:3917623 original size:18 final size:18
Alignment explanation
Indices: 3917602--3917641 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3917592 GAAATATTTA
*
3917602 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
3917620 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
3917638 TTTT
1 TTTT
3917642 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:3917673 original size:12 final size:12
Alignment explanation
Indices: 3917643--3917675 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3917633 TATATTTTTT
3917643 AAAATT-ATATA
1 AAAATTAATATA
3917654 AAAA-TAATATA
1 AAAATTAATATA
3917665 AAAATTAATAT
1 AAAATTAATAT
3917676 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3922780 original size:31 final size:31
Alignment explanation
Indices: 3922745--3922805 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3922735 CTAAACGAAC
*
3922745 ACTATGTCAAGACCATTGTCTCTATCTATCA
1 ACTATGTCAAGACCATCGTCTCTATCTATCA
3922776 ACTATGTCAAGACCATCGTCTCTATCTATC
1 ACTATGTCAAGACCATCGTCTCTATCTATC
3922806 TCCACTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (31 bp):
ACTATGTCAAGACCATCGTCTCTATCTATCA
Found at i:3924929 original size:24 final size:27
Alignment explanation
Indices: 3924884--3924935 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
3924874 TTTTAAAAAA
*
3924884 TATTAATTAAAAAAATTAAAAGATAATT
1 TATTAATT-AAAAAATTAAAAGAAAATT
3924912 TATTAATT-AAAAA-T-AAAGAAAATT
1 TATTAATTAAAAAATTAAAAGAAAATT
3924936 AAAAATAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 5 0.22
28 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TATTAATTAAAAAATTAAAAGAAAATT
Found at i:3929037 original size:12 final size:13
Alignment explanation
Indices: 3929019--3929055 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
3929009 CGCGTCATTG
3929019 AAAGGTATGAGGC
1 AAAGGTATGAGGC
3929032 -AAGGTATGAGGC
1 AAAGGTATGAGGC
3929044 AAAGG-ATGAGGC
1 AAAGGTATGAGGC
3929056 TAGAAGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.38, C:0.08, G:0.41, T:0.14
Consensus pattern (13 bp):
AAAGGTATGAGGC
Found at i:3931484 original size:26 final size:26
Alignment explanation
Indices: 3931455--3931535 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
3931445 CTATATATAT
*
3931455 ATACATATAATATAGCTATTAAGAAA
1 ATACATATAATATAGATATTAAGAAA
* * *
3931481 ATACATACAATATATAATATTAAGAAT
1 ATACATATAATATA-GATATTAAGAAA
* *
3931508 ATATATAATAATAT-GGTATTAA-AAA
1 ATACAT-ATAATATAGATATTAAGAAA
3931533 ATA
1 ATA
3931536 TAGTATTGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
25 5 0.11
26 19 0.43
27 14 0.32
28 6 0.14
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (26 bp):
ATACATATAATATAGATATTAAGAAA
Found at i:3932023 original size:21 final size:22
Alignment explanation
Indices: 3931999--3932054 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
3931989 ATACATATAT
3931999 AAATAATA-ATAATAATGTTAG
1 AAATAATACATAATAATGTTAG
* *
3932020 AAAT-ATACCAT-ATAGTATTAG
1 AAATAATA-CATAATAATGTTAG
3932041 AAAT-ATACATAATA
1 AAATAATACATAATA
3932055 TATATACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
AAATAATACATAATAATGTTAG
Found at i:3935698 original size:33 final size:35
Alignment explanation
Indices: 3935661--3935731 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
3935651 AAGGAAACGT
*
3935661 GAAAA-AGAAA-CATATTTGTTGAGAAATAATGTA
1 GAAAACAGAAACCATATTTATTGAGAAATAATGTA
*
3935694 GAAAACATAAACTCATATTTATTGAGAAATAATGTA
1 GAAAACAGAAAC-CATATTTATTGAGAAATAATGTA
3935730 GA
1 GA
3935732 GAGCATGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 5 0.15
34 4 0.12
36 24 0.73
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (35 bp):
GAAAACAGAAACCATATTTATTGAGAAATAATGTA
Found at i:3936765 original size:8 final size:7
Alignment explanation
Indices: 3936717--3936768 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
3936707 TTTCTTCTTT
3936717 TTTTTTA
1 TTTTTTA
3936724 TTTTTTA
1 TTTTTTA
3936731 TTTTTTA
1 TTTTTTA
*
3936738 TTTTTAAA
1 TTTTT-TA
3936746 TTTTATTA
1 TTTT-TTA
*
3936754 TTATTTA
1 TTTTTTA
3936761 TTTATTTA
1 TTT-TTTA
3936769 GGAATATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 24 0.63
8 13 0.34
9 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:3937657 original size:5 final size:5
Alignment explanation
Indices: 3937647--3937720 Score: 51
Period size: 5 Copynumber: 13.8 Consensus size: 5
3937637 AATATTTAAC
* * * *
3937647 TAAAA TAAAA TAAAA TAATAA -ATAA TAAAA GAAAA TAAAG GAAAA TAATAAA
1 TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA T-A-AAA
3937699 TAAAAA TAAAAA TAAAAA TAAA
1 T-AAAA T-AAAA T-AAAA TAAA
3937721 GATTGGGTTG
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 2 0.04
5 30 0.53
6 19 0.33
7 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:3937682 original size:30 final size:29
Alignment explanation
Indices: 3937649--3937720 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
3937639 TATTTAACTA
3937649 AAATAAAATAAAATAATAAATAATAAA-AGA
1 AAATAAAATAAAATAATAAATAA-AAATA-A
**
3937679 AAATAAAGGAAAATAATAAATAAAAATAA
1 AAATAAAATAAAATAATAAATAAAAATAA
3937708 AAATAAAAATAAA
1 AAAT-AAAATAAA
3937721 GATTGGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.22
30 28 0.78
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (29 bp):
AAATAAAATAAAATAATAAATAAAAATAA
Found at i:3937693 original size:20 final size:19
Alignment explanation
Indices: 3937648--3937715 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
3937638 ATATTTAACT
*
3937648 AAAATAAAATAAAATAATA
1 AAAATAAAAGAAAATAATA
3937667 AATAATAAAAGAAAATAA-A
1 AA-AATAAAAGAAAATAATA
3937686 GGAAAATAATAA-ATAAA-AATA
1 --AAAATAA-AAGA-AAATAATA
3937707 AAAATAAAA
1 AAAATAAAA
3937716 ATAAAGATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
18 2 0.05
19 10 0.24
20 22 0.52
21 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAATAAAAGAAAATAATA
Found at i:3944116 original size:10 final size:10
Alignment explanation
Indices: 3944101--3944128 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3944091 TAAATACATT
3944101 TAATTAAAGA
1 TAATTAAAGA
3944111 TAATTAAAGA
1 TAATTAAAGA
3944121 TAATTAAA
1 TAATTAAA
3944129 ATTAAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:3949677 original size:12 final size:12
Alignment explanation
Indices: 3949660--3949692 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3949650 CGGCCTGTCC
3949660 ATATTAATTTTT
1 ATATTAATTTTT
3949672 ATATT-ATTTTT
1 ATATTAATTTTT
3949683 ATA-TAATTTT
1 ATATTAATTTT
3949693 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3949933 original size:22 final size:22
Alignment explanation
Indices: 3949908--3949950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3949898 TATCCAAACA
3949908 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
3949930 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
3949951 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:3949954 original size:11 final size:11
Alignment explanation
Indices: 3949915--3949955 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3949905 ACAATAACAA
3949915 CAAAATAGTAG
1 CAAAATAGTAG
* *
3949926 CAACATAATAG
1 CAAAATAGTAG
*
3949937 TAAAATAGTAG
1 CAAAATAGTAG
3949948 CAAAATAG
1 CAAAATAG
3949956 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:3952776 original size:23 final size:23
Alignment explanation
Indices: 3952750--3952795 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3952740 TGAAAAGATT
*
3952750 TAAATCCAAAATTAATTAAATCC
1 TAAACCCAAAATTAATTAAATCC
* *
3952773 TAAACCCAAAATTATTTGAATCC
1 TAAACCCAAAATTAATTAAATCC
3952796 ACTTATCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAACCCAAAATTAATTAAATCC
Found at i:3954703 original size:19 final size:19
Alignment explanation
Indices: 3954663--3954704 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3954653 CCAAATAAAT
* *
3954663 TTTTTATTTTTAAATTATA
1 TTTTTATTTTTAAATAACA
3954682 TTTTTATTTTT-AATAAACA
1 TTTTTATTTTTAAAT-AACA
3954701 TTTT
1 TTTT
3954705 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTTAAATAACA
Found at i:3963096 original size:24 final size:24
Alignment explanation
Indices: 3963069--3963120 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3963059 TTAGTAAGTC
*
3963069 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3963093 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3963117 AAAT
1 AAAT
3963121 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3965065 original size:24 final size:24
Alignment explanation
Indices: 3965038--3965089 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3965028 TTAGTAAGTC
*
3965038 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3965062 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3965086 AAAT
1 AAAT
3965090 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3967841 original size:47 final size:47
Alignment explanation
Indices: 3967772--3967865 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
3967762 GCACCCACAT
3967772 TGTAATCCAAGTAACATACTCGTGTCTGATGGTAATATCTATAACAG
1 TGTAATCCAAGTAACATACTCGTGTCTGATGGTAATATCTATAACAG
3967819 TGTAATCCAAGTAACATACTCGTGTCTGATGGTAATATCTATAACAG
1 TGTAATCCAAGTAACATACTCGTGTCTGATGGTAATATCTATAACAG
3967866 GGCGGAGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (47 bp):
TGTAATCCAAGTAACATACTCGTGTCTGATGGTAATATCTATAACAG
Found at i:3969385 original size:68 final size:66
Alignment explanation
Indices: 3969307--3969442 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 66
3969297 TAAATATTTC
* * *
3969307 TTGGGTAATTGATAGTTTCGAAAAAATGCAAATTGGTCCCTTAAAAAATTATCAAAAAAGTCAAA
1 TTGGGTAATTGACAGTCTCGAAAAAATGCAAATAGGTCCCTTAAAAAATTAT-AAAAAA-TCAAA
3969372 ATA
64 ATA
* *
3969375 TTGGGTAATTGACAGTCTCGAAAATATGCAAATAGGTCCCTTAAAAAATTATAAAAAATTAAAAT
1 TTGGGTAATTGACAGTCTCGAAAAAATGCAAATAGGTCCCTTAAAAAATTATAAAAAATCAAAAT
3969440 A
66 A
3969441 TT
1 TT
3969443 TATAAACTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 9 0.14
67 6 0.10
68 48 0.76
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (66 bp):
TTGGGTAATTGACAGTCTCGAAAAAATGCAAATAGGTCCCTTAAAAAATTATAAAAAATCAAAAT
A
Found at i:3969559 original size:29 final size:30
Alignment explanation
Indices: 3969506--3969569 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3969496 CAAATTACTG
* * *
3969506 AAATTTTTTTTAAAAATCTAAAAAAA-GCT
1 AAATTATTTTTAAAAATCAAAAAAAACGAT
3969535 AAATTATTTTTAAAAAT-AAATAAAAACGAT
1 AAATTATTTTTAAAAATCAAA-AAAAACGAT
3969565 AAATT
1 AAATT
3969570 TAATGCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTATTTTTAAAAATCAAAAAAAACGAT
Found at i:3970835 original size:54 final size:53
Alignment explanation
Indices: 3970690--3970823 Score: 209
Period size: 51 Copynumber: 2.5 Consensus size: 53
3970680 TATTCCGCTG
* *
3970690 CCACCACCACCTAGACCTCCAGCTCCACCGCCTACACCACCTGTATCTGGACA
1 CCACCACCACCTAGACCTCCAGCTCCGCCGCCTACACCACCTGTACCTGGACA
*
3970743 --ACCACCACCTAGACCTCCAGCTCCGCTGCCTACACCACCTGTACCTGGACAA
1 CCACCACCACCTAGACCTCCAGCTCCGCCGCCTACACCACCTGTACCTGGAC-A
*
3970795 CCACCACCACCTAGACCTCCAACTCCGCC
1 CCACCACCACCTAGACCTCCAGCTCCGCC
3970824 CCCGGTCCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
51 47 0.64
52 1 0.01
54 25 0.34
ACGTcount: A:0.25, C:0.50, G:0.11, T:0.14
Consensus pattern (53 bp):
CCACCACCACCTAGACCTCCAGCTCCGCCGCCTACACCACCTGTACCTGGACA
Found at i:3970841 original size:33 final size:33
Alignment explanation
Indices: 3970798--3970873 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
3970788 TGGACAACCA
*
3970798 CCACCACCTAGACCTCCAACTCCGCCCCCGGTC
1 CCACCACCTAGACCTCCAACTCCGCCACCGGTC
* *
3970831 CCACCGCCTAGACCTCCAACTCCGCCACCGGTT
1 CCACCACCTAGACCTCCAACTCCGCCACCGGTC
*
3970864 CCACCCCCTA
1 CCACCACCTA
3970874 AACCACCTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.18, C:0.57, G:0.12, T:0.13
Consensus pattern (33 bp):
CCACCACCTAGACCTCCAACTCCGCCACCGGTC
Found at i:3970888 original size:42 final size:42
Alignment explanation
Indices: 3970837--3970933 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
3970827 GGTCCCACCG
*
3970837 CCTAGACCTCCAACTCCGCCACCGGTTCCACCCCCTAAACCA
1 CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
* *
3970879 CCTAGACCTCCACCTCCGCCACCAGTTCCACCCCCTAACCCA
1 CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
3970921 CCTAGACCTCCAA
1 CCTAGACCTCCAA
3970934 TTCCACCGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.54, G:0.08, T:0.14
Consensus pattern (42 bp):
CCTAGACCTCCAACTCCGCCACCAGTTCCACCCCCTAAACCA
Found at i:3970938 original size:30 final size:30
Alignment explanation
Indices: 3970897--3970964 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
3970887 TCCACCTCCG
*
3970897 CCACCAGTTCCACCCCCT-AACCCACCTAGA
1 CCACCAATTCCACCCCCTAAACCC-CCTAGA
* *
3970927 CCTCCAATTCCACCGCCTAAACCCCCTAGA
1 CCACCAATTCCACCCCCTAAACCCCCTAGA
3970957 CCACCAAT
1 CCACCAAT
3970965 GCCTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.28, C:0.51, G:0.06, T:0.15
Consensus pattern (30 bp):
CCACCAATTCCACCCCCTAAACCCCCTAGA
Found at i:3973952 original size:15 final size:16
Alignment explanation
Indices: 3973932--3973969 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3973922 TACATTATTA
3973932 TTATTTTCTTT-CTAT
1 TTATTTTCTTTCCTAT
* *
3973947 TTATTTTTTTTCCTTT
1 TTATTTTCTTTCCTAT
3973963 TTATTTT
1 TTATTTT
3973970 ATTTTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTCCTAT
Found at i:3973967 original size:20 final size:20
Alignment explanation
Indices: 3973935--3973974 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3973925 ATTATTATTA
3973935 TTTTCTTTCTA-TTTATTTT
1 TTTTCTTTCTATTTTATTTT
*
3973954 TTTTCCTTTTTATTTTATTTT
1 TTTT-CTTTCTATTTTATTTT
3973975 CGAATTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTCTATTTTATTTT
Found at i:3974712 original size:12 final size:12
Alignment explanation
Indices: 3974697--3974744 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3974687 TATTTATCTC
3974697 TTTATATTTATG
1 TTTATATTTATG
3974709 TTTATATTTTATG
1 TTTATA-TTTATG
** *
3974722 TATTATACCTATC
1 T-TTATATTTATG
3974735 TTTATATTTA
1 TTTATATTTA
3974745 CACATGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:3974923 original size:22 final size:22
Alignment explanation
Indices: 3974898--3974939 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3974888 TAACGTGCTA
*
3974898 TTATTACTATTACTT-TTATTTT
1 TTATTACCATTA-TTATTATTTT
3974920 TTATTACCATTATTATTATT
1 TTATTACCATTATTATTATT
3974940 GTACTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTACCATTATTATTATTTT
Found at i:3975147 original size:28 final size:30
Alignment explanation
Indices: 3975097--3975153 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
3975087 ACATATACGT
3975097 TATTATTTATATTATTACAATTAT-TATTG
1 TATTATTTATATTATTACAATTATGTATTG
* * *
3975126 TATT-TTTATATTCTTTCTATTATGTATT
1 TATTATTTATATTATTACAATTATGTATT
3975154 ACTCATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (30 bp):
TATTATTTATATTATTACAATTATGTATTG
Found at i:3975566 original size:26 final size:26
Alignment explanation
Indices: 3975537--3975592 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3975527 TGGTACAAAT
3975537 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3975563 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3975589 TGAT
1 TGAT
3975593 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3983157 original size:26 final size:26
Alignment explanation
Indices: 3983126--3983181 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3983116 TGAAATTCCC
3983126 ATCATGGAACATTTACCTAAACC-ATT
1 ATCATGGAACATTTACCT-AACCTATT
3983152 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCTATT
3983178 ATCA
1 ATCA
3983182 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCTATT
Found at i:3987947 original size:33 final size:32
Alignment explanation
Indices: 3987910--3987972 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
3987900 TTACTCCAAT
3987910 TTGGAATTAAATTATTCTCTTTTCCTATTTCTA
1 TTGGAATTAAATTATTCTCTTTTCC-ATTTCTA
* *
3987943 TTGGAATTGAATTATTTTCTTTTCCATTTC
1 TTGGAATTAAATTATTCTCTTTTCCATTTC
3987973 ATTTCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (32 bp):
TTGGAATTAAATTATTCTCTTTTCCATTTCTA
Found at i:3990152 original size:23 final size:23
Alignment explanation
Indices: 3990126--3990228 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 23
3990116 GTTTTTATGT
* *
3990126 TTCTATTTCTATTTATTTTGTTA
1 TTCTATTTCTATTTATTATATTA
* *
3990149 TTCTAATACTATTT-TTAT-TTA
1 TTCTATTTCTATTTATTATATTA
* *
3990170 -TCTATTTATATTT-CTACTATTA
1 TTCTATTTCTATTTATTA-TATTA
*
3990192 TTATATTTCTATTTATTATATT-
1 TTCTATTTCTATTTATTATATTA
3990214 TT-TATTTCTATTTAT
1 TTCTATTTCTATTTAT
3990229 ATACTAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 12 0.18
21 17 0.26
22 8 0.12
23 27 0.41
24 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (23 bp):
TTCTATTTCTATTTATTATATTA
Found at i:3990164 original size:43 final size:42
Alignment explanation
Indices: 3990117--3990229 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 42
3990107 GAGGGCTTTG
** * *
3990117 TTTTTATGTTTCTATTTCTATTTATTTTGTTATTCTAATACTA
1 TTTTTAT-TTTCTATTTCTATTTATACTATTATTATAATACTA
* * * *
3990160 TTTTTATTTATCTATTTATATTTCTACTATTATTATATTTCTA
1 TTTTTATTT-TCTATTTCTATTTATACTATTATTATAATACTA
*
3990203 TTTATTATATTTTTATTTCTATTTATA
1 TTT-TTAT-TTTCTATTTCTATTTATA
3990230 TACTAATATT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.04
43 35 0.62
44 17 0.30
45 2 0.04
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (42 bp):
TTTTTATTTTCTATTTCTATTTATACTATTATTATAATACTA
Found at i:3990178 original size:29 final size:28
Alignment explanation
Indices: 3990128--3990208 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 28
3990118 TTTTATGTTT
* *
3990128 CTATTTCTATTTAT-TTTGTTATTCTAATA
1 CTATTTTTATTTATCTAT-TTATT-TAATA
**
3990157 CTATTTTTATTTATCTATTTATATTTCTA
1 CTATTTTTATTTATCTATTTAT-TTAATA
*
3990186 CTATTATTATATT-TCTATTTATT
1 CTATTTTTAT-TTATCTATTTATT
3990209 ATATTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.02
29 38 0.86
30 5 0.11
ACGTcount: A:0.25, C:0.10, G:0.01, T:0.64
Consensus pattern (28 bp):
CTATTTTTATTTATCTATTTATTTAATA
Found at i:3990207 original size:15 final size:15
Alignment explanation
Indices: 3990175--3990220 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3990165 ATTTATCTAT
3990175 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
3990192 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
3990207 TTATATTTTTATTT
1 TTATATTTCTATTT
3990221 CTATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:3990419 original size:25 final size:24
Alignment explanation
Indices: 3990358--3990437 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
3990348 TATAATGCTC
* *
3990358 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATACATTATAT
*
3990382 ACTTT-AATATTTTCATATATTATAT
1 A-TTTCAA-ATTTTCATACATTATAT
* *
3990407 ATTTCAAACTTTTTTTACACATTATAT
1 ATTTCAAA---TTTTCATACATTATAT
3990434 ATTT
1 ATTT
3990438 TGAATTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.16
25 20 0.45
27 17 0.39
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTCAAATTTTCATACATTATAT
Found at i:3992668 original size:20 final size:21
Alignment explanation
Indices: 3992633--3992683 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
3992623 AATACTATAT
3992633 ATAAAATATGTATGTAAGAATA
1 ATAAAATA-GTATGTAAGAATA
*
3992655 ATAAAATA-TATGTAATAATA
1 ATAAAATAGTATGTAAGAATA
*
3992675 TTAATAATA
1 ATAA-AATA
3992684 AATATAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
ATAAAATAGTATGTAAGAATA
Found at i:3993331 original size:30 final size:27
Alignment explanation
Indices: 3993297--3993378 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
3993287 TAGTATATAT
3993297 ATACATATAATATAGTTATTAAGAAAATAC
1 ATACA-AT-ATATAG-TATTAAGAAAATAC
* *
3993327 ATACACTATATAGTATTAAGAATATAC
1 ATACAATATATAGTATTAAGAAAATAC
3993354 --ACAATATATAGGGTATTAA-AAAATA
1 ATACAATATATA--GTATTAAGAAAATA
3993379 TAGTATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 9 0.20
26 5 0.11
27 20 0.43
28 6 0.13
29 1 0.02
30 5 0.11
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (27 bp):
ATACAATATATAGTATTAAGAAAATAC
Found at i:3993570 original size:3 final size:3
Alignment explanation
Indices: 3993562--3993763 Score: 65
Period size: 3 Copynumber: 70.0 Consensus size: 3
3993552 AATATTGTAT
* ** * *
3993562 ATA ATA ATA ATA ATA CTA GCA ATA ATA ATA AGA TATA A-A AAA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * * *
3993606 ATA AT- ATA ATA ATA ATG TTA AAA ATA GAGTA ATAA ATA TTA ATA GAGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA AT-A ATA ATA ATA -ATA
* * * *
3993654 A-A ATA ACA A-A GATA ATA GTA AT- ATA ATA GTA A-A A-A AT- GTA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
3993694 ATA TTA A-A A-A ATA ATA CTA A-A TATA A-C ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* *
3993735 A-A ATA ATA ATA ATG ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3993764 TAAAAAATAG
Statistics
Matches: 145, Mismatches: 34, Indels: 40
0.66 0.16 0.18
Matches are distributed among these distances:
2 26 0.18
3 106 0.73
4 11 0.08
5 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3993588 original size:33 final size:31
Alignment explanation
Indices: 3993527--3993588 Score: 72
Period size: 31 Copynumber: 1.9 Consensus size: 31
3993517 CCATGTATAA
*
3993527 GTATATATATAATATAACATACACTAATATT
1 GTATATATATAATATAACATACAATAATATT
*
3993558 GTATATA-ATAATAATAATACTAGCAATAATA
1 GTATATATATAAT-ATAACA-TA-CAATAATA
3993589 ATAAGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 5 0.19
31 12 0.46
32 2 0.08
33 7 0.27
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (31 bp):
GTATATATATAATATAACATACAATAATATT
Found at i:3993729 original size:33 final size:33
Alignment explanation
Indices: 3993692--3993772 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
3993682 GTAAAAAATG
*
3993692 TAATATTAAAAAATAATACTAAAT-ATAACA-TAA
1 TAATA-TAAAAAATAATAAT-AATGATAACAGTAA
* *
3993725 TAATAATATAAAATAATAATAATGATAATAGTAA
1 TAAT-ATAAAAAATAATAATAATGATAACAGTAA
3993759 TAATATAAAAAATA
1 TAATATAAAAAATA
3993773 GCAATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 3 0.07
33 30 0.73
34 8 0.20
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (33 bp):
TAATATAAAAAATAATAATAATGATAACAGTAA
Found at i:3993734 original size:16 final size:15
Alignment explanation
Indices: 3993702--3993786 Score: 73
Period size: 15 Copynumber: 5.4 Consensus size: 15
3993692 TAATATTAAA
*
3993702 AAATAATACTAAATAT
1 AAATAATAAT-AATAT
3993718 AACATAATAATAATAT
1 AA-ATAATAATAATAT
3993734 AAAATAATAATAATGAT
1 -AAATAATAATAAT-AT
*
3993751 -AATAGTAATAATAT
1 AAATAATAATAATAT
* **
3993765 AAAAAATAGCAATAT
1 AAATAATAATAATAT
3993780 ATAATAA
1 A-AATAA
3993787 AAACTTAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 2 0.04
15 22 0.39
16 22 0.39
17 11 0.19
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (15 bp):
AAATAATAATAATAT
Found at i:3993783 original size:17 final size:19
Alignment explanation
Indices: 3993736--3993788 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3993726 AATAATATAA
* *
3993736 AATAATAATAATGATAATAGT
1 AATAAT-ATAAT-AAAATAGC
3993757 AATAATATAA-AAAATAGC
1 AATAATATAATAAAATAGC
3993775 AAT-ATATAATAAAA
1 AATAATATAATAAAA
3993789 ACTTAATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 13 0.45
20 4 0.14
21 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (19 bp):
AATAATATAATAAAATAGC
Found at i:3995874 original size:26 final size:26
Alignment explanation
Indices: 3995843--3995950 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3995833 TGAAATGCCC
*
3995843 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
3995869 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
3995895 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
3995921 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
3995947 ATCA
1 ATCA
3995951 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:3998653 original size:12 final size:12
Alignment explanation
Indices: 3998636--3998660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3998626 ACCGAAGCTC
3998636 CTCTAAGTTGGT
1 CTCTAAGTTGGT
3998648 CTCTAAGTTGGT
1 CTCTAAGTTGGT
3998660 C
1 C
3998661 AAATAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CTCTAAGTTGGT
Found at i:3999864 original size:177 final size:177
Alignment explanation
Indices: 3999568--3999917 Score: 700
Period size: 177 Copynumber: 2.0 Consensus size: 177
3999558 ATCATCCTCG
3999568 GCACCGCGGTCATGAGACTCTACCTCTGTTGCCGGTGGTATCGGTGCATCCACCACCGGTATATG
1 GCACCGCGGTCATGAGACTCTACCTCTGTTGCCGGTGGTATCGGTGCATCCACCACCGGTATATG
3999633 TCTCGAAGATAAAGATCTCGCTCGAGCACTTCCTCAGCTCCGTCCACGGCCTCTTGTACTCATAT
66 TCTCGAAGATAAAGATCTCGCTCGAGCACTTCCTCAGCTCCGTCCACGGCCTCTTGTACTCATAT
3999698 CGTATTATCTTGATTACGAATTTTTATACATCAATTAATATTCTAAT
131 CGTATTATCTTGATTACGAATTTTTATACATCAATTAATATTCTAAT
3999745 GCACCGCGGTCATGAGACTCTACCTCTGTTGCCGGTGGTATCGGTGCATCCACCACCGGTATATG
1 GCACCGCGGTCATGAGACTCTACCTCTGTTGCCGGTGGTATCGGTGCATCCACCACCGGTATATG
3999810 TCTCGAAGATAAAGATCTCGCTCGAGCACTTCCTCAGCTCCGTCCACGGCCTCTTGTACTCATAT
66 TCTCGAAGATAAAGATCTCGCTCGAGCACTTCCTCAGCTCCGTCCACGGCCTCTTGTACTCATAT
3999875 CGTATTATCTTGATTACGAATTTTTATACATCAATTAATATTC
131 CGTATTATCTTGATTACGAATTTTTATACATCAATTAATATTC
3999918 CAGTGTTTAT
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 173 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (177 bp):
GCACCGCGGTCATGAGACTCTACCTCTGTTGCCGGTGGTATCGGTGCATCCACCACCGGTATATG
TCTCGAAGATAAAGATCTCGCTCGAGCACTTCCTCAGCTCCGTCCACGGCCTCTTGTACTCATAT
CGTATTATCTTGATTACGAATTTTTATACATCAATTAATATTCTAAT
Found at i:4002900 original size:26 final size:26
Alignment explanation
Indices: 4002869--4002976 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
4002859 TGAAATGCCC
*
4002869 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
4002895 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4002921 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
4002947 ATCATGAAACATTTACCTAACCCAGT
1 ATCATGGAACATTTACCTAACCCATT
4002973 ATCA
1 ATCA
4002977 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4003544 original size:6 final size:7
Alignment explanation
Indices: 4003533--4003557 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4003523 GAGAGAAGGG
4003533 AGGGGGA
1 AGGGGGA
4003540 AGGGGGA
1 AGGGGGA
4003547 AGGGGGA
1 AGGGGGA
4003554 AGGG
1 AGGG
4003558 ATTCCCGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
AGGGGGA
Found at i:4004263 original size:20 final size:20
Alignment explanation
Indices: 4004238--4004276 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4004228 GTGAAATTGG
* *
4004238 GTTTAATTTGTTGGGTTTTA
1 GTTTAATGTGTTAGGTTTTA
4004258 GTTTAATGTGTTAGGTTTT
1 GTTTAATGTGTTAGGTTTT
4004277 GGGGTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (20 bp):
GTTTAATGTGTTAGGTTTTA
Found at i:4004296 original size:22 final size:22
Alignment explanation
Indices: 4004271--4004316 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4004261 TAATGTGTTA
* * *
4004271 GGTTTTGGGGTTTAGTATGAAG
1 GGTTTTGGAGTTTAATATAAAG
4004293 GGTTTTGGAGTTTAATATAAAG
1 GGTTTTGGAGTTTAATATAAAG
4004315 GG
1 GG
4004317 GCCAAAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
GGTTTTGGAGTTTAATATAAAG
Found at i:4007801 original size:31 final size:33
Alignment explanation
Indices: 4007766--4007833 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 33
4007756 ATCTTTATAG
*
4007766 TTTTTTAAAAAATTA-AAT-CAAAATTTTA-TCA
1 TTTTTTAAAAAATCAGAATGCAAAATTTTACT-A
*
4007797 -TTTTTAAAAAGTCAGAATGCAAAATTTTACTA
1 TTTTTTAAAAAATCAGAATGCAAAATTTTACTA
4007829 TTTTT
1 TTTTT
4007834 CAAATTAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
30 12 0.39
31 3 0.10
32 11 0.35
33 5 0.16
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (33 bp):
TTTTTTAAAAAATCAGAATGCAAAATTTTACTA
Found at i:4007825 original size:32 final size:30
Alignment explanation
Indices: 4007767--4007833 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
4007757 TCTTTATAGT
*
4007767 TTTTTAAAAAATTAAATCAAAATTTTA-TCA
1 TTTTTAAAAAATCAAATCAAAATTTTACT-A
*
4007797 TTTTTAAAAAGTCAGAATGCAAAATTTTACTA
1 TTTTTAAAAAATCA-AAT-CAAAATTTTACTA
4007829 TTTTT
1 TTTTT
4007834 CAAATTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 12 0.38
31 3 0.09
32 16 0.50
33 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (30 bp):
TTTTTAAAAAATCAAATCAAAATTTTACTA
Found at i:4008136 original size:25 final size:26
Alignment explanation
Indices: 4008108--4008160 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
4008098 AAAACATTTT
*
4008108 AATTTT-TTTTAATATATTTTAAATA
1 AATTTTCTTTTAATATATTCTAAATA
*
4008133 AATTTTCTTTTAATATATTCTAATTA
1 AATTTTCTTTTAATATATTCTAAATA
4008159 AA
1 AA
4008161 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTTTCTTTTAATATATTCTAAATA
Found at i:4012175 original size:10 final size:10
Alignment explanation
Indices: 4012160--4012184 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4012150 CAAATTAAAA
4012160 ATATTAATCT
1 ATATTAATCT
4012170 ATATTAATCT
1 ATATTAATCT
4012180 ATATT
1 ATATT
4012185 TTAAGTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATTAATCT
Found at i:4026004 original size:21 final size:20
Alignment explanation
Indices: 4025967--4026006 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4025957 TTAATGTTCG
*
4025967 AGTTTATGTTTTAGGTTTGT
1 AGTTTAAGTTTTAGGTTTGT
*
4025987 AGTTTAAGATTTTGGGTTTG
1 AGTTTAAG-TTTTAGGTTTG
4026007 AGATTCTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (20 bp):
AGTTTAAGTTTTAGGTTTGT
Found at i:4038263 original size:90 final size:90
Alignment explanation
Indices: 4038130--4038298 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 90
4038120 AATAATTCTC
* * *
4038130 ACATTGGGGTTTCAACTTTTTTTTGTCCAAATTAATCTATAAACTTGGCAATTGTTCACATGTTA
1 ACATTGGGGTATCAACTTTTTTTTGTCCAAATTAATCCATAAACTTGGCAATTGATCACATGTT-
4038195 AG-GCTTGAACTAGGTAATTGTTCCT
65 AGTGCTTGAACTAGGTAATTGTTCCT
** * * * * *
4038220 ACATTGGGGTATGGACTTTTTTTTGTTCAAGTTAATCCCTAAACTTGGTAATTGATCTCATGTTA
1 ACATTGGGGTATCAACTTTTTTTTGTCCAAATTAATCCATAAACTTGGCAATTGATCACATGTTA
4038285 GTGCTTGAACTAGG
66 GTGCTTGAACTAGG
4038299 CTTGAGCATT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
89 2 0.03
90 66 0.97
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (90 bp):
ACATTGGGGTATCAACTTTTTTTTGTCCAAATTAATCCATAAACTTGGCAATTGATCACATGTTA
GTGCTTGAACTAGGTAATTGTTCCT
Found at i:4043604 original size:20 final size:20
Alignment explanation
Indices: 4043579--4043622 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
4043569 TAGGAAATTA
4043579 CTAAAAAAATATTTAATTTG
1 CTAAAAAAATATTTAATTTG
4043599 CTAAAAAAATATTTAATTTG
1 CTAAAAAAATATTTAATTTG
4043619 CTAA
1 CTAA
4043623 GTAACTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
CTAAAAAAATATTTAATTTG
Found at i:4046711 original size:24 final size:27
Alignment explanation
Indices: 4046684--4046735 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4046674 AAAAAAATTA
4046684 TACATA-ATATA-ATATT-GAAATATT
1 TACATAGATATACATATTAGAAATATT
4046708 TACATAGTATATACATATTAGAAATATT
1 TACATAG-ATATACATATTAGAAATATT
4046736 AATAATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.25
26 5 0.21
27 5 0.21
28 8 0.33
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (27 bp):
TACATAGATATACATATTAGAAATATT
Found at i:4047024 original size:3 final size:3
Alignment explanation
Indices: 4047018--4047436 Score: 140
Period size: 3 Copynumber: 140.7 Consensus size: 3
4047008 TACTACCACC
* * * *
4047018 AAT AAT AAT AAT AGTT AA- AAT AAT AAT AAT ACT AGT AAT AGT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
4047063 TAC AAC AAT GAT AAT AGT AAT AA- AAT AA- GAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
4047109 ATT AAT AAT AA- AAGT AA- AA- AAT AA- AAT AGT AAT AAT AAT AAA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * *
4047151 AAT AAT AAT AGC AAT AAT AAGT -AT ATT AAT AAC AGT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
* *
4047196 AAT GAT ACA- AAT AAT AAT AAT ATAT ATAT AAAT AAT AAT AGTT AA-
1 AAT AAT A-AT AAT AAT AAT AAT A-AT A-AT -AAT AAT AAT A-AT AAT
* * * ** * *
4047241 AAA AAT AAT AGA- AGT AAT AAC AAT AAT GGT -AT TAG AAT AA- AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
4047284 AA- ATAT AAAT ACA- AGT -AT AAT AAT AAT AAT GGT AAT AAA AAT AAA
1 AAT A-AT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
4047329 AAT AAT AGT AAT AAT AAT ACGTT AAGT TAT AAT AGT AA- AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT A--AT AA-T AAT AAT AAT AAT AAT AAT AAT
* * * * *
4047376 AAT TAT GAT AAT AAA AAT -AT ATT ATAT AAT AAT AGT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
*
4047420 AAT AGT AA- ATAT AAT AA
1 AAT AAT AAT A-AT AAT AA
4047437 CATTAAACCA
Statistics
Matches: 300, Mismatches: 81, Indels: 70
0.67 0.18 0.16
Matches are distributed among these distances:
2 29 0.10
3 242 0.81
4 25 0.08
5 4 0.01
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4047098 original size:22 final size:21
Alignment explanation
Indices: 4047069--4047151 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 21
4047059 TAATTACAAC
*
4047069 AATGATAATAGTAATAAAATA
1 AATGATAATAATAATAAAATA
* *
4047090 AGATGATAATAATAATAATATT
1 A-ATGATAATAATAATAAAATA
*
4047112 AATAATAA-AAGTAA-AAAATAA
1 AATGATAATAA-TAATAAAAT-A
4047133 AAT-AGTAATAATAATAAAA
1 AATGA-TAATAATAATAAAA
4047152 ATAATAATAG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.14
21 19 0.38
22 24 0.48
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
AATGATAATAATAATAAAATA
Found at i:4047374 original size:47 final size:47
Alignment explanation
Indices: 4047306--4047421 Score: 128
Period size: 47 Copynumber: 2.4 Consensus size: 47
4047296 AAGTATAATA
* * * *
4047306 ATAATAATGGTAATAAAAATAAAAATAAT-AGTAATAATAATACGTTA-
1 ATAATAATAGTAA-AATAATAAAAATAATGA-TAATAAAAATACATTAT
* * *
4047353 AGTTATAATAGTAAAATAATAAAAATTATGATAATAAAAATATATTAT
1 A-TAATAATAGTAAAATAATAAAAATAATGATAATAAAAATACATTAT
4047401 ATAATAATAGTAAAATAATAA
1 ATAATAATAGTAAAATAATAA
4047422 TAGTAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 46 0.79
48 12 0.21
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (47 bp):
ATAATAATAGTAAAATAATAAAAATAATGATAATAAAAATACATTAT
Found at i:4047420 original size:14 final size:15
Alignment explanation
Indices: 4047399--4047436 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
4047389 AAAATATATT
4047399 ATATAATAATAGTAA
1 ATATAATAATAGTAA
4047414 A-ATAATAATAGTAA
1 ATATAATAATAGTAA
4047428 ATATAATAA
1 ATATAATAA
4047437 CATTAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATATAATAATAGTAA
Found at i:4050149 original size:57 final size:57
Alignment explanation
Indices: 4050074--4050237 Score: 208
Period size: 57 Copynumber: 2.9 Consensus size: 57
4050064 GTGAGCTTTG
* *
4050074 ATAATAAATTATAAAAACAACAGTCATTTTGGACAACCATTTCTTCAAATGTCAGAC
1 ATAATAAATTCTGAAAACAACAGTCATTTTGGACAACCATTTCTTCAAATGTCAGAC
* * * *
4050131 ATAATAAATTCTGGAAACAGCA-TCCATTTTAGG-CAATCATTTCTTCATATGTCAGAC
1 ATAATAAATTCTGAAAACAACAGT-CATTTT-GGACAACCATTTCTTCAAATGTCAGAC
* *
4050188 ATGATATA-TCATGAAAACAACAGTCATTTTGGACAACCATTTCTTCAAAT
1 ATAATAAATTC-TGAAAACAACAGTCATTTTGGACAACCATTTCTTCAAAT
4050238 TTCTAGCACG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.06
57 82 0.91
58 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (57 bp):
ATAATAAATTCTGAAAACAACAGTCATTTTGGACAACCATTTCTTCAAATGTCAGAC
Found at i:4053384 original size:15 final size:15
Alignment explanation
Indices: 4053366--4053399 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4053356 GCAGAAAAAA
*
4053366 TAAGGGTTGAAAATT
1 TAAGGATTGAAAATT
*
4053381 TAAGTATTGAAAATT
1 TAAGGATTGAAAATT
4053396 TAAG
1 TAAG
4053400 TACTGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TAAGGATTGAAAATT
Found at i:4053400 original size:15 final size:15
Alignment explanation
Indices: 4053372--4053406 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4053362 AAAATAAGGG
4053372 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
4053387 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
*
4053402 CTGAA
1 TTGAA
4053407 TTTAAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (15 bp):
TTGAAAATTTAAGTA
Found at i:4053410 original size:13 final size:14
Alignment explanation
Indices: 4053376--4053413 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4053366 TAAGGGTTGA
*
4053376 AAATTTAAGTATTG
1 AAATTTAAGTACTG
4053390 AAAATTTAAGTACTG
1 -AAATTTAAGTACTG
4053405 -AATTTAAGT
1 AAATTTAAGT
4053414 TATAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
15 13 0.59
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (14 bp):
AAATTTAAGTACTG
Found at i:4058908 original size:10 final size:10
Alignment explanation
Indices: 4058889--4058924 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
4058879 TTTGGTTTGT
4058889 ATAT-AAATG
1 ATATGAAATG
4058898 ATATGAAATG
1 ATATGAAATG
4058908 ATATGAAATG
1 ATATGAAATG
*
4058918 TTATGAA
1 ATATGAA
4058925 TTTAATTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (10 bp):
ATATGAAATG
Found at i:4069832 original size:296 final size:296
Alignment explanation
Indices: 4069298--4069888 Score: 1173
Period size: 296 Copynumber: 2.0 Consensus size: 296
4069288 CCAACGGTGC
*
4069298 AAAATTAAGTACATCAACGGCTATGATTAAAGGGCACCTACCACCAAATCTTTAAGAATATAAAA
1 AAAATTAAGTACATCAACGGCTATGATTAAAGGGCACCTACCACCAAATCTTTAAAAATATAAAA
4069363 TCATATCTTCTAAGATTACATATCTTATCTAAGATATGTAATCTTATAAAATAATATCTTATATT
66 TCATATCTTCTAAGATTACATATCTTATCTAAGATATGTAATCTTATAAAATAATATCTTATATT
4069428 TGTCTAACTTGTAGATGAGCCTTCAATCTCTTCAAGCAACGGGCCGGTCCGATTGGGTCAAATGA
131 TGTCTAACTTGTAGATGAGCCTTCAATCTCTTCAAGCAACGGGCCGGTCCGATTGGGTCAAATGA
4069493 CCTCCTTCCTTTTTGATGGTTCACACAGATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCATG
196 CCTCCTTCCTTTTTGATGGTTCACACAGATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCATG
4069558 ACACTAGTCCGTACGTTTTCAGAGTAATTTGGGCTT
261 ACACTAGTCCGTACGTTTTCAGAGTAATTTGGGCTT
4069594 AAAATTAAGTACATCAACGGCTATGATTAAAGGGCACCTACCACCAAATCTTTAAAAATATAAAA
1 AAAATTAAGTACATCAACGGCTATGATTAAAGGGCACCTACCACCAAATCTTTAAAAATATAAAA
4069659 TCATATCTTCTAAGATTACATATCTTATCTAAGATATGTAATCTTATAAAATAATATCTTATATT
66 TCATATCTTCTAAGATTACATATCTTATCTAAGATATGTAATCTTATAAAATAATATCTTATATT
4069724 TGTCTAACTTGTAGATGAGCCTTCAATCTCTTCAAGCAACGGGCCGGTCCGATTGGGTCAAATGA
131 TGTCTAACTTGTAGATGAGCCTTCAATCTCTTCAAGCAACGGGCCGGTCCGATTGGGTCAAATGA
4069789 CCTCCTTCCTTTTTGATGGTTCACACAGATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCATG
196 CCTCCTTCCTTTTTGATGGTTCACACAGATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCATG
4069854 ACACTAGTCCGTACGTTTTCAGAGTAATTTGGGCT
261 ACACTAGTCCGTACGTTTTCAGAGTAATTTGGGCT
4069889 CTGAAACTCA
Statistics
Matches: 294, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
296 294 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (296 bp):
AAAATTAAGTACATCAACGGCTATGATTAAAGGGCACCTACCACCAAATCTTTAAAAATATAAAA
TCATATCTTCTAAGATTACATATCTTATCTAAGATATGTAATCTTATAAAATAATATCTTATATT
TGTCTAACTTGTAGATGAGCCTTCAATCTCTTCAAGCAACGGGCCGGTCCGATTGGGTCAAATGA
CCTCCTTCCTTTTTGATGGTTCACACAGATGTGTCATGGTTGCGGGCTCCCATGCGCAACCCATG
ACACTAGTCCGTACGTTTTCAGAGTAATTTGGGCTT
Found at i:4075282 original size:6 final size:6
Alignment explanation
Indices: 4075271--4075309 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
4075261 TTATTGATTT
*
4075271 TTTATA TTTATA TTTATA TTTATTTA TCTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTA--TA TTTATA TTTATA T
4075310 CCAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.83
8 5 0.17
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:4077117 original size:19 final size:18
Alignment explanation
Indices: 4077093--4077135 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
4077083 TTCAGAACAA
4077093 TCATTT-ATCAAATATCAT
1 TCATTTAAT-AAATATCAT
4077111 CTCATTTCAATAAATATCAT
1 -TCATTT-AATAAATATCAT
4077131 TCATT
1 TCATT
4077136 CACATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (18 bp):
TCATTTAATAAATATCAT
Found at i:4078678 original size:23 final size:23
Alignment explanation
Indices: 4078652--4078712 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
4078642 TGAGCAATAA
4078652 TCTATTGAGCTGAAACGGTAAGC
1 TCTATTGAGCTGAAACGGTAAGC
*
4078675 TCTATCGAGCTGAAACGGTAAGC
1 TCTATTGAGCTGAAACGGTAAGC
*
4078698 TCTAATGAGCTGAAA
1 TCTATTGAGCTGAAA
4078713 ATAGTAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (23 bp):
TCTATTGAGCTGAAACGGTAAGC
Found at i:4078733 original size:47 final size:49
Alignment explanation
Indices: 4078652--4078758 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 49
4078642 TGAGCAATAA
* * *
4078652 TCTATTGAGCTGAAACGGTAAGCTCTATCGAGCTGA-A-A-CGGTAAGC
1 TCTAATGAGCTGAAACAGTAAGCTCTATCAAGCTGATATATCGGTAAGC
*
4078698 TCTAATGAGCTGAAAATAGTAAGCTCT-TACAAGCTGATATATCGGTAAGC
1 TCTAATGAGCTG-AAACAGTAAGCTCTAT-CAAGCTGATATATCGGTAAGC
4078748 TC-ATATGAGCT
1 TCTA-ATGAGCT
4078759 ATGGTAAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
46 12 0.24
47 19 0.37
48 1 0.02
49 2 0.04
50 17 0.33
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (49 bp):
TCTAATGAGCTGAAACAGTAAGCTCTATCAAGCTGATATATCGGTAAGC
Found at i:4085000 original size:24 final size:25
Alignment explanation
Indices: 4084976--4085035 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
4084966 GCTTTTTTTA
4084976 TTTTATTTAATATTAATACAATTAT
1 TTTTATTTAATATTAATACAATTAT
* *
4085001 TTTTATTTAATATTAATATAA-AAT
1 TTTTATTTAATATTAATACAATTAT
4085025 TTTTATTTAAT
1 TTTTATTTAAT
4085036 TATATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTATTTAATATTAATACAATTAT
Found at i:4085072 original size:17 final size:17
Alignment explanation
Indices: 4085050--4085084 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4085040 TTTTAATGAG
4085050 TAGTGACATGACACTTT
1 TAGTGACATGACACTTT
4085067 TAGTGACATGACACTTT
1 TAGTGACATGACACTTT
4085084 T
1 T
4085085 TGATTGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (17 bp):
TAGTGACATGACACTTT
Found at i:4091718 original size:12 final size:12
Alignment explanation
Indices: 4091701--4091725 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4091691 AATCTTGTTC
4091701 ATTTCTTTATTT
1 ATTTCTTTATTT
4091713 ATTTCTTTATTT
1 ATTTCTTTATTT
4091725 A
1 A
4091726 CATTTTCATC
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTCTTTATTT
Found at i:4099883 original size:32 final size:31
Alignment explanation
Indices: 4099819--4099895 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 31
4099809 TTTTTGGGGC
4099819 TTAATAAGAATTTTTAAAAATTTTGAAAAAT
1 TTAATAAGAATTTTTAAAAATTTTGAAAAAT
* *
4099850 TTAATGAGAACTTTTTAAAAA-TTTGAGAGAAT
1 TTAATAAGAA-TTTTTAAAAATTTTGA-AAAAT
*
4099882 TTAAATAAAAATTT
1 TT-AATAAGAATTT
4099896 CGGATTGTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 14 0.36
32 19 0.49
33 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (31 bp):
TTAATAAGAATTTTTAAAAATTTTGAAAAAT
Found at i:4103193 original size:18 final size:18
Alignment explanation
Indices: 4103139--4103194 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
4103129 ATAATATTTT
4103139 TTTAAGTTAATTAAGAAA
1 TTTAAGTTAATTAAGAAA
* * *
4103157 TTGAA-ATACA-TATATAAA
1 TTTAAGTTA-ATTA-AGAAA
4103175 TTTAAGTTAATTAAGAAA
1 TTTAAGTTAATTAAGAAA
4103193 TT
1 TT
4103195 GAAATATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (18 bp):
TTTAAGTTAATTAAGAAA
Found at i:4103211 original size:18 final size:18
Alignment explanation
Indices: 4103154--4103212 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
4103144 GTTAATTAAG
*
4103154 AAATTGAAATACATATAT
1 AAATTGAAATATATATAT
* * *
4103172 AAATTTAAGT-TA-ATTAAG
1 AAATTGAAATATATA-T-AT
4103190 AAATTGAAATATATATAT
1 AAATTGAAATATATATAT
4103208 AAATT
1 AAATT
4103213 TACTTTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
16 1 0.03
17 2 0.07
18 23 0.77
19 3 0.10
20 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
AAATTGAAATATATATAT
Found at i:4103221 original size:36 final size:36
Alignment explanation
Indices: 4103139--4103214 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
4103129 ATAATATTTT
4103139 TTTAAGTTAATTAAGAAATTGAAATACATATATAAA
1 TTTAAGTTAATTAAGAAATTGAAATACATATATAAA
*
4103175 TTTAAGTTAATTAAGAAATTGAAATATATATATAAA
1 TTTAAGTTAATTAAGAAATTGAAATACATATATAAA
4103211 TTTA
1 TTTA
4103215 CTTTAATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (36 bp):
TTTAAGTTAATTAAGAAATTGAAATACATATATAAA
Found at i:4105777 original size:15 final size:15
Alignment explanation
Indices: 4105757--4105787 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4105747 ATGGCTGACC
4105757 TCGTTTTAGGAATAG
1 TCGTTTTAGGAATAG
4105772 TCGTTTTAGGAATAG
1 TCGTTTTAGGAATAG
4105787 T
1 T
4105788 TATTCATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (15 bp):
TCGTTTTAGGAATAG
Found at i:4112205 original size:21 final size:21
Alignment explanation
Indices: 4112180--4112222 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4112170 AATAATATAT
4112180 TTTAAGTTTAACAA-TTTACTA
1 TTTAAGTTTAA-AATTTTACTA
4112201 TTTAAGTTTAAAATTTTACTA
1 TTTAAGTTTAAAATTTTACTA
4112222 T
1 T
4112223 ATATATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTAAGTTTAAAATTTTACTA
Found at i:4116212 original size:22 final size:22
Alignment explanation
Indices: 4116187--4116234 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4116177 GTTGAGGTGA
4116187 GGATGGTGG-GGGGCAGGGAGAG
1 GGATGGTGGAGGGG-AGGGAGAG
*
4116209 GGATGGTGGAGGGGTGGGAGAG
1 GGATGGTGGAGGGGAGGGAGAG
4116231 GGAT
1 GGAT
4116235 CGGGTGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.67, T:0.12
Consensus pattern (22 bp):
GGATGGTGGAGGGGAGGGAGAG
Found at i:4117305 original size:22 final size:21
Alignment explanation
Indices: 4117280--4117338 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
4117270 TTTTTAAATC
*
4117280 TTTTAAAAATTTTAATTACAAG
1 TTTTAAAAA-TTTAATGACAAG
* *
4117302 TTTTGAAAAATTTAATGAGAAT
1 TTTT-AAAAATTTAATGACAAG
4117324 TTTTAAAAAGTTTAA
1 TTTTAAAAA-TTTAA
4117339 GAGAACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.16
22 22 0.69
23 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTTAAAAATTTAATGACAAG
Found at i:4117331 original size:21 final size:23
Alignment explanation
Indices: 4117280--4117343 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 23
4117270 TTTTTAAATC
* * *
4117280 TTTTAAAAATTTTAATTACAAGT
1 TTTTAAAAAGTTTAATGAGAAGT
*
4117303 TTTGAAAAA-TTTAATGAGAA-T
1 TTTTAAAAAGTTTAATGAGAAGT
4117324 TTTTAAAAAGTTTAA-GAGAA
1 TTTTAAAAAGTTTAATGAGAA
4117344 CTTAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.39
22 14 0.39
23 8 0.22
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.41
Consensus pattern (23 bp):
TTTTAAAAAGTTTAATGAGAAGT
Found at i:4125025 original size:22 final size:22
Alignment explanation
Indices: 4125000--4125044 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4124990 TTACTATTTG
4125000 TATTTACCA-TTATTATTACTAT
1 TATTT-CCATTTATTATTACTAT
* *
4125022 TATTTTCATTTTTTATTACTAT
1 TATTTCCATTTATTATTACTAT
4125044 T
1 T
4125045 TCTAATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTCCATTTATTATTACTAT
Found at i:4131214 original size:35 final size:34
Alignment explanation
Indices: 4131136--4131300 Score: 161
Period size: 35 Copynumber: 4.7 Consensus size: 34
4131126 TCCTCATTGA
* * * **
4131136 AATACCATACCTACATTTTACAACTCGGTATGGGG
1 AATACCATACCTACGTTTCACAACTCAGTAT-GAT
* ** *
4131171 AA-AGCCATACCTACATTTCTTAAGTCAGTATCGAT
1 AATA-CCATACCTACGTTTCACAACTCAGTAT-GAT
* *
4131206 AATACCATACCTATGTTTCACAACTCAGTATGGTT
1 AATACCATACCTACGTTTCACAACTCAGTAT-GAT
4131241 AATACCATACCTACGTTTCACAACTCAGTATGAAT
1 AATACCATACCTACGTTTCACAACTCAGTATG-AT
* *
4131276 GATACCATAGCTACGTTTCACAACT
1 AATACCATACCTACGTTTCACAACT
4131301 TTGCCATGGA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
34 2 0.02
35 105 0.97
36 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (34 bp):
AATACCATACCTACGTTTCACAACTCAGTATGAT
Found at i:4131229 original size:70 final size:70
Alignment explanation
Indices: 4131136--4131300 Score: 190
Period size: 70 Copynumber: 2.4 Consensus size: 70
4131126 TCCTCATTGA
* * * ** *
4131136 AATACCATACCTACATTTTACAACTCGGTATGGGGAA-AGCCATACCTACATTTCTTAAGTCAGT
1 AATACCATACCTACGTTTCACAACTCAGTATGGGGAATA-CCATACCTACATTTCACAACTCAGT
4131200 ATCG-AT
65 AT-GAAT
* ** *
4131206 AATACCATACCTATGTTTCACAACTCAGTATGGTTAATACCATACCTACGTTTCACAACTCAGTA
1 AATACCATACCTACGTTTCACAACTCAGTATGGGGAATACCATACCTACATTTCACAACTCAGTA
4131271 TGAAT
66 TGAAT
* *
4131276 GATACCATAGCTACGTTTCACAACT
1 AATACCATACCTACGTTTCACAACT
4131301 TTGCCATGGA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
69 1 0.01
70 78 0.98
71 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (70 bp):
AATACCATACCTACGTTTCACAACTCAGTATGGGGAATACCATACCTACATTTCACAACTCAGTA
TGAAT
Found at i:4135012 original size:31 final size:32
Alignment explanation
Indices: 4134932--4135020 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
4134922 TTTTTGGGGC
* *
4134932 TTAATAAGAATTTTTAAAACTTTT-AAAAATT
1 TTAATAAGAATTTTTAAAAATTTTGAAAAATA
* * *
4134963 TTTATTACAATTTTTTAAAAATTTTGAAAAA-A
1 TTAATAAGAA-TTTTTAAAAATTTTGAAAAATA
* *
4134995 TTAATGAGAATTTTTAAAAAGTTTGA
1 TTAATAAGAATTTTTAAAAATTTTGA
4135021 GAGAACTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 22 0.47
32 20 0.43
33 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (32 bp):
TTAATAAGAATTTTTAAAAATTTTGAAAAATA
Found at i:4138995 original size:21 final size:21
Alignment explanation
Indices: 4138966--4139008 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4138956 AATAATATAT
4138966 TTTAAGTTTAAAAGCTTACTA
1 TTTAAGTTTAAAAGCTTACTA
* **
4138987 TTTACGTTTAAAATTTTACTA
1 TTTAAGTTTAAAAGCTTACTA
4139008 T
1 T
4139009 ATATATTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAAGTTTAAAAGCTTACTA
Found at i:4142568 original size:17 final size:17
Alignment explanation
Indices: 4142546--4142587 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4142536 ATAGAAATTA
4142546 AATAAAATTAAAATTTT
1 AATAAAATTAAAATTTT
* *
4142563 AATAAAAATATAATTTT
1 AATAAAATTAAAATTTT
4142580 AA-AAAATT
1 AATAAAATT
4142588 CATTTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAAATTAAAATTTT
Found at i:4142783 original size:4 final size:4
Alignment explanation
Indices: 4142774--4142799 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4142764 ATATATACCA
4142774 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
4142800 TTACAATAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:4153224 original size:25 final size:25
Alignment explanation
Indices: 4153196--4153245 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4153186 TGAATTTGGG
4153196 TCATTCAGCATAAGGGTCATTTTAA
1 TCATTCAGCATAAGGGTCATTTTAA
4153221 TCATTCAGCATAAGGGTCATTTTAA
1 TCATTCAGCATAAGGGTCATTTTAA
4153246 GGTCGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (25 bp):
TCATTCAGCATAAGGGTCATTTTAA
Found at i:4179289 original size:10 final size:11
Alignment explanation
Indices: 4179265--4179297 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
4179255 AAAGTTAGTA
4179265 AAAAAAATTCAT
1 AAAAAAATT-AT
4179277 AAAAAAATT-T
1 AAAAAAATTAT
4179287 AAAAAAATTAT
1 AAAAAAATTAT
4179298 TCATGTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 1 0.05
12 9 0.45
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAAAATTAT
Done.