Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 91 of 186
Found at i:29602207 original size:46 final size:45
Alignment explanation
Indices: 29602106--29602231 Score: 134
Period size: 46 Copynumber: 2.7 Consensus size: 45
29602096 GATGGTATGT
29602106 GAGCTAGTGTAAGACATGTCTGAGACATGCATCGGCCACATTATGAGA
1 GAGCTAGTGTAAGACATGTCTG-GACATGCATCGG-C-CATTATGAGA
* *
29602154 -A-CCAGTGTAAGACATGTCTAGGACATGCATCTG-CATTGA-GACGA
1 GAGCTAGTGTAAGACATGTCT-GGACATGCATCGGCCATT-ATGA-GA
*
29602198 GAGCTAGTGTAAGACATGTATGGGACATGCATCG
1 GAGCTAGTGTAAGACATGTCT-GGACATGCATCG
29602232 TCCTCGGGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
43 6 0.09
44 3 0.04
45 1 0.01
46 55 0.82
47 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGACATGCATCGGCCATTATGAGA
Found at i:29605768 original size:20 final size:20
Alignment explanation
Indices: 29605743--29605791 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
29605733 TAGGGATCAA
29605743 TTTGAAACAAAATAGAAAAC
1 TTTGAAACAAAATAGAAAAC
* * *
29605763 TTTGAAA-AAACTTGAAAAT
1 TTTGAAACAAAATAGAAAAC
29605782 TTTAGAAACA
1 TTT-GAAACA
29605792 GGGGTCACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 11 0.46
21 1 0.04
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (20 bp):
TTTGAAACAAAATAGAAAAC
Found at i:29607403 original size:24 final size:24
Alignment explanation
Indices: 29607370--29607416 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29607360 ATTGATATAA
* **
29607370 TGGTATCCTTTTTGACCTTTTCAT
1 TGGTAACCTTTTCAACCTTTTCAT
29607394 TGGTAACCTTTTCAACCTTTTCA
1 TGGTAACCTTTTCAACCTTTTCA
29607417 CTGTTTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (24 bp):
TGGTAACCTTTTCAACCTTTTCAT
Found at i:29613550 original size:21 final size:21
Alignment explanation
Indices: 29613520--29613560 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29613510 GAAATGTTAA
*
29613520 TATGATTTGTATTACTACGCT
1 TATGAGTTGTATTACTACGCT
*
29613541 TATGAGTTGTATTCCTACGC
1 TATGAGTTGTATTACTACGC
29613561 CATTAGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (21 bp):
TATGAGTTGTATTACTACGCT
Found at i:29618024 original size:24 final size:24
Alignment explanation
Indices: 29617947--29618025 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
29617937 TCGAAACAAA
*
29617947 ATCCCGTTATTAGCTC-TCATGAGC
1 ATCCCGTTAATAGCTCTTCA-GAGC
* *
29617971 TTCCCGTTATATAGTTCTTGCA-AGC
1 ATCCCGTTA-ATAGCTCTT-CAGAGC
* *
29617996 TTCCCATTAATAGCTCTTCAGAGC
1 ATCCCGTTAATAGCTCTTCAGAGC
29618020 ATCCCG
1 ATCCCG
29618026 ATTGGTTATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
23 2 0.05
24 23 0.52
25 16 0.36
26 1 0.02
27 2 0.05
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (24 bp):
ATCCCGTTAATAGCTCTTCAGAGC
Found at i:29619453 original size:43 final size:43
Alignment explanation
Indices: 29619406--29619558 Score: 164
Period size: 43 Copynumber: 3.6 Consensus size: 43
29619396 ATATAGGATT
* * *
29619406 TCGATATGTGATTTCGTGTAAGACTATGTCTGGGAAATTGGCA
1 TCGATATGTGATTTCATGTAAGACCATGTCTGGGACATTGGCA
* * *
29619449 TCGATTTGAGATTTGCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATGTGATTT-CATGTAAGACCATGTCTGGGACATTGGCA
* * * * * *
29619493 TTG-TATTTGATTTCATGTAAAACCCTGTTTGGGACAGTGGCA
1 TCGATATGTGATTTCATGTAAGACCATGTCTGGGACATTGGCA
* *
29619535 TCGATATTTGATTACATGTAAGAC
1 TCGATATGTGATTTCATGTAAGAC
29619559 TACATCTAGG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 26 0.28
43 37 0.40
44 29 0.32
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (43 bp):
TCGATATGTGATTTCATGTAAGACCATGTCTGGGACATTGGCA
Found at i:29619479 original size:44 final size:43
Alignment explanation
Indices: 29619406--29619539 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 43
29619396 ATATAGGATT
* * *
29619406 TCGATATGTGATTTCGTGTAAGACTATGTCTGGGAAATTGGCA
1 TCGATTTGAGATTTCGTGTAAGACCATGTCTGGGAAATTGGCA
*
29619449 TCGATTTGAGATTTGCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATTTGAGATTT-CGTGTAAGACCATGTCTGGGAAATTGGCA
* * * * * * *
29619493 TTGTATTT--GATTTCATGTAAAACCCTGTTTGGGACAGTGGCA
1 TCG-ATTTGAGATTTCGTGTAAGACCATGTCTGGGAAATTGGCA
29619535 TCGAT
1 TCGAT
29619540 ATTTGATTAC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 26 0.33
43 17 0.22
44 29 0.37
45 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (43 bp):
TCGATTTGAGATTTCGTGTAAGACCATGTCTGGGAAATTGGCA
Found at i:29619527 original size:42 final size:43
Alignment explanation
Indices: 29619406--29619555 Score: 124
Period size: 44 Copynumber: 3.5 Consensus size: 43
29619396 ATATAGGATT
* * * * * * *
29619406 TCGATATGTGATTTCGTGTAAGACTATGTCTGGGAAATTGGCA
1 TCGATATTTGATTACATGTAAAACCATGTCTGGGACAGTGGCA
* * * * *
29619449 TCGAT-TTGAGATTTGCGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATT-TGA-TTACATGTAAAACCATGTCTGGGACAGTGGCA
* * * *
29619493 TTG-TATTTGATTTCATGTAAAACCCTGTTTGGGACAGTGGCA
1 TCGATATTTGATTACATGTAAAACCATGTCTGGGACAGTGGCA
29619535 TCGATATTTGATTACATGTAA
1 TCGATATTTGATTACATGTAA
29619556 GACTACATCT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 29 0.33
43 26 0.30
44 33 0.38
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (43 bp):
TCGATATTTGATTACATGTAAAACCATGTCTGGGACAGTGGCA
Found at i:29627135 original size:42 final size:42
Alignment explanation
Indices: 29627025--29627189 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 42
29627015 TTCCGATATG
* *
29627025 TGATTTCGTGTAAGA-CCAGATCTGGGACGTTGGCATCG-ATT
1 TGATTTCGTGTAAGACCCTG-TCTGGGACATTGGCATCGTATT
* * * *
29627066 TGAGATTTATGTGTAAGGCCATGTCTGGGACATTAGCATCGTATT
1 T--GATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATCGTATT
*
29627111 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCG-TATT
* * * *
29627154 TGATTACATGTAAGACCAC-GTTTGGGACGTTGGCAT
1 TGATTTCGTGTAAGACC-CTGTCTGGGACATTGGCAT
29627190 TGTACGTGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 27 0.27
43 43 0.43
44 24 0.24
45 6 0.06
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGTATT
Found at i:29628965 original size:58 final size:58
Alignment explanation
Indices: 29628892--29629009 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
29628882 TACTTGAATG
29628892 TGGAACTTGCTTGATGACCCTGTTCATCCATGATCAATGGCTATTATATGTGATTATA
1 TGGAACTTGCTTGATGACCCTGTTCATCCATGATCAATGGCTATTATATGTGATTATA
29628950 TGGAACTTGCTTGATGACCCTGTTCATCCATGATCAATGGCTATTATATGTGATTATA
1 TGGAACTTGCTTGATGACCCTGTTCATCCATGATCAATGGCTATTATATGTGATTATA
29629008 TG
1 TG
29629010 ACTAACATGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (58 bp):
TGGAACTTGCTTGATGACCCTGTTCATCCATGATCAATGGCTATTATATGTGATTATA
Found at i:29636087 original size:25 final size:25
Alignment explanation
Indices: 29636059--29636126 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
29636049 TCCGATATAT
*
29636059 GGATCTTCGGAGCTTCCCGATTAAA
1 GGATCTTCGGAGCTTCCCAATTAAA
* * *
29636084 GGATCTTTCATGAGCTTCCTAATTAAT
1 GGATC-TTC-GGAGCTTCCCAATTAAA
* *
29636111 GGCTCTCCGGAGCTTC
1 GGATCTTCGGAGCTTC
29636127 TATATATTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
25 12 0.35
26 5 0.15
27 17 0.50
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (25 bp):
GGATCTTCGGAGCTTCCCAATTAAA
Found at i:29636150 original size:24 final size:24
Alignment explanation
Indices: 29636123--29636198 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
29636113 CTCTCCGGAG
*
29636123 CTTCTATATATTGGCTCACTTGAA
1 CTTCTAGATATTGGCTCACTTGAA
* *
29636147 CTTCTCGATATTGGCTCGCTTGAA
1 CTTCTAGATATTGGCTCACTTGAA
** * * *
29636171 CTTCCCGATACTGGCTCACATGAG
1 CTTCTAGATATTGGCTCACTTGAA
29636195 CTTC
1 CTTC
29636199 CCATTATATG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (24 bp):
CTTCTAGATATTGGCTCACTTGAA
Found at i:29636199 original size:24 final size:24
Alignment explanation
Indices: 29636134--29636200 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
29636124 TTCTATATAT
* *
29636134 TGGCTCACTTGAACTTCTCGATAT
1 TGGCTCACTTGAACTTCCCGATAC
*
29636158 TGGCTCGCTTGAACTTCCCGATAC
1 TGGCTCACTTGAACTTCCCGATAC
* *
29636182 TGGCTCACATGAGCTTCCC
1 TGGCTCACTTGAACTTCCC
29636201 ATTATATGGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (24 bp):
TGGCTCACTTGAACTTCCCGATAC
Found at i:29636212 original size:25 final size:24
Alignment explanation
Indices: 29636182--29636247 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 24
29636172 TTCCCGATAC
29636182 TGGCTCACATGAGCTTCCCATTATA
1 TGGCTCACATGAGCTTCCCATT-TA
* *
29636207 TGGCTCGAAAGAGAGCTTCCCATTTA
1 TGGCTC-ACA-TGAGCTTCCCATTTA
29636233 TGTGCTC-CTATGAGC
1 TG-GCTCAC-ATGAGC
29636248 ACTCCTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
25 10 0.30
26 7 0.21
27 16 0.48
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (24 bp):
TGGCTCACATGAGCTTCCCATTTA
Found at i:29642088 original size:16 final size:16
Alignment explanation
Indices: 29642067--29642097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29642057 AAGTGAAAAA
*
29642067 TCCTATTAATTGTTTT
1 TCCTATTAACTGTTTT
29642083 TCCTATTAACTGTTT
1 TCCTATTAACTGTTT
29642098 CAGGCTAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (16 bp):
TCCTATTAACTGTTTT
Found at i:29656132 original size:39 final size:39
Alignment explanation
Indices: 29656074--29656170 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
29656064 TGAACTGAAA
* * * *
29656074 CCCGAAGTCTAACTGAAGCACATAAGTGCTAAACGGAAT
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
29656113 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
29656152 CCCGAAGGCTAACTAAAGC
1 CCCGAAGGCTAACTAAAGC
29656171 TCATCAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (39 bp):
CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
Found at i:29658392 original size:15 final size:15
Alignment explanation
Indices: 29658354--29658395 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
29658344 GAAGCCCAGA
29658354 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
29658369 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
*
29658384 ATAGGGAAATCC
1 ATAAGGAAATCC
29658396 TATTTACAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:29659694 original size:72 final size:72
Alignment explanation
Indices: 29659605--29659752 Score: 260
Period size: 72 Copynumber: 2.1 Consensus size: 72
29659595 CAACCAATAT
* *
29659605 ATATGAATATTCATCTTATCAATATTTTTGATAAGTTACTCAAACACATGCATTTGTTCAAATAA
1 ATATGAATATTCATCTTATCAATATTTTTAATAAGTTACTCAAACACATGCATTTGTACAAATAA
*
29659670 ATCGATC
66 ATCAATC
*
29659677 ATATGAATATTCATCTTATTAATATTTTTAATAAGTTACTCAAACACATGCATTTGTACAAATAA
1 ATATGAATATTCATCTTATCAATATTTTTAATAAGTTACTCAAACACATGCATTTGTACAAATAA
29659742 ATCAATC
66 ATCAATC
29659749 ATAT
1 ATAT
29659753 ACATCATGGA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (72 bp):
ATATGAATATTCATCTTATCAATATTTTTAATAAGTTACTCAAACACATGCATTTGTACAAATAA
ATCAATC
Found at i:29661781 original size:19 final size:19
Alignment explanation
Indices: 29661713--29661814 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 19
29661703 ACATCGTGAT
* *
29661713 CTGAAGCTCGAAGT-CTAA
1 CTGAAGCCCAAAGTGCTAA
* *
29661731 CTGAAGCACACAAGTTCTAA
1 CTGAAGCCCA-AAGTGCTAA
*
29661751 ATGGAAGCCCAAAG-GCTAA
1 CT-GAAGCCCAAAGTGCTAA
29661770 CTGAAGCACC-AAGTGCTAAA
1 CTGAAGC-CCAAAGTGCT-AA
* *
29661790 CAGAAGCCCGAAG-GCTAA
1 CTGAAGCCCAAAGTGCTAA
*
29661808 CTAAAGC
1 CTGAAGC
29661815 TCATCAGAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
18 23 0.34
19 19 0.28
20 19 0.28
21 7 0.10
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.15
Consensus pattern (19 bp):
CTGAAGCCCAAAGTGCTAA
Found at i:29661796 original size:38 final size:39
Alignment explanation
Indices: 29661727--29661814 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 39
29661717 AGCTCGAAGT
* **
29661727 CTAACTGAAGCACACAAGTTCTAAATGGAAGCCCAAAGG
1 CTAACTGAAGCACACAAGTGCTAAACAGAAGCCCAAAGG
*
29661766 CTAACTGAAGCAC-CAAGTGCTAAACAGAAGCCCGAAGG
1 CTAACTGAAGCACACAAGTGCTAAACAGAAGCCCAAAGG
*
29661804 CTAACTAAAGC
1 CTAACTGAAGC
29661815 TCATCAGAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 31 0.70
39 13 0.30
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (39 bp):
CTAACTGAAGCACACAAGTGCTAAACAGAAGCCCAAAGG
Found at i:29666994 original size:4 final size:4
Alignment explanation
Indices: 29666985--29667142 Score: 316
Period size: 4 Copynumber: 39.5 Consensus size: 4
29666975 AGGAGTTGCA
29666985 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29667033 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29667081 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
29667129 GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GT
29667143 TTATGTGTTT
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 154 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:29672241 original size:28 final size:29
Alignment explanation
Indices: 29672201--29672255 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
29672191 CACGGGAGAA
*
29672201 GACACGGGCGTGT-CTAGGCCGTGTGAGG
1 GACACGGGCGTGTGCTACGCCGTGTGAGG
* *
29672229 GACATGGGCGTGTGCTTCGCCGTGTGA
1 GACACGGGCGTGTGCTACGCCGTGTGA
29672256 AAACCCCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.13, C:0.22, G:0.44, T:0.22
Consensus pattern (29 bp):
GACACGGGCGTGTGCTACGCCGTGTGAGG
Found at i:29673821 original size:25 final size:25
Alignment explanation
Indices: 29673792--29673844 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
29673782 AGCCAAACCG
*
29673792 AGCCTTTGTGGCGAGTAATCTGTAA
1 AGCCTTTGTGGCAAGTAATCTGTAA
*
29673817 AGCCTTTGTGGCAAGTTATCTGTAA
1 AGCCTTTGTGGCAAGTAATCTGTAA
29673842 AGC
1 AGC
29673845 TGTAACAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (25 bp):
AGCCTTTGTGGCAAGTAATCTGTAA
Found at i:29683201 original size:19 final size:19
Alignment explanation
Indices: 29683177--29683218 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
29683167 GTCAAAAGTT
29683177 TAGAGGTAAATTTGTAATC
1 TAGAGGTAAATTTGTAATC
*
29683196 TAGAGGTAAATTTGTAATT
1 TAGAGGTAAATTTGTAATC
29683215 TAGA
1 TAGA
29683219 CAAAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (19 bp):
TAGAGGTAAATTTGTAATC
Found at i:29683706 original size:22 final size:22
Alignment explanation
Indices: 29683678--29683734 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
29683668 TGCTCGTATA
*
29683678 AGCTTACTATTTAGC-AGAATAG
1 AGCTTACTATTCAGCTAG-ATAG
* *
29683700 AGCTTACTGTTCAGCTTGATAG
1 AGCTTACTATTCAGCTAGATAG
29683722 AGCTTACTATTCA
1 AGCTTACTATTCA
29683735 TCAGCTCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (22 bp):
AGCTTACTATTCAGCTAGATAG
Found at i:29691371 original size:2 final size:2
Alignment explanation
Indices: 29691364--29691389 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29691354 GCTAGGTCAA
29691364 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
29691390 CTTGGGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29691597 original size:16 final size:16
Alignment explanation
Indices: 29691576--29691609 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29691566 AACCGCCATA
29691576 GCCAATATAAGAATCT
1 GCCAATATAAGAATCT
* *
29691592 GCCAATATTAGTATCT
1 GCCAATATAAGAATCT
29691608 GC
1 GC
29691610 ATGTATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (16 bp):
GCCAATATAAGAATCT
Found at i:29700565 original size:45 final size:45
Alignment explanation
Indices: 29700501--29700590 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
29700491 CATCAATAAG
29700501 AGGTATGTTGATTTTTACCTTTCGAAAGTTGTCGAGGATCTTCTT
1 AGGTATGTTGATTTTTACCTTTCGAAAGTTGTCGAGGATCTTCTT
*
29700546 AGGTATGTTGATTTTTACCTTTCGAAAGTTGTCGAGTATCTTCTT
1 AGGTATGTTGATTTTTACCTTTCGAAAGTTGTCGAGGATCTTCTT
29700591 CTCTTTTCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.20, C:0.13, G:0.21, T:0.46
Consensus pattern (45 bp):
AGGTATGTTGATTTTTACCTTTCGAAAGTTGTCGAGGATCTTCTT
Found at i:29702465 original size:12 final size:12
Alignment explanation
Indices: 29702450--29702480 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29702440 ATAATTAAAT
29702450 AATTAAATTAGA
1 AATTAAATTAGA
*
29702462 AATTAAATTGGA
1 AATTAAATTAGA
29702474 AATTAAA
1 AATTAAA
29702481 CTCAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (12 bp):
AATTAAATTAGA
Found at i:29711885 original size:13 final size:12
Alignment explanation
Indices: 29711867--29711918 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
29711857 ATTTTAAATC
29711867 AAACTTTTTAAA
1 AAACTTTTTAAA
*
29711879 AACACTTTTAAAA
1 AA-ACTTTTTAAA
* *
29711892 AATATTTTTTTACA
1 AA-A-CTTTTTAAA
29711906 AAACTTTTTAAA
1 AAACTTTTTAAA
29711918 A
1 A
29711919 GCATTAACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 10 0.32
13 13 0.42
14 8 0.26
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (12 bp):
AAACTTTTTAAA
Found at i:29713138 original size:24 final size:26
Alignment explanation
Indices: 29713092--29713144 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
29713082 TTTATTTTGG
*
29713092 TTAGTGAAAGTCAATTGAGTTTT-TT
1 TTAGTGAAAGACAATTGAGTTTTGTT
*
29713117 TTAGTG-AAGACAATTGATTTTTGTT
1 TTAGTGAAAGACAATTGAGTTTTGTT
29713142 TTA
1 TTA
29713145 CCCTAATGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (26 bp):
TTAGTGAAAGACAATTGAGTTTTGTT
Found at i:29714486 original size:16 final size:16
Alignment explanation
Indices: 29714465--29714496 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29714455 GTTCTGTTGA
29714465 GACCCATCTCTTCCAT
1 GACCCATCTCTTCCAT
29714481 GACCCATCTCTTCCAT
1 GACCCATCTCTTCCAT
29714497 TGATGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (16 bp):
GACCCATCTCTTCCAT
Found at i:29729401 original size:36 final size:35
Alignment explanation
Indices: 29729322--29729392 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
29729312 TGATTTAGCA
* *
29729322 AACAATAAGTATTAAAAGAAACGAAAATTTTTAACT
1 AACAATAAGTATTAAAAGAAACGAAAA-TATTAAAT
*
29729358 AACAATAAGTGTTAAAAGAAACGAAAA-ATTAAAT
1 AACAATAAGTATTAAAAGAAACGAAAATATTAAAT
29729392 A
1 A
29729393 GAAGAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 6 0.19
36 26 0.81
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (35 bp):
AACAATAAGTATTAAAAGAAACGAAAATATTAAAT
Found at i:29736960 original size:74 final size:75
Alignment explanation
Indices: 29736839--29736987 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 75
29736829 AATTAGTTGT
*
29736839 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTT-TTGTATAAGGACTA
1 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
*
29736903 AACTGTGTAC
66 AACCGTGTAC
29736913 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
1 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
29736978 AACCGTGTAC
66 AACCGTGTAC
29736988 AGGATAAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 50 0.69
75 22 0.31
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (75 bp):
GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
AACCGTGTAC
Found at i:29737253 original size:15 final size:15
Alignment explanation
Indices: 29737228--29737262 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29737218 ATTAAATAGG
29737228 AAAGA-AAAGAAAGA
1 AAAGAGAAAGAAAGA
*
29737242 AAAGAGAAAGAAATA
1 AAAGAGAAAGAAAGA
29737257 AAAGAG
1 AAAGAG
29737263 GAGAAAGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAGAGAAAGAAAGA
Found at i:29738870 original size:21 final size:21
Alignment explanation
Indices: 29738846--29738889 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29738836 AAATGTGGTG
29738846 ATGTTTACCTTTTGTGACGGC
1 ATGTTTACCTTTTGTGACGGC
29738867 ATGTTTACCTTTTGTGACGGC
1 ATGTTTACCTTTTGTGACGGC
29738888 AT
1 AT
29738890 ATATGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (21 bp):
ATGTTTACCTTTTGTGACGGC
Found at i:29744180 original size:39 final size:39
Alignment explanation
Indices: 29744133--29744264 Score: 219
Period size: 39 Copynumber: 3.4 Consensus size: 39
29744123 TATATGAGAT
29744133 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
29744172 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
* * **
29744211 TGGAAATATATCCGGACTTGAGGTCCACAGGCTACGTGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
*
29744250 TGGAAAAATATCCGG
1 TGGAAATATATCCGG
29744265 GTTAAAGACC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (39 bp):
TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
Found at i:29744278 original size:78 final size:78
Alignment explanation
Indices: 29744133--29744282 Score: 194
Period size: 78 Copynumber: 1.9 Consensus size: 78
29744123 TATATGAGAT
* * * * **
29744133 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAATATATCCGGACATGAGGTCC
1 TGGAAATATATCCGGACATGAGGTCCACAGGCTACATGCTGGAAAAATATCCGGACATAAGACCC
29744198 GCAGGCTATATGC
66 GCAGGCTATATGC
* * **
29744211 TGGAAATATATCCGGACTTGAGGTCCACAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACC
1 TGGAAATATATCCGGACATGAGGTCCACAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACC
29744275 CGCAGGCT
65 CGCAGGCT
29744283 TACGCTAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 1 0.02
78 60 0.98
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (78 bp):
TGGAAATATATCCGGACATGAGGTCCACAGGCTACATGCTGGAAAAATATCCGGACATAAGACCC
GCAGGCTATATGC
Found at i:29747942 original size:11 final size:11
Alignment explanation
Indices: 29747926--29747968 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
29747916 ACCTCGTGAA
29747926 AATATATTAAT
1 AATATATTAAT
*
29747937 AATATATAAAT
1 AATATATTAAT
29747948 -A-ATATTAAT
1 AATATATTAAT
*
29747957 AATATAATAAT
1 AATATATTAAT
29747968 A
1 A
29747969 TAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATTAAT
Found at i:29747968 original size:20 final size:20
Alignment explanation
Indices: 29747925--29747962 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29747915 AACCTCGTGA
29747925 AAAT-ATATTAATAATATAT
1 AAATAATATTAATAATATAT
29747944 AAATAATATTAATAATATA
1 AAATAATATTAATAATATA
29747963 ATAATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAATATTAATAATATAT
Found at i:29755611 original size:25 final size:25
Alignment explanation
Indices: 29755582--29755634 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
29755572 TACCAATTAG
*
29755582 ACCGAAACCATCTACATTTAAAACT
1 ACCGAAACCAACTACATTTAAAACT
29755607 ACCGAAACCAACTACATTTAAAACT
1 ACCGAAACCAACTACATTTAAAACT
29755632 ACC
1 ACC
29755635 ATACCATTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (25 bp):
ACCGAAACCAACTACATTTAAAACT
Found at i:29769845 original size:37 final size:37
Alignment explanation
Indices: 29769791--29769883 Score: 168
Period size: 37 Copynumber: 2.5 Consensus size: 37
29769781 TATTATAATT
29769791 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
1 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
*
29769828 CCGGTGAGTGTTGGGCACACATTTTATTTTGGTTATG
1 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
*
29769865 CCGATGAGCGTTGGGCACA
1 CCGATGAGTGTTGGGCACA
29769884 AGTTATACTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.35
Consensus pattern (37 bp):
CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
Found at i:29777989 original size:15 final size:15
Alignment explanation
Indices: 29777969--29777998 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29777959 CATTATTAGA
29777969 TCTATTTTTGTTTGG
1 TCTATTTTTGTTTGG
29777984 TCTATTTTTGTTTGG
1 TCTATTTTTGTTTGG
29777999 ACATAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (15 bp):
TCTATTTTTGTTTGG
Found at i:29778037 original size:24 final size:24
Alignment explanation
Indices: 29778010--29778056 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29778000 CATAGATATG
29778010 GTTGCTTTCACACCTCGCTTTCTT
1 GTTGCTTTCACACCTCGCTTTCTT
29778034 GTTGCTTTCACACCTCGCTTTCT
1 GTTGCTTTCACACCTCGCTTTCT
29778057 CATGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.13, T:0.45
Consensus pattern (24 bp):
GTTGCTTTCACACCTCGCTTTCTT
Found at i:29784972 original size:25 final size:25
Alignment explanation
Indices: 29784938--29784988 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29784928 TTCCTTATAA
**
29784938 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
29784963 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
29784988 A
1 A
29784989 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:29784987 original size:12 final size:12
Alignment explanation
Indices: 29784941--29784988 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
29784931 CTTATAAACT
29784941 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
29784953 TTCTATTAGGACT
1 TTAAATTAGGA-A
29784966 TTAAATTAGGAA
1 TTAAATTAGGAA
*
29784978 TTAGATTAGGA
1 TTAAATTAGGA
29784989 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:29787613 original size:38 final size:38
Alignment explanation
Indices: 29787558--29787637 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
29787548 TAGTTACAAA
*
29787558 AAATTTTAAATAATTATATGTAGGATGATAAAAGAAAT
1 AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
*
29787596 AAATTATAAATAGTTATATGTAGGATGATAAAAGAAAT
1 AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
29787634 AAAT
1 AAAT
29787638 GATTCAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.33
Consensus pattern (38 bp):
AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
Found at i:29799460 original size:18 final size:18
Alignment explanation
Indices: 29799437--29799479 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29799427 AAATAATTAC
29799437 GTAAGC-AATGAATGCTTA
1 GTAAGCTAA-GAATGCTTA
*
29799455 GTAAGCTCAGAATGCTTA
1 GTAAGCTAAGAATGCTTA
29799473 GTAAGCT
1 GTAAGCT
29799480 CATATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (18 bp):
GTAAGCTAAGAATGCTTA
Found at i:29799480 original size:18 final size:18
Alignment explanation
Indices: 29799446--29799481 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29799436 CGTAAGCAAT
29799446 GAATGCTTAGTAAGCTCA
1 GAATGCTTAGTAAGCTCA
29799464 GAATGCTTAGTAAGCTCA
1 GAATGCTTAGTAAGCTCA
29799482 TATAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
GAATGCTTAGTAAGCTCA
Found at i:29800187 original size:35 final size:35
Alignment explanation
Indices: 29800125--29800206 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
29800115 AATCTAACTG
29800125 AAACACACCAGATGCTCATAAGAGCTAATCCATCCC
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATCCC
* **
29800161 AAACACACCAATGCTCATAAGGGCTAATCCATCTG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCC
29800196 AAACACACCAA
1 AAACACACCAA
29800207 AACATAGAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
35 33 0.77
36 10 0.23
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATCCC
Found at i:29801556 original size:28 final size:29
Alignment explanation
Indices: 29801501--29801557 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
29801491 TACAAGGGTT
*
29801501 TTCACATGACCAAGCACACGCCTGTGTCC
1 TTCACACGACCAAGCACACGCCTGTGTCC
*
29801530 TTCACACGACCTAGACACAC-CC-GTGTCC
1 TTCACACGACCAAG-CACACGCCTGTGTCC
29801558 AAAAACCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 14 0.56
30 5 0.20
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (29 bp):
TTCACACGACCAAGCACACGCCTGTGTCC
Found at i:29804340 original size:12 final size:12
Alignment explanation
Indices: 29804323--29804354 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29804313 ATATAACTTT
29804323 AATATTTATTAA
1 AATATTTATTAA
*
29804335 AATATTTATTAC
1 AATATTTATTAA
29804347 AATATTTA
1 AATATTTA
29804355 CAGCTCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
AATATTTATTAA
Found at i:29806526 original size:16 final size:17
Alignment explanation
Indices: 29806505--29806574 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 17
29806495 TTTGGTTCAC
*
29806505 TGTAATGGAATAAG-GT
1 TGTAATTGAATAAGAGT
29806521 TGTAATTGAAT-AGAGT
1 TGTAATTGAATAAGAGT
*
29806537 TGTAATTGAAT-AGAGC
1 TGTAATTGAATAAGAGT
* *
29806553 TGTAATAGAAT-AGAGC
1 TGTAATTGAATAAGAGT
29806569 TGTAAT
1 TGTAAT
29806575 AAGTAATTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
15 2 0.04
16 48 0.96
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (17 bp):
TGTAATTGAATAAGAGT
Found at i:29806548 original size:32 final size:32
Alignment explanation
Indices: 29806504--29806574 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
29806494 GTTTGGTTCA
* *
29806504 CTGTAATGGAATA-AGGTTGTAATTGAATAGAG
1 CTGTAATGGAATAGA-GCTGTAATAGAATAGAG
* *
29806536 TTGTAATTGAATAGAGCTGTAATAGAATAGAG
1 CTGTAATGGAATAGAGCTGTAATAGAATAGAG
29806568 CTGTAAT
1 CTGTAAT
29806575 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.32
Consensus pattern (32 bp):
CTGTAATGGAATAGAGCTGTAATAGAATAGAG
Found at i:29806575 original size:16 final size:16
Alignment explanation
Indices: 29806521--29806575 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
29806511 GGAATAAGGT
* *
29806521 TGTAATTGAATAGAGT
1 TGTAATAGAATAGAGC
*
29806537 TGTAATTGAATAGAGC
1 TGTAATAGAATAGAGC
29806553 TGTAATAGAATAGAGC
1 TGTAATAGAATAGAGC
29806569 TGTAATA
1 TGTAATA
29806576 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (16 bp):
TGTAATAGAATAGAGC
Found at i:29806645 original size:44 final size:46
Alignment explanation
Indices: 29806560--29806649 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
29806550 AGCTGTAATA
*
29806560 GAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
***
29806606 GAATAGAACTGTAAT-AGT-ATTCTTTTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
29806650 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 23 0.57
45 3 0.08
46 14 0.35
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (46 bp):
GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:29807259 original size:18 final size:18
Alignment explanation
Indices: 29807236--29807271 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29807226 ACGTGGTAGT
29807236 CCAACTAGATTTTAAGTA
1 CCAACTAGATTTTAAGTA
29807254 CCAACTAGATTTTAAGTA
1 CCAACTAGATTTTAAGTA
29807272 TATCTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
CCAACTAGATTTTAAGTA
Found at i:29807355 original size:40 final size:40
Alignment explanation
Indices: 29807278--29807355 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
29807268 AGTATATCTG
* *
29807278 TTAATACATACTTCATCCGGTTAAATTATACAGTTTTCTA
1 TTAATACATACTTCATCCGGCTAAATTATACAATTTTCTA
*
29807318 TTAATACATACTTCATCCGGCTAAATTATATAATTTTC
1 TTAATACATACTTCATCCGGCTAAATTATACAATTTTC
29807356 ACGCAAATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (40 bp):
TTAATACATACTTCATCCGGCTAAATTATACAATTTTCTA
Found at i:29809260 original size:17 final size:16
Alignment explanation
Indices: 29809240--29809298 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
29809230 ATATTTAATG
29809240 ATATAATATAT-AAAT
1 ATATAATATATAAAAT
*
29809255 ATAT-ATTTATAAGAAT
1 ATATAATATATAA-AAT
29809271 A-ATAATTATATAAAA-
1 ATATAA-TATATAAAAT
*
29809286 ATATAAAATATAA
1 ATATAATATATAA
29809299 TGGTTTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 5 0.14
15 14 0.39
16 11 0.31
17 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATAATATATAAAAT
Found at i:29809606 original size:23 final size:23
Alignment explanation
Indices: 29809592--29809709 Score: 71
Period size: 26 Copynumber: 4.7 Consensus size: 23
29809582 AAATGACATA
29809592 ATAATATAAAATAAATATAATAT
1 ATAATATAAAATAAATATAATAT
* *
29809615 ATAATATAAAAGTATGTATGTGAA-A-
1 ATAATATAAAA-TA--AATAT-AATAT
29809640 ATAATATATAATATATAA-ATAATAT
1 ATAATATA-AA-ATA-AATATAATAT
29809665 GAGTAATATATAAAATAATTATATAATAT
1 -A-T-A-ATATAAAATAA--ATATAATAT
29809694 ATAATATAAAAATAAA
1 ATAATAT-AAAATAAA
29809710 AATGAAGCAA
Statistics
Matches: 74, Mismatches: 5, Indels: 31
0.67 0.05 0.28
Matches are distributed among these distances:
23 13 0.18
24 5 0.07
25 13 0.18
26 18 0.24
27 8 0.11
28 5 0.07
29 12 0.16
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (23 bp):
ATAATATAAAATAAATATAATAT
Found at i:29809616 original size:7 final size:7
Alignment explanation
Indices: 29809589--29809701 Score: 63
Period size: 7 Copynumber: 17.1 Consensus size: 7
29809579 ATAAAATGAC
29809589 ATAATAAT
1 ATAAT-AT
29809597 ATAA-A-
1 ATAATAT
29809602 ATAA-AT
1 ATAATAT
29809608 ATAATAT
1 ATAATAT
29809615 ATAATAT
1 ATAATAT
29809622 A-AA-AGT
1 ATAATA-T
*
29809628 AT-GTAT
1 ATAATAT
*
29809634 GTGAA-A-
1 AT-AATAT
29809640 ATAATAT
1 ATAATAT
29809647 ATAATAT
1 ATAATAT
29809654 AT-A-A-
1 ATAATAT
29809658 ATAATAT
1 ATAATAT
29809665 GAGTAATAT
1 -A-TAATAT
29809674 ATAA-A-
1 ATAATAT
29809679 ATAATTAT
1 ATAA-TAT
29809687 ATAATAT
1 ATAATAT
29809694 ATAATAT
1 ATAATAT
29809701 A
1 A
29809702 AAAATAAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 35
0.68 0.03 0.28
Matches are distributed among these distances:
4 2 0.02
5 14 0.17
6 16 0.19
7 36 0.43
8 10 0.12
9 6 0.07
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:29809616 original size:18 final size:19
Alignment explanation
Indices: 29809589--29809702 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 19
29809579 ATAAAATGAC
29809589 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
* *
29809608 ATAATATATAATATAAAAGT
1 ATAATATATAAAATAATA-T
* *
29809628 AT-GTATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
29809647 ATAATATAT-AAATAATAT
1 ATAATATATAAAATAATAT
29809665 GAGTAATATATAAAATAATTAT
1 -A-TAATATATAAAATAA-TAT
*
29809687 ATAATATATAATATAA
1 ATAATATATAAAATAA
29809703 AAATAAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
18 19 0.24
19 14 0.18
20 36 0.46
21 7 0.09
22 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:29809673 original size:20 final size:18
Alignment explanation
Indices: 29809561--29809702 Score: 96
Period size: 20 Copynumber: 7.4 Consensus size: 18
29809551 CAATATATAG
*
29809561 ATAAA-AATATTTAATAGT
1 ATAAATAATATATAATA-T
29809579 ATAAAATGACATA-ATAATAT
1 AT-AAAT-A-ATATATAATAT
29809599 A-AAATAA-ATATAATAT
1 ATAAATAATATATAATAT
* *
29809615 ATAATATAAAAGTAT-GTAT
1 ATAA-ATAATA-TATAATAT
*
29809634 GTGAAAATAATATATAATAT
1 AT--AAATAATATATAATAT
29809654 ATAAATAATATGAGTAATAT
1 ATAAATAATAT-A-TAATAT
29809674 ATAAAATAATTATATAATAT
1 AT-AAATAA-TATATAATAT
29809694 ATAATATAA
1 ATAA-ATAA
29809703 AAATAAAAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 32
0.73 0.04 0.23
Matches are distributed among these distances:
15 1 0.01
16 9 0.09
17 3 0.03
18 19 0.19
19 14 0.14
20 34 0.34
21 15 0.15
22 6 0.06
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (18 bp):
ATAAATAATATATAATAT
Found at i:29809708 original size:18 final size:18
Alignment explanation
Indices: 29809589--29809694 Score: 76
Period size: 18 Copynumber: 5.8 Consensus size: 18
29809579 ATAAAATGAC
* *
29809589 ATAATAATATAAAATAAAT
1 ATAAT-ATATAATATAAAA
29809608 ATAATATATAATAT--AA
1 ATAATATATAATATAAAA
* * * *
29809624 A-AGTATGT-ATGTGAAA
1 ATAATATATAATATAAAA
*
29809640 ATAATATATAATATATAA
1 ATAATATATAATATAAAA
29809658 ATAATATGAGTAATATATAAA
1 ATAATAT-A-TAATATA-AAA
29809679 ATAATTATATAATATA
1 ATAA-TATATAATATA
29809695 TAATATAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 3 0.04
15 5 0.07
16 5 0.07
17 5 0.07
18 20 0.29
19 6 0.09
20 14 0.21
21 7 0.10
22 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
ATAATATATAATATAAAA
Found at i:29810120 original size:18 final size:19
Alignment explanation
Indices: 29810093--29810201 Score: 100
Period size: 20 Copynumber: 5.6 Consensus size: 19
29810083 ATTTAATGAC
29810093 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
*
29810112 ATAATATATAATATGAA-AGT
1 ATAATATATAAAAT-AATA-T
* *
29810132 AT-GTATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
29810151 ATAATATAT-AAATAATAT
1 ATAATATATAAAATAATAT
29810169 GAGTAATATATAAAATAATCAT
1 -A-TAATATATAAAATAAT-AT
29810191 ATAATATATAA
1 ATAATATATAA
29810202 TTTAAAAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
18 17 0.23
19 18 0.24
20 30 0.40
21 8 0.11
22 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:29810149 original size:504 final size:507
Alignment explanation
Indices: 29809583--29810555 Score: 1880
Period size: 507 Copynumber: 1.9 Consensus size: 507
29809573 AATAGTATAA
29809583 AATGACATAATAATATAAAATAAATATAATATATAATATAAAAGTATGTATGTGAAAATAATATA
1 AATGACATAATAATATAAAATAAATATAATATATAATATAAAAGTATGTATGTGAAAATAATATA
*
29809648 TAATATATAAATAATATGAGTAATATATAAAATAATTATATAATATATAATAT-AAAAATAAAAA
66 TAATATATAAATAATATGAGTAATATATAAAATAATCATATAATATATAATATAAAAAATAAAAA
29809712 TGAAGCAAATAACAATAAAAATTTATATTTATATAATAATAGAAATAAATATATAGGGTTAAATT
131 TGAAGCAAATAACAATAAAAATTTATATTTATATAATAATAGAAATAAATATATAGGGTTAAATT
29809777 TGAAGTTTAATAAAATTACAGGGGCGAATTTAAAAAAAAAAACTGAATTAAGGT-C-AATTAAAA
196 TGAAGTTTAATAAAATTACAGGGGCGAATTTAAAAAAAAAAACTGAATTAAGGTCCTAATTAAAA
29809840 CACGCGTAAAACAAAAGGGACTCATTGGGCAAATCGCCCTATTCCCAAAACAACAGCGTTTTCCC
261 CACGCGTAAAACAAAAGGGACTCATTGGGCAAATCGCCCTATTCCCAAAACAACAGCGTTTTCCC
29809905 TAATGCGGTTGTAAATCACTGGGAGGGCCAAATTGAAACAGAATTAAAACATTAAAGCTAAATTA
326 TAATGCGGTTGTAAATCACTGGGAGGGCCAAATTGAAACAGAATTAAAACATTAAAGCTAAATTA
*
29809970 AAAAATAAATAAAATTAAATTAAAAATATAAAAATTGCGAGAGGACCAATTGGGCAATTAACCCA
391 AAAAATAAATAAAATGAAATTAAAAATATAAAAATTGCGAGAGGACCAATTGGGCAATTAACCCA
29810035 TTTCATGAAAACACAAACTTTTAATGATAACAATACGTAGATAAAAATATTT
456 TTTCATGAAAACACAAACTTTTAATGATAACAATACGTAGATAAAAATATTT
*
29810087 AATGACATAATAATATAAAATAAATATAATATATAATATGAAAGTATGTATGTGAAAATAATATA
1 AATGACATAATAATATAAAATAAATATAATATATAATATAAAAGTATGTATGTGAAAATAATATA
*
29810152 TAATATATAAATAATATGAGTAATATATAAAATAATCATATAATATATAATTTAAAAAATAAAAA
66 TAATATATAAATAATATGAGTAATATATAAAATAATCATATAATATATAATATAAAAAATAAAAA
29810217 TGAAGCAAATAACAATAAAAATTTATATTTATATAATAATAGAAATAAATATATAGGGTTAAATT
131 TGAAGCAAATAACAATAAAAATTTATATTTATATAATAATAGAAATAAATATATAGGGTTAAATT
29810282 TGAAGTTTAATAAAATTACAGGGGCGAATTTAAAAAAAAAAACTGAATTAAGGTCCTAATTAAAA
196 TGAAGTTTAATAAAATTACAGGGGCGAATTTAAAAAAAAAAACTGAATTAAGGTCCTAATTAAAA
29810347 CACGCGTAAAACAAAAGGGACTCATTGGGCAAATCGCCCTATTCCCAAAACAACAGCGTTTTCCC
261 CACGCGTAAAACAAAAGGGACTCATTGGGCAAATCGCCCTATTCCCAAAACAACAGCGTTTTCCC
*
29810412 TAATGCGGTTGTAAATCACTGGGAGGGCCAAATTGAAACAGAATTAAAACATTAAGGCTAAATTA
326 TAATGCGGTTGTAAATCACTGGGAGGGCCAAATTGAAACAGAATTAAAACATTAAAGCTAAATTA
29810477 AAAAATAAATAAAATGAAATTAAAAATATAAAAATTGCGAGAGGACCAATTGGGCAATTAACCCA
391 AAAAATAAATAAAATGAAATTAAAAATATAAAAATTGCGAGAGGACCAATTGGGCAATTAACCCA
29810542 TTTCATGAAAACAC
456 TTTCATGAAAACAC
29810556 GCGGATCCTC
Statistics
Matches: 461, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
504 115 0.25
505 130 0.28
506 1 0.00
507 215 0.47
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (507 bp):
AATGACATAATAATATAAAATAAATATAATATATAATATAAAAGTATGTATGTGAAAATAATATA
TAATATATAAATAATATGAGTAATATATAAAATAATCATATAATATATAATATAAAAAATAAAAA
TGAAGCAAATAACAATAAAAATTTATATTTATATAATAATAGAAATAAATATATAGGGTTAAATT
TGAAGTTTAATAAAATTACAGGGGCGAATTTAAAAAAAAAAACTGAATTAAGGTCCTAATTAAAA
CACGCGTAAAACAAAAGGGACTCATTGGGCAAATCGCCCTATTCCCAAAACAACAGCGTTTTCCC
TAATGCGGTTGTAAATCACTGGGAGGGCCAAATTGAAACAGAATTAAAACATTAAAGCTAAATTA
AAAAATAAATAAAATGAAATTAAAAATATAAAAATTGCGAGAGGACCAATTGGGCAATTAACCCA
TTTCATGAAAACACAAACTTTTAATGATAACAATACGTAGATAAAAATATTT
Found at i:29810156 original size:7 final size:7
Alignment explanation
Indices: 29810144--29810202 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
29810134 GTATGTGAAA
29810144 ATAATAT
1 ATAATAT
29810151 ATAATAT
1 ATAATAT
29810158 AT-A-A-
1 ATAATAT
29810162 ATAATAT
1 ATAATAT
29810169 GAGTAATAT
1 -A-TAATAT
29810178 ATAA-A-
1 ATAATAT
29810183 ATAATCAT
1 ATAAT-AT
29810191 ATAATAT
1 ATAATAT
29810198 ATAAT
1 ATAAT
29810203 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 3 0.07
7 20 0.45
8 7 0.16
9 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:29810202 original size:27 final size:27
Alignment explanation
Indices: 29810144--29810217 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
29810134 GTATGTGAAA
*
29810144 ATAATATATAATAT-ATAAATAATATG
1 ATAATATATAAAATAATAAATAATATG
*
29810170 AGTAATATATAAAATAATCATATAATAT-
1 A-TAATATATAAAATAAT-AAATAATATG
* *
29810198 ATAATTTAAAAAATAA-AAAT
1 ATAATATATAAAATAATAAAT
29810218 GAAGCAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 25 0.62
28 3 0.08
29 8 0.20
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (27 bp):
ATAATATATAAAATAATAAATAATATG
Found at i:29811122 original size:434 final size:434
Alignment explanation
Indices: 29810314--29811180 Score: 1725
Period size: 434 Copynumber: 2.0 Consensus size: 434
29810304 GGCGAATTTA
29810314 AAAAAAAAAACTGAATTAAGGTCCTAATTAAAACACGCGTAAAACAAAAGGGACTCATTGGGCAA
1 AAAAAAAAAACTGAATTAAGGTCCTAATTAAAACACGCGTAAAACAAAAGGGACTCATTGGGCAA
29810379 ATCGCCCTATTCCCAAAACAACAGCGTTTTCCCTAATGCGGTTGTAAATCACTGGGAGGGCCAAA
66 ATCGCCCTATTCCCAAAACAACAGCGTTTTCCCTAATGCGGTTGTAAATCACTGGGAGGGCCAAA
29810444 TTGAAACAGAATTAAAACATTAAGGCTAAATTAAAAAATAAATAAAATGAAATTAAAAATATAAA
131 TTGAAACAGAATTAAAACATTAAGGCTAAATTAAAAAATAAATAAAATGAAATTAAAAATATAAA
29810509 AATTGCGAGAGGACCAATTGGGCAATTAACCCATTTCATGAAAACACGCGGATCCTCCCCGGGTA
196 AATTGCGAGAGGACCAATTGGGCAATTAACCCATTTCATGAAAACACGCGGATCCTCCCCGGGTA
29810574 ATCGGGTCAACACGCGGATCCTCTGCCTAATACGGTGCCGTTTCATAGCTTATTGTTTAAACAGA
261 ATCGGGTCAACACGCGGATCCTCTGCCTAATACGGTGCCGTTTCATAGCTTATTGTTTAAACAGA
*
29810639 AACGATGTCATTTTTGCTGGATTATATAAGCTAAAACTTAAGCCTAAAACTTATTTAGCAATCAG
326 AACAATGTCATTTTTGCTGGATTATATAAGCTAAAACTTAAGCCTAAAACTTATTTAGCAATCAG
29810704 TTTAGAAGAAAAAAATCTAAAAAATCCTCTGAATAAAGAGACAT
391 TTTAGAAGAAAAAAATCTAAAAAATCCTCTGAATAAAGAGACAT
29810748 AAAAAAAAAACTGAATTAAGGTCCTAATTAAAACACGCGTAAAACAAAAGGGACTCATTGGGCAA
1 AAAAAAAAAACTGAATTAAGGTCCTAATTAAAACACGCGTAAAACAAAAGGGACTCATTGGGCAA
29810813 ATCGCCCTATTCCCAAAACAACAGCGTTTTCCCTAATGCGGTTGTAAATCACTGGGAGGGCCAAA
66 ATCGCCCTATTCCCAAAACAACAGCGTTTTCCCTAATGCGGTTGTAAATCACTGGGAGGGCCAAA
29810878 TTGAAACAGAATTAAAACATTAAGGCTAAATTAAAAAATAAATAAAATGAAATTAAAAATATAAA
131 TTGAAACAGAATTAAAACATTAAGGCTAAATTAAAAAATAAATAAAATGAAATTAAAAATATAAA
29810943 AATTGCGAGAGGACCAATTGGGCAATTAACCCATTTCATGAAAACACGCGGATCCTCCCCGGGTA
196 AATTGCGAGAGGACCAATTGGGCAATTAACCCATTTCATGAAAACACGCGGATCCTCCCCGGGTA
29811008 ATCGGGTCAACACGCGGATCCTCTGCCTAATACGGTGCCGTTTCATAGCTTATTGTTTAAACAGA
261 ATCGGGTCAACACGCGGATCCTCTGCCTAATACGGTGCCGTTTCATAGCTTATTGTTTAAACAGA
29811073 AACAATGTCATTTTTGCTGGATTATATAAGCTAAAACTTAAGCCTAAAACTTATTTAGCAATCAG
326 AACAATGTCATTTTTGCTGGATTATATAAGCTAAAACTTAAGCCTAAAACTTATTTAGCAATCAG
29811138 TTTAGAAGAAAAAAATCTAAAAAATCCTCTGAATAAAGAGACA
391 TTTAGAAGAAAAAAATCTAAAAAATCCTCTGAATAAAGAGACA
29811181 GAGGGGTTCT
Statistics
Matches: 432, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
434 432 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (434 bp):
AAAAAAAAAACTGAATTAAGGTCCTAATTAAAACACGCGTAAAACAAAAGGGACTCATTGGGCAA
ATCGCCCTATTCCCAAAACAACAGCGTTTTCCCTAATGCGGTTGTAAATCACTGGGAGGGCCAAA
TTGAAACAGAATTAAAACATTAAGGCTAAATTAAAAAATAAATAAAATGAAATTAAAAATATAAA
AATTGCGAGAGGACCAATTGGGCAATTAACCCATTTCATGAAAACACGCGGATCCTCCCCGGGTA
ATCGGGTCAACACGCGGATCCTCTGCCTAATACGGTGCCGTTTCATAGCTTATTGTTTAAACAGA
AACAATGTCATTTTTGCTGGATTATATAAGCTAAAACTTAAGCCTAAAACTTATTTAGCAATCAG
TTTAGAAGAAAAAAATCTAAAAAATCCTCTGAATAAAGAGACAT
Found at i:29818621 original size:17 final size:19
Alignment explanation
Indices: 29818599--29818644 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29818589 TAATTACAAC
29818599 ATAATTTAATAA-A-TAAA
1 ATAATTTAATAACATTAAA
*
29818616 ATAA-TTACATAACATTAAT
1 ATAATTTA-ATAACATTAAA
29818635 ATAATTTAAT
1 ATAATTTAAT
29818645 GATTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 1 0.04
19 9 0.38
20 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATTTAATAACATTAAA
Found at i:29820593 original size:21 final size:20
Alignment explanation
Indices: 29820560--29820621 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
29820550 ATTGGGTGGA
29820560 TCAGCTTTCACGAGCTTCTGT
1 TCAGCTTT-ACGAGCTTCTGT
* *
29820581 TTAGCTCTTACGAGCTTATGT
1 TCAGCT-TTACGAGCTTCTGT
*
29820602 TCAGCTTT-CGAGATTCTGT
1 TCAGCTTTACGAGCTTCTGT
29820621 T
1 T
29820622 GGCGTATTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 21 0.60
22 2 0.06
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (20 bp):
TCAGCTTTACGAGCTTCTGT
Found at i:29835459 original size:16 final size:17
Alignment explanation
Indices: 29835427--29835459 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29835417 TTTATAAGTA
*
29835427 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
29835444 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
29835460 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:29841838 original size:13 final size:13
Alignment explanation
Indices: 29841820--29841856 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29841810 GCCTGAGACA
29841820 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
29841833 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
* *
29841846 CAGCCGTGTGT
1 CGGGCGTGTGT
29841857 GACACAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.24, G:0.43, T:0.30
Consensus pattern (13 bp):
CGGGCGTGTGTCT
Found at i:29841977 original size:30 final size:30
Alignment explanation
Indices: 29841941--29841997 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
29841931 GCACGTGGTA
29841941 GTGTGAGATCATTTCGAAGGGTACACGAGC
1 GTGTGAGATCATTTCGAAGGGTACACGAGC
* *
29841971 GTGTGAGATTATTTTGAAGGGTACACG
1 GTGTGAGATCATTTCGAAGGGTACACG
29841998 GCCTGACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.28
Consensus pattern (30 bp):
GTGTGAGATCATTTCGAAGGGTACACGAGC
Found at i:29847094 original size:26 final size:25
Alignment explanation
Indices: 29847013--29847094 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
29847003 CAACTACCTA
* *
29847013 TAAATAATTCAAATAAAAT-TATATT
1 TAAAAAATTAAAATAAAATCTA-ATT
*
29847038 TAGAAAATTAAAAT--AATCTAACTT
1 TAAAAAATTAAAATAAAATCTAA-TT
*
29847062 CCTAAAAGATTAAAATAAAATCTAATT
1 --TAAAAAATTAAAATAAAATCTAATT
29847089 TAAAAA
1 TAAAAA
29847095 TAAATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 16 0.36
26 12 0.27
27 2 0.04
28 7 0.16
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAATCTAATT
Found at i:29847811 original size:29 final size:30
Alignment explanation
Indices: 29847769--29847827 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
29847759 ACTTAACAAG
29847769 CAAATGCCTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
29847798 CAAATTCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
29847828 TAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:29849012 original size:64 final size:64
Alignment explanation
Indices: 29848911--29849036 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
29848901 GGATAACTTT
** ** *
29848911 AGTCAAAAGTATAAAATGGCATGTATCAATTATTCAATAGATTAATGTGCCACATCAATAATAG
1 AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAATAG
* * *
29848975 AGTCAAAAGTATAAAATGGCACATGTCAAAAATTCAATAAATTAATGTGTCACATCAGTAAT
1 AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAAT
29849037 CTATTGGTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (64 bp):
AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAATAG
Found at i:29850646 original size:31 final size:31
Alignment explanation
Indices: 29850611--29850698 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 31
29850601 AAAGTTTTAG
29850611 TTTCACCCAATAAGTATTTTTGAAAG-TCTGA
1 TTTCA-CCAATAAGTATTTTTGAAAGTTCTGA
* * ** *
29850642 TTTCA--ACTATGTTCATTTTCAAAAGTTCTGG
1 TTTCACCAATAAG-T-ATTTTTGAAAGTTCTGA
29850673 TTTCACCTAATAAGTATTTTTGAAAG
1 TTTCACC-AATAAGTATTTTTGAAAG
29850699 CTCATCTTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 11
0.68 0.15 0.18
Matches are distributed among these distances:
28 4 0.10
29 1 0.02
30 9 0.21
31 14 0.33
32 9 0.21
33 1 0.02
34 4 0.10
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (31 bp):
TTTCACCAATAAGTATTTTTGAAAGTTCTGA
Found at i:29850875 original size:60 final size:60
Alignment explanation
Indices: 29850761--29850876 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
29850751 TTTATCCTGT
* * * ** *
29850761 TTCATTTTCAAAAGTTTTGGTTCAATCCAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAG
1 TTCATTTTCAAAAGTTCTAGTTCAATCCAGTAAGTATTTTAGAAAGACTAGTTCCGCAAG
*
29850821 TTCATTTTCAAAAGTTCTAGTTCCA-CCTAGT-AGATATTTTAGAAAGACTAGTTCCG
1 TTCATTTTCAAAAGTTCTAGTTCAATCC-AGTAAG-TATTTTAGAAAGACTAGTTCCG
29850877 TCTAGGTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (60 bp):
TTCATTTTCAAAAGTTCTAGTTCAATCCAGTAAGTATTTTAGAAAGACTAGTTCCGCAAG
Found at i:29864832 original size:71 final size:71
Alignment explanation
Indices: 29864713--29864845 Score: 221
Period size: 71 Copynumber: 1.9 Consensus size: 71
29864703 ATATTGGGAG
*
29864713 AATGGATATTATCCAAAAGAGATTAAGCATATCTTACGAGAGTAACTCATTTATAACAAGGTCAG
1 AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGTCAG
29864778 TGGACA
66 TGGACA
* * * *
29864784 AATGGATATTATCCCAAAGAGATTAAGCTTATCCTATGAGAGTCACTCATTTATAACAAGGT
1 AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGT
29864846 TATTAGACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (71 bp):
AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGTCAG
TGGACA
Found at i:29865149 original size:6 final size:6
Alignment explanation
Indices: 29865138--29865172 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
29865128 GGTTTTCTCC
29865138 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
29865173 TCATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:29865196 original size:63 final size:63
Alignment explanation
Indices: 29865093--29865223 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
29865083 AGAATTGGTG
* * *
29865093 AAATGGAGAAATAGGAAACATTTGAAAATGATTAAGGTTTTCTCCAAAATGAAAATGAAAATGA
1 AAATGGAGAAATA-GAAACATTTAAAAATGATTAAGGTTTTCTCCAAAATAAAAATAAAAATGA
29865157 AAATGGAGAAAT-GAAATCATTTAAAAATGAATGT-A-GTTTTCTCCAAAATAAAAATAAAAATG
1 AAATGGAGAAATAGAAA-CATTTAAAAATG-AT-TAAGGTTTTCTCCAAAATAAAAATAAAAATG
29865219 A
63 A
29865220 AAAT
1 AAAT
29865224 AAAAAATGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
62 4 0.07
63 41 0.67
64 15 0.25
65 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (63 bp):
AAATGGAGAAATAGAAACATTTAAAAATGATTAAGGTTTTCTCCAAAATAAAAATAAAAATGA
Found at i:29865222 original size:12 final size:13
Alignment explanation
Indices: 29865201--29865236 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29865191 AGTTTTCTCC
*
29865201 AAAATAAAAAT-A
1 AAAATGAAAATAA
29865213 AAAATGAAAATAA
1 AAAATGAAAATAA
29865226 AAAATGAAAAT
1 AAAATGAAAAT
29865237 GTCCTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAATGAAAATAA
Found at i:29868050 original size:12 final size:12
Alignment explanation
Indices: 29868006--29868053 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
29867996 TATTTAAATT
*
29868006 TTTTATTAATTA
1 TTTTATTAATAA
*
29868018 TTGTATT--TAA
1 TTTTATTAATAA
29868028 TTTTATTAATAA
1 TTTTATTAATAA
29868040 TTTTATTAATAA
1 TTTTATTAATAA
29868052 TT
1 TT
29868054 AAAATGTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 8 0.26
12 23 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TTTTATTAATAA
Found at i:29868580 original size:59 final size:59
Alignment explanation
Indices: 29868505--29868629 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 59
29868495 AGGGTTTGAA
*
29868505 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCTCACATTGGAGCCTAAAC
1 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
* * ** * *
29868564 TTTTTTTTGTCTAAGTTAGGCCTTGAACTTGAAAATTGTTCCCACATTGGAGCTTAAAC
1 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
29868623 TTTTTTT
1 TTTTTTT
29868630 CATGTCCAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (59 bp):
TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
Found at i:29871873 original size:12 final size:12
Alignment explanation
Indices: 29871856--29871890 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
29871846 GACCTTATAA
* *
29871856 TATATATGTGTG
1 TATATATATATG
29871868 TATATATATATG
1 TATATATATATG
29871880 TATATATATAT
1 TATATATATAT
29871891 AAATGCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:29871874 original size:14 final size:14
Alignment explanation
Indices: 29871855--29871891 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29871845 AGACCTTATA
* *
29871855 ATATATATGTGTGT
1 ATATATATATGTAT
29871869 ATATATATATGTAT
1 ATATATATATGTAT
29871883 ATATATATA
1 ATATATATA
29871892 AATGCAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:29876063 original size:21 final size:21
Alignment explanation
Indices: 29876037--29876076 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29876027 CATTTGGGTG
*
29876037 TTCGATGCTTTTGAGAAAACT
1 TTCGATGCTTTTGAAAAAACT
29876058 TTCGATGCTTTTGAAAAAA
1 TTCGATGCTTTTGAAAAAA
29876077 GTCTAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (21 bp):
TTCGATGCTTTTGAAAAAACT
Found at i:29878004 original size:59 final size:59
Alignment explanation
Indices: 29877941--29878114 Score: 158
Period size: 59 Copynumber: 3.1 Consensus size: 59
29877931 GATGTTGAAT
29877941 TTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCA
1 TTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCA
* * * * **
29878000 TTTTT-TTCTTCGTT-GTTTA--TT-ACTAG--C---AGTTTTA-ACT-TTAGGATGTT-GAA
1 TTTTTCTCCTT--TTCGTTTATCTTGTCT-GTTCTTTA-TTTTATAGTCTTAGGGTGTTCTCA
29878050 TTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCA
1 -TTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCA
29878110 TTTTT
1 TTTTT
29878115 TTCTTCGTTG
Statistics
Matches: 85, Mismatches: 12, Indels: 36
0.64 0.09 0.27
Matches are distributed among these distances:
50 3 0.04
51 19 0.22
52 7 0.08
53 8 0.09
54 2 0.02
55 2 0.02
56 2 0.02
57 8 0.09
58 7 0.08
59 24 0.28
60 3 0.04
ACGTcount: A:0.13, C:0.14, G:0.14, T:0.59
Consensus pattern (59 bp):
TTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCA
Found at i:29878019 original size:110 final size:110
Alignment explanation
Indices: 29877826--29878156 Score: 662
Period size: 110 Copynumber: 3.0 Consensus size: 110
29877816 TATATGTTTA
29877826 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
1 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
29877891 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
66 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
29877936 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
1 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
29878001 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
66 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
29878046 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
1 TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
29878111 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
66 TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
29878156 T
1 T
29878157 TTCGTGTTGA
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 221 1.00
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.57
Consensus pattern (110 bp):
TGAATTTTTTCTCCTTTTCGTTTATCTTGTCTGTTCTTTATTTTATAGTCTTAGGGTGTTCTCAT
TTTTTTCTTCGTTGTTTATTACTAGCAGTTTTAACTTTAGGATGT
Found at i:29878069 original size:51 final size:51
Alignment explanation
Indices: 29877904--29878070 Score: 137
Period size: 51 Copynumber: 3.1 Consensus size: 51
29877894 TTTCTTCGTT
29877904 GTTTATTACTAGCAGTTTTAACTTTAGGATGTTGAATTTTTTCTCCTTTTC
1 GTTTATTACTAGCAGTTTTAACTTTAGGATGTTGAATTTTTTCTCCTTTTC
* * * **
29877955 GTTTATCTTGTCT-GTTCTTTA-TTTTATAGTCTTAGGGTGTTCTCATTTTTT-T-CTTCGTT-
1 GTTTA--TT-ACTAG--C---AGTTTTA-ACT-TTAGGATGTT-GAATTTTTTCTCCTT--TTC
29878014 GTTTATTACTAGCAGTTTTAACTTTAGGATGTTGAATTTTTTCTCCTTTTC
1 GTTTATTACTAGCAGTTTTAACTTTAGGATGTTGAATTTTTTCTCCTTTTC
29878065 GTTTAT
1 GTTTAT
29878071 CTTGTCTGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 36
0.66 0.07 0.27
Matches are distributed among these distances:
50 9 0.10
51 21 0.24
52 6 0.07
53 8 0.09
54 2 0.02
55 2 0.02
56 2 0.02
57 8 0.09
58 6 0.07
59 15 0.17
60 9 0.10
ACGTcount: A:0.16, C:0.13, G:0.14, T:0.56
Consensus pattern (51 bp):
GTTTATTACTAGCAGTTTTAACTTTAGGATGTTGAATTTTTTCTCCTTTTC
Found at i:29880963 original size:44 final size:44
Alignment explanation
Indices: 29880875--29880965 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
29880865 ATAGGTCAAA
* **
29880875 TAATATTAAAATAACCTACACTAATAAGAGTTTAGGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAAAAAC
*
29880919 TAATATTAAAATAATCTACACTAATCAA-AGTTTAAGTGAAAAAC
1 TAATATTAAAATAACCTACACTAAT-AAGAGTTTAAGTGAAAAAC
29880963 TAA
1 TAA
29880966 AAATAGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAAAAAC
Found at i:29882139 original size:102 final size:103
Alignment explanation
Indices: 29881969--29882156 Score: 229
Period size: 102 Copynumber: 1.8 Consensus size: 103
29881959 TATCAATACA
* * * * * **
29881969 GTATCGATACTTTGTAGGTTTTGTGAGAAACATAATGCTATTTTGATATTGCTTTTAAGAAGGGG
1 GTATCGATACTTTGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAGG
29882034 TATCGA-AATTTCAAAAAATATTGACACTTAATCAAAAG
66 TATCGATAA-TTCAAAAAATATTGACACTTAATCAAAAG
* * * *
29882072 GTATCGATACTTAT-TAGGGTTTGTGA-AAACAAAATTCCACTTTGGTATCGTTTTTAAGAAAAT
1 GTATCGATACTT-TGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAG
*
29882135 GTATCGATAATTCAGAAAATAT
65 GTATCGATAATTCAAAAAATAT
29882157 CAATACTTGG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
102 45 0.63
103 25 0.35
104 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (103 bp):
GTATCGATACTTTGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAGG
TATCGATAATTCAAAAAATATTGACACTTAATCAAAAG
Found at i:29884574 original size:36 final size:37
Alignment explanation
Indices: 29884506--29884580 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
29884496 AAAGAACCAT
29884506 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
1 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
29884543 TTTACATAGTTTAGAAATACAAAAAAA-GGCCTCTCA
1 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
29884579 TT
1 TT
29884581 AAATCATTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 11 0.29
37 27 0.71
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (37 bp):
TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
Found at i:29893729 original size:25 final size:25
Alignment explanation
Indices: 29893698--29893747 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
29893688 CAGCATTGAG
**
29893698 AAAATCTGGGAAAGCATTGAGAAAA
1 AAAATCTAAGAAAGCATTGAGAAAA
29893723 AAAATCTAAGAAAGCATTGAGAAAA
1 AAAATCTAAGAAAGCATTGAGAAAA
29893748 TTTTTTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAATCTAAGAAAGCATTGAGAAAA
Found at i:29893747 original size:21 final size:21
Alignment explanation
Indices: 29893689--29893748 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
29893679 CTCCAAATTC
**
29893689 AGCATTGAGAAAATCTGGGAA
1 AGCATTGAGAAAATCTAAGAA
29893710 AGCATTGAGAAAAAAAATCTAAGAA
1 AGCATTGAG----AAAATCTAAGAA
29893735 AGCATTGAGAAAAT
1 AGCATTGAGAAAAT
29893749 TTTTTTGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 14 0.42
25 19 0.58
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (21 bp):
AGCATTGAGAAAATCTAAGAA
Found at i:29894296 original size:10 final size:10
Alignment explanation
Indices: 29894281--29894310 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29894271 GAGAGAAGAA
29894281 GAAAAAAAAT
1 GAAAAAAAAT
*
29894291 GGAAAAAAAT
1 GAAAAAAAAT
29894301 GAAAAAAAAT
1 GAAAAAAAAT
29894311 TATTTTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:29895369 original size:38 final size:37
Alignment explanation
Indices: 29895287--29895392 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 37
29895277 ACAATACATA
29895287 AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
1 AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
* * *
29895324 AGGCAGTAGACATGCTTAATATGTATTCAAT-TCAACAG
1 A-ACAGTAGACATGCTTAACATGTATTCAGTCT-AACAG
* * * *
29895362 TAACAGTAGGCATGCTGAGCATGTAATCAGT
1 -AACAGTAGACATGCTTAACATGTATTCAGT
29895393 AATACAGTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 2 0.04
38 53 0.95
39 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (37 bp):
AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
Found at i:29899870 original size:26 final size:26
Alignment explanation
Indices: 29899839--29899893 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
29899829 CTTTCATTTT
* *
29899839 CATGTTGAACATCTCTCTGCCTTCAA
1 CATGTTGAACACCTCTCTACCTTCAA
29899865 CATGTTGAACACCTCTCTACCTTCAA
1 CATGTTGAACACCTCTCTACCTTCAA
29899891 CAT
1 CAT
29899894 CTCTAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (26 bp):
CATGTTGAACACCTCTCTACCTTCAA
Found at i:29923328 original size:19 final size:20
Alignment explanation
Indices: 29923304--29923360 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
29923294 CAATGACTAA
29923304 AATGGAAATGAGAAA-AATT
1 AATGGAAATGAGAAATAATT
*
29923323 AATGG--ATGATAAATAATT
1 AATGGAAATGAGAAATAATT
*
29923341 AATAGGAAAT-AAAAATAATT
1 AAT-GGAAATGAGAAATAATT
29923361 TTATGTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 7 0.22
18 7 0.22
19 7 0.22
20 9 0.28
21 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (20 bp):
AATGGAAATGAGAAATAATT
Found at i:29926105 original size:40 final size:40
Alignment explanation
Indices: 29926061--29926173 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
29926051 GTAATTTGGT
* * *
29926061 CAAGCCACTAGTAATGCAGATAAATTGCCAGTGGTACAGA
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
* * * *
29926101 CAAGCTACCAGTAATGCAAATAAACTGCTAGTAGTGCAGA
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
* * *
29926141 AAAGCTGCCAGAAATGCAGATAAACTGCCAGTG
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTG
29926174 ATGTAAAAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (40 bp):
CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
Found at i:29938671 original size:20 final size:21
Alignment explanation
Indices: 29938633--29938672 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
29938623 CACGCCACAC
29938633 GCCCGTGCTCGCCCCCAACAT
1 GCCCGTGCTCGCCCCCAACAT
29938654 GCCCGTG-T-GCCACCCAACA
1 GCCCGTGCTCGCC-CCCAACA
29938673 GCAGCTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.12
Consensus pattern (21 bp):
GCCCGTGCTCGCCCCCAACAT
Found at i:29945990 original size:45 final size:45
Alignment explanation
Indices: 29945926--29946016 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
29945916 TGCCCGAGAG
29945926 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
1 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
29945971 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
1 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
29946016 T
1 T
29946017 TGAATAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (45 bp):
TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
Found at i:29948444 original size:20 final size:20
Alignment explanation
Indices: 29948421--29948479 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
29948411 TAAACATGGT
29948421 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
29948441 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
29948461 AAGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
29948480 TGTATTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:29948613 original size:24 final size:24
Alignment explanation
Indices: 29948529--29948674 Score: 179
Period size: 25 Copynumber: 6.0 Consensus size: 24
29948519 GGAGGAAGTG
29948529 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* *
29948553 GATAAATGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
29948578 GATATAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
29948603 TAATAGGGCTTATGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
29948627 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
29948650 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
29948675 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
23 18 0.17
24 38 0.35
25 53 0.49
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:29948673 original size:72 final size:74
Alignment explanation
Indices: 29948533--29948674 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 74
29948523 GAAGTGTAAA
* * *
29948533 AGGGCTTATGCCCCAGTTATGATAAATGGCTTATGCCCCAGTTATGATATAGGGCTTATGCCCCA
1 AGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCCCA
29948598 GTTATTAAT
66 GTTATTAAT
* * *
29948607 AGGGCTTATGCCCTAGTTATTA-AAAGGGCTT-TGCCCCAGTTATTA-AAAGAGGC-TAGGCCTC
1 AGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAG-GGCTTAGGCC-C
29948668 CAGTTAT
64 CAGTTAT
29948675 ATGATAAAGC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 8 0.13
72 24 0.40
73 8 0.13
74 20 0.33
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (74 bp):
AGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCCCA
GTTATTAAT
Found at i:29956451 original size:33 final size:34
Alignment explanation
Indices: 29956395--29956462 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
29956385 TGGTTAGATT
29956395 AAGTTAACTTTAATATATAAAATGATAAATAAAA
1 AAGTTAACTTTAATATATAAAATGATAAATAAAA
*
29956429 AAGTTAACTTTCA-ATATAAAATGATAAATAAAA
1 AAGTTAACTTTAATATATAAAATGATAAATAAAA
29956462 A
1 A
29956463 TTAAAGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (34 bp):
AAGTTAACTTTAATATATAAAATGATAAATAAAA
Found at i:29959186 original size:21 final size:21
Alignment explanation
Indices: 29959160--29959205 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
29959150 TGTTACATAG
* *
29959160 TGACTGTTTGAAAGCTGTTTC
1 TGACTGGTTGAAAGATGTTTC
29959181 TGACTGGTTGAAAGATGTTTC
1 TGACTGGTTGAAAGATGTTTC
29959202 TGAC
1 TGAC
29959206 CGTCAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (21 bp):
TGACTGGTTGAAAGATGTTTC
Found at i:29969597 original size:10 final size:10
Alignment explanation
Indices: 29969582--29969614 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
29969572 CATGGGCTTA
29969582 GGCCGTGTTG
1 GGCCGTGTTG
29969592 GGCCGTGTTG
1 GGCCGTGTTG
*
29969602 GGCCATGTTG
1 GGCCGTGTTG
29969612 GGC
1 GGC
29969615 TAAAATCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.21, G:0.48, T:0.27
Consensus pattern (10 bp):
GGCCGTGTTG
Found at i:29982203 original size:14 final size:14
Alignment explanation
Indices: 29982184--29982210 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29982174 CTGTTTTTAT
29982184 TATGTGTGAAATTC
1 TATGTGTGAAATTC
29982198 TATGTGTGAAATT
1 TATGTGTGAAATT
29982211 TTCGTGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (14 bp):
TATGTGTGAAATTC
Found at i:29982743 original size:15 final size:15
Alignment explanation
Indices: 29982723--29982752 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29982713 ATTATGAAAT
29982723 ATATGTTTTGGATTG
1 ATATGTTTTGGATTG
*
29982738 ATATGTTTTGTATTG
1 ATATGTTTTGGATTG
29982753 GAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTG
Found at i:29984728 original size:3 final size:3
Alignment explanation
Indices: 29984720--29984754 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
29984710 ACATACCTCA
* *
29984720 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
29984755 TGAGGAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:29988147 original size:24 final size:22
Alignment explanation
Indices: 29988111--29988157 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
29988101 TATATAAGAT
**
29988111 TTTTAAATAAATTTGTTTAAAA
1 TTTTAAATAAATTAATTTAAAA
29988133 TTTTAATATTAAATTAATTTAAAA
1 TTTTAA-A-TAAATTAATTTAAAA
29988157 T
1 T
29988158 ATAAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAATAAATTAATTTAAAA
Found at i:29988194 original size:21 final size:22
Alignment explanation
Indices: 29988152--29988207 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
29988142 TAAATTAATT
* *
29988152 TAAAATATAAACATAATTTTTTA
1 TAAAA-ATAAAAATAATATTTTA
29988175 TAAAAATAAAAAT-ATATTTTA
1 TAAAAATAAAAATAATATTTTA
* *
29988196 AAAAAATTAAAA
1 TAAAAATAAAAA
29988208 CAATTTAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.59
22 7 0.24
23 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAATAAAAATAATATTTTA
Found at i:29988213 original size:20 final size:21
Alignment explanation
Indices: 29988170--29988213 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29988160 AAACATAATT
* *
29988170 TTTTATAAAAATAAAAATATA
1 TTTTAAAAAAATAAAAACATA
*
29988191 TTTTAAAAAAATTAAAACA-A
1 TTTTAAAAAAATAAAAACATA
29988211 TTT
1 TTT
29988214 AACAAGCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTTAAAAAAATAAAAACATA
Found at i:29990294 original size:12 final size:12
Alignment explanation
Indices: 29990272--29990308 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
29990262 AATGATTAAT
29990272 TAAGTTCAAGTGG
1 TAAG-TCAAGTGG
29990285 TAAGTCAAGTGG
1 TAAGTCAAGTGG
29990297 TAAGTCAAGTGG
1 TAAGTCAAGTGG
29990309 CTTTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (12 bp):
TAAGTCAAGTGG
Found at i:29999155 original size:19 final size:19
Alignment explanation
Indices: 29999131--29999168 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29999121 AATTTGTCAC
29999131 TGTTATTGGAGTATGCTAA
1 TGTTATTGGAGTATGCTAA
29999150 TGTTATTGGAGTATGCTAA
1 TGTTATTGGAGTATGCTAA
29999169 GGGCTTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TGTTATTGGAGTATGCTAA
Found at i:29999504 original size:131 final size:131
Alignment explanation
Indices: 29999270--29999532 Score: 490
Period size: 131 Copynumber: 2.0 Consensus size: 131
29999260 AGGCACTTTT
*
29999270 CAATCAGCTGAAGTTGGTGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
*
29999335 GGACCGTCAGGTAGAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
29999400 G
131 G
*
29999401 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
*
29999466 GGACTGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
29999531 G
131 G
29999532 C
1 C
29999533 CTCATACATA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (131 bp):
CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
G
Found at i:30004513 original size:12 final size:12
Alignment explanation
Indices: 30004496--30004547 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
30004486 CTGTTATGAG
30004496 TAGCAA-TTCTGT
1 TAGCAAGTT-TGT
30004508 TAGCAAGTTTGT
1 TAGCAAGTTTGT
*
30004520 TAGCTAAGCTTGT
1 TAGC-AAGTTTGT
*
30004533 TAGCTAAGTCTGT
1 TAGC-AAGTTTGT
30004546 TA
1 TA
30004548 ACTAAGTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.37
13 22 0.63
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (12 bp):
TAGCAAGTTTGT
Found at i:30004555 original size:13 final size:13
Alignment explanation
Indices: 30004503--30004556 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
30004493 GAGTAGCAAT
30004503 TCTGTTAGC-AAG
1 TCTGTTAGCTAAG
*
30004515 TTTGTTAGCTAAG
1 TCTGTTAGCTAAG
30004528 -CTTGTTAGCTAAG
1 TC-TGTTAGCTAAG
*
30004541 TCTGTTAACTAAG
1 TCTGTTAGCTAAG
30004554 TCT
1 TCT
30004557 ATAAATACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.22
13 27 0.75
14 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (13 bp):
TCTGTTAGCTAAG
Done.