Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 89
Found at i:11809762 original size:17 final size:16
Alignment explanation
Indices: 11809740--11809793 Score: 69
Period size: 15 Copynumber: 3.4 Consensus size: 16
11809730 ATAAAATAAA
11809740 AGTAATTTGAAAGTTAG
1 AGTAA-TTGAAAGTTAG
11809757 AGTAATT-AAA-TTAGG
1 AGTAATTGAAAGTTA-G
11809772 AGTAATTGAAAGTTA-
1 AGTAATTGAAAGTTAG
11809787 AGTAATT
1 AGTAATT
11809794 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.09
15 18 0.53
16 5 0.15
17 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.35
Consensus pattern (16 bp):
AGTAATTGAAAGTTAG
Found at i:11809776 original size:15 final size:14
Alignment explanation
Indices: 11809753--11809799 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
11809743 AATTTGAAAG
11809753 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
11809767 TTAGGAGTAATTGAAA
1 TTA-GAGTAATT-AAA
11809783 GTTA-AGTAATTAAA
1 -TTAGAGTAATTAAA
11809797 TTA
1 TTA
11809800 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 15 0.50
16 3 0.10
17 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:11809793 original size:30 final size:32
Alignment explanation
Indices: 11809740--11809799 Score: 106
Period size: 30 Copynumber: 1.9 Consensus size: 32
11809730 ATAAAATAAA
11809740 AGTAATTTGAAAGTTAGAGTAATTAAATTAGG
1 AGTAATTTGAAAGTTAGAGTAATTAAATTAGG
11809772 AGTAA-TTGAAAGTTA-AGTAATTAAATTA
1 AGTAATTTGAAAGTTAGAGTAATTAAATTA
11809800 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 13 0.46
31 10 0.36
32 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (32 bp):
AGTAATTTGAAAGTTAGAGTAATTAAATTAGG
Found at i:11809985 original size:21 final size:21
Alignment explanation
Indices: 11809961--11810005 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11809951 TGGTTTTGAA
*
11809961 AAAATTAAAAGTTTAAATACT
1 AAAACTAAAAGTTTAAATACT
* *
11809982 AAAACTAATAGTTTAAGTACT
1 AAAACTAAAAGTTTAAATACT
11810003 AAA
1 AAA
11810006 TGCATAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (21 bp):
AAAACTAAAAGTTTAAATACT
Found at i:11812915 original size:10 final size:10
Alignment explanation
Indices: 11812900--11812928 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
11812890 CGAATTAACC
11812900 AATTTTTTAT
1 AATTTTTTAT
11812910 AATTTTTTAT
1 AATTTTTTAT
11812920 AATTTTTTA
1 AATTTTTTA
11812929 ATTAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:11815084 original size:33 final size:33
Alignment explanation
Indices: 11815042--11815107 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11815032 GAATATTGAT
11815042 ATTGCCAAGAGAGTATCGATATTCCCACTACAG
1 ATTGCCAAGAGAGTATCGATATTCCCACTACAG
11815075 ATTGCCAAGAGAGTATCGATATTCCCACTACAG
1 ATTGCCAAGAGAGTATCGATATTCCCACTACAG
11815108 TATCGATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (33 bp):
ATTGCCAAGAGAGTATCGATATTCCCACTACAG
Found at i:11816985 original size:18 final size:17
Alignment explanation
Indices: 11816948--11816979 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11816938 TTATTTAATC
11816948 TAAAATGTTACAGTTAA
1 TAAAATGTTACAGTTAA
11816965 TAAAATGTTA-AGTTA
1 TAAAATGTTACAGTTA
11816980 TAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (17 bp):
TAAAATGTTACAGTTAA
Found at i:11818475 original size:193 final size:185
Alignment explanation
Indices: 11818125--11818498 Score: 658
Period size: 193 Copynumber: 2.0 Consensus size: 185
11818115 AATTAGGTCA
*
11818125 GTTCGATAAAAAAATTAGAACCTTTTTTCTCATATACCCCCTTTTTCTCTTTAACTCGCCTCTTA
1 GTTCGATAAAAAAATTAGAACCTTTTTTCTCATATACCCCCTTTTTCTCTTTAACTCGACTCTTA
11818190 GCTTTTTTTCTATAACATAACCCAACAACCTACCAAGAATAATTTTTAGTGTCACTATCAACCAT
66 GCTTTTTTTCTATAACATAACCCAACAACCTACCAAGAATAATTTTTAGTGTCACTATCAACCAT
*
11818255 TGCCGTATGTCGATCACTATAGACAATGATACATGAATCCCAAATTTCATCTCAT
131 TGCCGTATATCGATCACTATAGACAATGATACATGAATCCCAAATTTCATCTCAT
11818310 GTTCGATAAAAAAATTAGAACCTTTTTTTCTTCATATACCCCCTTTTTTCTCTTTAACTCGACTC
1 GTTCGATAAAAAAATTAGAACC-TTTTTTC-TCATATACCCCC-TTTTTCTCTTTAACTCGACTC
11818375 TTAGCCTTTTTTTTCTATAACATAACCCAACAACCTACCAAGAAATAATTTTTAGTGTCACTATA
63 TTAG-C-TTTTTTTCTATAACATAACCCAACAACCTACCAAG-AATAATTTTTAGTGTCAC--TA
11818440 TCAACCATTGCCGTATATCGATCACTATAGACAATGATACATGAATCCCAAATTTCATC
123 TCAACCATTGCCGTATATCGATCACTATAGACAATGATACATGAATCCCAAATTTCATC
11818499 ATAAGATTTA
Statistics
Matches: 179, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
185 22 0.12
186 7 0.04
187 12 0.07
188 24 0.13
189 1 0.01
190 35 0.20
191 18 0.10
193 60 0.34
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (185 bp):
GTTCGATAAAAAAATTAGAACCTTTTTTCTCATATACCCCCTTTTTCTCTTTAACTCGACTCTTA
GCTTTTTTTCTATAACATAACCCAACAACCTACCAAGAATAATTTTTAGTGTCACTATCAACCAT
TGCCGTATATCGATCACTATAGACAATGATACATGAATCCCAAATTTCATCTCAT
Found at i:11819660 original size:48 final size:47
Alignment explanation
Indices: 11819565--11819660 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 47
11819555 ATTCGTCACG
* *
11819565 TCGACGTGACAGTTTCAATAAAAATATTTTTTATTTAAACTCGTTATC
1 TCGACGTGAAAGTTTCAATAAAAATATTTTTTATTTAAAATC-TTATC
*
11819613 TCGACGTGATAAGTTTTAATAAAATATAATTTTTTA-TTAAAAT-TTATC
1 TCGACGTGA-AAGTTTCAATAAAA-AT-ATTTTTTATTTAAAATCTTATC
11819661 ACTTCAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 14 0.33
49 12 0.29
50 8 0.19
51 8 0.19
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (47 bp):
TCGACGTGAAAGTTTCAATAAAAATATTTTTTATTTAAAATCTTATC
Found at i:11826521 original size:2 final size:2
Alignment explanation
Indices: 11826514--11826558 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11826504 TTAACATAAT
11826514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11826556 TA T
1 TA T
11826559 TTGATGTGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11831267 original size:25 final size:25
Alignment explanation
Indices: 11831233--11831298 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
11831223 TGCATTTGTT
*
11831233 TATGTTGAGAAAACAATAGCAGGCA
1 TATGTCGAGAAAACAATAGCAGGCA
11831258 TATGTCGAGAAAACAATAGCAGGCA
1 TATGTCGAGAAAACAATAGCAGGCA
11831283 TATGTCGAGAAAACAA
1 TATGTCGAGAAAACAA
11831299 GTTTAAACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (25 bp):
TATGTCGAGAAAACAATAGCAGGCA
Found at i:11831914 original size:22 final size:24
Alignment explanation
Indices: 11831870--11831923 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
11831860 AAAAACCCAG
* *
11831870 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
*
11831894 ACCGGTTTTTAT-CCGAAAAAAAAA
1 ACCGGTTTTTATACCG-GAAAAAAA
11831918 ACCGGT
1 ACCGGT
11831924 CTGGGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGAAAAAAA
Found at i:11834183 original size:21 final size:21
Alignment explanation
Indices: 11834159--11834198 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11834149 TTTATTTTAT
11834159 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
11834180 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
11834199 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:11834245 original size:32 final size:32
Alignment explanation
Indices: 11834193--11834284 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
11834183 TTTGTTTCAA
11834193 TTATCGAACTT-GAAGTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
11834224 TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
*
11834256 TTATCAAACTTGGAAGTATTTAAGTATTT
1 TTATCGAACTTGGAAGT-TTTAAGTATTT
11834285 CATTATGTGA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 11 0.19
32 36 0.62
33 11 0.19
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
Found at i:11834546 original size:21 final size:21
Alignment explanation
Indices: 11834520--11834576 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
11834510 TGGAGCATGG
*
11834520 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
11834541 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
11834562 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
11834577 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:11834789 original size:15 final size:15
Alignment explanation
Indices: 11834746--11834792 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
11834736 ACTATTAAAT
*
11834746 CGGTTTTTTTATAA-
1 CGGTTTTTTTAAAAC
*
11834760 CGGTTTTTTAAAAAAC
1 CGGTTTTTT-TAAAAC
11834776 CGGTTTTTTTAAAAC
1 CGGTTTTTTTAAAAC
11834791 CG
1 CG
11834793 AAACCGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.32
15 10 0.36
16 9 0.32
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (15 bp):
CGGTTTTTTTAAAAC
Found at i:11834895 original size:14 final size:14
Alignment explanation
Indices: 11834843--11834914 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 14
11834833 GTTAGAACCG
*
11834843 AACCGGTTATTTAT
1 AACCGGTTTTTTAT
*
11834857 AACCGGTTTTTTTTT
1 AACCGG-TTTTTTAT
*
11834872 CAAATC-GTTTTTTAT
1 --AACCGGTTTTTTAT
*
11834887 AACCGGTTTTTTAAAA
1 AACCGGTTTTTT--AT
11834903 AACCGGTTTTTT
1 AACCGGTTTTTT
11834915 TAAAACCGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 3 0.07
14 13 0.28
15 13 0.28
16 14 0.30
17 3 0.07
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (14 bp):
AACCGGTTTTTTAT
Found at i:11834898 original size:16 final size:16
Alignment explanation
Indices: 11834887--11834919 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11834877 CGTTTTTTAT
*
11834887 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTTAAA
11834903 AACCGGTTTTTTTAAA
1 AACCGGTTTTTTTAAA
11834919 A
1 A
11834920 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
AACCGGTTTTTTTAAA
Found at i:11834899 original size:130 final size:133
Alignment explanation
Indices: 11834750--11835006 Score: 477
Period size: 130 Copynumber: 2.0 Consensus size: 133
11834740 TTAAATCGGT
11834750 TTTTTTATAACGGTTTTTTAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGA
1 TTTTTTATAACGGTTTTTTAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGA
11834815 TAT-CGGCCCTCCAAACCGGTTAG-AACCGAACCGGTTA-TTTAT-AACCGGTTTTTTTTTCAAA
66 TATCCGGCCCTCCAAACCGGTTAGAAACCGAACCGGTTATTTTATAAACCGGTTTTTTTTTCAAA
11834876 TCG
131 TCG
11834879 TTTTTTATAACCGGTTTTTTAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGG
1 TTTTTTATAA-CGGTTTTTTAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGG
11834944 ATATCCGGCCCTCCAAACCGGTTAGAAACCGAACCGGTTATTTTATAAACCGGTTTTTTTTTC
65 ATATCCGGCCCTCCAAACCGGTTAGAAACCGAACCGGTTATTTTATAAACCGGTTTTTTTTTC
11835007 TATGGGAAAA
Statistics
Matches: 123, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
129 10 0.08
130 58 0.47
131 20 0.16
132 14 0.11
133 5 0.04
134 16 0.13
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (133 bp):
TTTTTTATAACGGTTTTTTAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGA
TATCCGGCCCTCCAAACCGGTTAGAAACCGAACCGGTTATTTTATAAACCGGTTTTTTTTTCAAA
TCG
Found at i:11834912 original size:30 final size:31
Alignment explanation
Indices: 11834843--11834914 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
11834833 GTTAGAACCG
* ***
11834843 AACCGGTTATTTATAACCGGTTTTTTTTTCA
1 AACCGGTTTTTTATAACCGGTTTTTTTAAAA
*
11834874 AATC-GTTTTTTATAACCGG-TTTTTTAAAA
1 AACCGGTTTTTTATAACCGGTTTTTTTAAAA
11834903 AACCGGTTTTTT
1 AACCGGTTTTTT
11834915 TAAAACCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 10 0.29
30 21 0.62
31 3 0.09
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (31 bp):
AACCGGTTTTTTATAACCGGTTTTTTTAAAA
Found at i:11834915 original size:17 final size:16
Alignment explanation
Indices: 11834887--11834919 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
11834877 CGTTTTTTAT
11834887 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
11834903 AACCGGTTTTTTTAAAA
1 AACCGG-TTTTTTAAAA
11834920 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
AACCGGTTTTTTAAAA
Found at i:11835037 original size:130 final size:129
Alignment explanation
Indices: 11834768--11835034 Score: 369
Period size: 130 Copynumber: 2.0 Consensus size: 129
11834758 AACGGTTTTT
11834768 TAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGATATCGGCCCTCCAAACCG
1 TAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGATATCGGCCCTCCAAACCG
**** * ****
11834833 GTTAGAACCGAACCGGTTATTTATAACCGGTTTTTTTTTCAAATCGTTTTTTATAACCGGTTTTT
66 GTTAGAACCGAACCGGTTATTTATAACCGGTTTTTTTTTCAAATCG-TGGAAAAAACCGGTCGGA
11834898 TAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGATATCCGGCCCTCCAAACC
1 TAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGATAT-CGGCCCTCCAAACC
*
11834963 GGTTAGAAACCGAACCGGTTATTTTATAAACCGGTTTTTTTTTC-TAT-G-GGAAAAAACCGGAT
65 GGTTAG-AACCGAACCGGTTA-TTTAT-AACCGGTTTTTTTTTCAAATCGTGGAAAAAACCGG-T
11835025 CGGA
126 CGGA
11835029 TAAAAA
1 TAAAAA
11835035 CCGATCCGGA
Statistics
Matches: 122, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
130 57 0.47
131 27 0.22
132 15 0.12
133 7 0.06
134 16 0.13
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (129 bp):
TAAAAAACCGGTTTTTTTAAAACCGAAACCGGTTACACCGGTTAGGATATCGGCCCTCCAAACCG
GTTAGAACCGAACCGGTTATTTATAACCGGTTTTTTTTTCAAATCGTGGAAAAAACCGGTCGGA
Found at i:11835040 original size:15 final size:17
Alignment explanation
Indices: 11835014--11835045 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11835004 TTCTATGGGA
11835014 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
11835030 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
11835046 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:11839323 original size:100 final size:100
Alignment explanation
Indices: 11839187--11839432 Score: 253
Period size: 100 Copynumber: 2.4 Consensus size: 100
11839177 ATATATGAGG
* * *
11839187 TATTAAACAAAAATATGGATTAACTTTGATCTAAATAGGT-TTTCAGAGACCAGATGTAACAAAA
1 TATTAAAC-AAAAT-TGGATTAATTTTGATTTAAATAGGTCTTTCA-AGACCAAATGTAACAAAA
* *
11839251 ATATTTTGATA-TTACAATATCAGACTAAATTATGATA
63 ATATTATAATATTTACAATATCAGACTAAATTATGATA
* ** * ** **
11839288 TATTAAACAAAATTGCGATTAATTTTGGTTTAAATAAATCTTTCACGTTCAAATGTAACCCAAAT
1 TATTAAACAAAATTG-GATTAATTTTGATTTAAATAGGTCTTTCAAGACCAAATGTAACAAAAAT
* * *
11839353 ATTATAATATTTATAATATTATACTAAATTATGATA
65 ATTATAATATTTACAATATCAGACTAAATTATGATA
* * *
11839389 TATTAAACAAAAATAAGAATTAATTTTAATTTAAATAGGTCTTT
1 TATTAAAC-AAAAT-TGGATTAATTTTGATTTAAATAGGTCTTT
11839433 TATAGACTGG
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
99 2 0.02
100 44 0.37
101 44 0.37
102 27 0.23
103 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (100 bp):
TATTAAACAAAATTGGATTAATTTTGATTTAAATAGGTCTTTCAAGACCAAATGTAACAAAAATA
TTATAATATTTACAATATCAGACTAAATTATGATA
Found at i:11839332 original size:101 final size:100
Alignment explanation
Indices: 11839187--11839400 Score: 234
Period size: 101 Copynumber: 2.1 Consensus size: 100
11839177 ATATATGAGG
** *
11839187 TATTAAACAAAAATATGGATTAACTTTGATCTAAATAGGTTTTCAGAGACCAGATGTAACAAAAA
1 TATTAAAC-AAAATATGGATTAACTTTGATCTAAATAAATTTTCA-AGACCAAATGTAACAAAAA
* *
11839252 TATTTTGATA-TTACAATATCAGACTAAATTATGATA
64 TATTATAATATTTACAATATCAGACTAAATTATGATA
* * * * ** **
11839288 TATTAAACAAAAT-TGCGATTAATTTTGGTTTAAATAAATCTTTCACGTTCAAATGTAACCCAAA
1 TATTAAACAAAATATG-GATTAACTTTGATCTAAATAAAT-TTTCAAGACCAAATGTAACAAAAA
* * *
11839352 TATTATAATATTTATAATATTATACTAAATTATGATA
64 TATTATAATATTTACAATATCAGACTAAATTATGATA
11839389 TATTAAACAAAA
1 TATTAAACAAAA
11839401 ATAAGAATTA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
99 2 0.02
100 44 0.47
101 48 0.51
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (100 bp):
TATTAAACAAAATATGGATTAACTTTGATCTAAATAAATTTTCAAGACCAAATGTAACAAAAATA
TTATAATATTTACAATATCAGACTAAATTATGATA
Found at i:11839485 original size:15 final size:17
Alignment explanation
Indices: 11839452--11839486 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11839442 GATCTAACCC
11839452 AAATATTATAATATTAA
1 AAATATTATAATATTAA
11839469 AAATATTA-AAT-TTAA
1 AAATATTATAATATTAA
11839484 AAA
1 AAA
11839487 GTCAATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATTATAATATTAA
Found at i:11839925 original size:108 final size:108
Alignment explanation
Indices: 11839713--11839930 Score: 323
Period size: 109 Copynumber: 2.0 Consensus size: 108
11839703 TACATGAACT
* * *
11839713 TTAGGGTGCTTGCATTTGGTTACCTAATTTTTGAAACTTACAATACAGTCATCGAACTTTTAGTT
1 TTAGGGTGCTTGCATTTGGTCACCTAACTTTTAAAACTTACAATACAGTCATCGAACTTTTAGTT
* *
11839778 CGTTTTCAGTAACATCCCTCCCATTACTTGCCGTTAGTTTTTG
66 CGTTTTCAGTAACATCCCTACCATTACTTGCCATTAGTTTTTG
*
11839821 TTAGGGTGCTTGCATTCTGGTCA-TTCAACTTTTAAAACTTACAATACAGTCATCGAACTTTTAG
1 TTAGGGTGCTTGCATT-TGGTCACCT-AACTTTTAAAACTTACAATACAGTCATCGAACTTTTAG
* * *
11839885 TTCGTTTTTA-TAAGATCCCTACCGTTACTTGCCATTAGTTTTTG
64 TTCGTTTTCAGTAACATCCCTACCATTACTTGCCATTAGTTTTTG
11839929 TT
1 TT
11839931 GACGTGACAC
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
108 49 0.49
109 50 0.51
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (108 bp):
TTAGGGTGCTTGCATTTGGTCACCTAACTTTTAAAACTTACAATACAGTCATCGAACTTTTAGTT
CGTTTTCAGTAACATCCCTACCATTACTTGCCATTAGTTTTTG
Found at i:11844708 original size:21 final size:21
Alignment explanation
Indices: 11844682--11844723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11844672 TACTAATATG
11844682 GGAGTGCACAATTGCACTAAT
1 GGAGTGCACAATTGCACTAAT
** *
11844703 GGAGTGCGTATTTGCACTAAT
1 GGAGTGCACAATTGCACTAAT
11844724 ACAAAGTGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (21 bp):
GGAGTGCACAATTGCACTAAT
Found at i:11846244 original size:27 final size:27
Alignment explanation
Indices: 11846208--11846260 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
11846198 AACATATGCC
*
11846208 TTTTTTTTT-CAATTTGGTGTCTAACT
1 TTTTTTTTTCCAATTTGGTGCCTAACT
*
11846234 TTTTTTATTTCCAGTTTGGTGCCTAAC
1 TTTTTT-TTTCCAATTTGGTGCCTAAC
11846261 AGTCCGTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 14 0.61
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (27 bp):
TTTTTTTTTCCAATTTGGTGCCTAACT
Found at i:11846473 original size:15 final size:15
Alignment explanation
Indices: 11846450--11846479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11846440 TTTCTCTCCT
*
11846450 CTTCCCTCTCTTCCC
1 CTTCACTCTCTTCCC
11846465 CTTCACTCTCTTCCC
1 CTTCACTCTCTTCCC
11846480 ATGCAATCGA
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:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTCACTCTCTTCCC
Found at i:11847630 original size:20 final size:21
Alignment explanation
Indices: 11847599--11847639 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
11847589 TTAATAATTA
11847599 TTATTATTTTAATTATAAAAT
1 TTATTATTTTAATTATAAAAT
*
11847620 TTATT-TTTTAATTATTAAAT
1 TTATTATTTTAATTATAAAAT
11847640 AATGCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTATTTTAATTATAAAAT
Found at i:11849266 original size:192 final size:189
Alignment explanation
Indices: 11848891--11849271 Score: 719
Period size: 192 Copynumber: 2.0 Consensus size: 189
11848881 GCATCCTTGT
11848891 TCGCTTTATGGAAGCAATCATTTTGATTTCTAACATTAGCAAGGGTTTGCGTAGTGTGTTTATTT
1 TCGCTTTATGGAAGCAATCATTTTGATTTCTAACATTAGCAAGGGTTTGCGTAGTGTGTTTATTT
11848956 CTTTTACAGGAATTTTCGAGAAGTGTTAGGTGATCCACCTGACAGATTACCAGAAAATAGGAAAA
66 CTTTTACAGGAATTTTCGAGAAGTGTTAGGTGATCCACCTGACAGATTACCAGAAAATAGGAAAA
11849021 AACACCAAACTATTATAATTCAAGGTTCTTTTATACCTCATCAGACAAATAATCTCGAA
131 AACACCAAACTATTATAATTCAAGGTTCTTTTATACCTCATCAGACAAATAATCTCGAA
11849080 TCGCTTTATGGAAGCAATCATTTTGATTTCTAACATTAGCAAGGGTTTGCGTAGTGTGTTTATTT
1 TCGCTTTATGGAAGCAATCATTTTGATTTCTAACATTAGCAAGGGTTTGCGTAGTGTGTTTATTT
11849145 CTTTCTTACAGGAA-TTTCGAGAAGTGTTAGGTGATCCACCTGACAGATTACCACAGAAAATAGG
66 C-TT-TTACAGGAATTTTCGAGAAGTGTTAGGTGATCCACCTGACAGATTA-C-CAGAAAATAGG
11849209 AAAAAACACCAAACTATTATAATTCAAGGTTCTTTTATACCTCATCAGACAAATAATCTCGAA
127 AAAAAACACCAAACTATTATAATTCAAGGTTCTTTTATACCTCATCAGACAAATAATCTCGAA
11849272 GAAACCAAAG
Statistics
Matches: 188, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
189 66 0.35
190 38 0.20
191 10 0.05
192 74 0.39
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (189 bp):
TCGCTTTATGGAAGCAATCATTTTGATTTCTAACATTAGCAAGGGTTTGCGTAGTGTGTTTATTT
CTTTTACAGGAATTTTCGAGAAGTGTTAGGTGATCCACCTGACAGATTACCAGAAAATAGGAAAA
AACACCAAACTATTATAATTCAAGGTTCTTTTATACCTCATCAGACAAATAATCTCGAA
Found at i:11850160 original size:24 final size:24
Alignment explanation
Indices: 11850133--11850194 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 24
11850123 GGAGAGAATG
11850133 AATGATACATGCTTCAGAGTCCAA
1 AATGATACATGCTTCAGAGTCCAA
*
11850157 AATGATAATGCATGCTTCAGATTCCAA
1 AATGAT-A--CATGCTTCAGAGTCCAA
11850184 AATGATA-ATGC
1 AATGATACATGC
11850195 ATGCTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 4 0.12
24 6 0.18
25 1 0.03
26 1 0.03
27 22 0.65
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
AATGATACATGCTTCAGAGTCCAA
Found at i:11850173 original size:27 final size:27
Alignment explanation
Indices: 11850140--11850201 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
11850130 ATGAATGATA
11850140 CATGCTTCAGAGTCCAAAATGATAATG
1 CATGCTTCAGAGTCCAAAATGATAATG
*
11850167 CATGCTTCAGATTCCAAAATGATAATG
1 CATGCTTCAGAGTCCAAAATGATAATG
11850194 CATGCTTC
1 CATGCTTC
11850202 TTTGGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (27 bp):
CATGCTTCAGAGTCCAAAATGATAATG
Found at i:11851935 original size:71 final size:71
Alignment explanation
Indices: 11851826--11852022 Score: 253
Period size: 71 Copynumber: 2.8 Consensus size: 71
11851816 TAAAACATCT
* * *
11851826 TAAATCCTAATT-AACACTTAAACTATTTAAACT-AAATACCTAAAACAAAAATAATATTTAAAA
1 TAAATCCTAATTAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAA-A-TAAAAA
11851889 T-A-ATCC
64 TAATATCC
*
11851895 TAAATCCTAATTAAAATACTAAAACTA-TTAAACTAAAATACCTAAAAC-AAGATAAATAAAAAT
1 TAAATCCTAATT-AAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAATAAAAAT
11851958 AATATCC
65 AATATCC
* * *
11851965 TAAAACTTAATTAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAATATAAA
1 TAAATCCTAATTAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAAATAAA
11852023 GTATAATGTT
Statistics
Matches: 113, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
68 6 0.05
69 26 0.23
70 29 0.26
71 45 0.40
72 7 0.06
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (71 bp):
TAAATCCTAATTAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAATAAAAATA
ATATCC
Found at i:11851954 original size:23 final size:22
Alignment explanation
Indices: 11851906--11851955 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
11851896 AAATCCTAAT
* *
11851906 TAAAATACTAAAACTATTAAAC
1 TAAAATACTAAAACAAATAAAC
11851928 TAAAATACCTAAAACAAGATAAA-
1 TAAAATA-CTAAAACAA-ATAAAC
11851951 TAAAA
1 TAAAA
11851956 ATAATATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 13 0.54
24 4 0.17
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAAATACTAAAACAAATAAAC
Found at i:11855664 original size:2 final size:2
Alignment explanation
Indices: 11855616--11855644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11855606 ATGGTTTTAA
11855616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11855645 AGTTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11856688 original size:8 final size:8
Alignment explanation
Indices: 11856675--11856713 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
11856665 AAGAAAAAGA
*
11856675 GAGAGAGC
1 GAGAGAGG
11856683 GAGAGAGG
1 GAGAGAGG
*
11856691 GAGGGAGG
1 GAGAGAGG
*
11856699 GAGGGAGG
1 GAGAGAGG
11856707 GAGAGAG
1 GAGAGAG
11856714 TTGAAAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.64, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:11856689 original size:12 final size:12
Alignment explanation
Indices: 11856672--11856713 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
11856662 GGAAAGAAAA
* *
11856672 AGAGAGAGAGCG
1 AGAGAGGGAGGG
11856684 AGAGAGGGAGGG
1 AGAGAGGGAGGG
*
11856696 AGGGAGGGAGGG
1 AGAGAGGGAGGG
11856708 AGAGAG
1 AGAGAG
11856714 TTGAAAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.62, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGGG
Found at i:11861205 original size:42 final size:42
Alignment explanation
Indices: 11861144--11861264 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 42
11861134 ATCTGGCCGA
* *
11861144 AAAGAATATCTCACTTGGCTTTCCCGTGAAGGGGAGTAATCC
1 AAAGAATATCTCACATGGCTTTCCCATGAAGGGGAGTAATCC
* *
11861186 GAAGAATATCTCACATGGCTTTCCCATGAAGGGGAGTCATCC
1 AAAGAATATCTCACATGGCTTTCCCATGAAGGGGAGTAATCC
** *
11861228 AAAGAGCATCTCACCTGG-TTTAGACCCATGAAGGGGA
1 AAAGAATATCTCACATGGCTTT---CCCATGAAGGGGA
11861265 ACCACTTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.04
42 52 0.76
44 13 0.19
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (42 bp):
AAAGAATATCTCACATGGCTTTCCCATGAAGGGGAGTAATCC
Found at i:11861958 original size:202 final size:201
Alignment explanation
Indices: 11861605--11861967 Score: 453
Period size: 202 Copynumber: 1.8 Consensus size: 201
11861595 CTCATCCTAG
* ** *
11861605 ATTTTGACATAGCTTAAATCGAGAAGAGATATCCGTCGACCATCGCTTTCAAGTTTAATTCCACT
1 ATTTTGACATAGCTTAAATCAAGAAGAGATATCCGTCGACCAAAGCTTTCAAGTTCAATTCCACT
* * ** *
11861670 CAACTCGAGAGCACATTAACTGCATGGTAGCAACAATGAACTATTTTAAGGTCAAAATTCAAACC
66 CAACTCGAGAGCACATTAACCGCATGGTAGCAACAAGGAACTACCTTAAGGTCAAAATTCAAAAC
* *
11861735 GAGGTCTTTAGGTCAAGAAGAAGACCCCAAATGGGTTCTGATTTAGCAATAAAGAACTATTTCCC
131 GAGGTCTTTAAGTCAAGAAGAA-AACCCAAATGGGTTCTGATTTAGCAATAAAGAACTATTTCCC
11861800 AACTCAT
195 AACTCAT
* * *
11861807 ATTTTGACATAGCTTAATTCAAGAAGAGTTATATGC-T-GACCAAAGCTTTCAAGTTCGATTCCA
1 ATTTTGACATAGCTTAAATCAAGAAGAG--ATATCCGTCGACCAAAGCTTTCAAGTTCAATTCCA
* * * * * * **
11861870 CTCAGCTCGAGAGCACATTGACCGCTTGGTTGCAACGAGGAATTACCTTCTGGTCAAAATTCAAA
64 CTCAACTCGAGAGCACATTAACCGCATGGTAGCAACAAGGAACTACCTTAAGGTCAAAATTCAAA
* *
11861935 AGGAGGT-TTTCAAGTCTAGAAGAAAACCCAAAT
129 ACGAGGTCTTT-AAGTCAAGAAGAAAACCCAAAT
11861968 CGACTGCAAT
Statistics
Matches: 134, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
201 11 0.08
202 117 0.87
203 1 0.01
204 5 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (201 bp):
ATTTTGACATAGCTTAAATCAAGAAGAGATATCCGTCGACCAAAGCTTTCAAGTTCAATTCCACT
CAACTCGAGAGCACATTAACCGCATGGTAGCAACAAGGAACTACCTTAAGGTCAAAATTCAAAAC
GAGGTCTTTAAGTCAAGAAGAAAACCCAAATGGGTTCTGATTTAGCAATAAAGAACTATTTCCCA
ACTCAT
Found at i:11862059 original size:26 final size:26
Alignment explanation
Indices: 11862023--11862081 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
11862013 GACATAGCTT
11862023 AAATCAAGAAGAGTTATTTGTGGACC
1 AAATCAAGAAGAGTTATTTGTGGACC
11862049 AAATCAAGAAGAGTTATTTGTGGACC
1 AAATCAAGAAGAGTTATTTGTGGACC
11862075 AAATCAA
1 AAATCAA
11862082 CTATTTGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (26 bp):
AAATCAAGAAGAGTTATTTGTGGACC
Found at i:11870671 original size:19 final size:19
Alignment explanation
Indices: 11870647--11870703 Score: 98
Period size: 18 Copynumber: 3.1 Consensus size: 19
11870637 TTCCATCCAT
*
11870647 TTTCATCTTCTTTGAACTC
1 TTTCATTTTCTTTGAACTC
11870666 TTTCATTTTCTTTGAACT-
1 TTTCATTTTCTTTGAACTC
11870684 TTTCATTTTCTTTGAACTC
1 TTTCATTTTCTTTGAACTC
11870703 T
1 T
11870704 AAGCTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 18 0.50
19 18 0.50
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTCATTTTCTTTGAACTC
Found at i:11870712 original size:37 final size:35
Alignment explanation
Indices: 11870645--11870722 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 35
11870635 ATTTCCATCC
**
11870645 ATTTTCATCTTCTTTGAACTCTTTCATTTTCTTTGA
1 ATTTTCATCTTCTTTGAACTCTAGCATTTTCTTT-A
*
11870681 ACTTTTCATTTTCTTTGAACTCTAAGC-TTTTCTTTA
1 A-TTTTCATCTTCTTTGAACTCT-AGCATTTTCTTTA
11870717 ATTTTC
1 ATTTTC
11870723 GTTGCTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.14
36 3 0.08
37 28 0.76
38 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.05, T:0.58
Consensus pattern (35 bp):
ATTTTCATCTTCTTTGAACTCTAGCATTTTCTTTA
Found at i:11872311 original size:19 final size:20
Alignment explanation
Indices: 11872287--11872324 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11872277 ATATAAAACT
11872287 AATTATATA-CTTTATAATA
1 AATTATATAGCTTTATAATA
*
11872306 AATTATATAGGTTTATAAT
1 AATTATATAGCTTTATAAT
11872325 TTATTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
AATTATATAGCTTTATAATA
Found at i:11874552 original size:64 final size:67
Alignment explanation
Indices: 11874466--11874635 Score: 170
Period size: 64 Copynumber: 2.6 Consensus size: 67
11874456 AAAATGTATT
* * * * *
11874466 TATTATCTATTTAACTGTGAATATTAAAAGTTAAT-TATATCTTTTTAAATATCTCAAATTAA-A
1 TATTATATATTTAAATTTGAATATTAAAAGTT-ATCTATATC-ATTTAAATATCTCAAACTAATA
11874529 -ATA
64 GATA
* * * *
11874532 -A-TATATATTTAAGTTTGAATAGTAAAAGTTATCTATATCATTTGAATATTTCAAACTAATAGA
1 TATTATATATTTAAATTTGAATATTAAAAGTTATCTATATCATTTAAATATCTCAAACTAATAGA
11874595 TA
66 TA
* * *
11874597 TTATTATCTATTTAAATTTGAATATTATAAGATATCTAT
1 -TATTATATATTTAAATTTGAATATTAAAAGTTATCTAT
11874636 TTTTGAGTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
63 18 0.21
64 32 0.38
65 4 0.05
67 1 0.01
68 30 0.35
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (67 bp):
TATTATATATTTAAATTTGAATATTAAAAGTTATCTATATCATTTAAATATCTCAAACTAATAGA
TA
Found at i:11876074 original size:52 final size:52
Alignment explanation
Indices: 11876018--11876121 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
11876008 AGATTGGGCA
*
11876018 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGAATTACAACTAATTACAAGG
1 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGAATTACAACCAATTACAAGG
* *
11876070 CACAGAAATAGGAAGCTAGCCTAGAGTTGGGGGATTACAACCAATTACAAGG
1 CACAGAAATAGGAAACTAGCCTAGAGTTGGGGAATTACAACCAATTACAAGG
11876122 ATATTATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.18
Consensus pattern (52 bp):
CACAGAAATAGGAAACTAGCCTAGAGTTGGGGAATTACAACCAATTACAAGG
Found at i:11880598 original size:52 final size:52
Alignment explanation
Indices: 11880542--11880641 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
11880532 TAGGCACACA
11880542 GAAATAAGAAACTAGCATAGAGTTGGGGAATTACAACTAATTACAAGGCACG
1 GAAATAAGAAACTAGCATAGAGTTGGGGAATTACAACTAATTACAAGGCACG
* * * *
11880594 GAAATAGGAAGCTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
1 GAAATAAGAAACTAGCATAGAGTTGGGGAATTACAACTAATTACAAGG
11880642 ATATTATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (52 bp):
GAAATAAGAAACTAGCATAGAGTTGGGGAATTACAACTAATTACAAGGCACG
Found at i:11882243 original size:34 final size:33
Alignment explanation
Indices: 11882204--11882308 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 33
11882194 AACTTTAAAC
11882204 ATTAAAAGATAATTATATCATTTGAATATTTTAT
1 ATTAAAA-ATAATTATATCATTTGAATATTTTAT
* *
11882238 ATT-AAAATAA-TAT-TTATTT-AA-ATTTAAAT
1 ATTAAAAATAATTATATCATTTGAATATTT-TAT
* * *
11882267 AGT-AAAATATATCTATATCTTTTGAATATTTTAA
1 ATTAAAAATA-AT-TATATCATTTGAATATTTTAT
11882301 ATTAAAAA
1 ATTAAAAA
11882309 ATCATACGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
28 4 0.07
29 12 0.22
30 6 0.11
31 3 0.05
32 7 0.13
33 7 0.13
34 8 0.15
35 8 0.15
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (33 bp):
ATTAAAAATAATTATATCATTTGAATATTTTAT
Found at i:11882339 original size:34 final size:32
Alignment explanation
Indices: 11882252--11882347 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 32
11882242 AAATAATATT
* * *
11882252 TATTTAAATTTAAATAGTAAAATATATCTATA
1 TATTTAAATTTAAATATTAAAAAATATCGATA
* *
11882284 TCTTTTGAATATTTTAA-ATTAAAAAATCATACGATA
1 T-ATTT-AA-ATTTAAATATTAAAAAAT-AT-CGATA
11882320 TATTTAAATTTAAATATTAAAAAATATC
1 TATTTAAATTTAAATATTAAAAAATATC
11882348 TATTTTAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
32 2 0.04
33 11 0.22
34 22 0.43
35 11 0.22
36 5 0.10
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (32 bp):
TATTTAAATTTAAATATTAAAAAATATCGATA
Found at i:11882347 original size:68 final size:63
Alignment explanation
Indices: 11882189--11882350 Score: 184
Period size: 63 Copynumber: 2.5 Consensus size: 63
11882179 ATTTATTATC
* * * *
11882189 TATTTAACTTTAAACATTAAAAGATAAT-TATATCATTTGAATATTTTATATTAAAATAATATT
1 TATTTAAATTTAAATATTAAAAAAT-ATCTATATCATTTGAATATTTTAAATTAAAATAATATT
* * *
11882252 TATTTAAATTTAAATAGTAAAATATATCTATATCTTTTGAATATTTTAAATTAAAA-AATCATAC
1 TATTTAAATTTAAATATTAAAAAATATCTATATCATTTGAATATTTTAAATTAAAATAAT-AT--
11882316 GAT
63 --T
11882319 ATATTTAAATTTAAATATTAAAAAATATCTAT
1 -TATTTAAATTTAAATATTAAAAAATATCTAT
11882351 TTTAAGTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
62 5 0.06
63 49 0.58
67 1 0.01
68 29 0.35
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (63 bp):
TATTTAAATTTAAATATTAAAAAATATCTATATCATTTGAATATTTTAAATTAAAATAATATT
Found at i:11884015 original size:3 final size:3
Alignment explanation
Indices: 11884007--11884054 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
11883997 ATTTCATTTA
11884007 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11884055 GCTATAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11884695 original size:6 final size:6
Alignment explanation
Indices: 11884684--11884729 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
11884674 CATAAATCAA
11884684 AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGT
1 AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGT
11884730 CAGGTAGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (6 bp):
AGGTTT
Found at i:11886131 original size:31 final size:32
Alignment explanation
Indices: 11886096--11886180 Score: 145
Period size: 31 Copynumber: 2.7 Consensus size: 32
11886086 TCATACCTAA
11886096 TGTTTACTTTTTGTTTCATTTTAGTA-CTCGG
1 TGTTTACTTTTTGTTTCATTTTAGTACCTCGG
*
11886127 TGTTTACTTTTTGTTTCATTTTAGTACCTCGT
1 TGTTTACTTTTTGTTTCATTTTAGTACCTCGG
*
11886159 TGTTAACTTTTTGTTTCATTTT
1 TGTTTACTTTTTGTTTCATTTT
11886181 GGAACCTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (32 bp):
TGTTTACTTTTTGTTTCATTTTAGTACCTCGG
Found at i:11887481 original size:41 final size:40
Alignment explanation
Indices: 11887443--11887820 Score: 296
Period size: 40 Copynumber: 9.2 Consensus size: 40
11887433 CATTTTTTGA
*
11887443 ACAAACGCCGGTAAATACTCGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATACT-GTACTTTAGTGGCGTTTTTAT
* * * * *
11887484 ATAAACACCGCTAAATATTATACTTTAGTGGCATTTTTATATAT
1 ACAAACGCCGCTAAATACTGTACTTTAGTGGC--GTTT-T-TAT
* * * *
11887528 AAAAAACGCCGCTAAATACTGTACTTTAATGGCATTTTAAGCT
1 -ACAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTTA--T
* * * * *
11887571 -CAAACGCTGCTAAAGACTCCTACTTTAGTGGCATTTGTAT
1 ACAAACGCCGCTAAATACT-GTACTTTAGTGGCGTTTTTAT
* * * *
11887611 A-TAACGCCGCTAAATACTATACTTTAGTGGCGTTTTAAGC
1 ACAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTTA-T
* * * * *
11887651 ACAAACACCGCTAAATACTCATACTTTAGTAGAGTTTTTGT
1 ACAAACGCCGCTAAATACT-GTACTTTAGTGGCGTTTTTAT
* * * *
11887692 ATAAAC-CCGTTAAATATTGTACTTTAGTGGC-ATTTTAT
1 ACAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTTAT
* * ***
11887730 ACAAACACCGCTAAAGACTAGTACTTTAGTGATTTTTTTAT
1 ACAAACGCCGCTAAATACT-GTACTTTAGTGGCGTTTTTAT
* * *
11887771 ACAAACGCCGCTAAAGAATGTACTTTGGTGGCGTTTTTAT
1 ACAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTTAT
11887811 ACAAACGCCG
1 ACAAACGCCG
11887821 TAATAGGACA
Statistics
Matches: 266, Mismatches: 56, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
38 10 0.04
39 35 0.13
40 76 0.29
41 74 0.28
42 36 0.14
43 5 0.02
44 3 0.01
45 27 0.10
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (40 bp):
ACAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTTAT
Found at i:11887635 original size:81 final size:82
Alignment explanation
Indices: 11887531--11887807 Score: 282
Period size: 81 Copynumber: 3.4 Consensus size: 82
11887521 TATATATAAA
* * * * *
11887531 AAACGCCGCTAAATACTGTACTTTAATGGCATTTTAAGCTCAAACGCTGCTAAAGACTCCTACTT
1 AAACGCCGCTAAATACTGTACTTTAGTGGCATTTTAAGCACAAACACCGCTAAAGACTCATACTT
11887596 TAGT-G-GCATTTGTAT
66 TAGTAGAGCATTTGTAT
* * *
11887611 ATAACGCCGCTAAATACTATACTTTAGTGGCGTTTTAAGCACAAACACCGCTAAATACTCATACT
1 A-AACGCCGCTAAATACTGTACTTTAGTGGCATTTTAAGCACAAACACCGCTAAAGACTCATACT
**
11887676 TTAGTAGAGTTTTTGTAT
65 TTAGTAGAGCATTTGTAT
* * *
11887694 AAAC-CCGTTAAATATTGTACTTTAGTGGCATTTT-A-TACAAACACCGCTAAAGACT-AGTACT
1 AAACGCCGCTAAATACTGTACTTTAGTGGCATTTTAAGCACAAACACCGCTAAAGACTCA-TACT
** *
11887755 TTAGT-GA-TTTTTTTAT
65 TTAGTAGAGCATTTGTAT
* * * *
11887771 ACAAACGCCGCTAAAGAATGTACTTTGGTGGCGTTTT
1 --AAACGCCGCTAAATACTGTACTTTAGTGGCATTTT
11887808 TATACAAACG
Statistics
Matches: 168, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
77 8 0.05
78 3 0.02
79 31 0.18
80 27 0.16
81 86 0.51
82 4 0.02
83 9 0.05
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (82 bp):
AAACGCCGCTAAATACTGTACTTTAGTGGCATTTTAAGCACAAACACCGCTAAAGACTCATACTT
TAGTAGAGCATTTGTAT
Found at i:11888388 original size:21 final size:22
Alignment explanation
Indices: 11888348--11888394 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
11888338 TTTTTTAGAA
11888348 AAAATAAAAATAATTTAAATAC
1 AAAATAAAAATAATTTAAATAC
*
11888370 AAAATATAAAA-AA-TTAAATAT
1 AAAATA-AAAATAATTTAAATAC
11888391 AAAA
1 AAAA
11888395 AATGCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 8 0.35
23 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATAAAAATAATTTAAATAC
Found at i:11888390 original size:14 final size:14
Alignment explanation
Indices: 11888371--11888397 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11888361 TTTAAATACA
11888371 AAATATAAAAAATT
1 AAATATAAAAAATT
11888385 AAATATAAAAAAT
1 AAATATAAAAAAT
11888398 GCCAAAAATT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATAAAAAATT
Found at i:11888395 original size:22 final size:22
Alignment explanation
Indices: 11888346--11888397 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
11888336 TATTTTTTAG
11888346 AAAAAATAAAAATAATTTAAAT
1 AAAAAATAAAAATAATTTAAAT
* *
11888368 ACAAAATATAAAA-AATTAAATAT
1 AAAAAATA-AAAATAATTTAA-AT
11888391 AAAAAAT
1 AAAAAAT
11888398 GCCAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAAAATAAAAATAATTTAAAT
Found at i:11888396 original size:23 final size:22
Alignment explanation
Indices: 11888346--11888415 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
11888336 TATTTTTTAG
*
11888346 AAAAAATAAAAATAATTTAA-AT
1 AAAAAATAAAAA-AATTAAATAT
*
11888368 ACAAAATATAAAAAATTAAATAT
1 AAAAAATA-AAAAAATTAAATAT
**
11888391 AAAAAATGCCAAAAATTAAAT-T
1 AAAAAAT-AAAAAAATTAAATAT
11888413 AAA
1 AAA
11888416 TTACTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 17 0.43
23 23 0.57
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (22 bp):
AAAAAATAAAAAAATTAAATAT
Found at i:11888444 original size:21 final size:20
Alignment explanation
Indices: 11888401--11888447 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11888391 AAAAAATGCC
*
11888401 AAAAATTAAATTAAATTACT
1 AAAAATTAAAATAAATTACT
* *
11888421 AAAAATTAAAATATATATATT
1 AAAAATTAAAATAAAT-TACT
11888442 AAAAAT
1 AAAAAT
11888448 ACTAAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTAAAATAAATTACT
Found at i:11888900 original size:58 final size:58
Alignment explanation
Indices: 11888792--11888902 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 58
11888782 ATAGTTTGTG
* * *
11888792 ATTTTTTTAATTTTTATTATTTTTAATATATATTTAGAATATTAGTAATTTAATTTTT
1 ATTTTTTTAATTTTTATTATTTTAAATATAAATTTAGAATATTAGAAATTTAATTTTT
11888850 ATTTTTTTATATTTTTGA-TATTTTAAATTATAAATTATA-AAT-TTA-AAATTTAA
1 ATTTTTTTA-ATTTTT-ATTATTTTAAA-TATAAATT-TAGAATATTAGAAATTTAA
11888903 AATATTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
58 16 0.35
59 17 0.37
60 11 0.24
61 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (58 bp):
ATTTTTTTAATTTTTATTATTTTAAATATAAATTTAGAATATTAGAAATTTAATTTTT
Found at i:11891787 original size:31 final size:31
Alignment explanation
Indices: 11891749--11891811 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
11891739 GAGTCGAGGG
*
11891749 TTACCTATGTTCTACGGAACATATGGACAGT
1 TTACCTATGTTATACGGAACATATGGACAGT
** *
11891780 TTACCTATGTTATTTGGATCATATGGACAGT
1 TTACCTATGTTATACGGAACATATGGACAGT
11891811 T
1 T
11891812 ACATAGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTATACGGAACATATGGACAGT
Found at i:11892543 original size:12 final size:12
Alignment explanation
Indices: 11892526--11892593 Score: 63
Period size: 12 Copynumber: 6.0 Consensus size: 12
11892516 TTTTAACATT
11892526 CGGTACTGTTCA
1 CGGTACTGTTCA
11892538 CGGTACTGTTCA
1 CGGTACTGTTCA
* *
11892550 C--TATTGTACA
1 CGGTACTGTTCA
*
11892560 TGGTACTGTTCA
1 CGGTACTGTTCA
* *
11892572 --TTATTGTTCA
1 CGGTACTGTTCA
11892582 CGGTACTGTTCA
1 CGGTACTGTTCA
11892594 TACCTTATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
10 15 0.35
12 28 0.65
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:11892594 original size:22 final size:22
Alignment explanation
Indices: 11892532--11892594 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
11892522 CATTCGGTAC
*
11892532 TGTTCACGGTACTGTTCACTAT
1 TGTTCACGGTACTGTTCATTAT
* *
11892554 TGTACATGGTACTGTTCATTAT
1 TGTTCACGGTACTGTTCATTAT
11892576 TGTTCACGGTACTGTTCAT
1 TGTTCACGGTACTGTTCAT
11892595 ACCTTATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAT
Found at i:11897643 original size:31 final size:31
Alignment explanation
Indices: 11897605--11897664 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
11897595 GAGTCGAGGG
* *
11897605 TTACCTATGTTCTACGGAACATATGGACAAA
1 TTACCTATATTCTACAGAACATATGGACAAA
**
11897636 TTACCTATATTCTTTAGAACATATGGACA
1 TTACCTATATTCTACAGAACATATGGACA
11897665 GTTACATAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (31 bp):
TTACCTATATTCTACAGAACATATGGACAAA
Found at i:11898399 original size:22 final size:22
Alignment explanation
Indices: 11898374--11898428 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
11898364 TTTAACATTC
* *
11898374 GGTATTGTTCACTACTGTACAT
1 GGTAATGTTCACCACTGTACAT
* *
11898396 GGTACTGTTCACCACTGTTCAT
1 GGTAATGTTCACCACTGTACAT
11898418 GGTAATGTTCA
1 GGTAATGTTCA
11898429 TACCATATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (22 bp):
GGTAATGTTCACCACTGTACAT
Found at i:11899141 original size:97 final size:97
Alignment explanation
Indices: 11898975--11899181 Score: 315
Period size: 97 Copynumber: 2.1 Consensus size: 97
11898965 AAAATTAGAA
* * *
11898975 GAAGAAGAAGAAGGTGTTGATGTTACCGTTGAGAGAATGATGTTGTCGTGAGAGAAGAAAACAAG
1 GAAGAAGAAGAAGGTGTTGATGTTACCGTTGAGAGAATGATGTTATCGTGAAAGAAGAAAACAAA
* *
11899040 GTGATGTCATGAGAGATGAGGAGGATGAGGAG
66 GTGATGTCATGAGAGAGGAGGAGGAGGAGGAG
* ** * *
11899072 GAAGAAGAAGAAGGTGTTGATTTTGTCGTTGAGAGAATGATGTTATCGTGAAAGAAGATAATAAA
1 GAAGAAGAAGAAGGTGTTGATGTTACCGTTGAGAGAATGATGTTATCGTGAAAGAAGAAAACAAA
11899137 GTGATGTCATGAGAGAGGAGGAGGAGGAGGAG
66 GTGATGTCATGAGAGAGGAGGAGGAGGAGGAG
*
11899169 GAGGAAGAAGAAG
1 GAAGAAGAAGAAG
11899182 AAGAAGAAGA
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.20
Consensus pattern (97 bp):
GAAGAAGAAGAAGGTGTTGATGTTACCGTTGAGAGAATGATGTTATCGTGAAAGAAGAAAACAAA
GTGATGTCATGAGAGAGGAGGAGGAGGAGGAG
Found at i:11899267 original size:26 final size:27
Alignment explanation
Indices: 11899224--11899282 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
11899214 GAGAGGAATA
11899224 TGTTGTCGTGAGAAAAG-AGAAGAAGG
1 TGTTGTCGTGAGAAAAGAAGAAGAAGG
* **
11899250 TGTTGTCTTGAGGGAAGAAGAAGAAGG
1 TGTTGTCGTGAGAAAAGAAGAAGAAGG
11899277 TGTTGT
1 TGTTGT
11899283 TGTTACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.32, C:0.03, G:0.39, T:0.25
Consensus pattern (27 bp):
TGTTGTCGTGAGAAAAGAAGAAGAAGG
Found at i:11899341 original size:79 final size:79
Alignment explanation
Indices: 11899184--11899353 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 79
11899174 AGAAGAAGAA
* * * * * * *
11899184 GAAGAAGAAGAATGTGATGTTGTTTCTGTTGAGAGGAATATGTTGTCGTGAGAAAAGAGAAGAAG
1 GAAGAAGAAGAAGGTGATGTTGTTACTGTTGAGAGAAAGATGTTGTCATAAGAAAAGACAAGAAG
*
11899249 GTGTTGTCTTGAGG
66 GTGTTGTCGTGAGG
* * **
11899263 GAAGAAGAAGAAGGTGTTGTTGTTACTGTTTAGAGAAAGATGTTGTCATAAGTGAAGACAAG-AG
1 GAAGAAGAAGAAGGTGATGTTGTTACTGTTGAGAGAAAGATGTTGTCATAAGAAAAGACAAGAAG
11899327 TGTGCTT-TCGTGAGG
66 -GTG-TTGTCGTGAGG
*
11899342 GAGGAAGAAGAA
1 GAAGAAGAAGAA
11899354 TAAAAAGAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 2 0.03
79 72 0.95
80 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.35, T:0.27
Consensus pattern (79 bp):
GAAGAAGAAGAAGGTGATGTTGTTACTGTTGAGAGAAAGATGTTGTCATAAGAAAAGACAAGAAG
GTGTTGTCGTGAGG
Found at i:11900652 original size:30 final size:29
Alignment explanation
Indices: 11900588--11900755 Score: 117
Period size: 29 Copynumber: 5.8 Consensus size: 29
11900578 AAAGCACAAT
* *
11900588 CAGGATGAGGATATAAACCCATGAAAAAA
1 CAGGACGAGGATATAATCCCATGAAAAAA
* * * *
11900617 TAGGACATAGGATATAATCCCATGTAGAAA
1 CAGGAC-GAGGATATAATCCCATGAAAAAA
*
11900647 CAGGACGAGAATATAATCCCAT-ACAAAAA
1 CAGGACGAGGATATAATCCCATGA-AAAAA
*
11900676 CAGGACG-GGATATAATCTCAT-ACAAAAA
1 CAGGACGAGGATATAATCCCATGA-AAAAA
** * * * * * *
11900704 CAAAATGGGGATATAATCTCATGCAGAGA
1 CAGGACGAGGATATAATCCCATGAAAAAA
* * *
11900733 CAGGACGTGGATAAAATCTCATG
1 CAGGACGAGGATATAATCCCATG
11900756 CGGATGATAT
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
28 23 0.21
29 64 0.58
30 24 0.22
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (29 bp):
CAGGACGAGGATATAATCCCATGAAAAAA
Found at i:11900715 original size:29 final size:28
Alignment explanation
Indices: 11900657--11900725 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
11900647 CAGGACGAGA
* **
11900657 ATATAATCCCATACAAAAACAGGACGGG
1 ATATAATCTCATACAAAAACAAAACGGG
*
11900685 ATATAATCTCATACAAAAACAAAATGGGG
1 ATATAATCTCATACAAAAACAAAA-CGGG
11900714 ATATAATCTCAT
1 ATATAATCTCAT
11900726 GCAGAGACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 21 0.58
29 15 0.42
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (28 bp):
ATATAATCTCATACAAAAACAAAACGGG
Found at i:11900744 original size:29 final size:28
Alignment explanation
Indices: 11900626--11900756 Score: 118
Period size: 29 Copynumber: 4.6 Consensus size: 28
11900616 ATAGGACATA
* * *
11900626 GGATATAATCCCATGTAGAAACAGGACG
1 GGATATAATCTCATGCAAAAACAGGACG
* * *
11900654 AGAATATAATCCCATACAAAAACAGGACG
1 -GGATATAATCTCATGCAAAAACAGGACG
* ** *
11900683 GGATATAATCTCATACAAAAACAAAATGG
1 GGATATAATCTCATGCAAAAACAGGA-CG
* *
11900712 GGATATAATCTCATGCAGAGACAGGACG
1 GGATATAATCTCATGCAAAAACAGGACG
*
11900740 TGGATAAAATCTCATGC
1 -GGATATAATCTCATGC
11900757 GGATGATATA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 23 0.27
29 61 0.73
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.19
Consensus pattern (28 bp):
GGATATAATCTCATGCAAAAACAGGACG
Found at i:11907293 original size:29 final size:29
Alignment explanation
Indices: 11907239--11907386 Score: 181
Period size: 29 Copynumber: 5.1 Consensus size: 29
11907229 AAGCATAATT
* *
11907239 AGGATGAAGATATAATCCTATACAGAAAC
1 AGGATGAGGATATAATCCCATACAGAAAC
* * *
11907268 CGGACGAGGATATAATCCCATGCAGAAAC
1 AGGATGAGGATATAATCCCATACAGAAAC
* *
11907297 ATGATGATGATATAATCCCA-AGCAGAAAC
1 AGGATGAGGATATAATCCCATA-CAGAAAC
* *
11907326 ATGATGAGGATATAATCACATACAGAAAC
1 AGGATGAGGATATAATCCCATACAGAAAC
* *
11907355 AGGAAGAAGATATAATCCCATACAGAAAC
1 AGGATGAGGATATAATCCCATACAGAAAC
11907384 AGG
1 AGG
11907387 GCATGGATAA
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
29 100 0.99
30 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.18
Consensus pattern (29 bp):
AGGATGAGGATATAATCCCATACAGAAAC
Found at i:11907395 original size:29 final size:28
Alignment explanation
Indices: 11907247--11907406 Score: 123
Period size: 29 Copynumber: 5.5 Consensus size: 28
11907237 TTAGGATGAA
* *
11907247 GATATAATCCTATACAGAAACCGGACGA-G
1 GATATAATCCCATACAGAAACAGG--GATG
* *
11907276 GATATAATCCCATGCAGAAACA-TGATG
1 GATATAATCCCATACAGAAACAGGGATG
*
11907303 ATGATATAATCCCA-AGCAGAAACA-TGATGAG
1 --GATATAATCCCATA-CAGAAACAGGGAT--G
* *
11907334 GATATAATCACATACAGAAACAGGAAGA-A
1 GATATAATCCCATACAGAAACAGG--GATG
11907363 GATATAATCCCATACAGAAACAGGGCATG
1 GATATAATCCCATACAGAAACAGGG-ATG
*
11907392 GATAAAATCCCATAC
1 GATATAATCCCATAC
11907407 GAATGATAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 24
0.76 0.08 0.17
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 1 0.01
29 99 0.92
30 1 0.01
31 1 0.01
32 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (28 bp):
GATATAATCCCATACAGAAACAGGGATG
Found at i:11907395 original size:58 final size:58
Alignment explanation
Indices: 11907239--11907406 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 58
11907229 AAGCATAATT
* * * *
11907239 AGGATGAAGATATAATCCTATACAGAAACCGGACGA-GGATATAATCCCATGCAGAAAC
1 AGGATGAAGATATAATCCCATACAGAAACAGGGC-ATGGATATAATCCCATACAGAAAC
* * * *
11907297 ATGATGATGATATAATCCCA-AGCAGAAACA-TG-ATGAGGATATAATCACATACAGAAAC
1 AGGATGAAGATATAATCCCATA-CAGAAACAGGGCAT--GGATATAATCCCATACAGAAAC
* *
11907355 AGGAAGAAGATATAATCCCATACAGAAACAGGGCATGGATAAAATCCCATAC
1 AGGATGAAGATATAATCCCATACAGAAACAGGGCATGGATATAATCCCATAC
11907407 GAATGATAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
55 1 0.01
57 1 0.01
58 83 0.93
59 2 0.02
60 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (58 bp):
AGGATGAAGATATAATCCCATACAGAAACAGGGCATGGATATAATCCCATACAGAAAC
Found at i:11907401 original size:87 final size:86
Alignment explanation
Indices: 11907241--11907403 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 86
11907231 GCATAATTAG
* * * * *
11907241 GATGAAGATATAATCCTATACAGAAACCGGACGAGGATATAATCCCATGCAGAAACATGATGATG
1 GATGAAGATATAATCCTATACAGAAACAGGAAGAAGATATAATCCCATACAGAAACAGGATGA-G
*
11907306 ATATAATCCCAAGCAGAAACAT
65 ATAAAATCCCAAGCAGAAACAT
*
11907328 GATGAGGATATAATCAC-ATACAGAAACAGGAAGAAGATATAATCCCATACAGAAACAGGGCATG
1 GATGAAGATATAATC-CTATACAGAAACAGGAAGAAGATATAATCCCATACAGAAACA-GG-ATG
11907392 -GATAAAATCCCA
63 AGATAAAATCCCA
11907404 TACGAATGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
87 61 0.92
88 2 0.03
89 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (86 bp):
GATGAAGATATAATCCTATACAGAAACAGGAAGAAGATATAATCCCATACAGAAACAGGATGAGA
TAAAATCCCAAGCAGAAACAT
Found at i:11912709 original size:20 final size:22
Alignment explanation
Indices: 11912684--11912723 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11912674 AGTCGTATAT
11912684 AGCCG-TTGGGGA-TATTTTGG
1 AGCCGTTTGGGGATTATTTTGG
11912704 AGCCGTTTGGGGATTATTTT
1 AGCCGTTTGGGGATTATTTT
11912724 TCTACAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (22 bp):
AGCCGTTTGGGGATTATTTTGG
Found at i:11912972 original size:19 final size:20
Alignment explanation
Indices: 11912909--11912978 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
11912899 TACTATTCAT
**
11912909 TACTATTCCCACAGTATCGG
1 TACTATTCATACAGTATCGG
*
11912929 TACTATTTATACAGTATCGG
1 TACTATTCATACAGTATCGG
*
11912949 TACTATTCATACAGTA-CAG
1 TACTATTCATACAGTATCGG
11912968 TACTATTCATA
1 TACTATTCATA
11912979 AAAACATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 13 0.29
20 32 0.71
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:11913239 original size:18 final size:18
Alignment explanation
Indices: 11913192--11913249 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
11913182 ATGTTTAATG
* *
11913192 AAAAAGAAATCAATTGATA
1 AAAAAGATATCAATTG-TT
11913211 ACAAAATGATATCAATTGTT
1 A-AAAA-GATATCAATTGTT
*
11913231 AAAAAGATAACAATTGTT
1 AAAAAGATATCAATTGTT
11913249 A
1 A
11913250 CCAATTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 6 0.18
21 10 0.29
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (18 bp):
AAAAAGATATCAATTGTT
Found at i:11917168 original size:36 final size:36
Alignment explanation
Indices: 11917116--11917231 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
11917106 TACAATCTGT
*
11917116 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
* *
11917152 TCATCACCATAGTCCATCACCATTATCATGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
11917188 TCATCACTATATTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
11917223 TTATCACCA
1 TCATCACCA
11917232 ACTTCTAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 19 0.26
36 53 0.74
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.31
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:11917364 original size:63 final size:63
Alignment explanation
Indices: 11917291--11917417 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
11917281 ACAAGGCATT
11917291 CATCCATTACCACTATTGGAGGCCGAATCCATCATCACTTGAAGGATCATTCTACAACACTTC
1 CATCCATTACCACTATTGGAGGCCGAATCCATCATCACTTGAAGGATCATTCTACAACACTTC
11917354 CATCCATTACCACTATTGGAGGCCGAATCCATCATCACTTGAAGGATCATTCTACAACACTTC
1 CATCCATTACCACTATTGGAGGCCGAATCCATCATCACTTGAAGGATCATTCTACAACACTTC
11917417 C
1 C
11917418 GTAACCCTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.27
Consensus pattern (63 bp):
CATCCATTACCACTATTGGAGGCCGAATCCATCATCACTTGAAGGATCATTCTACAACACTTC
Found at i:11921333 original size:36 final size:36
Alignment explanation
Indices: 11921293--11921393 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
11921283 ACCATTTTCC
*
11921293 ATCACCATTATCACACCTATATAATCACCATAGGT-A
1 ATCACCATTATCACGCCTATATAATCACCATA-GTCA
* * *
11921329 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATAATCACCATAGTCA
*
11921365 ATCACCA-TATCACGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATAATCACCA
11921394 ACTTCTAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
35 22 0.37
36 37 0.63
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.29
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATAATCACCATAGTCA
Found at i:11922511 original size:20 final size:20
Alignment explanation
Indices: 11922481--11922545 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
11922471 TTCATTATTG
*
11922481 TTCACACAGTA-TCGATACTA
1 TTCATACAGTACT-GATACTA
*
11922501 TTTATACAGTACTGATACTA
1 TTCATACAGTACTGATACTA
11922521 TTCATACAGTAC--ATTACTA
1 TTCATACAGTACTGA-TACTA
11922540 TTCATA
1 TTCATA
11922546 AAAATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 1 0.03
19 11 0.28
20 27 0.68
21 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (20 bp):
TTCATACAGTACTGATACTA
Found at i:11923223 original size:54 final size:54
Alignment explanation
Indices: 11923136--11923517 Score: 484
Period size: 54 Copynumber: 7.1 Consensus size: 54
11923126 TATGTATTGC
*
11923136 ATTTACCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAA
1 ATTT-CCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * *
11923191 ATTTCCGTATTGTCACTATGTTTGCAACCTAAGAAA-TCATAATAAGTTTATCA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * *
11923244 ATTTCTGTATTTGCACTATGTGTACAACCTATA-AAATTCATAATAAGTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTA-AGAAATTCATAATAAGTTTATGA
* * *
11923298 ATTTTCGTATTGGCACTATGTGTGCAACCCTAA-AAATTCATAATAAGTTAATAA
1 ATTTCCGTATTGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGA
* * ** *
11923352 ATTTCCTTGTTGGTTCTCTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
** *
11923406 ATTTTTGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTCTATGA
1 ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
* * * * *
11923460 ATTTCCGTATTGCCACTATGTGTGCAATCCCACA-TAATTCATAATGAGTTTACGA
1 ATTTCCGTATTGGCACTATGTGTGCAA-CCTA-AGAAATTCATAATAAGTTTATGA
11923515 ATT
1 ATT
11923518 AATGTATCGA
Statistics
Matches: 282, Mismatches: 39, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
53 50 0.18
54 200 0.71
55 31 0.11
56 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (54 bp):
ATTTCCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
Found at i:11927505 original size:14 final size:14
Alignment explanation
Indices: 11927486--11927514 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11927476 ATTGGTGGCC
11927486 TGACATGAAAAGAG
1 TGACATGAAAAGAG
11927500 TGACATGAAAAGAG
1 TGACATGAAAAGAG
11927514 T
1 T
11927515 TATATAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.28, T:0.17
Consensus pattern (14 bp):
TGACATGAAAAGAG
Found at i:11930068 original size:54 final size:54
Alignment explanation
Indices: 11929979--11930223 Score: 294
Period size: 54 Copynumber: 4.5 Consensus size: 54
11929969 TATGTATTGC
*
11929979 ATTTACTGTATTGGCACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATAA
1 ATTTAC-GTATTGGCACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGA
* * *
11930034 ATTTTCGTATTGCCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGA
1 ATTTACGTATTGGCACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGA
* * * * *
11930088 ATTTCCGTATCGACACTATTTGTGCAACCAAAGAAATTTATAATAAGTTTATGA
1 ATTTACGTATTGGCACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGA
* * * * * *
11930142 ATTTACGTATTGGCACTATGTGTGCAACCCCACGTAATTAATAATGAGTTTGTGA
1 ATTTACGTATTGGCACTATGTGTGCAA-CCTAAGAAATTTATAATAAGTTTATGA
* * *
11930197 A-TTACTGTATCGACACTACGTGTGCAA
1 ATTTAC-GTATTGGCACTATGTGTGCAA
11930224 AACCATAGAA
Statistics
Matches: 165, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 120 0.73
55 45 0.27
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (54 bp):
ATTTACGTATTGGCACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGA
Found at i:11935122 original size:21 final size:21
Alignment explanation
Indices: 11935082--11935122 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11935072 TGTACACATG
*
11935082 TTTGTAATATGATTATATTTA
1 TTTGTAATATGATTAAATTTA
11935103 TTTGTAATAT-ATCTAAATTT
1 TTTGTAATATGAT-TAAATTT
11935123 TGATTAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTGTAATATGATTAAATTTA
Found at i:11935239 original size:29 final size:29
Alignment explanation
Indices: 11935178--11935318 Score: 167
Period size: 29 Copynumber: 4.9 Consensus size: 29
11935168 GTCATTGTAT
* **
11935178 ATGGGATTATAT-CCCTTCCTGATTCTAT
1 ATGGGATTATATCCCCATCCTGATTCTGC
* *
11935206 GTGGGATTATATCCCCATCCTGATTTTGC
1 ATGGGATTATATCCCCATCCTGATTCTGC
* *
11935235 ATGGGATTATATCCCCTTCTTGATTCTGC
1 ATGGGATTATATCCCCATCCTGATTCTGC
* * * *
11935264 ATGGGATAATATCCCCGTCATGATTCTAC
1 ATGGGATTATATCCCCATCCTGATTCTGC
*
11935293 ATGGGATAATATCCCCATCCTGATTC
1 ATGGGATTATATCCCCATCCTGATTC
11935319 CATTTTGGAT
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 11 0.11
29 86 0.89
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (29 bp):
ATGGGATTATATCCCCATCCTGATTCTGC
Found at i:11942571 original size:17 final size:17
Alignment explanation
Indices: 11942549--11942609 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
11942539 ATAAAGTTAG
11942549 TTCATTAATTAAACTAA
1 TTCATTAATTAAACTAA
* * *
11942566 TTCATTCATCAAACTAG
1 TTCATTAATTAAACTAA
* * *
11942583 TCCATTTATTAGACTAA
1 TTCATTAATTAAACTAA
*
11942600 CTC-TTAATTA
1 TTCATTAATTA
11942610 TTCCATGCAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (17 bp):
TTCATTAATTAAACTAA
Found at i:11947005 original size:18 final size:19
Alignment explanation
Indices: 11946968--11947012 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
11946958 TATGATTTCA
* *
11946968 AAAATAAAAATTAGATTTT
1 AAAATAAAAATTAAACTTT
11946987 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
11947005 ATAATAAA
1 AAAATAAA
11947013 TATCAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:11948771 original size:22 final size:21
Alignment explanation
Indices: 11948746--11948786 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
11948736 TATAAAAAAT
11948746 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
11948768 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
11948787 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:11949588 original size:27 final size:27
Alignment explanation
Indices: 11949550--11949613 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
11949540 AACTAACCCT
11949550 AAACCATATTAATTCAACAATATAAAA
1 AAACCATATTAATTCAACAATATAAAA
11949577 AAACCATATTAATTCAACAATATAAAA
1 AAACCATATTAATTCAACAATATAAAA
*
11949604 AAAACATATT
1 AAACCATATT
11949614 TAACAGTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (27 bp):
AAACCATATTAATTCAACAATATAAAA
Found at i:11952525 original size:23 final size:23
Alignment explanation
Indices: 11952462--11952531 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
11952452 ATATTAAATA
*
11952462 TTTTTTAATAATATTAAAGAATT
1 TTTTTTATTAATATTAAAGAATT
11952485 TTATTTTGGATTGAATATTAAAGAA-T
1 TT-TTTT--ATT-AATATTAAAGAATT
11952511 TTTTTTATTACATATTAAAGA
1 TTTTTTATTA-ATATTAAAGA
11952532 GTAAAAAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 1 0.02
23 15 0.37
24 4 0.10
25 4 0.10
26 5 0.12
27 12 0.29
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTTTATTAATATTAAAGAATT
Found at i:11957573 original size:44 final size:44
Alignment explanation
Indices: 11957510--11957594 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
11957500 CTTCATCTAA
*
11957510 ATTCAAAGCATTCAAAGCTGATTGTTATCATCTAAATTCAACCC
1 ATTCAAAGCATTCAAAGCTGATTGTTATCATCGAAATTCAACCC
*
11957554 ATTCAAGGCATTCAAAGCTGATTGTTATCATCGAAATTCAA
1 ATTCAAAGCATTCAAAGCTGATTGTTATCATCGAAATTCAA
11957595 GGGTTGTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (44 bp):
ATTCAAAGCATTCAAAGCTGATTGTTATCATCGAAATTCAACCC
Found at i:11958917 original size:10 final size:10
Alignment explanation
Indices: 11958902--11958957 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
11958892 CAACCCATTC
11958902 TATTT-ATTAT
1 TATTTGATT-T
*
11958912 TATTTAATTT
1 TATTTGATTT
*
11958922 TATTT-TTGTT
1 TATTTGAT-TT
11958932 TATTTGATTT
1 TATTTGATTT
11958942 TATTTGATTT
1 TATTTGATTT
11958952 TATTTG
1 TATTTG
11958958 TGTCACAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 1 0.02
10 36 0.88
11 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (10 bp):
TATTTGATTT
Found at i:11958923 original size:6 final size:5
Alignment explanation
Indices: 11958904--11958956 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
11958894 ACCCATTCTA
* * *
11958904 TTTAT TATTAT TTAAT TTTAT TTT-T GTTTAT TTGAT TTTAT TTGAT TTTAT
1 TTTAT T-TTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT
11958955 TT
1 TT
11958957 GTGTCACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 1 0.03
5 32 0.82
6 6 0.15
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:11959252 original size:3 final size:3
Alignment explanation
Indices: 11959244--11959287 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11959234 TTTAAATAAC
11959244 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11959288 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11959292 original size:3 final size:3
Alignment explanation
Indices: 11959286--11959330 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
11959276 AATAATAATA
11959286 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11959331 CTACTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11959313 original size:20 final size:20
Alignment explanation
Indices: 11959288--11959328 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11959278 TAATAATAAT
11959288 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
11959308 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
11959328 T
1 T
11959329 TACTACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATTATTATTATTA
Found at i:11963369 original size:22 final size:22
Alignment explanation
Indices: 11963344--11963392 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
11963334 TTGTAAGAGT
11963344 TTGGAAACATGTTTCTAACGAC
1 TTGGAAACATGTTTCTAACGAC
*
11963366 TTGGAAACATGTTTCTAATGAC
1 TTGGAAACATGTTTCTAACGAC
11963388 TTGGA
1 TTGGA
11963393 GCATTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (22 bp):
TTGGAAACATGTTTCTAACGAC
Found at i:11983291 original size:17 final size:18
Alignment explanation
Indices: 11983269--11983321 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
11983259 TTTTCTTTTC
11983269 TTTTTTTGTTTTTGTT-T
1 TTTTTTTGTTTTTGTTCT
*
11983286 TTTTTTTGTTTTTCTTCT
1 TTTTTTTGTTTTTGTTCT
*
11983304 TTCTTGTTGCTTTTTGTT
1 TT-TTTTTG-TTTTTGTT
11983322 GCAGCACTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.50
18 3 0.10
19 5 0.17
20 7 0.23
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTTTTGTTTTTGTTCT
Found at i:11987302 original size:12 final size:12
Alignment explanation
Indices: 11987285--11987313 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11987275 CAATAATTAT
11987285 GAATTCTTTCTA
1 GAATTCTTTCTA
11987297 GAATTCTTTCTA
1 GAATTCTTTCTA
11987309 GAATT
1 GAATT
11987314 TACCTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (12 bp):
GAATTCTTTCTA
Found at i:11999454 original size:26 final size:28
Alignment explanation
Indices: 11999424--11999483 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
11999414 CATCCTTATT
* *
11999424 TCATTTCATTTCAT-TT-CTTAATTTTA
1 TCATTTCATTTAATCTTACTTAATTTAA
*
11999450 TCATTTCATTTAATCTTACTTTATTTAA
1 TCATTTCATTTAATCTTACTTAATTTAA
11999478 TCATTT
1 TCATTT
11999484 TCCTTCCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.45
27 2 0.07
28 14 0.48
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (28 bp):
TCATTTCATTTAATCTTACTTAATTTAA
Found at i:12001409 original size:24 final size:23
Alignment explanation
Indices: 12001365--12001409 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12001355 TCAGTAATAG
* *
12001365 TAGTTTTTGTTTGTATATTTTTT
1 TAGTTTTTGATTGAATATTTTTT
12001388 TAGTTGTTTGATTGAAT-TTTTT
1 TAGTT-TTTGATTGAATATTTTT
12001410 AAATTATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (23 bp):
TAGTTTTTGATTGAATATTTTTT
Found at i:12002340 original size:14 final size:13
Alignment explanation
Indices: 12002307--12002343 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12002297 TATATATAAC
12002307 TACTAATAAAAAA
1 TACTAATAAAAAA
*
12002320 TACTAATAAAAAG
1 TACTAATAAAAAA
12002333 TACATAATAAA
1 TAC-TAATAAA
12002344 TAAAGGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (13 bp):
TACTAATAAAAAA
Found at i:12002549 original size:30 final size:30
Alignment explanation
Indices: 12002491--12002550 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
12002481 AGTTAATGTT
*
12002491 TATTAATTATTAAATTTTCTAAAGTTACAA
1 TATTAATTATTAAATTTTCTAAAATTACAA
12002521 TATT-ATTATTAAA-TTTCTAAACAATTACAA
1 TATTAATTATTAAATTTTCT-AA-AATTACAA
12002551 AATGGTCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (30 bp):
TATTAATTATTAAATTTTCTAAAATTACAA
Found at i:12005192 original size:22 final size:22
Alignment explanation
Indices: 12005162--12005241 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
12005152 GATTTCCTCC
*
12005162 TATCAGTGCTAAGGTACTTTAG
1 TATCAGTGCTAAGGAACTTTAG
* * * * **
12005184 TGTCAGTGCAAATGCACTTCCG
1 TATCAGTGCTAAGGAACTTTAG
* *
12005206 TTTCAGTGCTACGGAACTTTAG
1 TATCAGTGCTAAGGAACTTTAG
*
12005228 TATCATTGCTAAGG
1 TATCAGTGCTAAGG
12005242 CACCTCCTTT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (22 bp):
TATCAGTGCTAAGGAACTTTAG
Found at i:12011391 original size:24 final size:24
Alignment explanation
Indices: 12011364--12011409 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12011354 ACAACAAGTC
*
12011364 TTTTTT-TGCTGTTCGAAACAATA
1 TTTTTTCTACTGTTCGAAACAATA
*
12011387 TTTTTTCTACTTTTCGAAACAAT
1 TTTTTTCTACTGTTCGAAACAAT
12011410 GAACAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (24 bp):
TTTTTTCTACTGTTCGAAACAATA
Found at i:12018742 original size:17 final size:17
Alignment explanation
Indices: 12018717--12018760 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
12018707 TAGACTGTAC
*
12018717 AATAAAAATAAATAAAT
1 AATAAAAATAAAAAAAT
*
12018734 AATAGAAATAAAAAAATT
1 AATAAAAATAAAAAAA-T
12018752 AAATAAAAA
1 -AATAAAAA
12018761 AGACCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAAAATAAAAAAAT
Found at i:12019271 original size:21 final size:21
Alignment explanation
Indices: 12019187--12019261 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
12019177 AGAGTTCCCC
* *
12019187 CCGTAACTTCCATGTCCACCT
1 CCGTAACTTCCACGTCCACCA
* *
12019208 CCGTAGCTTCCACGACCACCA
1 CCGTAACTTCCACGTCCACCA
* *
12019229 CCATAGCTTCCACGTCCACCA
1 CCGTAACTTCCACGTCCACCA
12019250 CCGTAACTTCCA
1 CCGTAACTTCCA
12019262 TGTTTACCAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.45, G:0.11, T:0.21
Consensus pattern (21 bp):
CCGTAACTTCCACGTCCACCA
Found at i:12020237 original size:36 final size:36
Alignment explanation
Indices: 12020147--12020431 Score: 232
Period size: 36 Copynumber: 7.9 Consensus size: 36
12020137 AAAGGGTTTT
*
12020147 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* * *
12020184 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
12020220 TTTCAAGAGAAATTGTCTCAAGAGAGAAAAAGACACAATTTG
1 TTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAATTTG
12020262 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATCTTAG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-TT-G
* * * * *
12020299 TTCCAAAAGTAACTGTCTCAAGGGAGACGAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
12020335 TTT-AATGTA-AAACT-TATTC-A-A-AG----ATTTTG
1 TTTCAA-G-AGAAACTGT-CTCAAGAGAGACAAAATTTG
*
12020364 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
12020400 TTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
12020432 AAGAGAGACA
Statistics
Matches: 200, Mismatches: 26, Indels: 45
0.74 0.10 0.17
Matches are distributed among these distances:
29 16 0.08
30 4 0.02
31 1 0.00
32 2 0.01
33 2 0.01
35 7 0.04
36 70 0.35
37 58 0.29
38 8 0.04
40 4 0.02
41 1 0.00
42 27 0.14
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:12020282 original size:78 final size:73
Alignment explanation
Indices: 12020147--12020431 Score: 218
Period size: 65 Copynumber: 3.9 Consensus size: 73
12020137 AAAGGGTTTT
* *
12020147 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAT
1 TTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAT
12020212 AAAATTTA
66 AAAATTTA
* *
12020220 TTTCAAGAGAAATTGTCTCAAGAGAGAAAAAGACACAATTTGTTTCAAGAGAAACTGTCTCAAGA
1 TTTCAAGAGAAACTATCTCAAGAGAG-AAAA-A-AC--TTTGTTTCAAGAGAAACTGTCTCAAGA
*
12020285 GAGA-CAAATCTTA
61 GAGATAAAAT-TTA
* * * * * ** *
12020298 GTTCCAAAAGTAACTGTCTCAAGGGAGACGAAA-TTTGTTT-AATGTA-AAACT-TATTC-A-A-
1 -TTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAA-G-AGAAACTGT-CTCAAGAG
*
12020356 AGAT----TTTG
62 AGATAAAATTTA
* * * * *
12020364 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAGAT
1 TTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAT
12020428 AAAA
66 AAAA
12020432 AAGAGAGACA
Statistics
Matches: 169, Mismatches: 22, Indels: 43
0.72 0.09 0.18
Matches are distributed among these distances:
65 41 0.24
66 6 0.04
67 2 0.01
68 4 0.02
70 3 0.02
71 1 0.01
72 4 0.02
73 39 0.23
74 4 0.02
75 1 0.01
76 3 0.02
77 5 0.03
78 35 0.21
79 21 0.12
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (73 bp):
TTTCAAGAGAAACTATCTCAAGAGAGAAAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAT
AAAATTTA
Found at i:12024726 original size:14 final size:14
Alignment explanation
Indices: 12024704--12024739 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12024694 TAGACTATAT
12024704 AATAAAAATAAATA
1 AATAAAAATAAATA
*
12024718 AATAGAAATAAATA
1 AATAAAAATAAATA
12024732 AATAAAAA
1 AATAAAAA
12024740 CACCAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:12025268 original size:21 final size:21
Alignment explanation
Indices: 12025163--12025261 Score: 144
Period size: 21 Copynumber: 4.7 Consensus size: 21
12025153 AGAGTGCCCC
*
12025163 CCGTAGCTTCCATGTCCACCT
1 CCGTAGCTTCCATGTCCACCA
*
12025184 CCGTAGCTTCCATGTCCACCT
1 CCGTAGCTTCCATGTCCACCA
* *
12025205 CCGTAGCTTCCACGACCACCA
1 CCGTAGCTTCCATGTCCACCA
*
12025226 CCATAGCTTCCATGTCCACCA
1 CCGTAGCTTCCATGTCCACCA
*
12025247 CCGTAACTTCCATGT
1 CCGTAGCTTCCATGT
12025262 TTACCACTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.19, C:0.42, G:0.13, T:0.25
Consensus pattern (21 bp):
CCGTAGCTTCCATGTCCACCA
Found at i:12026255 original size:76 final size:74
Alignment explanation
Indices: 12026104--12026270 Score: 185
Period size: 76 Copynumber: 2.2 Consensus size: 74
12026094 AAAAAACAAT
* * * * * *
12026104 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAATTACCTAAAACAAAGAT
1 ATAATATCCTAAA-CTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAAAAAAAAT
12026169 AAAATATAAAA
65 AAAATAT-AAA
12026180 ATAATATCCTTAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATA-C-AAAGATAAAAA
1 ATAATATCC-TAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAA-A-AAAAA
** *
12026243 ATAATGTTTAAA
63 ATAAAATATAAA
*
12026255 ATATTATCCTAAACTT
1 ATAATATCCTAAACTT
12026271 GAGTTTAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
74 10 0.13
75 13 0.17
76 51 0.65
77 4 0.05
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (74 bp):
ATAATATCCTAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAAAAAAAATA
AAATATAAA
Found at i:12037394 original size:17 final size:18
Alignment explanation
Indices: 12037355--12037396 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
12037345 GTTGTTTTTA
*
12037355 AAATAAAAGATAACAATT
1 AAATAAAAGATAAAAATT
12037373 AAATAAAAGA-AAAAATT
1 AAATAAAAGATAAAAATT
*
12037390 TAATAAA
1 AAATAAA
12037397 TAAATTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAAAATT
Found at i:12039899 original size:14 final size:15
Alignment explanation
Indices: 12039872--12039917 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
12039862 GCATCTGATA
12039872 AAATAAAAT-AAAAT
1 AAATAAAATGAAAAT
**
12039886 AAATGGAATG-AAAT
1 AAATAAAATGAAAAT
12039900 AAATAAAATGAAAAT
1 AAATAAAATGAAAAT
12039915 AAA
1 AAA
12039918 ACGAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (15 bp):
AAATAAAATGAAAAT
Found at i:12039903 original size:4 final size:5
Alignment explanation
Indices: 12039869--12039918 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
12039859 TAAGCATCTG
** *
12039869 ATAAA ATAAA ATAAA AT-AA ATGGA ATGAA AT-AA ATAAA ATGAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
12039918 A
1 A
12039919 CGAAATGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:12042919 original size:18 final size:18
Alignment explanation
Indices: 12042898--12042940 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
12042888 GTTGTTTTTA
*
12042898 AAATAAAAGATAACAATT
1 AAATAAAAGAAAACAATT
12042916 AAATAAAAGAAAACAATT
1 AAATAAAAGAAAACAATT
12042934 AAATAAA
1 AAATAAA
12042941 TAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAACAATT
Done.