Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 53 of 109
Found at i:17269813 original size:23 final size:24
Alignment explanation
Indices: 17269778--17269822 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
17269768 AAGTTAAACC
*
17269778 TTTTTTTTATTATAAAAATGATAA
1 TTTTTATTATTATAAAAATGATAA
**
17269802 TTTTTATT-TTATTTAAATGAT
1 TTTTTATTATTATAAAAATGAT
17269823 GTGAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTTATTATTATAAAAATGATAA
Found at i:17275339 original size:18 final size:19
Alignment explanation
Indices: 17275302--17275339 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17275292 GTTTCAAACA
*
17275302 ATATGTTTAATTATTTATT
1 ATATGTTTAATTAATTATT
*
17275321 ATATG-TTATTTAATTATT
1 ATATGTTTAATTAATTATT
17275339 A
1 A
17275340 AATTAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
ATATGTTTAATTAATTATT
Found at i:17276369 original size:18 final size:18
Alignment explanation
Indices: 17276332--17276369 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17276322 ATTTATTATA
*
17276332 TAAATAATTTTATCATTT
1 TAAATAATTTTATCAGTT
17276350 TAAATATATTTTATC-GTT
1 TAAATA-ATTTTATCAGTT
17276368 TA
1 TA
17276370 CAAATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TAAATAATTTTATCAGTT
Found at i:17279666 original size:14 final size:14
Alignment explanation
Indices: 17279647--17279673 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17279637 CATATATGTA
17279647 TAATAAAAATAGTT
1 TAATAAAAATAGTT
17279661 TAATAAAAATAGT
1 TAATAAAAATAGT
17279674 ATATCCATAT
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:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
TAATAAAAATAGTT
Found at i:17280339 original size:16 final size:16
Alignment explanation
Indices: 17280318--17280359 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
17280308 CGAGACCAAA
17280318 ACGCGCGGGTCTGGCC
1 ACGCGCGGGTCTGGCC
17280334 ACGCGCGGGTCTGGCC
1 ACGCGCGGGTCTGGCC
*
17280350 ACGCTCGGGT
1 ACGCGCGGGT
17280360 TGGGTCATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.36, G:0.43, T:0.14
Consensus pattern (16 bp):
ACGCGCGGGTCTGGCC
Found at i:17281226 original size:16 final size:16
Alignment explanation
Indices: 17281202--17281244 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
17281192 CGAGACCAAA
*
17281202 ACGCGCGGGTCTGGCC
1 ACGCACGGGTCTGGCC
17281218 ACGCACGGGTCTGGCC
1 ACGCACGGGTCTGGCC
*
17281234 ACGCTCGGGTC
1 ACGCACGGGTC
17281245 AGGTCATCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.37, G:0.40, T:0.14
Consensus pattern (16 bp):
ACGCACGGGTCTGGCC
Found at i:17281734 original size:880 final size:881
Alignment explanation
Indices: 17280031--17281774 Score: 3305
Period size: 880 Copynumber: 2.0 Consensus size: 881
17280021 CAAACAAGCA
17280031 TAATAGTAAGCTAAAAAAAACAAAAGGGATTAAATCGAAGCTAAAACAGAATTACTAGGGAACAA
1 TAATAGTAAGCTAAAAAAAACAAAAGGGATTAAATCGAAGCTAAAACAGAATTACTAGGGAACAA
* *
17280096 ACATAAATAAAGCCAAACAAGGACCCATGTGCAATGCGCACACAACTTGGAGGATTAATCGGAAA
66 ACATAAATAAAGCCAAACAAGGACCCATGTGCAATGCACACACAACATGGAGGATTAATCGGAAA
* *
17280161 TATTTCCGTCCCCCTCAAAACATAACGTTTTTGCGCGGGTCAAAATGAAACCAACCAAAAATTAC
131 TATTTCCCTCCCCCTCAAAACACAACGTTTTTGCGCGGGTCAAAATGAAACCAACCAAAAATTAC
17280226 ATAGCCAGAATTAAAAAAAACCAGGGGACTAGATTGGGTTTCGGCACAAAAGAAAAAGGACTTGG
196 ATAGCCAGAATTAAAAAAAACCAGGGGACTAGATTGGGTTTCGGCACAAAAGAAAAAGGACTTGG
* *
17280291 CGTGTAAATATCCCCTCCGAGACCAAAACGCGCGGGTCTGGCCACGCGCGGGTCTGGCCACGCTC
261 CGTGCAAATATCCCCTCCGAGACCAAAACGCGCGGGTCTGGCCACGCACGGGTCTGGCCACGCTC
**
17280356 GGGTTGGGTCATCGGGTATAGGCCAATACGGTGCCGTTTTAAACCATTGAAACAAGGTTTAAACG
326 GGGTCAGGTCATCGGGTATAGGCCAATACGGTGCCGTTTTAAACCATTGAAACAAGGTTTAAACG
17280421 ACACCATTTCAATAATCAGTATAAGATTAAAAAAAACAAACCCTAAACACCCTATCCCCCTTTTA
391 ACACCATTTCAATAATCAGTATAAGATT-AAAAAAACAAACCCTAAACACCCTATCCCCCTTTTA
17280486 GCAACCAGAAAGAAAAAAAAAAAGAAAAAGACTGAAGGCCACCCCTCAGAGCGCCGTTCTGGCGA
455 GCAACCAGAAAG-AAAAAAAAAAGAAAAAGACTGAAGGCCACCCCTCAGAGCGCCGTTCTGGCGA
* *
17280551 TTCGTCACCTTCGAAGACCTCCGGTCATTGCTTCAACTTCGATGACTGCGGAGAGAGCAAAAATC
519 TTCGTCACCTTCGAAGACCTCCGATCATTGCTTCAACTCCGATGACTGCGGAGAGAGCAAAAATC
17280616 GAGCCTCCAGGTACGCTCACTCTCTCTAATCTCTCTTTTTTATTAAGAATCAAACATCCAAAACA
584 GAGCCTCCAGGTACGCTCACTCTCTCTAATCTCTCTTTTTTATTAAGAATCAAACATCCAAAACA
17280681 CACAGGAAAGAAAAAGAAAATAAAAAACAGAACAAAAACCGAAGCAAAAGTTGAATCACCTTTCG
649 CACAGGAAAGAAAAAGAAAATAAAAAACAGAACAAAAACCGAAGCAAAAGTTGAATCACCTTTCG
17280746 TATCTTTTGAAATTTCTCTGATGATTTTCTTATTTCAATATGCGTGTCTTTTTTTTTTACAAATT
714 TATCTTTTGAAATTTCTCTGATGATTTTCTTATTTCAATATGCGTGTCTTTTTTTTTTACAAATT
17280811 GAAAAATGACTTTTATATAGCCGAATCGAAAAGAAAAATAAATCAAAATACATCATTTTTCTCTA
779 GAAAAATGACTTTTATATAGCCGAATCGAAAAGAAAAATAAATCAAAATACATCATTTTTCTCTA
17280876 CCATCCTTTTATATTTTCTCAATAAGAGTAATAATAAT
844 CCATCCTTTTATATTTTCTCAATAAGAGTAATAATAAT
17280914 TAATAGTAAGCTAAAAAAAACAAAAGGGATTAAATCGAAGCTAAAACAGAATTACTAGGGAACAA
1 TAATAGTAAGCTAAAAAAAACAAAAGGGATTAAATCGAAGCTAAAACAGAATTACTAGGGAACAA
* *
17280979 ACATAAATAAAGCCAAACAAGGACCCATGTGCAATGCACGCACAACATGGAGGATTAATTGGAAA
66 ACATAAATAAAGCCAAACAAGGACCCATGTGCAATGCACACACAACATGGAGGATTAATCGGAAA
17281044 TATTTCCCTCCCCCTCAAAACACAGA-GTTTTTGCGCGGGTCAAAATGAAACCAACCAAAAATTA
131 TATTTCCCTCCCCCTCAAAACACA-ACGTTTTTGCGCGGGTCAAAATGAAACCAACCAAAAATTA
17281108 CATAGCCAGAATTAAAAAAAACCAGGGGACTAGATTGGGTTTCGGCACAAAAGAAAAAAGGACTT
195 CATAGCCAGAATTAAAAAAAACCAGGGGACTAGATTGGGTTTCGGCACAAAAG-AAAAAGGACTT
17281173 GGCGTGCAAATATCCCCTCCGAGACCAAAACGCGCGGGTCTGGCCACGCACGGGTCTGGCCACGC
259 GGCGTGCAAATATCCCCTCCGAGACCAAAACGCGCGGGTCTGGCCACGCACGGGTCTGGCCACGC
17281238 TCGGGTCAGGTCATCGGGTATAGGCCAATACGGTGCCGTTTTAAACCATTGAAACAAGGTTTAAA
324 TCGGGTCAGGTCATCGGGTATAGGCCAATACGGTGCCGTTTTAAACCATTGAAACAAGGTTTAAA
* *
17281303 CGACACCGTTTCAATAATTAGTATAAGATT-AAAAAACAAACCCTAAACACCCTATCCCCCTTTT
389 CGACACCATTTCAATAATCAGTATAAGATTAAAAAAACAAACCCTAAACACCCTATCCCCCTTTT
17281367 AGCAACCAGAAAG-AAAAAAAAAGAAAAAGACTGAAGGCCACCCCTCAGAGCGCCGTTCTGGCGA
454 AGCAACCAGAAAGAAAAAAAAAAGAAAAAGACTGAAGGCCACCCCTCAGAGCGCCGTTCTGGCGA
17281431 TTCGTCACCTTCGAAGACCTCCGATCATTGCTTCAACTCCGATGACTGCGGAGAGAGCAAAAATC
519 TTCGTCACCTTCGAAGACCTCCGATCATTGCTTCAACTCCGATGACTGCGGAGAGAGCAAAAATC
17281496 GAGCCTCCAGGTACGCTCACTCTCTCTAATCTCTCTTTTTTATTAAGAATCAAACATCCAAAACA
584 GAGCCTCCAGGTACGCTCACTCTCTCTAATCTCTCTTTTTTATTAAGAATCAAACATCCAAAACA
17281561 CACAGGAAAGAAAAAGAAAATAAAAAACAGAACAAAAACCGAAGCAAAAGTTGAATCACCTTTCG
649 CACAGGAAAGAAAAAGAAAATAAAAAACAGAACAAAAACCGAAGCAAAAGTTGAATCACCTTTCG
17281626 TATCTTTTGAAATTTCTCTGATGATTTTCTTATTTCAATATGCGTGTCTTTTTTTTTTACAAATT
714 TATCTTTTGAAATTTCTCTGATGATTTTCTTATTTCAATATGCGTGTCTTTTTTTTTTACAAATT
17281691 GAAAAATGACTTTTATATAGCCGAATCGAAAAGAAAAATAAATCAAAATACATCATTTTTCTCTA
779 GAAAAATGACTTTTATATAGCCGAATCGAAAAGAAAAATAAATCAAAATACATCATTTTTCTCTA
17281756 CCATCCTTTTATATTTTCT
844 CCATCCTTTTATATTTTCT
17281775 ATTTTTTTAC
Statistics
Matches: 845, Mismatches: 14, Indels: 7
0.98 0.02 0.01
Matches are distributed among these distances:
880 393 0.47
882 47 0.06
883 239 0.28
884 166 0.20
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (881 bp):
TAATAGTAAGCTAAAAAAAACAAAAGGGATTAAATCGAAGCTAAAACAGAATTACTAGGGAACAA
ACATAAATAAAGCCAAACAAGGACCCATGTGCAATGCACACACAACATGGAGGATTAATCGGAAA
TATTTCCCTCCCCCTCAAAACACAACGTTTTTGCGCGGGTCAAAATGAAACCAACCAAAAATTAC
ATAGCCAGAATTAAAAAAAACCAGGGGACTAGATTGGGTTTCGGCACAAAAGAAAAAGGACTTGG
CGTGCAAATATCCCCTCCGAGACCAAAACGCGCGGGTCTGGCCACGCACGGGTCTGGCCACGCTC
GGGTCAGGTCATCGGGTATAGGCCAATACGGTGCCGTTTTAAACCATTGAAACAAGGTTTAAACG
ACACCATTTCAATAATCAGTATAAGATTAAAAAAACAAACCCTAAACACCCTATCCCCCTTTTAG
CAACCAGAAAGAAAAAAAAAAGAAAAAGACTGAAGGCCACCCCTCAGAGCGCCGTTCTGGCGATT
CGTCACCTTCGAAGACCTCCGATCATTGCTTCAACTCCGATGACTGCGGAGAGAGCAAAAATCGA
GCCTCCAGGTACGCTCACTCTCTCTAATCTCTCTTTTTTATTAAGAATCAAACATCCAAAACACA
CAGGAAAGAAAAAGAAAATAAAAAACAGAACAAAAACCGAAGCAAAAGTTGAATCACCTTTCGTA
TCTTTTGAAATTTCTCTGATGATTTTCTTATTTCAATATGCGTGTCTTTTTTTTTTACAAATTGA
AAAATGACTTTTATATAGCCGAATCGAAAAGAAAAATAAATCAAAATACATCATTTTTCTCTACC
ATCCTTTTATATTTTCTCAATAAGAGTAATAATAAT
Found at i:17282018 original size:26 final size:27
Alignment explanation
Indices: 17281989--17282039 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
17281979 CCACATTAGC
*
17281989 TGGGCTAGGTTAATTGGGT-TTTGGTT
1 TGGGCTAGGTTAAGTGGGTATTTGGTT
17282015 TGGGCTAGGTTAAGTGGGTATTTGG
1 TGGGCTAGGTTAAGTGGGTATTTGG
17282040 GATCTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.14, C:0.04, G:0.41, T:0.41
Consensus pattern (27 bp):
TGGGCTAGGTTAAGTGGGTATTTGGTT
Found at i:17282156 original size:23 final size:24
Alignment explanation
Indices: 17282122--17282167 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
17282112 TTAATAACTT
17282122 TATTTTTATTTTTTATTT-ATTTA
1 TATTTTTATTTTTTATTTGATTTA
17282145 TATTTTGT-TTTTTTATTTGATTT
1 TATTTT-TATTTTTTATTTGATTT
17282168 GGGCCGGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (24 bp):
TATTTTTATTTTTTATTTGATTTA
Found at i:17282797 original size:44 final size:44
Alignment explanation
Indices: 17282745--17282861 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
17282735 TTTTAATCCG
*
17282745 CTCCACTGTAACTTCAAGGAGATAGGATTATC-GGCTTCAATATA
1 CTCCACTGTAACTTCAAGGAGATAAGATT-TCTGGCTTCAATATA
* * * *
17282789 CTCTACTGTAATCTT-AGGGAGATAAGATTTCTGGCTTCAATCTG
1 CTCCACTGTAA-CTTCAAGGAGATAAGATTTCTGGCTTCAATATA
* *
17282833 CTCCACTGTAACCTCAAGAAGATAAGATT
1 CTCCACTGTAACTTCAAGGAGATAAGATT
17282862 CACCATTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
43 4 0.07
44 54 0.89
45 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAACTTCAAGGAGATAAGATTTCTGGCTTCAATATA
Found at i:17282978 original size:233 final size:233
Alignment explanation
Indices: 17282571--17283302 Score: 1302
Period size: 233 Copynumber: 3.1 Consensus size: 233
17282561 GCTATACCGC
* * *
17282571 AGGGAGATAAGATTTCTGGCTTCAATTTGCTCCATTGTAACCTCAAGGAGATAATATTCACCATT
1 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATTCACCATT
* *
17282636 TTCGATTAGGAGTTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
66 TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
* *
17282701 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGAG
131 CTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGAG
* * *
17282766 ATAGGATTATCGGCTTCAATATACTCTACTGTAATCTT
196 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTT
*
17282804 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAAGAAGATAAGATTCACCATT
1 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATTCACCATT
*
17282869 TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTA
66 TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
*
17282934 CTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAACCTCAAGGAG
131 CTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGAG
17282999 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTT
196 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTT
*
17283037 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATT
1 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATTCACCATT
17283102 TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
66 TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
* *
17283167 TTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCATTGTAACTTCAAGGAG
131 CTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGAG
*
17283232 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTC
196 ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTT
*
17283270 AGGGAGATAAGATTTTTGGCTTCAATCTGCTCC
1 AGGGAGATAAGATTTCTGGCTTCAATCTGCTCC
17283303 CTCACTCTTG
Statistics
Matches: 478, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 478 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (233 bp):
AGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATTCACCATT
TTCGATTAGGAATTCTTCGGTCTATTCTACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
CTCTACTGTAATTTTAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAACTTCAAGGAG
ATAGGATTATCGGCTTCAATCTGCTCCACTGTAATCTT
Found at i:17283025 original size:44 final size:44
Alignment explanation
Indices: 17282972--17283094 Score: 185
Period size: 44 Copynumber: 2.8 Consensus size: 44
17282962 CCTTTATTTT
* * *
17282972 AATCCGCTCCACTGTAACCTCAAGGAGATAGGATTATC-GGCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATT-TCTGGCTTC
* *
17283016 AATCTGCTCCACTGTAATCTTAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTCTGGCTTC
17283060 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATT
17283095 CACCATTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
43 2 0.03
44 69 0.97
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACCTCAGGGAGATAAGATTTCTGGCTTC
Found at i:17283258 original size:44 final size:44
Alignment explanation
Indices: 17283205--17283302 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
17283195 CCTTTATTTT
* * *
17283205 AATCCGCTCCATTGTAA-CTTCAAGGAGATAGGATTATCGGCTTC
1 AATCTGCTCCACTGTAATC-TCAAGGAGATAAGATTATCGGCTTC
* * *
17283249 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTTGGCTTC
1 AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTATCGGCTTC
17283293 AATCTGCTCC
1 AATCTGCTCC
17283303 CTCACTCTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTATCGGCTTC
Found at i:17295780 original size:18 final size:18
Alignment explanation
Indices: 17295753--17295793 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17295743 ACGAATAATT
17295753 AATAAATACAAATAAG-C
1 AATAAATACAAATAAGAC
*
17295770 AATACAATACACATAAGAC
1 AATA-AATACAAATAAGAC
17295789 AATAA
1 AATAA
17295794 GCTCACATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAATACAAATAAGAC
Found at i:17295973 original size:14 final size:14
Alignment explanation
Indices: 17295954--17295980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17295944 CATATATGTA
17295954 TAATAAAAATAGTT
1 TAATAAAAATAGTT
17295968 TAATAAAAATAGT
1 TAATAAAAATAGT
17295981 ATATCCATAT
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:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
TAATAAAAATAGTT
Found at i:17296676 original size:16 final size:16
Alignment explanation
Indices: 17296655--17296696 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
17296645 CGAGACCAAA
17296655 ACGCGCGGGTCTGGCC
1 ACGCGCGGGTCTGGCC
17296671 ACGCGCGGGTCTGGCC
1 ACGCGCGGGTCTGGCC
*
17296687 ACGCTCGGGT
1 ACGCGCGGGT
17296697 TGGGTCATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.36, G:0.43, T:0.14
Consensus pattern (16 bp):
ACGCGCGGGTCTGGCC
Found at i:17297598 original size:11 final size:11
Alignment explanation
Indices: 17297582--17297633 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
17297572 TTTTAATAAC
17297582 TTTATTTTTGT
1 TTTATTTTTGT
*
17297593 TTTATTTTTTT
1 TTTATTTTTGT
17297604 ATTTATTATTT-T
1 -TTTATT-TTTGT
17297616 TTTATATTTTG-
1 TTTAT-TTTTGT
17297627 TTTATTT
1 TTTATTT
17297634 ATTTGATTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 2 0.06
11 23 0.64
12 8 0.22
13 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTATTTTTGT
Found at i:17297612 original size:26 final size:26
Alignment explanation
Indices: 17297583--17297636 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
17297573 TTTAATAACT
*
17297583 TTATTTTTGTTTTATTTT-TTTATTTA
1 TTATTTTT-TTATATTTTGTTTATTTA
17297609 TTATTTTTTTATATTTTGTTTATTTA
1 TTATTTTTTTATATTTTGTTTATTTA
17297635 TT
1 TT
17297637 TGATTTGGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.80
Consensus pattern (26 bp):
TTATTTTTTTATATTTTGTTTATTTA
Found at i:17299169 original size:7 final size:7
Alignment explanation
Indices: 17299157--17299200 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
17299147 GAAATCTCTC
17299157 CTCCCTA
1 CTCCCTA
17299164 CTCCCTA
1 CTCCCTA
17299171 CTCCCTA
1 CTCCCTA
17299178 CTCCCTA
1 CTCCCTA
17299185 CTCCCTA
1 CTCCCTA
17299192 CTCCCTA
1 CTCCCTA
17299199 CT
1 CT
17299201 GTCCGACATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
CTCCCTA
Found at i:17302709 original size:19 final size:19
Alignment explanation
Indices: 17302687--17302737 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
17302677 ATGGGGCATG
17302687 AAGCGCATCCTAGCAAACA
1 AAGCGCATCCTAGCAAACA
* * **
17302706 AAGCGTATCCTGGTGAACA
1 AAGCGCATCCTAGCAAACA
*
17302725 AAGCGCATTCTAG
1 AAGCGCATCCTAG
17302738 TGCGTAAGCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (19 bp):
AAGCGCATCCTAGCAAACA
Found at i:17309966 original size:26 final size:26
Alignment explanation
Indices: 17309865--17309958 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 26
17309855 ACACATAGTA
**
17309865 CCTACTAAATAAACACTGGCTCAAAG
1 CCTACTAAATAAACACCAGCTCAAAG
* ** *
17309891 CCTGCTAAATAAGTACCAGCTCATAG
1 CCTACTAAATAAACACCAGCTCAAAG
* * *
17309917 CCTGCTAAGTAATCACCAGCTCAAAG
1 CCTACTAAATAAACACCAGCTCAAAG
17309943 CCTACTAAATAAACAC
1 CCTACTAAATAAACAC
17309959 TTGTTCAAGG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (26 bp):
CCTACTAAATAAACACCAGCTCAAAG
Found at i:17316335 original size:45 final size:45
Alignment explanation
Indices: 17316285--17316374 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
17316275 TGAGTATTGA
*
17316285 GAGCACTTGTCTATTCATTGTGGAACGTATTTTGTGAGTGTATTT
1 GAGCACTTGTCTATTCATCGTGGAACGTATTTTGTGAGTGTATTT
* *
17316330 GAGCACTTGTCTGTTCATCGTGGAATGTATTTTGTGAGTGTATTT
1 GAGCACTTGTCTATTCATCGTGGAACGTATTTTGTGAGTGTATTT
17316375 TAGTGAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.44
Consensus pattern (45 bp):
GAGCACTTGTCTATTCATCGTGGAACGTATTTTGTGAGTGTATTT
Found at i:17318052 original size:4 final size:4
Alignment explanation
Indices: 17318045--17318095 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
17318035 ATGAAATATG
17318045 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
17318093 ATA
1 ATA
17318096 GAGACTAGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:17323745 original size:21 final size:21
Alignment explanation
Indices: 17323721--17323762 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17323711 TAACATTTTT
17323721 TTTTCAATTTGGTA-TTTATTA
1 TTTT-AATTTGGTATTTTATTA
* *
17323742 TTTTTATTTTGTATTTTATTA
1 TTTTAATTTGGTATTTTATTA
17323763 ATTGTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTTAATTTGGTATTTTATTA
Found at i:17323758 original size:90 final size:91
Alignment explanation
Indices: 17323647--17323836 Score: 364
Period size: 90 Copynumber: 2.1 Consensus size: 91
17323637 ACTTAAATAC
17323647 TTATGTTTTATTTTGTTATTTTATTAATTGTTATCTAATAGGTTAAGGTTATTATTTTTTAACGT
1 TTAT-TTTTATTTTGTTATTTTATTAATTGTTATCTAATAGGTTAAGGTTATTATTTTTTAACGT
17323712 AACATTTTTTTTTCAATTTGGTATTTA
65 AACATTTTTTTTTCAATTTGGTATTTA
17323739 TTATTTTTATTTTG-TATTTTATTAATTGTTATCTAATAGGTTAAGGTTATTATTTTTTAACGTA
1 TTATTTTTATTTTGTTATTTTATTAATTGTTATCTAATAGGTTAAGGTTATTATTTTTTAACGTA
17323803 ACATTTTTTTTTCAATTTGGTATTTA
66 ACATTTTTTTTTCAATTTGGTATTTA
17323829 TTATTTTT
1 TTATTTTT
17323837 TTGAGCTAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
90 84 0.86
91 10 0.10
92 4 0.04
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (91 bp):
TTATTTTTATTTTGTTATTTTATTAATTGTTATCTAATAGGTTAAGGTTATTATTTTTTAACGTA
ACATTTTTTTTTCAATTTGGTATTTA
Found at i:17338231 original size:18 final size:18
Alignment explanation
Indices: 17338208--17338250 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17338198 GAATAGATTT
17338208 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
17338226 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
17338244 TTAATTA
1 TTAATTA
17338251 CACCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:17339225 original size:62 final size:62
Alignment explanation
Indices: 17339155--17339276 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 62
17339145 CTTGAAAATA
*
17339155 TTTCTAATCACCTTCAAAAAAAAAAAAAAAAAAAAGGAAAAATAAAATTTTTACCTTGGGGG
1 TTTCTAATCACCTTCAAAAAAAAAAAAAAAAAAAAGGAAAAATAAAATTGTTACCTTGGGGG
* * *
17339217 TTTCTAATCCCCTTCAAAAAAAAAAAAAAAAAAAAGGATAAATCAAATTGTTACCTTGGG
1 TTTCTAATCACCTTCAAAAAAAAAAAAAAAAAAAAGGAAAAATAAAATTGTTACCTTGGG
17339277 AGTATCCACA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.25
Consensus pattern (62 bp):
TTTCTAATCACCTTCAAAAAAAAAAAAAAAAAAAAGGAAAAATAAAATTGTTACCTTGGGGG
Found at i:17339992 original size:16 final size:16
Alignment explanation
Indices: 17339942--17339992 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
17339932 ATTGTAGCTA
*
17339942 AAATAAAAAATAACAAT
1 AAATAAATAATAA-AAT
17339959 AAATAAAT-ATAAATAT
1 AAATAAATAATAAA-AT
17339975 AAA-AAACTAATAAAAT
1 AAATAAA-TAATAAAAT
17339991 AA
1 AA
17339993 TTTAAATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 14 0.47
17 12 0.40
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAATAATAAAAT
Found at i:17341598 original size:25 final size:25
Alignment explanation
Indices: 17341570--17341618 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17341560 AGTTTTTTAG
*
17341570 TTTT-CTTCTCTCAGTTAAACTCTAT
1 TTTTACTT-TCTCACTTAAACTCTAT
*
17341595 TTTTAGTTTCTCACTTAAACTCTA
1 TTTTACTTTCTCACTTAAACTCTA
17341619 GTTAGCCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (25 bp):
TTTTACTTTCTCACTTAAACTCTAT
Found at i:17349952 original size:31 final size:31
Alignment explanation
Indices: 17349883--17349954 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
17349873 GATTTGATGT
* *
17349883 AATTATACATATAAAACTTTAATTATAGGTC
1 AATTGTACACATAAAACTTTAATTATAGGTC
* *
17349914 -ATGTGTACACATAAAACTTTAATT-TTGCTTC
1 AAT-TGTACACATAAAACTTTAATTATAG-GTC
17349945 AATTGTACAC
1 AATTGTACAC
17349955 CTTTAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 4 0.12
31 28 0.82
32 2 0.06
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (31 bp):
AATTGTACACATAAAACTTTAATTATAGGTC
Found at i:17354284 original size:12 final size:11
Alignment explanation
Indices: 17354238--17354280 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
17354228 AGTTAAATAT
17354238 TATTTTATTAA
1 TATTTTATTAA
17354249 TATTTTAATTAGA
1 TATTTT-ATTA-A
17354262 TA-TTTATTAA
1 TATTTTATTAA
17354272 TATTTTATT
1 TATTTTATT
17354281 TAATTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.10
11 16 0.55
12 7 0.24
13 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:17374025 original size:17 final size:17
Alignment explanation
Indices: 17374003--17374062 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
17373993 ACAAGTAGGG
17374003 TAAAATGAGCATGTGAT
1 TAAAATGAGCATGTGAT
* * *
17374020 TAAAATCATCCCATGATTG-G
1 TAAAATGA--GCATG--TGAT
17374040 TAAAATGAGCATGTGAT
1 TAAAATGAGCATGTGAT
17374057 TAAAAT
1 TAAAAT
17374063 CATCCCATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 4 0.12
19 4 0.12
20 7 0.22
21 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (17 bp):
TAAAATGAGCATGTGAT
Found at i:17374051 original size:37 final size:37
Alignment explanation
Indices: 17374001--17374077 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
17373991 TAACAAGTAG
17374001 GGTAAAATGAGCATGTGATTAAAATCATCCCATGATT
1 GGTAAAATGAGCATGTGATTAAAATCATCCCATGATT
17374038 GGTAAAATGAGCATGTGATTAAAATCATCCCATGATT
1 GGTAAAATGAGCATGTGATTAAAATCATCCCATGATT
17374075 GGT
1 GGT
17374078 CTTTGGCCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
GGTAAAATGAGCATGTGATTAAAATCATCCCATGATT
Found at i:17390768 original size:16 final size:15
Alignment explanation
Indices: 17390749--17390778 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17390739 TTCATTTCAT
17390749 TTGCATTTAGGTTAAC
1 TTGCATTTA-GTTAAC
17390765 TTGCATTTAGTTAA
1 TTGCATTTAGTTAA
17390779 TTAACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (15 bp):
TTGCATTTAGTTAAC
Found at i:17405183 original size:17 final size:17
Alignment explanation
Indices: 17405161--17405199 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17405151 TTCAATTTAT
17405161 TAAATTAAATTTAA-TAA
1 TAAATTAAA-TTAATTAA
*
17405178 TAAATTATATTAATTAA
1 TAAATTAAATTAATTAA
17405195 TAAAT
1 TAAAT
17405200 ACAATAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAAATTAATTAA
Found at i:17406879 original size:20 final size:20
Alignment explanation
Indices: 17406829--17406871 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17406819 AAAAAAATTC
* *
17406829 AAAATTTTAAAATATTTATA
1 AAAATTATAAAATATTCATA
*
17406849 ACAATTATAAAAT-TTCATA
1 AAAATTATAAAATATTCATA
17406868 AAAA
1 AAAA
17406872 ATTCTAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTATAAAATATTCATA
Found at i:17407856 original size:17 final size:18
Alignment explanation
Indices: 17407834--17407868 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17407824 CTAATAATAA
17407834 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
17407851 TTTAAATGTTTAATTATT
1 TTTAAATGTCTAATTATT
17407869 ATAACTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:17408942 original size:44 final size:44
Alignment explanation
Indices: 17408883--17408972 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
17408873 TAATTGTAAT
* * * * * *
17408883 TTAAATTCTATTTATTTTTAAATGTGTAATTCTCACTATTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
17408927 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
17408971 TT
1 TT
17408973 TTATTTTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
Found at i:17410877 original size:18 final size:18
Alignment explanation
Indices: 17410840--17410877 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
17410830 TTAATTTTTT
17410840 AAAATTTAAAAAGTTCAAA
1 AAAATTTAAAAAGTT-AAA
*
17410859 AAATTTTAAAAA-TTAAA
1 AAAATTTAAAAAGTTAAA
17410876 AA
1 AA
17410878 TCATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 2 0.11
19 11 0.61
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATTTAAAAAGTTAAA
Found at i:17411628 original size:5 final size:5
Alignment explanation
Indices: 17411620--17411649 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
17411610 TTACATTTCT
17411620 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
17411650 TTGTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:17411633 original size:10 final size:11
Alignment explanation
Indices: 17411595--17411649 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
17411585 CATCTCTTCC
*
17411595 TTTTTATTTTT
1 TTTTTATTTTA
* *
17411606 TGTTTTACATTTC
1 T-TTTTA-TTTTA
17411619 TTTTTATTTTA
1 TTTTTATTTTA
17411630 -TTTTATTTTA
1 TTTTTATTTTA
17411640 TTTTTATTTT
1 TTTTTATTTT
17411650 TTGTTTACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 10 0.27
11 13 0.35
12 10 0.27
13 4 0.11
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:17425030 original size:44 final size:43
Alignment explanation
Indices: 17424966--17425557 Score: 329
Period size: 44 Copynumber: 13.8 Consensus size: 43
17424956 AGAATCTCAG
* * *
17424966 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAG-A
* * * * ** *
17425010 ATCCTATCTCTCTGAGATTACAATGGAGTGGATT-AAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCT--AGA
* * * * * *
17425054 ATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCGTATC-AG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATTGAAGCTAGA
* * * * *
17425095 GTCTTATCTCTCTGAGATTATAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAG-A
** *
17425139 ATCTTA--TCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCT--AGA
* * * * * * *
17425181 ATCTTATCTCTCTGA-AGTGACAGTAGAGTGGATCGTATC-AG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATTGAAGCTAGA
* * * *
17425222 GTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAG-A
* * *
17425266 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG-TAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCT--AGA
* * * * * * *
17425310 ATCTTATCTCTCTGA-AGTGACAGTAGAGTGGATCGTATC-AG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATTGAAGCTAGA
* * * *
17425351 GTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAG-A
* * *
17425395 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG-TAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCT--AGA
* * * * * * *
17425439 ATCTTATCTCTCTGA-AGTGACAGTAGAGTGGATCGTATC-AG-
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATTGAAGCTAGA
* * * *
17425480 GTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAG-A
*
17425524 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATT
17425558 AAAATAAAGG
Statistics
Matches: 402, Mismatches: 112, Indels: 68
0.69 0.19 0.12
Matches are distributed among these distances:
41 109 0.27
42 48 0.12
43 11 0.03
44 226 0.56
45 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCGGATTGAAGCTAGA
Found at i:17425143 original size:85 final size:84
Alignment explanation
Indices: 17425054--17425427 Score: 242
Period size: 85 Copynumber: 4.4 Consensus size: 84
17425044 AAAATAAAGG
* * * * * *
17425054 ATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATCGTATCAGGTCTTATCTCTCTGAGATTATAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
17425118 CGGAGCAGATTGAAGCTAGTA
65 CGGAGCAGATTGAAGCTAG-A
** * * *
17425139 ATCTTA--TCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTGA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGA-TCGAAT-CAGG-TCTTATCTCCCTGAGA-TTA
** ** * * *
17425201 CAGTAGAGTGGATCGTATC-AG-
62 CAGCGGAGCAGATTGAAGCTAGA
* * * * * * * *
17425222 GTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGATCGAATC-AG--GTCTTATCTCCCTGAGATTAC
* * * *
17425287 AGTGGAGCGGATTAAAG-TAAAGG
63 AGCGGAGCAGATTGAAGCT--AGA
* * * * * *
17425310 ATCTTATCTCTCTGA-AGTGACAGTAGAGTGGATCGTATCAGGTCTTATCGCCCTGAGATTACAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCGGATCGAATCAGGTCTTATCTCCCTGAGATTACAG
17425374 CGGAGCAGATTGAAGCTAGTA
65 CGGAGCAGATTGAAGCTAG-A
*
17425395 ATCCTATCTCCCTGAGATTACAGTGGAGCGGAT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCGGAT
17425428 TAAAGTAAAG
Statistics
Matches: 213, Mismatches: 57, Indels: 38
0.69 0.19 0.12
Matches are distributed among these distances:
83 24 0.11
84 11 0.05
85 117 0.55
86 30 0.14
87 5 0.02
88 26 0.12
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (84 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCGGATCGAATCAGGTCTTATCTCCCTGAGATTACAGC
GGAGCAGATTGAAGCTAGA
Found at i:17425344 original size:129 final size:129
Alignment explanation
Indices: 17424962--17425621 Score: 1153
Period size: 129 Copynumber: 5.1 Consensus size: 129
17424952 TCAAAGAATC
* * * *
17424962 TCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCTCTGAGA
1 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
17425027 TTACAATGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
* * * *
17425091 TCAGGTCTTATCTCTCTGAGATTATAGCGGAGCAGATTGAAGCTAGTAAT-CT-TATCCCTGAGA
1 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
17425154 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
17425218 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
17425283 TTACAGTGGAGCGGATTAAAGTAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
17425347 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
17425412 TTACAGTGGAGCGGATTAAAGTAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
17425476 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
17425541 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCATA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
* *
17425605 TCAGATCTTATCTCCCT
1 TCAGGTCTTATCGCCCT
17425622 AAGCAGTAGT
Statistics
Matches: 510, Mismatches: 19, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
127 117 0.23
128 4 0.01
129 389 0.76
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (129 bp):
TCAGGTCTTATCGCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
Found at i:17429713 original size:17 final size:17
Alignment explanation
Indices: 17429693--17429727 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17429683 TCGATTTGAT
17429693 ACCCTAATCAATTTCTA
1 ACCCTAATCAATTTCTA
*
17429710 ACCCTGATCAATTTCTA
1 ACCCTAATCAATTTCTA
17429727 A
1 A
17429728 TCCAACTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (17 bp):
ACCCTAATCAATTTCTA
Found at i:17430352 original size:17 final size:18
Alignment explanation
Indices: 17430314--17430353 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17430304 AAAAATTATT
*
17430314 TAAAATTAATATTAAATA
1 TAAAATTAATATTAAAAA
17430332 -AAAATTAA-ATTAAAAA
1 TAAAATTAATATTAAAAA
17430348 TAAAAT
1 TAAAAT
17430354 ATCATATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAATATTAAAAA
Found at i:17433984 original size:18 final size:17
Alignment explanation
Indices: 17433961--17433994 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17433951 GACCCAAATT
17433961 TAAAGGCTTGGTTGAATC
1 TAAAGGCTTGG-TGAATC
17433979 TAAAGGCTTGGTGAAT
1 TAAAGGCTTGGTGAAT
17433995 AAGTCTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (17 bp):
TAAAGGCTTGGTGAATC
Found at i:17436144 original size:20 final size:21
Alignment explanation
Indices: 17436119--17436160 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17436109 TAATACTAGA
17436119 AAAAATGAAATTTAATA-TTT
1 AAAAATGAAATTTAATAGTTT
* *
17436139 AAAAATTAGATTTAATAGTTT
1 AAAAATGAAATTTAATAGTTT
17436160 A
1 A
17436161 CGAGAGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATGAAATTTAATAGTTT
Found at i:17463726 original size:21 final size:22
Alignment explanation
Indices: 17463684--17463726 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
17463674 AACAAAAAAT
*
17463684 AAAAAAATAGAAAAGAGGAAGAA
1 AAAAAAAGAGAAAAGA-GAAGAA
*
17463707 AAAAAAAGAGACAAGA-AAGA
1 AAAAAAAGAGAAAAGAGAAGA
17463727 TTGATGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (22 bp):
AAAAAAAGAGAAAAGAGAAGAA
Found at i:17480706 original size:31 final size:31
Alignment explanation
Indices: 17480668--17480729 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
17480658 CCTCAGTGGG
* *
17480668 ATTGTTAATATAGTGGAAGAGAGGTTTGTCT
1 ATTGTTAATATAGTAGAAGAGAGGTTCGTCT
*
17480699 ATTGTTAATATAGTAGAAGAGCGGTTCGTCT
1 ATTGTTAATATAGTAGAAGAGAGGTTCGTCT
17480730 CCTCCATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (31 bp):
ATTGTTAATATAGTAGAAGAGAGGTTCGTCT
Found at i:17494715 original size:17 final size:17
Alignment explanation
Indices: 17494695--17494731 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17494685 GAGATTTTTA
17494695 TTTTAGTTTAAT-TTAAT
1 TTTTA-TTTAATATTAAT
17494712 TTTTATTTAATATTAAT
1 TTTTATTTAATATTAAT
17494729 TTT
1 TTT
17494732 AAATGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATTTAATATTAAT
Found at i:17494727 original size:22 final size:22
Alignment explanation
Indices: 17494688--17494730 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17494678 GAGAGATGAG
*
17494688 ATTTTTATTTTAGTTTAATTTA
1 ATTTTTATTTTAATTTAATTTA
17494710 ATTTTTA-TTTAATATTAATTT
1 ATTTTTATTTTAAT-TTAATTT
17494731 TAAATGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTTTATTTTAATTTAATTTA
Found at i:17494732 original size:16 final size:16
Alignment explanation
Indices: 17494694--17494732 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
17494684 TGAGATTTTT
17494694 ATTTTAGTTTAATTTA
1 ATTTTAGTTTAATTTA
17494710 ATTTTTA-TTTAATATTA
1 A-TTTTAGTTTAAT-TTA
17494727 ATTTTA
1 ATTTTA
17494733 AATGTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTTTAGTTTAATTTA
Found at i:17500413 original size:25 final size:26
Alignment explanation
Indices: 17500379--17500433 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
17500369 CGAGAAGTTC
* *
17500379 TGTCTTGC-AATGACTTCATGTTTGA
1 TGTCTTGCAAATGACTTAATGGTTGA
17500404 TGTCTTGCAAAATGACTTAATGGTTGA
1 TGTCTTGC-AAATGACTTAATGGTTGA
17500431 TGT
1 TGT
17500434 TATAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 8 0.31
27 18 0.69
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.42
Consensus pattern (26 bp):
TGTCTTGCAAATGACTTAATGGTTGA
Found at i:17505740 original size:21 final size:21
Alignment explanation
Indices: 17505714--17505755 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17505704 ATCAAAACGA
*
17505714 AATAGTTTTGCCTTTTAACTT
1 AATAGTTTTGACTTTTAACTT
17505735 AATAGTTTTGACTTTTAACTT
1 AATAGTTTTGACTTTTAACTT
17505756 TAGAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (21 bp):
AATAGTTTTGACTTTTAACTT
Found at i:17506031 original size:23 final size:24
Alignment explanation
Indices: 17506000--17506052 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
17505990 CCCTGATCAA
**
17506000 TTTTT-AATTTAAATAT-TTTTAT
1 TTTTTAAATTTAAATATATTGAAT
*
17506022 TTTTTAAATTTATATATATTGAAT
1 TTTTTAAATTTAAATATATTGAAT
17506046 TTTTTAA
1 TTTTTAA
17506053 TTTCATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 10 0.38
24 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTAAATTTAAATATATTGAAT
Found at i:17506052 original size:24 final size:23
Alignment explanation
Indices: 17506020--17506065 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
17506010 AAATATTTTT
17506020 ATTTTTTAAATTT-ATATATATTGA
1 ATTTTTT-AATTTCATATA-ATTGA
17506044 ATTTTTTAATTTCATATAATTG
1 ATTTTTTAATTTCATATAATTG
17506066 TATATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
ATTTTTTAATTTCATATAATTGA
Found at i:17506054 original size:23 final size:23
Alignment explanation
Indices: 17506000--17506065 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
17505990 CCCTGATCAA
* **
17506000 TTTTTAATTTAAATAT-TTTTAT
1 TTTTTAATTTATATATATTGAAT
17506022 TTTTTAAATTTATATATATTGAAT
1 TTTTT-AATTTATATATATTGAAT
17506046 TTTTTAATTTCATATA-ATTG
1 TTTTTAATTT-ATATATATTG
17506066 TATATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 5 0.13
23 19 0.50
24 14 0.37
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (23 bp):
TTTTTAATTTATATATATTGAAT
Found at i:17509345 original size:18 final size:19
Alignment explanation
Indices: 17509315--17509355 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17509305 TTATAAAAAA
*
17509315 AAATTATACTCC-ATACAT
1 AAATTATACTCCAATAAAT
17509333 AAATCTATA-TCCAATAAAT
1 AAAT-TATACTCCAATAAAT
17509352 AAAT
1 AAAT
17509356 ATGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTATACTCCAATAAAT
Found at i:17509539 original size:12 final size:12
Alignment explanation
Indices: 17509522--17509547 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17509512 CCTTTTAAAG
17509522 TTAATATGTAAT
1 TTAATATGTAAT
17509534 TTAATATGTAAT
1 TTAATATGTAAT
17509546 TT
1 TT
17509548 GATTCATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTAATATGTAAT
Found at i:17512934 original size:86 final size:87
Alignment explanation
Indices: 17512830--17513007 Score: 245
Period size: 86 Copynumber: 2.1 Consensus size: 87
17512820 TTGAAGAAGT
* * **
17512830 GTGGCAAAACTGTAAAATCTGGAA-AACCAGTGGAAAAATTTTAAAATCTGGAATAA-TAGTGGT
1 GTGGCAAAACTGTAAAATCTGGAATAA-CAGTGGAAAAACTATAAAATCTGGAA-AATTAGTGAC
*
17512893 AGAATTGTAAAATTTGGAAAACCA
64 AAAATTGTAAAATTTGGAAAACCA
* * *
17512917 GTGGCAGAACTG-AAAATCTGGAATAACAGTGGCAAAACTATAAAATTTGGAAAATTAGTGACAA
1 GTGGCAAAACTGTAAAATCTGGAATAACAGTGGAAAAACTATAAAATCTGGAAAATTAGTGACAA
17512981 AATTGTAAAATTTGGAAAACCA
66 AATTGTAAAATTTGGAAAACCA
17513003 GTGGC
1 GTGGC
17513008 TCGAGACCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 2 0.02
86 66 0.81
87 13 0.16
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (87 bp):
GTGGCAAAACTGTAAAATCTGGAATAACAGTGGAAAAACTATAAAATCTGGAAAATTAGTGACAA
AATTGTAAAATTTGGAAAACCA
Found at i:17512946 original size:28 final size:29
Alignment explanation
Indices: 17512830--17513007 Score: 173
Period size: 29 Copynumber: 6.2 Consensus size: 29
17512820 TTGAAGAAGT
17512830 GTGGCAAAACTGTAAAATCTGGAAAACCA
1 GTGGCAAAACTGTAAAATCTGGAAAACCA
* * * *
17512859 GTGGAAAAATTTTAAAATCTGGAATAA-TA
1 GTGGCAAAACTGTAAAATCTGGAA-AACCA
* * * *
17512888 GTGGTAGAATTGTAAAATTTGGAAAACCA
1 GTGGCAAAACTGTAAAATCTGGAAAACCA
*
17512917 GTGGCAGAACTG-AAAATCTGGAATAA-CA
1 GTGGCAAAACTGTAAAATCTGGAA-AACCA
* * **
17512945 GTGGCAAAACTATAAAATTTGGAAAATTA
1 GTGGCAAAACTGTAAAATCTGGAAAACCA
* * *
17512974 GTGACAAAATTGTAAAATTTGGAAAACCA
1 GTGGCAAAACTGTAAAATCTGGAAAACCA
17513003 GTGGC
1 GTGGC
17513008 TCGAGACCTT
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
28 26 0.21
29 94 0.77
30 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (29 bp):
GTGGCAAAACTGTAAAATCTGGAAAACCA
Found at i:17512961 original size:57 final size:58
Alignment explanation
Indices: 17512830--17512970 Score: 185
Period size: 57 Copynumber: 2.4 Consensus size: 58
17512820 TTGAAGAAGT
* * * *
17512830 GTGGCAAAACTGTAAAATCTGGAAAACCAGTGGAAAAATTTTAAAATCTGGAATAATA
1 GTGGCAAAACTGTAAAATTTGGAAAACCAGTGGAAAAATCTGAAAATCTGGAATAACA
* * * * *
17512888 GTGGTAGAATTGTAAAATTTGGAAAACCAGTGGCAGAA-CTGAAAATCTGGAATAACA
1 GTGGCAAAACTGTAAAATTTGGAAAACCAGTGGAAAAATCTGAAAATCTGGAATAACA
*
17512945 GTGGCAAAACTATAAAATTTGGAAAA
1 GTGGCAAAACTGTAAAATTTGGAAAA
17512971 TTAGTGACAA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
57 38 0.54
58 32 0.46
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.23
Consensus pattern (58 bp):
GTGGCAAAACTGTAAAATTTGGAAAACCAGTGGAAAAATCTGAAAATCTGGAATAACA
Found at i:17516286 original size:45 final size:45
Alignment explanation
Indices: 17516176--17516287 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 45
17516166 GTTTCTTCTG
** *
17516176 TCTGCTCCACTGCAACTTCAGGGAGAT-AGAATTAT-CGGT-TTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG-ATT-TGCCATCTTCGA
*
17516220 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGA
*
17516265 TCTG-TCCCACTGTAACTTCAGGG
1 TCTGCT-CCACTGCAACTTCAGGG
17516288 GGATTGTAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.02
44 32 0.55
45 25 0.43
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGA
Found at i:17516617 original size:129 final size:129
Alignment explanation
Indices: 17516478--17516762 Score: 489
Period size: 129 Copynumber: 2.2 Consensus size: 129
17516468 ACTCAGTCTG
* * * *
17516478 CTCCGCTGCAACCTCAGGGAGATAAGACCTGATGCGATTCACTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACCGCAACTTCAGAGAGATA
*
17516543 AGATCCATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTA
66 AGATCCATTACTTTAATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTA
* *
17516607 CTCCACTGCAACCTCAGGGAGATAAGACTTGTTACGATCCACTCTACCGCAACTTCAGAGAGATA
1 CTCCACTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACCGCAACTTCAGAGAGATA
* *
17516672 AGATCTATTACTTTAATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTG
66 AGATCCATTACTTTAATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTA
17516736 CTCCACTGCAACCTCAGGGAGATAAGA
1 CTCCACTGCAACCTCAGGGAGATAAGA
17516763 TTTGCCATCT
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 147 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (129 bp):
CTCCACTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACCGCAACTTCAGAGAGATA
AGATCCATTACTTTAATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTA
Found at i:17516739 original size:44 final size:43
Alignment explanation
Indices: 17516523--17516764 Score: 202
Period size: 44 Copynumber: 5.6 Consensus size: 43
17516513 GATTCACTCT
* * ** *
17516523 ACTGCAACTTCAGAGAGATAAGATCCATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TATGGCTTCAATCCGCTCC
* * **
17516567 ACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCC
1 ACTGCAACTTCAGGGAGATAAGATTAT-GGCTTCAATCCGCTCC
* * * * *
17516611 ACTGCAACCTCAGGGAGATAAGACT-T-G-TTACGATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATTATGGCTT-CAATCCGCTCC
* * ** *
17516652 ACCGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TATGGCTTCAATCCGCTCC
* * * *
17516696 ACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAT-GGCTTCAATCCGCTCC
*
17516740 ACTGCAACCTCAGGGAGATAAGATT
1 ACTGCAACTTCAGGGAGATAAGATT
17516765 TGCCATCTCC
Statistics
Matches: 153, Mismatches: 38, Indels: 14
0.75 0.19 0.07
Matches are distributed among these distances:
40 2 0.01
41 29 0.19
42 1 0.01
43 7 0.05
44 112 0.73
45 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGATTATGGCTTCAATCCGCTCC
Found at i:17529257 original size:25 final size:27
Alignment explanation
Indices: 17529195--17529258 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
17529185 TTATTCATAC
17529195 ATATATATAAAAATATATAAATTAACTT
1 ATAT-TATAAAAATATATAAATTAACTT
17529223 -T-TTATAAAAATATA-AAATTAA-TT
1 ATATTATAAAAATATATAAATTAACTT
17529246 ATATGTATAAAAA
1 ATAT-TATAAAAA
17529259 AACAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATTATAAAAATATATAAATTAACTT
Found at i:17534094 original size:28 final size:30
Alignment explanation
Indices: 17534041--17534106 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
17534031 TAAAATTTTT
*
17534041 TTTAT-AAATTTGTAAAAAATTATT-AAAA
1 TTTATAAAATTTGTAAAAAAATATTAAAAA
17534069 TTTATAAAATTT-TAAATAAAAT-TTAAAAA
1 TTTATAAAATTTGTAAA-AAAATATTAAAAA
*
17534098 TTAATAAAA
1 TTTATAAAA
17534107 AAACCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TTTATAAAATTTGTAAAAAAATATTAAAAA
Found at i:17534105 original size:21 final size:21
Alignment explanation
Indices: 17534064--17534124 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
17534054 AAAAAATTAT
*
17534064 TAAAATTTATAAAATT-TTAAA
1 TAAAATTTA-AAAATTAATAAA
17534085 TAAAATTTAAAAATTAATAAA
1 TAAAATTTAAAAATTAATAAA
* *
17534106 AAAACCATTTAACAATTAA
1 TAAA--ATTTAAAAATTAA
17534125 GTCTAGAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 16 0.47
23 12 0.35
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAATTTAAAAATTAATAAA
Found at i:17555103 original size:9 final size:9
Alignment explanation
Indices: 17555086--17555122 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17555076 TGAGTTTTCG
17555086 AATTCGAAT
1 AATTCGAAT
*
17555095 AACTCGAAT
1 AATTCGAAT
17555104 AATTCGAAT
1 AATTCGAAT
17555113 AATTCGAAT
1 AATTCGAAT
17555122 A
1 A
17555123 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17555849 original size:5 final size:5
Alignment explanation
Indices: 17555839--17555864 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17555829 CTCGAAAATT
17555839 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
17555865 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:17556507 original size:28 final size:28
Alignment explanation
Indices: 17556475--17556528 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
17556465 CAGAAAACTG
*
17556475 CTTTAAGGGGTTAAAAGTA-AATTTTAAA
1 CTTTAAGGGGGT-AAAGTATAATTTTAAA
17556503 CTTTAAGGGGGTAAAGTATAATTTTA
1 CTTTAAGGGGGTAAAGTATAATTTTA
17556529 TCATTATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (28 bp):
CTTTAAGGGGGTAAAGTATAATTTTAAA
Found at i:17557012 original size:22 final size:22
Alignment explanation
Indices: 17556987--17557054 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
17556977 TCTCACTCAC
17556987 ATTTCTCACAATTCTCTCAAAA
1 ATTTCTCACAATTCTCTCAAAA
17557009 ATTTCTCAATCAA--CTCTCAAAA
1 ATTTCTC-A-CAATTCTCTCAAAA
* *
17557031 ATCTCTCA-AATTCTCT-AATA
1 ATTTCTCACAATTCTCTCAAAA
17557051 ATTT
1 ATTT
17557055 TTTTCCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 5 0.13
22 22 0.56
23 1 0.03
24 3 0.08
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTCTCACAATTCTCTCAAAA
Found at i:17557273 original size:19 final size:18
Alignment explanation
Indices: 17557249--17557304 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
17557239 TATTGTTTAA
17557249 ATTTTTATTTCACTGTTAT
1 ATTTTTATTT-ACTGTTAT
17557268 ATTTTTATTTA---TT-T
1 ATTTTTATTTACTGTTAT
17557282 -TTTTTATTTTACTGTTAT
1 ATTTTTA-TTTACTGTTAT
17557300 ATTTT
1 ATTTT
17557305 AACTTAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 2 0.06
17 2 0.06
18 2 0.06
19 14 0.45
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (18 bp):
ATTTTTATTTACTGTTAT
Found at i:17557318 original size:32 final size:32
Alignment explanation
Indices: 17557249--17557318 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
17557239 TATTGTTTAA
* * *
17557249 ATTTTTATTTCACTGTTATATTTTTATTTATT
1 ATTTTTATTTCACTGTTATATTTTAACTTAGT
* *
17557281 TTTTTTATTTTACTGTTATATTTTAACTTAGT
1 ATTTTTATTTCACTGTTATATTTTAACTTAGT
17557313 ATTTTT
1 ATTTTT
17557319 TATATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (32 bp):
ATTTTTATTTCACTGTTATATTTTAACTTAGT
Found at i:17558640 original size:17 final size:17
Alignment explanation
Indices: 17558618--17558651 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17558608 TGATTTGCTA
17558618 TCAATGCCTTGCTATAC
1 TCAATGCCTTGCTATAC
17558635 TCAATGCCTTGCTATAC
1 TCAATGCCTTGCTATAC
17558652 CAAGGCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
TCAATGCCTTGCTATAC
Found at i:17560642 original size:29 final size:29
Alignment explanation
Indices: 17560610--17560677 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
17560600 AATCCTGGGA
* *
17560610 TATTTTTTCAAAACTCATCTTGTCAAAAT
1 TATTTTTTCAAAACCCATCTCGTCAAAAT
17560639 TATTTTTTCAAAACCCATCTCGTCAAAAT
1 TATTTTTTCAAAACCCATCTCGTCAAAAT
17560668 TATTTTTTCA
1 TATTTTTTCA
17560678 GAACACTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.46
Consensus pattern (29 bp):
TATTTTTTCAAAACCCATCTCGTCAAAAT
Found at i:17560850 original size:22 final size:22
Alignment explanation
Indices: 17560824--17560878 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
17560814 TGCAATGCTA
*
17560824 AAACCCTAATTTAATTAACCCT
1 AAACCCTAATTTAATAAACCCT
* * *
17560846 AAACCATACTTTAATAAACCTT
1 AAACCCTAATTTAATAAACCCT
17560868 AAACCCTAATT
1 AAACCCTAATT
17560879 AAACAATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (22 bp):
AAACCCTAATTTAATAAACCCT
Found at i:17561707 original size:9 final size:9
Alignment explanation
Indices: 17561687--17561811 Score: 78
Period size: 9 Copynumber: 13.6 Consensus size: 9
17561677 GAATTTAAAC
17561687 TTTTATATAT
1 TTTTATA-AT
17561697 TTTTATAAT
1 TTTTATAAT
*
17561706 TTTCTATACT
1 TTT-TATAAT
17561716 TTTTATAAT
1 TTTTATAAT
* *
17561725 TTTTACACGT
1 TTTTATA-AT
*
17561735 TTCTAT-A-
1 TTTTATAAT
17561742 TTTT-TAAT
1 TTTTATAAT
*
17561750 TTTTAATAAA
1 TTTT-ATAAT
*
17561760 TTATATATAT
1 TTTTATA-AT
* *
17561770 ATTTGTAAT
1 TTTTATAAT
*
17561779 TTTTATGAT
1 TTTTATAAT
17561788 TTTCTATCAA-
1 TTT-TAT-AAT
17561798 TTTTATAAT
1 TTTTATAAT
17561807 TTTTA
1 TTTTA
17561812 ACTTTTTTTT
Statistics
Matches: 87, Mismatches: 18, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 6 0.07
9 38 0.44
10 37 0.43
11 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:17561717 original size:28 final size:25
Alignment explanation
Indices: 17561695--17561811 Score: 90
Period size: 28 Copynumber: 4.3 Consensus size: 25
17561685 ACTTTTATAT
17561695 ATTTTTATAATTTTCTATACTTTTTATA
1 ATTTTTATAATTTTCTATA--TTTT-TA
* **
17561723 ATTTTTACACGTTTCTATATTTTTA
1 ATTTTTATAATTTTCTATATTTTTA
* *
17561748 ATTTTTAATAAATTATATATATATTTGTA
1 ATTTTT-AT-AATT-T-TCTATATTTTTA
*
17561777 ATTTTTATGATTTTCTATCAATTTTATA
1 ATTTTTATAATTTTCTAT--ATTTT-TA
17561805 ATTTTTA
1 ATTTTTA
17561812 ACTTTTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
25 12 0.17
26 6 0.08
27 9 0.13
28 28 0.39
29 16 0.23
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (25 bp):
ATTTTTATAATTTTCTATATTTTTA
Found at i:17563221 original size:7 final size:7
Alignment explanation
Indices: 17563211--17563246 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
17563201 TTTATAATGA
17563211 TTATTAT
1 TTATTAT
17563218 TTATTAT
1 TTATTAT
17563225 TTATTAT
1 TTATTAT
17563232 TTATTAT
1 TTATTAT
17563239 TTATTAT
1 TTATTAT
17563246 T
1 T
17563247 ATTTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:17563225 original size:10 final size:10
Alignment explanation
Indices: 17563210--17563251 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
17563200 ATTTATAATG
17563210 ATTATTATTT
1 ATTATTATTT
17563220 ATTATT-TATT
1 ATTATTAT-TT
17563230 ATTTATTATTT
1 A-TTATTATTT
17563241 ATTATTATTT
1 ATTATTATTT
17563251 A
1 A
17563252 AAAATTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.03
10 19 0.66
11 8 0.28
12 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTATTATTT
Found at i:17565648 original size:12 final size:12
Alignment explanation
Indices: 17565631--17565655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17565621 TCAAGTACTA
17565631 TTATTTGTAACT
1 TTATTTGTAACT
17565643 TTATTTGTAACT
1 TTATTTGTAACT
17565655 T
1 T
17565656 AGTTACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATTTGTAACT
Found at i:17570139 original size:18 final size:17
Alignment explanation
Indices: 17570099--17570142 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
17570089 TCAACATCTA
17570099 AATATTTTCATTTTATT
1 AATATTTTCATTTTATT
17570116 ATATATTTTCATAATTT-TT
1 A-ATATTTTCAT--TTTATT
17570135 AATATTTT
1 AATATTTT
17570143 TTTATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 3 0.12
20 3 0.12
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
AATATTTTCATTTTATT
Found at i:17575638 original size:43 final size:44
Alignment explanation
Indices: 17575553--17575678 Score: 119
Period size: 43 Copynumber: 2.8 Consensus size: 44
17575543 AAATGAGAAA
* * *
17575553 AACCTATCTAAATCCTAAGATCTAAATTAGAAAAAATAAAATAAAATTCT
1 AACCTATTTGAATCCTAAGATCTAAATTAG-----A-AAAATAAAATTCC
* * * *
17575603 ATCTTTTTTGAATCCTAATAT-TAAATTAGAAAAATAAAATTCC
1 AACCTATTTGAATCCTAAGATCTAAATTAGAAAAATAAAATTCC
*
17575646 AACCTATTTGAATCCTTAGATCTAAATTAGAAA
1 AACCTATTTGAATCCTAAGATCTAAATTAGAAA
17575679 GAAAAAAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
43 28 0.44
44 12 0.19
49 8 0.13
50 15 0.24
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (44 bp):
AACCTATTTGAATCCTAAGATCTAAATTAGAAAAATAAAATTCC
Found at i:17577520 original size:30 final size:30
Alignment explanation
Indices: 17577486--17577547 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
17577476 TTTATTTTTA
*
17577486 TTTTTTAATTTTAAAATACTTTTAAAATAT
1 TTTTTTAATTTTAAAATAATTTTAAAATAT
* **
17577516 TTTTTTATTTTTAAAATAATTTTTTAATAT
1 TTTTTTAATTTTAAAATAATTTTAAAATAT
17577546 TT
1 TT
17577548 ATTAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATAATTTTAAAATAT
Found at i:17577539 original size:20 final size:20
Alignment explanation
Indices: 17577505--17577554 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 20
17577495 TTTAAAATAC
17577505 TTTTAAAATATTTTTT-TAT
1 TTTTAAAATATTTTTTATAT
17577524 TTTTAAAATAATTTTTTAATAT
1 TTTTAAAAT-ATTTTTT-ATAT
17577546 TTATTAAAA
1 TT-TTAAAA
17577555 AATAAGCCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
22 5 0.19
23 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATATTTTTTATAT
Found at i:17578645 original size:21 final size:23
Alignment explanation
Indices: 17578601--17578645 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
17578591 TGATATATAC
*
17578601 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
17578624 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
17578645 A
1 A
17578646 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:17578791 original size:20 final size:22
Alignment explanation
Indices: 17578766--17578806 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
17578756 TACTATTTTC
*
17578766 TTTTTTTTCTT-TTT-CGATTA
1 TTTTTTTACTTATTTACGATTA
17578786 TTTTTTTACTTATTTACGATT
1 TTTTTTTACTTATTTACGATT
17578807 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTTTTACTTATTTACGATTA
Found at i:17579136 original size:29 final size:31
Alignment explanation
Indices: 17579074--17579136 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
17579064 CATATGCATG
* **
17579074 TTAATATATATACATATATATTTTAAATGTT
1 TTAATATATATACATATATATTATAAATACT
*
17579105 TTAATATATATACATAT-TA-TATACATACT
1 TTAATATATATACATATATATTATAAATACT
17579134 TTA
1 TTA
17579137 TTATTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.32
30 2 0.07
31 17 0.61
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (31 bp):
TTAATATATATACATATATATTATAAATACT
Found at i:17579395 original size:52 final size:51
Alignment explanation
Indices: 17579314--17579413 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
17579304 GTTTTTATAT
17579314 TATACTTATATATTTCATTTTTTAGTAAATGCATGAATATATTTTATATGTG
1 TATACTTATATATTTCATTTTTTAGTAAATGCAT-AATATATTTTATATGTG
* * * *
17579366 TATATTTATAT-TTTCCTTGTTTTCA-TAAATGCATTATGTATTTTATAT
1 TATACTTATATATTTCATT-TTTT-AGTAAATGCATAATATATTTTATAT
17579414 ATATATAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 18 0.43
52 23 0.55
53 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (51 bp):
TATACTTATATATTTCATTTTTTAGTAAATGCATAATATATTTTATATGTG
Found at i:17584539 original size:179 final size:180
Alignment explanation
Indices: 17584235--17584693 Score: 843
Period size: 181 Copynumber: 2.6 Consensus size: 180
17584225 CGAGGAGCAG
*
17584235 AGAACGAAATGACAAATTCTGATGCATATTCAAAGAAGAAAGGCATTTGAATCCCGAACAT-A-A
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
* *
17584298 CAATTCAACACAAAATTGTTGTTTTTAGTTATACAACATCATATTGGGGGGGACACCACTAATTT
66 TAATTCAATACAAAATTGTTGTTTTTAGTTATACAACATCATATTGGGGGGGACACCACTAATTT
*
17584363 TTAGATGTCACGGCTCTCTACTTTTCCACTTGAAAAAAACAG-GACTATT
131 TTAGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAGAGACTATT
17584412 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
*
17584477 TAATTCAATACAAAATTGTTGTTTTTAGTTATTCAACATCATATTGGGGGGGACACCACTAATTT
66 TAATTCAATACAAAATTGTTGTTTTTAGTTATACAACATCATATTGGGGGGGACACCACTAATTT
17584542 TTAGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAGAAGACTATT
131 TTAGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAG-AGACTATT
17584593 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
1 AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
17584658 TAATTCAATACAAAATTGTTGTTTTTAGTTATACAA
66 TAATTCAATACAAAATTGTTGTTTTTAGTTATACAA
17584694 TGTCAGATGA
Statistics
Matches: 272, Mismatches: 6, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
177 60 0.22
178 1 0.00
179 104 0.38
181 107 0.39
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (180 bp):
AGAACGAAATGACAAATTCTGATACATATTCAAAGAAGAAAGGCATTTGAATCCCGAACATGATA
TAATTCAATACAAAATTGTTGTTTTTAGTTATACAACATCATATTGGGGGGGACACCACTAATTT
TTAGATGTCACGGCTCTCTACTTTTCCACTAGAAAAAAACAGAGACTATT
Found at i:17588391 original size:21 final size:24
Alignment explanation
Indices: 17588351--17588393 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
17588341 ATTGCGCCAC
17588351 CAATTTTTCTATTGTAAATATATA
1 CAATTTTTCTATTGTAAATATATA
17588375 CAATTTTT-TA-T-TAAATATA
1 CAATTTTTCTATTGTAAATATA
17588394 CACATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 2 0.11
24 8 0.42
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (24 bp):
CAATTTTTCTATTGTAAATATATA
Found at i:17598129 original size:26 final size:25
Alignment explanation
Indices: 17598096--17598146 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
17598086 TTTGACTAGG
* *
17598096 CTTAATTA-ATTAACTGATGTTGATT
1 CTTAATTATAATAACT-AGGTTGATT
17598121 CTTATATTATAATAACTAGGTTGATT
1 CTTA-ATTATAATAACTAGGTTGATT
17598147 ATTTGTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (25 bp):
CTTAATTATAATAACTAGGTTGATT
Found at i:17599159 original size:26 final size:26
Alignment explanation
Indices: 17599130--17599183 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
17599120 GAGAGTTCTC
*
17599130 AAGATAACTTTTCAAATGGTGAAGAT
1 AAGATAACTTTTCAAAGGGTGAAGAT
17599156 AAGATAACTTTTCAAAGGGTGAAGAT
1 AAGATAACTTTTCAAAGGGTGAAGAT
17599182 AA
1 AA
17599184 CTTATGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (26 bp):
AAGATAACTTTTCAAAGGGTGAAGAT
Found at i:17606347 original size:36 final size:36
Alignment explanation
Indices: 17606300--17606407 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
17606290 TTATGAGCAT
17606300 CCCATTATCAATGAACACCACTTTGATGATTTGTTA
1 CCCATTATCAATGAACACCACTTTGATGATTTGTTA
*
17606336 CCCATTATCAATGAACACCATTTTGATGATTTGTTA
1 CCCATTATCAATGAACACCACTTTGATGATTTGTTA
17606372 CCCATTATCAATGAACACCACTTTGATGATTTGTTA
1 CCCATTATCAATGAACACCACTTTGATGATTTGTTA
17606408 ACAACTCTGT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (36 bp):
CCCATTATCAATGAACACCACTTTGATGATTTGTTA
Found at i:17607963 original size:21 final size:21
Alignment explanation
Indices: 17607902--17607985 Score: 84
Period size: 20 Copynumber: 4.0 Consensus size: 21
17607892 TTTAAAATCT
*
17607902 ATATTTATCAAATAA-TTTAA
1 ATATATATCAAATAATTTTAA
* *
17607922 TTATAT-TCCGTAATTAATTTTAA
1 ATATATAT-C--AAATAATTTTAA
17607945 ATAATATATCAAAT-ATTTTAA
1 AT-ATATATCAAATAATTTTAA
17607966 ATATATATCAAATAATTTTA
1 ATATATATCAAATAATTTTA
17607986 TAATTTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.02
20 16 0.31
21 15 0.29
22 8 0.15
23 6 0.12
24 5 0.10
25 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (21 bp):
ATATATATCAAATAATTTTAA
Found at i:17607973 original size:20 final size:22
Alignment explanation
Indices: 17607936--17607985 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
17607926 ATTCCGTAAT
17607936 TAATTTTAAATAATATATCAAA
1 TAATTTTAAATAATATATCAAA
17607958 T-ATTTTAAAT-ATATATCAAA
1 TAATTTTAAATAATATATCAAA
17607978 TAATTTTA
1 TAATTTTA
17607986 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.41
21 15 0.56
22 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTTTAAATAATATATCAAA
Found at i:17608286 original size:14 final size:14
Alignment explanation
Indices: 17608267--17608302 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17608257 TTGTTTCACT
*
17608267 AAAAATGATTTTTG
1 AAAAATAATTTTTG
17608281 AAAAATAATTTTTG
1 AAAAATAATTTTTG
*
17608295 GAAAATAA
1 AAAAATAA
17608303 CTTGTTTTTT
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:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (14 bp):
AAAAATAATTTTTG
Found at i:17608900 original size:18 final size:18
Alignment explanation
Indices: 17608877--17608916 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
17608867 TTATTATTTT
*
17608877 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
17608895 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
17608913 TAAA
1 TAAA
17608917 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:17608923 original size:19 final size:19
Alignment explanation
Indices: 17608887--17608937 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
17608877 TAAAATTTAC
*
17608887 TATTAAAATAAAAT-TTAAA
1 TATT-AAATAAATTATTAAA
17608906 TATTAAATAAATTATTAAA
1 TATTAAATAAATTATTAAA
*
17608925 -AAT-AATAAATTAT
1 TATTAAATAAATTAT
17608938 ATTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATAAATTATTAAA
Found at i:17613491 original size:2 final size:2
Alignment explanation
Indices: 17613420--17613476 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
17613410 GTTGGGGAAA
17613420 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
17613462 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
17613477 AACCTGTTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17623515 original size:15 final size:17
Alignment explanation
Indices: 17623495--17623528 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17623485 CTATTTACTT
17623495 TTCCTC-AAA-TTTTTA
1 TTCCTCAAAACTTTTTA
17623510 TTCCTCAAAACTTTTTA
1 TTCCTCAAAACTTTTTA
17623527 TT
1 TT
17623529 TTCCCCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
TTCCTCAAAACTTTTTA
Found at i:17633269 original size:27 final size:27
Alignment explanation
Indices: 17633231--17633283 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
17633221 AGAAATCATG
17633231 GATAGCTAAACAGATGACAATTGAGCA
1 GATAGCTAAACAGATGACAATTGAGCA
*
17633258 GATAGCTAAACAGATGGCAATTGAGC
1 GATAGCTAAACAGATGACAATTGAGC
17633284 TGTTGTACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (27 bp):
GATAGCTAAACAGATGACAATTGAGCA
Found at i:17634982 original size:13 final size:13
Alignment explanation
Indices: 17634944--17634984 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
17634934 TGAATCTAAT
*
17634944 TTTTGCATGTATA
1 TTTTGCATGTATG
*
17634957 TTTCTGTATGTATG
1 TTT-TGCATGTATG
17634971 TTTTGCATGTATG
1 TTTTGCATGTATG
17634984 T
1 T
17634985 AAGTCGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (13 bp):
TTTTGCATGTATG
Found at i:17636426 original size:21 final size:22
Alignment explanation
Indices: 17636382--17636433 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
17636372 CCATTTTCAT
* *
17636382 ATTTTGACCCCTATTTTAATCC
1 ATTTTGACCACTATTTTAACCC
*
17636404 ATTTTGACCAGTA-TTTAACCC
1 ATTTTGACCACTATTTTAACCC
17636425 ATTTTGACC
1 ATTTTGACC
17636434 TATATACGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (22 bp):
ATTTTGACCACTATTTTAACCC
Found at i:17642174 original size:49 final size:49
Alignment explanation
Indices: 17642106--17642200 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
17642096 TGACTGCTGG
17642106 GTACTGTTCACGTACGACGCAAATCACGTCCACGTAAGCGCGATTTGCT
1 GTACTGTTCACGTACGACGCAAATCACGTCCACGTAAGCGCGATTTGCT
*
17642155 GTACTGTTCACGTACGACGCAAATCACGTCCACGTAAGTGCGATTT
1 GTACTGTTCACGTACGACGCAAATCACGTCCACGTAAGCGCGATTT
17642201 TCTTCCACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (49 bp):
GTACTGTTCACGTACGACGCAAATCACGTCCACGTAAGCGCGATTTGCT
Found at i:17642269 original size:39 final size:41
Alignment explanation
Indices: 17642216--17642321 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 41
17642206 CACGTCAGCA
* * * *
17642216 AATCGCGCTTACGTGGACGCGATTTGTTGCCACGT-AAGT-
1 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
**
17642255 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCCCCTG
1 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
*
17642296 ACATCGCGCTGACGTGGACGCAATTT
1 A-ATCGCGCTGACGTGGACGCGATTT
17642322 AGGGGAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
39 32 0.56
40 1 0.02
41 1 0.02
42 23 0.40
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (41 bp):
AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
Found at i:17644249 original size:13 final size:13
Alignment explanation
Indices: 17644227--17644267 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
17644217 GTTTCTTTTA
17644227 TTTT-ATTTTAAT
1 TTTTAATTTTAAT
17644239 TTTTAATTTTAAAT
1 TTTTAATTTT-AAT
17644253 TTCTTAA-TTTAAT
1 TT-TTAATTTTAAT
17644266 TT
1 TT
17644268 AATTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 10 0.38
14 8 0.31
15 4 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:17647915 original size:19 final size:21
Alignment explanation
Indices: 17647871--17647917 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
17647861 CGCCTCTCTT
*
17647871 TGCATTCATTTTTCATTCATCA
1 TGCATT-ATATTTCATTCATCA
17647893 -GCATTATATTTCA-TCAT-A
1 TGCATTATATTTCATTCATCA
17647911 TGCATTA
1 TGCATTA
17647918 AGTTTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 10 0.43
20 7 0.30
21 5 0.22
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (21 bp):
TGCATTATATTTCATTCATCA
Found at i:17655812 original size:44 final size:44
Alignment explanation
Indices: 17655753--17656005 Score: 272
Period size: 44 Copynumber: 5.8 Consensus size: 44
17655743 AGCGAATCTT
* * *
17655753 ATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCTACGATTCTC
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
* * * ** * *
17655797 ATCTTCCTGAAGTTGCAGTGGAGCAAATGGAAGTTACAAGTCTT
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
* *
17655841 ATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTTACAAGTCTC
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
* * * * * * * *
17655885 ATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGATTCGAGTCTC
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
* *
17655929 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTA
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
* * **
17655973 ATCTTCCTGAAGTTGCAGTGGAATAGATTAAAG
1 ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG
17656006 TGACAAATCC
Statistics
Matches: 169, Mismatches: 40, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 169 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAGTCTC
Found at i:17655863 original size:88 final size:88
Alignment explanation
Indices: 17655700--17655994 Score: 387
Period size: 88 Copynumber: 3.3 Consensus size: 88
17655690 GTCATCGTGG
* * * * * *
17655700 CAAATCTTATCTCCCTGAATTTGTAGTAGAGCAAATTGAAGATAGCGAA-TCTTATCTCCCTAAA
1 CAAATCTCATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGTTA-C-AAGTCTTATCTCCCTAAA
17655764 GTTGCAATGGAGCAGATTAAAGCTA
64 GTTGCAATGGAGCAGATTAAAGCTA
* * *
17655789 CGATTCTCATCTTCCTGAAGTTGCAGTGGAGCAAATGGAAGTTACAAGTCTTATCTCCCTAAAGT
1 CAAATCTCATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGTTACAAGTCTTATCTCCCTAAAGT
*
17655854 TGCAATGGAGCAGATTAAAGTTA
66 TGCAATGGAGCAGATTAAAGCTA
* * * * * *
17655877 CAAGTCTCATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGATT-CGAGTCTCATCTCCCTAAAG
1 CAAATCTCATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAG-TTACAAGTCTTATCTCCCTAAAG
*
17655941 TTGCAGTGGAGCAGATTAAAGCTA
65 TTGCAATGGAGCAGATTAAAGCTA
*
17655965 CAAATCTAATCTTCCTGAAGTTGCAGTGGA
1 CAAATCTCATCTTCCTGAAGTTGCAGTGGA
17655995 ATAGATTAAA
Statistics
Matches: 181, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
87 2 0.01
88 142 0.78
89 37 0.20
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (88 bp):
CAAATCTCATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGTTACAAGTCTTATCTCCCTAAAGT
TGCAATGGAGCAGATTAAAGCTA
Found at i:17655932 original size:132 final size:132
Alignment explanation
Indices: 17655762--17656011 Score: 320
Period size: 132 Copynumber: 1.9 Consensus size: 132
17655752 TATCTCCCTA
* * * * *
17655762 AAGTTGCAATGGAGCAGATTAAAGCTACGATTCTCATCTTCCTGAAGTTGCAGTGGAGCAAATGG
1 AAGTTGCAATGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAAATGA
* * * * *
17655827 AAGTTACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTTACAAGTCTCATCTTCT
66 AAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAAGTCTCATCTTCT
17655892 TG
131 TG
* * * * * *
17655894 AAGTTGCAGTGGAGTAGATTGAAGATTCGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTA
1 AAGTTGCAATGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAAATGA
* * * *
17655959 AAGCTACAAATCTAATCTTCCTGAAGTTGCAGTGGAATAGATTAAAGTGACAA
66 AAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAA
17656012 ATCCTGTACC
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
132 98 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (132 bp):
AAGTTGCAATGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAAATGA
AAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAAGTCTCATCTTCT
TG
Found at i:17656012 original size:44 final size:44
Alignment explanation
Indices: 17655700--17656037 Score: 268
Period size: 44 Copynumber: 7.7 Consensus size: 44
17655690 GTCATCGTGG
* * * * * * * *
17655700 CAAATCTTATCTCCCTGAATTTGTAGTAGAGCAAATTGAAGATA
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* * *
17655744 GCGAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCTA
1 -CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * ** *
17655789 CGATTCTCATCTTCCTGAAGTTGCAGTGGAGCAAATGGAAGTTA
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * *
17655833 CAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTTA
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * * * *
17655877 CAAGTCTCATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGATT
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* *
17655921 CGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * **
17655965 CAAATCTAATCTTCCTGAAGTTGCAGTGGAATAGATTAAAG-TGA
1 CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCT-A
*
17656009 CAAATC-C-TGTACCTCTAAAGTTGCAGTGG
1 CAAATCTCATCT-CC-CTAAAGTTGCAGTGG
17656038 GTTAGAATGA
Statistics
Matches: 235, Mismatches: 55, Indels: 7
0.79 0.19 0.02
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 196 0.83
45 35 0.15
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CAAATCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA
Found at i:17656030 original size:132 final size:131
Alignment explanation
Indices: 17655759--17656037 Score: 308
Period size: 132 Copynumber: 2.1 Consensus size: 131
17655749 TCTTATCTCC
* * * * *
17655759 CTAAAGTTGCAATGGAGCAGATTAAAGCTACGATTCTCATCTTCCTGAAGTTGCAGTGGAGCAAA
1 CTAAAGTTGCAGTGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAAA
* * * * * * * *
17655824 TGGAAGTTACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTTACAAGTCTCATCT
66 TGAAAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAAATCTCATCC
17655889 T
131 T
* * * * *
17655890 CTTGAAGTTGCAGTGGAGTAGATTGAAGATTCGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAG
1 C-TAAAGTTGCAGTGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAA
* * * * * *
17655955 ATTAAAGCTACAAATCTAATCTTCCTGAAGTTGCAGTGGAATAGATTAAAGTGACAAATC-CTGT
65 ATGAAAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAAATCTC-AT
17656019 ACCT
129 -CCT
17656023 CTAAAGTTGCAGTGG
1 CTAAAGTTGCAGTGG
17656038 GTTAGAATGA
Statistics
Matches: 120, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
131 2 0.02
132 115 0.96
133 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (131 bp):
CTAAAGTTGCAGTGGAGCAGATTAAAGATACGAGTCTCATCTCCCTAAAGTTGCAGTGGAGCAAA
TGAAAGCTACAAATCTAATCTCCCTAAAGTTGCAATGGAACAGATTAAAGTGACAAATCTCATCC
T
Found at i:17656037 original size:88 final size:85
Alignment explanation
Indices: 17655757--17656033 Score: 306
Period size: 88 Copynumber: 3.2 Consensus size: 85
17655747 AATCTTATCT
* * *
17655757 CCCTAAAGTTGCAATGGAGCAGATTAAAGCTACGATTCTCATCTTCCTGAAGTTGCAGTGGAGCA
1 CCCTAAAGTTGCAATGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTGCAGTGGAGTA
* *
17655822 AATGGAAGTTACAAGT-CTTA
66 GATTGAAG-TACAAGTCCTTA
* * *
17655842 TCTCCCTAAAGTTGCAATGGAGCAGATTAAAGTTACAAGTCTCATCTTCTTGAAGTTGCAGTGGA
1 ---CCCTAAAGTTGCAATGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTGCAGTGGA
* *
17655907 GTAGATTGAAGATTCGAGTCTCATCT-
63 GTAGATTGAAG-TACAAGTC-C-T-TA
* * *
17655933 CCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTAATCTTCCTGAAGTTGCAGTGGAATA
1 CCCTAAAGTTGCAATGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTGCAGTGGAGTA
* *
17655998 GATTAAAGTGACAAATCCTGTA
66 GATTGAAGT-ACAAGTCCT-TA
17656020 CCTCTAAAGTTGCA
1 CC-CTAAAGTTGCA
17656034 GTGGGTTAGA
Statistics
Matches: 161, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
86 2 0.01
87 4 0.02
88 152 0.94
90 1 0.01
91 1 0.01
92 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (85 bp):
CCCTAAAGTTGCAATGGAGCAGATTAAAGCTACAAATCTCATCTTCCTGAAGTTGCAGTGGAGTA
GATTGAAGTACAAGTCCTTA
Found at i:17659101 original size:23 final size:23
Alignment explanation
Indices: 17659061--17659106 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17659051 TTTAGATTAT
** *
17659061 TTATTTTAATTTTTAAATTTTAA
1 TTATTTTAATTTAAAAATGTTAA
*
17659084 TTATTTTGATTTAAAAATGTTAA
1 TTATTTTAATTTAAAAATGTTAA
17659107 AAATTCCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTATTTTAATTTAAAAATGTTAA
Found at i:17660545 original size:5 final size:5
Alignment explanation
Indices: 17660535--17660561 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17660525 TGAAATAGAG
17660535 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
17660562 AAGGATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:17661010 original size:16 final size:17
Alignment explanation
Indices: 17660986--17661019 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17660976 TATAAATTTA
*
17660986 ATTATAATT-ATTAAAT
1 ATTAAAATTGATTAAAT
17661002 ATTAAAATTGATTAAAT
1 ATTAAAATTGATTAAAT
17661019 A
1 A
17661020 CACAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTAAAATTGATTAAAT
Found at i:17669052 original size:25 final size:25
Alignment explanation
Indices: 17668924--17669052 Score: 127
Period size: 25 Copynumber: 5.2 Consensus size: 25
17668914 TATGCCCATG
* * *
17668924 CGAGC-ATGTAATCGGAAAGCTCTTT
1 CGAGCGATGTAA-CGGGAAGCTCATA
* *
17668949 CGAGCCATATAACGGGAAGCTCATA
1 CGAGCGATGTAACGGGAAGCTCATA
*
17668974 TGAGCGATGTAACGGGAAGCTCATA
1 CGAGCGATGTAACGGGAAGCTCATA
* * *
17668999 TGAGCGATGTAACGGGAAGCTCTTG
1 CGAGCGATGTAACGGGAAGCTCATA
* *
17669024 CGAGCCAAT-TATCGGGAAGCTCATA
1 CGAG-CGATGTAACGGGAAGCTCATA
17669049 CGAG
1 CGAG
17669053 TTATAAACAG
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
25 80 0.91
26 8 0.09
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (25 bp):
CGAGCGATGTAACGGGAAGCTCATA
Done.