Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 116 of 145
Found at i:38887628 original size:3 final size:3
Alignment explanation
Indices: 38887622--38887659 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38887612 ATTAAACACA
38887622 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38887660 CCAAGTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38887982 original size:49 final size:48
Alignment explanation
Indices: 38887922--38888153 Score: 216
Period size: 49 Copynumber: 4.7 Consensus size: 48
38887912 GATAATAACA
* * *
38887922 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGT-TCTCATAT-CG
* * *
38887971 AGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-GTTCTCATATC-G
* * * *
38888021 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGG-TTCTCATATC-G
* ** * *
38888070 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-GTTCTCATATC-G
* * *
38888120 TACCAACGCCATGTCCCAAACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
38888154 TGACCTCTCA
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
48 2 0.01
49 80 0.51
50 75 0.48
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGGTTCTCATATCG
Found at i:38888046 original size:50 final size:50
Alignment explanation
Indices: 38887922--38888164 Score: 253
Period size: 50 Copynumber: 4.9 Consensus size: 50
38887912 GATAATAACA
* * * *
38887922 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGG-GTGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCT-CGG
* * * * * *
38887971 AGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * *
38888021 TGCCCATGCCATGTCCCAGACATGGTCTTAC--GGGGGCCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCTCGG
* *
38888070 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
* * * *
38888120 TACCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT
38888165 GATCTCAAGG
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
48 5 0.03
49 77 0.47
50 80 0.48
51 3 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCGG
Found at i:38888075 original size:99 final size:99
Alignment explanation
Indices: 38887924--38888151 Score: 262
Period size: 99 Copynumber: 2.3 Consensus size: 99
38887914 TAATAACATG
* * ** * * *
38887924 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTACAGCCAATGCCATATCCCA
1 CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTACAGCCAACGCCATATCCCA
* ** *
38887989 GATATGGTCTTACATGGGAGTTCTCATATCGGTG
66 GACATGGTCTTACATGGGACCTCTCATATCGGTA
* * * *
38888023 CCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCT-CGGTGCCAACGCCATGTCC
1 CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTAC--AGCCAACGCCATATCC
* *
38888086 CAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
64 CAGACATGGTCTTACATGGGACCTCTCATATCGGTA
*
38888122 CCAACGCCATGTCCCAAACATGGTCTTACA
1 CCAACGCCATGTCCCAGACATGGTCTTACA
38888152 TGTGACCTCT
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
97 1 0.01
98 10 0.09
99 96 0.90
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (99 bp):
CCAACGCCATGTCCCAGACATGGTCTTACAGGGGGCCTCTCATCTACAGCCAACGCCATATCCCA
GACATGGTCTTACATGGGACCTCTCATATCGGTA
Found at i:38888188 original size:56 final size:50
Alignment explanation
Indices: 38887924--38888200 Score: 236
Period size: 50 Copynumber: 5.5 Consensus size: 50
38887914 TAATAACATG
* *** * * * *
38887924 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTTCATGTACAG--
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCT-CGGTA
* * * ** * * *
38887973 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
* * * * * *
38888023 CCCATGCCATGTCCCAGACATGGTCTTAC-GGGGGCCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
38888072 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
* *
38888122 CCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCATGATCTCAAGGATA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TCTC--GG-TA
* *
38888178 CCAATGCCATGTCCTAGACATGG
1 CCAACGCCATGTCCCAGACATGG
38888201 AATCTCTTTA
Statistics
Matches: 191, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.01
49 79 0.41
50 81 0.42
52 1 0.01
53 4 0.02
55 2 0.01
56 22 0.12
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTA
Found at i:38889791 original size:50 final size:51
Alignment explanation
Indices: 38889623--38889804 Score: 206
Period size: 51 Copynumber: 3.6 Consensus size: 51
38889613 TGTCTGCGAA
* * * ****
38889623 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAAATAACGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
* * *
38889674 CACGTGTGTAGTACTAAGTGCAAGCTACTATGTGAACC-AGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAG-CTTGGT
* * *
38889725 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGA-AAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
* *
38889775 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
38889805 TGTGTATCAA
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
50 37 0.33
51 74 0.66
52 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAGAAAGCTTGGT
Found at i:38892726 original size:25 final size:25
Alignment explanation
Indices: 38892692--38892778 Score: 156
Period size: 25 Copynumber: 3.5 Consensus size: 25
38892682 TACGAGCACT
38892692 TAACGGGAAGCTCATGTGAGCTGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
38892717 TAACGGGAAGCTCATGTGAGCCGTA
1 TAACGGGAAGCTCATGTGAGCTGTA
*
38892742 TAACGGGAAGCTCATGTGAGCTCTA
1 TAACGGGAAGCTCATGTGAGCTGTA
38892767 TAACGGGAAGCT
1 TAACGGGAAGCT
38892779 TATCCAGGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (25 bp):
TAACGGGAAGCTCATGTGAGCTGTA
Found at i:38892802 original size:50 final size:50
Alignment explanation
Indices: 38892698--38892806 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
38892688 CACTTAACGG
* ** **
38892698 GAAGCTCATGTGAGCTGTATAACGGGAAGCTCATGTGAGCCGTATAACGG
1 GAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCAGAGCCGTATAACAA
* **
38892748 GAAGCTCATGTGAGCTCTATAACGGGAAGCTTATCCAG-GTTGTATAACAA
1 GAAGCTCATGTGAGCTCTATAACGGGAAGCTCAT-CAGAGCCGTATAACAA
38892798 GAAGCTCAT
1 GAAGCTCAT
38892807 AAGAGCCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (50 bp):
GAAGCTCATGTGAGCTCTATAACGGGAAGCTCATCAGAGCCGTATAACAA
Found at i:38897284 original size:2 final size:2
Alignment explanation
Indices: 38897271--38897302 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
38897261 AAAATTTATC
38897271 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38897303 TTACGGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38907548 original size:87 final size:88
Alignment explanation
Indices: 38907434--38907608 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 88
38907424 CTTTGAAAAT
38907434 CAATAATTCCATTTTTTTTAAAATTTTTGAAGTTAATAAAATTTTAAAAGATATATATTTAAAAA
1 CAATAATTCCATTTTTTTTAAAATTTTTGAAGTTAATAAAATTTTAAAAGATATATATTTAAAAA
38907499 ATAAAAAATTAAAACATAATTCA
66 ATAAAAAATTAAAACATAATTCA
38907522 CAATAATTCC-TTTTTTTTAAAATTTTTGAAGTTAATAAAATTTTAAAAGATATATATTTAAAAA
1 CAATAATTCCATTTTTTTTAAAATTTTTGAAGTTAATAAAATTTTAAAAGATATATATTTAAAAA
38907586 ATAAAAAATTAAAACATAATTCA
66 ATAAAAAATTAAAACATAATTCA
38907609 AAATTCAAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 77 0.89
88 10 0.11
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (88 bp):
CAATAATTCCATTTTTTTTAAAATTTTTGAAGTTAATAAAATTTTAAAAGATATATATTTAAAAA
ATAAAAAATTAAAACATAATTCA
Found at i:38915566 original size:20 final size:19
Alignment explanation
Indices: 38915522--38915560 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38915512 GCTCTTGAAC
38915522 TATACTCATTTTTCTATAT
1 TATACTCATTTTTCTATAT
38915541 TATACTCATTTTTCTATAT
1 TATACTCATTTTTCTATAT
38915560 T
1 T
38915561 GGTACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (19 bp):
TATACTCATTTTTCTATAT
Found at i:38918400 original size:10 final size:10
Alignment explanation
Indices: 38918372--38918405 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38918362 TTTCATATTA
38918372 AAATTAAAAT
1 AAATTAAAAT
*
38918382 ATA-TAAAAT
1 AAATTAAAAT
38918391 AAATTAAAAT
1 AAATTAAAAT
38918401 AAATT
1 AAATT
38918406 TTTGGTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:38922984 original size:23 final size:23
Alignment explanation
Indices: 38922923--38922987 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
38922913 ATAAGTGCCA
*
38922923 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38922946 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
38922969 CACTGAAATGTAGCCGAAG
1 CACTGATATGTAGCCGAAG
38922988 TATGTAGCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38922994 original size:13 final size:13
Alignment explanation
Indices: 38922976--38923000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38922966 TACCACTGAA
38922976 ATGTAGCCGAAGT
1 ATGTAGCCGAAGT
38922989 ATGTAGCCGAAG
1 ATGTAGCCGAAG
38923001 CTATCACTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (13 bp):
ATGTAGCCGAAGT
Found at i:38925184 original size:24 final size:23
Alignment explanation
Indices: 38925126--38925196 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
38925116 ACTTTCTGTC
* *
38925126 TTTTTATTTTATAACATTTTTATTGA
1 TTTTTAATTTAT-ACATATTT-TT-A
*
38925152 TTTTTAATTTTTACATATTTTTA
1 TTTTTAATTTATACATATTTTTA
*
38925175 TTTTTCAATTTATATATATTTT
1 TTTTT-AATTTATACATATTTT
38925197 GGAGTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 6 0.15
24 16 0.41
25 7 0.18
26 10 0.26
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTTTAATTTATACATATTTTTA
Found at i:38935723 original size:58 final size:58
Alignment explanation
Indices: 38935582--38935728 Score: 159
Period size: 58 Copynumber: 2.5 Consensus size: 58
38935572 GTACGTAGTG
* * * * * *
38935582 TAAGACCATGGATGAAAGATGTTATGGTAGCATGGTACAAGGTAAAATGTATATAGCG
1 TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
* ** * * * *
38935640 TAAGACCATGGAAGAAAGACACTATGGCGGCACGGTACAAGGTATAAGGTATACGGTA
1 TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
* *
38935698 TAAGACCATAGATGAAAGATGCTATGACAGC
1 TAAGACCATGGATGAAAGATGCTATGGCAGC
38935729 CAGGCATGAT
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (58 bp):
TAAGACCATGGATGAAAGATGCTATGGCAGCACGGTACAAGGTAAAAGGTATACAGCA
Found at i:38935815 original size:32 final size:32
Alignment explanation
Indices: 38935778--38935839 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
38935768 GCATCCACAG
38935778 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
1 AGATAAGCCTGCTGAGACAGTAAACACAGAAT
* *
38935810 AGATAAGTCTGCTGGGACAGTAAACACAGA
1 AGATAAGCCTGCTGAGACAGTAAACACAGA
38935840 TGAATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (32 bp):
AGATAAGCCTGCTGAGACAGTAAACACAGAAT
Found at i:38937344 original size:22 final size:22
Alignment explanation
Indices: 38937319--38937362 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38937309 TCAAAAATAC
*
38937319 AGGAGCACATAAA-TGCTAAATT
1 AGGAGAAC-TAAAGTGCTAAATT
*
38937341 AGGAGAACTAAAGTGTTAAATT
1 AGGAGAACTAAAGTGCTAAATT
38937363 GATTGCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (22 bp):
AGGAGAACTAAAGTGCTAAATT
Found at i:38943041 original size:13 final size:13
Alignment explanation
Indices: 38943023--38943047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38943013 ATAAGGGGAT
38943023 TTAAAATTAAAAA
1 TTAAAATTAAAAA
38943036 TTAAAATTAAAA
1 TTAAAATTAAAA
38943048 CAAATTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:38954442 original size:27 final size:27
Alignment explanation
Indices: 38954412--38954479 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
38954402 GTCTATCTCA
38954412 GAGGCGCCAATGGTGGTGCC-TATCTGG
1 GAGGCGCCAATGGTGGTGCCATA-CTGG
* **
38954439 GAGGCGCCATTATTGGTGCCATACTGG
1 GAGGCGCCAATGGTGGTGCCATACTGG
38954466 GAGGCGCCAATGGT
1 GAGGCGCCAATGGT
38954480 CTGATTTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.22
Consensus pattern (27 bp):
GAGGCGCCAATGGTGGTGCCATACTGG
Found at i:38954569 original size:18 final size:18
Alignment explanation
Indices: 38954533--38954584 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
38954523 ACTAGAGAAA
38954533 CAGAAGAAATAAGAAGGAAG
1 CAGAAGAAA-AA-AAGGAAG
38954553 CAGAAGAAAAAAAGGAAG
1 CAGAAGAAAAAAAGGAAG
* *
38954571 GAAAAGAAGAAAAA
1 CAGAAGAA-AAAAA
38954585 AATGTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 13 0.45
19 7 0.24
20 9 0.31
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (18 bp):
CAGAAGAAAAAAAGGAAG
Found at i:38954585 original size:20 final size:19
Alignment explanation
Indices: 38954529--38954585 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
38954519 TTTTACTAGA
*
38954529 GAAACAGAAGAAATAAGAAG
1 GAAA-AGAAGAAAAAAGAAG
*
38954549 GAAGCAGAAGAAAAAAAGGAAG
1 GAA-AAGAAG-AAAAAA-GAAG
38954571 GAAAAGAAGAAAAAA
1 GAAAAGAAGAAAAAA
38954586 ATGTATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.45
21 10 0.32
22 7 0.23
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (19 bp):
GAAAAGAAGAAAAAAGAAG
Found at i:38957939 original size:6 final size:6
Alignment explanation
Indices: 38957931--38957962 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
38957921 GTCTCTAGCA
*
38957931 CTGGCA CTGGCT CTGGCT CTGGCT CTGGCT CT
1 CTGGCT CTGGCT CTGGCT CTGGCT CTGGCT CT
38957963 AGTGCATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.34, G:0.31, T:0.31
Consensus pattern (6 bp):
CTGGCT
Found at i:38959892 original size:21 final size:21
Alignment explanation
Indices: 38959866--38960013 Score: 116
Period size: 21 Copynumber: 7.2 Consensus size: 21
38959856 NNNNNNNNNN
38959866 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
38959887 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
38959908 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
38959926 TATAAA-TACAA-ATTTAATTAT
1 AAAAAATTACAATA-TTCA-TAC
38959947 AAAATAATTACAATATTCAT--
1 AAAA-AATTACAATATTCATAC
38959967 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
38959988 AAAAAAATTAGAATATTCATA-
1 -AAAAAATTACAATATTCATAC
38960009 AAAAA
1 AAAAA
38960014 TTCTAATCCA
Statistics
Matches: 103, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.03
18 7 0.07
19 19 0.18
20 18 0.17
21 25 0.24
22 22 0.21
23 8 0.08
24 1 0.01
ACGTcount: A:0.59, C:0.11, G:0.01, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:38959976 original size:19 final size:19
Alignment explanation
Indices: 38959866--38960015 Score: 110
Period size: 19 Copynumber: 7.4 Consensus size: 19
38959856 NNNNNNNNNN
38959866 AAAAAATTACAATATTCAT
1 AAAAAATTACAATATTCAT
38959885 ACAAAAAATTACAATATTCAT
1 --AAAAAATTACAATATTCAT
* * *
38959906 ACAAAA-TACTA-ATCCA-
1 AAAAAATTACAATATTCAT
*
38959922 AAACTATAAATACAAATTTAATT-AT
1 AAA--A-AATTAC-AA--T-ATTCAT
38959947 AAAATAATTACAATATTCAT
1 AAAA-AATTACAATATTCAT
38959967 AAAAAATTACAATATTCAT
1 AAAAAATTACAATATTCAT
*
38959986 ACAAAAAAATTAGAATATTCAT
1 ---AAAAAATTACAATATTCAT
38960008 AAAAAATT
1 AAAAAATT
38960016 CTAATCCAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 30
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.02
17 4 0.04
18 5 0.05
19 33 0.31
20 10 0.09
21 20 0.19
22 20 0.19
23 7 0.07
24 1 0.01
25 5 0.05
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAAATTACAATATTCAT
Found at i:38959997 original size:41 final size:41
Alignment explanation
Indices: 38959866--38960015 Score: 125
Period size: 41 Copynumber: 3.7 Consensus size: 41
38959856 NNNNNNNNNN
38959866 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATAC-
1 AAAAAATTACAATATTCAT--AAAAAATTACAATATTCATACA
* * * * *
38959908 --AAAA-TACTA-ATCCA-AAACTATAAATACAA-ATTTAATTATA
1 AAAAAATTACAATATTCATAAA--A-AATTACAATA-TTCA-TACA
*
38959948 AAATAATTACAATATTCATAAAAAATTACAATATTCATACA
1 AAAAAATTACAATATTCATAAAAAATTACAATATTCATACA
*
38959989 AAAAAATTAGAATATTCATAAAAAATT
1 AAAAAATTACAATATTCATAAAAAATT
38960016 CTAATCCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 25
0.69 0.11 0.21
Matches are distributed among these distances:
35 3 0.04
37 2 0.02
38 14 0.17
39 6 0.07
40 4 0.05
41 28 0.34
42 13 0.16
43 6 0.07
44 4 0.05
45 3 0.04
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (41 bp):
AAAAAATTACAATATTCATAAAAAATTACAATATTCATACA
Found at i:38960058 original size:102 final size:101
Alignment explanation
Indices: 38959866--38960049 Score: 280
Period size: 102 Copynumber: 1.8 Consensus size: 101
38959856 NNNNNNNNNN
*
38959866 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCCAAAACTATAA
1 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATAAAAAATACTAATCCAAAACTATAA
* * *
38959931 ATACAAATTTAATTATAAAATAATTACAATATTCAT
66 ACACAAATATAATAATAAAATAATTACAATATTCAT
* *
38959967 AAAAAATTACAATATTCATACAAAAAAATTAGAATATTCATAAAAAATTCTAATCC-AAACTATA
1 AAAAAATTACAATATTCATAC-AAAAAATTACAATATTCATAAAAAATACTAATCCAAAACTATA
38960031 AACACTAAATATAGATAAT
65 AACAC-AAATATA-ATAAT
38960050 TTATAATTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
101 33 0.45
102 37 0.50
103 4 0.05
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (101 bp):
AAAAAATTACAATATTCATACAAAAAATTACAATATTCATAAAAAATACTAATCCAAAACTATAA
ACACAAATATAATAATAAAATAATTACAATATTCAT
Found at i:38960156 original size:3 final size:3
Alignment explanation
Indices: 38960150--38960201 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
38960140 TTTTTTTTCT
*
38960150 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC -TC TTC TTC TCC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
38960195 TTC TTC T
1 TTC TTC T
38960202 CCTTTCTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:38960168 original size:11 final size:11
Alignment explanation
Indices: 38960154--38960198 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
38960144 TTTTCTTTCT
38960154 TCTTCTTCTTC
1 TCTTCTTCTTC
38960165 TCTTCTTCTTC
1 TCTTCTTCTTC
38960176 T-TCTCTTCTTC
1 TCT-TCTTCTTC
38960187 TCCTTC-TCTTC
1 T-CTTCTTCTTC
38960198 T
1 T
38960199 TCTCCTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.87
12 2 0.06
13 1 0.03
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:38960170 original size:14 final size:14
Alignment explanation
Indices: 38960146--38960201 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
38960136 CCTTTTTTTT
38960146 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
38960159 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
38960173 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
*
38960187 TCCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
38960201 T
1 T
38960202 CCTTTCTCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
13 5 0.12
14 36 0.88
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:38960201 original size:17 final size:17
Alignment explanation
Indices: 38960146--38960198 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
38960136 CCTTTTTTTT
38960146 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
38960162 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
*
38960179 -TCTTCTTCTCCTTC-TC
1 TTC-TCTTCTTCTTCTTC
38960195 TTCT
1 TTCT
38960199 TCTCCTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:38960211 original size:17 final size:16
Alignment explanation
Indices: 38960145--38960213 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 16
38960135 ACCTTTTTTT
*
38960145 TTTCTTTCTTCTTCTTC
1 TTTC-TTCTTCTTCTCC
*
38960162 -TTC-TCTTCTTCTTC
1 TTTCTTCTTCTTCTCC
38960176 -TTC-TCTTCTTCTCC
1 TTTCTTCTTCTTCTCC
38960190 -TTC-TCTTCTTCTCC
1 TTTCTTCTTCTTCTCC
38960204 TTTCTCTCTT
1 TTTCT-TCTT
38960214 TTTTTTTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
14 38 0.79
15 3 0.06
16 3 0.06
17 4 0.08
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTTCTTCTTCTCC
Found at i:38960213 original size:14 final size:14
Alignment explanation
Indices: 38960151--38960210 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
38960141 TTTTTTTCTT
*
38960151 TCTTCTTCTTCTTC
1 TCTTCTTCTCCTTC
*
38960165 TCTTCTTCTTCTTC
1 TCTTCTTCTCCTTC
38960179 TCTTCTTCTCCTTC
1 TCTTCTTCTCCTTC
38960193 TCTTCTTCTCCTTTC
1 TCTTCTTCTCC-TTC
38960208 TCT
1 TCT
38960211 CTTTTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
14 38 0.86
15 6 0.14
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTCTTCTCCTTC
Found at i:38961409 original size:26 final size:26
Alignment explanation
Indices: 38961351--38961411 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
38961341 TAAATTTATC
* * *
38961351 AAAAATATTTTTCAAAAGTACTTTTC
1 AAAAACATTTTTCAAAAGTACTTCTA
* * *
38961377 CATAACATTTTTTAAAAGTACTTCTA
1 AAAAACATTTTTCAAAAGTACTTCTA
38961403 AAAAACATT
1 AAAAACATT
38961412 GCTACTAGCC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (26 bp):
AAAAACATTTTTCAAAAGTACTTCTA
Found at i:38974808 original size:14 final size:13
Alignment explanation
Indices: 38974781--38974819 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
38974771 CCCTCCTTTC
*
38974781 TTTCTTTCTTTTT
1 TTTCTTTGTTTTT
38974794 TTT-TTTGGTTTTT
1 TTTCTTT-GTTTTT
38974807 TTTCTTTGTTTTT
1 TTTCTTTGTTTTT
38974820 GTTGCAGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTCTTTGTTTTT
Found at i:38978731 original size:32 final size:31
Alignment explanation
Indices: 38978650--38978732 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
38978640 CATAACTTTT
* * * **
38978650 TTGAAAATTTCAATTAGGCTCTTCCAAATATT
1 TTGAAAA-TTCAATTAAGCTCTTCAAAAAAAA
*
38978682 TTAGAAAATTCTCATTAAGCTCTTCAAAAAAAA
1 TT-GAAAATTC-AATTAAGCTCTTCAAAAAAAA
38978715 TTGAAAAGTTCAATTAAG
1 TTGAAAA-TTCAATTAAG
38978733 TCCCCAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
32 16 0.39
33 25 0.61
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (31 bp):
TTGAAAATTCAATTAAGCTCTTCAAAAAAAA
Found at i:38979018 original size:91 final size:88
Alignment explanation
Indices: 38978879--38979050 Score: 218
Period size: 91 Copynumber: 1.9 Consensus size: 88
38978869 AAAAAAAAAG
* * * * * *
38978879 AAAAACAAAGTAATTAAGCTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTTAAAATGCAT
1 AAAAAAAAAGCAATTAAACTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATACAC
* *
38978944 CAAAAAGGCTCTCAAACTTCTTC
66 CAAAAAGACCCTCAAACTTCTTC
* * *
38978967 AAAAAAAAAGCAATTAAACTCCTACTTTTTTTTTCACTTAATTGGGTACTTGAACTTTCAAAATA
1 AAAAAAAAAGCAATTAAACTCCT-C--TTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATA
38979032 CACCAAAAAGACCCTCAAA
63 CACCAAAAAGACCCTCAAA
38979051 ATTTTTAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
88 20 0.29
89 1 0.01
91 49 0.70
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (88 bp):
AAAAAAAAAGCAATTAAACTCCTCTTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAATACAC
CAAAAAGACCCTCAAACTTCTTC
Found at i:38979661 original size:89 final size:87
Alignment explanation
Indices: 38979525--38979715 Score: 253
Period size: 89 Copynumber: 2.2 Consensus size: 87
38979515 CAGGGGTTTA
*
38979525 AATTGTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA-CCAAATTGA
1 AATTGTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAAA-TGA
*
38979589 GTGCAAAAAAAAAGTAGGGAA-TT
65 GTGCAAAAAAAAAGTA-AGAACTT
* *
38979612 AATTGTTTTTTTTTAAAAGGTTTGA-GGTCTTTTTTATGTATTTTAAAAGTTCAAGTACCCAAAT
1 AATTGTTTTTTTTT--AA-GTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAAAT
*
38979676 GAGTGCGAAAAAAAAGTAAGAACTT
63 GAGTGCAAAAAAAAAGTAAGAACTT
*
38979701 AATTACTTTTTTTTT
1 AATT-GTTTTTTTTT
38979716 TTTAAAATTG
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
87 14 0.15
88 3 0.03
89 55 0.60
90 20 0.22
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (87 bp):
AATTGTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTACCCAAATGAG
TGCAAAAAAAAAGTAAGAACTT
Found at i:38979735 original size:89 final size:85
Alignment explanation
Indices: 38979525--38979737 Score: 232
Period size: 89 Copynumber: 2.4 Consensus size: 85
38979515 CAGGGGTTTA
** *
38979525 AATTGTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCAAATTGAG
1 AATTGTTTTTTTTTAAAATTGA-GGTCTTTTT-ATGCATTTTAAAAGTTCAAGTACCAAATTGAG
*
38979590 TGCAAAAAAAAAGTAGGGAATT
64 TGCAAAAAAAAAGTAGAGAATT
*
38979612 AATTGTTTTTTTTTAAAAGGTTTGAGGTCTTTTTTATGTATTTTAAAAGTTCAAGTACCCAAA-T
1 AATTGTTTTTTTTTAAAA---TTGAGGTC-TTTTTATGCATTTTAAAAGTTCAAGTA-CCAAATT
*
38979676 GAGTGCGAAAAAAAAGTA-AGAACTT
61 GAGTGCAAAAAAAAAGTAGAGAA-TT
* *
38979701 AATTACTTTTTTTTTTTTAAAATTGAGGACTTTTTAT
1 -A--A-TTGTTTTTTTTTAAAATTGAGGTCTTTTTAT
38979738 CCACTTAAAC
Statistics
Matches: 108, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
87 16 0.15
88 3 0.03
89 51 0.47
90 22 0.20
92 1 0.01
93 15 0.14
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (85 bp):
AATTGTTTTTTTTTAAAATTGAGGTCTTTTTATGCATTTTAAAAGTTCAAGTACCAAATTGAGTG
CAAAAAAAAAGTAGAGAATT
Found at i:38988479 original size:30 final size:30
Alignment explanation
Indices: 38988439--38988724 Score: 320
Period size: 30 Copynumber: 9.3 Consensus size: 30
38988429 ATATATGTAA
* *
38988439 ACATATACAAATCATTTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
38988469 ACATGTACAAATCCATTCGGCAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
38988499 CCATATAAAAATCAATTCGGCAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* **
38988529 ACATATACAAATCAATTTGATAATGTATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* * *
38988559 CCATATACAAATCAATTCGGCTATGCATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
38988589 CCATATACAAATCAATTCGGCAATATATAT
1 ACATATACAAATCAATTCGGCAATGTATAT
* *
38988619 ATCCATATACAAATCAATTCGACAATATATATGT
1 A--CATATACAAATCAATTCGGCAATGTATA--T
* * *
38988653 AAACATATACAAATCATTTCGACAATATATAT
1 --ACATATACAAATCAATTCGGCAATGTATAT
* *
38988685 ACATGTACAAATCAATTCGGCAATGTATAAA
1 ACATATACAAATCAATTCGGCAATGTAT-AT
38988716 ACATATACA
1 ACATATACA
38988725 TTTGAATTCA
Statistics
Matches: 218, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
30 152 0.70
31 9 0.04
32 28 0.13
34 28 0.13
36 1 0.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (30 bp):
ACATATACAAATCAATTCGGCAATGTATAT
Found at i:38993358 original size:30 final size:30
Alignment explanation
Indices: 38993324--38993383 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
38993314 TATTTTATTA
38993324 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
38993354 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
38993384 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:39002906 original size:13 final size:13
Alignment explanation
Indices: 39002888--39002915 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39002878 TGAACCCGAG
39002888 AACCAAAACCCAA
1 AACCAAAACCCAA
39002901 AACCAAAACCCAA
1 AACCAAAACCCAA
39002914 AA
1 AA
39002916 ACTGGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (13 bp):
AACCAAAACCCAA
Found at i:39003176 original size:13 final size:13
Alignment explanation
Indices: 39003158--39003185 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39003148 TGAACCCGAG
39003158 AACCAAAACCCAA
1 AACCAAAACCCAA
39003171 AACCAAAACCCAA
1 AACCAAAACCCAA
39003184 AA
1 AA
39003186 ACTGGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (13 bp):
AACCAAAACCCAA
Found at i:39003255 original size:270 final size:271
Alignment explanation
Indices: 39002754--39003294 Score: 1059
Period size: 270 Copynumber: 2.0 Consensus size: 271
39002744 TAATTTGGAT
39002754 AAAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATAATATTTTTTGAATTTAATTTTCAA
1 AAAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATAATATTTTTTGAATTTAATTTTCAA
39002819 GTCAAATAATTGGCCCGATAGGTAATTGAACTTGAAAATTGGACCCAAGATAAAAAAATTGAACC
66 GTCAAATAATTGGCCCGATAGGTAATTGAACTTGAAAATTGGACCCAAGATAAAAAAATTGAACC
39002884 CGAGAACCAAAACCCAAAACCAAAACCCAAAAACTGGTTGAATTGGGCCCTGTGTATAAAGCTAA
131 CGAGAACCAAAACCCAAAACCAAAACCCAAAAACTGGTTGAATTGGGCCCTGTGTATAAAGCTAA
39002949 GCTGACGGTCCATCCAGTGGCTGGATCAGACCGGTCGGGCAATCATTGGCCCTGACCGAACCGGC
196 GCTGACGGTCCATCCAGTGGCTGGATCAGACCGGTCGGGCAATCATTGGCCCTGACCGAACCGGC
39003014 TAGACCTATTA
261 TAGACCTATTA
39003025 AAAGTAAAA-TAAATTTAAT-AAATTAATTAAAATAAATATAATATTTTTTGAATTTAATTTTCA
1 AAAGTAAAATTAAA-TTAATCAAATTAATTAAAATAAATATAATATTTTTTGAATTTAATTTTCA
39003088 AGTCAAATAATTGGCCCGATAGGTAATTGAACTTGAAAATTGGACCCAAGATAAAAAAATTGAAC
65 AGTCAAATAATTGGCCCGATAGGTAATTGAACTTGAAAATTGGACCCAAGATAAAAAAATTGAAC
39003153 CCGAGAACCAAAACCCAAAACCAAAACCCAAAAACTGGTTGAATTGGGCCCTGTGTATAAAGCTA
130 CCGAGAACCAAAACCCAAAACCAAAACCCAAAAACTGGTTGAATTGGGCCCTGTGTATAAAGCTA
39003218 AGCTGACGGTCCATCCAGTGGCTGGATCAGACCGGTCGGGCAATCATTGGCCCTGACCGAACCGG
195 AGCTGACGGTCCATCCAGTGGCTGGATCAGACCGGTCGGGCAATCATTGGCCCTGACCGAACCGG
39003283 CTAGACCTATTA
260 CTAGACCTATTA
39003295 GGGGAAAACG
Statistics
Matches: 269, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
270 255 0.95
271 14 0.05
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (271 bp):
AAAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATAATATTTTTTGAATTTAATTTTCAA
GTCAAATAATTGGCCCGATAGGTAATTGAACTTGAAAATTGGACCCAAGATAAAAAAATTGAACC
CGAGAACCAAAACCCAAAACCAAAACCCAAAAACTGGTTGAATTGGGCCCTGTGTATAAAGCTAA
GCTGACGGTCCATCCAGTGGCTGGATCAGACCGGTCGGGCAATCATTGGCCCTGACCGAACCGGC
TAGACCTATTA
Found at i:39020017 original size:1 final size:1
Alignment explanation
Indices: 39020013--39020076 Score: 83
Period size: 1 Copynumber: 64.0 Consensus size: 1
39020003 TTTTTCGTTC
** * * *
39020013 TTTTTTTTTTTTTTTTTTTTTTTTTTACTTTCTTTTTTTGTTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39020077 GTGATTGTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.02, C:0.05, G:0.02, T:0.92
Consensus pattern (1 bp):
T
Found at i:39020017 original size:12 final size:10
Alignment explanation
Indices: 39020000--39020073 Score: 78
Period size: 10 Copynumber: 7.0 Consensus size: 10
39019990 TGGTGGTGTA
39020000 CTTTTTTTCGTT
1 CTTTTTTT--TT
39020012 CTTTTTTTTT
1 CTTTTTTTTT
*
39020022 TTTTTTTTTT
1 CTTTTTTTTT
*
39020032 TTTTTTTACTTT
1 CTTTTTT--TTT
39020044 CTTTTTTTGTT
1 CTTTTTTT-TT
39020055 CTTTTTTTTT
1 CTTTTTTTTT
39020065 -TTTTTTTTT
1 CTTTTTTTTT
39020074 TTTGTGATTG
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.16
10 21 0.37
11 10 0.18
12 17 0.30
ACGTcount: A:0.01, C:0.08, G:0.03, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:39020046 original size:32 final size:33
Alignment explanation
Indices: 39020001--39020072 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 33
39019991 GGTGGTGTAC
39020001 TTTTTTTCGTTCTTTTTTT-TT-TTTTTTTTTT
1 TTTTTTTCGTTCTTTTTTTGTTCTTTTTTTTTT
*
39020032 TTTTTTTACTTTCTTTTTTTGTTCTTTTTTTTTT
1 TTTTTTT-CGTTCTTTTTTTGTTCTTTTTTTTTT
39020066 TTTTTTT
1 TTTTTTT
39020073 TTTTGTGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 7 0.19
32 11 0.30
33 2 0.05
34 17 0.46
ACGTcount: A:0.01, C:0.07, G:0.03, T:0.89
Consensus pattern (33 bp):
TTTTTTTCGTTCTTTTTTTGTTCTTTTTTTTTT
Found at i:39025180 original size:23 final size:23
Alignment explanation
Indices: 39025136--39025180 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39025126 CGAAAACCCT
*
39025136 TAAAACAAAAACCCTAATCCTAA
1 TAAAACAAAAACCCTAACCCTAA
* **
39025159 TAAAATAAAAACTTTAACCCTA
1 TAAAACAAAAACCCTAACCCTA
39025181 GGAGAGAACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (23 bp):
TAAAACAAAAACCCTAACCCTAA
Found at i:39030021 original size:2 final size:2
Alignment explanation
Indices: 39030014--39030038 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39030004 ACTTATATTA
39030014 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
39030039 AAAAGCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:39031294 original size:10 final size:9
Alignment explanation
Indices: 39031280--39031387 Score: 87
Period size: 9 Copynumber: 11.7 Consensus size: 9
39031270 ACATATGGCA
39031280 AAAAATTAT
1 AAAAATTAT
39031289 AAAAA--AT
1 AAAAATTAT
*
39031296 AAAAGTTAT
1 AAAAATTAT
39031305 AAAAATTAT
1 AAAAATTAT
*
39031314 -TAAATTAT
1 AAAAATTAT
39031322 AAAAAAATTAT
1 --AAAAATTAT
*
39031333 AAAAATCAT
1 AAAAATTAT
*
39031342 AAAAATATAAA
1 AAAAAT-T-AT
39031353 AAAATATTAT
1 AAAA-ATTAT
*
39031363 AAAATTTTAT
1 AAAA-ATTAT
*
39031373 AAAAATCAT
1 AAAAATTAT
39031382 AAAAAT
1 AAAAAT
39031388 AGATATAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.08
8 7 0.09
9 38 0.47
10 14 0.17
11 13 0.16
12 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:39031304 original size:16 final size:15
Alignment explanation
Indices: 39031281--39031355 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 15
39031271 CATATGGCAA
39031281 AAAATTATAAAAAAT
1 AAAATTATAAAAAAT
39031296 AAAAGTTATAAAAATTAT
1 AAAA-TTATAAAAA--AT
*
39031314 TAAATTAT---AAA-
1 AAAATTATAAAAAAT
39031325 AAAATTATAAAAATCAT
1 AAAATTATAAAAA--AT
*
39031342 AAAAATATAAAAAA
1 AAAATTATAAAAAA
39031356 ATATTATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
11 7 0.15
12 1 0.02
14 4 0.08
15 5 0.10
16 10 0.21
17 16 0.33
18 5 0.10
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (15 bp):
AAAATTATAAAAAAT
Found at i:39031327 original size:19 final size:20
Alignment explanation
Indices: 39031305--39031407 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
39031295 TAAAAGTTAT
* *
39031305 AAAAATTAT-TAAATTATAA
1 AAAAATTATAAAAATCATAA
39031324 AAAAATTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
* *
39031344 AAATA-TAAAAAAAT-ATTATA
1 AAAAATTATAAAAATCA-TA-A
**
39031364 AAATTTTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
39031384 AAATAGA-TAT-AAAATGCATAA
1 AAA-A-ATTATAAAAAT-CATAA
39031405 AAA
1 AAA
39031408 TGACCTTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.01
19 19 0.28
20 26 0.38
21 21 0.31
22 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:39031362 original size:30 final size:29
Alignment explanation
Indices: 39031291--39031408 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 29
39031281 AAAATTATAA
* * *
39031291 AAAATAAAAGTTATAAAAATTATTAAATTAT
1 AAAA-AAAA-TTATAAAAATCATAAAAATAT
39031322 -AAAAAAATTATAAAAATCATAAAAATAT
1 AAAAAAAATTATAAAAATCATAAAAATAT
* *
39031350 AAAAAAATATTATAAAATTTTATAAAAATCAT
1 AAAAAAA-ATTATAAAA-ATCATAAAAAT-AT
*
39031382 AAAAATAGA-TAT-AAAATGCATAAAAAT
1 AAAAA-AAATTATAAAAAT-CATAAAAAT
39031409 GACCTTTAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
28 18 0.25
29 11 0.15
30 23 0.32
31 12 0.16
32 8 0.11
33 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAAAAATTATAAAAATCATAAAAATAT
Found at i:39031377 original size:11 final size:11
Alignment explanation
Indices: 39031317--39031378 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 11
39031307 AAATTATTAA
*
39031317 ATTATAAAAAA
1 ATTATAAAAAT
39031328 ATTAT-AAAA-
1 ATTATAAAAAT
*
39031337 ATCATAAAAAT
1 ATTATAAAAAT
*
39031348 A-TAAAAAAAT
1 ATTATAAAAAT
39031358 ATTAT-AAAAT
1 ATTATAAAAAT
*
39031368 TTTATAAAAAT
1 ATTATAAAAAT
39031379 CATAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 4 0.10
10 25 0.60
11 13 0.31
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTATAAAAAT
Found at i:39031394 original size:21 final size:19
Alignment explanation
Indices: 39031324--39031408 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 19
39031314 TAAATTATAA
39031324 AAAAAT-TATAAAAATCAT
1 AAAAATATATAAAAATCAT
*
39031342 AAAAATATAAAAAAAT-ATT
1 AAAAATATATAAAAATCA-T
*
39031361 ATAAAATTTTATAAAAATCAT
1 A-AAAA-TATATAAAAATCAT
*
39031382 AAAAATAGATATAAAATGCAT
1 AAAAATATATA-AAAAT-CAT
39031403 AAAAAT
1 AAAAAT
39031409 GACCTTTAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
18 7 0.13
19 14 0.25
20 13 0.24
21 20 0.36
22 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATATATAAAAATCAT
Found at i:39031395 original size:31 final size:31
Alignment explanation
Indices: 39031296--39031398 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 31
39031286 TATAAAAAAT
* * *
39031296 AAAAG-TTATAAAA-ATTATTAAATTAT-AA
1 AAAAGATTATAAAATTTTATAAAAATATAAA
* *
39031324 AAAA-ATTATAAAA-ATCATAAAAATATAAA
1 AAAAGATTATAAAATTTTATAAAAATATAAA
*
39031353 AAAATATTATAAAATTTTATAAAAATCATAAA
1 AAAAGATTATAAAATTTTATAAAAAT-ATAAA
*
39031385 AATAGA-TATAAAAT
1 AAAAGATTATAAAAT
39031399 GCATAAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 22 0.35
29 6 0.10
30 9 0.14
31 17 0.27
32 9 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (31 bp):
AAAAGATTATAAAATTTTATAAAAATATAAA
Found at i:39031405 original size:40 final size:40
Alignment explanation
Indices: 39031329--39031406 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
39031319 TATAAAAAAA
* **
39031329 TTATAAAAATCATAAAAATATAAAAAAATATTATAAAATT
1 TTATAAAAATCATAAAAATAGAAAAAAATAGCATAAAATT
*
39031369 TTATAAAAATCATAAAAATAGATATAAAAT-GCATAAAA
1 TTATAAAAATCATAAAAATAGA-AAAAAATAGCATAAAA
39031407 ATGACCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (40 bp):
TTATAAAAATCATAAAAATAGAAAAAAATAGCATAAAATT
Found at i:39031871 original size:16 final size:17
Alignment explanation
Indices: 39031837--39031871 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39031827 AAAGTTAGAG
*
39031837 AGCCTTTTATACCATTA
1 AGCCTTTTATACAATTA
39031854 AGCCTTTTATA-AATTA
1 AGCCTTTTATACAATTA
39031870 AG
1 AG
39031872 TGTTTAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (17 bp):
AGCCTTTTATACAATTA
Found at i:39038619 original size:41 final size:41
Alignment explanation
Indices: 39038572--39038711 Score: 210
Period size: 41 Copynumber: 3.4 Consensus size: 41
39038562 TATATGATTG
* *
39038572 GCACTAAGTGTGCGAAATTAAATAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
39038613 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
* * * *
39038654 ACACTAAGTGTGCGAAACCAAGTAATTATGTT-AATAACGG
1 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
*
39038694 GCACTAAGTGTGCAAAAC
1 GCACTAAGTGTGCGAAAC
39038712 CGAGATCAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 23 0.25
41 68 0.75
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
Found at i:39042729 original size:264 final size:265
Alignment explanation
Indices: 39042232--39042739 Score: 874
Period size: 265 Copynumber: 1.9 Consensus size: 265
39042222 TTCTCCCACT
39042232 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
1 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
* * * *
39042297 CTAGTGGCATTCTTACCTAATTTACATGTCATGCTTCCAGTATATGCATGACATGTTATGAAAAT
66 CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
**
39042362 TTTATAATATTCACATTCATTCATTCAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
131 TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
*
39042427 CTCCACAATTTTTCGTTTAAGGGAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
196 CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
39042492 TTACA
261 TTACA
*
39042497 CAATATTTTAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
1 CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
* * * *
39042562 CTAGTAGCATTCTTACCTAATCTATATGACATGCTTTCAGTATATGCATGACATGCTATGATAGT
66 CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
* *
39042627 TTTATAATATTCACATTCATTTA-GAAGAAGAATCAATCAACCATAAAAACAAACAATTTTGATT
131 TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
*
39042691 CTCCACAATTTTTCGTTTAAGGAAAAAACCGAAGAAGTGAATGTGAACA
196 CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACA
39042740 GTGCACCAGG
Statistics
Matches: 228, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
264 85 0.37
265 143 0.63
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (265 bp):
CAATATTTAAAAAAAAATATGCAAGGTTTTTTATCCTAGATTTCAAGAATGATGATACAATAGTC
CTAGTAGCATTCTTACCTAATCTACATGACATGCTTCCAGTATATGCATGACATGCTATGAAAAT
TTTATAATATTCACATTCATTCATGAAGAAGAATCAATCAACCATAAAAACAAACAAATTTGATT
CTCCACAATTTTTCGTTTAAGGAAAAAACCAAAGAAGTGAATGTGAACATTTCAGGGACCTTCTC
TTACA
Found at i:39045544 original size:23 final size:23
Alignment explanation
Indices: 39045514--39045561 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
39045504 TATCATCTGT
* *
39045514 TTTATGATATGAGATTAGTCTTA
1 TTTATGATATGAGATCACTCTTA
39045537 TTTATGATATGAGATCACTCTTA
1 TTTATGATATGAGATCACTCTTA
39045560 TT
1 TT
39045562 GGATTAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (23 bp):
TTTATGATATGAGATCACTCTTA
Found at i:39053231 original size:13 final size:13
Alignment explanation
Indices: 39053213--39053239 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39053203 TTTTCAAAAC
39053213 TTAGAAACATGTA
1 TTAGAAACATGTA
39053226 TTAGAAACATGTA
1 TTAGAAACATGTA
39053239 T
1 T
39053240 CAATACCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TTAGAAACATGTA
Found at i:39053408 original size:19 final size:20
Alignment explanation
Indices: 39053384--39053434 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
39053374 CCAATCATAT
39053384 GTATCGATACCTT-TGTAAA
1 GTATCGATACCTTGTGTAAA
**
39053403 GTATCGATACCTTGGTGTAGG
1 GTATCGATACCTT-GTGTAAA
39053424 GTATCGATACC
1 GTATCGATACC
39053435 AAATTGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
GTATCGATACCTTGTGTAAA
Found at i:39054549 original size:21 final size:21
Alignment explanation
Indices: 39054524--39054572 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39054514 AGCGGTGGCA
*
39054524 GTGAGATCAGTTACTGTAGCG
1 GTGAGATCAGATACTGTAGCG
**
39054545 GTGAGATTGGATACTGTAGCG
1 GTGAGATCAGATACTGTAGCG
39054566 GTGAGAT
1 GTGAGAT
39054573 TAGAAACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.37, T:0.29
Consensus pattern (21 bp):
GTGAGATCAGATACTGTAGCG
Found at i:39062185 original size:46 final size:46
Alignment explanation
Indices: 39062128--39062217 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
39062118 GGTAACACAC
*
39062128 ATATGACAAGGTCATTGGAAAAAACAGTTGGACGAATTGCTTTCGT
1 ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTCGT
* *
39062174 ATATGATAAGGTCATTGGAAAAAGCAGTTGGACAAATTGCTTTC
1 ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTC
39062218 ATAAAGAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (46 bp):
ATATGACAAGGTCATTGGAAAAAACAGTTGGACAAATTGCTTTCGT
Found at i:39064537 original size:25 final size:25
Alignment explanation
Indices: 39064472--39064527 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
39064462 AGCAAAAAAT
* *
39064472 GGTAAGCTCCTCCGAGTTGGATATC
1 GGTAAGCTCATACGAGTTGGATATC
39064497 GGTAAGCTCATACGAGTTGTGA-ATC
1 GGTAAGCTCATACGAGTTG-GATATC
39064522 GGTAAG
1 GGTAAG
39064528 TTCTGACGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCATACGAGTTGGATATC
Found at i:39075353 original size:41 final size:40
Alignment explanation
Indices: 39075308--39075456 Score: 118
Period size: 41 Copynumber: 3.6 Consensus size: 40
39075298 AGTGCCTAGA
* *
39075308 AGGCTTATTGCCAATGAGATAATTCAAACTCTATGTCTAAC
1 AGGCTTA-TGCCAATGAAACAATTCAAACTCTATGTCTAAC
* ** * *
39075349 AGGCTGGATGCCGGTGAAACAATTCAGACTCTATGTCTAGC
1 AGGCT-TATGCCAATGAAACAATTCAAACTCTATGTCTAAC
* * * * * *
39075390 AGGCTTGATACCAGTAAAACAATTCAGACTTTATGTCTAGC
1 AGGCTT-ATGCCAATGAAACAATTCAAACTCTATGTCTAAC
** *
39075431 AGGCTTGATGCCTGTGAAACATTTCA
1 AGGCTT-ATGCCAATGAAACAATTCA
39075457 GACTTTAAGT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
41 89 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (40 bp):
AGGCTTATGCCAATGAAACAATTCAAACTCTATGTCTAAC
Found at i:39075457 original size:41 final size:41
Alignment explanation
Indices: 39075328--39075472 Score: 191
Period size: 41 Copynumber: 3.5 Consensus size: 41
39075318 CCAATGAGAT
* * * *
39075328 AATTCAAACTCTATGTCTAACAGGCTGGATGCCGGTGAAAC
1 AATTCAGACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* *
39075369 AATTCAGACTCTATGTCTAGCAGGCTTGATACCAGTAAAAC
1 AATTCAGACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* *
39075410 AATTCAGACTTTATGTCTAGCAGGCTTGATGCCTGTGAAAC
1 AATTCAGACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
* * *
39075451 ATTTCAGACTTTAAGTCTAGCA
1 AATTCAGACTCTATGTCTAGCA
39075473 AGCCAAAAGC
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
AATTCAGACTCTATGTCTAGCAGGCTTGATGCCAGTGAAAC
Found at i:39081986 original size:4 final size:4
Alignment explanation
Indices: 39081977--39082005 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39081967 TGTTAGACAT
39081977 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
39082006 GTGTGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:39087509 original size:25 final size:22
Alignment explanation
Indices: 39087466--39087511 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39087456 GATGTTTAGA
*
39087466 ATTTTACTCAAATAATAACTTT
1 ATTTTACTCAAAAAATAACTTT
39087488 ATTTTACATCAATAAAATTAACTT
1 ATTTTAC-TCAA-AAAA-TAACTT
39087512 AACTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 3 0.15
25 6 0.30
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTACTCAAAAAATAACTTT
Found at i:39088672 original size:25 final size:24
Alignment explanation
Indices: 39088642--39088695 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
39088632 ACGAACGAAC
*
39088642 GAAAAAAGAGAAATAGTAGCAAAAAA
1 GAAAAAAGA-AAATAGGAG-AAAAAA
*
39088668 GAAAAAAGAAAATAGGAGAAAAAC
1 GAAAAAAGAAAATAGGAGAAAAAA
39088692 GAAA
1 GAAA
39088696 TACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 8 0.31
26 9 0.35
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.06
Consensus pattern (24 bp):
GAAAAAAGAAAATAGGAGAAAAAA
Found at i:39089763 original size:17 final size:17
Alignment explanation
Indices: 39089737--39090268 Score: 211
Period size: 17 Copynumber: 32.1 Consensus size: 17
39089727 AATTTTTATG
39089737 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
*
39089755 ACACGAAAATTTCGAAA
1 ACACGAAAATTTTGAAA
* * *
39089772 ACATG-AATTTTTTAAA
1 ACACGAAAATTTTGAAA
** *
39089788 ACACGAATTTTTTTAAA
1 ACACGAAAATTTTGAAA
*
39089805 ACACGAGAATTTTTTTTGAAA
1 ACACGA-AA---ATTTTGAAA
39089826 ACACG---------AAA
1 ACACGAAAATTTTGAAA
*
39089834 ACATGAAAATTTTGAAA
1 ACACGAAAATTTTGAAA
39089851 ACACGAAAATTTTTG-AA
1 ACACGAAAA-TTTTGAAA
* * **
39089868 ACACGAGAATTTTTATG
1 ACACGAAAATTTTGAAA
39089885 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
*
39089903 ACACGAAAATTTCGAAA
1 ACACGAAAATTTTGAAA
* * *
39089920 ACATG-AATTTTTTAAA
1 ACACGAAAATTTTGAAA
** *
39089936 ACACGAATTTTTTTAAA
1 ACACGAAAATTTTGAAA
*
39089953 ACACGAGAATTTT----
1 ACACGAAAATTTTGAAA
**** ***
39089966 TTTTGAAAA-CACGAAA
1 ACACGAAAATTTTGAAA
*
39089982 ACATGAAAATTTTGAAA
1 ACACGAAAATTTTGAAA
39089999 ACACGAAAATTTTTG-AA
1 ACACGAAAA-TTTTGAAA
* * **
39090016 ACACGAGAATTTTTATG
1 ACACGAAAATTTTGAAA
39090033 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
*
39090051 ACACGAAAATTTCGAAA
1 ACACGAAAATTTTGAAA
* * *
39090068 ACATG-AATTTTTTAAA
1 ACACGAAAATTTTGAAA
* ** *
39090084 ACATGAATTTTTTTTAAA
1 ACACGAA-AATTTTGAAA
*
39090102 ACACGAGAATTTT----
1 ACACGAAAATTTTGAAA
**** ***
39090115 TTTTGAAAA-CACGAAA
1 ACACGAAAATTTTGAAA
*
39090131 ACATGAAAATTTTGAAA
1 ACACGAAAATTTTGAAA
39090148 ACACGAAAATTTTTG-AA
1 ACACGAAAA-TTTTGAAA
* * **
39090165 ACACGAGAATTTTTATG
1 ACACGAAAATTTTGAAA
39090182 ACACGAAAAATTTTGAAA
1 ACACG-AAAATTTTGAAA
39090200 ACACGAAAATTTTTG-AA
1 ACACGAAAA-TTTTGAAA
*
39090217 ACACAAAAATTTT-AAA
1 ACACGAAAATTTTGAAA
* *
39090233 ACACTAACATTTGTG-AA
1 ACACGAAAATTT-TGAAA
*
39090250 ACACGAAAACTCTTGAAA
1 ACACGAAAA-TTTTGAAA
39090268 A
1 A
39090269 TGTTAAAAGT
Statistics
Matches: 381, Mismatches: 91, Indels: 84
0.69 0.16 0.15
Matches are distributed among these distances:
8 7 0.02
13 8 0.02
16 77 0.20
17 192 0.50
18 84 0.22
21 13 0.03
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (17 bp):
ACACGAAAATTTTGAAA
Found at i:39089982 original size:131 final size:128
Alignment explanation
Indices: 39089847--39090107 Score: 305
Period size: 131 Copynumber: 2.0 Consensus size: 128
39089837 TGAAAATTTT
* *
39089847 GAAAACACGAAAATTTTTG-AAACACGAGAATTTTT-ATGACACGAAAAATTTTGAAAACACG-A
1 GAAAACACGAAAA-TTTTGAAAACACGAAAATTTTTGA-AACACG-AAAATTTTGAAAACACGAA
* * **
39089909 AAATTTCGAAAACATG-AATTTTTTAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAA
63 AAATTTCGAAAACACGAAAATTTCGAAAACACGAA-TTTTTTAAAACA--AGAATTTTTTTT-AA
39089973 AACAC
124 AACAC
* * * **
39089978 GAAAACATGAAAATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAA
1 GAAAACACGAAAATTTTGAAAACACGAAAATTTTTGAAACACGAAAATTTTGAAAACACGAAAAA
* * *
39090043 TTTTGAAAACACGAAAATTTCGAAAACATGAATTTTTTAAAACATGAATTTTTTTTAAAACAC
66 TTTCGAAAACACGAAAATTTCGAAAACACGAATTTTTTAAAACAAGAATTTTTTTTAAAACAC
39090106 GA
1 GA
39090108 GAATTTTTTT
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
128 9 0.08
129 11 0.10
130 18 0.16
131 59 0.53
132 15 0.13
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (128 bp):
GAAAACACGAAAATTTTGAAAACACGAAAATTTTTGAAACACGAAAATTTTGAAAACACGAAAAA
TTTCGAAAACACGAAAATTTCGAAAACACGAATTTTTTAAAACAAGAATTTTTTTTAAAACAC
Found at i:39090094 original size:15 final size:16
Alignment explanation
Indices: 39090065--39090096 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39090055 GAAAATTTCG
39090065 AAAACATGAATTTTTT
1 AAAACATGAATTTTTT
39090081 AAAACATGAATTTTTT
1 AAAACATGAATTTTTT
39090097 TTAAAACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
AAAACATGAATTTTTT
Found at i:39090111 original size:20 final size:20
Alignment explanation
Indices: 39090075--39090128 Score: 76
Period size: 18 Copynumber: 2.8 Consensus size: 20
39090065 AAAACATGAA
*
39090075 TTTTTTAAAACA--TGAATT
1 TTTTTTAAAACACGAGAATT
39090093 TTTTTTAAAACACGAGAATT
1 TTTTTTAAAACACGAGAATT
39090113 TTTTTTGAAAACACGA
1 TTTTTT-AAAACACGA
39090129 AAACATGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 12 0.38
20 11 0.34
21 9 0.28
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTTTTAAAACACGAGAATT
Found at i:39090219 original size:149 final size:148
Alignment explanation
Indices: 39089719--39090211 Score: 968
Period size: 148 Copynumber: 3.3 Consensus size: 148
39089709 ATGTATAATT
39089719 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
1 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
39089784 TAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTGA
66 TAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTGA
39089849 AAACACGAAAATTTTTGA
131 AAACACGAAAATTTTTGA
39089867 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
1 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
39089932 TAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTGA
66 TAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTGA
39089997 AAACACGAAAATTTTTGA
131 AAACACGAAAATTTTTGA
39090015 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
1 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
*
39090080 TAAAACATGAATTTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTG
66 TAAAACACGAA-TTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTG
39090145 AAAACACGAAAATTTTTGA
130 AAAACACGAAAATTTTTGA
39090164 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTT
1 AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTT
39090212 TTGAAACACA
Statistics
Matches: 343, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
148 223 0.65
149 120 0.35
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (148 bp):
AACACGAGAATTTTTATGACACGAAAAATTTTGAAAACACGAAAATTTCGAAAACATGAATTTTT
TAAAACACGAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAAATTTTGA
AAACACGAAAATTTTTGA
Found at i:39090602 original size:95 final size:95
Alignment explanation
Indices: 39090467--39090657 Score: 346
Period size: 95 Copynumber: 2.0 Consensus size: 95
39090457 CTAATAAAAT
*
39090467 ACGAGAATTTTTATTAAAATACGAGGAATTTTGAATATTTTCGATTTTTAGAAGGGCGTCCCGTA
1 ACGAAAATTTTTATTAAAATACGAGGAATTTTGAATATTTTCGATTTTTAGAAGGGCGTCCCGTA
*
39090532 TTTAACACGAGCCATCGATATTCACCCAAC
66 TTTAACACGAGCCATCAATATTCACCCAAC
**
39090562 ACGAAAATTTTTATTAAAATACGAGGAATTTTGAATATTTTTTATTTTTAGAAGGGCGTCCCGTA
1 ACGAAAATTTTTATTAAAATACGAGGAATTTTGAATATTTTCGATTTTTAGAAGGGCGTCCCGTA
39090627 TTTAACACGAGCCATCAATATTCACCCAAC
66 TTTAACACGAGCCATCAATATTCACCCAAC
39090657 A
1 A
39090658 TAGCAATGAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (95 bp):
ACGAAAATTTTTATTAAAATACGAGGAATTTTGAATATTTTCGATTTTTAGAAGGGCGTCCCGTA
TTTAACACGAGCCATCAATATTCACCCAAC
Found at i:39091078 original size:18 final size:18
Alignment explanation
Indices: 39091030--39091078 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
39091020 TTGGGCCTGC
*
39091030 TTTGTTCTTTTTTGCTAT
1 TTTGTTTTTTTTTGCTAT
* * *
39091048 TCTGTTTCTTTTTGCTGT
1 TTTGTTTTTTTTTGCTAT
39091066 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
39091079 TGGGGGCGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (18 bp):
TTTGTTTTTTTTTGCTAT
Found at i:39091207 original size:11 final size:11
Alignment explanation
Indices: 39091178--39091242 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
39091168 AAAATATATA
**
39091178 TTTTTTCTTTT
1 TTTTTTCTTCC
39091189 TTTTTTCTTCC
1 TTTTTTCTTCC
*
39091200 TTTCTTC-T-C
1 TTTTTTCTTCC
*
39091209 TCTTTTC-TCC
1 TTTTTTCTTCC
39091219 TTTTTTCTTCC
1 TTTTTTCTTCC
39091230 TTTTTTCCTTCC
1 TTTTTT-CTTCC
39091242 T
1 T
39091243 CTTCGGGGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 7 0.16
10 8 0.18
11 24 0.53
12 6 0.13
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTCTTCC
Found at i:39091219 original size:19 final size:19
Alignment explanation
Indices: 39091191--39091239 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
39091181 TTTCTTTTTT
39091191 TTTTCTTCCTTTCTTC-TCTC
1 TTTTC-TCCTTTCTTCTTC-C
*
39091211 TTTTCTCCTTTTTTCTTCC
1 TTTTCTCCTTTCTTCTTCC
*
39091230 TTTTTTCCTT
1 TTTTCTCCTT
39091240 CCTCTTCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTCTCCTTTCTTCTTCC
Found at i:39091924 original size:29 final size:29
Alignment explanation
Indices: 39091797--39091985 Score: 125
Period size: 30 Copynumber: 6.4 Consensus size: 29
39091787 CGAAGTTTCT
*
39091797 GGGGT-AAAAGTGTAATTTTAGCAAA--ATA
1 GGGGTCAAAA-TGTAATTTTAG-AAAGTTTA
* * * *
39091825 TGGGCCAAAATGTAATTTCTTGAGAGTTTA
1 GGGGTCAAAATGTAATTT-TAGAAAGTTTA
** * *
39091855 GGGGTCAAGGTGCAATTTTGAGAAAGTATA
1 GGGGTCAAAATGTAATTTT-AGAAAGTTTA
* * *
39091885 AGGGTCGAAATGTAATTTTAGAAAGTTTT
1 GGGGTCAAAATGTAATTTTAGAAAGTTTA
* * *
39091914 GGGGCCAAAATGTAAATTTTAGAAAATTTT
1 GGGGTCAAAATGT-AATTTTAGAAAGTTTA
*
39091944 GGGGTCAAAATGTAAATTTT-GAAAAGTATA
1 GGGGTCAAAATGT-AATTTTAG-AAAGTTTA
* *
39091974 AGGGTTAAAATG
1 GGGGTCAAAATG
39091986 CAAAAAATAA
Statistics
Matches: 124, Mismatches: 30, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
28 13 0.10
29 26 0.21
30 85 0.69
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAGAAAGTTTA
Found at i:39094416 original size:20 final size:20
Alignment explanation
Indices: 39094355--39094424 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
39094345 ATTAGACAGA
39094355 TATTGAATTAATCAATTTTAT
1 TATTGAATTAATCAATTTT-T
* ** * *
39094376 GATT-TCTTATTGAATTTTTT
1 TATTGAATTAATCAA-TTTTT
39094396 TATTGAATTAATCAATTTTT
1 TATTGAATTAATCAATTTTT
39094416 TATTGAATT
1 TATTGAATT
39094425 TTTTATTTAC
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
20 24 0.65
21 13 0.35
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (20 bp):
TATTGAATTAATCAATTTTT
Found at i:39097398 original size:22 final size:23
Alignment explanation
Indices: 39097370--39097414 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
39097360 ATGCAATCTT
39097370 ATATATGA-TATGTAATCTTAGA
1 ATATATGATTATGTAATCTTAGA
*
39097392 ATATATGATTCTGTAATCTTAGA
1 ATATATGATTATGTAATCTTAGA
39097415 GATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATATGATTATGTAATCTTAGA
Found at i:39103644 original size:125 final size:125
Alignment explanation
Indices: 39103414--39103837 Score: 591
Period size: 125 Copynumber: 3.4 Consensus size: 125
39103404 ACGTGGACGC
** * * * *
39103414 GAAGAATTTGTGAAATTGCGCTCTCTTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
*
39103479 TTTCGAGTTGACATTTCTGAGAAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
* * * * * *
39103539 GAAGAATTTGTTAAATCACGCCCACACGGGCGCACTTTTGCTACAGTAGGTCCT-GAAAAAATTA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* * * *
39103603 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATT-TGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCT-TTATGA
* * * *
39103664 GAAGAATTTCTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
* *
39103729 TTTTGAGTTGACATTTCTGAGCAAATAGTTTAAAATCGCTTCTACCAGGATGCTTTATGA
66 TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
**
39103789 GAAGAATTTGTGAAATTGCGCCCACATGGACGCGCTTTTGCTACAGTAG
1 GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAG
39103838 CATGTTTGGG
Statistics
Matches: 256, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
124 39 0.15
125 179 0.70
126 38 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (125 bp):
GAAGAATTTGTGAAATCACGCCCACATGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAA
TTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
Found at i:39105822 original size:21 final size:21
Alignment explanation
Indices: 39105789--39105836 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
39105779 TTGTCTAGCT
* * *
39105789 TCCGGCGGCGATTGTTGTTCC
1 TCCGGTGGCGATTCTGGTTCC
* *
39105810 TCCGGTGGGGATTCTGGTTCT
1 TCCGGTGGCGATTCTGGTTCC
39105831 TCCGGT
1 TCCGGT
39105837 ACGACATCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.25, G:0.35, T:0.35
Consensus pattern (21 bp):
TCCGGTGGCGATTCTGGTTCC
Found at i:39106129 original size:18 final size:18
Alignment explanation
Indices: 39106091--39106130 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39106081 GACTCGGAAA
**
39106091 AGGATACATATAAGGGTT
1 AGGATACATATAAGGACT
39106109 AGGATACATATAAGGACT
1 AGGATACATATAAGGACT
39106127 AGGA
1 AGGA
39106131 AACACACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGACT
Found at i:39109674 original size:33 final size:34
Alignment explanation
Indices: 39109623--39109754 Score: 108
Period size: 33 Copynumber: 3.7 Consensus size: 34
39109613 TCAACCTTTA
* *
39109623 TCGGTGGATTCAGCACTTAGCAATCACCAGTGAT
1 TCGGTGGAATCAGCACTTAGCAATCACCAATGAT
*
39109657 TCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGTGGAATCAGCACTTAGCAA------TCAC---CAATGAT
*
39109699 AT-GGTGGAATCAGCACTTAGCAACCACCAATGAT
1 -TCGGTGGAATCAGCACTTAGCAATCACCAATGAT
*
39109733 TCGG-GGAATCAACACTTAGCAA
1 TCGGTGGAATCAGCACTTAGCAA
39109755 CCCCTTGGGG
Statistics
Matches: 80, Mismatches: 6, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
33 35 0.44
34 12 0.15
37 3 0.04
39 4 0.05
42 7 0.09
43 19 0.24
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (34 bp):
TCGGTGGAATCAGCACTTAGCAATCACCAATGAT
Found at i:39109755 original size:33 final size:33
Alignment explanation
Indices: 39109704--39109962 Score: 130
Period size: 33 Copynumber: 7.6 Consensus size: 33
39109694 AAGATATGGT
39109704 GGAATCAGCACTTAGCAACCACCAATGATTCGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
* *
39109737 GGAATCAACACTTAGCAACC-CC-----TTGGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
* * *
39109764 GGAATCAGCGCTTAGCAACCCCCTTCACATTTAAAGATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T---GATTCGG
* * *
39109806 TGGAATCATCACTTAGCAACCACCAATGAATCAG
1 -GGAATCAGCACTTAGCAACCACCAATGATTCGG
*
39109840 GGAATCAACACTTAGCAACC-CC-----TTCGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
*
39109867 GGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATAT-GG
1 GGAATCAGCACTTAGCAACCACC---A-A--T---GAT-TCGG
* *
39109909 TGGAATCAACACTTAGCAACCACCAATGAGTCGG
1 -GGAATCAGCACTTAGCAACCACCAATGATTCGG
39109943 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
39109963 CCTTCATATT
Statistics
Matches: 172, Mismatches: 20, Indels: 68
0.66 0.08 0.26
Matches are distributed among these distances:
27 42 0.24
28 4 0.02
29 1 0.01
31 1 0.01
32 4 0.02
33 58 0.34
34 8 0.05
37 2 0.01
39 2 0.01
40 3 0.02
42 9 0.05
43 38 0.22
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGATTCGG
Found at i:39109781 original size:103 final size:103
Alignment explanation
Indices: 39109656--39109967 Score: 500
Period size: 103 Copynumber: 3.0 Consensus size: 103
39109646 TCACCAGTGA
* *
39109656 TTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCA
1 TTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAAGATATGGTGGAATCAACACTTAGCA
*
39109721 ACCACCAATGATTCGGGGAATCAACACTTAGCAACCCC
66 ACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC
* * * * *
39109759 TTGGGGGAATCAGCGCTTAGCAACCCCCTTCACATTTAAAGATACGGTGGAATCATCACTTAGCA
1 TTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAAGATATGGTGGAATCAACACTTAGCA
*
39109824 ACCACCAATGAATCAGGGAATCAACACTTAGCAACCCC
66 ACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC
*
39109862 TTCGGGGAATCAGCACTTAGCAACCCCCTTT-ATATTTAAAGATATGGTGGAATCAACACTTAGC
1 TTCGGGGAATCAGCACTTAGCAA-CCCCTTTCACATTTAAAGATATGGTGGAATCAACACTTAGC
* *
39109926 AACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC
65 AACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC
39109965 TTC
1 TTC
39109968 ATATTCAATG
Statistics
Matches: 191, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
103 185 0.97
104 6 0.03
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (103 bp):
TTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAAGATATGGTGGAATCAACACTTAGCA
ACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC
Found at i:39111489 original size:14 final size:13
Alignment explanation
Indices: 39111465--39111494 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
39111455 GAGGGGGGAG
39111465 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
39111478 AAAGAGAAGAAAGA
1 AAAGA-AAGAAAGA
39111492 AAA
1 AAA
39111495 AGTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:39115267 original size:62 final size:61
Alignment explanation
Indices: 39115185--39115419 Score: 407
Period size: 62 Copynumber: 3.8 Consensus size: 61
39115175 CAATGTACCT
39115185 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTGTTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TTTAATTTATATTACAA
* * *
39115247 AACTAATATTACAAAGTTTGTTTCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TTTAATTTATATTACAA
*
39115309 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTTTAATTTATATTACAA
*
39115370 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAAT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTTTAAT
39115420 GTTGTAATAT
Statistics
Matches: 163, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
61 64 0.39
62 99 0.61
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (61 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTTTAATTTATATTACAA
Found at i:39115314 original size:14 final size:14
Alignment explanation
Indices: 39115295--39115323 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39115285 TAATGTATTT
39115295 AATTTATATTACAA
1 AATTTATATTACAA
39115309 AATTTATATTACAA
1 AATTTATATTACAA
39115323 A
1 A
39115324 GTTTGTTCCA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:39115375 original size:14 final size:14
Alignment explanation
Indices: 39115356--39115384 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39115346 GTAATGTATT
39115356 AATTTATATTACAA
1 AATTTATATTACAA
39115370 AATTTATATTACAA
1 AATTTATATTACAA
39115384 A
1 A
39115385 GTTTGTTCCA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:39115406 original size:123 final size:124
Alignment explanation
Indices: 39115185--39115413 Score: 415
Period size: 123 Copynumber: 1.9 Consensus size: 124
39115175 CAATGTACCT
*
39115185 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTGTTTAATTTATATTACAAAAC
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTGATTAATTTATATTACAAAAC
*
39115250 TAATATTACAAAGTTTGTTTCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAA
66 TAATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAA
*
39115309 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-ATTAATTTATATTACAAAAT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTGATTAATTTATATTACAAAAC
*
39115373 TTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
66 TAATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
39115414 TGTAATGTTG
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
123 57 0.56
124 44 0.44
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (124 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTGATTAATTTATATTACAAAAC
TAATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAA
Found at i:39115413 original size:8 final size:8
Alignment explanation
Indices: 39115400--39115427 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
39115390 TTCCAAGTTT
39115400 TAATGTTG
1 TAATGTTG
39115408 TAATGTTG
1 TAATGTTG
39115416 TAATGTTG
1 TAATGTTG
39115424 TAAT
1 TAAT
39115428 ATTGCAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (8 bp):
TAATGTTG
Found at i:39117240 original size:4 final size:4
Alignment explanation
Indices: 39117231--39117291 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
39117221 TAATAGAACT
*
39117231 AGTA AGTA AGTT AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA
1 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA
39117279 AGTA AGTA AGTA A
1 AGTA AGTA AGTA A
39117292 TAATAATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.26
Consensus pattern (4 bp):
AGTA
Found at i:39117344 original size:3 final size:3
Alignment explanation
Indices: 39117289--39117330 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39117279 AGTAAGTAAG
39117289 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39117331 AAGGCTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39118868 original size:18 final size:18
Alignment explanation
Indices: 39118826--39118882 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
39118816 CCGGTCGGGA
*
39118826 TCGGGCTTGGGCTCTAGG
1 TCGGGCTTGGGCTCTAGC
* * *
39118844 TCTGGCTCGGCCTCTAGC
1 TCGGGCTTGGGCTCTAGC
*
39118862 TCGGGCTTGGGCTCTGGC
1 TCGGGCTTGGGCTCTAGC
39118880 TCG
1 TCG
39118883 TATGCCCCAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.04, C:0.30, G:0.39, T:0.28
Consensus pattern (18 bp):
TCGGGCTTGGGCTCTAGC
Found at i:39119518 original size:14 final size:14
Alignment explanation
Indices: 39119499--39119528 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39119489 AAATTACATG
*
39119499 TTAGAATAGTATCA
1 TTAGAATAATATCA
39119513 TTAGAATAATATCA
1 TTAGAATAATATCA
39119527 TT
1 TT
39119529 TGAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (14 bp):
TTAGAATAATATCA
Found at i:39122980 original size:194 final size:194
Alignment explanation
Indices: 39122651--39123040 Score: 771
Period size: 194 Copynumber: 2.0 Consensus size: 194
39122641 CTTTTTTTTC
39122651 TTTTCTATTTTTTAAAAATAGAAAATATGATTGGTAAATGAAAATAGAAATTTGTTAAATAATGA
1 TTTTCTATTTTTTAAAAATAGAAAATATGATTGGTAAATGAAAATAGAAATTTGTTAAATAATGA
39122716 AATAATGAAAACACGTTTGATATGTATTTTTCAAAATAAAAATAAAAATAAATTAATTAATTAAA
66 AATAATGAAAACACGTTTGATATGTATTTTTCAAAATAAAAATAAAAATAAATTAATTAATTAAA
*
39122781 ATATAATTTATTTAAAATGTATTACAATAAAGTAAAATATAATTAAATAAAATAGTTTTAAAAT
131 ATATAATTTATTTAAAATGTATTACAATAAAGTAAAATATAATTAAATAAAATAGTTTAAAAAT
39122845 TTTTCTATTTTTTAAAAATAGAAAATATGATTGGTAAATGAAAATAGAAATTTGTTAAATAATGA
1 TTTTCTATTTTTTAAAAATAGAAAATATGATTGGTAAATGAAAATAGAAATTTGTTAAATAATGA
39122910 AATAATGAAAACACGTTTGATATGTATTTTTCAAAATAAAAATAAAAATAAATTAATTAATTAAA
66 AATAATGAAAACACGTTTGATATGTATTTTTCAAAATAAAAATAAAAATAAATTAATTAATTAAA
39122975 ATATAATTTATTTAAAATGTATTACAATAAAGTAAAATATAATTAAATAAAATAGTTTAAAAAT
131 ATATAATTTATTTAAAATGTATTACAATAAAGTAAAATATAATTAAATAAAATAGTTTAAAAAT
39123039 TT
1 TT
39123041 CAAAAATAAA
Statistics
Matches: 195, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 195 1.00
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (194 bp):
TTTTCTATTTTTTAAAAATAGAAAATATGATTGGTAAATGAAAATAGAAATTTGTTAAATAATGA
AATAATGAAAACACGTTTGATATGTATTTTTCAAAATAAAAATAAAAATAAATTAATTAATTAAA
ATATAATTTATTTAAAATGTATTACAATAAAGTAAAATATAATTAAATAAAATAGTTTAAAAAT
Found at i:39125834 original size:3 final size:3
Alignment explanation
Indices: 39125826--39125852 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39125816 TAATTTCATG
39125826 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
39125853 CAACAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39127196 original size:25 final size:25
Alignment explanation
Indices: 39127115--39127209 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 25
39127105 GCGGATACAC
* * *
39127115 TACAGCTCTCTTGAGCTTCTCGATA
1 TACAGCTCACATGAGCTTCCCGATA
*** * *
39127140 TTTGGCTCATAAGAGCTTCCCGATA
1 TACAGCTCACATGAGCTTCCCGATA
**
39127165 TACAGCTCGTATGAGCTTCCCG-T-
1 TACAGCTCACATGAGCTTCCCGATA
39127188 TACTTAGCTCACATGAGCTTCC
1 TAC--AGCTCACATGAGCTTCC
39127210 TATTATATGG
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
23 3 0.06
24 1 0.02
25 49 0.92
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (25 bp):
TACAGCTCACATGAGCTTCCCGATA
Found at i:39131184 original size:26 final size:27
Alignment explanation
Indices: 39131133--39131195 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
39131123 TTTAAAATAC
* *
39131133 TTTTAAAATAATTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
39131160 TTTTAAAATAATTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
*
39131186 TTTAAAAATA
1 TTTTAAAATA
39131196 GGTCTGGCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATATGTTTAT
Found at i:39140276 original size:16 final size:16
Alignment explanation
Indices: 39140257--39140296 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
39140247 TAAAGTTAAT
*
39140257 TATATATAAA-AACAAA
1 TATA-ATAAATAAAAAA
39140273 TATAATAAATAAAAAA
1 TATAATAAATAAAAAA
39140289 TATAATAA
1 TATAATAA
39140297 TACAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TATAATAAATAAAAAA
Found at i:39141389 original size:15 final size:15
Alignment explanation
Indices: 39141348--39141398 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
39141338 TGACTCTGGT
*
39141348 TTAGGCTAGTTGGGC
1 TTAGGCTAATTGGGC
*
39141363 -TAGGGT-ATTGGGC
1 TTAGGCTAATTGGGC
*
39141376 TTAGGCTAATTGGGT
1 TTAGGCTAATTGGGC
39141391 TTAGGCTA
1 TTAGGCTA
39141399 GCCTAGAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 6 0.20
14 10 0.33
15 14 0.47
ACGTcount: A:0.18, C:0.10, G:0.37, T:0.35
Consensus pattern (15 bp):
TTAGGCTAATTGGGC
Found at i:39154344 original size:14 final size:15
Alignment explanation
Indices: 39154279--39154348 Score: 90
Period size: 15 Copynumber: 4.8 Consensus size: 15
39154269 AAACTCTAGC
39154279 CTAGCCTAAACCCAA
1 CTAGCCTAAACCCAA
39154294 CTAGCCTAAACCCAA
1 CTAGCCTAAACCCAA
* *
39154309 TTAGCCTAAGCCCAA
1 CTAGCCTAAACCCAA
* *
39154324 -TACCCT-AGCCCAA
1 CTAGCCTAAACCCAA
39154337 CTAGCCTAAACC
1 CTAGCCTAAACC
39154349 AGAAGTCAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
13 7 0.15
14 10 0.21
15 31 0.65
ACGTcount: A:0.36, C:0.40, G:0.09, T:0.16
Consensus pattern (15 bp):
CTAGCCTAAACCCAA
Found at i:39154344 original size:28 final size:30
Alignment explanation
Indices: 39154279--39154348 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
39154269 AAACTCTAGC
*
39154279 CTAGCCTAAACCCAACTAGCCTAAACCCAA
1 CTAGCCTAAACCCAACTACCCTAAACCCAA
* * *
39154309 TTAGCCTAAGCCCAA-TACCCT-AGCCCAA
1 CTAGCCTAAACCCAACTACCCTAAACCCAA
39154337 CTAGCCTAAACC
1 CTAGCCTAAACC
39154349 AGAAGTCAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 16 0.47
29 5 0.15
30 13 0.38
ACGTcount: A:0.36, C:0.40, G:0.09, T:0.16
Consensus pattern (30 bp):
CTAGCCTAAACCCAACTACCCTAAACCCAA
Found at i:39164505 original size:19 final size:19
Alignment explanation
Indices: 39164481--39164521 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
39164471 CGATTTATTC
*
39164481 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTACCTAAA
39164500 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
39164519 TAA
1 TAA
39164522 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:39165222 original size:3 final size:3
Alignment explanation
Indices: 39165214--39165245 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39165204 AAATAAAAGA
39165214 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39165246 CAACAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39170479 original size:10 final size:10
Alignment explanation
Indices: 39170464--39170489 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39170454 AAAGAAACTG
39170464 TTTTTTTTCT
1 TTTTTTTTCT
39170474 TTTTTTTTCT
1 TTTTTTTTCT
39170484 TTTTTT
1 TTTTTT
39170490 GCTGCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:39170604 original size:12 final size:11
Alignment explanation
Indices: 39170585--39170615 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
39170575 TTTATAATTG
39170585 TTATTTTATTA
1 TTATTTTATTA
39170596 TTAATTTTATTA
1 TT-ATTTTATTA
39170608 TTATTTTA
1 TTATTTTA
39170616 GAGGCGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:39171481 original size:24 final size:22
Alignment explanation
Indices: 39171414--39171481 Score: 54
Period size: 24 Copynumber: 3.1 Consensus size: 22
39171404 TATATCCAAT
39171414 TTTTTAAATTAATAGAAAATGATA
1 TTTTTAAATTAATAG-AAAT-ATA
* *
39171438 TTTTAAAATT-AT---AATCTA
1 TTTTTAAATTAATAGAAATATA
39171456 TTTTTAAATTAATAGAAGATAATA
1 TTTTTAAATTAATAGAA-AT-ATA
39171480 TT
1 TT
39171482 AAACTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
18 11 0.32
19 5 0.15
22 1 0.03
23 4 0.12
24 13 0.38
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTTAAATTAATAGAAATATA
Found at i:39171499 original size:42 final size:42
Alignment explanation
Indices: 39171414--39171502 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
39171404 TATATCCAAT
* *
39171414 TTTTTAAATTAATAGAAAATGATATTTTAAAATTATAATCTA
1 TTTTTAAATTAATAGAAAATGATATATTAAAATTATAAACTA
* *
39171456 TTTTTAAATTAATAGAAGAT-A-ATATTAAACTTATAAAAACTA
1 TTTTTAAATTAATAGAAAATGATATATTAAAATTAT--AAACTA
39171498 TTTTT
1 TTTTT
39171503 TTCACGCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 11 0.27
41 1 0.02
42 29 0.71
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (42 bp):
TTTTTAAATTAATAGAAAATGATATATTAAAATTATAAACTA
Found at i:39172012 original size:17 final size:17
Alignment explanation
Indices: 39171990--39172025 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39171980 TATTTTCTGT
39171990 TGTTGTTTTTTAAAATA
1 TGTTGTTTTTTAAAATA
39172007 TGTTGTTTTTTAAAATA
1 TGTTGTTTTTTAAAATA
39172024 TG
1 TG
39172026 AGTAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (17 bp):
TGTTGTTTTTTAAAATA
Found at i:39176029 original size:22 final size:20
Alignment explanation
Indices: 39176004--39176051 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
39175994 AATATAAAAT
39176004 AAAATAATTAATAATAA-AGCTC
1 AAAATAA-TAATAA-AACA-CTC
39176026 AAAATTAATAATAAAACACTC
1 AAAA-TAATAATAAAACACTC
39176047 AAAAT
1 AAAAT
39176052 TTAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 11 0.46
23 3 0.12
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATAATAATAAAACACTC
Found at i:39176055 original size:22 final size:19
Alignment explanation
Indices: 39176009--39176052 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
39175999 AAAATAAAAT
*
39176009 AATTAATAATAAAGCTCAA
1 AATTAATAATAAAACTCAA
39176028 AATTAATAATAAAACACTCAA
1 AATTAATAAT-AAA-ACTCAA
39176049 AATT
1 AATT
39176053 TAAGAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 9 0.41
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (19 bp):
AATTAATAATAAAACTCAA
Found at i:39179304 original size:21 final size:21
Alignment explanation
Indices: 39179278--39179329 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
39179268 ACCGAGGCTT
*
39179278 AAGGATTGAGATAGATGGTTG
1 AAGGATTGAGACAGATGGTTG
*
39179299 AAGGATAGAGACAGATGGTTG
1 AAGGATTGAGACAGATGGTTG
*
39179320 GAGGA-TGAGA
1 AAGGATTGAGA
39179330 AAGAGATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.37, C:0.02, G:0.40, T:0.21
Consensus pattern (21 bp):
AAGGATTGAGACAGATGGTTG
Found at i:39183247 original size:45 final size:45
Alignment explanation
Indices: 39183149--39183334 Score: 209
Period size: 45 Copynumber: 4.2 Consensus size: 45
39183139 AATAATAACA
* * * * *
39183149 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAACACACAGCAACCACCTTTATAATCAAT
* *
39183192 GATACTCGGTGGAATCAACACATAGCAACCA-CTTTCATAATCAAT
1 GATACCCGGTGGAATCAACACACAGCAACCACCTTT-ATAATCAAT
* *
39183237 -AGTACCCGGTGGAATCAGCACACAGTAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAACACACAGCAACCACCTTTATAATCAAT
* * *
39183282 GATACTCGGTGGAATTAACACACAGCAATCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAACACACAGCAACCACCTTTATAATCAAT
*
39183327 GGTACCCG
1 GATACCCG
39183335 ATACACGTAG
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
43 11 0.09
44 16 0.13
45 90 0.74
46 5 0.04
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (45 bp):
GATACCCGGTGGAATCAACACACAGCAACCACCTTTATAATCAAT
Found at i:39183284 original size:90 final size:88
Alignment explanation
Indices: 39183155--39183334 Score: 254
Period size: 90 Copynumber: 2.0 Consensus size: 88
39183145 AACAGATACA
* * * *
39183155 CGGTGGATCAGCACATAGCACCACCCTTATAGTCAATGATACTCGGTGGAATCAACACATAGCAA
1 CGGTGGATCAGCACACAGAACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGCAA
39183220 CCA-CTTTCATAATCAATAGTACC
66 CCACCTTT-ATAATCAATAGTACC
* *
39183243 CGGTGGAATCAGCACACAGTAACCACCTTTATAATCAATGATACTCGGTGGAATTAACACACAGC
1 CGGTGG-ATCAGCACACAG-AACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGC
* *
39183308 AATCACCTTTATAATCAATGGTACC
64 AACCACCTTTATAATCAATAGTACC
39183333 CG
1 CG
39183335 ATACACGTAG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 6 0.07
89 11 0.14
90 60 0.74
91 4 0.05
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (88 bp):
CGGTGGATCAGCACACAGAACCACCCTTATAATCAATGATACTCGGTGGAATCAACACACAGCAA
CCACCTTTATAATCAATAGTACC
Found at i:39189617 original size:21 final size:21
Alignment explanation
Indices: 39189591--39189633 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
39189581 GAAAAAGTCG
39189591 TTACACTCAAAATTGACCATA
1 TTACACTCAAAATTGACCATA
39189612 TTACACTCAAAATTGACCATA
1 TTACACTCAAAATTGACCATA
39189633 T
1 T
39189634 GACAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (21 bp):
TTACACTCAAAATTGACCATA
Done.