Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 40 of 131
Found at i:13230836 original size:55 final size:54
Alignment explanation
Indices: 13230775--13230930 Score: 233
Period size: 55 Copynumber: 2.9 Consensus size: 54
13230765 GCGTTTTTTA
*
13230775 GCAAAAAATATTCAAAATCCTGCTCACTCCCAACAAAAAAAATTTTTAAAACGCC
1 GCAAAAAATATTCAAAATCCTGCTCACTCCCAACAAAAAAAA-TTTTAAAAAGCC
* *
13230830 GCAAAAAATATTCAAAAT-CTCGCTTACTCCCAACAAAAAAAAATTTAAAAAGCC
1 GCAAAAAATATTCAAAATCCT-GCTCACTCCCAACAAAAAAAATTTTAAAAAGCC
* *
13230884 TCAAAAAATATTCAAAATCCCGCTCACTCCCAACAAAAAAAAATTTT
1 GCAAAAAATATTCAAAATCCTGCTCACTCCCAAC-AAAAAAAATTTT
13230931 GGTTACTCGC
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
54 41 0.45
55 50 0.55
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (54 bp):
GCAAAAAATATTCAAAATCCTGCTCACTCCCAACAAAAAAAATTTTAAAAAGCC
Found at i:13230877 original size:54 final size:53
Alignment explanation
Indices: 13230775--13230929 Score: 238
Period size: 54 Copynumber: 2.8 Consensus size: 53
13230765 GCGTTTTTTA
* *
13230775 GCAAAAAATATTCAAAATCCTGCTCACTCCCAACAAAAAAAATTTTTAAAACGCC
1 GCAAAAAATATTCAAAATCC-GCTCACTCCCAACAAAAAAAA-ATTTAAAAAGCC
*
13230830 GCAAAAAATATTCAAAATCTCGCTTACTCCCAACAAAAAAAAATTTAAAAAGCC
1 GCAAAAAATATTCAAAATC-CGCTCACTCCCAACAAAAAAAAATTTAAAAAGCC
*
13230884 TCAAAAAATATTCAAAATCCCGCTCACTCCCAACAAAAAAAAATTT
1 GCAAAAAATATTCAAAAT-CCGCTCACTCCCAACAAAAAAAAATTT
13230930 TGGTTACTCG
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
54 52 0.56
55 40 0.43
56 1 0.01
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.21
Consensus pattern (53 bp):
GCAAAAAATATTCAAAATCCGCTCACTCCCAACAAAAAAAAATTTAAAAAGCC
Found at i:13234013 original size:20 final size:22
Alignment explanation
Indices: 13233985--13234029 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
13233975 GTCTTGTAGC
*
13233985 AAGTGCTTG-CTATGAGCAGCA
1 AAGTGCTTGTATATGAGCAGCA
13234006 AAGT-CTTGTATATGAGCAGCA
1 AAGTGCTTGTATATGAGCAGCA
13234027 AAG
1 AAG
13234030 GATATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (22 bp):
AAGTGCTTGTATATGAGCAGCA
Found at i:13234066 original size:16 final size:16
Alignment explanation
Indices: 13234045--13234079 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13234035 TCAAAAGGTA
*
13234045 TTGCCTTTGTTATATT
1 TTGCCTTTGTTATAAT
13234061 TTGCCTTTGTTATAAT
1 TTGCCTTTGTTATAAT
13234077 TTG
1 TTG
13234080 TCGGTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.60
Consensus pattern (16 bp):
TTGCCTTTGTTATAAT
Found at i:13234857 original size:27 final size:26
Alignment explanation
Indices: 13234827--13234884 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
13234817 AATTTTGAGG
*
13234827 TTTATAATTTATAATTTTTATTAATT
1 TTTATAATTTATAACTTTTATTAATT
* * * *
13234853 ATTTACATTTTCTCACTTTTATTAATT
1 -TTTATAATTTATAACTTTTATTAATT
13234880 TTTAT
1 TTTAT
13234885 TATTATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATAATTTATAACTTTTATTAATT
Found at i:13235137 original size:43 final size:43
Alignment explanation
Indices: 13235090--13235193 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
13235080 TTTTGGCGAG
* *
13235090 AAGCGCCGCTAAAGGTCACGTTCTTTAGAGGCGTTTGTGACAA
1 AAGCGCCGCTAAAGGTCACGGTCTATAGAGGCGTTTGTGACAA
* * * **
13235133 AAGCGCCGCTAAAGGCCATGGTCTATAGCGGCGTTTGTGAGTA
1 AAGCGCCGCTAAAGGTCACGGTCTATAGAGGCGTTTGTGACAA
*
13235176 AAGCGCCACTAAAGGTCA
1 AAGCGCCGCTAAAGGTCA
13235194 TAGAATTTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCACGGTCTATAGAGGCGTTTGTGACAA
Found at i:13235205 original size:43 final size:43
Alignment explanation
Indices: 13235113--13235220 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
13235103 GGTCACGTTC
* * * * **
13235113 TTTAGAGGCGTTTGTGACAAAAGCGCCGCTAAAGGCCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGCCATAGAA
* * *
13235156 TATAGCGGCGTTTGTGAGTAAAGCGCCACTAAAGGTCATAGAA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGCCATAGAA
*
13235199 TTTAGC-GTGTTTGTGAGAAAAG
1 TTTAGCGGCGTTTGTGAGAAAAG
13235221 TCATGGTCTA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 14 0.26
43 39 0.74
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGCCATAGAA
Found at i:13236615 original size:15 final size:15
Alignment explanation
Indices: 13236595--13236626 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
13236585 ACCATATAGT
13236595 GCAGACCATGGTTAG
1 GCAGACCATGGTTAG
13236610 GCAGACCATGGTTAG
1 GCAGACCATGGTTAG
13236625 GC
1 GC
13236627 TATGGCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.19
Consensus pattern (15 bp):
GCAGACCATGGTTAG
Found at i:13236912 original size:29 final size:29
Alignment explanation
Indices: 13236880--13237041 Score: 114
Period size: 28 Copynumber: 5.7 Consensus size: 29
13236870 GAAATTTTCA
* *
13236880 TAAAAGTAAGTCTTTGTGGCGATCTCTGT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTGT
** ** * * *
13236909 TAAAAGGGAGGTTTTATGGCTATCTCTGC
1 TAAAAGAAAGCCTTTGTGGCGATCTCTGT
* * ** *
13236938 T-AAAGGAAGCCTTTGTTGTTATCTTTGT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTGT
*
13236966 TAAAA-AAAGTCTTTGTGGCGATCTCTGT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTGT
* * *
13236994 TAAAAGAAAACCTTTCTGGCAATCTCTGT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTGT
* * *
13237023 CAAAA-TATGCCTTTGTGGC
1 TAAAAGAAAGCCTTTGTGGC
13237042 AAGACTCTAA
Statistics
Matches: 101, Mismatches: 30, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
28 52 0.51
29 49 0.49
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (29 bp):
TAAAAGAAAGCCTTTGTGGCGATCTCTGT
Found at i:13240831 original size:17 final size:17
Alignment explanation
Indices: 13240805--13240849 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
13240795 AATCACACAA
13240805 ATCT-AATTGAGTCAGG
1 ATCTAAATTGAGTCAGG
13240821 ATCTAAATTGAGTCAGG
1 ATCTAAATTGAGTCAGG
13240838 ATCTAAATTGAG
1 ATCTAAATTGAG
13240850 AATGCACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (17 bp):
ATCTAAATTGAGTCAGG
Found at i:13244045 original size:23 final size:23
Alignment explanation
Indices: 13243966--13244043 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
13243956 CCCAAGGGCA
* *
13243966 TTACAGAATATGCCACACAGGCA
1 TTACAGAATATGCCACAAAGGCT
* *
13243989 TCACAGAATATGCCATAAAGGCT
1 TTACAGAATATGCCACAAAGGCT
*
13244012 TTACAGAATGTGCCACAAAGGCT
1 TTACAGAATATGCCACAAAGGCT
13244035 TTACAGAAT
1 TTACAGAAT
13244044 GTTATGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (23 bp):
TTACAGAATATGCCACAAAGGCT
Found at i:13247538 original size:46 final size:46
Alignment explanation
Indices: 13247486--13247577 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
13247476 CAAGTCACAC
13247486 ATAGCATTCACATATATAATACCATCCATAAAATGCTTAACCATAA
1 ATAGCATTCACATATATAATACCATCCATAAAATGCTTAACCATAA
*
13247532 ATAGCATTCACATATATAATCCCATCCATAAAATGCTTAACCATAA
1 ATAGCATTCACATATATAATACCATCCATAAAATGCTTAACCATAA
13247578 TCAAAATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (46 bp):
ATAGCATTCACATATATAATACCATCCATAAAATGCTTAACCATAA
Found at i:13252415 original size:30 final size:30
Alignment explanation
Indices: 13252381--13252445 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
13252371 ACTTATTTTA
*
13252381 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATAATTTTAAAGGCAT
*
13252411 TTGTTAATTTTGTTATAATTTTAGAGGCAT
1 TTGTTAATTTTGTTATAATTTTAAAGGCAT
13252441 TTGTT
1 TTGTT
13252446 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATAATTTTAAAGGCAT
Found at i:13253118 original size:19 final size:19
Alignment explanation
Indices: 13253073--13253118 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
13253063 AAATTCTATC
*
13253073 TAATAAATTTATTATAAAT
1 TAATAAATATATTATAAAT
13253092 T-ATCAAATATATT-TAAAT
1 TAAT-AAATATATTATAAAT
13253110 TAAATAAAT
1 T-AATAAAT
13253119 TACTGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATAAATATATTATAAAT
Found at i:13260635 original size:22 final size:20
Alignment explanation
Indices: 13260608--13260647 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13260598 AATCCTTTTT
13260608 ATAATACCAAAATTATATAAAA
1 ATAATA-CAAAATT-TATAAAA
*
13260630 ATAATATAAAATTTATAA
1 ATAATACAAAATTTATAA
13260648 TATATATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATACAAAATTTATAAAA
Found at i:13260859 original size:85 final size:85
Alignment explanation
Indices: 13260767--13261315 Score: 1064
Period size: 85 Copynumber: 6.4 Consensus size: 85
13260757 AAAATTCATT
13260767 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13260832 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
13260852 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13260917 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
13260937 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13261002 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
13261022 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13261087 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
13261107 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13261172 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
13261192 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
1 TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
13261257 TATTTTTTTTGCTATAACTA
66 TATTTTTTTTGCTATAACTA
*
13261277 TTTACAAATAAGTATATTATAATAT-TTTTATAACATATA
1 TTTACAAATAAGTATATTAT--TATGTTTTATAATATATA
13261316 AGTTATTTTT
Statistics
Matches: 461, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
85 445 0.97
86 13 0.03
87 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (85 bp):
TTTACAAATAAGTATATTATTATGTTTTATAATATATAGCATGGAACATAAATAAGTTATGTCTA
TATTTTTTTTGCTATAACTA
Found at i:13265206 original size:24 final size:24
Alignment explanation
Indices: 13265178--13265223 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13265168 TTTGAAATTT
*
13265178 AATTT-GTGTATTTATATTTTTAAG
1 AATTTAGTCTATTTAT-TTTTTAAG
*
13265202 AATTTAGTCTCTTTATTTTTTA
1 AATTTAGTCTATTTATTTTTTA
13265224 GATTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
AATTTAGTCTATTTATTTTTTAAG
Found at i:13266888 original size:11 final size:10
Alignment explanation
Indices: 13266862--13266886 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13266852 CCCTAGATGT
13266862 AAAAACAAAA
1 AAAAACAAAA
13266872 AAAAACAAAA
1 AAAAACAAAA
13266882 AAAAA
1 AAAAA
13266887 ACCCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:13268377 original size:51 final size:50
Alignment explanation
Indices: 13268254--13268492 Score: 230
Period size: 51 Copynumber: 4.7 Consensus size: 50
13268244 AAAGTGATGG
* * *** *
13268254 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATA-AAAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG-ATAGTTTGA
* * * * *
13268304 TCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-TTTGA
* * * *
13268355 TCACGTGTGTAGTACTACGTGCAGGCTGCTATGTGTATCGGATA-TTAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTT--TGA
* * * *
13268406 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTTTGA
* * *
13268456 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTA
13268493 TCGAATGATA
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
49 5 0.03
50 71 0.46
51 76 0.49
52 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTTTGA
Found at i:13268458 original size:101 final size:101
Alignment explanation
Indices: 13268254--13268530 Score: 308
Period size: 101 Copynumber: 2.7 Consensus size: 101
13268244 AAAGTGATGG
* * *
13268254 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATAAAAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGAATAAAAGGTCACATGTGTAGTAC
* * * *
13268319 TATGTGCAAGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAAGCTACTACGCGAACCGAAAAGCTTCGA
* * * * * * *
13268355 TCACGTGTGTAGTACTACGTGCAGGCTGCTATGTGTATCGGATATTAATGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGA-ATAAAAGGTCACATGTGTAGTA
* * *
13268420 CTATGTGCAGGCTACTACGTGAACCGAAAAG-TTTGA
65 CTATGTGCAAGCTACTACGCGAACCGAAAAGCTTCGA
* * * *
13268456 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGTATC-GAATGATAATA-GTTAAATGAGTAG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGAAT-A-AA-AGGTCACATGTGTAG
13268519 TACTATGTGCAA
63 TACTATGTGCAA
13268531 ACCACCGAAT
Statistics
Matches: 144, Mismatches: 28, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
99 2 0.01
100 2 0.01
101 97 0.67
102 43 0.30
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGAATAAAAGGTCACATGTGTAGTAC
TATGTGCAAGCTACTACGCGAACCGAAAAGCTTCGA
Found at i:13268473 original size:50 final size:49
Alignment explanation
Indices: 13268254--13268497 Score: 211
Period size: 50 Copynumber: 4.9 Consensus size: 49
13268244 AAAGTGATGG
* ** *
13268254 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATAA-AAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAA-AATTTGA
* * * * * ** *
13268304 TCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GA-AAATTTGA
* * * * * * *
13268355 TCACGTGTGTAGTACTACGTGCAGGCTGCTATGTGTATCGGATATTAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAATT--TGA
*
13268406 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAA-TTTGA
* * *
13268456 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGTATCGAA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
13268498 TGATAATAGT
Statistics
Matches: 154, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
49 3 0.02
50 77 0.50
51 72 0.47
52 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAATTTGA
Found at i:13274202 original size:13 final size:13
Alignment explanation
Indices: 13274184--13274210 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13274174 AATTATCACA
13274184 TAGGCATGATTTG
1 TAGGCATGATTTG
13274197 TAGGCATGATTTG
1 TAGGCATGATTTG
13274210 T
1 T
13274211 GAATCAATTC
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:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (13 bp):
TAGGCATGATTTG
Found at i:13276650 original size:101 final size:101
Alignment explanation
Indices: 13276496--13276892 Score: 564
Period size: 101 Copynumber: 3.9 Consensus size: 101
13276486 AAAAAGTTAT
* *
13276496 TACTAATATCTGATTCTGACACGAAAAATAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGG
1 TACTGATATCTGATTCTAACACGAAAAA-AAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGG
13276561 CCATTGACAGACCAACACCCAAAATTTTTTTTTCGTA
65 CCATTGACAGACCAACACCCAAAATTTTTTTTTCGTA
*
13276598 TACTGATATTTGATTCTAACACGAAAAAAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGGC
1 TACTGATATCTGATTCTAACACGAAAAAAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGGC
13276663 CATTGACAGACCAACACCCAAAATTTTTTTTTCGTA
66 CATTGACAGACCAACACCCAAAATTTTTTTTTCGTA
* *
13276699 TACTGATATTTGATTCTAACACGAAAAAAAAAGAAATTTTTTTTGAAATTGTACTGGGTGCCGGC
1 TACTGATATCTGATTCTAACACGAAAAAAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGGC
* ** * *
13276764 CATTGACAGGCCAGTACTCAAATTTTTTTTTACTTTTTTCGTA
66 CATTGACAGACCAACACCCAAA-----ATTT--TTTTTTCGTA
* * * *
13276807 TATTGATATCTGATTCTGACACG-AAAAAAAA-TATTTTTTTTTGAAATTGTACTGGGTACCGGC
1 TACTGATATCTGATTCTAACACGAAAAAAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGGC
* *
13276870 CATTGACAGGCCAGCACCCAAAA
66 CATTGACAGACCAACACCCAAAA
13276893 AATATTTTTT
Statistics
Matches: 270, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
101 155 0.57
102 25 0.09
106 52 0.19
107 8 0.03
108 30 0.11
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (101 bp):
TACTGATATCTGATTCTAACACGAAAAAAAAAGAATTTTTTTTTGAAATTGTACTGGGTGCCGGC
CATTGACAGACCAACACCCAAAATTTTTTTTTCGTA
Found at i:13282743 original size:21 final size:22
Alignment explanation
Indices: 13282719--13282759 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13282709 ATTTAAACAT
*
13282719 ACATCTCATATAAT-ATCATAA
1 ACATATCATATAATAATCATAA
*
13282740 ACATATGATATAATAATCAT
1 ACATATCATATAATAATCAT
13282760 CTACATACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (22 bp):
ACATATCATATAATAATCATAA
Found at i:13289252 original size:25 final size:25
Alignment explanation
Indices: 13289197--13289254 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
13289187 ATAGATCTGA
*
13289197 ATTTTAATTTTAGTTATTTTTATTTG
1 ATTTTAATTTTAGTTA-TTTAATTTG
*
13289223 A-TTTAATTTTAAGTTA-TTAATTTT
1 ATTTTAATTTT-AGTTATTTAATTTG
13289247 ATTTTAAT
1 ATTTTAAT
13289255 GTCTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 7 0.25
25 15 0.54
26 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (25 bp):
ATTTTAATTTTAGTTATTTAATTTG
Found at i:13289265 original size:20 final size:18
Alignment explanation
Indices: 13289219--13289267 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
13289209 GTTATTTTTA
*
13289219 TTTGATTTAATTTTAAGT
1 TTTGATTTTATTTTAAGT
*
13289237 TATTAATTTTATTTTAATGT
1 T-TTGATTTTATTTTAA-GT
13289257 CTTTGATTTTA
1 -TTTGATTTTA
13289268 GTGTATGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 10 0.40
21 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTGATTTTATTTTAAGT
Found at i:13291130 original size:20 final size:20
Alignment explanation
Indices: 13291105--13291147 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13291095 AGAGATAGTG
*
13291105 GTGTAACAACCCATTTTTTA
1 GTGTAACAACCCAGTTTTTA
*
13291125 GTGTAACAGCCCAGTTTTTA
1 GTGTAACAACCCAGTTTTTA
13291145 GTG
1 GTG
13291148 GTACCAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
GTGTAACAACCCAGTTTTTA
Found at i:13292610 original size:26 final size:26
Alignment explanation
Indices: 13292574--13292636 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
13292564 CCTGTAAGTG
13292574 TTCTGAAACTAATATATGTTATGATA
1 TTCTGAAACTAATATATGTTATGATA
13292600 TTCTGAAACTAATATATGTTATGATA
1 TTCTGAAACTAATATATGTTATGATA
*
13292626 TTTTGAAACTA
1 TTCTGAAACTA
13292637 CTGTAGGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (26 bp):
TTCTGAAACTAATATATGTTATGATA
Found at i:13298985 original size:42 final size:41
Alignment explanation
Indices: 13298935--13299018 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
13298925 ATATTATCAG
* * *
13298935 ATATCGATGCCACTGTCCTAAACAGGGTCTTATATGAAATC
1 ATATCGATGCCAATGTCCTAAACAGGGTCTTACACGAAATC
* *
13298976 ATATACGATGCCAATGTCCTAGACATGGTCTTACACGAAATC
1 ATAT-CGATGCCAATGTCCTAAACAGGGTCTTACACGAAATC
13299018 A
1 A
13299019 CACCTCAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
ATATCGATGCCAATGTCCTAAACAGGGTCTTACACGAAATC
Found at i:13302736 original size:16 final size:17
Alignment explanation
Indices: 13302715--13302746 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13302705 TATTGTGTTA
13302715 TTTAATTGTT-TAATAG
1 TTTAATTGTTGTAATAG
13302731 TTTAATTGTTGTAATA
1 TTTAATTGTTGTAATA
13302747 CAATACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TTTAATTGTTGTAATAG
Found at i:13310156 original size:26 final size:27
Alignment explanation
Indices: 13310127--13310188 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
13310117 AGCGGTAAAA
13310127 TGGTAATTTTACCC-CCAAGGGTATTT
1 TGGTAATTTTACCCTCCAAGGGTATTT
* * *
13310153 TGGTTATTTTACCCTTCGAGGGTATTT
1 TGGTAATTTTACCCTCCAAGGGTATTT
*
13310180 TGGTCATTT
1 TGGTAATTT
13310189 AACAATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
TGGTAATTTTACCCTCCAAGGGTATTT
Found at i:13310456 original size:10 final size:10
Alignment explanation
Indices: 13310441--13310471 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
13310431 AGCCAAACAA
13310441 GGCCCATAAC
1 GGCCCATAAC
*
13310451 GGCCCATAAT
1 GGCCCATAAC
13310461 GGCCCATAAC
1 GGCCCATAAC
13310471 G
1 G
13310472 CTCGTGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (10 bp):
GGCCCATAAC
Found at i:13313401 original size:19 final size:19
Alignment explanation
Indices: 13313377--13313417 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
13313367 ACACGGTTAG
13313377 ACATAGGACCGTGTGCCAT
1 ACATAGGACCGTGTGCCAT
13313396 ACATAGGACCGTGTGCCAT
1 ACATAGGACCGTGTGCCAT
13313415 ACA
1 ACA
13313418 CAAGCATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (19 bp):
ACATAGGACCGTGTGCCAT
Found at i:13320402 original size:5 final size:5
Alignment explanation
Indices: 13320391--13320472 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
13320381 AAAGAAAAGC
* * * *
13320391 AAAAT AAGAT AAAAT AAAA- ATAAAT AAAAAG AAAAG AAAAT AATAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
* *
13320442 AATAT AAAAAT ATTAACT -AAAT AAAAT AAAA
1 AAAAT -AAAAT A--AAAT AAAAT AAAAT AAAA
13320473 AAAGGAAGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
4 4 0.07
5 45 0.75
6 7 0.12
7 4 0.07
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:13320410 original size:16 final size:15
Alignment explanation
Indices: 13320391--13320473 Score: 62
Period size: 15 Copynumber: 5.3 Consensus size: 15
13320381 AAAGAAAAGC
13320391 AAAATAAGATAAAATA
1 AAAATAA-ATAAAATA
13320407 AAAATAAATAAAA-A
1 AAAATAAATAAAATA
* *
13320421 GAAAAGAAA-ATAATA
1 -AAAATAAATAAAATA
13320436 TAAAATAATATAAAAATA
1 -AAAATAA-AT-AAAATA
* *
13320454 TTAACTAAATAAAATA
1 -AAAATAAATAAAATA
13320470 AAAA
1 AAAA
13320474 AAGGAAGGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.08
15 22 0.42
16 14 0.26
17 2 0.04
18 11 0.21
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:13320425 original size:21 final size:22
Alignment explanation
Indices: 13320401--13320453 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
13320391 AAAATAAGAT
13320401 AAAATAAAAATAAATA-AAAAG
1 AAAATAAAAATAAATATAAAAG
* *
13320422 AAAA-GAAAAT-AATATAAAAT
1 AAAATAAAAATAAATATAAAAG
*
13320442 AATATAAAAATA
1 AAAATAAAAATA
13320454 TTAACTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAATAAAAATAAATATAAAAG
Found at i:13335363 original size:3 final size:3
Alignment explanation
Indices: 13335355--13335404 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
13335345 TGACGAGGGA
13335355 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
13335403 GA
1 GA
13335405 GCCTTTTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:13343458 original size:73 final size:72
Alignment explanation
Indices: 13343381--13343527 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 72
13343371 CTTGAATGCA
*
13343381 TTGTTTGATGAGTTTGACCTTGTAACGGTCCACCCCTCTCTCCAATCTTTTCTCCTTTTTTTTTT
1 TTGTTTGATGAGTTTGACCTTGTAACCGTCCACCCCTCTCTCCAATCTTTTCTCC-TTTTTTTTT
*
13343446 GTTTGATC
65 GTTTCATC
*
13343454 TTGTTTGATGAGTTTGACCTTGTAACCGTCCACCCCTCTCTCCCATCTTTTCTCCTTTTTTTTTG
1 TTGTTTGATGAGTTTGACCTTGTAACCGTCCACCCCTCTCTCCAATCTTTTCTCCTTTTTTTTTG
13343519 TTTCATC
66 TTTCATC
13343526 TT
1 TT
13343528 TTCTCTCTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 18 0.25
73 53 0.75
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.50
Consensus pattern (72 bp):
TTGTTTGATGAGTTTGACCTTGTAACCGTCCACCCCTCTCTCCAATCTTTTCTCCTTTTTTTTTG
TTTCATC
Found at i:13343642 original size:11 final size:11
Alignment explanation
Indices: 13343626--13343665 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
13343616 AAAACTGAAA
*
13343626 CACCACCATAT
1 CACCACCATAC
13343637 CACCACCATAC
1 CACCACCATAC
*
13343648 CACCACCATAG
1 CACCACCATAC
13343659 CACCACC
1 CACCACC
13343666 GTCTCACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.35, C:0.53, G:0.03, T:0.10
Consensus pattern (11 bp):
CACCACCATAC
Found at i:13344445 original size:47 final size:47
Alignment explanation
Indices: 13344382--13344482 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
13344372 GCGTTTCAGT
* * **
13344382 AGCTTGTCTGCAATTTTGGTGGCTTGA-CCACAACTATGTGTATTGGC
1 AGCTTGTCTGCAATTTTAGTGACTT-ATCCACAACTATGTGTATTGAA
** *
13344429 AGCTTGTCTGGGATTTTAGTGACTTATCCACTACTATGTGTATTGAA
1 AGCTTGTCTGCAATTTTAGTGACTTATCCACAACTATGTGTATTGAA
13344476 AGCTTGT
1 AGCTTGT
13344483 TTGTAAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.39
Consensus pattern (47 bp):
AGCTTGTCTGCAATTTTAGTGACTTATCCACAACTATGTGTATTGAA
Found at i:13354955 original size:14 final size:15
Alignment explanation
Indices: 13354926--13354958 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
13354916 AGAGAGAGCC
*
13354926 TTCTTTTTTCTTTCT
1 TTCTTTCTTCTTTCT
13354941 TTCTTTCTT-TTTCT
1 TTCTTTCTTCTTTCT
13354955 TTCT
1 TTCT
13354959 ATTATTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTCTTCTTTCT
Found at i:13361554 original size:12 final size:12
Alignment explanation
Indices: 13361537--13361561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13361527 ATTTGGGTTG
13361537 AAAATAATTTTT
1 AAAATAATTTTT
13361549 AAAATAATTTTT
1 AAAATAATTTTT
13361561 A
1 A
13361562 TTGGGGGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATAATTTTT
Found at i:13372122 original size:15 final size:14
Alignment explanation
Indices: 13372102--13372158 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
13372092 ATTGATACAA
13372102 ATTTTTATTTTAGTT
1 ATTTTTATTTTA-TT
*
13372117 ATTTTTATTTGATTT
1 ATTTTTATTTTA-TT
**
13372132 AATTTTTAGGTTATT
1 -ATTTTTATTTTATT
*
13372147 AATTTTATTTTA
1 ATTTTTATTTTA
13372159 ATTTCTCCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
14 9 0.27
15 15 0.45
16 9 0.27
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:13375672 original size:27 final size:28
Alignment explanation
Indices: 13375642--13375694 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
13375632 CAAAATTCAT
* *
13375642 ACTTTAATTA-TAAAATAATTAATTTGC
1 ACTTAAATTATTAAAATAATCAATTTGC
*
13375669 ACTTAAATTATTAACATAATCAATTT
1 ACTTAAATTATTAAAATAATCAATTT
13375695 AAATTATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATCAATTTGC
Found at i:13375709 original size:21 final size:22
Alignment explanation
Indices: 13375671--13375715 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
13375661 TAATTTGCAC
*
13375671 TTAAATTATTAACATAATCAAT
1 TTAAATTATTAACATAATAAAT
*
13375693 TTAAATTATT-TCATAATAAAT
1 TTAAATTATTAACATAATAAAT
13375714 TT
1 TT
13375716 TTAGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATTATTAACATAATAAAT
Found at i:13375899 original size:14 final size:15
Alignment explanation
Indices: 13375880--13375911 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13375870 TTTTTAATAA
13375880 AAATTTT-AAAACTT
1 AAATTTTGAAAACTT
13375894 AAATTTTGAAAACTT
1 AAATTTTGAAAACTT
13375909 AAA
1 AAA
13375912 AATTTGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATTTTGAAAACTT
Found at i:13375926 original size:18 final size:19
Alignment explanation
Indices: 13375894--13375943 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
13375884 TTTAAAACTT
*
13375894 AAATTTTGA-AAAC-TTAA
1 AAATTTGGAGAAACTTTAA
13375911 AAATTTGGAGAAACTTTAA
1 AAATTTGGAGAAACTTTAA
*
13375930 AACTTTGGAGAAAC
1 AAATTTGGAGAAAC
13375944 AAGTTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.28
18 4 0.14
19 17 0.59
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (19 bp):
AAATTTGGAGAAACTTTAA
Found at i:13387780 original size:45 final size:45
Alignment explanation
Indices: 13387716--13387806 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
13387706 ACCAATCAAG
* * *
13387716 TAGCGCCAGGAAGACGAGTCGCAGGAATACATGAAGTGGATGCTC
1 TAGCGCCAAGAAGACGAGTCGCAAGAATACATGAAGTAGATGCTC
*
13387761 TAGCGCCAAGAAGACGAGTCGCAAGAATACATGAAGTATATGCTC
1 TAGCGCCAAGAAGACGAGTCGCAAGAATACATGAAGTAGATGCTC
13387806 T
1 T
13387807 CACTTCACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.18
Consensus pattern (45 bp):
TAGCGCCAAGAAGACGAGTCGCAAGAATACATGAAGTAGATGCTC
Found at i:13412141 original size:104 final size:105
Alignment explanation
Indices: 13411983--13412191 Score: 402
Period size: 104 Copynumber: 2.0 Consensus size: 105
13411973 TGAAATTAGC
13411983 TATCTTTTTCTGTAAATATTTTAATAAGGGTAAAATAAAGGTTTTAAGTTTTTAGTTTTAATAAA
1 TATCTTTTTCTGTAAATATTTTAATAAGGGTAAAATAAAGGTTTTAAGTTTTTAGTTTTAATAAA
*
13412048 ATAGGATGATAACAACTAATATATAATTATATTTTATATA
66 ATAGGATGATAACAACTAATATATAAATATATTTTATATA
13412088 TATCTTTTTC-GTAAATATTTTAATAAGGGTAAAATAAAGGTTTTAAGTTTTTAGTTTTAATAAA
1 TATCTTTTTCTGTAAATATTTTAATAAGGGTAAAATAAAGGTTTTAAGTTTTTAGTTTTAATAAA
13412152 ATAGGATGATAACAACTAATATATAAATATATTTTATATA
66 ATAGGATGATAACAACTAATATATAAATATATTTTATATA
13412192 ATATATATTA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 93 0.90
105 10 0.10
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (105 bp):
TATCTTTTTCTGTAAATATTTTAATAAGGGTAAAATAAAGGTTTTAAGTTTTTAGTTTTAATAAA
ATAGGATGATAACAACTAATATATAAATATATTTTATATA
Found at i:13412191 original size:15 final size:16
Alignment explanation
Indices: 13412171--13412200 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13412161 TAACAACTAA
13412171 TATATAA-ATATATTT
1 TATATAATATATATTT
13412186 TATATAATATATATT
1 TATATAATATATATT
13412201 AATTGTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:13432508 original size:50 final size:50
Alignment explanation
Indices: 13432451--13432595 Score: 155
Period size: 50 Copynumber: 2.9 Consensus size: 50
13432441 CATTGAGATT
* ** * *
13432451 ATGAGAGGTCCCATGTAGGACCATGTCTTTGACATGGCGTTGACACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGACACCGAG
** * *
13432501 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGACACCGAG
* ** * * *
13432551 ATGAAAACTCCCATGTAAGACCATATCTGGGATATGGCATTGACA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGACA
13432596 GTACAAGAAA
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGACACCGAG
Found at i:13441417 original size:19 final size:19
Alignment explanation
Indices: 13441375--13441415 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13441365 GGTTTGGTTA
*
13441375 TTTTACTTAATTTCATTAG
1 TTTTACTTAATTTCAGTAG
*
13441394 TTTTATTTAATTT-AGTAG
1 TTTTACTTAATTTCAGTAG
13441412 TTTT
1 TTTT
13441416 TAATTTCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTACTTAATTTCAGTAG
Found at i:13447738 original size:15 final size:15
Alignment explanation
Indices: 13447720--13447759 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
13447710 CCATTCAATA
13447720 TGGAGCAATCGATAT
1 TGGAGCAATCGATAT
*
13447735 TGGAGCAATTGATAT
1 TGGAGCAATCGATAT
13447750 TGGAGCAATC
1 TGGAGCAATC
13447760 CTTAGCACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (15 bp):
TGGAGCAATCGATAT
Found at i:13459034 original size:135 final size:134
Alignment explanation
Indices: 13458793--13459062 Score: 441
Period size: 135 Copynumber: 2.0 Consensus size: 134
13458783 CTTTTTTCAT
* ** *
13458793 TAACTCTTTGATTTTCCTCTTGGAATCGGTTTCAATTCAAGAATTCTTTTCAATATTGAAGTATT
1 TAACTCTTTAATTTTCCTCTTGGAATCAATTTCAATCCAAGAATTCTTTTCAATATTGAAGTATT
* * *
13458858 TCCATTATCTGCCTTTGTGAGTGACATTATTCATTATTTCGATTGAGAGATTTATTACTCCATTC
66 TCCATTATCTACCTTTGTGAGTGACATTATTCATTATTTCGATCGAGAGATTTAGTACTCCATTC
13458923 TATA
131 TATA
* *
13458927 TAACTCTTTAATTTTCCTCTTGGAATCAATTTCTATCCAAGAATTCTTTTCTAATATTGAATTAT
1 TAACTCTTTAATTTTCCTCTTGGAATCAATTTCAATCCAAGAATTCTTTTC-AATATTGAAGTAT
*
13458992 TTCCGTTATCTACCTTTGTGAGTGACATTATTCATTATTTCGATCGAGAGATTTAGTACTCCATT
65 TTCCATTATCTACCTTTGTGAGTGACATTATTCATTATTTCGATCGAGAGATTTAGTACTCCATT
13459057 CTATA
130 CTATA
13459062 T
1 T
13459063 TTGACATTGA
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 46 0.37
135 79 0.63
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (134 bp):
TAACTCTTTAATTTTCCTCTTGGAATCAATTTCAATCCAAGAATTCTTTTCAATATTGAAGTATT
TCCATTATCTACCTTTGTGAGTGACATTATTCATTATTTCGATCGAGAGATTTAGTACTCCATTC
TATA
Found at i:13460646 original size:12 final size:12
Alignment explanation
Indices: 13460629--13460658 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
13460619 TAGGTTTTCA
13460629 TTTTTTTTCCAT
1 TTTTTTTTCCAT
13460641 TTTTTTTTCCAT
1 TTTTTTTTCCAT
13460653 TTTTTT
1 TTTTTT
13460659 CTTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCCAT
Found at i:13460659 original size:10 final size:11
Alignment explanation
Indices: 13460623--13460658 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
13460613 TTAGTTTAGG
13460623 TTTT-CATTTT
1 TTTTCCATTTT
13460633 TTTTCCATTTTT
1 TTTTCCA-TTTT
13460645 TTTTCCATTTT
1 TTTTCCATTTT
13460656 TTT
1 TTT
13460659 CTTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCCATTTT
Found at i:13470473 original size:91 final size:92
Alignment explanation
Indices: 13470358--13470540 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 92
13470348 TATGTTAAAC
13470358 TTAGAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTTACAATGATTTTAATGAA
1 TTAGAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTTACAATGATTTTAATGAA
13470423 ATTAGGATCGAATTGTGAAAATTACTT
66 ATTAGGATCGAATTGTGAAAATTACTT
13470450 TTAGAAATA-TAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTTACAATGATTTTAATGAA
1 TTAGAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTTACAATGATTTTAATGAA
13470514 ATTAGGATCGAATTGTGAAAATTACTT
66 ATTAGGATCGAATTGTGAAAATTACTT
13470541 AATCTGAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 82 0.90
92 9 0.10
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (92 bp):
TTAGAAATATTAAATATATTTTCTCATAGATTCTTTTACGGTAAAGTTACAATGATTTTAATGAA
ATTAGGATCGAATTGTGAAAATTACTT
Found at i:13475074 original size:29 final size:30
Alignment explanation
Indices: 13475040--13475109 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
13475030 AAATTAAAAA
*
13475040 AATAAAAATTAT-A-AACTATATTAAATTTT
1 AATAAAAATTATAAGAAATAT-TTAAATTTT
* *
13475069 AATAAAAAATATAAGAAATATTTAATTTTT
1 AATAAAAATTATAAGAAATATTTAAATTTT
*
13475099 ATTAAAAATTA
1 AATAAAAATTA
13475110 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 11 0.32
30 18 0.53
31 5 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
AATAAAAATTATAAGAAATATTTAAATTTT
Found at i:13475126 original size:9 final size:9
Alignment explanation
Indices: 13475114--13475177 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
13475104 AAATTAGAAA
13475114 AAAAATTAT
1 AAAAATTAT
*
13475123 AAAAATCAT
1 AAAAATTAT
13475132 AAAAATTAT
1 AAAAATTAT
13475141 -AAAATGTAT
1 AAAAAT-TAT
* *
13475150 AGAAATATAG
1 AAAAAT-TAT
13475160 AAAAATATAT
1 AAAAAT-TAT
13475170 ATAAAATT
1 A-AAAATT
13475178 TTATAAAGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
8 5 0.11
9 19 0.42
10 16 0.36
11 5 0.11
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:13477036 original size:114 final size:114
Alignment explanation
Indices: 13476841--13477261 Score: 620
Period size: 114 Copynumber: 3.7 Consensus size: 114
13476831 TAAGCATTAG
* * *
13476841 GAAAGCGCCGC-GAAAAACCTAAGGCC-A--ACGCCG-TTTCAGAGCTTTCGGGGATTTAGCGGC
1 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* *
13476901 GTTTTTAAGAAAGCGCCGCTAATGCTGAGGGCTTTAGCGGCGTTTTTGA
66 ATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
*
13476950 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTTGCGGC
1 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* *
13477015 ATTTTTAAGAAAGCGCCGCTAATACTCAAGGCTTTAGCGGCGTTTTTGA
66 ATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* * * * *
13477064 GAAAGCGCCACAAAAATACCTAAGCCCAACGACGTCATTTTCTGAGCTTTTGGGGATTTAGCGGC
1 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
*
13477129 GA-TTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
66 -ATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* * *
13477178 GAAAGCGCCGCAAAAAAACTTTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAACGGC
1 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* *
13477243 GTTTTTGAGAAAGCGCCGC
66 ATTTTTAAGAAAGCGCCGC
13477262 AAAAAAACCT
Statistics
Matches: 277, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
109 11 0.04
110 13 0.05
111 1 0.00
113 6 0.02
114 245 0.88
115 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
ATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
Found at i:13477257 original size:73 final size:73
Alignment explanation
Indices: 13477161--13477334 Score: 285
Period size: 73 Copynumber: 2.4 Consensus size: 73
13477151 TGCTCAGGGC
* * *
13477161 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTTAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCT
13477226 TTCGGGGA
66 TTCGGGGA
*
13477234 TTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCT
13477299 TTCGGGGA
66 TTCGGGGA
* * *
13477307 TTTAGTGGCGTTTTTAAGACAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
13477335 TAATGCTCAG
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 93 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCT
TTCGGGGA
Found at i:13477279 original size:187 final size:187
Alignment explanation
Indices: 13477047--13477515 Score: 740
Period size: 187 Copynumber: 2.5 Consensus size: 187
13477037 TACTCAAGGC
* * * *
13477047 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAATACCTAAGCCCAACGACGTCATTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
13477112 TTTGGGGATTTAGCGGCGATTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTG
* *
13477177 AGAAAGCGCCGCAAAAAAACTTTAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
131 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* *
13477234 TTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
13477299 TTCGGGGATTTAGTGGCGTTTTTAAGACAGCGCCGCTAATGCTCAGGGCTTTAGTGGCATTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTG
*
13477364 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTTTCGGGGA
131 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
* ** * * *
13477421 TTTAGCGGCATTTTCAAGAAAGCGCCGCAAAAAAATCTAAGCCCAACGTCGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
13477486 TTCGGGGATTTAGCGGCGTTTTTAAGAAAG
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAG
13477516 AGATAGTATT
Statistics
Matches: 256, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
187 256 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (187 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATTTTTG
AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGA
Found at i:13477467 original size:73 final size:73
Alignment explanation
Indices: 13477348--13477515 Score: 266
Period size: 73 Copynumber: 2.3 Consensus size: 73
13477338 TGCTCAGGGC
* *
13477348 TTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGAT-GCCGTTTTCTGAGC
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACG-TCGCCGTTTTCTGAGC
13477412 TTTCGGGGA
65 TTTCGGGGA
* * *
13477421 TTTAGCGGCATTTTCAAGAAAGCGCCGCAAAAAAATCTAAGCCCAACGTCGCCGTTTTTTGAGCT
1 TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGTCGCCGTTTTCTGAGCT
13477486 TTCGGGGA
66 TTCGGGGA
*
13477494 TTTAGCGGCGTTTTTAAGAAAG
1 TTTAGCGGCATTTTTAAGAAAG
13477516 AGATAGTATT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 1 0.01
73 86 0.99
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCATTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGTCGCCGTTTTCTGAGCT
TTCGGGGA
Found at i:13477761 original size:7 final size:7
Alignment explanation
Indices: 13477734--13477773 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
13477724 TTTTAAGGTA
*
13477734 TATGGAG
1 TATGGAT
*
13477741 TATGGGT
1 TATGGAT
*
13477748 TAGGGAT
1 TATGGAT
13477755 TATGGAT
1 TATGGAT
13477762 TATGGAT
1 TATGGAT
13477769 TATGG
1 TATGG
13477774 TTTAAGGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (7 bp):
TATGGAT
Found at i:13478074 original size:14 final size:16
Alignment explanation
Indices: 13478031--13478076 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
13478021 TTTTAAGGTT
*
13478031 AGGGAGTATGGATTT-
1 AGGGATTATGGATTTA
13478046 AGGGATTATGG-TTTA
1 AGGGATTATGGATTTA
13478061 AGGG-TTA-GGATTTA
1 AGGGATTATGGATTTA
13478075 AG
1 AG
13478077 ATTTAGGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 12 0.43
15 14 0.50
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
AGGGATTATGGATTTA
Found at i:13478089 original size:14 final size:14
Alignment explanation
Indices: 13478058--13478127 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
13478048 GGATTATGGT
* **
13478058 TTAAGGGTTAGGAT
1 TTAAGAGTTAGGGG
*
13478072 TTAAGATTTAGGGG
1 TTAAGAGTTAGGGG
*
13478086 TTAAGGGTTTAGGGG
1 TTAAGAG-TTAGGGG
13478101 TT-AGACGTTAGGGG
1 TTAAGA-GTTAGGGG
13478115 TTAAGAGTTAGGG
1 TTAAGAGTTAGGG
13478128 ATTTAAGGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 33 0.72
15 13 0.28
ACGTcount: A:0.26, C:0.01, G:0.40, T:0.33
Consensus pattern (14 bp):
TTAAGAGTTAGGGG
Found at i:13478098 original size:15 final size:15
Alignment explanation
Indices: 13478078--13478140 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
13478068 GGATTTAAGA
13478078 TTTAGGGGTTAAGGG
1 TTTAGGGGTTAAGGG
*
13478093 TTTAGGGGTT-AGACG
1 TTTAGGGGTTAAG-GG
*
13478108 -TTAGGGGTTAAGAG
1 TTTAGGGGTTAAGGG
*
13478122 -TTAGGGATTTAA-GG
1 TTTAGGG-GTTAAGGG
13478136 TTTAG
1 TTTAG
13478141 AGATTCAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.47
15 21 0.52
ACGTcount: A:0.24, C:0.02, G:0.40, T:0.35
Consensus pattern (15 bp):
TTTAGGGGTTAAGGG
Found at i:13478098 original size:29 final size:28
Alignment explanation
Indices: 13478058--13478140 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
13478048 GGATTATGGT
13478058 TTAAGGGTTAGGATTTAAGATTTAGGGG
1 TTAAGGGTTAGGATTTAAGATTTAGGGG
** *
13478086 TTAAGGGTTTAGGGGTT-AGACGTTAGGGG
1 TTAAGGG-TTAGGATTTAAGA-TTTAGGGG
* *
13478115 TTAAGAGTTAGGGATTTAAGGTTTAG
1 TTAAGGGTTA-GGATTTAAGATTTAG
13478141 AGATTCAGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 13 0.30
29 28 0.65
30 2 0.05
ACGTcount: A:0.27, C:0.01, G:0.37, T:0.35
Consensus pattern (28 bp):
TTAAGGGTTAGGATTTAAGATTTAGGGG
Found at i:13483691 original size:44 final size:43
Alignment explanation
Indices: 13483579--13483758 Score: 252
Period size: 43 Copynumber: 4.2 Consensus size: 43
13483569 GACTTATAGT
* * * *
13483579 GGCGTTTGCGGTAGAAGCGCCTCTAAAGGTCATGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGC
* * *
13483622 GGTGTTTGTGGCAAAAGCGCCGCTAAAGGTTATGGTCTTTAGCC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAG-C
*
13483666 GGCGTTTGTGGGAAAAGCGCAGCTAAAGGTCATGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGC
* * *
13483709 GACATTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGC
13483752 GGCGTTT
1 GGCGTTT
13483759 ATTTTCTGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 81 0.68
44 39 0.32
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGC
Found at i:13486143 original size:43 final size:43
Alignment explanation
Indices: 13486031--13486144 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
13486021 GTGCTTTTCG
* * * * **
13486031 TGTAAGACCACGTATGGGACGTTGACATCGATTTGTGTTTATG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
* *
13486074 TGTAAGACC-CTGTCTGGAACAG-TGGCATCGATATGTGATTGCA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACA
13486117 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
13486145 TGTACGAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
42 2 0.03
43 54 0.93
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACA
Found at i:13499174 original size:129 final size:129
Alignment explanation
Indices: 13498964--13499198 Score: 407
Period size: 129 Copynumber: 1.8 Consensus size: 129
13498954 TATTTTTGCC
* *
13498964 AGATTTTCTTTTACCTACCCTAGATTAGGTAAGGAAATCAGGAGATCGAGAATATATTTATGGGA
1 AGATTTTCTTTTACCTACCCTAGATTAGGTAAGGAAATCAGGAGACCGAGAATATATTTATAGGA
13499029 AGTGGACACTTGGAATGGTTTTTGGCTATCTACTTAATGCTCAACAGTGAGGTTAATCATCACT
66 AGTGGACACTTGGAATGGTTTTTGGCTATCTACTTAATGCTCAACAGTGAGGTTAATCATCACT
* * *
13499093 AGATTTTCTTTTACCTACCCTGGATTAGGTAAGGAAATCAGGGGACCGAGAATGTATTTATAGGA
1 AGATTTTCTTTTACCTACCCTAGATTAGGTAAGGAAATCAGGAGACCGAGAATATATTTATAGGA
* *
13499158 AGTGGACACTTTGAATGGTTTTTGGCTATCTGCTTAATGCT
66 AGTGGACACTTGGAATGGTTTTTGGCTATCTACTTAATGCT
13499199 TAGGTTCTTC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 99 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (129 bp):
AGATTTTCTTTTACCTACCCTAGATTAGGTAAGGAAATCAGGAGACCGAGAATATATTTATAGGA
AGTGGACACTTGGAATGGTTTTTGGCTATCTACTTAATGCTCAACAGTGAGGTTAATCATCACT
Found at i:13501295 original size:61 final size:60
Alignment explanation
Indices: 13501201--13501425 Score: 252
Period size: 61 Copynumber: 3.7 Consensus size: 60
13501191 ATATTTGTTT
* * *
13501201 AAGAATGCCTTTGTGGAAAAGCTTTGGATAGGAAAGCATTTGTGGCGAGTACTGAATGTAA
1 AAGAATGCCTTTGTGGAAAAACTTTGGACAGGAAAGCCTTTGTGGCGAGTACTGAATGT-A
* * * * * *
13501262 AAGATTGCCTTTATGGAAAAACTCTAGACAGGAAAGCCTCTGTAGCGAGTACTGAATGTA
1 AAGAATGCCTTTGTGGAAAAACTTTGGACAGGAAAGCCTTTGTGGCGAGTACTGAATGTA
* * * *
13501322 AAGAAATGCCTTTGTGGAAAAAACTTTGGACAAGAAAGCCTTTGTGGCGAGCATTAAATGTA
1 AAG-AATGCCTTTGTGG-AAAAACTTTGGACAGGAAAGCCTTTGTGGCGAGTACTGAATGTA
** * * *
13501384 AAGGAACACCTTTGTGGAAAAGCTCTGGATAGGAAAGCCTTT
1 AA-GAATGCCTTTGTGGAAAAACTTTGGACAGGAAAGCCTTT
13501426 ATGGAGAATA
Statistics
Matches: 136, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
60 4 0.03
61 82 0.60
62 49 0.36
63 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (60 bp):
AAGAATGCCTTTGTGGAAAAACTTTGGACAGGAAAGCCTTTGTGGCGAGTACTGAATGTA
Found at i:13505536 original size:17 final size:17
Alignment explanation
Indices: 13505500--13505537 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
13505490 TTGTAGGGTC
*
13505500 GGAATAGGAGGAAGGTA
1 GGAATAGGAGGAAGGCA
*
13505517 GGAATAGGAGGAATGCA
1 GGAATAGGAGGAAGGCA
13505534 GGAA
1 GGAA
13505538 CTAAAGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.45, T:0.11
Consensus pattern (17 bp):
GGAATAGGAGGAAGGCA
Found at i:13507968 original size:25 final size:25
Alignment explanation
Indices: 13507920--13507973 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
13507910 TATGCCAGAG
* * *
13507920 AGGCAACATGCAGAATACGTCACAA
1 AGGCAACATACAGAATAAGCCACAA
*
13507945 AGGCAACATACAGAATAAGCCACAT
1 AGGCAACATACAGAATAAGCCACAA
13507970 AGGC
1 AGGC
13507974 CAAAAAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (25 bp):
AGGCAACATACAGAATAAGCCACAA
Found at i:13511632 original size:23 final size:23
Alignment explanation
Indices: 13511601--13511651 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
13511591 ACCTACTTTC
* *
13511601 TTACTGTAGTAATTTTCGGGGTG
1 TTACAGTAGTAATTTTCGGGGTA
13511624 TTACAGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGGTA
13511647 TTACA
1 TTACA
13511652 TTTTTAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGGTA
Found at i:13512933 original size:4 final size:4
Alignment explanation
Indices: 13512924--13512958 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
13512914 GGTTTTTATT
13512924 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
13512959 TAACCCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:13513691 original size:39 final size:40
Alignment explanation
Indices: 13513632--13513711 Score: 153
Period size: 39 Copynumber: 2.0 Consensus size: 40
13513622 AAGATTTAAG
13513632 GAATCACTTCGTAAGTGTCCTCATCATGGGATTCCTCATT
1 GAATCACTTCGTAAGTGTCCTCATCATGGGATTCCTCATT
13513672 GAATCACTTC-TAAGTGTCCTCATCATGGGATTCCTCATT
1 GAATCACTTCGTAAGTGTCCTCATCATGGGATTCCTCATT
13513711 G
1 G
13513712 TGTCCAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 30 0.75
40 10 0.25
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (40 bp):
GAATCACTTCGTAAGTGTCCTCATCATGGGATTCCTCATT
Found at i:13514363 original size:21 final size:21
Alignment explanation
Indices: 13514339--13514379 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13514329 TGATGTCTTC
* *
13514339 ATCCAAAGTCAAGCAACAACG
1 ATCCAAAGCCAAGAAACAACG
13514360 ATCCAAAGCCAAGAAACAAC
1 ATCCAAAGCCAAGAAACAAC
13514380 ATTGAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (21 bp):
ATCCAAAGCCAAGAAACAACG
Found at i:13516045 original size:21 final size:21
Alignment explanation
Indices: 13516021--13516061 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13516011 TGATGTCTTC
* *
13516021 ATCCAAAGTCAAGCAACAACG
1 ATCCAAAGCCAAGAAACAACG
13516042 ATCCAAAGCCAAGAAACAAC
1 ATCCAAAGCCAAGAAACAAC
13516062 ATTGAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (21 bp):
ATCCAAAGCCAAGAAACAACG
Found at i:13521517 original size:294 final size:294
Alignment explanation
Indices: 13520981--13521563 Score: 925
Period size: 294 Copynumber: 2.0 Consensus size: 294
13520971 TCCAAGCCAC
* *
13520981 TGCCAAAAATACCATTGTGATTCTAGATGAAGAAGTGAAAGAGAGGTTTGATTCAATCTTTAAGA
1 TGCCAAAAATACCATTGTGATTCAAGATGAAAAAGTGAAAGAGAGGTTTGATTCAATCTTTAAGA
13521046 ATCAACCTATGATGCAAGAAAAAGGTTTCAACTTGGAAAGCAATGATAAGATGATTGTGCCTTTG
66 ATCAACCTATGATGCAAGAAAAAGGTTTCAACTTGGAAAGCAATGATAAGATGATTGTGCCTTTG
* * * *
13521111 CTGATTTGAAAGACGATTGATGCCCTCAATTGGAATTATTTTTGTGATGCATAATGATTACCCAA
131 CCGATTCGAAAGACAATTGATGCCCTCAATTGGAATTATTTTTGTGATGCACAATGATTACCCAA
* * * * * *
13521176 TGAGGAGTTAGTTTGAGAGTTCTATGCCAATTTGACTAAGTCAGATGCTACTGAAGTTCTTGTTG
196 TGAGAAGTTAGTTCGAAAGTTCTATGCCAATTTGACTAAGCCAGATGCTACCGAAGTTCTTCTTG
* *
13521241 GCAAGAAGAAGGTACCCTTAACTTTTAAGACCTT
261 GCAAAAAGAAGGTACCCTTAACTTCTAAGACCTT
* *
13521275 TGCCGAAAATACCATTGTGGTTCAAGATGAAAAAGTGAAAGAGAGGTTTGATTCAATCTTTAAGA
1 TGCCAAAAATACCATTGTGATTCAAGATGAAAAAGTGAAAGAGAGGTTTGATTCAATCTTTAAGA
* * *
13521340 ATCAACCTATGATGC-CGAAAAAAGGTTTCAACTTGGAAAGCAATGATAAGATGGTTGTGTCTTT
66 ATCAACCTATGATGCAAG-AAAAAGGTTTCAACTTGGAAAGCAATGATAAGATGATTGTGCCTTT
* * *
13521404 GCCGATTCGAAAGACAATTGATGCCCTCAATTGGAATTATTTTTGTGATGCACGATTATTACCCG
130 GCCGATTCGAAAGACAATTGATGCCCTCAATTGGAATTATTTTTGTGATGCACAATGATTACCCA
* *
13521469 ATGAGAAGTTAGTTCGAAAGTTCTATGCCAGTTTGACTAAGCCAGATGCTACCGGAGTTCTTCTT
195 ATGAGAAGTTAGTTCGAAAGTTCTATGCCAATTTGACTAAGCCAGATGCTACCGAAGTTCTTCTT
*
13521534 TGCAAAAAGAAGGTACCCTTAACTTCTAAG
260 GGCAAAAAGAAGGTACCCTTAACTTCTAAG
13521564 TCCATTAAGG
Statistics
Matches: 263, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
293 1 0.00
294 262 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (294 bp):
TGCCAAAAATACCATTGTGATTCAAGATGAAAAAGTGAAAGAGAGGTTTGATTCAATCTTTAAGA
ATCAACCTATGATGCAAGAAAAAGGTTTCAACTTGGAAAGCAATGATAAGATGATTGTGCCTTTG
CCGATTCGAAAGACAATTGATGCCCTCAATTGGAATTATTTTTGTGATGCACAATGATTACCCAA
TGAGAAGTTAGTTCGAAAGTTCTATGCCAATTTGACTAAGCCAGATGCTACCGAAGTTCTTCTTG
GCAAAAAGAAGGTACCCTTAACTTCTAAGACCTT
Found at i:13522577 original size:25 final size:25
Alignment explanation
Indices: 13522530--13522577 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
13522520 AATTCTTTTC
*
13522530 GTTTAGTTTTAATTTCTTTTTAGGT
1 GTTTAGTTTTAATTTCTTGTTAGGT
*
13522555 GTTTA-TTTTTATTTCTTAGTTAG
1 GTTTAGTTTTAATTTCTT-GTTAG
13522578 AATTTTGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.65
Consensus pattern (25 bp):
GTTTAGTTTTAATTTCTTGTTAGGT
Found at i:13524306 original size:15 final size:16
Alignment explanation
Indices: 13524277--13524306 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13524267 CAAACATCCT
13524277 TTAACACATTATCAAA
1 TTAACACATTATCAAA
13524293 TTAACACA-TATCAA
1 TTAACACATTATCAA
13524307 CAAGGCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:13530548 original size:25 final size:25
Alignment explanation
Indices: 13530510--13530568 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
13530500 CTGTACCTGT
13530510 ATGCTCACAGGAGCTATGAATCAGA
1 ATGCTCACAGGAGCTATGAATCAGA
* *
13530535 ATGCTCACATGAGCTTTGAATCAGA
1 ATGCTCACAGGAGCTATGAATCAGA
13530560 ATGCTCACA
1 ATGCTCACA
13530569 CGATTTGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (25 bp):
ATGCTCACAGGAGCTATGAATCAGA
Found at i:13558347 original size:13 final size:14
Alignment explanation
Indices: 13558329--13558358 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
13558319 TAAAATTTTG
13558329 TTTTTAAGTTAT-T
1 TTTTTAAGTTATGT
13558342 TTTTTAAGTTATGT
1 TTTTTAAGTTATGT
13558356 TTT
1 TTT
13558359 ATGTTTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (14 bp):
TTTTTAAGTTATGT
Found at i:13563365 original size:20 final size:22
Alignment explanation
Indices: 13563321--13563392 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
13563311 AAAATAAGAA
*
13563321 GTGCCTC--TATTTGCACTTCG
1 GTGCCTCTATATTTGCACTACG
* *
13563341 ATGCCT-T-TGTTTGCACTACG
1 GTGCCTCTATATTTGCACTACG
13563361 GTGCCTCTATATTTGCACTACG
1 GTGCCTCTATATTTGCACTACG
13563383 GTGCCTCTAT
1 GTGCCTCTAT
13563393 TAGCATTTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 21 0.48
21 1 0.02
22 22 0.50
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (22 bp):
GTGCCTCTATATTTGCACTACG
Found at i:13563392 original size:22 final size:21
Alignment explanation
Indices: 13563321--13563390 Score: 90
Period size: 20 Copynumber: 3.4 Consensus size: 21
13563311 AAAATAAGAA
*
13563321 GTGCCTC-TATTTGCACTTCG
1 GTGCCTCTTATTTGCACTACG
* *
13563341 ATGCCT-TTGTTTGCACTACG
1 GTGCCTCTTATTTGCACTACG
13563361 GTGCCTCTATATTTGCACTACG
1 GTGCCTCT-TATTTGCACTACG
13563383 GTGCCTCT
1 GTGCCTCT
13563391 ATTAGCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 21 0.50
21 1 0.02
22 20 0.48
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.39
Consensus pattern (21 bp):
GTGCCTCTTATTTGCACTACG
Found at i:13565740 original size:21 final size:20
Alignment explanation
Indices: 13565700--13565740 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
13565690 AAATGATATG
* *
13565700 ATGCTATATTATACATACAA
1 ATGCTATATAATAAATACAA
13565720 ATGCTATAATAATAAATACAA
1 ATGCTAT-ATAATAAATACAA
13565741 CAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (20 bp):
ATGCTATATAATAAATACAA
Found at i:13567984 original size:82 final size:82
Alignment explanation
Indices: 13567845--13568007 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
13567835 ATATGTTCAG
* *
13567845 TAGTTAGGTTACCTATATACGAACTTACTAAGCATTATTTCTTACGTTAGTTGTTTTCTTTTCCT
1 TAGTTAGGTTACCTATATACGAACTTACTAACCATTATTGCTTACGTTAGTTGTTTTCTTTTCCT
13567910 GTAGGTCATCGGAAAGC
66 GTAGGTCATCGGAAAGC
* * *
13567927 TAGTTAGGTTACCTTTATATGAACTTACTAACCATTATTGCTTACGTTAGTTTTTTTCTTTTCCT
1 TAGTTAGGTTACCTATATACGAACTTACTAACCATTATTGCTTACGTTAGTTGTTTTCTTTTCCT
13567992 GTAGGTCATCGGAAAG
66 GTAGGTCATCGGAAAG
13568008 ATCGATTGGG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (82 bp):
TAGTTAGGTTACCTATATACGAACTTACTAACCATTATTGCTTACGTTAGTTGTTTTCTTTTCCT
GTAGGTCATCGGAAAGC
Found at i:13568625 original size:17 final size:17
Alignment explanation
Indices: 13568603--13568645 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
13568593 ATGTGTCTCA
13568603 ACCGTGTGTGACACACG
1 ACCGTGTGTGACACACG
*
13568620 ACCGTGTGCGACACACG
1 ACCGTGTGTGACACACG
13568637 ACCGTGTGT
1 ACCGTGTGT
13568646 CCCTTGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (17 bp):
ACCGTGTGTGACACACG
Found at i:13571524 original size:21 final size:21
Alignment explanation
Indices: 13571499--13571543 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13571489 TTTGTTTTTC
13571499 TTTTCCCTCCTTTCCTTCCCT
1 TTTTCCCTCCTTTCCTTCCCT
** * *
13571520 TTTTCTTTCCTTTTCTTCTCT
1 TTTTCCCTCCTTTCCTTCCCT
13571541 TTT
1 TTT
13571544 CATAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTCCCTCCTTTCCTTCCCT
Found at i:13572300 original size:215 final size:218
Alignment explanation
Indices: 13571828--13572417 Score: 744
Period size: 216 Copynumber: 2.7 Consensus size: 218
13571818 ACTTTTCTTG
* * *
13571828 CTAGCCAAACAAGCTTTCATCAGTCCTCTTTTTCTTTTTGTTATGCATCATCATATTTTTTAGTT
1 CTAGCCAAACAGGCTTTCACCAGTCCTCTTTTTCTTTTTGTTATGCATCATCCTATTTTTTAGTT
** ** **
13571893 CTTTTGG-AAAGAAAAGAAACCTTTTTCTTTAACTGAAAACTCATGAGAAACCATGAATGAGATG
66 C-TTTGGAAAAGAAAAGAAACC-CCTTCAATAACTGAAAACTCAAAAGAAACCATGAATGAGATG
* * * **
13571957 GAAAAGAATATGTTCTTCTAGGAAGATTGTTTGGCTTCCTAGAAAATCTGGGTTTTCTTCCTTCC
129 GAAAAGAACAAG--C-TCT-------TT-TTTGGCTTCCTAGAAAATATGGACTTTCTTCCTTCC
*
13572022 CACTTTTTTTTCTTTTCTCATTCATTTTTTTCCTCA
183 CACTTTTTTTTCGTTTCTCATTCATTTTTTTCCTCA
13572058 CTAGCCAAACAGGCTTTCACCAGTCCTCTTTTTCTTTTTGTTATGCATCA-CCTATTTTTTAGTT
1 CTAGCCAAACAGGCTTTCACCAGTCCTCTTTTTCTTTTTGTTATGCATCATCCTATTTTTTAGTT
* *
13572122 CTTTGGAAAAGAAAAG-AACCCTCTTC-ATCAACTGAAAACTTAAAAGAAGCCATGAATGAGATG
66 CTTTGGAAAAGAAAAGAAACCC-CTTCAAT-AACTGAAAACTCAAAAGAAACCATGAATGAGATG
*
13572185 GAAAAGAACAAGCTCTTTTTTGGCTTCCTAGAAAATATGGACTTTCTTCC-TCGC-CTCTTTTTT
129 GAAAAGAACAAGCTCTTTTTTGGCTTCCTAGAAAATATGGACTTTCTTCCTTCCCACT-TTTTTT
** *
13572248 TCGTTTCTTGTT-ATTTTTTTCCTCG
193 TCGTTTCTCATTCATTTTTTTCCTCA
* * *
13572273 CTAGCCAAATAGGCTTTCACTAGTCCTCTTTTTCTTTTTGTTATGCATCATCGTATTTTTTAGTT
1 CTAGCCAAACAGGCTTTCACCAGTCCTCTTTTTCTTTTTGTTATGCATCATCCTATTTTTTAGTT
* * *
13572338 CTTTGGGAAAGAAAAGAAACCCCTTCAATAACTGAAAACTCAAGAGAAACTATGAATGAGATGGA
66 CTTTGGAAAAGAAAAGAAACCCCTTCAATAACTGAAAACTCAAAAGAAACCATGAATGAGATGGA
13572403 AAAGAACAAGCTCTT
131 AAAGAACAAGCTCTT
13572418 CTAGGAAGCT
Statistics
Matches: 325, Mismatches: 28, Indels: 28
0.85 0.07 0.07
Matches are distributed among these distances:
215 62 0.19
216 97 0.30
217 36 0.11
218 2 0.01
225 3 0.01
226 1 0.00
227 1 0.00
228 52 0.16
229 23 0.07
230 48 0.15
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (218 bp):
CTAGCCAAACAGGCTTTCACCAGTCCTCTTTTTCTTTTTGTTATGCATCATCCTATTTTTTAGTT
CTTTGGAAAAGAAAAGAAACCCCTTCAATAACTGAAAACTCAAAAGAAACCATGAATGAGATGGA
AAAGAACAAGCTCTTTTTTGGCTTCCTAGAAAATATGGACTTTCTTCCTTCCCACTTTTTTTTCG
TTTCTCATTCATTTTTTTCCTCA
Found at i:13576015 original size:29 final size:29
Alignment explanation
Indices: 13575954--13576023 Score: 117
Period size: 27 Copynumber: 2.5 Consensus size: 29
13575944 TTGCAAAATA
*
13575954 AAAAAAAAACATTATAATTTTATTTACAT
1 AAAAAAAACCATTATAATTTTATTTACAT
13575983 --AAAAAACCATTATAATTTTATTTACAT
1 AAAAAAAACCATTATAATTTTATTTACAT
13576010 AAAAAAAACCATTA
1 AAAAAAAACCATTA
13576024 AATATGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 26 0.68
29 12 0.32
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAAAAACCATTATAATTTTATTTACAT
Found at i:13576271 original size:10 final size:11
Alignment explanation
Indices: 13576243--13576277 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
13576233 CCGTATTTTT
13576243 TTAAAAAAATTA
1 TTAAAAAAA-TA
13576255 TTAAAAAAATA
1 TTAAAAAAATA
13576266 TT-AAAAAATA
1 TTAAAAAAATA
13576276 TT
1 TT
13576278 TTATTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 4 0.17
12 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:13576615 original size:20 final size:21
Alignment explanation
Indices: 13576590--13576629 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
13576580 TAACAAAAAA
*
13576590 TTAAAAATT-ACTTAAATATT
1 TTAAAAATTAAATTAAATATT
13576610 TTAAAAATTAAATTAAATAT
1 TTAAAAATTAAATTAAATAT
13576630 AAATATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAATTAAATTAAATATT
Found at i:13580280 original size:6 final size:6
Alignment explanation
Indices: 13580262--13580307 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
13580252 GTCGTAGTTT
*
13580262 ATGTGT ATG-GG ATGTGG ATGTGG ATGTGG ATGTGG ATGTGG ATGTG
1 ATGTGG ATGTGG ATGTGG ATGTGG ATGTGG ATGTGG ATGTGG ATGTG
13580308 TGATCTAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
ATGTGG
Found at i:13593956 original size:25 final size:25
Alignment explanation
Indices: 13593934--13593982 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
13593924 TAAAGCTCGG
*
13593934 ATAAGCTTCCTATTACATGGCTCAC
1 ATAAGCTTCCCATTACATGGCTCAC
* *
13593959 ATGAGCTTCCCATTATATGGCTCA
1 ATAAGCTTCCCATTACATGGCTCA
13593983 AGAGAGTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (25 bp):
ATAAGCTTCCCATTACATGGCTCAC
Found at i:13595182 original size:73 final size:73
Alignment explanation
Indices: 13595061--13595248 Score: 313
Period size: 73 Copynumber: 2.6 Consensus size: 73
13595051 CGTGTGTGAC
* ** * * *
13595061 ACACGGCCTAGCACACGGGCATATGTCTTGGCCGTGTGACCCCTGCACCTAGTTATTTCAAATGA
1 ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCCCGGCACCTAGTTATTTCAAATGA
13595126 AATTGTTT
66 AATTGTTT
13595134 ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCCCGGCACCTAGTTATTTCAAATGA
1 ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCCCGGCACCTAGTTATTTCAAATGA
13595199 AATTGTTT
66 AATTGTTT
*
13595207 ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGGGTGACCC
1 ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCC
13595249 AAGTCAGAGA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 108 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (73 bp):
ACACGGCCTAGCACATGGGTGTGTGGCTTGGCCGTGTGACCCCGGCACCTAGTTATTTCAAATGA
AATTGTTT
Found at i:13598020 original size:48 final size:48
Alignment explanation
Indices: 13597953--13598138 Score: 246
Period size: 48 Copynumber: 3.9 Consensus size: 48
13597943 GCATCAATAT
*
13597953 TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATAT
1 TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATAA
* * * *
13598001 TCTATTATGATACAAGGGTGGCAAGGACTGTGTGCAGGCCACCAATAA
1 TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATAA
* * * * * *
13598049 CCTGTTAAGATACAAGGGTGGCACGAACTATGTGCAGGCCACCGAGAA
1 TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATAA
* * *
13598097 TCTGTTATTACACAAAGGTGGTACGGACTGTGTGCAGGCCAC
1 TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
13598139 TGAGAAATTT
Statistics
Matches: 117, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 117 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (48 bp):
TCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGATAA
Found at i:13598983 original size:2 final size:2
Alignment explanation
Indices: 13598976--13599000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13598966 TTAAATTTAA
13598976 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13599001 AATGATTTGT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13602522 original size:45 final size:46
Alignment explanation
Indices: 13602473--13602589 Score: 211
Period size: 45 Copynumber: 2.6 Consensus size: 46
13602463 TGGTTATGAT
*
13602473 ATCTAAAGTAATAAACACTTAATCAAAA-TTGTACCTTTTTTATTC
1 ATCTAAAGTAATAAACACTTAATCAAAACATGTACCTTTTTTATTC
13602518 ATCTAAAGTAATAAACACTTAAT-AAAACATGTACCTTTTTTATTC
1 ATCTAAAGTAATAAACACTTAATCAAAACATGTACCTTTTTTATTC
13602563 ATCTAAAGTAATAAACACTTAATCAAA
1 ATCTAAAGTAATAAACACTTAATCAAA
13602590 CGAGTAATCT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
44 4 0.06
45 62 0.90
46 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.36
Consensus pattern (46 bp):
ATCTAAAGTAATAAACACTTAATCAAAACATGTACCTTTTTTATTC
Found at i:13607381 original size:29 final size:29
Alignment explanation
Indices: 13607339--13607401 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
13607329 ACCATCTTTC
*
13607339 ACGAGTCTAGTGATTCTTTCTTGGTTAAT
1 ACGAGTCTAGTGATTCTTTCTTGGTGAAT
13607368 ACGAGTCTAGTGATTCTTTCTTGGTGAAT
1 ACGAGTCTAGTGATTCTTTCTTGGTGAAT
13607397 A-GAGT
1 ACGAGT
13607402 GAGAAGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (29 bp):
ACGAGTCTAGTGATTCTTTCTTGGTGAAT
Found at i:13613613 original size:21 final size:21
Alignment explanation
Indices: 13613560--13613614 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
13613550 GAGCTAAATA
*
13613560 GAAACCCATAAGGGATGAACG
1 GAAACCCATAAGGCATGAACG
* * *
13613581 GAAGCTCGTAAGAGCA-GAACG
1 GAAACCCATAAG-GCATGAACG
13613602 GAAACCCATAAGG
1 GAAACCCATAAGG
13613615 GTTAAACAGA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.42, C:0.20, G:0.29, T:0.09
Consensus pattern (21 bp):
GAAACCCATAAGGCATGAACG
Found at i:13613637 original size:42 final size:42
Alignment explanation
Indices: 13613533--13613689 Score: 115
Period size: 42 Copynumber: 3.7 Consensus size: 42
13613523 GCTCGAAGGC
* * ** *
13613533 TAAATAGAAGCTCATGAGAGCTA-AATAGAAACCCATAAGGGA
1 TAAACAGAAGCTCATAAGAGC-AGAACGGAAACCCATAAGGGT
* * *
13613575 TGAACGGAAGCTCGTAAGAGCAGAACGGAAACCCATAAGGGT
1 TAAACAGAAGCTCATAAGAGCAGAACGGAAACCCATAAGGGT
* * * *
13613617 TAAACAGAAGCTCA-ATAGAGCTGAATGGAAACTCATATA-AGT
1 TAAACAGAAGCTCATA-AGAGCAGAACGGAAACCCATA-AGGGT
* * *
13613659 TAAATAGAAGCTCGTATGAGC-GAAACGGAAA
1 TAAACAGAAGCTCATAAGAGCAG-AACGGAAA
13613690 GTAAACACAA
Statistics
Matches: 91, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
41 3 0.03
42 86 0.95
43 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (42 bp):
TAAACAGAAGCTCATAAGAGCAGAACGGAAACCCATAAGGGT
Found at i:13615445 original size:40 final size:40
Alignment explanation
Indices: 13615390--13615466 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
13615380 ATATAATGGA
* * * *
13615390 CCACTAGTTAGGCATGTTAGTTGTTAATCAGGTTGGCGGG
1 CCACTAGTTAGGCATGATAGTTGCTAACCAGATTGGCGGG
13615430 CCACTAG-TAGGGCATGATAGTTGCTAACCAGATTGGC
1 CCACTAGTTA-GGCATGATAGTTGCTAACCAGATTGGC
13615467 ATGTATGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (40 bp):
CCACTAGTTAGGCATGATAGTTGCTAACCAGATTGGCGGG
Found at i:13622638 original size:12 final size:12
Alignment explanation
Indices: 13622623--13622665 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
13622613 AGATCACAAA
13622623 GAAGATCTTGAG
1 GAAGATCTTGAG
** *
13622635 GAAGATCCCGAA
1 GAAGATCTTGAG
13622647 GAAGATCTTGAG
1 GAAGATCTTGAG
13622659 GAAGATC
1 GAAGATC
13622666 CAGAGGAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (12 bp):
GAAGATCTTGAG
Found at i:13622671 original size:12 final size:12
Alignment explanation
Indices: 13622608--13622674 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
13622598 ATCAAAAGAT
13622608 GAGGAAGATCACA
1 GAGGAAGATC-CA
* **
13622621 -AAGAAGATCTT
1 GAGGAAGATCCA
*
13622632 GAGGAAGATCCC
1 GAGGAAGATCCA
* **
13622644 GAAGAAGATCTT
1 GAGGAAGATCCA
13622656 GAGGAAGATCCA
1 GAGGAAGATCCA
13622668 GAGGAAG
1 GAGGAAG
13622675 TTTCAAAAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.31, T:0.13
Consensus pattern (12 bp):
GAGGAAGATCCA
Found at i:13622674 original size:24 final size:24
Alignment explanation
Indices: 13622607--13622674 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
13622597 AATCAAAAGA
13622607 TGAGGAAGATCACA-AAGAAGATCT
1 TGAGGAAGATC-CAGAAGAAGATCT
*
13622631 TGAGGAAGATCCCGAAGAAGATCT
1 TGAGGAAGATCCAGAAGAAGATCT
*
13622655 TGAGGAAGATCCAGAGGAAG
1 TGAGGAAGATCCAGAAGAAG
13622675 TTTCAAAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.41, C:0.13, G:0.31, T:0.15
Consensus pattern (24 bp):
TGAGGAAGATCCAGAAGAAGATCT
Found at i:13630939 original size:17 final size:19
Alignment explanation
Indices: 13630909--13630948 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
13630899 TTGTATTATT
13630909 ATGTGGAATGTATA-TGATC
1 ATGTGGAATGTATAGT-ATC
13630928 ATGTGG-AT-TATAGTATC
1 ATGTGGAATGTATAGTATC
13630945 ATGT
1 ATGT
13630949 TATAAAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.55
18 3 0.15
19 6 0.30
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (19 bp):
ATGTGGAATGTATAGTATC
Found at i:13631726 original size:5 final size:5
Alignment explanation
Indices: 13631716--13631753 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
13631706 TCACTTTGAT
13631716 ATTAA ATTAA ATTAA GA-TAA TATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA -ATTAA -ATTAA ATTAA ATTAA AT
13631754 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:13631742 original size:16 final size:17
Alignment explanation
Indices: 13631714--13631761 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 17
13631704 AATCACTTTG
13631714 ATATTAAATTAAATTAAGATA
1 ATATTAAATTAAATT---A-A
13631735 ATATTAAATTAAATTAA
1 ATATTAAATTAAATTAA
13631752 ATATTAAATT
1 ATATTAAATT
13631762 TATTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
21 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATTAAATTAAATTAA
Found at i:13631766 original size:21 final size:20
Alignment explanation
Indices: 13631714--13631782 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
13631704 AATCACTTTG
* *
13631714 ATATTAAATTAAATTAAGATA
1 ATATTAAATT-TATTAAAATA
*
13631735 ATATT-AA---ATTAAATTAA
1 ATATTAAATTTATTAAAAT-A
13631752 ATATTAAATTTATTAAAATA
1 ATATTAAATTTATTAAAATA
*
13631772 ATATTATATTT
1 ATATTAAATTT
13631783 GGAATACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
16 6 0.15
17 6 0.15
18 2 0.05
20 13 0.33
21 12 0.31
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
ATATTAAATTTATTAAAATA
Found at i:13631771 original size:17 final size:17
Alignment explanation
Indices: 13631674--13631761 Score: 70
Period size: 17 Copynumber: 4.8 Consensus size: 17
13631664 ATCTACAAGA
*
13631674 TAAACATTAAATTAAAT
1 TAAATATTAAATTAAAT
13631691 TAAATATTAAGA-TAATCACT
1 TAAATATTAA-ATTAA--A-T
**
13631711 TTGATATTAAATTAAAT
1 TAAATATTAAATTAAAT
13631728 TAAGATAATATTAAATTAAAT
1 T---A-AATATTAAATTAAAT
13631749 TAAATATTAAATT
1 TAAATATTAAATT
13631762 TATTAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
17 25 0.44
18 3 0.05
19 2 0.04
20 12 0.21
21 15 0.26
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:13631781 original size:16 final size:16
Alignment explanation
Indices: 13631721--13631761 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
13631711 TTGATATTAA
*
13631721 ATTAAATTAAGATAAT
1 ATTAAATTAAAATAAT
*
13631737 ATTAAATTAAATTAAAT
1 ATTAAATTAAAAT-AAT
13631754 ATTAAATT
1 ATTAAATT
13631762 TATTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTAAATTAAAATAAT
Found at i:13637267 original size:16 final size:16
Alignment explanation
Indices: 13637229--13637261 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13637219 GAATCGACTC
13637229 AAAACTTTATCACGCT
1 AAAACTTTATCACGCT
13637245 AAAACTTTATCACGCT
1 AAAACTTTATCACGCT
13637261 A
1 A
13637262 TTACTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (16 bp):
AAAACTTTATCACGCT
Found at i:13638878 original size:61 final size:57
Alignment explanation
Indices: 13638765--13638897 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 57
13638755 AATTACTTTA
* * *
13638765 TTATTAAATTTATATAATACTTATCAAGAAAAATATTATATTAAATTTAATATTAAAT
1 TTATTAAATTAATAGAATACTTATCAAGAAAAATA-TATATTAAATTAAATATTAAAT
* *
13638823 CTTATTAAATTAATAGAATATTTACCTACAAGATAAAATA-ATATTAAATTAAATATTAAGT
1 -TTATTAAATTAATAGAATACTTA--T-CAAGA-AAAATATATATTAAATTAAATATTAAAT
*
13638884 TTATTAAAATAATA
1 TTATTAAATTAATA
13638898 TTATTTTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 20 0.31
60 13 0.20
61 20 0.31
62 5 0.08
63 6 0.09
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (57 bp):
TTATTAAATTAATAGAATACTTATCAAGAAAAATATATATTAAATTAAATATTAAAT
Found at i:13641725 original size:61 final size:57
Alignment explanation
Indices: 13641612--13641744 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 57
13641602 AATTACTTTA
* * *
13641612 TTATTAAATTTATATAATACTTATCAAGAAAAATATTATATTAAATTTAATATTAAAT
1 TTATTAAATTAATAGAATACTTATCAAGAAAAATA-TATATTAAATTAAATATTAAAT
* *
13641670 CTTATTAAATTAATAGAATATTTACCTACAAGATAAAATA-ATATTAAATTAAATATTAAGT
1 -TTATTAAATTAATAGAATACTTA--T-CAAGA-AAAATATATATTAAATTAAATATTAAAT
*
13641731 TTATTAAAATAATA
1 TTATTAAATTAATA
13641745 TTATTTTTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 20 0.31
60 13 0.20
61 20 0.31
62 5 0.08
63 6 0.09
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (57 bp):
TTATTAAATTAATAGAATACTTATCAAGAAAAATATATATTAAATTAAATATTAAAT
Found at i:13656301 original size:116 final size:117
Alignment explanation
Indices: 13656072--13656304 Score: 378
Period size: 116 Copynumber: 2.0 Consensus size: 117
13656062 TTGCTTCGAT
*
13656072 CAAACCCCATCCACTAAGGTAGGTCTCACTTGTAACTTCGCAAGCAAACCTCTATCATCAGTCAA
1 CAAACCCCATCCACTAAGGTAGGTATCACTTGTAACTTCGCAAGCAAACCTC--TCATCAGTCAA
**
13656137 ACTCTACTTAGCAAACATCGCTCTCAAATCAGTCATCAGTTTTTTGCTCAGTTC
64 ACTCTACTTAGCAAACATCGCTCTCAAATCAGTCATCAGTTTCATGCTCAGTTC
* *
13656191 CAAACCCCATCCATTAAGGTAGGTATCACTTGTAACTTTGCAAGCAAACCTC-CATCAGTCAAAC
1 CAAACCCCATCCACTAAGGTAGGTATCACTTGTAACTTCGCAAGCAAACCTCTCATCAGTCAAAC
* *
13656255 TCTACTTAGCGAACATCGCTCTCAAATCAGTCATCGGTTTCATGCTCAGT
66 TCTACTTAGCAAACATCGCTCTCAAATCAGTCATCAGTTTCATGCTCAGT
13656305 GCATCAACCA
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
116 58 0.54
119 49 0.46
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (117 bp):
CAAACCCCATCCACTAAGGTAGGTATCACTTGTAACTTCGCAAGCAAACCTCTCATCAGTCAAAC
TCTACTTAGCAAACATCGCTCTCAAATCAGTCATCAGTTTCATGCTCAGTTC
Found at i:13658988 original size:15 final size:16
Alignment explanation
Indices: 13658968--13659001 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13658958 CACAGTTCCA
13658968 CTATAG-TTTCAAAAT
1 CTATAGTTTTCAAAAT
*
13658983 CTATAGTTTTCAGAAT
1 CTATAGTTTTCAAAAT
13658999 CTA
1 CTA
13659002 AAATTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
CTATAGTTTTCAAAAT
Found at i:13659761 original size:42 final size:42
Alignment explanation
Indices: 13659714--13659806 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
13659704 CCCTTATGGC
* *
13659714 CAGGCCGTGCTTCTAACACGGTCAAGAGACACGTCCGTGTCT
1 CAGGCCGTGCATCTAACACGGTCAAGAGACACGCCCGTGTCT
* *
13659756 TAGGCCGTGCATCTCACACGGTCAAGAGACACGCCCGTGTCT
1 CAGGCCGTGCATCTAACACGGTCAAGAGACACGCCCGTGTCT
*
13659798 CAGGTCGTG
1 CAGGCCGTG
13659807 TGGACATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.20
Consensus pattern (42 bp):
CAGGCCGTGCATCTAACACGGTCAAGAGACACGCCCGTGTCT
Found at i:13662306 original size:28 final size:27
Alignment explanation
Indices: 13662274--13662328 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
13662264 TAAAATAATT
*
13662274 AAAATTCAA-TATGTTAATAATTTAAGTG
1 AAAATT-AATTAT-TTAATAATTAAAGTG
*
13662302 AAAATTAATTATTTTATAATTAAAGTG
1 AAAATTAATTATTTAATAATTAAAGTG
13662329 TGAATTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (27 bp):
AAAATTAATTATTTAATAATTAAAGTG
Done.