Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 21 of 39
Found at i:3094970 original size:53 final size:52
Alignment explanation
Indices: 3094836--3095142 Score: 255
Period size: 53 Copynumber: 5.8 Consensus size: 52
3094826 TTATTTCTCT
* *
3094836 AAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAAGGCATTATTTTAGT
1 AAGTGACA-CAAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTTTAGC
* * * *
3094889 GAGTGACACCAGTCACTATTCACCCTAATCACCACTAAGGCATTA-TTTAGC
1 AAGTGACACAAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTTTAGC
* * * *
3094940 AAGTGACTGCTAATTCACTATTCACTCTAATCGCCACCGAGGCATTATTTCT--C
1 AAGTGAC-AC-AAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTT-TAGC
* ** * *
3094993 TAAGTGACACCAAGTCACCATTTTCTCTAATCGCCACCAAGGCATTATTTTAGT
1 -AAGTGACA-CAAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTTTAGC
* ** * ** *
3095047 AAGTGACACCAAGTCGCTATTTGCCCTAATCGCCACTAAGGTGTTATTTCA-C
1 AAGTGACA-CAAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTTTAGC
* * **
3095099 TAAATGACACCAAGTCCCTATTCTACCC-GCTCGCCACCAAGGCA
1 -AAGTGACA-CAAGTCACTATTC-ACCCTAATCGCCACCAAGGCA
3095143 ACACTAAATC
Statistics
Matches: 205, Mismatches: 39, Indels: 20
0.78 0.15 0.08
Matches are distributed among these distances:
51 11 0.05
52 35 0.17
53 145 0.71
54 13 0.06
55 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (52 bp):
AAGTGACACAAGTCACTATTCACCCTAATCGCCACCAAGGCATTATTTTAGC
Found at i:3095022 original size:27 final size:27
Alignment explanation
Indices: 3094987--3095061 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
3094977 CGAGGCATTA
3094987 TTTCTCTAAGTGACACCAAGTCACCAT
1 TTTCTCTAAGTGACACCAAGTCACCAT
* * **
3095014 TTTCTCTAA-TCGCCACCAAGGCATTAT
1 TTTCTCTAAGT-GACACCAAGTCACCAT
**
3095041 TTT-AGTAAGTGACACCAAGTC
1 TTTCTCTAAGTGACACCAAGTC
3095062 GCTATTTGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
26 13 0.34
27 25 0.66
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (27 bp):
TTTCTCTAAGTGACACCAAGTCACCAT
Found at i:3095133 original size:106 final size:104
Alignment explanation
Indices: 3094835--3095142 Score: 311
Period size: 106 Copynumber: 2.9 Consensus size: 104
3094825 GTTATTTCTC
* * *
3094835 TAAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAAGGCATTATTTTAGTGAGTGACACC-
1 TAAGTGACACCAAGTCACTATT-TCCCTAATCGCCACCAAGGCATTATTTCACTAAGTGACACCA
* * *
3094899 AGTCACTATTC-ACCCTAATCACCACTAAGGCATTATTTAG
65 AGTCCCTATTCTACCC-AATCGCCACCAAGGCATTATTTAG
* * * * * *
3094939 CAAGTGACTGCTAATTCACTA-TTCACTCTAATCGCCACCGAGGCATTATTTCTCTAAGTGACAC
1 TAAGTGAC-ACCAAGTCACTATTTC-C-CTAATCGCCACCAAGGCATTATTTCACTAAGTGACAC
* *
3095003 CAAGTCACC-ATT-TTCTCTAATCGCCACCAAGGCATTATTTTAG
63 CAAGTC-CCTATTCTAC-CCAATCGCCACCAAGGCATTA-TTTAG
* * ** *
3095046 TAAGTGACACCAAGTCGCTATTTGCCCTAATCGCCACTAAGGTGTTATTTCACTAAATGACACCA
1 TAAGTGACACCAAGTCACTATTT-CCCTAATCGCCACCAAGGCATTATTTCACTAAGTGACACCA
**
3095111 AGTCCCTATTCTACCCGCTCGCCACCAAGGCA
65 AGTCCCTATTCTACCCAATCGCCACCAAGGCA
3095143 ACACTAAATC
Statistics
Matches: 163, Mismatches: 29, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
103 2 0.01
104 9 0.06
105 44 0.27
106 88 0.54
107 19 0.12
108 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (104 bp):
TAAGTGACACCAAGTCACTATTTCCCTAATCGCCACCAAGGCATTATTTCACTAAGTGACACCAA
GTCCCTATTCTACCCAATCGCCACCAAGGCATTATTTAG
Found at i:3098937 original size:20 final size:20
Alignment explanation
Indices: 3098912--3098985 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3098902 AAAAAGATAG
3098912 AATGTATCAATACATTGAAA
1 AATGTATCAATACATTGAAA
* * * *
3098932 AATGTATCGATATATTCATA
1 AATGTATCAATACATTGAAA
* ** *
3098952 CATGTATTGATACGTTG-AA
1 AATGTATCAATACATTGAAA
3098971 AATGTATCAATACAT
1 AATGTATCAATACAT
3098986 CTGCGTAAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCAATACATTGAAA
Found at i:3099942 original size:31 final size:31
Alignment explanation
Indices: 3099903--3100019 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
3099893 CCAGCGACAT
3099903 TAGG-TTTAGAAGGGTTGCCACCAACTCGTG
1 TAGGCTTTAGAAGGGTTGCCACCAACTCGTG
* * *
3099933 TAGGCTTTAGAGAAGGTTGCTACCAACTTGTG
1 TAGGCTTTAGA-AGGGTTGCCACCAACTCGTG
* * *
3099965 TGGGCTTTAGAAGGGTTGCTACCGAC-CTGTG
1 TAGGCTTTAGAAGGGTTGCCACCAACTC-GTG
3099996 T-GGACTTTAGAAGAGGTTGCCACC
1 TAGG-CTTTAGAAG-GGTTGCCACC
3100020 GACTTGTGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
30 6 0.08
31 32 0.43
32 36 0.49
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (31 bp):
TAGGCTTTAGAAGGGTTGCCACCAACTCGTG
Found at i:3100006 original size:63 final size:63
Alignment explanation
Indices: 3099907--3100027 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
3099897 CGACATTAGG
*
3099907 TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAG-AGAAGGTTGCTACCAACTTGTGTGGGC
1 TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAGAAG-AGGTTGCCACCAACTTGTGTGGGC
* * *
3099970 TTTAGAAGGGTTGCTACCGAC-CTGTGT-GGACTTTAGAAGAGGTTGCCACCGACTTGTG
1 TTTAGAAGGGTTGCCACCAACTC-GTGTAGG-CTTTAGAAGAGGTTGCCACCAACTTGTG
3100028 GGCTTTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
62 3 0.06
63 46 0.90
64 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (63 bp):
TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAGAAGAGGTTGCCACCAACTTGTGTGGGC
Found at i:3100021 original size:32 final size:32
Alignment explanation
Indices: 3099907--3100046 Score: 134
Period size: 31 Copynumber: 4.6 Consensus size: 32
3099897 CGACATTAGG
* *
3099907 TTTAGAAG-GGTTGCCACC-AACTCGTGTAGGC
1 TTTAGAAGAGGTTGCCACCGACCT-GTGTGGGC
* * *
3099938 TTTAG-AGAAGGTTGCTACCAACTTGTGTGGGC
1 TTTAGAAG-AGGTTGCCACCGACCTGTGTGGGC
* *
3099970 TTTAGAAG-GGTTGCTACCGACCTGTGTGGAC
1 TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
3100001 TTTAGAAGAGGTTGCCACCGA-CT-TGTGGGC
1 TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
*
3100031 TTT-GAAAAGG-TGCCAC
1 TTTAGAAGAGGTTGCCAC
3100047 TGACTTATGG
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.06
29 6 0.06
30 11 0.12
31 35 0.37
32 32 0.34
33 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (32 bp):
TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
Found at i:3100045 original size:28 final size:29
Alignment explanation
Indices: 3099994--3100158 Score: 171
Period size: 28 Copynumber: 5.9 Consensus size: 29
3099984 TACCGACCTG
* * * *
3099994 TGTGGACTTTAGAAGAGGTTGCCACCGACT
1 TGTGGGCTTT-GAAAAGGATGCCACTGACT
3100024 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
3100052 TATGGGTTTTGAAATGG-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
3100080 T-TGGGCTTTG-AAAGGAAGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
3100107 TGTGGGCTTTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
3100135 TATAGGCTTTGAAAAAG-TGCCACT
1 TGTGGGCTTTGAAAAGGATGCCACT
3100159 AATTTTCAGG
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.03
27 19 0.16
28 76 0.64
29 10 0.08
30 9 0.08
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:3100080 original size:56 final size:56
Alignment explanation
Indices: 3100013--3100375 Score: 310
Period size: 56 Copynumber: 6.6 Consensus size: 56
3100003 TAGAAGAGGT
* *
3100013 TGCCACCGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTATGGGTTTTGAAATGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAA-GG
* *
3100069 TGCCACTGACTT-TGGGCTTTG-AAAGGAAGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
* * * * *
3100123 ATGCCACTAACTTATAGGCTTTGAAAAAG-TGCCACT-A---AT----TTT--CAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
* * *
3100169 CGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTACGGGCTTTGAAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAAGG
** * * * * *
3100225 TGCCACTGACTTACGAGCTTTGAAAAGG-TCCCACTGACTTGTTGGTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAA-GG
* * * * **
3100282 TTGCCACTGACTTGTGGGCTCTG-AAAGGATGCCACTAACCTGTGGGCTTTGAAAATA
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAAGG
3100339 TGCCACTGACTTGTGGGCTTTGAAAAGGGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAA-GGATGCCACT
3100376 AACTCGGGAG
Statistics
Matches: 245, Mismatches: 40, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
44 4 0.02
45 25 0.10
46 4 0.02
48 3 0.01
49 1 0.00
52 1 0.00
53 3 0.01
54 7 0.03
55 43 0.18
56 87 0.36
57 18 0.07
58 49 0.20
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
Found at i:3100160 original size:28 final size:28
Alignment explanation
Indices: 3100013--3100158 Score: 172
Period size: 28 Copynumber: 5.2 Consensus size: 28
3100003 TAGAAGAGGT
* *
3100013 TGCCACCGACTTGTGGGCTTTGAAAAGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
* *
3100041 TGCCACTGACTTATGGGTTTTGAAATGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
3100069 TGCCACTGACTT-TGGGCTTTG-AAAGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
* *
3100095 AAGCCACTGACTTGTGGGCTTTG-AAAGG
1 -TGCCACTGACTTATGGGCTTTGAAAAGG
* * *
3100123 ATGCCACTAACTTATAGGCTTTGAAAAAG
1 -TGCCACTGACTTATGGGCTTTGAAAAGG
3100152 TGCCACT
1 TGCCACT
3100159 AATTTTCAGG
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.04
27 19 0.18
28 76 0.74
29 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTATGGGCTTTGAAAAGG
Found at i:3100214 original size:28 final size:28
Alignment explanation
Indices: 3100170--3100393 Score: 211
Period size: 28 Copynumber: 7.9 Consensus size: 28
3100160 ATTTTCAGGC
3100170 GCCACTGACTTGTGGGCTTTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
** *
3100198 GCCACTGACTTACGGGCTTTGAAA-AAGT
1 GCCACTGACTTGTGGGCTTTGAAAGGA-T
** *
3100226 GCCACTGACTTACGAGCTTTGAAAAGG-T
1 GCCACTGACTTGTGGGCTTTG-AAAGGAT
* * * *
3100254 CCCACTGACTTGTTGGTTTTGAAAAGGGTT
1 GCCACTGACTTGTGGGCTTTG-AAA-GGAT
*
3100284 GCCACTGACTTGTGGGCTCTGAAAGGAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
* * **
3100312 GCCACTAACCTGTGGGCTTTGAAAATAT
1 GCCACTGACTTGTGGGCTTTGAAAGGAT
3100340 GCCACTGACTTGTGGGCTTTGAAAAGGGAT
1 GCCACTGACTTGTGGGCTTTG-AAA-GGAT
* *
3100370 GCCACTAACTCG-GGAGCTTTGAAA
1 GCCACTGACTTGTGG-GCTTTGAAA
3100394 ATGTGTCATA
Statistics
Matches: 161, Mismatches: 27, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
27 1 0.01
28 108 0.67
29 16 0.10
30 36 0.22
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (28 bp):
GCCACTGACTTGTGGGCTTTGAAAGGAT
Found at i:3100259 original size:101 final size:100
Alignment explanation
Indices: 3100070--3100259 Score: 267
Period size: 101 Copynumber: 1.9 Consensus size: 100
3100060 TTGAAATGGT
** *
3100070 GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1 GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTACGGGCTTTGAAAAGATGCCACTAACT
* *
3100135 TATAGGCTTTGAAAAAGTGCCACTAATTTTCAGGC
66 TAGAGGCTTTGAAAAAGTCCCACTAATTTTCAGGC
* *
3100170 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTACGGGCTTTGAAAA-AGTGCCACTGA
1 GCCACTGACTT-TGGGCTTTGAAAGGAAGCCACTGACTTACGGGCTTTGAAAAGA-TGCCACTAA
*
3100234 CTTACGA-GCTTTGAAAAGGTCCCACT
64 CTTA-GAGGCTTTGAAAAAGTCCCACT
3100260 GACTTGTTGG
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
100 12 0.15
101 66 0.84
102 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (100 bp):
GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTACGGGCTTTGAAAAGATGCCACTAACT
TAGAGGCTTTGAAAAAGTCCCACTAATTTTCAGGC
Found at i:3100315 original size:86 final size:86
Alignment explanation
Indices: 3100171--3100375 Score: 245
Period size: 86 Copynumber: 2.4 Consensus size: 86
3100161 TTTTCAGGCG
* *
3100171 CCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACTTACGGGCTTTGAAAAAGTGCCACTGA
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTACGGGCTCTGAAAAAGTGCCACTAA
* *
3100234 CTTACGAGCTTTGAAAAGGTC
66 CCTACGAGCTTTGAAAAGATC
* * * ** *
3100255 CCACTGACTTGTTGGTTTTGAAAAGGGTTGCCACTGACTTGTGGGCTCTG-AAAGGATGCCACTA
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTACGGGCTCTGAAAAAG-TGCCACTA
** * * *
3100319 ACCTGTGGGCTTTGAAAATATG
65 ACCTACGAGCTTTGAAAAGATC
3100341 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACT
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACT
3100376 AACTCGGGAG
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
84 18 0.18
85 7 0.07
86 75 0.75
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (86 bp):
CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTACGGGCTCTGAAAAAGTGCCACTAA
CCTACGAGCTTTGAAAAGATC
Found at i:3100459 original size:26 final size:26
Alignment explanation
Indices: 3100404--3100459 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
3100394 ATGTGTCATA
* * *
3100404 TTAACAAAAATTTCTTGACAAAGTTT
1 TTAACAAAAATTTCTCGACAAAGCTC
*
3100430 TTAACAAACA-TTCTCGACAAAAGCTC
1 TTAACAAAAATTTCTCGAC-AAAGCTC
3100456 TTAA
1 TTAA
3100460 TGGTAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (26 bp):
TTAACAAAAATTTCTCGACAAAGCTC
Found at i:3101708 original size:14 final size:14
Alignment explanation
Indices: 3101689--3101732 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
3101679 GATCCCTCCC
3101689 TTTTTGTATTGTTT
1 TTTTTGTATTGTTT
*
3101703 TTTTTGTTTTTGTTT
1 TTTTTG-TATTGTTT
*
3101718 TTTTTTTATT-TTT
1 TTTTTGTATTGTTT
3101731 TT
1 TT
3101733 GCTTTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 9 0.35
15 12 0.46
ACGTcount: A:0.05, C:0.00, G:0.09, T:0.86
Consensus pattern (14 bp):
TTTTTGTATTGTTT
Found at i:3101714 original size:20 final size:18
Alignment explanation
Indices: 3101689--3101739 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
3101679 GATCCCTCCC
3101689 TTTTTGTATTGTTTTTTTTG
1 TTTTTGT-TT-TTTTTTTTG
*
3101709 TTTTTGTTTTTTTTTTATT
1 TTTTTGTTTTTTTTTT-TG
3101728 TTTTTGCTTTTT
1 TTTTTG-TTTTT
3101740 GAGAATGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.25
19 9 0.32
20 12 0.43
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (18 bp):
TTTTTGTTTTTTTTTTTG
Found at i:3115625 original size:20 final size:19
Alignment explanation
Indices: 3115573--3115626 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
3115563 AAAAAGACAG
* *
3115573 AATGTATTGATACATTGAA
1 AATGTATCGATACATTCAA
3115592 AATGTATC-ATTACATTCATA
1 AATGTATCGA-TACATTCA-A
*
3115612 CATGTATCGATACAT
1 AATGTATCGATACAT
3115627 CTGGGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 13 0.45
21 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:3120581 original size:20 final size:21
Alignment explanation
Indices: 3120548--3120604 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
3120538 TTTATTAGCA
3120548 ATGTAT-TTTAATATAATAATT
1 ATGTATATTT-ATATAATAATT
* *
3120569 -TGTATATTTATATCATATTT
1 ATGTATATTTATATAATAATT
*
3120589 ATATCATATTTATATA
1 ATGT-ATATTTATATA
3120605 TTTTTATGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 14 0.48
21 5 0.17
22 10 0.34
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
ATGTATATTTATATAATAATT
Found at i:3120588 original size:11 final size:11
Alignment explanation
Indices: 3120572--3120603 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3120562 AATAATTTGT
3120572 ATATTTATATC
1 ATATTTATATC
3120583 ATATTTATATC
1 ATATTTATATC
3120594 ATATTTATAT
1 ATATTTATAT
3120604 ATTTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTATATC
Found at i:3120658 original size:30 final size:32
Alignment explanation
Indices: 3120622--3120681 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3120612 GTGTCATAAT
3120622 TATATTTA-AA-AAATATTATATAAATTTTGA
1 TATATTTATAATAAATATTATATAAATTTTGA
**
3120652 TATATTTATAATTTATATTATATAAATTTT
1 TATATTTATAATAAATATTATATAAATTTT
3120682 AATACGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 2 0.08
32 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
TATATTTATAATAAATATTATATAAATTTTGA
Found at i:3120661 original size:18 final size:17
Alignment explanation
Indices: 3120634--3120682 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
3120624 TATTTAAAAA
3120634 ATATTATATAAATTTTGAT
1 ATATT-TATAAATTTT-AT
3120653 ATATTTAT-AA-TTTAT
1 ATATTTATAAATTTTAT
*
3120668 AT-TATATAAATTTTA
1 ATATTTATAAATTTTA
3120683 ATACGTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 6 0.22
16 7 0.26
17 2 0.07
18 3 0.11
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATTTATAAATTTTAT
Found at i:3120725 original size:23 final size:22
Alignment explanation
Indices: 3120698--3120771 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 22
3120688 TTTGTATATT
3120698 TATATCATATTCATATTATTTTG
1 TATATCATATT-ATATTATTTTG
*
3120721 TATATCATATTATATT-TTATG
1 TATATCATATTATATTATTTTG
*
3120742 T-TAT-ATATTA-ATTATTTTT
1 TATATCATATTATATTATTTTG
*
3120761 TATATTATATT
1 TATATCATATT
3120772 TTTATCATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 3 0.07
19 10 0.22
20 6 0.13
21 10 0.22
22 5 0.11
23 11 0.24
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (22 bp):
TATATCATATTATATTATTTTG
Found at i:3120740 original size:40 final size:39
Alignment explanation
Indices: 3120692--3120771 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 39
3120682 AATACGTTTG
3120692 TATATTTATATCATAT-TCATATTATTTTGTATATCATAT
1 TATATTTATATCATATATCA-ATTATTTTGTATATCATAT
* * * * *
3120731 TATATTTTATGTTATATATTAATTATTTTTTATATTATAT
1 TATA-TTTATATCATATATCAATTATTTTGTATATCATAT
3120771 T
1 T
3120772 TTTATCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (39 bp):
TATATTTATATCATATATCAATTATTTTGTATATCATAT
Found at i:3120747 original size:12 final size:12
Alignment explanation
Indices: 3120727--3120773 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3120717 TTTGTATATC
3120727 ATATTATATTTT
1 ATATTATATTTT
* *
3120739 ATGTTATATATT
1 ATATTATATTTT
*
3120751 A-ATTATTTTTT
1 ATATTATATTTT
3120762 ATATTATATTTT
1 ATATTATATTTT
3120774 TATCATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:3121083 original size:4 final size:4
Alignment explanation
Indices: 3121074--3121102 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3121064 AAAGGGGTTC
3121074 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
3121103 ATATACTTTT
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:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:3122340 original size:16 final size:17
Alignment explanation
Indices: 3122314--3122345 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3122304 ATTAGATAAT
3122314 TTTTTTCTTTTTCTTTG
1 TTTTTTCTTTTTCTTTG
3122331 TTTTTT-TTTTTCTTT
1 TTTTTTCTTTTTCTTT
3122346 TTTGGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTG
Found at i:3132417 original size:101 final size:101
Alignment explanation
Indices: 3132299--3132499 Score: 402
Period size: 101 Copynumber: 2.0 Consensus size: 101
3132289 GCAGATTGCA
3132299 TACGAATTCTAAATCGTCTCATGAATTATCATACAAATTTACTTATTTAAATACATAATTTAAAA
1 TACGAATTCTAAATCGTCTCATGAATTATCATACAAATTTACTTATTTAAATACATAATTTAAAA
3132364 ATAAAATAAAAATTAAATATAAAAAATTATAAAATT
66 ATAAAATAAAAATTAAATATAAAAAATTATAAAATT
3132400 TACGAATTCTAAATCGTCTCATGAATTATCATACAAATTTACTTATTTAAATACATAATTTAAAA
1 TACGAATTCTAAATCGTCTCATGAATTATCATACAAATTTACTTATTTAAATACATAATTTAAAA
3132465 ATAAAATAAAAATTAAATATAAAAAATTATAAAAT
66 ATAAAATAAAAATTAAATATAAAAAATTATAAAAT
3132500 AATTAATAAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (101 bp):
TACGAATTCTAAATCGTCTCATGAATTATCATACAAATTTACTTATTTAAATACATAATTTAAAA
ATAAAATAAAAATTAAATATAAAAAATTATAAAATT
Found at i:3132510 original size:12 final size:11
Alignment explanation
Indices: 3132482--3132514 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3132472 AAAAATTAAA
3132482 TATAAAA-AAT
1 TATAAAATAAT
3132492 TATAAAATAAT
1 TATAAAATAAT
3132503 TAATAAAATAAT
1 T-ATAAAATAAT
3132515 GTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:3132791 original size:21 final size:19
Alignment explanation
Indices: 3132734--3132792 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
3132724 TTTTAAAATA
* *
3132734 ATAAAACATAAACCCTAA-
1 ATAAAAAATAAAACCTAAT
3132752 ATAAAAAATAAAA--TAAT
1 ATAAAAAATAAAACCTAAT
3132769 ATAATAAAATAAGAACCTAAT
1 ATAA-AAAATAA-AACCTAAT
3132790 ATA
1 ATA
3132793 TAATGAGCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 18 0.53
19 2 0.06
21 7 0.21
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAAATAAAACCTAAT
Found at i:3133880 original size:16 final size:17
Alignment explanation
Indices: 3133859--3133891 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3133849 GTGTATTATT
3133859 CAAAATGA-TTTTATAA
1 CAAAATGATTTTTATAA
*
3133875 CAAAATTATTTTTATAA
1 CAAAATGATTTTTATAA
3133892 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
CAAAATGATTTTTATAA
Found at i:3135081 original size:23 final size:23
Alignment explanation
Indices: 3135055--3135101 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3135045 CAACTAACAC
3135055 AGCAAAAATTGACAACAATAATG
1 AGCAAAAATTGACAACAATAATG
*
3135078 AGCAAAAATTGACAGCAATAATG
1 AGCAAAAATTGACAACAATAATG
3135101 A
1 A
3135102 ATAGAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (23 bp):
AGCAAAAATTGACAACAATAATG
Found at i:3139196 original size:20 final size:18
Alignment explanation
Indices: 3139161--3139195 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3139151 TAAAATTTTT
3139161 AATT-AAAATATAATATA
1 AATTAAAAATATAATATA
*
3139178 AATTAAAAATATATTATA
1 AATTAAAAATATAATATA
3139196 TTAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAAAAATATAATATA
Found at i:3139201 original size:20 final size:18
Alignment explanation
Indices: 3139159--3139202 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
3139149 ATTAAAATTT
3139159 TTAATT-AAAATATAATA
1 TTAATTAAAAATATAATA
*
3139176 TAAATTAAAAATATATTATA
1 TTAATTAAAAATATA--ATA
3139196 TTAATTA
1 TTAATTA
3139203 TATTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
20 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATTAAAAATATAATA
Found at i:3139234 original size:38 final size:36
Alignment explanation
Indices: 3139175--3139275 Score: 102
Period size: 38 Copynumber: 2.8 Consensus size: 36
3139165 AAAATATAAT
* *
3139175 ATAAAT-TAAAAATATATTATATTA-ATTATATTTAA
1 ATAAATATATAAATTTATTATATTATATTATATTT-A
*
3139210 ATAAATAATATTAAATTTATTATATTATTTTTATATTTA
1 ATAAAT-ATA-TAAATTTATTATATTA-TATTATATTTA
*
3139249 ATAAATATAT-AATAT-TTATATTATATT
1 ATAAATATATAAATTTATTATATTATATT
3139276 TTTATATAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
34 3 0.05
35 14 0.25
36 4 0.07
37 3 0.05
38 17 0.30
39 7 0.12
40 8 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
ATAAATATATAAATTTATTATATTATATTATATTTA
Found at i:3139235 original size:43 final size:36
Alignment explanation
Indices: 3139187--3139286 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 36
3139177 AAATTAAAAA
*
3139187 TATATTATATTAATTATATTTAAATAAATAATATTAAATTTAT
1 TATATTATATT--TTATATTT-AATAAAT-ATA-T-AATAT-T
3139230 TATATTAT-TTTTATATTTAATAAATATATAATATT
1 TATATTATATTTTATATTTAATAAATATATAATATT
*
3139265 TATATTATATTTT-TATATAATA
1 TATATTATATTTTATATTTAATA
3139287 TTTAAAATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
35 17 0.31
36 8 0.15
37 1 0.02
38 3 0.06
39 7 0.13
40 8 0.15
42 2 0.04
43 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
TATATTATATTTTATATTTAATAAATATATAATATT
Found at i:3139269 original size:13 final size:13
Alignment explanation
Indices: 3139253--3139290 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3139243 TATTTAATAA
3139253 ATATATAATATTT
1 ATATATAATATTT
3139266 ATAT-T-ATATTT
1 ATATATAATATTT
*
3139277 TTATATAATATTT
1 ATATATAATATTT
3139290 A
1 A
3139291 AAATTATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATATAATATTT
Found at i:3144641 original size:2 final size:2
Alignment explanation
Indices: 3144634--3144662 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3144624 CATTTTATGA
3144634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3144663 ACTATCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3147825 original size:23 final size:23
Alignment explanation
Indices: 3147787--3147875 Score: 66
Period size: 22 Copynumber: 4.1 Consensus size: 23
3147777 AAGATCATTT
3147787 TATTATTTTTA-A--AATAAAAA
1 TATTATTTTTATATTAATAAAAA
***
3147807 TATTATTTTTATATTAATATTTA
1 TATTATTTTTATATTAATAAAAA
3147830 TA-TATTTTTATAATT-ATAAAAA
1 TATTATTTTTAT-ATTAATAAAAA
* *
3147852 -ATTATATTTAT-TAAATAAATAA
1 TATTATTTTTATATTAATAAA-AA
3147874 TA
1 TA
3147876 AATCAGATCG
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
20 12 0.23
21 7 0.13
22 23 0.43
23 11 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTTTTATATTAATAAAAA
Found at i:3147864 original size:42 final size:41
Alignment explanation
Indices: 3147785--3147865 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
3147775 ATAAGATCAT
*
3147785 TTTATTATTTTTAAAATAAAAATATTATTTTTATATTAATA
1 TTTATTATTTTTAAAATAAAAATATTATTATTATATTAATA
3147826 TTTATATATTTTTATAATTATAAAAA-ATTA-TATT-TATTAA
1 TTTAT-TATTTTTA-AA--ATAAAAATATTATTATTATATTAA
3147866 ATAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
41 5 0.14
42 14 0.40
43 5 0.14
44 4 0.11
45 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (41 bp):
TTTATTATTTTTAAAATAAAAATATTATTATTATATTAATA
Found at i:3147905 original size:13 final size:14
Alignment explanation
Indices: 3147874--3147906 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3147864 AAATAAATAA
*
3147874 TAAATCAGATCGAT
1 TAAATCAAATCGAT
3147888 TAAATCAAATCG-T
1 TAAATCAAATCGAT
3147901 TAAATC
1 TAAATC
3147907 TTATGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAATCAAATCGAT
Found at i:3151242 original size:6 final size:6
Alignment explanation
Indices: 3151233--3151257 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3151223 AATTAAAATG
3151233 TGATTA TGATTA TGATTA TGATTA T
1 TGATTA TGATTA TGATTA TGATTA T
3151258 AATTTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTA
Found at i:3151696 original size:29 final size:29
Alignment explanation
Indices: 3151639--3151697 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
3151629 TTTATATTTT
* *
3151639 AAATATAAAATATTTTAAATATTATTATA
1 AAATATAAAATATTTCAAATATGATTATA
3151668 AAATATAAAATATATTCAAATATGA-TATA
1 AAATATAAAATAT-TTCAAATATGATTATA
3151697 A
1 A
3151698 TATGACTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
AAATATAAAATATTTCAAATATGATTATA
Found at i:3152952 original size:14 final size:15
Alignment explanation
Indices: 3152926--3152965 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3152916 AATTTTTCAT
3152926 TAAAATT-ATTTAA-
1 TAAAATTAATTTAAG
3152939 TAAAATTAATTTAAG
1 TAAAATTAATTTAAG
*
3152954 T-AATTTAATTTA
1 TAAAATTAATTTA
3152966 TTAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 16 0.67
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TAAAATTAATTTAAG
Found at i:3155473 original size:5 final size:5
Alignment explanation
Indices: 3155465--3155490 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3155455 AGCTCATACC
3155465 ATATT ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT A
3155491 ATATATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:3155986 original size:2 final size:2
Alignment explanation
Indices: 3155979--3156011 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3155969 TGTAGACAAC
3155979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3156012 CACCATTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3157750 original size:34 final size:34
Alignment explanation
Indices: 3157682--3157753 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
3157672 ATAAATTCAT
* *
3157682 CTAACACACCTAATATGTTTACTTAATACAACAC
1 CTAACACACCTAATATGATTACTCAATACAACAC
*
3157716 CTAACACACTTAATAT-ATTACTCAACTA-ATACAC
1 CTAACACACCTAATATGATTACTCAA-TACA-ACAC
3157750 CTAA
1 CTAA
3157754 TATGTTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.29
Consensus pattern (34 bp):
CTAACACACCTAATATGATTACTCAATACAACAC
Found at i:3157771 original size:22 final size:24
Alignment explanation
Indices: 3157716--3157777 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
3157706 AATACAACAC
3157716 CTAACACACTTAATATATTACTCAA
1 CTAACACACTTAATATATTA-TCAA
* * *
3157741 CTAATACACCTAATATGTT-T-AA
1 CTAACACACTTAATATATTATCAA
3157763 CTAACACACTTAATA
1 CTAACACACTTAATA
3157778 AAGATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.47
23 1 0.03
25 16 0.50
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.32
Consensus pattern (24 bp):
CTAACACACTTAATATATTATCAA
Found at i:3162391 original size:22 final size:22
Alignment explanation
Indices: 3162352--3162407 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3162342 AGATAAGATC
* * *
3162352 ACCTAATACATCTAATATCTTT
1 ACCTAACACACCTAATATATTT
*
3162374 ACTTAACACACCTAATATATTT
1 ACCTAACACACCTAATATATTT
3162396 ACCTAACACACC
1 ACCTAACACACC
3162408 ACCTAACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (22 bp):
ACCTAACACACCTAATATATTT
Found at i:3162483 original size:12 final size:12
Alignment explanation
Indices: 3162466--3162491 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3162456 CCTAATACAC
3162466 TTAATAAAAATA
1 TTAATAAAAATA
3162478 TTAATAAAAATA
1 TTAATAAAAATA
3162490 TT
1 TT
3162492 CTAACATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:3165234 original size:6 final size:6
Alignment explanation
Indices: 3165217--3165254 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
3165207 ATGAATTAAA
3165217 TAAATT TAAAATT TAAATT TAAA-T TAAA-T TAAATT TAA
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAA
3165255 TAATTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.33
6 14 0.47
7 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:3165248 original size:16 final size:16
Alignment explanation
Indices: 3165210--3165254 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
3165200 TTGGATTATG
3165210 AATTAAA-TAAATTT-
1 AATTAAATTAAATTTA
*
3165224 AA--AATTTAAATTTA
1 AATTAAATTAAATTTA
3165238 AATTAAATTAAATTTA
1 AATTAAATTAAATTTA
3165254 A
1 A
3165255 TAATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 7 0.28
14 4 0.16
16 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAATTAAATTTA
Found at i:3165259 original size:24 final size:23
Alignment explanation
Indices: 3165212--3165254 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3165202 GGATTATGAA
3165212 TTAAATAAATTTAAAATTTAAAT
1 TTAAATAAATTTAAAATTTAAAT
3165235 TTAAATTAAA-TT-AAATTTAA
1 TTAAA-TAAATTTAAAATTTAA
3165255 TAATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAATAAATTTAAAATTTAAAT
Found at i:3165414 original size:9 final size:9
Alignment explanation
Indices: 3165400--3165440 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
3165390 TCAATATCAA
3165400 ATTAAATTT
1 ATTAAATTT
3165409 ATTAAATTT
1 ATTAAATTT
*
3165418 AATAAA-TT
1 ATTAAATTT
*
3165426 ATTTAATTT
1 ATTAAATTT
3165435 -TTAAAT
1 ATTAAAT
3165441 AAATTTACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTAAATTT
Found at i:3167264 original size:15 final size:15
Alignment explanation
Indices: 3167241--3167271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3167231 TAAATGTTAA
*
3167241 ATATGAATATATTTT
1 ATATAAATATATTTT
3167256 ATATAAATATATTTT
1 ATATAAATATATTTT
3167271 A
1 A
3167272 ATTTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATAAATATATTTT
Found at i:3167298 original size:18 final size:17
Alignment explanation
Indices: 3167277--3167315 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
3167267 TTTTAATTTT
3167277 TTTAAAAAAATTAATATA
1 TTTAAAAAAATT-ATATA
*
3167295 TTTATAAAAATTATATA
1 TTTAAAAAAATTATATA
3167312 TTTA
1 TTTA
3167316 TATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAAAAATTATATA
Found at i:3167310 original size:17 final size:18
Alignment explanation
Indices: 3167277--3167317 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
3167267 TTTTAATTTT
*
3167277 TTTAAAAAAATTAATATA
1 TTTATAAAAATTAATATA
3167295 TTTATAAAAATT-ATATA
1 TTTATAAAAATTAATATA
3167312 TTTATA
1 TTTATA
3167318 TTTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTATAAAAATTAATATA
Found at i:3168087 original size:23 final size:24
Alignment explanation
Indices: 3168011--3168089 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 24
3168001 CAATAATGTG
*
3168011 TTAA-ATATTATAAATTATTTTTAGT
1 TTAATATATTAT--ATTATTTTTAGA
*
3168036 TTAAT-TATT-TATTAATTTTGAGA
1 TTAATATATTATATT-ATTTTTAGA
*
3168059 TGAATATATTATATTATTTTTA-A
1 TTAATATATTATATTATTTTTAGA
3168082 TTAATATA
1 TTAATATA
3168090 ATTTAGTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.07
23 19 0.42
24 11 0.24
25 12 0.27
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (24 bp):
TTAATATATTATATTATTTTTAGA
Found at i:3168400 original size:28 final size:28
Alignment explanation
Indices: 3168360--3168423 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
3168350 TTTTAAGTAA
3168360 TTTTATATTTTTATTATATCA-AAATAAAT
1 TTTTATATTTTTATT-TA-CATAAATAAAT
3168389 TTTTATA-TTTTATTTACACTTAAATAAAT
1 TTTTATATTTTTATTTACA--TAAATAAAT
3168418 TTTTAT
1 TTTTAT
3168424 TTCACATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 7 0.22
29 21 0.66
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTATATTTTTATTTACATAAATAAAT
Found at i:3168490 original size:30 final size:30
Alignment explanation
Indices: 3168450--3168551 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
3168440 AATTTATGTC
*
3168450 AAAAACTTATTTAAGTATAAATTAAAAATT
1 AAAAATTTATTTAAGTATAAATTAAAAATT
* * *
3168480 AAGAATTTATTT-TGATATAAATTAAAGATT
1 AAAAATTTATTTAAG-TATAAATTAAAAATT
* *
3168510 AAAAATTTATTTAAATACAAATTAAAAATT
1 AAAAATTTATTTAAGTATAAATTAAAAATT
*
3168540 AAAAACTTATTT
1 AAAAATTTATTT
3168552 GAATGTAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 59 0.98
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAAATTTATTTAAGTATAAATTAAAAATT
Found at i:3170597 original size:23 final size:24
Alignment explanation
Indices: 3170566--3170610 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3170556 TAACAATTTA
*
3170566 TTTATTTATATCATATTCATATAT
1 TTTATTTATATCATAATCATATAT
*
3170590 TTTA-TTATGTCATAATCATAT
1 TTTATTTATATCATAATCATAT
3170611 TTTAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTATTTATATCATAATCATATAT
Found at i:3170711 original size:15 final size:14
Alignment explanation
Indices: 3170675--3170724 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
3170665 AAATTTTAAT
3170675 ATTATATTT-T-T-
1 ATTATATTTATATA
3170686 ATTAT-TTTATATAA
1 ATTATATTTATAT-A
3170700 ATTATATTTATATA
1 ATTATATTTATATA
3170714 ATTATATTTAT
1 ATTATATTTAT
3170725 TATTATCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.09
11 6 0.18
12 1 0.03
14 17 0.50
15 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:3171231 original size:6 final size:6
Alignment explanation
Indices: 3171220--3171249 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3171210 ATAACATAAA
3171220 ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT
3171250 TAATAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:3172867 original size:12 final size:12
Alignment explanation
Indices: 3172850--3172893 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
3172840 TTTTTTTATC
3172850 ATATTATATTTT
1 ATATTATATTTT
3172862 ATATTATATTTT
1 ATATTATATTTT
*
3172874 A-ATTATTTTTT
1 ATATTATATTTT
3172885 ATATTATAT
1 ATATTATAT
3172894 AATCAGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:3173262 original size:29 final size:29
Alignment explanation
Indices: 3173217--3173272 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3173207 ATTTATTATA
*
3173217 ATTTTAAATATATAAAAATAAAAATATTT
1 ATTTTAAATATAAAAAAATAAAAATATTT
*
3173246 ATTTT-AATAATAAAAAAATTAAAATAT
1 ATTTTAAAT-ATAAAAAAATAAAAATAT
3173273 ACTTTTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTTAAATATAAAAAAATAAAAATATTT
Found at i:3173278 original size:28 final size:27
Alignment explanation
Indices: 3173217--3173281 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
3173207 ATTTATTATA
*
3173217 ATTTTAAATATATAAAAATAAAAATATTT
1 ATTTTAAATATAAAAAAATAAAAATA--T
*
3173246 ATTTT-AATAATAAAAAAATTAAAATAT
1 ATTTTAAAT-ATAAAAAAATAAAAATAT
3173273 ACTTTTAAA
1 A-TTTTAAA
3173282 GATAGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 7 0.23
29 22 0.71
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTTTAAATATAAAAAAATAAAAATAT
Found at i:3173651 original size:18 final size:19
Alignment explanation
Indices: 3173632--3173670 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3173622 TCAATTATTA
3173632 TTATATTAAATATTAATAT
1 TTATATTAAATATTAATAT
* *
3173651 TTTTATTAAAT-TTAAGAT
1 TTATATTAAATATTAATAT
3173669 TT
1 TT
3173671 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATATTAAATATTAATAT
Found at i:3173671 original size:18 final size:19
Alignment explanation
Indices: 3173635--3173671 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3173625 ATTATTATTA
*
3173635 TATTAAATATTAATATTTT
1 TATTAAATATTAAGATTTT
3173654 TATTAAAT-TTAAGATTTT
1 TATTAAATATTAAGATTTT
3173672 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTAAATATTAAGATTTT
Found at i:3174234 original size:30 final size:29
Alignment explanation
Indices: 3174200--3174263 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
3174190 CTCAAAATAA
*
3174200 AAAAAATTTATTACTAAATTAATTTCAAAT
1 AAAAAATTTATTACTAAA-CAATTTCAAAT
* * *
3174230 AAAAAGTTTATTATTAAACCATTTCAAAT
1 AAAAAATTTATTACTAAACAATTTCAAAT
3174259 AAAAA
1 AAAAA
3174264 CAAAATCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAAATTTATTACTAAACAATTTCAAAT
Found at i:3175733 original size:11 final size:11
Alignment explanation
Indices: 3175696--3175735 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3175686 AAATAATTAA
3175696 AATATG-ACAT
1 AATATGAACAT
* *
3175706 AATATAAAAAT
1 AATATGAACAT
3175717 AATATGAACAT
1 AATATGAACAT
3175728 AATATGAA
1 AATATGAA
3175736 TACTAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (11 bp):
AATATGAACAT
Found at i:3176119 original size:30 final size:30
Alignment explanation
Indices: 3176075--3176141 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
3176065 GTTATAATCT
* * *
3176075 AAAAAATAATATAAACACA-AATAAATATATA
1 AAAAAAT-CTATAAAAACATAA-AAATAAATA
*
3176106 TAAAAATCTATAAAAACATAAAAATAAATA
1 AAAAAATCTATAAAAACATAAAAATAAATA
3176136 AAAAAA
1 AAAAAA
3176142 AAGCAAAGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (30 bp):
AAAAAATCTATAAAAACATAAAAATAAATA
Found at i:3176136 original size:18 final size:18
Alignment explanation
Indices: 3176105--3176139 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3176095 ATAAATATAT
**
3176105 ATAAAAATCTATAAAAAC
1 ATAAAAATAAATAAAAAC
3176123 ATAAAAATAAATAAAAA
1 ATAAAAATAAATAAAAA
3176140 AAAAGCAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
ATAAAAATAAATAAAAAC
Found at i:3176517 original size:19 final size:20
Alignment explanation
Indices: 3176493--3176532 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3176483 ACTTAATCAT
*
3176493 TTAAATT-ATATTAAAAAAA
1 TTAAATTGAAATTAAAAAAA
*
3176512 TTAAATTGAAATTTAAAAAA
1 TTAAATTGAAATTAAAAAAA
3176532 T
1 T
3176533 AGTGAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAATTGAAATTAAAAAAA
Found at i:3177450 original size:3 final size:3
Alignment explanation
Indices: 3177442--3177466 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3177432 TAAAAGTAAA
3177442 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3177467 GAAGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3177903 original size:6 final size:6
Alignment explanation
Indices: 3177902--3177929 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3177892 AGTAAAAATA
3177902 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
3177930 GCCTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3179562 original size:58 final size:58
Alignment explanation
Indices: 3179497--3179616 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
3179487 TATTTGTTGA
3179497 TTTTATATGGGAAATTGCTATATTGATTAGTGTCAAAGTTTAGGGTAAAATTCTGAAT
1 TTTTATATGGGAAATTGCTATATTGATTAGTGTCAAAGTTTAGGGTAAAATTCTGAAT
3179555 TTTTATATGGGAAATTGCTATATTGATTAGTGTCAAAGTTTAGGGTAAAATTCTGAAT
1 TTTTATATGGGAAATTGCTATATTGATTAGTGTCAAAGTTTAGGGTAAAATTCTGAAT
3179613 TTTT
1 TTTT
3179617 GTCTTATTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (58 bp):
TTTTATATGGGAAATTGCTATATTGATTAGTGTCAAAGTTTAGGGTAAAATTCTGAAT
Found at i:3179899 original size:36 final size:36
Alignment explanation
Indices: 3179817--3179891 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
3179807 GATTACTAGC
3179817 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
1 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
3179853 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
1 TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
3179889 TAA
1 TAA
3179892 GTATCTTCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (36 bp):
TAACAGTCTTCTAACACTTCCTTTCATGCTGGAGAA
Found at i:3181768 original size:18 final size:18
Alignment explanation
Indices: 3181720--3181840 Score: 68
Period size: 18 Copynumber: 6.7 Consensus size: 18
3181710 TGACTCAGCC
3181720 TGGTTTTGAGACTTAGAT
1 TGGTTTTGAGACTTAGAT
* * * *
3181738 T-GTGGTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
* *
3181756 TGGTTTTGAGACTCAGAA
1 TGGTTTTGAGACTTAGAT
* * *
3181774 T-GTGTTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
* *
3181792 TGGTTTTGAGACTCAGAA
1 TGGTTTTGAGACTTAGAT
* * *
3181810 T-GTGTTAGTGACTTAGCT
1 TGGT-TTTGAGACTTAGAT
3181828 TGGTTTTGAGACT
1 TGGTTTTGAGACT
3181841 CAGAATGTGT
Statistics
Matches: 70, Mismatches: 27, Indels: 12
0.64 0.25 0.11
Matches are distributed among these distances:
17 6 0.09
18 58 0.83
19 6 0.09
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (18 bp):
TGGTTTTGAGACTTAGAT
Found at i:3181870 original size:36 final size:36
Alignment explanation
Indices: 3181707--3181857 Score: 257
Period size: 36 Copynumber: 4.2 Consensus size: 36
3181697 GGGACAAAGG
* * * * *
3181707 TAGTGACTCAGCCTGGTTTTGAGACTTAGATTGTGG
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3181743 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3181779 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3181815 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
1 TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
3181851 TAGTGAC
1 TAGTGAC
3181858 AGATTTTGGT
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 110 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (36 bp):
TAGTGACTTAGCTTGGTTTTGAGACTCAGAATGTGT
Found at i:3210475 original size:2 final size:2
Alignment explanation
Indices: 3210470--3210496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3210460 TATATATATA
3210470 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3210497 ATTTAAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3210819 original size:9 final size:9
Alignment explanation
Indices: 3210805--3210836 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3210795 TCCCAAGAAT
3210805 TTTTTATTA
1 TTTTTATTA
3210814 TTTTTATTA
1 TTTTTATTA
*
3210823 TTATTATTA
1 TTTTTATTA
3210832 TTTTT
1 TTTTT
3210837 TATAACTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3212042 original size:4 final size:4
Alignment explanation
Indices: 3212033--3212079 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
3212023 AGATTTCTTT
3212033 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3212080 TATATATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:3212694 original size:16 final size:17
Alignment explanation
Indices: 3212669--3212704 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3212659 ATAAATATGT
3212669 TTTTTATTAATTGTTTA
1 TTTTTATTAATTGTTTA
*
3212686 TTTTT-TTAATTTTTTA
1 TTTTTATTAATTGTTTA
3212702 TTT
1 TTT
3212705 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTATTAATTGTTTA
Found at i:3218213 original size:16 final size:16
Alignment explanation
Indices: 3218187--3218232 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3218177 TTTGAATATA
*
3218187 AAATGAATTAAATTCG
1 AAATGATTTAAATTCG
*
3218203 AAAT-AGTTTAAAATCG
1 AAATGA-TTTAAATTCG
3218219 AAATGATTTAAATT
1 AAATGATTTAAATT
3218233 TAAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (16 bp):
AAATGATTTAAATTCG
Found at i:3218259 original size:15 final size:16
Alignment explanation
Indices: 3218219--3218262 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3218209 TTTAAAATCG
3218219 AAATGATTTAAATTTAA
1 AAATGA-TTAAATTTAA
**
3218236 AAAAAATTAAATTT-A
1 AAATGATTAAATTTAA
3218251 AAATGATTAAAT
1 AAATGATTAAAT
3218263 ACGAATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
17 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (16 bp):
AAATGATTAAATTTAA
Found at i:3218347 original size:22 final size:22
Alignment explanation
Indices: 3218322--3218365 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3218312 TTAAAAATAA
* *
3218322 ATTAAATTTAATTAATTTAAAT
1 ATTAAATTAAATTAATTAAAAT
*
3218344 ATTAAATTAAATTGATTAAAAT
1 ATTAAATTAAATTAATTAAAAT
3218366 TTATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAATTAAATTAATTAAAAT
Found at i:3218409 original size:15 final size:15
Alignment explanation
Indices: 3218389--3218421 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3218379 ATATTTAAAA
3218389 AATTTAAAATAATAT
1 AATTTAAAATAATAT
*
3218404 AATTTAAAATAATTT
1 AATTTAAAATAATAT
3218419 AAT
1 AAT
3218422 CTAATTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTAAAATAATAT
Found at i:3218431 original size:9 final size:9
Alignment explanation
Indices: 3218417--3218460 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
3218407 TTAAAATAAT
3218417 TTAATCTAA
1 TTAATCTAA
3218426 TTAATCTAA
1 TTAATCTAA
* *
3218435 TTCATTTAA
1 TTAATCTAA
3218444 TTAAT-TAA
1 TTAATCTAA
*
3218452 TTGATCTAA
1 TTAATCTAA
3218461 AAATTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (9 bp):
TTAATCTAA
Found at i:3220261 original size:2 final size:2
Alignment explanation
Indices: 3220254--3220289 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3220244 CAACATCCTC
3220254 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3220290 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3220294 original size:2 final size:2
Alignment explanation
Indices: 3220289--3220323 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3220279 TCTCTCTCTC
3220289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3220324 TTCAGTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3220984 original size:3 final size:3
Alignment explanation
Indices: 3220976--3221007 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3220966 GGTTAGACTT
3220976 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3221008 TGTTATTACT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3224004 original size:6 final size:6
Alignment explanation
Indices: 3223993--3224017 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3223983 TTTCCGGTGC
3223993 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3224018 TTAATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3224253 original size:24 final size:25
Alignment explanation
Indices: 3224191--3224274 Score: 91
Period size: 24 Copynumber: 3.3 Consensus size: 25
3224181 AATTTTTTTA
*
3224191 AAATTTAATAGTAAGAATTTAGTAATAT
1 AAATTTAAT--TAAAAATTTAGT-ATAT
*
3224219 CAATTTAATTAAAAATTTAGTAT-T
1 AAATTTAATTAAAAATTTAGTATAT
* *
3224243 AAATTTGATTAAAAATTTAGTA-AA
1 AAATTTAATTAAAAATTTAGTATAT
3224267 AAATTTAA
1 AAATTTAA
3224275 AATTATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 28 0.57
25 2 0.04
26 11 0.22
28 8 0.16
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (25 bp):
AAATTTAATTAAAAATTTAGTATAT
Found at i:3224268 original size:11 final size:11
Alignment explanation
Indices: 3224199--3224273 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 11
3224189 TAAAATTTAA
*
3224199 TAGTAAGAATT
1 TAGTAAAAATT
3224210 TAGTAATATCAATT
1 TAGTAA-A--AATT
*
3224224 TAATTAAAAATT
1 T-AGTAAAAATT
*
3224236 TAGTATTAAATT
1 TAGTA-AAAATT
*
3224248 TGATTAAAAATT
1 T-AGTAAAAATT
3224260 TAGTAAAAAATT
1 TAGT-AAAAATT
3224272 TA
1 TA
3224274 AAATTATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
11 11 0.22
12 26 0.52
13 3 0.06
14 6 0.12
15 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (11 bp):
TAGTAAAAATT
Found at i:3228166 original size:21 final size:21
Alignment explanation
Indices: 3228136--3228175 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3228126 AAAACAAAAC
* *
3228136 AAAATTAAAAAAATAAAAATA
1 AAAATAAAAAAAAGAAAAATA
*
3228157 AAAATAAAAAGAAGAAAAA
1 AAAATAAAAAAAAGAAAAA
3228176 AAATACTAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAATAAAAAAAAGAAAAATA
Found at i:3231066 original size:32 final size:32
Alignment explanation
Indices: 3231000--3231062 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3230990 ATAATATATA
** *
3231000 AATTTCATTCATTATTTTTTGAATTACGTTTT
1 AATTTCATTCATTATAATTTGAATCACGTTTT
*
3231032 AATTTCATTCATTA-AATTTGAATCACATTTT
1 AATTTCATTCATTATAATTTGAATCACGTTTT
3231063 TAATATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (32 bp):
AATTTCATTCATTATAATTTGAATCACGTTTT
Found at i:3232121 original size:24 final size:22
Alignment explanation
Indices: 3232078--3232121 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3232068 AAAATAGGAT
*
3232078 TTTAATTTTTTATGATTTGAAA
1 TTTAATTTTTTATGAATTGAAA
3232100 TTTAATTTTTTTATTGAATTGA
1 TTTAA-TTTTTTA-TGAATTGA
3232122 TTTATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAATTTTTTATGAATTGAAA
Found at i:3232124 original size:22 final size:23
Alignment explanation
Indices: 3232078--3232135 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
3232068 AAAATAGGAT
*
3232078 TTTAA-TTTTTTA-TGATTTGAAA
1 TTTAATTTTTTTATTGAATTG-AA
3232100 TTTAATTTTTTTATTGAATTG-A
1 TTTAATTTTTTTATTGAATTGAA
*
3232122 TTT-ATTTTTGTATT
1 TTTAATTTTTTTATT
3232136 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 10 0.31
22 9 0.28
23 7 0.22
24 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTAATTTTTTTATTGAATTGAA
Found at i:3232598 original size:14 final size:14
Alignment explanation
Indices: 3232551--3232598 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3232541 TATAATTCAA
3232551 AAAATATATAAATT
1 AAAATATATAAATT
* *
3232565 TAAATAT-TAATTT
1 AAAATATATAAATT
*
3232578 AATAATATATAAACT
1 AA-AATATATAAATT
3232593 AAAATA
1 AAAATA
3232599 CTTCATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 6 0.22
14 15 0.56
15 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATATAAATT
Found at i:3233329 original size:3 final size:3
Alignment explanation
Indices: 3233321--3233345 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3233311 TGATGTTTGA
3233321 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3233346 GTAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3236763 original size:19 final size:19
Alignment explanation
Indices: 3236739--3236775 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3236729 GATCAATTTT
3236739 TTTAATATTTAAA-AAATAA
1 TTTAATA-TTAAATAAATAA
3236758 TTTAATATTAAATAAATA
1 TTTAATATTAAATAAATA
3236776 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATATTAAATAAATAA
Found at i:3237172 original size:14 final size:13
Alignment explanation
Indices: 3237144--3237202 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
3237134 AGTGAAAGAA
*
3237144 ATATTTTAATTTTT
1 ATATTTTAA-ATTT
3237158 ATATTATTAAATTT
1 ATATT-TTAAATTT
*
3237172 AATATTTTAATTTTT
1 -ATATTTTAA-ATTT
*
3237187 ATATTTTAAAATT
1 ATATTTTAAATTT
3237200 ATA
1 ATA
3237203 ACAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.13
14 21 0.55
15 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATTTTAAATTT
Found at i:3237182 original size:8 final size:8
Alignment explanation
Indices: 3237143--3237195 Score: 55
Period size: 7 Copynumber: 7.2 Consensus size: 8
3237133 GAGTGAAAGA
3237143 AATATTTT
1 AATATTTT
3237151 AAT-TTTT
1 AATATTTT
3237158 -ATATTATT
1 AATATT-TT
3237166 AA-A-TTT
1 AATATTTT
3237172 AATATTTT
1 AATATTTT
3237180 AAT-TTTT
1 AATATTTT
3237187 -ATATTTT
1 AATATTTT
3237194 AA
1 AA
3237196 AATTATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
6 8 0.21
7 16 0.42
8 13 0.34
9 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AATATTTT
Found at i:3237425 original size:15 final size:14
Alignment explanation
Indices: 3237407--3237458 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
3237397 TATTATAATT
3237407 TTAAAAGTATAAAAA
1 TTAAAA-TATAAAAA
* *
3237422 TTAAAATATTAAAT
1 TTAAAATATAAAAA
3237436 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
3237451 TTAAAATA
1 TTAAAATA
3237459 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:3237446 original size:29 final size:31
Alignment explanation
Indices: 3237397--3237458 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
3237387 TTTTTTTATT
3237397 TATTATAATTTTAAAAGTATAAAAATTAAAA
1 TATTATAATTTTAAAAGTATAAAAATTAAAA
3237428 TATTA-AA-TTTAATAA-TATAAAAATTAAAA
1 TATTATAATTTTAA-AAGTATAAAAATTAAAA
3237457 TA
1 TA
3237459 ATTTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 21 0.70
30 4 0.13
31 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
TATTATAATTTTAAAAGTATAAAAATTAAAA
Found at i:3237832 original size:24 final size:22
Alignment explanation
Indices: 3237797--3237843 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
3237787 ACATATTCTA
3237797 AATATATTTATTAAATAATAAT
1 AATATATTTATTAAATAATAAT
*
3237819 AATATATTTATATTAAATATTAAT
1 AATATA-TT-TATTAAATAATAAT
3237843 A
1 A
3237844 CATAGTGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
24 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATTTATTAAATAATAAT
Found at i:3243927 original size:16 final size:17
Alignment explanation
Indices: 3243901--3243932 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3243891 ATTCCGTATA
3243901 TATATTATAAATTTTAT
1 TATATTATAAATTTTAT
3243918 TATA-TATAAATTTTA
1 TATATTATAAATTTTA
3243933 ATCTAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAAATTTTAT
Found at i:3244148 original size:21 final size:21
Alignment explanation
Indices: 3244124--3244169 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3244114 AATGATGAAG
*
3244124 TTAATTATTATAACGATAAGA
1 TTAAGTATTATAACGATAAGA
**
3244145 TTAAGTATTATAATTATAAGA
1 TTAAGTATTATAACGATAAGA
3244166 TTAA
1 TTAA
3244170 AATGATTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (21 bp):
TTAAGTATTATAACGATAAGA
Found at i:3245241 original size:2 final size:2
Alignment explanation
Indices: 3245193--3245223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3245183 TCTTTTAATT
3245193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3245224 CTTAAATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3245557 original size:2 final size:2
Alignment explanation
Indices: 3245550--3245576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3245540 ATTTTCTGCC
3245550 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3245577 TTCTTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3248495 original size:3 final size:3
Alignment explanation
Indices: 3248487--3248524 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3248477 GACCAAGTAA
3248487 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
3248525 AAGAGATTGA
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:3251942 original size:25 final size:26
Alignment explanation
Indices: 3251914--3251966 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3251904 GATTTGAGAT
3251914 TAATTCGAT-TTATTTTT-TAATTATA
1 TAATT-GATATTATTTTTATAATTATA
* *
3251939 TAATTTATATTATTTTTATATTTATA
1 TAATTGATATTATTTTTATAATTATA
3251965 TA
1 TA
3251967 TTATGCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 13 0.54
26 9 0.38
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TAATTGATATTATTTTTATAATTATA
Found at i:3253710 original size:13 final size:13
Alignment explanation
Indices: 3253692--3253717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3253682 ATATAAAAAA
3253692 TTAAATATATATT
1 TTAAATATATATT
3253705 TTAAATATATATT
1 TTAAATATATATT
3253718 CATATCTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAAATATATATT
Found at i:3253711 original size:29 final size:31
Alignment explanation
Indices: 3253658--3253715 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
3253648 TTAATATTTT
* *
3253658 AAATATAAATATAATTTTTTTAATATATAAA
1 AAATATAAATATAATATTTTAAATATATAAA
3253689 AAAT-TAAATAT-ATATTTTAAATATATA
1 AAATATAAATATAATATTTTAAATATATA
3253716 TTCATATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 7 0.28
31 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AAATATAAATATAATATTTTAAATATATAAA
Found at i:3254908 original size:16 final size:17
Alignment explanation
Indices: 3254889--3254921 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3254879 TTTTTAATTT
3254889 TTTAA-AAATATTTTTA
1 TTTAATAAATATTTTTA
*
3254905 TTTAATACATATTTTTA
1 TTTAATAAATATTTTTA
3254922 ATCTACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATAAATATTTTTA
Found at i:3255739 original size:2 final size:2
Alignment explanation
Indices: 3255695--3255722 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3255685 TGAAAAAAAA
3255695 AT AT 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
3255723 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3256501 original size:3 final size:3
Alignment explanation
Indices: 3256493--3256536 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3256483 AGACCAAGTA
3256493 AAT AAT 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 AAT AAT AA
3256537 GAGATTGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3256665 original size:18 final size:19
Alignment explanation
Indices: 3256629--3256666 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3256619 TATATTTTAT
3256629 TAAATTAATTATGAAATTA
1 TAAATTAATTATGAAATTA
3256648 TAAATATAA-TAT-AAATTA
1 TAAAT-TAATTATGAAATTA
3256666 T
1 T
3256667 TTAATGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATTAATTATGAAATTA
Found at i:3257230 original size:2 final size:2
Alignment explanation
Indices: 3257223--3257269 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3257213 GCTCAAACCA
3257223 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT
*
3257265 GT AT A
1 AT AT A
3257270 AAACCCCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3257611 original size:15 final size:15
Alignment explanation
Indices: 3257593--3257622 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3257583 TAAATAATAA
*
3257593 TAATTTAAATTAAAT
1 TAATTCAAATTAAAT
3257608 TAATTCAAATTAAAT
1 TAATTCAAATTAAAT
3257623 AAAATCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTCAAATTAAAT
Found at i:3258695 original size:18 final size:19
Alignment explanation
Indices: 3258663--3258700 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3258653 AGATATTATT
*
3258663 TTTTAAATATATAAA-ATA
1 TTTTAAAAATATAAATATA
*
3258681 TTTTAAAAATTTAAATATA
1 TTTTAAAAATATAAATATA
3258700 T
1 T
3258701 ACATATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTAAAAATATAAATATA
Done.