Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 177 of 185
Found at i:53663205 original size:14 final size:15
Alignment explanation
Indices: 53663186--53663218 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53663176 TATTTAGTAA
*
53663186 ATTTTTTTAAAAT-T
1 ATTTTTTAAAAATAT
53663200 ATTTTTTAAAAATAT
1 ATTTTTTAAAAATAT
53663215 ATTT
1 ATTT
53663219 ATAGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTTAAAAATAT
Found at i:53663314 original size:12 final size:13
Alignment explanation
Indices: 53663291--53663316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53663281 TTTATAACAT
53663291 AAAATTGAAAAAA
1 AAAATTGAAAAAA
53663304 AAAATTGAAAAAA
1 AAAATTGAAAAAA
53663317 GCAAATGACC
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAATTGAAAAAA
Found at i:53671778 original size:20 final size:21
Alignment explanation
Indices: 53671737--53671782 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
53671727 AGTTGGACTT
53671737 AAGAT-TAAAAGAATTTACTA
1 AAGATATAAAAGAATTTACTA
* *
53671757 AAGATATAAAAGAGTTT-TTA
1 AAGATATAAAAGAATTTACTA
53671777 AAGATA
1 AAGATA
53671783 CCAACTGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.30
Consensus pattern (21 bp):
AAGATATAAAAGAATTTACTA
Found at i:53678506 original size:13 final size:13
Alignment explanation
Indices: 53678488--53678512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53678478 ACTAGCAGCG
53678488 AAGCTAGAATTTT
1 AAGCTAGAATTTT
53678501 AAGCTAGAATTT
1 AAGCTAGAATTT
53678513 GAATTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AAGCTAGAATTTT
Found at i:53682698 original size:22 final size:22
Alignment explanation
Indices: 53682670--53682711 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
53682660 TTAGCCATTT
53682670 AGCTTTGATGGGTTTACCTTTA
1 AGCTTTGATGGGTTTACCTTTA
53682692 AGCTTTGATGGGTTTACCTT
1 AGCTTTGATGGGTTTACCTT
53682712 ATTTAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (22 bp):
AGCTTTGATGGGTTTACCTTTA
Found at i:53689134 original size:20 final size:19
Alignment explanation
Indices: 53689082--53689140 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
53689072 AAAAACTATA
* *
53689082 AAAAAATTATAAATATTTTT
1 AAAAATTTA-AAATATTTAT
* *
53689102 AAAATTTTCAAATAATTTAT
1 AAAAATTTAAAAT-ATTTAT
53689122 AAAAATTTAAAAT-TTTAT
1 AAAAATTTAAAATATTTAT
53689140 A
1 A
53689141 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 22 0.69
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:53689208 original size:10 final size:9
Alignment explanation
Indices: 53689083--53689213 Score: 51
Period size: 9 Copynumber: 14.7 Consensus size: 9
53689073 AAAACTATAA
*
53689083 AAAAATTAT
1 AAAAATTTT
*
53689092 AAATATTTT
1 AAAAATTTT
*
53689101 TAAAATTTT
1 AAAAATTTT
53689110 CAAATAATTTAT
1 -AAA-AATTT-T
53689122 AAAAA-TTT
1 AAAAATTTT
53689130 -AAAATTTT
1 AAAAATTTT
* *
53689138 -ATATTTTT
1 AAAAATTTT
53689146 AAAAA---T
1 AAAAATTTT
* *
53689152 ATAAATATT
1 AAAAATTTT
* *
53689161 GAAAATATT
1 AAAAATTTT
*
53689170 AAAAATTATAAA
1 AAAAATT-T--T
*
53689182 AAAAAATTT
1 AAAAATTTT
53689191 -AAAATTTT
1 AAAAATTTT
53689199 AAAAATTTT
1 AAAAATTTT
*
53689208 TAAAAT
1 AAAAAT
53689214 AATATTTTTT
Statistics
Matches: 91, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
6 5 0.05
7 4 0.04
8 17 0.19
9 44 0.48
10 5 0.05
11 9 0.10
12 7 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (9 bp):
AAAAATTTT
Found at i:53691612 original size:33 final size:35
Alignment explanation
Indices: 53691575--53691671 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
53691565 ATAGTTATAT
53691575 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
53691608 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
53691643 --AAATATTTAAAATTTATATTTTATATATT
1 TTAAATATTTAAAA--TATAATTTATATATT
53691672 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 7 0.14
35 10 0.20
37 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:53692401 original size:7 final size:7
Alignment explanation
Indices: 53692389--53692414 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53692379 ATTATTTTAA
53692389 AAAAGTG
1 AAAAGTG
53692396 AAAAGTG
1 AAAAGTG
53692403 AAAAGTG
1 AAAAGTG
53692410 AAAAG
1 AAAAG
53692415 AAAGAGACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.12
Consensus pattern (7 bp):
AAAAGTG
Found at i:53694359 original size:24 final size:24
Alignment explanation
Indices: 53694331--53694383 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
53694321 CACCTTTGAA
*
53694331 ACCCTTTCCACAGCTCCTTTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
53694355 ACCCTTTCCACAGCTCCTCTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
53694379 ACCCT
1 ACCCT
53694384 ATCGATTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.49, G:0.04, T:0.34
Consensus pattern (24 bp):
ACCCTTTCCACAGCTCCTCTCTTC
Found at i:53697435 original size:50 final size:50
Alignment explanation
Indices: 53697380--53697480 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
53697370 AAAGATAGTT
53697380 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAAA
53697430 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAAA
53697480 A
1 A
53697481 TATTAAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.32
Consensus pattern (50 bp):
AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAAA
Found at i:53697769 original size:20 final size:20
Alignment explanation
Indices: 53697744--53697783 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53697734 AATATTTTTT
*
53697744 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
53697764 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
53697784 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:53697790 original size:14 final size:14
Alignment explanation
Indices: 53697767--53697806 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53697757 ACAGAAAAGT
*
53697767 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
53697781 AAATCATTTTACGG
1 AAAACATTTTACAG
53697795 AAAACATTTTAC
1 AAAACATTTTAC
53697807 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:53702139 original size:60 final size:59
Alignment explanation
Indices: 53702011--53702156 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 59
53702001 AATTATAATT
* * * *
53702011 TTTTTCTTTTTTAGTCATTCAATTATGAAAAGTTACAAAATTGTCATTCAACTGTTAGTA
1 TTTTTCTTTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTCATTCAACTATTAG-A
** * *
53702071 AATTTCTTTTTTAGTCACCCAACTATGAAATGTTACAAAATAGTCA-TCTAACTATTCA-A
1 TTTTTCTTTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTCATTC-AACTATT-AGA
53702130 TTTTGTCTTTTTT-GATCACTCAACTAT
1 TTTT-TCTTTTTTAG-TCACTCAACTAT
53702157 TCAGTATTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 6 0.08
60 64 0.90
61 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (59 bp):
TTTTTCTTTTTTAGTCACTCAACTATGAAAAGTTACAAAATAGTCATTCAACTATTAGA
Found at i:53708566 original size:50 final size:50
Alignment explanation
Indices: 53708506--53708606 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
53708496 TATAAACCCA
53708506 TCATTGTTGGCATCGAATAACCGAAACATCTATTACCGAACCAGGGATTT
1 TCATTGTTGGCATCGAATAACCGAAACATCTATTACCGAACCAGGGATTT
53708556 TCATTGTTGGCATCGAATAACCGAAACATCTATTACCGAACCAGGGATTT
1 TCATTGTTGGCATCGAATAACCGAAACATCTATTACCGAACCAGGGATTT
53708606 T
1 T
53708607 TGTCAATTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (50 bp):
TCATTGTTGGCATCGAATAACCGAAACATCTATTACCGAACCAGGGATTT
Found at i:53711578 original size:20 final size:23
Alignment explanation
Indices: 53711531--53711578 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
53711521 TTTAATATTT
*
53711531 TTTAGATAGATTTACAAATTTGAA
1 TTTAGATAGATTTACAAAATTG-A
53711555 TTTAGATA-ATTTA-AAAATTG-
1 TTTAGATAGATTTACAAAATTGA
53711575 TTTA
1 TTTA
53711579 TTTCCAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
22 6 0.26
23 5 0.22
24 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (23 bp):
TTTAGATAGATTTACAAAATTGA
Found at i:53721514 original size:30 final size:30
Alignment explanation
Indices: 53721479--53721537 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
53721469 TATTTTATTA
* *
53721479 TTAATTTTGTTATTGTTATAAAGGTATTTG
1 TTAATTTTATTATTATTATAAAGGTATTTG
* *
53721509 TTAATTTTATTATTATTTTAGAGGTATTT
1 TTAATTTTATTATTATTATAAAGGTATTT
53721538 CCTTGTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (30 bp):
TTAATTTTATTATTATTATAAAGGTATTTG
Found at i:53721636 original size:21 final size:22
Alignment explanation
Indices: 53721581--53721640 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
53721571 AAGTTTACAT
53721581 ATTTTTTAAA-ATTTATTTTCA
1 ATTTTTTAAATATTTATTTTCA
*
53721602 ATTTGTTAGAAAATATTTATTTT-A
1 ATTT-TT--TAAATATTTATTTTCA
53721626 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
53721641 TTGATGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 12 0.36
22 2 0.06
23 2 0.06
24 8 0.24
25 9 0.27
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
ATTTTTTAAATATTTATTTTCA
Found at i:53723128 original size:39 final size:40
Alignment explanation
Indices: 53723073--53723157 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
53723063 TCAAATACAT
53723073 TTAAAACAAATATTAAAACAAAAAACAAA-TAAAAATATA
1 TTAAAACAAATATTAAAACAAAAAACAAATTAAAAATATA
* * * *
53723112 TTAAAACAATTTTTAAAACAATACACAAATTAAAAATATA
1 TTAAAACAAATATTAAAACAAAAAACAAATTAAAAATATA
*
53723152 ATAAAA
1 TTAAAA
53723158 ATTAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 25 0.62
40 15 0.38
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAAAAACAAATTAAAAATATA
Found at i:53723218 original size:24 final size:23
Alignment explanation
Indices: 53723173--53723218 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53723163 TTTTATTAAA
* * *
53723173 ATTAAAATTAAAATATAAATATG
1 ATTAAAAATAAAAAAGAAATATG
53723196 ATTAAAAATAAAAAAGAATATAT
1 ATTAAAAATAAAAAAGAA-ATAT
53723219 ATTTAGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTAAAAATAAAAAAGAAATATG
Found at i:53730112 original size:29 final size:29
Alignment explanation
Indices: 53730079--53730138 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
53730069 AATTTTGGAT
53730079 TTTAGTTT-TTGTACTTTT-ATTTTCAGAAA
1 TTTAGTTTCTT-TACTTTTAATTTTCA-AAA
53730108 TTTAGTTTCTTTACTTTTCAATTTTCAAAA
1 TTTAGTTTCTTTACTTTT-AATTTTCAAAA
53730138 T
1 T
53730139 GCATGACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 15 0.54
30 6 0.21
31 7 0.25
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTAGTTTCTTTACTTTTAATTTTCAAAA
Found at i:53733830 original size:21 final size:21
Alignment explanation
Indices: 53733801--53733841 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53733791 AAGTGATAAG
53733801 ATTTAAATTTAAAA-TATTAAC
1 ATTTAAA-TTAAAATTATTAAC
*
53733822 ATTTTAATTAAAATTATTAA
1 ATTTAAATTAAAATTATTAA
53733842 TTTTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTAAATTAAAATTATTAAC
Found at i:53734699 original size:7 final size:7
Alignment explanation
Indices: 53734687--53734715 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53734677 TAAATTTCAA
53734687 AAATTTT
1 AAATTTT
53734694 AAATTTT
1 AAATTTT
53734701 AAATTTT
1 AAATTTT
53734708 AAATTTT
1 AAATTTT
53734715 A
1 A
53734716 TACATGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AAATTTT
Found at i:53735249 original size:9 final size:10
Alignment explanation
Indices: 53735222--53735253 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
53735212 AAAAAATATT
53735222 TTTTAAAAAA
1 TTTTAAAAAA
53735232 TTTTAAAAAA
1 TTTTAAAAAA
53735242 TTTTAAAAAA
1 TTTTAAAAAA
53735252 TT
1 TT
53735254 AATTAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:53736024 original size:11 final size:11
Alignment explanation
Indices: 53735996--53736025 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
53735986 ATTGTTATTA
53735996 TAATTAAATTT
1 TAATTAAATTT
53736007 TAA-TAAATTT
1 TAATTAAATTT
53736017 TAATTAAAT
1 TAATTAAAT
53736026 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTAAATTT
Found at i:53737779 original size:30 final size:31
Alignment explanation
Indices: 53737724--53737781 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
53737714 TTTACTTTTT
*
53737724 AAGTATAAAAACTAAATATTTAATTTTACTA
1 AAGTATAAAAACTAAATAATTAATTTTACTA
**
53737755 AAGTATAAGGACT-AATAATTAATTTTA
1 AAGTATAAAAACTAAATAATTAATTTTA
53737782 ACCTTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (31 bp):
AAGTATAAAAACTAAATAATTAATTTTACTA
Found at i:53761321 original size:20 final size:20
Alignment explanation
Indices: 53761281--53761322 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53761271 TTAATATCAA
* **
53761281 AATAATAACAACATGGTAAT
1 AATAATAAAAACATGAAAAT
53761301 AATAATAAAAACATGAAAAT
1 AATAATAAAAACATGAAAAT
53761321 AA
1 AA
53761323 GAATCCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (20 bp):
AATAATAAAAACATGAAAAT
Found at i:53775880 original size:37 final size:37
Alignment explanation
Indices: 53775830--53775905 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
53775820 AAAGATTGAG
*
53775830 AAAGATCTGACAAAGCCTCCTTTCTTTCGGTCATGAA
1 AAAGATCTGACAAAGCCTCCTTCCTTTCGGTCATGAA
53775867 AAAGATCTGACAAAGCCTCCTTCCTTTCGGTCATGAA
1 AAAGATCTGACAAAGCCTCCTTCCTTTCGGTCATGAA
53775904 AA
1 AA
53775906 TGGACCCACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (37 bp):
AAAGATCTGACAAAGCCTCCTTCCTTTCGGTCATGAA
Found at i:53791592 original size:22 final size:22
Alignment explanation
Indices: 53791566--53791611 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
53791556 TTTTTTTCCA
53791566 ATAACTTGAATATACATCACAC
1 ATAACTTGAATATACATCACAC
53791588 ATAACTTGAATATACATCACAC
1 ATAACTTGAATATACATCACAC
53791610 AT
1 AT
53791612 TCAAAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (22 bp):
ATAACTTGAATATACATCACAC
Found at i:53794621 original size:26 final size:26
Alignment explanation
Indices: 53794558--53794621 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 26
53794548 CTTTTATATA
53794558 TAATAATATAATATAATATAATATACT
1 TAATAATA-AATATAATATAATATACT
* *
53794585 TAATTATTAAATA-AATAT-ATATATTT
1 TAA-TAATAAATATAATATAATATA-CT
53794611 TAATCAATAAA
1 TAAT-AATAAA
53794622 ATCTTTGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 6 0.19
26 14 0.45
27 7 0.23
28 4 0.13
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATAATAAATATAATATAATATACT
Found at i:53797191 original size:22 final size:22
Alignment explanation
Indices: 53797160--53797202 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53797150 ATAAAATTGT
*
53797160 AGAAGTTTTTAAAATTTATTTA
1 AGAAGCTTTTAAAATTTATTTA
53797182 AGAAGCTTTTAAAATTTATTT
1 AGAAGCTTTTAAAATTTATTT
53797203 GAGTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
AGAAGCTTTTAAAATTTATTTA
Found at i:53797701 original size:20 final size:21
Alignment explanation
Indices: 53797676--53797715 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53797666 AATATTTTTC
*
53797676 AAATATTTAAGC-CTTTTAAA
1 AAATATATAAGCACTTTTAAA
*
53797696 AAATATATAATCACTTTTAA
1 AAATATATAAGCACTTTTAA
53797716 TTATAGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATATATAAGCACTTTTAAA
Found at i:53798261 original size:12 final size:12
Alignment explanation
Indices: 53798244--53798270 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53798234 CTGATATACG
53798244 AAAAAGAAAAAA
1 AAAAAGAAAAAA
53798256 AAAAAGAAAAAA
1 AAAAAGAAAAAA
53798268 AAA
1 AAA
53798271 TTTTGGGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:53798711 original size:12 final size:11
Alignment explanation
Indices: 53798682--53798710 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53798672 TCCTTTTCCT
53798682 TCTTTTTTCTC
1 TCTTTTTTCTC
53798693 TC-TTTTTCTC
1 TCTTTTTTCTC
53798703 TCTTTTTT
1 TCTTTTTT
53798711 TGTTTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:53808786 original size:21 final size:21
Alignment explanation
Indices: 53808756--53808817 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
53808746 TAACAGAACC
*
53808756 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCCAGTTAACTA
*
53808777 GCTGACGTGGCCAGTTAACTA
1 GCTGATGTGGCCAGTTAACTA
53808798 GCTGATGTGGCCAGTTAACT
1 GCTGATGTGGCCAGTTAACT
53808818 TGCCACATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGATGTGGCCAGTTAACTA
Found at i:53809901 original size:30 final size:31
Alignment explanation
Indices: 53809830--53809893 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
53809820 GGAAACCGTT
*
53809830 AGTTAGTGACTGTTTTGTCACTTTTTTATAA
1 AGTTAGTGACTGTTTTGTCACTTTTTCATAA
* *
53809861 CGTTAGTGACTGTTTTGTTA-TTTTTCA-AA
1 AGTTAGTGACTGTTTTGTCACTTTTTCATAA
53809890 AGTT
1 AGTT
53809894 GGGTGACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.17
30 6 0.21
31 18 0.62
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.52
Consensus pattern (31 bp):
AGTTAGTGACTGTTTTGTCACTTTTTCATAA
Found at i:53816231 original size:13 final size:13
Alignment explanation
Indices: 53816213--53816242 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
53816203 TCCTGCCTTT
53816213 AATGGAGATGGAA
1 AATGGAGATGGAA
53816226 AATGGAGATGGAA
1 AATGGAGATGGAA
53816239 AATG
1 AATG
53816243 ACTGAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (13 bp):
AATGGAGATGGAA
Found at i:53819325 original size:3 final size:3
Alignment explanation
Indices: 53819317--53819345 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53819307 AAATGTAAAT
53819317 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
53819346 AAATCCCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:53823569 original size:29 final size:28
Alignment explanation
Indices: 53823531--53823630 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
53823521 ATAAAGAGAT
*
53823531 GCACCAAAGTGCAATGATAGAACAGAGTG
1 GCACCGAAGTGCAAT-ATAGAACAGAGTG
*
53823560 GCACCGAAGTGCAATATTAGAACAGAATG
1 GCACCGAAGTGCAATA-TAGAACAGAGTG
* * ** * *
53823589 ACACTGAAGTGCTTTAACAAAACAGAGTG
1 GCACCGAAGTGCAAT-ATAGAACAGAGTG
53823618 GCACCGAAGTGCA
1 GCACCGAAGTGCA
53823631 TTAACAGTAC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.02
29 55 0.96
30 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (28 bp):
GCACCGAAGTGCAATATAGAACAGAGTG
Found at i:53827291 original size:24 final size:24
Alignment explanation
Indices: 53827246--53827292 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53827236 TATATATACC
53827246 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
53827270 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
53827293 CTATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:53827993 original size:26 final size:27
Alignment explanation
Indices: 53827956--53828006 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
53827946 TTTCACCTTT
*
53827956 TCTTTCCTTTTTCTCTTCTGTTTCTGG
1 TCTTTCCTTTTTCTATTCTGTTTCTGG
*
53827983 TCTTT-CTTTTTCTATTCTTTTTCT
1 TCTTTCCTTTTTCTATTCTGTTTCT
53828007 TTTATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.69
Consensus pattern (27 bp):
TCTTTCCTTTTTCTATTCTGTTTCTGG
Found at i:53828052 original size:28 final size:28
Alignment explanation
Indices: 53828021--53828096 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
53828011 TTTAATTATA
*
53828021 ATAATATAATAATATATATTATAA-TATT
1 ATAATATTATAATATATATTATAACT-TT
* *
53828049 ATAATATTATGATATTATATTTTAACTTT
1 ATAATATTATAATA-TATATTATAACTTT
53828078 A-AATATTTATAATATATAT
1 ATAATA-TTATAATATATAT
53828097 ACACTTATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 21 0.51
29 19 0.46
30 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATAATATTATAATATATATTATAACTTT
Found at i:53828055 original size:8 final size:8
Alignment explanation
Indices: 53828015--53828067 Score: 72
Period size: 8 Copynumber: 6.8 Consensus size: 8
53828005 CTTTTATTTA
53828015 ATTATAAT
1 ATTATAAT
*
53828023 AATATAAT
1 ATTATAAT
*
53828031 AATAT-AT
1 ATTATAAT
53828038 ATTATAAT
1 ATTATAAT
53828046 ATTATAAT
1 ATTATAAT
*
53828054 ATTATGAT
1 ATTATAAT
53828062 ATTATA
1 ATTATA
53828068 TTTTAACTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 6 0.15
8 34 0.85
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
ATTATAAT
Found at i:53835220 original size:32 final size:31
Alignment explanation
Indices: 53835175--53835270 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
53835165 CTTAGATAAT
53835175 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
53835206 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
53835238 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
53835269 TT
1 TT
53835271 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:53845192 original size:26 final size:27
Alignment explanation
Indices: 53845137--53845194 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
53845127 ATCACGTAGG
53845137 AATAGGAAAGATATATAATATATTCCTA
1 AATAGGAAAGATATATAATATATT-CTA
*
53845165 AATAGGAATGATATATAATATATT-TA
1 AATAGGAAAGATATATAATATATTCTA
53845191 AATA
1 AATA
53845195 TTTCTAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
28 23 0.79
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (27 bp):
AATAGGAAAGATATATAATATATTCTA
Found at i:53846477 original size:16 final size:17
Alignment explanation
Indices: 53846458--53846497 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
53846448 AATTTTTAGA
53846458 ATTTTT-AATAACATTT
1 ATTTTTAAATAACATTT
*
53846474 ATTTTTAAATAACTTTT
1 ATTTTTAAATAACATTT
53846491 ATATTTT
1 AT-TTTT
53846498 TTTTGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTAAATAACATTT
Found at i:53846497 original size:19 final size:19
Alignment explanation
Indices: 53846444--53846498 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
53846434 AATATTAACA
* *
53846444 AAATAATTTTTAGAATTTTT
1 AAATAACTTTTA-TATTTTT
*
53846464 -AATAAC-ATT-TATTTTT
1 AAATAACTTTTATATTTTT
53846480 AAATAACTTTTATATTTTT
1 AAATAACTTTTATATTTTT
53846499 TTTGAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 4 0.14
19 12 0.43
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
AAATAACTTTTATATTTTT
Found at i:53850341 original size:17 final size:16
Alignment explanation
Indices: 53850311--53850347 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53850301 TAATTAATTC
*
53850311 TATTTT-ATTTTAT-T
1 TATTTTAATATTATAT
53850325 TATTTTAATATTATAT
1 TATTTTAATATTATAT
53850341 TATTTTA
1 TATTTTA
53850348 TAAAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTAATATTATAT
Found at i:53856591 original size:18 final size:19
Alignment explanation
Indices: 53856555--53856594 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
53856545 CATATGCCAC
*
53856555 ATTAAAAAATCATTTAAAA
1 ATTAAAAAATCATTCAAAA
*
53856574 ATTATAAAA-CATTCAAAA
1 ATTAAAAAATCATTCAAAA
53856592 ATT
1 ATT
53856595 TAACGTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATCATTCAAAA
Found at i:53857556 original size:23 final size:24
Alignment explanation
Indices: 53857525--53857576 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
53857515 TTTAAACACT
*
53857525 AAAAGTTGCTTTCTTGGA-GAAAA
1 AAAAATTGCTTTCTTGGAGGAAAA
53857548 AAAAATTGCTTTCTTGGAGGAAAA
1 AAAAATTGCTTTCTTGGAGGAAAA
53857572 AAAAA
1 AAAAA
53857577 CTCCAAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (24 bp):
AAAAATTGCTTTCTTGGAGGAAAA
Found at i:53861335 original size:43 final size:43
Alignment explanation
Indices: 53861287--53861385 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
53861277 GGAAAGTTTG
*
53861287 ATGGTAGTTATAACAACGTTAAATGTCCAATTAA-GCAACACTA
1 ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGC-ACACTA
* * * *
53861330 ATGGTAATCATAACCATGCTAAATGTCCAATTAAGGCACACTA
1 ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGCACACTA
53861373 ATGGTAGTTATAA
1 ATGGTAGTTATAA
53861386 GAGAGAGCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTAGTTATAACAACGCTAAATGTCCAATTAAGGCACACTA
Found at i:53862127 original size:17 final size:17
Alignment explanation
Indices: 53862105--53862137 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53862095 CCCAAATTGA
53862105 GAACTAAAGATAAACCG
1 GAACTAAAGATAAACCG
53862122 GAACTAAAGATAAACC
1 GAACTAAAGATAAACC
53862138 ATGATCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (17 bp):
GAACTAAAGATAAACCG
Found at i:53864233 original size:17 final size:18
Alignment explanation
Indices: 53864207--53864244 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53864197 ATAAATATTT
* *
53864207 ATATTTATA-TAATTAAA
1 ATATTCATATTAAATAAA
53864224 ATATTCATATTAAATAAA
1 ATATTCATATTAAATAAA
53864242 ATA
1 ATA
53864245 GTGTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTCATATTAAATAAA
Found at i:53864314 original size:17 final size:17
Alignment explanation
Indices: 53864294--53864335 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
53864284 TTACTAATGT
*
53864294 TAAATTTT-TTATTGAAA
1 TAAATTTTAATATT-AAA
53864311 TAAAATTTTAATATTAAA
1 T-AAATTTTAATATTAAA
53864329 TAAATTT
1 TAAATTT
53864336 ATCAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAATTTTAATATTAAA
Found at i:53869281 original size:31 final size:31
Alignment explanation
Indices: 53869246--53869304 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53869236 AACCATCCAG
*
53869246 TGATTTGAAT-AAAAACTTTCAAATAATTTAA
1 TGATTTAAATGAAAAA-TTTCAAATAATTTAA
*
53869277 TGATTTAAATGAAAAATTTTAAATAATT
1 TGATTTAAATGAAAAATTTCAAATAATT
53869305 AAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (31 bp):
TGATTTAAATGAAAAATTTCAAATAATTTAA
Found at i:53896528 original size:3 final size:3
Alignment explanation
Indices: 53896509--53896565 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
53896499 TTTCAATTGA
*
53896509 ATT ATC ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53896555 ATT ATT ATT AT
1 ATT ATT ATT AT
53896566 ACATATAGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:53896663 original size:13 final size:15
Alignment explanation
Indices: 53896631--53896667 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53896621 ATACATGTTC
53896631 ATATTTTATATATAT
1 ATATTTTATATATAT
*
53896646 ATATTTTTTAT-TAT
1 ATATTTTATATATAT
53896660 -TATTTTAT
1 ATATTTTAT
53896668 TTTCATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 7 0.35
14 3 0.15
15 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATTTTATATATAT
Found at i:53896710 original size:22 final size:24
Alignment explanation
Indices: 53896682--53896728 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53896672 ATAACTCTTG
53896682 TATACA-TGGAT-ATATATATACA
1 TATACATTGGATAATATATATACA
**
53896704 TATACATTTTATAATATATATACA
1 TATACATTGGATAATATATATACA
53896728 T
1 T
53896729 TTTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 3 0.14
24 12 0.57
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (24 bp):
TATACATTGGATAATATATATACA
Found at i:53896733 original size:20 final size:20
Alignment explanation
Indices: 53896710--53896748 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53896700 TACATATACA
53896710 TTTTATAATATATATACATT
1 TTTTATAATATATATACATT
* *
53896730 TTTTATATTGTATATACAT
1 TTTTATAATATATATACAT
53896749 ACATTTCCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTATAATATATATACATT
Found at i:53898229 original size:25 final size:25
Alignment explanation
Indices: 53898197--53898248 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
53898187 ACACTTCAAT
53898197 AAATGAATAAATAAATATCAAATAA
1 AAATGAATAAATAAATATCAAATAA
53898222 AAATGAATAAATAAATATCAAATAA
1 AAATGAATAAATAAATATCAAATAA
53898247 AA
1 AA
53898249 CAACGATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (25 bp):
AAATGAATAAATAAATATCAAATAA
Found at i:53898571 original size:3 final size:3
Alignment explanation
Indices: 53898563--53898611 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
53898553 CAAGACATAG
* *
53898563 ATA ATA ATA ATA TTA ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53898611 A
1 A
53898612 CCTAAATACA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:53899658 original size:15 final size:16
Alignment explanation
Indices: 53899621--53899665 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
53899611 ATATTTTAGG
53899621 TGTTTGGGCTTGGGTT
1 TGTTTGGGCTTGGGTT
* *
53899637 AGTTTGGGCTT-GTTT
1 TGTTTGGGCTTGGGTT
*
53899652 TGTTTGGGTTTGGG
1 TGTTTGGGCTTGGG
53899666 AAGGGTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.02, C:0.04, G:0.42, T:0.51
Consensus pattern (16 bp):
TGTTTGGGCTTGGGTT
Found at i:53907518 original size:11 final size:11
Alignment explanation
Indices: 53907483--53907511 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53907473 TTATCAAACA
53907483 AAAAAAGAGAG
1 AAAAAAGAGAG
53907494 -AAAAAGAGAG
1 AAAAAAGAGAG
53907504 AAAAAAGA
1 AAAAAAGA
53907512 AGGAAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:53909031 original size:93 final size:93
Alignment explanation
Indices: 53908914--53909212 Score: 582
Period size: 93 Copynumber: 3.2 Consensus size: 93
53908904 TGTCAGACTT
53908914 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
1 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
53908979 TTGTATAATACTGATATACGAAAAAGAA
66 TTGTATAATACTGATATACGAAAAAGAA
53909007 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
1 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
53909072 TTGTATAATACTGATATACGAAAAAGAA
66 TTGTATAATACTGATATACGAAAAAGAA
53909100 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
1 AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
53909165 TTGTATAATACTGATATACGAAAAAGAA
66 TTGTATAATACTGATATACGAAAAAGAA
*
53909193 AAAAAAACT-TTTTTTTGGGT
1 AAAAAAATTATTTTTTTGGGT
53909213 GCTGGCCTAT
Statistics
Matches: 205, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 11 0.05
93 194 0.95
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (93 bp):
AAAAAAATTATTTTTTTGGGTTTTGGTTTGTTAATGTCCGGAACCCATGTATTTTTTTAAAAAAA
TTGTATAATACTGATATACGAAAAAGAA
Found at i:53909583 original size:107 final size:107
Alignment explanation
Indices: 53909308--53909831 Score: 847
Period size: 107 Copynumber: 5.0 Consensus size: 107
53909298 TTAATTTTTT
* *
53909308 TTTTGGTGCTGGCCTATCAATGGCCGGCACCCAGTGA-ACAAT-AAA-TTTTTTTTCTTTTTTTT
1 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGT-ACACAGTAAAATTTTTTTTTCTTTTTTTT
** * *
53909370 TATGTCAGAATCATATATAAAAATAC------GA-AAAAAAAA
65 CGTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
* *
53909406 TTTTGATGCTCGCCTGTCAATGGCCGGCACCCAGTGA-ACAGT-AAATTTTTTTTTCTTTTTTTT
1 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGT-ACACAGTAAAATTTTTTTTTCTTTTTTTT
53909469 CGTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
65 CGTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
53909512 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
1 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
53909577 GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
66 GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
53909619 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
1 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
53909684 GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
66 GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
53909726 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
1 TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
* * *
53909791 GTGTTAGAATCAGATATAAAAATACGATAAAAATAAAAAAA
66 GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAA
53909832 TTTCTATTTC
Statistics
Matches: 403, Mismatches: 13, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
98 41 0.10
99 40 0.10
105 2 0.00
106 46 0.11
107 274 0.68
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (107 bp):
TTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAATTTTTTTTTCTTTTTTTTC
GTGTCAGAATCAGATATAAAAATACAAAAAAAATAAAAAAAA
Found at i:53910130 original size:106 final size:108
Alignment explanation
Indices: 53909940--53910607 Score: 789
Period size: 106 Copynumber: 6.2 Consensus size: 108
53909930 AAGTCCTAAA
* * ****
53909940 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTTTGACACG-AAAAAAATAAAATTTTTTTAC
1 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTTAC
53910004 TGTGT-ACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AAAA-
66 TGT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAG
53910044 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTTA
1 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAG-AAAAAAAATTTA
53910109 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AAAA-
65 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAG
53910150 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTTA
1 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAG-AAAAAAAATTTA
53910215 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAG
65 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAG
* *****
53910260 TTTTATTATTATTATTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTT
1 TTTT-TT-TTA-T-TTTTTTT-GTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAA
* *
53910325 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAATTTTAT
61 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAA----AG
*
53910378 TTATTTATTTATTTTTTTTGTATTTTTATATCTGATTCTGATAC---------GAAAAAAAA-TT
1 TT-TTT-TTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTT
53910433 ACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAG
64 ACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAG
* *****
53910479 TTTTATTATTATTATTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTT
1 TTTT-TT-TTA-T-TTTTTTT-GTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAA
* *
53910544 TTTACTGTTCACTGGGTGCCGGCCATTGAAAGGCCAGCACCC-AAAAT
61 TTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAG
*
53910591 TTTTTTTTCTTTTTTTT
1 TTTTTTTTATTTTTTTT
53910608 TTTCTTTTTC
Statistics
Matches: 498, Mismatches: 33, Indels: 62
0.84 0.06 0.10
Matches are distributed among these distances:
100 3 0.01
101 7 0.01
102 1 0.00
103 7 0.01
104 65 0.13
105 53 0.11
106 151 0.30
107 2 0.00
108 7 0.01
109 5 0.01
110 6 0.01
111 4 0.01
112 11 0.02
113 5 0.01
114 96 0.19
115 57 0.11
116 7 0.01
117 1 0.00
118 7 0.01
119 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (108 bp):
TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTTAC
TGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAG
Found at i:53910357 original size:114 final size:114
Alignment explanation
Indices: 53910156--53910589 Score: 640
Period size: 114 Copynumber: 3.9 Consensus size: 114
53910146 AAAATTTTTT
* *****
53910156 TTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTTACTGTTC
1 TTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAG-AAATTTTTTTTACTGTTC
53910221 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTA
65 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTA
*
53910271 TTATTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCA
1 TTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTACTGTTCA
*
53910336 CTGGGTGCCGGCCATTGACAGGCCAACACCC-AAAAA-TTTTATTTATTTA
66 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTA-TTA-TTA
* *
53910385 TTTATTTTTTTTGTATTTTTATATCTGATTCTGATACG---AAAAA-AAA------TTACTGTTC
1 -TTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTACTGTTC
53910440 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTA
65 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTA
*
53910490 TTATTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCA
1 TTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTACTGTTCA
*
53910555 CTGGGTGCCGGCCATTGAAAGGCCAGCACCCAAAA
66 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
53910590 TTTTTTTTTC
Statistics
Matches: 288, Mismatches: 16, Indels: 31
0.86 0.05 0.09
Matches are distributed among these distances:
104 34 0.12
105 43 0.15
106 8 0.03
107 10 0.03
108 3 0.01
111 3 0.01
112 10 0.03
113 8 0.03
114 91 0.32
115 78 0.27
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (114 bp):
TTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTACTGTTCA
CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTA
Found at i:53910476 original size:219 final size:219
Alignment explanation
Indices: 53909940--53910610 Score: 902
Period size: 219 Copynumber: 3.1 Consensus size: 219
53909930 AAGTCCTAAA
*
53909940 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTTTGACACGAAAAAAATAAAATTTTTTTACT
1 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACG--AAAAA-AAAA----TTTACT
53910005 GTGT-ACTGGGTGCCGGCCATTGACAGGCCAGCA-CC--AAAA-TTTT-TT-TTA-T-TTTTTTT
59 GT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTTT
* *****
53910061 -GTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTTACTGTTCACTGGGTGCC
123 CGTATTTTTATATCTGATTCTTACACGAAAAAAAAG-AAATTTTTTTTACTGTTCACTGGGTGCC
53910125 GGCCATTGACAGGCCAGCA-CC--AAA----A-
187 GGCCATTGACAGGCCAGCACCCAAAAATTTTAT
53910150 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAAATTTA
1 TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACAC---------GAAAAAAAAATTTA
53910215 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTT
57 CTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTT
53910280 TCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCACTGGGTGCC
122 TCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCACTGGGTGCC
*
53910345 GGCCATTGACAGGCCAACACCCAAAAATTTTAT
187 GGCCATTGACAGGCCAGCACCCAAAAATTTTAT
*
53910378 TTATTTATTTATTTTTTTTGTATTTTTATATCTGATTCTGATACG-AAAAAAAA-TTACTGTTCA
1 TT-TTT-TTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAATTTACTGTTCA
53910441 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTTTCGTATT
64 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTTTCGTATT
53910506 TTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCACTGGGTGCCGGCCATT
129 TTTATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCACTGGGTGCCGGCCATT
*
53910571 GAAAGGCCAGCACCC-AAAATTTT-T
194 GACAGGCCAGCACCCAAAAATTTTAT
*
53910595 TTTTCTTT-TTTTTTTT
1 TTTTTTTTATTTTTTTT
53910611 CTTTTTCGTA
Statistics
Matches: 420, Mismatches: 12, Indels: 54
0.86 0.02 0.11
Matches are distributed among these distances:
210 41 0.10
211 1 0.00
212 37 0.09
213 2 0.00
214 8 0.02
215 7 0.02
216 10 0.02
217 10 0.02
218 11 0.03
219 155 0.37
220 56 0.13
221 37 0.09
223 3 0.01
227 1 0.00
228 2 0.00
229 3 0.01
230 36 0.09
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (219 bp):
TTTTTTTTATTTTTTTTGTATTTTTATATCTGATTCTGACACGAAAAAAAAATTTACTGTTCACT
GGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAGTTTTATTATTATTATTTTTTTCGTATTTT
TATATCTGATTCTTACACGAAAAAAAAGAAATTTTTTTTACTGTTCACTGGGTGCCGGCCATTGA
CAGGCCAGCACCCAAAAATTTTAT
Found at i:53910607 original size:12 final size:12
Alignment explanation
Indices: 53910590--53910616 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53910580 GCACCCAAAA
53910590 TTTTTTTTTCTT
1 TTTTTTTTTCTT
53910602 TTTTTTTTTCTT
1 TTTTTTTTTCTT
53910614 TTT
1 TTT
53910617 CGTATATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:53918032 original size:29 final size:29
Alignment explanation
Indices: 53917977--53918043 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
53917967 AAAGGGACCT
* * *
53917977 GATCAAATTAATCCCTCTATTATTAAACA
1 GATCAAATTAATCCCTCTACTACTAAAAA
* * *
53918006 GATCAATTTAGTCCCTGTACTACTAAAAA
1 GATCAAATTAATCCCTCTACTACTAAAAA
53918035 GAATCAAAT
1 G-ATCAAAT
53918044 AAAACCAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.31
Consensus pattern (29 bp):
GATCAAATTAATCCCTCTACTACTAAAAA
Found at i:53954769 original size:16 final size:16
Alignment explanation
Indices: 53954748--53954778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53954738 CGCTGTATTA
*
53954748 GAATAGAGGCGTAATG
1 GAATAGAGACGTAATG
53954764 GAATAGAGACGTAAT
1 GAATAGAGACGTAAT
53954779 AGCAATTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (16 bp):
GAATAGAGACGTAATG
Found at i:53955028 original size:18 final size:17
Alignment explanation
Indices: 53955007--53955041 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53954997 TTATTATTAA
*
53955007 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53955025 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53955042 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53955115 original size:23 final size:21
Alignment explanation
Indices: 53955071--53955111 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53955061 TATATGAATT
53955071 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
53955092 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
53955112 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:53957447 original size:11 final size:12
Alignment explanation
Indices: 53957425--53957453 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
53957415 ATTTTAAAAA
53957425 TTAAAAAGTATT
1 TTAAAAAGTATT
53957437 TTAAAAA-TATT
1 TTAAAAAGTATT
53957448 TTAAAA
1 TTAAAA
53957454 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TTAAAAAGTATT
Found at i:53957459 original size:29 final size:28
Alignment explanation
Indices: 53957414--53957489 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
53957404 ACCAAAAATT
**
53957414 TATTTTAAAAATTAAAAAGTATTTTAAAAA-
1 TATTTT-AAAATTAAAAA--AAATTAAAAAG
53957444 TATTTTAAAATTAAAAAAAATTAAAAAG
1 TATTTTAAAATTAAAAAAAATTAAAAAG
*
53957472 TATTTTAAAATTTAAAAA
1 TATTTTAAAATTAAAAAA
53957490 TAAAAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 8 0.19
28 17 0.40
29 11 0.26
30 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
TATTTTAAAATTAAAAAAAATTAAAAAG
Found at i:53957470 original size:39 final size:38
Alignment explanation
Indices: 53957420--53957538 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 38
53957410 AATTTATTTT
53957420 AAAAATTAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAGTATTTT-AAAATATTTTAAAATTAAA
*
53957459 AAAAATTAAAAAGTATTTT-AAA-A-TTTAAAAAT-AA
1 AAAAATTAAAAAGTATTTTAAAATATTTTAAAATTAAA
53957493 AAAAATT------TATTTTAGAAATATTTTAAAATTAAA
1 AAAAATTAAAAAGTATTTTA-AAATATTTTAAAATTAAA
*
53957526 AAAATTTGAAAAA
1 AAAAATT-AAAAA
53957539 TAAATATATT
Statistics
Matches: 66, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
28 6 0.09
30 3 0.05
31 1 0.02
32 8 0.12
33 8 0.12
34 9 0.14
35 8 0.12
36 1 0.02
37 3 0.05
39 19 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (38 bp):
AAAAATTAAAAAGTATTTTAAAATATTTTAAAATTAAA
Found at i:53957497 original size:28 final size:27
Alignment explanation
Indices: 53957439--53957530 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 27
53957429 AAAGTATTTT
53957439 AAAAATATTTTAAAA-TTAAAAA-AAA
1 AAAAATATTTTAAAATTTAAAAATAAA
53957464 TTAAAAAGTATTTTAAAATTTAAAAATAAA
1 --AAAAA-TATTTTAAAATTTAAAAATAAA
* * *
53957494 AAAATTTATTTTAGAAATATTTTAAAATTAA
1 AAAA-ATATTTT--AAA-ATTTAAAAATAAA
53957525 AAAAAT
1 AAAAAT
53957531 TTGAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 5 0.09
28 20 0.37
29 7 0.13
30 7 0.13
31 15 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
AAAAATATTTTAAAATTTAAAAATAAA
Found at i:53957499 original size:16 final size:16
Alignment explanation
Indices: 53957478--53957542 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
53957468 AAAGTATTTT
53957478 AAAATTTAAAAATAAA
1 AAAATTTAAAAATAAA
***
53957494 AAAATTT-ATTTTAGAA
1 AAAATTTAAAAATA-AA
* * *
53957510 ATATTTTAAAATTAAA
1 AAAATTTAAAAATAAA
53957526 AAAATTTGAAAAATAAA
1 AAAATTT-AAAAATAAA
53957543 TATATTTATT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
15 3 0.08
16 21 0.58
17 12 0.33
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAATTTAAAAATAAA
Found at i:53961346 original size:22 final size:22
Alignment explanation
Indices: 53961318--53961362 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
53961308 ACGTTGAAAC
53961318 CCTCGGCGGGAATGACGATGGA
1 CCTCGGCGGGAATGACGATGGA
* *
53961340 CCTCGGCGTGAATGCCGATGGA
1 CCTCGGCGGGAATGACGATGGA
53961362 C
1 C
53961363 TTGACCACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.38, T:0.16
Consensus pattern (22 bp):
CCTCGGCGGGAATGACGATGGA
Found at i:53969407 original size:19 final size:19
Alignment explanation
Indices: 53969383--53969422 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
53969373 TCATTGTCAA
*
53969383 ATTGATACAAGGTTGAGTG
1 ATTGATACAAGGTCGAGTG
53969402 ATTGATACAAGGTCGAGTG
1 ATTGATACAAGGTCGAGTG
53969421 AT
1 AT
53969423 ACGAGCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGATACAAGGTCGAGTG
Found at i:53983928 original size:24 final size:25
Alignment explanation
Indices: 53983901--53983947 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
53983891 GGATTCTGAA
53983901 ATAGA-AGATCTTGTTTCTTTTGTG
1 ATAGATAGATCTTGTTTCTTTTGTG
* * *
53983925 ATAGATGGTTTTTGTTTCTTTTG
1 ATAGATAGATCTTGTTTCTTTTG
53983948 GTAACACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.17, C:0.06, G:0.21, T:0.55
Consensus pattern (25 bp):
ATAGATAGATCTTGTTTCTTTTGTG
Found at i:53984250 original size:79 final size:79
Alignment explanation
Indices: 53984154--53984311 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
53984144 AAACCAACAA
*
53984154 AAATTATTAACTTTATGACCAAACACTCGTACATGAATTCATTTGCTCCAAAATCACTACTGCAT
1 AAATTATGAACTTTATGACCAAACACTCGTACATGAATTCATTTGCTCCAAAATCACTACTGCAT
53984219 GAAACCAGTTTAAT
66 GAAACCAGTTTAAT
*
53984233 AAATTATGAACTTTATGACCAAACACTCGTACATGAATTCATTTGCTCCAAAATCTCTACTGCAT
1 AAATTATGAACTTTATGACCAAACACTCGTACATGAATTCATTTGCTCCAAAATCACTACTGCAT
53984298 GAAACCAGTTTAAT
66 GAAACCAGTTTAAT
53984312 TGAGGTGCAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (79 bp):
AAATTATGAACTTTATGACCAAACACTCGTACATGAATTCATTTGCTCCAAAATCACTACTGCAT
GAAACCAGTTTAAT
Found at i:53985536 original size:3 final size:3
Alignment explanation
Indices: 53985528--53985568 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
53985518 TTCCTTATCA
* *
53985528 TCG TCG TCG TCG TCG TCG TCA TCC TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
53985569 ATGTTCTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.02, C:0.37, G:0.27, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:53985555 original size:21 final size:21
Alignment explanation
Indices: 53985525--53985570 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
53985515 ATCTTCCTTA
*
53985525 TCATCGTCGTCGTCGTCGTCG
1 TCATCCTCGTCGTCGTCGTCG
53985546 TCATCCTCGTCGTCGTCGTCG
1 TCATCCTCGTCGTCGTCGTCG
53985567 TCAT
1 TCAT
53985571 GTTCTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.07, C:0.35, G:0.24, T:0.35
Consensus pattern (21 bp):
TCATCCTCGTCGTCGTCGTCG
Found at i:53986478 original size:20 final size:20
Alignment explanation
Indices: 53986455--53986510 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
53986445 TTATAAATCT
53986455 TAAAAAGTAAAAATAAT-ATA
1 TAAAAAGTAAAAA-AATGATA
* *
53986475 TAAAAATTAAAAAAATGTTA
1 TAAAAAGTAAAAAAATGATA
*
53986495 TAAGAAGTAAAAAAAT
1 TAAAAAGTAAAAAAAT
53986511 TTTAAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (20 bp):
TAAAAAGTAAAAAAATGATA
Found at i:53986700 original size:6 final size:6
Alignment explanation
Indices: 53986671--53986727 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
53986661 TCAGTTATCA
* * *
53986671 TATTTT TCTTTT T-TTTA TATTTT TACTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
53986718 CATATTTT TA
1 --TATTTT TA
53986728 GCGTGTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 4 0.09
6 33 0.77
8 6 0.14
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:53986982 original size:24 final size:23
Alignment explanation
Indices: 53986954--53986999 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
53986944 TCAAATCGTG
* *
53986954 AATAAAACCTTTTAAATTTAAAAA
1 AATAAAACATTTCAAA-TTAAAAA
53986978 AATAAAACATTTCAAATTAAAA
1 AATAAAACATTTCAAATTAAAA
53987000 TATTGTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
AATAAAACATTTCAAATTAAAAA
Found at i:53987173 original size:18 final size:17
Alignment explanation
Indices: 53987144--53987218 Score: 78
Period size: 17 Copynumber: 4.0 Consensus size: 17
53987134 GTCCTCAAAA
53987144 TTATTATTTTAAATTTTT
1 TTATT-TTTTAAATTTTT
53987162 TTACTTTTTTAAATATATTTT
1 TTA-TTTTTT-AA-AT-TTTT
*
53987183 TTAGTTTTTTTAAATTTAT
1 TTA--TTTTTTAAATTTTT
53987202 TTATTTTTTAAATTTTT
1 TTATTTTTTAAATTTTT
53987219 AAAAATTACT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
17 13 0.27
18 7 0.14
19 10 0.20
20 4 0.08
21 9 0.18
22 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (17 bp):
TTATTTTTTAAATTTTT
Found at i:53987184 original size:22 final size:23
Alignment explanation
Indices: 53987156--53987208 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
53987146 ATTATTTTAA
53987156 ATTTTTTTA-CTTTTTTAAATAT
1 ATTTTTTTAGCTTTTTTAAATAT
* *
53987178 A-TTTTTTAGTTTTTTTAAATTT
1 ATTTTTTTAGCTTTTTTAAATAT
53987200 ATTTATTTT
1 ATTT-TTTT
53987209 TTAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 2 0.08
24 4 0.15
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
ATTTTTTTAGCTTTTTTAAATAT
Found at i:53987217 original size:26 final size:27
Alignment explanation
Indices: 53987177--53987238 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
53987167 TTTTTAAATA
** * *
53987177 TATTTTTTAGTTTTTTTAAATTTA-TT
1 TATTTTTTAAATTTTTAAAAATTACTT
53987203 TATTTTTTAAATTTTTAAAAATTACTT
1 TATTTTTTAAATTTTTAAAAATTACTT
53987230 TGATTTTTT
1 T-ATTTTTT
53987239 TTGTAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.67
27 3 0.10
28 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (27 bp):
TATTTTTTAAATTTTTAAAAATTACTT
Found at i:53989914 original size:3 final size:3
Alignment explanation
Indices: 53989908--53989933 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53989898 CGACAGTGAG
53989908 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
53989934 GGGCGTCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:53995017 original size:21 final size:21
Alignment explanation
Indices: 53994992--53995031 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53994982 AAATTTAATG
*
53994992 GAAAAGATTAATTTCAAAACA
1 GAAAAGATTAATTTAAAAACA
**
53995013 GAAAATCTTAATTTAAAAA
1 GAAAAGATTAATTTAAAAA
53995032 GTGCATTAAT
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:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (21 bp):
GAAAAGATTAATTTAAAAACA
Found at i:54003904 original size:30 final size:31
Alignment explanation
Indices: 54003868--54003941 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
54003858 AATAGCTCAA
**
54003868 TGACTTAAAT-AAAACTTTTGAATACTTCAG
1 TGACTTAAATGAAAACTTTCAAATACTTCAG
* *
54003898 TGACTTAAATGGAAACTTTCAAATATTTCAG
1 TGACTTAAATGAAAACTTTCAAATACTTCAG
**
54003929 TGACCAAAATGAA
1 TGACTTAAATGAA
54003942 GATTACCCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATACTTCAG
Found at i:54006639 original size:47 final size:49
Alignment explanation
Indices: 54006564--54006672 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 49
54006554 CATGGCAATA
* * * *
54006564 TGTGATATGTGATTTCCTTATAAGACCATATCTGGGATATGGCATCG-G
1 TGTGATATGTGACTTCCGTATAAAACCATAGCTGGGATATGGCATCGAG
* * * *
54006612 TGTGATATGTG-CTTCCGTGTAAAACCATAGCTGGGCTATGGCTTTGATG
1 TGTGATATGTGACTTCCGTATAAAACCATAGCTGGGATATGGCATCGA-G
54006661 TGTGATATGTGA
1 TGTGATATGTGA
54006673 TTATGTGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 27 0.54
48 11 0.22
49 12 0.24
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.36
Consensus pattern (49 bp):
TGTGATATGTGACTTCCGTATAAAACCATAGCTGGGATATGGCATCGAG
Found at i:54007225 original size:25 final size:25
Alignment explanation
Indices: 54007196--54007309 Score: 156
Period size: 25 Copynumber: 4.6 Consensus size: 25
54007186 GAACCTTAGT
54007196 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
54007221 ATGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
54007246 GTGCTCTCTGATTATTAGTACATCC
1 GTGCTCTCTGATTATTAGCACATCA
** *
54007271 GTGCTCTCTGATTATTAGCATGTTA
1 GTGCTCTCTGATTATTAGCACATCA
*
54007296 GTGGTCTCTGATTA
1 GTGCTCTCTGATTA
54007310 GCACATTTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:54007276 original size:50 final size:50
Alignment explanation
Indices: 54007196--54007309 Score: 174
Period size: 50 Copynumber: 2.3 Consensus size: 50
54007186 GAACCTTAGT
54007196 GTGCTCTCTGATTATTAGCACATCAATGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCAATGCTCTCTGATTATTAGCACGTCA
* ** * *
54007246 GTGCTCTCTGATTATTAGTACATCCGTGCTCTCTGATTATTAGCATGTTA
1 GTGCTCTCTGATTATTAGCACATCAATGCTCTCTGATTATTAGCACGTCA
*
54007296 GTGGTCTCTGATTA
1 GTGCTCTCTGATTA
54007310 GCACATTTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (50 bp):
GTGCTCTCTGATTATTAGCACATCAATGCTCTCTGATTATTAGCACGTCA
Found at i:54007325 original size:22 final size:25
Alignment explanation
Indices: 54007271--54007327 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
54007261 TAGTACATCC
**
54007271 GTGCTCTCTGATTATTAGCATGTTA
1 GTGCTCTCTGATTAGCAGCATGTTA
*
54007296 GTGGTCTCTGATTAGCA-CAT-TT-
1 GTGCTCTCTGATTAGCAGCATGTTA
54007318 GTGCTCTCTG
1 GTGCTCTCTG
54007328 TATAACACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 3 0.11
25 14 0.50
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (25 bp):
GTGCTCTCTGATTAGCAGCATGTTA
Found at i:54007343 original size:22 final size:24
Alignment explanation
Indices: 54007271--54007350 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 24
54007261 TAGTACATCC
**
54007271 GTGCTCTCTG-ATTATTAGCATGTTA
1 GTGCTCTCTGTATTAACA-CAT-TTA
* *
54007296 GTGGTCTCTG-ATTAGCACATTT-
1 GTGCTCTCTGTATTAACACATTTA
54007318 GTGCTCTCTGTA-TAACAC-TTTA
1 GTGCTCTCTGTATTAACACATTTA
*
54007340 GTGCTATCTGT
1 GTGCTCTCTGT
54007351 TCATTAGTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.06
22 24 0.51
23 3 0.06
24 3 0.06
25 14 0.30
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (24 bp):
GTGCTCTCTGTATTAACACATTTA
Found at i:54008532 original size:5 final size:5
Alignment explanation
Indices: 54008522--54008593 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
54008512 TGTTAAAAAA
* *
54008522 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATCATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT AT-ATT
54008568 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
54008594 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 33 0.59
6 10 0.18
7 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:54008575 original size:19 final size:19
Alignment explanation
Indices: 54008551--54008593 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
54008541 ATTATGTTTT
54008551 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
54008570 TATATTATATTATATTATA
1 TATATTATATTATATTATA
54008589 TATAT
1 TATAT
54008594 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:54008625 original size:17 final size:17
Alignment explanation
Indices: 54008603--54008636 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54008593 TACATAAAAC
*
54008603 AAAAGAAAGAATAGAAA
1 AAAAGAAAGAAAAGAAA
54008620 AAAAGAAAGAAAAGAAA
1 AAAAGAAAGAAAAGAAA
54008637 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAGAAA
Found at i:54008632 original size:9 final size:9
Alignment explanation
Indices: 54008603--54008636 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
54008593 TACATAAAAC
54008603 AAAAGAAAG
1 AAAAGAAAG
*
54008612 AATAGAAA-
1 AAAAGAAAG
54008620 AAAAGAAAG
1 AAAAGAAAG
54008629 AAAAGAAA
1 AAAAGAAA
54008637 CAGAATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:54009265 original size:29 final size:30
Alignment explanation
Indices: 54009206--54009263 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54009196 TCCGAGCCTT
*
54009206 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
54009236 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
54009264 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:54009655 original size:46 final size:44
Alignment explanation
Indices: 54009603--54009688 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
54009593 AGAACAGAAA
*
54009603 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAAGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAAGAT
*
54009649 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACA
54009689 GGAATAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
46 21 0.55
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAAGAT
Found at i:54009702 original size:44 final size:45
Alignment explanation
Indices: 54009605--54009729 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 45
54009595 AACAGAAATG
* * *
54009605 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAAGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAAGAATA
* *
54009651 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
** * * *
54009695 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
54009730 CAGGGTATTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.53
45 1 0.02
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
Found at i:54016985 original size:13 final size:13
Alignment explanation
Indices: 54016967--54016991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54016957 TACTTATTGG
54016967 TTAAACCATAAAA
1 TTAAACCATAAAA
54016980 TTAAACCATAAA
1 TTAAACCATAAA
54016992 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAACCATAAAA
Found at i:54017858 original size:30 final size:30
Alignment explanation
Indices: 54017817--54017877 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
54017807 CATGTGTAAC
54017817 TATGACGATAAACATGTGAAAATTATTCAA
1 TATGACGATAAACATGTGAAAATTATTCAA
* *
54017847 TATGGCGATAAACATGTGACAATTATTCAA
1 TATGACGATAAACATGTGAAAATTATTCAA
54017877 T
1 T
54017878 TTTACATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (30 bp):
TATGACGATAAACATGTGAAAATTATTCAA
Found at i:54018602 original size:121 final size:122
Alignment explanation
Indices: 54018387--54018632 Score: 467
Period size: 121 Copynumber: 2.0 Consensus size: 122
54018377 GCTTAGTGGT
54018387 TAAGCATGAATAGTCATCATTGGAAATTTCATGAAACATTAAGGTTAATTTTGGAAATTATCAAT
1 TAAGCATGAATAGTCATCATTGGAAATTTCATGAAACATTAAGGTTAATTTTGGAAATTATCAAT
* *
54018452 TAAAATGATATTAAATAAAATAAAGTAAAAATCCTATTAT-ATCATCAACCTCCAAA
66 TAAAATGATATTAAATAAAATAAAATAAAAATCCTATTATCATCATCAACCACCAAA
54018508 TAAGCATGAATAGTCATCATTGGAAATTTCATGAAACATTAAGGTTAATTTTGGAAATTATCAAT
1 TAAGCATGAATAGTCATCATTGGAAATTTCATGAAACATTAAGGTTAATTTTGGAAATTATCAAT
54018573 TAAAATGATATTAAATAAAATAAAATAAAAATCCTATTATCATCATCAACCACCAAA
66 TAAAATGATATTAAATAAAATAAAATAAAAATCCTATTATCATCATCAACCACCAAA
54018630 TAA
1 TAA
54018633 AATAAAATAA
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
121 104 0.85
122 18 0.15
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (122 bp):
TAAGCATGAATAGTCATCATTGGAAATTTCATGAAACATTAAGGTTAATTTTGGAAATTATCAAT
TAAAATGATATTAAATAAAATAAAATAAAAATCCTATTATCATCATCAACCACCAAA
Found at i:54020326 original size:25 final size:24
Alignment explanation
Indices: 54020298--54020349 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
54020288 TCAACTCAAC
54020298 TTATTACAACGCGAGACCACTCCCT
1 TTATTACAACGCGAGACCACT-CCT
* *
54020323 TTATTGCAACGGGAGACCACTCCT
1 TTATTACAACGCGAGACCACTCCT
54020347 TTA
1 TTA
54020350 ACTGACCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (24 bp):
TTATTACAACGCGAGACCACTCCT
Found at i:54021400 original size:28 final size:26
Alignment explanation
Indices: 54021359--54021415 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
54021349 TCACGTAATT
54021359 AATAAATTATTATATATTTAATTTTACTA
1 AATAAATTATTATATA-TT-ATTTTA-TA
*
54021388 AATACATT-TTATATATTATTTTATA
1 AATAAATTATTATATATTATTTTATA
54021413 AAT
1 AAT
54021416 GTTATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 5 0.19
26 6 0.22
27 2 0.07
28 7 0.26
29 7 0.26
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AATAAATTATTATATATTATTTTATA
Found at i:54023529 original size:17 final size:16
Alignment explanation
Indices: 54023507--54023549 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
54023497 TACTAGTTCA
54023507 ATTAATATTTTAATAT
1 ATTAATATTTTAATAT
54023523 GATTAATATTTT--TAT
1 -ATTAATATTTTAATAT
54023538 A-TAATATTTTAA
1 ATTAATATTTTAA
54023550 GGATCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 3 0.12
17 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTAATATTTTAATAT
Found at i:54027566 original size:6 final size:6
Alignment explanation
Indices: 54027555--54027581 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54027545 GTCAAACATG
54027555 GGCTTC GGCTTC GGCTTC GGCTTC GGC
1 GGCTTC GGCTTC GGCTTC GGCTTC GGC
54027582 GTTTGGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.37, T:0.30
Consensus pattern (6 bp):
GGCTTC
Found at i:54033354 original size:2 final size:2
Alignment explanation
Indices: 54033347--54033371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54033337 TGGAACTTGA
54033347 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
54033372 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54035305 original size:18 final size:18
Alignment explanation
Indices: 54035278--54035370 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
54035268 TACGACCGTT
54035278 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54035296 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
54035314 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54035332 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54035350 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
54035368 TAC
1 TAC
54035371 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:54035325 original size:36 final size:36
Alignment explanation
Indices: 54035278--54035370 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
54035268 TACGACCGTT
54035278 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
54035314 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
54035350 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
54035371 AGTAGTTGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:54050746 original size:23 final size:23
Alignment explanation
Indices: 54050717--54050762 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
54050707 GATGCCCATC
54050717 TCTCTCCCTCCACCCAAAAAATA
1 TCTCTCCCTCCACCCAAAAAATA
*
54050740 TCTCTCCCTCCACCCGAAAAATA
1 TCTCTCCCTCCACCCAAAAAATA
54050763 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.22
Consensus pattern (23 bp):
TCTCTCCCTCCACCCAAAAAATA
Found at i:54051065 original size:170 final size:170
Alignment explanation
Indices: 54050878--54051213 Score: 618
Period size: 170 Copynumber: 2.0 Consensus size: 170
54050868 AAAAACATGG
54050878 ATGTCGTTCGTCTCTCTCCCTCCATCCCTGAAACCGTTTCAAACACCCTATTTTGGTAAATAATG
1 ATGTCGTTCGTCTCTCTCCCTCCATCCCTGAAACCGTTTCAAACACCCTATTTTGGTAAATAATG
54050943 ATATTGGCATACCATTTCAGTATTTAATTTTTTAATTTGTATTATACTAGTAAAAAAGCCCACTA
66 ATATTGGCATACCATTTCAGTATTTAATTTTTTAATTTGTATTATACTAGTAAAAAAGCCCACTA
* *
54051008 TCTTATAGATTTTATTAACACCGTATGTTTTCAACACCGC
131 TCTTATAAATTTTATTAACACCGTATGTTTTAAACACCGC
*
54051048 ATGTCGTTCGTCTCTCTCCCTCCATCCCTGAAACTGTTTCAAACACCCTATTTTGGTAAATAATG
1 ATGTCGTTCGTCTCTCTCCCTCCATCCCTGAAACCGTTTCAAACACCCTATTTTGGTAAATAATG
* * *
54051113 ATATTGGCATACCATTTCAGTATTTAATTTTTTAATTTGTGTTATACTGGTAAAAAAGTCCACTA
66 ATATTGGCATACCATTTCAGTATTTAATTTTTTAATTTGTATTATACTAGTAAAAAAGCCCACTA
54051178 TCTTATAAATTTTATTAACACCGTATGTTTTAAACA
131 TCTTATAAATTTTATTAACACCGTATGTTTTAAACA
54051214 TGTCTGATCT
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 160 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (170 bp):
ATGTCGTTCGTCTCTCTCCCTCCATCCCTGAAACCGTTTCAAACACCCTATTTTGGTAAATAATG
ATATTGGCATACCATTTCAGTATTTAATTTTTTAATTTGTATTATACTAGTAAAAAAGCCCACTA
TCTTATAAATTTTATTAACACCGTATGTTTTAAACACCGC
Found at i:54052482 original size:9 final size:9
Alignment explanation
Indices: 54052464--54052503 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
54052454 TTTGGTTAAA
54052464 AATTAACCG
1 AATTAACCG
*
54052473 AATTACCCG
1 AATTAACCG
*
54052482 AATTAACCA
1 AATTAACCG
*
54052491 AATTAACCA
1 AATTAACCG
54052500 AATT
1 AATT
54052504 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:54052619 original size:5 final size:5
Alignment explanation
Indices: 54052611--54052651 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
54052601 AATTTTATGA
54052611 TTGGG TTGGG TTGGG TAATTGGG TTGGG TTGGG TTGGG TTG
1 TTGGG TTGGG TTGGG ---TTGGG TTGGG TTGGG TTGGG TTG
54052652 AATACTTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 28 0.85
8 5 0.15
ACGTcount: A:0.05, C:0.00, G:0.54, T:0.41
Consensus pattern (5 bp):
TTGGG
Found at i:54052633 original size:18 final size:18
Alignment explanation
Indices: 54052610--54052644 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54052600 TAATTTTATG
54052610 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
54052628 ATTGGGTTGGGTTGGGT
1 ATTGGGTTGGGTTGGGT
54052645 TGGGTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.51, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Done.