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 24 of 39
Found at i:3484882 original size:16 final size:16
Alignment explanation
Indices: 3484855--3484893 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
3484845 TATGTGCATG
3484855 AAAAAATAATA-TTTT
1 AAAAAATAATATTTTT
3484870 AAAAAATATATATTTTT
1 AAAAAATA-ATATTTTT
3484887 AAAAAAT
1 AAAAAAT
3484894 TATTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAAATAATATTTTT
Found at i:3484951 original size:20 final size:18
Alignment explanation
Indices: 3484928--3484966 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
3484918 AGATAAAATT
3484928 TTTTAAAAGTGGATAATTAA
1 TTTTAAAAGT-GA-AATTAA
*
3484948 TTTTTAAAGTGAAATTAA
1 TTTTAAAAGTGAAATTAA
3484966 T
1 T
3484967 AGGAAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (18 bp):
TTTTAAAAGTGAAATTAA
Found at i:3484953 original size:21 final size:18
Alignment explanation
Indices: 3484927--3484966 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
3484917 TAGATAAAAT
3484927 TTTTTAAAAGTGGATAATTAA
1 TTTTT-AAAGT-GA-AATTAA
3484948 TTTTTAAAGTGAAATTAA
1 TTTTTAAAGTGAAATTAA
3484966 T
1 T
3484967 AGGAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 5 0.26
21 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTTAAAGTGAAATTAA
Found at i:3485088 original size:19 final size:18
Alignment explanation
Indices: 3485056--3485117 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
3485046 GGGTAGTTTT
* * *
3485056 TTTTTTTAATTTGAGTAG
1 TTTTTATAAATTGAGTAA
*
3485074 TTTTTATGAAATTGA-TAT
1 TTTTTAT-AAATTGAGTAA
3485092 TTTTTAATAAA-TGAGTAA
1 TTTTT-ATAAATTGAGTAA
3485110 TTTTTATA
1 TTTTTATA
3485118 TTTTTAAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.16
18 23 0.62
19 8 0.22
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTTTATAAATTGAGTAA
Found at i:3485258 original size:34 final size:34
Alignment explanation
Indices: 3485201--3485269 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 34
3485191 AATAATTTTT
3485201 ATTATATTTAATAAATATAAAAAA-TAATAAAATA
1 ATTATATTTAATAAATATAAAAAATTAA-AAAATA
3485235 ATTATATCTTAA-AAAT-TAAAAAAATTAAAAAATA
1 ATTATAT-TTAATAAATAT-AAAAAATTAAAAAATA
3485269 A
1 A
3485270 AACATACGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 1 0.03
34 24 0.75
35 7 0.22
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (34 bp):
ATTATATTTAATAAATATAAAAAATTAAAAAATA
Found at i:3486285 original size:10 final size:10
Alignment explanation
Indices: 3486270--3486373 Score: 66
Period size: 10 Copynumber: 9.7 Consensus size: 10
3486260 AAGTATAATA
*
3486270 TTATTTATAT
1 TTATTTAAAT
3486280 TTATTTAAAT
1 TTATTTAAAT
3486290 TTAATTTAAAAT
1 TT-ATTT-AAAT
*
3486302 ATAAATTTTAAATT
1 -T-TA-TTTAAA-T
3486316 TTATTTAAAT
1 TTATTTAAAT
*
3486326 TTATTTATAT
1 TTATTTAAAT
*
3486336 TTATAAATAAA-
1 TTAT--TTAAAT
*
3486347 TAATTTAAAT
1 TTATTTAAAT
**
3486357 TCGTTTAAAT
1 TTATTTAAAT
3486367 TTATTTA
1 TTATTTA
3486374 TATTATTTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
9 4 0.05
10 38 0.52
11 13 0.18
12 8 0.11
13 6 0.08
14 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:3486880 original size:21 final size:20
Alignment explanation
Indices: 3486854--3486923 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
3486844 TAAAAATTTG
3486854 ATATATTAAAATTATAAAATA
1 ATATATTAAAATTATAAAA-A
* * *
3486875 ATATA-TCATATGAATAAAAA
1 ATATATTAAAAT-TATAAAAA
*
3486895 ATATTATTATAATTATAAAAA
1 ATA-TATTAAAATTATAAAAA
3486916 ATA-ATTAA
1 ATATATTAA
3486924 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 8 0.21
21 23 0.61
22 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
ATATATTAAAATTATAAAAA
Found at i:3487211 original size:18 final size:17
Alignment explanation
Indices: 3487188--3487221 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3487178 AATAACCCCA
3487188 AAAAGCAAAAGCAGAAGC
1 AAAAGCAAAAGC-GAAGC
*
3487206 AAAAGCGAAAGCGAAG
1 AAAAGCAAAAGCGAAG
3487222 ATGATGGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAGCAAAAGCGAAGC
Found at i:3489305 original size:148 final size:148
Alignment explanation
Indices: 3489035--3489332 Score: 443
Period size: 148 Copynumber: 2.0 Consensus size: 148
3489025 AGGTACCTAA
* * * * *
3489035 TTTCCTAAAGGATCATGAATTTAATATTTACTTTGCTTGGCTTGCTTTTTGTGTTATCGGGGATG
1 TTTCCTAAAGGATCATGAACTCAATACTTACTTGGCTTGGCTTGCTTTTTGTGTTATCGAGGATG
* * *
3489100 CCCAGTTTGGTAAATCAGAATTAGTGGAGAAACCAAAATAGCATTTGCCTTTGCTTTGTACTTAG
66 CCCAGTTTGGTAAATCAGAATTAGTGGAGAAACCAAAATAGCATTCGCCTTTACTTTGTACTTAA
3489165 CAATGCACAATCTTCTGT
131 CAATGCACAATCTTCTGT
* *
3489183 TTTCCTAAAGGATCATGAGCTCAATACTTACTTGGCTTGGCTTGCTTTTTGTGTTATTGAGGATG
1 TTTCCTAAAGGATCATGAACTCAATACTTACTTGGCTTGGCTTGCTTTTTGTGTTATCGAGGATG
* * * * *
3489248 CTCAGTTTGGTAAATCAGAGTTATTTGAGAAACCAAAATAGCATTCGCTTTTACTTTGTACTTAA
66 CCCAGTTTGGTAAATCAGAATTAGTGGAGAAACCAAAATAGCATTCGCCTTTACTTTGTACTTAA
* *
3489313 TAATGCAGAATCTTCTGT
131 CAATGCACAATCTTCTGT
3489331 TT
1 TT
3489333 AAGCAAAACC
Statistics
Matches: 133, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
148 133 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (148 bp):
TTTCCTAAAGGATCATGAACTCAATACTTACTTGGCTTGGCTTGCTTTTTGTGTTATCGAGGATG
CCCAGTTTGGTAAATCAGAATTAGTGGAGAAACCAAAATAGCATTCGCCTTTACTTTGTACTTAA
CAATGCACAATCTTCTGT
Found at i:3495226 original size:2 final size:2
Alignment explanation
Indices: 3495219--3495256 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3495209 TCAGATGTGC
3495219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3495257 CATACAGCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3495411 original size:17 final size:17
Alignment explanation
Indices: 3495389--3495422 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3495379 CTAAAGTAAA
3495389 TGATATAAATATATATT
1 TGATATAAATATATATT
3495406 TGATATAAATATATATT
1 TGATATAAATATATATT
3495423 AAATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TGATATAAATATATATT
Found at i:3497341 original size:14 final size:14
Alignment explanation
Indices: 3497322--3497348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3497312 AAAAAATAAT
3497322 ATATTTAATTTTTC
1 ATATTTAATTTTTC
3497336 ATATTTAATTTTT
1 ATATTTAATTTTT
3497349 TTAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTAATTTTTC
Found at i:3500795 original size:14 final size:13
Alignment explanation
Indices: 3500767--3500814 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
3500757 TAAATAAGAT
*
3500767 TATTAT-TTAATA
1 TATTATATTAAAA
3500779 TATTATGATTAAAA
1 TATTAT-ATTAAAA
*
3500793 TATTATTTTAAAA
1 TATTATATTAAAA
3500806 TATATATAT
1 TAT-TATAT
3500815 ATATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 6 0.20
13 9 0.30
14 15 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATTATATTAAAA
Found at i:3500928 original size:17 final size:18
Alignment explanation
Indices: 3500902--3500935 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3500892 ATAATATTAC
*
3500902 TATAATAAAA-TAAATTT
1 TATAAAAAAATTAAATTT
3500919 TATAAAAAAATTAAATT
1 TATAAAAAAATTAAATT
3500936 AATAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAAAAAATTAAATTT
Found at i:3501151 original size:22 final size:22
Alignment explanation
Indices: 3501110--3501151 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3501100 ACATTCAAAC
*
3501110 TTTAAAAAATAATATCTATTAT
1 TTTAAAAAATAATATATATTAT
3501132 TTTAAATAAATAA-ATATATT
1 TTTAAA-AAATAATATATATT
3501152 TCCACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAAAATAATATATATTAT
Found at i:3501841 original size:15 final size:17
Alignment explanation
Indices: 3501801--3501842 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
3501791 TGAAGCATAT
*
3501801 AATATTTTTATTGTTGA
1 AATATTTTTATTGTTAA
*
3501818 AATAATTTTA-TG-TAA
1 AATATTTTTATTGTTAA
3501833 AATATTTTTA
1 AATATTTTTA
3501843 ATTATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 11 0.50
16 2 0.09
17 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
AATATTTTTATTGTTAA
Found at i:3502128 original size:28 final size:25
Alignment explanation
Indices: 3502097--3502162 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 25
3502087 AATATTTTTA
3502097 AAAAATTATTTTTTGTCAAACAAAATAT
1 AAAAATTATTTTTT-TCAAA-AAAAT-T
*
3502125 AAAAATT-TTTGTCTTTGAAAAAAATT
1 AAAAATTATTT-T-TTTCAAAAAAATT
3502151 AAAAA-TATTTTT
1 AAAAATTATTTTT
3502163 CAAGGTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 9 0.26
27 8 0.24
28 12 0.35
29 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (25 bp):
AAAAATTATTTTTTTCAAAAAAATT
Found at i:3502321 original size:2 final size:2
Alignment explanation
Indices: 3502314--3502341 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3502304 AACCGGCCAA
3502314 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
3502342 CTCTTAAAAT
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:3502820 original size:23 final size:23
Alignment explanation
Indices: 3502774--3502827 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3502764 ATAAAATTAT
*
3502774 AATAAAAT-ATTAATTTTATAAA
1 AATAAAATAATTAATTTAATAAA
3502796 AATAAAATAATTTAATTTAAT-AA
1 AATAAAATAA-TTAATTTAATAAA
3502819 AATAAAATA
1 AATAAAATA
3502828 TTATGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.28
23 12 0.41
24 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAAATAATTAATTTAATAAA
Found at i:3504088 original size:18 final size:19
Alignment explanation
Indices: 3504065--3504113 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3504055 GATAATTTTA
3504065 AATATAATATAAAAT-TAT
1 AATATAATATAAAATGTAT
* *
3504083 AATATAAATATAAGATGTTT
1 AATAT-AATATAAAATGTAT
3504103 AATA-AATATAA
1 AATATAATATAA
3504114 TATATCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 6 0.22
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
AATATAATATAAAATGTAT
Found at i:3507666 original size:17 final size:19
Alignment explanation
Indices: 3507632--3507666 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3507622 ATATATAATA
3507632 TAATATGATACAAATATTT
1 TAATATGATACAAATATTT
3507651 TAATAT-ATAC-AATATT
1 TAATATGATACAAATATT
3507667 AATATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (19 bp):
TAATATGATACAAATATTT
Found at i:3508727 original size:17 final size:17
Alignment explanation
Indices: 3508678--3508739 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
3508668 TTATTATTTT
*
3508678 TTATTAATTATA-TAAA
1 TTATTAAATATATTAAA
3508694 -TATTAACATA-ATATAAA
1 TTATTAA-ATATAT-TAAA
3508711 TTATTAAATATATTAAAA
1 TTATTAAATATATT-AAA
3508729 TT-TTAAATATA
1 TTATTAAATATA
3508740 AATATATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 7 0.18
16 2 0.05
17 17 0.44
18 13 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATTAAATATATTAAA
Found at i:3509144 original size:18 final size:19
Alignment explanation
Indices: 3509116--3509166 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
3509106 TTTAATATAA
*
3509116 ATTATTAAAATATTAAAAT
1 ATTATAAAAATATTAAAAT
*
3509135 -TTATATAAATA-TAAAAT
1 ATTATAAAAATATTAAAAT
*
3509152 ATTTTAAAAATATTA
1 ATTATAAAAATATTA
3509167 TGATATAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
18 18 0.69
19 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTATAAAAATATTAAAAT
Found at i:3510666 original size:2 final size:2
Alignment explanation
Indices: 3510659--3510687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3510649 AGCCTTTATT
3510659 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 T
3510688 TTAAATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3511504 original size:16 final size:15
Alignment explanation
Indices: 3511458--3511517 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
3511448 AATTTTCTTT
3511458 AGAAAAAA--AAAAA
1 AGAAAAAAGGAAAAA
*
3511471 AG-AAAAAGAAAGAGAA
1 AGAAAAAAGGAA-A-AA
*
3511487 AGAAAGGAAGGAAAAA
1 AGAAA-AAAGGAAAAA
3511503 AGAAAAAAGGAAAAA
1 AGAAAAAAGGAAAAA
3511518 TTTATGCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 5 0.13
13 2 0.05
14 2 0.05
15 10 0.26
16 11 0.29
17 3 0.08
18 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGGAAAAA
Found at i:3512085 original size:17 final size:17
Alignment explanation
Indices: 3512050--3512098 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
3512040 CTATTAAGTA
*
3512050 AAATATATATT-TTTATT
1 AAATATTTATTATTT-TT
3512067 AAATATTTATTATTTTT
1 AAATATTTATTATTTTT
3512084 -AATATTTATTATTTT
1 AAATATTTATTATTTT
3512099 AATATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 15 0.50
17 12 0.40
18 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATATTTATTATTTTT
Found at i:3512089 original size:16 final size:15
Alignment explanation
Indices: 3512056--3512103 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
3512046 AGTAAAATAT
*
3512056 ATATTT-TTA-TTAA
1 ATATTTATTATTTTA
3512069 ATATTTATTATTTTTA
1 ATATTTATTA-TTTTA
3512085 ATATTTATTATTTTA
1 ATATTTATTATTTTA
3512100 ATAT
1 ATAT
3512104 AATTAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 6 0.19
14 3 0.10
15 9 0.29
16 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTATTATTTTA
Found at i:3512505 original size:27 final size:26
Alignment explanation
Indices: 3512453--3512517 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
3512443 TCGATATTTA
*
3512453 ATTTAATTAATTAATAAGTTTAATTAAT
1 ATTTAA-TAATTAATAAATTTAATT-AT
*
3512481 ATTTAATAATT-TTAAATTTATATTAT
1 ATTTAATAATTAATAAATTTA-ATTAT
3512507 ATTTTAATAAT
1 A-TTTAATAAT
3512518 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 10 0.30
27 17 0.52
28 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTAATAATTAATAAATTTAATTAT
Found at i:3512589 original size:2 final size:2
Alignment explanation
Indices: 3512582--3512608 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3512572 ATCCCTTCAT
3512582 TC 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 TC T
3512609 GCGCTCATTT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3516708 original size:28 final size:27
Alignment explanation
Indices: 3516668--3516722 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3516658 TTGGGTTGAT
3516668 TCCACAATCAGATA-CTATAGATTTATAA
1 TCCACAATCAGATATC-ATAGA-TTATAA
*
3516696 TCCACGATCAGATATCATAGATTATAA
1 TCCACAATCAGATATCATAGATTATAA
3516723 CTTTGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 18 0.72
29 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
TCCACAATCAGATATCATAGATTATAA
Found at i:3520465 original size:2 final size:2
Alignment explanation
Indices: 3520458--3520489 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3520448 TGCTTTGATA
3520458 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
3520490 GCATATTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3520597 original size:18 final size:18
Alignment explanation
Indices: 3520574--3520614 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3520564 AACAAATTAT
*
3520574 TGATTATATAATAATAAA
1 TGATTATATAAGAATAAA
3520592 TGATTATATAAGAATAAA
1 TGATTATATAAGAATAAA
3520610 TGATT
1 TGATT
3520615 GGTACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
TGATTATATAAGAATAAA
Found at i:3521354 original size:2 final size:2
Alignment explanation
Indices: 3521349--3521377 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3521339 ACTAGTGTAC
3521349 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
3521378 CTGGAAGTTT
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:3521456 original size:28 final size:27
Alignment explanation
Indices: 3521387--3521456 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
3521377 ACTGGAAGTT
* *
3521387 TTTTTTCAATAAGTTGTAAATATATTA
1 TTTTTTAAATAATTTGTAAATATATTA
* * * *
3521414 TTTGTTGATTAAATTTGTAAATTTATTA
1 TTTTTTAAAT-AATTTGTAAATATATTA
3521442 TATTTTTAAATAATT
1 T-TTTTTAAATAATT
3521457 GCAGGAATCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
27 7 0.21
28 20 0.61
29 6 0.18
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (27 bp):
TTTTTTAAATAATTTGTAAATATATTA
Found at i:3523947 original size:22 final size:23
Alignment explanation
Indices: 3523892--3523955 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
3523882 TTATAATTAC
3523892 TTTAA-TTATAAAAATTTAAAAT
1 TTTAATTTATAAAAATTTAAAAT
* *
3523914 TTTTATAATATAAATAA-TTAAAA-
1 TTTAAT-TTATAAA-AATTTAAAAT
3523937 TTTAATTTATATAAAATTT
1 TTTAATTTATA-AAAATTT
3523956 TTAATTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAATTTATAAAAATTTAAAAT
Found at i:3527432 original size:7 final size:7
Alignment explanation
Indices: 3527420--3527454 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
3527410 ATGTTTATAT
3527420 TTGAATA
1 TTGAATA
3527427 TTGAATA
1 TTGAATA
3527434 TTGAATA
1 TTGAATA
3527441 TTGAATA
1 TTGAATA
3527448 TTGAATA
1 TTGAATA
3527455 GAGTATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TTGAATA
Found at i:3527504 original size:12 final size:12
Alignment explanation
Indices: 3527479--3527521 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
3527469 AATAAATATG
3527479 TTTA-ATTTTT-
1 TTTATATTTTTC
3527489 TTTATATTTTTC
1 TTTATATTTTTC
*
3527501 TTTATTTTTTTC
1 TTTATATTTTTC
3527513 TTTATATTT
1 TTTATATTT
3527522 GAAGGATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 4 0.14
11 6 0.21
12 19 0.66
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATATTTTTC
Found at i:3529164 original size:2 final size:2
Alignment explanation
Indices: 3529157--3529185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3529147 CGATATTTTG
3529157 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 T
3529186 TTGTGTGTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3529761 original size:18 final size:18
Alignment explanation
Indices: 3529740--3529782 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3529730 AAAAAGTAAG
3529740 ATTTTAATTT-TTTTCAAT
1 ATTTTAATTTATTTT-AAT
* *
3529758 ATTTGAATTTATTTTATT
1 ATTTTAATTTATTTTAAT
3529776 ATTTTAA
1 ATTTTAA
3529783 CTTGGCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTATTTTAAT
Found at i:3536960 original size:69 final size:67
Alignment explanation
Indices: 3536852--3536985 Score: 241
Period size: 69 Copynumber: 2.0 Consensus size: 67
3536842 GGCTCTCTAC
*
3536852 AATAAAATAAAGTGTGCAGTAGTAGTATGTGAGTAGTAGAGAGTGTGTGTGCAAAAAGTCAAGAG
1 AATAAAATAAAGTGTGCAGTAGTAATATGTGAGTAGTAGAGA--GTGTGTGCAAAAAGTCAAGAG
3536917 TTAA
64 TTAA
3536921 AATAAAATAAAGTGTGCAGTAGTAATATGTGAGTAGTAGAGAGTGTGTGCAAAAAGTCAAGAGTT
1 AATAAAATAAAGTGTGCAGTAGTAATATGTGAGTAGTAGAGAGTGTGTGCAAAAAGTCAAGAGTT
3536986 TGTATGAGGT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 23 0.36
69 41 0.64
ACGTcount: A:0.41, C:0.04, G:0.28, T:0.26
Consensus pattern (67 bp):
AATAAAATAAAGTGTGCAGTAGTAATATGTGAGTAGTAGAGAGTGTGTGCAAAAAGTCAAGAGTT
AA
Found at i:3537754 original size:14 final size:14
Alignment explanation
Indices: 3537706--3537755 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3537696 AAAACATAAA
3537706 AATATTAAA-TAATT
1 AATA-TAAATTAATT
* *
3537720 -ATATAATTTAATA
1 AATATAAATTAATT
3537733 AATATAAATTAATT
1 AATATAAATTAATT
*
3537747 AATTTAAAT
1 AATATAAAT
3537756 ATATCTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 3 0.10
13 7 0.24
14 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAAATTAATT
Found at i:3537964 original size:20 final size:22
Alignment explanation
Indices: 3537939--3537985 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3537929 TAAATATATT
3537939 TAAATTT-A-ATTTTAAAAATA
1 TAAATTTAATATTTTAAAAATA
*
3537959 TAAATTTAATATTTTAATAATA
1 TAAATTTAATATTTTAAAAATA
3537981 TAAAT
1 TAAAT
3537986 AAATAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTTAATATTTTAAAAATA
Found at i:3538351 original size:14 final size:15
Alignment explanation
Indices: 3538332--3538360 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3538322 TATTAAATGT
3538332 TTAATTTTTT-AAAA
1 TTAATTTTTTCAAAA
3538346 TTAATTTTTTCAAAA
1 TTAATTTTTTCAAAA
3538361 ATGTTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTTTTCAAAA
Found at i:3543445 original size:27 final size:28
Alignment explanation
Indices: 3543400--3543452 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
3543390 AAAATTAAAA
3543400 TATATTAAATAATTATATT-TATTTTAT
1 TATATTAAATAATTATATTATATTTTAT
*
3543427 TATATTAATTAAATT-TATTATATTTT
1 TATATTAAAT-AATTATATTATATTTT
3543453 TTCCTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TATATTAAATAATTATATTATATTTTAT
Found at i:3544762 original size:17 final size:17
Alignment explanation
Indices: 3544736--3544770 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3544726 ATATACTATG
*
3544736 TAAATTAGATAATATCA
1 TAAATCAGATAATATCA
*
3544753 TAAATCAGATGATATCA
1 TAAATCAGATAATATCA
3544770 T
1 T
3544771 CTTATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (17 bp):
TAAATCAGATAATATCA
Found at i:3544934 original size:2 final size:2
Alignment explanation
Indices: 3544927--3544975 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3544917 TTAAATTTAC
3544927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3544969 TA TA TA T
1 TA TA TA T
3544976 GCAGGTATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3545361 original size:17 final size:17
Alignment explanation
Indices: 3545341--3545374 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3545331 AATATTATCA
3545341 GTTAAATATTTGAATTC
1 GTTAAATATTTGAATTC
3545358 GTTAAATATTTGAATTC
1 GTTAAATATTTGAATTC
3545375 AATTTATAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (17 bp):
GTTAAATATTTGAATTC
Found at i:3547752 original size:22 final size:23
Alignment explanation
Indices: 3547713--3547755 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3547703 TCTAATCAAA
**
3547713 TTTTTATTTTATTTTTAATATAT
1 TTTTTATTTTATAATTAATATAT
3547736 TTTTTATTTTA-AATTAATAT
1 TTTTTATTTTATAATTAATAT
3547756 TGAACAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTATTTTATAATTAATATAT
Found at i:3555393 original size:2 final size:2
Alignment explanation
Indices: 3555388--3555442 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3555378 TAGATGTGTG
3555388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3555430 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3555443 GAGTTTAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3565665 original size:25 final size:26
Alignment explanation
Indices: 3565637--3565686 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3565627 TTTAGATATT
* *
3565637 CGTATCGTA-TTTATATTTTTTTTAC
1 CGTATCATATTTTATATTATTTTTAC
3565662 CGTATCATATTTTATATTATTTTTA
1 CGTATCATATTTTATATTATTTTTA
3565687 ATTTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (26 bp):
CGTATCATATTTTATATTATTTTTAC
Found at i:3566080 original size:19 final size:20
Alignment explanation
Indices: 3566056--3566094 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3566046 CATATTTAAA
*
3566056 TTATTAAAT-TATTTATATT
1 TTATTAAATATATTCATATT
3566075 TTATTAAATATATTCATATT
1 TTATTAAATATATTCATATT
3566095 GGTCCCGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTAAATATATTCATATT
Found at i:3566490 original size:33 final size:31
Alignment explanation
Indices: 3566398--3566490 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 31
3566388 TGATATAAAA
* *
3566398 ATAATATTAAATATATAAATATTTTAAAATTTT
1 ATAA-ATTAAATATATTAATA-ATTAAAATTTT
* *
3566431 ATATAATATGAAT-TATTAATGTATTAAAATTTAT
1 ATA-AAT-TAAATATATTAAT-AATTAAAATTT-T
3566465 ATAAATTAAATATAATTAATAATTAA
1 ATAAATTAAATAT-ATTAATAATTAA
3566491 TAAAAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
32 4 0.08
33 29 0.60
34 15 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (31 bp):
ATAAATTAAATATATTAATAATTAAAATTTT
Found at i:3566808 original size:14 final size:14
Alignment explanation
Indices: 3566789--3566849 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
3566779 GGATTTTAAT
3566789 TTTAAAATATTA-GA
1 TTTAAAAT-TTATGA
3566803 TTTAAAATTTATGA
1 TTTAAAATTTATGA
* *
3566817 TTTCCAAATTCATGAA
1 TTT-AAAATTTATG-A
*
3566833 TTTAAAATTTATTA
1 TTTAAAATTTATGA
3566847 TTT
1 TTT
3566850 GGATAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.08
14 17 0.44
15 15 0.38
16 4 0.10
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TTTAAAATTTATGA
Found at i:3567082 original size:19 final size:20
Alignment explanation
Indices: 3567048--3567092 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3567038 ATAAAATTTT
3567048 TAAATTTATAAATTTAAATA
1 TAAATTTATAAATTTAAATA
* *
3567068 TAAATTT-TTAATTTAAATT
1 TAAATTTATAAATTTAAATA
3567087 TAAATT
1 TAAATT
3567093 GTCGAACGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATTTATAAATTTAAATA
Found at i:3567090 original size:25 final size:25
Alignment explanation
Indices: 3567011--3567091 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
3567001 ATCCAAATCC
* * *
3567011 AAATAT-AATTTTTTATTTGATATTC
1 AAATATAAATTTTTAATTT-AAATTT
3567036 AAATA-AAATTTTTAAATTTATAAATTT
1 AAATATAAATTTTT-AA-TT-TAAATTT
3567063 AAATATAAATTTTTAATTTAAATTT
1 AAATATAAATTTTTAATTTAAATTT
3567088 AAAT
1 AAAT
3567092 TGTCGAACGG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 23 0.48
26 3 0.06
27 13 0.27
28 9 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
AAATATAAATTTTTAATTTAAATTT
Found at i:3571543 original size:21 final size:21
Alignment explanation
Indices: 3571518--3571566 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3571508 AAATTTTATT
3571518 TTATTTTATTTAT-TTTTAAAA
1 TTATTTT-TTTATGTTTTAAAA
*
3571539 TTATTATTTTATGTTTTAAAA
1 TTATTTTTTTATGTTTTAAAA
3571560 -TATTTTT
1 TTATTTTT
3571567 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTTTTATGTTTTAAAA
Found at i:3571549 original size:20 final size:18
Alignment explanation
Indices: 3571526--3571575 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
3571516 TTTTATTTTA
3571526 TTTATTTTTAAAATTATTAT
1 TTTATTTTTAAAA-TATT-T
3571546 TTTATGTTTTAAAATATTT
1 TTTAT-TTTTAAAATATTT
*
3571565 TTAATTTTTAA
1 TTTATTTTTAA
3571576 TTTTTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 9 0.32
21 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATTTTTAAAATATTT
Found at i:3580340 original size:5 final size:5
Alignment explanation
Indices: 3580332--3580372 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
3580322 ATTTAATAAT
*
3580332 TTATA TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TT
3580373 TAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 21 0.68
6 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:3580346 original size:11 final size:11
Alignment explanation
Indices: 3580330--3580393 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
3580320 AAATTTAATA
3580330 ATTTATATTAT
1 ATTTATATTAT
3580341 A-TT-TA-TAT
1 ATTTATATTAT
3580349 ATTT-TATTAT
1 ATTTATATTAT
3580359 A-TTATAATTAT
1 ATTTAT-ATTAT
* *
3580370 ATTTAAAATAT
1 ATTTATATTAT
3580381 -TTTATATTTAT
1 ATTTATA-TTAT
3580392 AT
1 AT
3580394 AATTTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
8 4 0.10
9 8 0.19
10 12 0.29
11 14 0.33
12 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3580358 original size:18 final size:19
Alignment explanation
Indices: 3580317--3580424 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 19
3580307 ATTTAAAAAA
*
3580317 ATTAAATTTAATAATTTAT
1 ATTATATTTAATAATTTAT
3580336 ATTATATTT-ATATATTT-T
1 ATTATATTTAATA-ATTTAT
3580354 ATTATATTATAATTATATTTAAAAT
1 ATTATATT-TAA-TA-ATTT---AT
3580379 ATTTTATATTTATATAATTT-T
1 A--TTATATTTA-ATAATTTAT
* *
3580400 AATATA-TTAATAATTAAT
1 ATTATATTTAATAATTTAT
3580418 ATTATAT
1 ATTATAT
3580425 AAATTTTAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
17 6 0.08
18 21 0.29
19 17 0.24
20 1 0.01
21 9 0.12
25 6 0.08
26 4 0.06
27 8 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATATTTAATAATTTAT
Found at i:3580397 original size:30 final size:29
Alignment explanation
Indices: 3580332--3580392 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
3580322 ATTTAATAAT
*
3580332 TTAT-ATTATATTTATATATTTTATTATA
1 TTATAATTATATTTAAATATTTTATTATA
3580360 TTATAATTATATTTAAAATATTTTA-TAT-
1 TTATAATTATATTT-AAATATTTTATTATA
3580388 TTATA
1 TTATA
3580393 TAATTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.30
29 12 0.40
30 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTATAATTATATTTAAATATTTTATTATA
Found at i:3582117 original size:16 final size:16
Alignment explanation
Indices: 3582069--3582167 Score: 76
Period size: 16 Copynumber: 6.2 Consensus size: 16
3582059 CGTGTTAAAG
*
3582069 TTTTAAATTTGACA-TA
1 TTTTAAATTT-AAATTA
* **
3582085 TTTTAAGTTCGAATTA
1 TTTTAAATTTAAATTA
* *
3582101 TTTTAGATTTAAGTTA
1 TTTTAAATTTAAATTA
* * * *
3582117 -TTTGAATCTAGATAA
1 TTTTAAATTTAAATTA
*
3582132 TTTTAAATTTAAATAA
1 TTTTAAATTTAAATTA
3582148 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
3582164 TTTT
1 TTTT
3582168 CATATTTAAT
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
15 10 0.16
16 52 0.84
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:3583162 original size:23 final size:22
Alignment explanation
Indices: 3583136--3583219 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 22
3583126 ATGAGATATA
3583136 ATAATTAAATTATTTTATTAAT
1 ATAATTAAATTATTTTATTAAT
*
3583158 AATAA--AAA-TA--TTAATAAT
1 -ATAATTAAATTATTTTATTAAT
3583176 ATAATATAATATATATTTTATATAAT
1 ATAAT-TAA-AT-TATTTTAT-TAAT
* *
3583202 ATATTTAAAATATTTTAT
1 ATAATTAAATTATTTTAT
3583220 ATTTATTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
17 4 0.08
18 7 0.15
20 4 0.08
21 4 0.08
23 14 0.29
24 1 0.02
25 6 0.12
26 8 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTAAATTATTTTATTAAT
Found at i:3583220 original size:23 final size:21
Alignment explanation
Indices: 3583131--3583221 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 21
3583121 GGTGAATGAG
*
3583131 ATATAATAATTAAATTATTTT
1 ATATAATAATTAAAATATTTT
* *
3583152 AT-TAATAATAAAAATA-TTA
1 ATATAATAATTAAAATATTTT
3583171 ATA-ATATAATATAATATATATTTT
1 ATATA-ATAAT-TAA-A-ATATTTT
3583195 ATATAATATATTTAAAATATTTT
1 ATATAATA-A-TTAAAATATTTT
3583218 ATAT
1 ATAT
3583222 TTATTATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.09
20 17 0.30
21 4 0.07
22 1 0.02
23 14 0.25
24 9 0.16
25 5 0.09
26 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAATAATTAAAATATTTT
Found at i:3583303 original size:28 final size:28
Alignment explanation
Indices: 3583185--3583306 Score: 76
Period size: 28 Copynumber: 4.3 Consensus size: 28
3583175 TATAATATAA
*
3583185 TATATATTTTATATAATATATTTAAAATATT
1 TATATA-TTTATAT--TATATTTAAATTATT
*
3583216 T-TATATTTATTATTA-ATTTTAATATATT
1 TATATATTTA-TATTATATTTAAAT-TATT
* * *
3583244 AATA-ATTTATGTTATA--AAAATT-TT
1 TATATATTTATATTATATTTAAATTATT
*
3583268 TAAAATATATTTATATTATATTTTAATTATT
1 T---ATATATTTATATTATATTTAAATTATT
3583299 TATATATT
1 TATATATT
3583307 ATTATAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 25
0.67 0.10 0.24
Matches are distributed among these distances:
24 2 0.03
25 1 0.01
26 3 0.04
27 13 0.19
28 30 0.43
29 6 0.09
30 11 0.16
31 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TATATATTTATATTATATTTAAATTATT
Found at i:3583652 original size:2 final size:2
Alignment explanation
Indices: 3583642--3583688 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3583632 ACACACTGTA
*
3583642 CT CT TT 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 CT CT CT
3583684 CT CT C
1 CT CT C
3583689 ATTAGTTTTC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3586886 original size:37 final size:37
Alignment explanation
Indices: 3586836--3586911 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
3586826 GTACTAGCGA
3586836 TTGAAATAAATTATATTATTTTTCAAACTGTAACCTT
1 TTGAAATAAATTATATTATTTTTCAAACTGTAACCTT
3586873 TTGAAATAAATTATATTATTTTTCAAACTGTAACCTT
1 TTGAAATAAATTATATTATTTTTCAAACTGTAACCTT
3586910 TT
1 TT
3586912 TTTCATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (37 bp):
TTGAAATAAATTATATTATTTTTCAAACTGTAACCTT
Found at i:3588850 original size:27 final size:27
Alignment explanation
Indices: 3588812--3588863 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3588802 GGTGTTTATC
* **
3588812 GATTGTGTTATCGGTTTAATTTGTAAA
1 GATTGAGTTATCAATTTAATTTGTAAA
3588839 GATTGAGTTATCAATTTAATTTGTA
1 GATTGAGTTATCAATTTAATTTGTA
3588864 TTAATTAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.19, T:0.48
Consensus pattern (27 bp):
GATTGAGTTATCAATTTAATTTGTAAA
Found at i:3588895 original size:100 final size:100
Alignment explanation
Indices: 3588719--3588906 Score: 236
Period size: 100 Copynumber: 1.9 Consensus size: 100
3588709 AAAGATTGGA
* * *
3588719 TTATCGGTTTCATTCGTAAAGATTAAGTTATCAGTTTAATTCATATTAATCGAGATTTGATCAAA
1 TTATCGGTTTAATTCGTAAAGATTAAGTTATCAATTTAATTCATATTAATAGAGATTTGATCAAA
3588784 GGTTTTCAAATTT-GAACAGGTGTTTATCGATTGTG
66 GGTTTTCAAATTTAG-ACAGGTGTTTATCGATTGTG
* * ** **
3588819 TTATCGGTTTAATTTGTAAAGATTGAGTTATCAATTTAATTTGTATTAATTAG-GATTTGATTGA
1 TTATCGGTTTAATTCGTAAAGATTAAGTTATCAATTTAATTCATATTAA-TAGAGATTTGATCAA
** *
3588883 ATTTTTTTAAATTTAGACAGGTGT
65 AGGTTTTCAAATTTAGACAGGTGT
3588907 AGTTTTATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
100 71 0.96
101 3 0.04
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (100 bp):
TTATCGGTTTAATTCGTAAAGATTAAGTTATCAATTTAATTCATATTAATAGAGATTTGATCAAA
GGTTTTCAAATTTAGACAGGTGTTTATCGATTGTG
Found at i:3592649 original size:20 final size:19
Alignment explanation
Indices: 3592615--3592659 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
3592605 TTTAATTTAA
*
3592615 TTAATTAATATAATTAATT
1 TTAAATAATATAATTAATT
3592634 TTAAATAATAATAATTAATT
1 TTAAATAAT-ATAATTAATT
3592654 TTAAAT
1 TTAAAT
3592660 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAATAATATAATTAATT
Found at i:3595658 original size:38 final size:37
Alignment explanation
Indices: 3595600--3595684 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 37
3595590 TTATGATATG
3595600 AATATAATAT-ATTTAATAAATATAAAAATAATAAAA
1 AATATAATATAATTTAATAAATATAAAAATAATAAAA
* **
3595636 AATATAATATAATTTATTTAAATATAATTATAATAAAA
1 AATATAATATAATTTA-ATAAATATAAAAATAATAAAA
* *
3595674 TATTTAATATA
1 AATATAATATA
3595685 CATATTTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 10 0.24
37 5 0.12
38 27 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (37 bp):
AATATAATATAATTTAATAAATATAAAAATAATAAAA
Found at i:3595829 original size:2 final size:2
Alignment explanation
Indices: 3595824--3595859 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3595814 TCTGCTTACA
*
3595824 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3595860 TCATGCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3597417 original size:31 final size:31
Alignment explanation
Indices: 3597359--3597419 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3597349 TATTTTATAT
* *
3597359 TAATATTTATATTTTTATAATTAAATTTAAA
1 TAATATTTATATTATTATAAGTAAATTTAAA
*
3597390 TAATATTTTTATTATTATATAGT-AATTTAA
1 TAATATTTATATTATTATA-AGTAAATTTAA
3597420 GTTAAATCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TAATATTTATATTATTATAAGTAAATTTAAA
Found at i:3598285 original size:21 final size:21
Alignment explanation
Indices: 3598259--3598298 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3598249 ATTGAAAATA
3598259 ATTATAA-ATATAAAATTAATT
1 ATTATAATA-ATAAAATTAATT
3598280 ATTATAATAATAAAATTAA
1 ATTATAATAATAAAATTAA
3598299 ATAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATAATAATAAAATTAATT
Found at i:3598477 original size:24 final size:24
Alignment explanation
Indices: 3598444--3598500 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
3598434 AATAATTAAA
*
3598444 AATTATTAAAAATATATTTAAATT
1 AATTAATAAAAATATATTTAAATT
*
3598468 AATTAATAAAATTATATTTAAATT
1 AATTAATAAAAATATATTTAAATT
*
3598492 AAATAATAA
1 AATTAATAA
3598501 TTAATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTAATAAAAATATATTTAAATT
Found at i:3598521 original size:35 final size:32
Alignment explanation
Indices: 3598463--3598546 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 32
3598453 AAATATATTT
3598463 AAAT-TAATTAATAAA-ATTATATTTAAATT-
1 AAATATAATTAATAAATATTATATTTAAATTA
*
3598492 AAATAATAATTAATAAATTATTTATTATTTATATTA
1 AAAT-ATAATTAATAAA-TA-TTA-TATTTAAATTA
3598528 AAATATAATTTAATAAATA
1 AAATATAA-TTAATAAATA
3598547 ATAAATAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
29 4 0.09
31 11 0.24
33 1 0.02
34 3 0.07
35 15 0.33
36 12 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATATAATTAATAAATATTATATTTAAATTA
Found at i:3598530 original size:52 final size:50
Alignment explanation
Indices: 3598436--3598556 Score: 126
Period size: 52 Copynumber: 2.4 Consensus size: 50
3598426 GACTGATAAA
*
3598436 TAATTAAA-AATTATTAAAAATATATTTAAATTAATTAATAAAAT-TATATT
1 TAATTAAATAATAATTAAAAATATATTT-AATTAATTAATAAAATATA-ATT
*
3598486 TAAATTAAATAATAATTAATAAAT-TATTT-ATTATTTATATTAAAATATAATT
1 T-AATTAAATAATAATTAA-AAATATATTTAATTAATTA-A-TAAAATATAATT
*
3598538 TAA-TAAATAATAAATAAAA
1 TAATTAAATAATAATTAAAA
3598557 GGGGGGTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
49 2 0.03
50 21 0.34
51 10 0.16
52 23 0.37
53 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (50 bp):
TAATTAAATAATAATTAAAAATATATTTAATTAATTAATAAAATATAATT
Found at i:3598803 original size:20 final size:20
Alignment explanation
Indices: 3598778--3598849 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
3598768 TTATTTTTAA
3598778 TTATATAATATAAATTATAT
1 TTATATAATATAAATTATAT
* * *
3598798 TTATATGATGTAATTTATA-
1 TTATATAATATAAATTATAT
*
3598817 TCATATAA-A-AAATTA-AT
1 TTATATAATATAAATTATAT
*
3598834 ATATTATAATATAAAT
1 TTA-TATAATATAAAT
3598850 ATTAAAATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
16 1 0.03
17 6 0.15
18 5 0.13
19 7 0.18
20 20 0.51
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATATAATATAAATTATAT
Found at i:3599179 original size:14 final size:13
Alignment explanation
Indices: 3599154--3599193 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3599144 AAAAAATAAT
3599154 AAATATAATATTA
1 AAATATAATATTA
*
3599167 TAATATAAGTATTA
1 AAATATAA-TATTA
3599181 AAATAT-ATATTA
1 AAATATAATATTA
3599193 A
1 A
3599194 GTTTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 8 0.33
14 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
AAATATAATATTA
Found at i:3599240 original size:26 final size:26
Alignment explanation
Indices: 3599204--3599256 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3599194 GTTTATTTAT
*
3599204 ATTTTAAAATTTAATAAAAATATTAA
1 ATTTTAAAATTTAATAAAAAAATTAA
* **
3599230 ATTTTTAAATTTTTTAAAAAAATTAA
1 ATTTTAAAATTTAATAAAAAAATTAA
3599256 A
1 A
3599257 AATATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTAAAATTTAATAAAAAAATTAA
Found at i:3600098 original size:24 final size:24
Alignment explanation
Indices: 3600071--3600116 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3600061 AAATTATTTT
*
3600071 AAAAAATTTT-AAATTCCACATAA
1 AAAAAATTTTAAAAATCCACATAA
3600094 AAAAAATTTTAAAAATCCACATA
1 AAAAAATTTTAAAAATCCACATA
3600117 GTCAAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATTTTAAAAATCCACATAA
Found at i:3601198 original size:12 final size:12
Alignment explanation
Indices: 3601183--3601208 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3601173 ATAATTTATC
3601183 TTTTAAAAATAA
1 TTTTAAAAATAA
3601195 TTTTAAAAATAA
1 TTTTAAAAATAA
3601207 TT
1 TT
3601209 AATAAAAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:3601742 original size:19 final size:20
Alignment explanation
Indices: 3601706--3601743 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3601696 TTAATTTAAT
* *
3601706 ATAAAAAATTATGTTAAAAA
1 ATAAAAAATAATGATAAAAA
3601726 ATAAAAAATAAT-ATAAAA
1 ATAAAAAATAATGATAAAA
3601744 TTAAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
ATAAAAAATAATGATAAAAA
Found at i:3602090 original size:2 final size:2
Alignment explanation
Indices: 3602083--3602134 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
3602073 TCCATGATAC
* *
3602083 AT AT AT AT AC AT AC 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
3602125 AT AT AT AT AT
1 AT AT AT AT AT
3602135 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3602410 original size:2 final size:2
Alignment explanation
Indices: 3602403--3602444 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3602393 CTCTAATCTT
3602403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3602445 AAAACATTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3603644 original size:23 final size:23
Alignment explanation
Indices: 3603614--3603673 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
3603604 AAATTCATTT
3603614 TATTATTTATTATAATATT-ATAA
1 TATTATTTATTATAATATTAAT-A
*
3603637 TATTATTTTAATATTAATATTAATA
1 TATTA-TTTATTA-TAATATTAATA
3603662 TATT-TTTATTAT
1 TATTATTTATTAT
3603674 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 6 0.19
25 12 0.38
26 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTTATTATAATATTAATA
Found at i:3603674 original size:23 final size:23
Alignment explanation
Indices: 3603614--3603676 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
3603604 AAATTCATTT
3603614 TATTATTTATTA-TAATATTATAA
1 TATT-TTTATTATTAATATTATAA
*
3603637 TATTATTTTAATATTAATATTA-ATA
1 TA-T-TTTTATTATTAATATTATA-A
3603662 TATTTTTATTATTAA
1 TATTTTTATTATTAA
3603677 ATTTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 13 0.38
24 9 0.26
25 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATTATTAATATTATAA
Found at i:3606286 original size:3 final size:3
Alignment explanation
Indices: 3606278--3606309 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3606268 ACCTGAAATT
*
3606278 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3606310 TCGGGCCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3607679 original size:24 final size:22
Alignment explanation
Indices: 3607637--3607710 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 22
3607627 ATAATCTTTG
3607637 AATTTTATTTATAA-A-ATTAAA
1 AATTTT-TTTATAATATATTAAA
*
3607658 AATTTTTACTTTTAATATATTAATA
1 AATTTTT--TTATAATATATTAA-A
3607683 ATATTTTTTTATAATATATCTAAA
1 A-ATTTTTTTATAATATAT-TAAA
3607707 AATT
1 AATT
3607711 ATGTATTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.02
21 6 0.14
22 5 0.11
23 4 0.09
24 17 0.39
25 5 0.11
26 6 0.14
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTTTTATAATATATTAAA
Found at i:3608164 original size:11 final size:10
Alignment explanation
Indices: 3608138--3608162 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3608128 TATTTAATTT
3608138 TATTTAAAAA
1 TATTTAAAAA
3608148 TATTTAAAAA
1 TATTTAAAAA
3608158 TATTT
1 TATTT
3608163 TATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:3608412 original size:3 final size:3
Alignment explanation
Indices: 3608404--3608437 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3608394 GAATTGATTA
3608404 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3608438 GTTAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3612442 original size:2 final size:2
Alignment explanation
Indices: 3612435--3612469 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3612425 AACAGCTCAC
3612435 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3612470 TTAAATTTCT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3617086 original size:29 final size:30
Alignment explanation
Indices: 3617060--3617116 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3617050 ATGTATTAAT
*
3617060 ATTATATTT-ATATATTTTATTATATTATA
1 ATTATATTTAAAATATTTTATTATATTATA
*
3617089 ATTTTATTTAAAATATTTTA-TAT-TTATA
1 ATTATATTTAAAATATTTTATTATATTATA
3617117 TAAATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTATATTTAAAATATTTTATTATATTATA
Found at i:3618564 original size:17 final size:18
Alignment explanation
Indices: 3618542--3618585 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3618532 TATTTTATTT
*
3618542 TATAAAAATT-ATAATTA
1 TATAAAAATTAATAAATA
3618559 TATAAAAATTAATAAATA
1 TATAAAAATTAATAAATA
*
3618577 TAGAAAAAT
1 TATAAAAAT
3618586 AATTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TATAAAAATTAATAAATA
Found at i:3619255 original size:24 final size:23
Alignment explanation
Indices: 3619182--3619255 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
3619172 AAAATTTGTG
* * *
3619182 ATAAATAAAAAAATTGAATGAGAA
1 ATAAAT-AAAAAATAGAATCATAA
* *
3619206 ATAATATAAAAAATAAAATTATTAA
1 ATAA-ATAAAAAATAGAATCA-TAA
3619231 AGTAAATAAAAAATAGAATCATAA
1 A-TAAATAAAAAATAGAATCATAA
3619255 A
1 A
3619256 AACAGTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
24 19 0.46
25 19 0.46
26 3 0.07
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (23 bp):
ATAAATAAAAAATAGAATCATAA
Found at i:3626453 original size:2 final size:2
Alignment explanation
Indices: 3626446--3626477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3626436 GGAGACTTTC
3626446 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
3626478 TAGGGTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3628211 original size:19 final size:19
Alignment explanation
Indices: 3628187--3628234 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
3628177 AATATTTAAA
3628187 TAATAATTATAATATTATT
1 TAATAATTATAATATTATT
3628206 TAATAATT-T--TATTATT
1 TAATAATTATAATATTATT
*
3628222 T-TTAATTATAATA
1 TAATAATTATAATA
3628235 GTTAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
18 3 0.12
19 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATAATTATAATATTATT
Found at i:3628584 original size:6 final size:6
Alignment explanation
Indices: 3628573--3628597 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3628563 TTTAAACCTA
3628573 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
3628598 GACCTCTTAA
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:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:3628657 original size:15 final size:16
Alignment explanation
Indices: 3628629--3628662 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3628619 AATTAAAAAA
3628629 TTTAAATTATAATTTT
1 TTTAAATTATAATTTT
*
3628645 TTTAATTTA-AATTTT
1 TTTAAATTATAATTTT
3628660 TTT
1 TTT
3628663 TGTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAAATTATAATTTT
Found at i:3629284 original size:37 final size:37
Alignment explanation
Indices: 3629183--3629287 Score: 90
Period size: 37 Copynumber: 2.8 Consensus size: 37
3629173 TTTATTTTAT
*
3629183 TAAAAT-ATTAATAT-TTAATATATTTACGAATATATAAAA
1 TAAAATAATTAATATATT--TATATTTA--AATATAAAAAA
* * *** *
3629222 -AATATAATTAATTTAAAAATTTTTAAATATAAAAAA
1 TAAAATAATTAATATATTTATATTTAAATATAAAAAA
3629258 TAAAATAATTAATATATTTATATTTAAATA
1 TAAAATAATTAATATATTTATATTTAAATA
3629288 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
36 10 0.20
37 23 0.46
38 10 0.20
39 7 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (37 bp):
TAAAATAATTAATATATTTATATTTAAATATAAAAAA
Found at i:3631300 original size:23 final size:24
Alignment explanation
Indices: 3631274--3631318 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3631264 AAATTATTTT
*
3631274 AAAAATTTT-AAATTCCACATAAA
1 AAAAATTTTAAAAATCCACATAAA
3631297 AAAAATTTTAAAAATCCACATA
1 AAAAATTTTAAAAATCCACATA
3631319 GTCAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAATTTTAAAAATCCACATAAA
Found at i:3632397 original size:12 final size:12
Alignment explanation
Indices: 3632382--3632407 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3632372 ATAATTTATC
3632382 TTTTAAAAATAA
1 TTTTAAAAATAA
3632394 TTTTAAAAATAA
1 TTTTAAAAATAA
3632406 TT
1 TT
3632408 AATAAAAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:3632940 original size:19 final size:20
Alignment explanation
Indices: 3632904--3632941 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3632894 TTAATTTAAT
* *
3632904 ATAAAAAATTATGTTAAAAA
1 ATAAAAAATAATGATAAAAA
3632924 ATAAAAAATAAT-ATAAAA
1 ATAAAAAATAATGATAAAA
3632942 TTAAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
ATAAAAAATAATGATAAAAA
Found at i:3633297 original size:2 final size:2
Alignment explanation
Indices: 3633280--3633327 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
3633270 TCCATGATAC
* *
3633280 AT AT AT AC AT AC 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
3633322 AT AT AT
1 AT AT AT
3633328 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3633443 original size:17 final size:19
Alignment explanation
Indices: 3633418--3633456 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3633408 GATGTTCTTT
3633418 TAATAT-AAA-AAAAATTA
1 TAATATAAAATAAAAATTA
*
3633435 TAATTTAAAATAAAAATTA
1 TAATATAAAATAAAAATTA
3633454 TAA
1 TAA
3633457 ATATTATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATATAAAATAAAAATTA
Found at i:3633610 original size:13 final size:13
Alignment explanation
Indices: 3633592--3633616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3633582 CTAATCTTTA
3633592 TATATATATATAT
1 TATATATATATAT
3633605 TATATATATATA
1 TATATATATATA
3633617 AAACATTAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:3634809 original size:23 final size:23
Alignment explanation
Indices: 3634779--3634838 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
3634769 AAATTCATTT
3634779 TATTATTTATTATAATATT-ATAA
1 TATTATTTATTATAATATTAAT-A
*
3634802 TATTATTTTAATATTAATATTAATA
1 TATTA-TTTATTA-TAATATTAATA
3634827 TATT-TTTATTAT
1 TATTATTTATTAT
3634839 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 6 0.19
25 12 0.38
26 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTTATTATAATATTAATA
Found at i:3634839 original size:23 final size:23
Alignment explanation
Indices: 3634779--3634841 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
3634769 AAATTCATTT
3634779 TATTATTTATTA-TAATATTATAA
1 TATT-TTTATTATTAATATTATAA
*
3634802 TATTATTTTAATATTAATATTA-ATA
1 TA-T-TTTTATTATTAATATTATA-A
3634827 TATTTTTATTATTAA
1 TATTTTTATTATTAA
3634842 ATTTAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 13 0.38
24 9 0.26
25 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATTATTAATATTATAA
Found at i:3637448 original size:3 final size:3
Alignment explanation
Indices: 3637440--3637471 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3637430 ACCTGAAATT
*
3637440 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3637472 TCGGGCCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3638842 original size:24 final size:22
Alignment explanation
Indices: 3638814--3638872 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
3638804 TTATTTATAA
*
3638814 ATTAAAAATTTTTACTTTTAATAT
1 ATTAAAAATTTTT--TTATAATAT
3638838 ATTAATAATATTTTTTTATAATAT
1 ATTAA-AA-ATTTTTTTATAATAT
3638862 ATCTAAAAATT
1 AT-TAAAAATT
3638873 ATGTATTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.10
24 17 0.55
25 5 0.16
26 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTAAAAATTTTTTTATAATAT
Found at i:3639571 original size:3 final size:3
Alignment explanation
Indices: 3639563--3639596 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3639553 GAATTGATTA
3639563 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3639597 ATAGTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3643596 original size:2 final size:2
Alignment explanation
Indices: 3643589--3643631 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3643579 AACAGCTCAC
3643589 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3643631 A
1 A
3643632 TTAAATTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3649705 original size:16 final size:18
Alignment explanation
Indices: 3649686--3649731 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3649676 TTATTTTATT
3649686 TTATA-AAAAATT-ATAA
1 TTATAGAAAAATTAATAA
*
3649702 TTATATAAAAATTAATAA
1 TTATAGAAAAATTAATAA
*
3649720 ATATAGAAAAAT
1 TTATAGAAAAAT
3649732 AATTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
18 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTATAGAAAAATTAATAA
Found at i:3649705 original size:21 final size:21
Alignment explanation
Indices: 3649666--3649705 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3649656 TAAATTTAAA
*
3649666 TATAAAATAATTATTTTATTT
1 TATAAAATAATTATATTATTT
3649687 TATAAAA-AATTATAATTAT
1 TATAAAATAATTAT-ATTAT
3649706 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAAAATAATTATATTATTT
Found at i:3657601 original size:2 final size:2
Alignment explanation
Indices: 3657594--3657625 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3657584 GGAGACTTTC
3657594 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
3657626 TAGGGTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3658910 original size:23 final size:24
Alignment explanation
Indices: 3658869--3658914 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3658859 TCTTATTATC
*
3658869 AATAAATTTATATTCTAATTAATA
1 AATAAATTTAAATTCTAATTAATA
3658893 AATAAATTTAAATT-TAATTAAT
1 AATAAATTTAAATTCTAATTAAT
3658915 TTTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAAATTTAAATTCTAATTAATA
Found at i:3659374 original size:16 final size:17
Alignment explanation
Indices: 3659352--3659435 Score: 70
Period size: 16 Copynumber: 5.1 Consensus size: 17
3659342 AATAATTATA
3659352 ATTATTATTTAATAATT
1 ATTATTATTTAATAATT
*
3659369 -TTATTATTT-TTAATT
1 ATTATTATTTAATAATT
* *
3659384 ATTAATATTTAAT-ATA
1 ATTATTATTTAATAATT
* *
3659400 ATTGATTATGATAATATTT
1 ATT-ATTAT-TTAATAATT
3659419 ATTA-TATTT-ATAATT
1 ATTATTATTTAATAATT
3659434 AT
1 AT
3659436 AATAAATATT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 12 0.23
16 23 0.44
17 8 0.15
18 5 0.10
19 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTATTATTTAATAATT
Found at i:3659738 original size:6 final size:6
Alignment explanation
Indices: 3659727--3659751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3659717 TTTAAACATA
3659727 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
3659752 GACCTCTTAA
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:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:3659805 original size:15 final size:15
Alignment explanation
Indices: 3659783--3659816 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3659773 ATTAAAAAAA
*
3659783 TTTAAATTATAATTTT
1 TTTAATTTA-AATTTT
3659799 TTTAATTTAAATTTT
1 TTTAATTTAAATTTT
3659814 TTT
1 TTT
3659817 TTTGTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAATTTAAATTTT
Found at i:3660832 original size:9 final size:9
Alignment explanation
Indices: 3660818--3660842 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3660808 TTAAAAATAT
3660818 ATTATATAA
1 ATTATATAA
3660827 ATTATATAA
1 ATTATATAA
3660836 ATTATAT
1 ATTATAT
3660843 TTTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTATATAA
Done.