Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 40 of 52
Found at i:6594992 original size:18 final size:18
Alignment explanation
Indices: 6594963--6595091 Score: 63
Period size: 20 Copynumber: 6.9 Consensus size: 18
6594953 ATAAAAATTT
6594963 ATATATTTATATAATATTA
1 ATATA-TTATATAATATTA
6594982 ATATATTATAT--TA-TA
1 ATATATTATATAATATTA
*
6594997 ATAATATT-TATACT-TT-
1 AT-ATATTATATAATATTA
* *
6595013 TTATATTCATATAATTTTTA
1 ATATATT-ATATAA-TATTA
6595033 ATATATTAATAATTAATATTA
1 ATATATT-AT-A-TAATATTA
* * * *
6595054 TATAAATTTTAAAATATAA
1 -ATATATTATATAATATTA
6595073 ATTTATATTATATAATATT
1 A--TATATTATATAATATT
6595092 TTATTTTAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
15 12 0.14
16 8 0.10
17 6 0.07
18 8 0.10
19 13 0.16
20 21 0.25
21 6 0.07
22 9 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATTATATAATATTA
Found at i:6595064 original size:32 final size:29
Alignment explanation
Indices: 6595015--6595094 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 29
6595005 TATACTTTTT
* *
6595015 ATATTCATATAATTTTTAATATATTAATAATTA
1 ATATT-ATATAAATTTTAAAATA-T-A-AATTA
*
6595048 ATATTATATAAATTTTAAAATATAAATTT
1 ATATTATATAAATTTTAAAATATAAATTA
6595077 ATATTATATAATATTTTA
1 ATATTATATAA-ATTTTA
6595095 TTTTAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.35
30 7 0.16
31 1 0.02
32 15 0.35
33 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATTATATAAATTTTAAAATATAAATTA
Found at i:6595096 original size:15 final size:15
Alignment explanation
Indices: 6595016--6595122 Score: 69
Period size: 15 Copynumber: 7.0 Consensus size: 15
6595006 ATACTTTTTA
6595016 TATTCATATAAT-TTT
1 TATT-ATATAATATTT
* *
6595031 TAATATATTAATAATTAA
1 TATTATA-TAAT-ATT-T
6595049 TATTATATAA-ATTT
1 TATTATATAATATTT
**
6595063 TAAAATATAA-ATTT
1 TATTATATAATATTT
6595077 ATATTATATAATATTT
1 -TATTATATAATATTT
* *
6595093 TATTTTA-AATAATT
1 TATTATATAATATTT
*
6595107 TATTACTATTATATTT
1 TATTA-TATAATATTT
6595123 ATTTAATTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
14 25 0.35
15 26 0.37
16 9 0.13
17 5 0.07
18 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATATAATATTT
Found at i:6596264 original size:18 final size:17
Alignment explanation
Indices: 6596232--6596265 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6596222 AATTTATAAG
6596232 TAAAAATTTTAATTTAT
1 TAAAAATTTTAATTTAT
*
6596249 TAAAATATTTTTATTTA
1 TAAAA-ATTTTAATTTA
6596266 ATAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAAATTTTAATTTAT
Found at i:6600662 original size:34 final size:34
Alignment explanation
Indices: 6600624--6600716 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 34
6600614 ATTTATTTCA
6600624 ATTTAAATTATTATTTAATAATAAAAAATTTTAT
1 ATTTAAATTATTATTTAATAATAAAAAATTTTAT
* * * **
6600658 ATTTAAA-TATAATTATATTAATATAATTTTTTAT
1 ATTTAAATTATTATT-TAATAATAAAAAATTTTAT
*
6600692 ATTTTAATT-TT-TTTAAATAATAAAA
1 ATTTAAATTATTATTT-AATAATAAAA
6600717 TAAGCAGTCC
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
32 1 0.02
33 16 0.34
34 29 0.62
35 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTTAAATTATTATTTAATAATAAAAAATTTTAT
Found at i:6602786 original size:11 final size:11
Alignment explanation
Indices: 6602757--6602794 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
6602747 TAATTTTAAA
6602757 TAAA-TAAAAT
1 TAAATTAAAAT
6602767 TAGAATTAAAAT
1 TA-AATTAAAAT
6602779 TAAATTAAAA-
1 TAAATTAAAAT
6602789 TAAATT
1 TAAATT
6602795 TATGATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 10 0.38
12 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TAAATTAAAAT
Found at i:6602828 original size:17 final size:17
Alignment explanation
Indices: 6602808--6602868 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
6602798 GATAAATTAT
6602808 TTAAAATATGAAATAAA
1 TTAAAATATGAAATAAA
6602825 TTAAAATAT-AATATAAAA
1 TTAAAATATGAA-AT-AAA
* * *
6602843 ATAACATAAGAAAATAAA
1 TTAAAATATG-AAATAAA
6602861 -TAAAATAT
1 TTAAAATAT
6602869 TATATGATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.06
17 17 0.49
18 12 0.34
19 2 0.06
20 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (17 bp):
TTAAAATATGAAATAAA
Found at i:6602831 original size:10 final size:12
Alignment explanation
Indices: 6602812--6602873 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 12
6602802 AATTATTTAA
*
6602812 AATATGAAATA-
1 AATATAAAATAT
6602823 AAT-TAAAATAT
1 AATATAAAATAT
6602834 AATATAAAA-AT
1 AATATAAAATAT
* *
6602845 AACATAAGAAAAT
1 AATATAA-AATAT
6602858 AA-ATAAAATAT
1 AATATAAAATAT
*
6602869 TATAT
1 AATAT
6602874 GATGTGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
10 6 0.14
11 19 0.45
12 13 0.31
13 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:6604525 original size:20 final size:22
Alignment explanation
Indices: 6604502--6604545 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
6604492 CAATTTAATC
6604502 ATTAAAATAATAA-A-AAATAA
1 ATTAAAATAATAATATAAATAA
6604522 ATTAAAATAATAATATAAATAA
1 ATTAAAATAATAATATAAATAA
6604544 AT
1 AT
6604546 GAAATTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATTAAAATAATAATATAAATAA
Found at i:6605722 original size:2 final size:2
Alignment explanation
Indices: 6605715--6605754 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6605705 AACTTTCCTT
6605715 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
6605755 ATAATTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6606180 original size:10 final size:10
Alignment explanation
Indices: 6606152--6606194 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
6606142 AAAAATAATT
* *
6606152 AAATAAATAT
1 AAATATATAA
6606162 AAATCATATAA
1 AAAT-ATATAA
6606173 AAATATATAA
1 AAATATATAA
6606183 AAATATATAA
1 AAATATATAA
6606193 AA
1 AA
6606195 TAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATATATAA
Found at i:6611499 original size:16 final size:15
Alignment explanation
Indices: 6611478--6611524 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
6611468 CAATAAATTC
6611478 GAATTTAAAATGACTT
1 GAATTTAAAATGA-TT
6611494 GAATTTAAAATGATT
1 GAATTTAAAATGATT
* *
6611509 CGAACTCAAAATGATT
1 -GAATTTAAAATGATT
6611525 TGAACCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 2 0.07
16 26 0.93
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (15 bp):
GAATTTAAAATGATT
Found at i:6611529 original size:16 final size:16
Alignment explanation
Indices: 6611484--6611529 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
6611474 ATTCGAATTT
* * *
6611484 AAAATGACTTGAATTT
1 AAAATGATTTGAACTC
*
6611500 AAAATGATTCGAACTC
1 AAAATGATTTGAACTC
6611516 AAAATGATTTGAAC
1 AAAATGATTTGAAC
6611530 CTGAAGTGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (16 bp):
AAAATGATTTGAACTC
Found at i:6615181 original size:23 final size:22
Alignment explanation
Indices: 6615136--6615219 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 22
6615126 TTAATTTTTT
* *
6615136 TATTAAAATTATTTAACGAATTAA
1 TATT-AAATAATTTAATG-ATTAA
*
6615160 TATTAAATAATTTAATTTATTAA
1 TATTAAATAATTTAA-TGATTAA
*
6615183 TAATAAA-AATTTTAATGATATAA
1 TATTAAATAA-TTTAATGAT-TAA
6615206 T-TTAATATAATTTA
1 TATTAA-ATAATTTA
6615220 TAATTTATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
22 8 0.16
23 35 0.71
24 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTAAATAATTTAATGATTAA
Found at i:6615211 original size:25 final size:25
Alignment explanation
Indices: 6615183--6615243 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
6615173 AATTTATTAA
6615183 TAATAAAAATTT-TAATGATATAATT
1 TAATAAAAATTTATAAT-ATATAATT
* *
6615208 TAAT-ATAATTTATAATTTATAATT
1 TAATAAAAATTTATAATATATAATT
6615232 TACATAAAAATT
1 TA-ATAAAAATT
6615244 AATACTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 15 0.50
25 10 0.33
26 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATAAAAATTTATAATATATAATT
Found at i:6615838 original size:16 final size:16
Alignment explanation
Indices: 6615817--6615857 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
6615807 GTAAAAAACA
6615817 CGAACTCAAAATAACT
1 CGAACTCAAAATAACT
*
6615833 CGAACTCAAAATAGCT
1 CGAACTCAAAATAACT
6615849 CGAACTCAA
1 CGAACTCAA
6615858 GACAGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.27, G:0.10, T:0.17
Consensus pattern (16 bp):
CGAACTCAAAATAACT
Found at i:6616378 original size:16 final size:15
Alignment explanation
Indices: 6616357--6616386 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6616347 ATGTTACACC
6616357 TAGAATAGTAATATAG
1 TAGAATAG-AATATAG
6616373 TAGAATAGAATATA
1 TAGAATAGAATATA
6616387 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:6618669 original size:20 final size:18
Alignment explanation
Indices: 6618634--6618696 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
6618624 ATTATTTAAA
6618634 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
6618652 AAATTAATTTTATAT-AT
1 AAATTAATTTTATATAAT
6618669 AAATATAGATTTTA-ATAAAT
1 AAAT-TA-ATTTTATAT-AAT
6618689 AAA-TAATT
1 AAATTAATT
6618697 AAATATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.22
18 21 0.51
19 6 0.15
20 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:6618899 original size:15 final size:16
Alignment explanation
Indices: 6618879--6618931 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
6618869 ATCGAAATTC
6618879 AAAAAAATTCAAA-CA
1 AAAAAAATTCAAATCA
*
6618894 AAAAAAATTTAAATTC-
1 AAAAAAATTCAAA-TCA
*
6618910 AAAAAAATTCGAATCCA
1 AAAAAAATTCAAAT-CA
6618927 AAAAA
1 AAAAA
6618932 TTTTAAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.42
16 12 0.39
17 6 0.19
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAAAAATTCAAATCA
Found at i:6618911 original size:31 final size:32
Alignment explanation
Indices: 6618873--6618947 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
6618863 ACTCTAATCG
6618873 AAATTCAAAAAAATTC-AAACAAAAAAAATTT
1 AAATTCAAAAAAATTCGAAACAAAAAAAATTT
* * *
6618904 AAATTCAAAAAAATTCGAATCCAAAAAATTTT
1 AAATTCAAAAAAATTCGAAACAAAAAAAATTT
* *
6618936 AAACTCCAAAAA
1 AAATTCAAAAAA
6618948 CACTCGTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 16 0.42
32 22 0.58
ACGTcount: A:0.63, C:0.13, G:0.01, T:0.23
Consensus pattern (32 bp):
AAATTCAAAAAAATTCGAAACAAAAAAAATTT
Found at i:6618913 original size:16 final size:16
Alignment explanation
Indices: 6618873--6618931 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
6618863 ACTCTAATCG
6618873 AAATTCAAAAAAATTC
1 AAATTCAAAAAAATTC
*
6618889 AAA--CAAAAAAAATTT
1 AAATTC-AAAAAAATTC
6618904 AAATTCAAAAAAATTC
1 AAATTCAAAAAAATTC
* *
6618920 GAATCCAAAAAA
1 AAATTCAAAAAA
6618932 TTTTAAACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.03
15 12 0.33
16 22 0.61
17 1 0.03
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20
Consensus pattern (16 bp):
AAATTCAAAAAAATTC
Found at i:6618980 original size:16 final size:16
Alignment explanation
Indices: 6618955--6619015 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
6618945 AAACACTCGT
*
6618955 ACCTACATAAA-TCTAA
1 ACCTAAATAAACTC-AA
6618971 ACCTAAATAAACTCAA
1 ACCTAAATAAACTCAA
* *
6618987 A-TTAAAATAAACTCCA
1 ACCT-AAATAAACTCAA
6619003 ACCTAAATAAACT
1 ACCTAAATAAACT
6619016 AAAATCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 1 0.03
16 34 0.89
17 3 0.08
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
ACCTAAATAAACTCAA
Found at i:6619730 original size:2 final size:2
Alignment explanation
Indices: 6619723--6619748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6619713 TGATTTAATG
6619723 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
6619749 GTGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6624845 original size:30 final size:30
Alignment explanation
Indices: 6624811--6624916 Score: 78
Period size: 30 Copynumber: 3.5 Consensus size: 30
6624801 CTGTTATTAT
6624811 ACTCAAATAAACTTTTAATCTTTATTTTAC
1 ACTCAAATAAACTTTTAATCTTTATTTTAC
* *
6624841 ACTCAAACAAA-TTATTAATTTTTAGTTTTA-
1 ACTCAAATAAACTT-TTAATCTTTA-TTTTAC
** *
6624871 A-TCTAAATAAACCCTTAAACTTTAATTTCTAC
1 ACTC-AAATAAACTTTTAATCTTT-ATTT-TAC
*
6624903 -CT-AAATAAATTTTT
1 ACTCAAATAAACTTTT
6624917 TAATTTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
29 4 0.07
30 45 0.78
31 8 0.14
32 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (30 bp):
ACTCAAATAAACTTTTAATCTTTATTTTAC
Found at i:6627529 original size:34 final size:34
Alignment explanation
Indices: 6627461--6627643 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
6627451 TGGCACTTTC
* * *
6627461 TGTTGATTAAAT-GGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
6627494 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
6627528 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
6627562 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
6627596 TGTTGACTAAATGGGAGATTTGGTAGGTTTCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
6627630 TGTTGATTAAATGG
1 TGTTGATTAAATGG
6627644 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 122 0.92
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:6627591 original size:102 final size:101
Alignment explanation
Indices: 6627461--6627643 Score: 312
Period size: 102 Copynumber: 1.8 Consensus size: 101
6627451 TGGCACTTTC
*
6627461 TGTTGATTAAATGGTGATTTGGTAGTTTATCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
6627526 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
6627562 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTTC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
6627627 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
6627644 TGGTTTTTAC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 12 0.16
102 64 0.84
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:6628004 original size:19 final size:19
Alignment explanation
Indices: 6627948--6628010 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
6627938 TGGTTGTCGA
**
6627948 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
6627967 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
6627986 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
6628005 GTTACT
1 GGTACT
6628011 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:6632142 original size:34 final size:34
Alignment explanation
Indices: 6632076--6632260 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
6632066 AAGTGGGAGA
* *
6632076 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
6632109 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
6632143 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
6632177 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
6632211 ATTGTTGACTAAATGGGAGATTTGGTAGGTTTCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
6632245 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
6632261 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:6632251 original size:102 final size:101
Alignment explanation
Indices: 6632076--6632260 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
6632066 AAGTGGGAGA
6632076 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
6632141 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
6632177 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
6632242 TCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
6632261 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:6640353 original size:78 final size:77
Alignment explanation
Indices: 6640173--6640407 Score: 256
Period size: 78 Copynumber: 3.0 Consensus size: 77
6640163 TTATTGATAT
* *
6640173 TTTTATTTCTAAAATACCGATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTCCGATGGGA
1 TTTTATTTCTAAAATACCGATTTTTCACAATC-GGGATACTCCAA-CTCGTTATTTCCGAGGGGA
6640238 TACTCCAACCTCGA
64 TACTCCAACCTCGA
* * * ** * *
6640252 TTTTATTTTTCAAACACTAATTTTTCACAATCGGAGATACTCCAACTTGTTATTTTCGAGGGGAT
1 TTTTATTTCTAAAATACCGATTTTTCACAATCGG-GATACTCCAACTCGTTATTTCCGAGGGGAT
* * *
6640317 GCTCTAACGC-CGG
65 ACTCCAAC-CTCGA
* ** * *
6640330 TTTTATTTCTAAAATACCGATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTTGAAGAGA
1 TTTTATTTCTAAAATACCGATTTTTCACAATC-GGGATACTCCAA-CTCGTTATTTCCGAGGGGA
6640395 TACTCCAACCTCG
64 TACTCCAACCTCG
6640408 TTATTTTCGA
Statistics
Matches: 127, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
78 65 0.51
79 62 0.49
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (77 bp):
TTTTATTTCTAAAATACCGATTTTTCACAATCGGGATACTCCAACTCGTTATTTCCGAGGGGATA
CTCCAACCTCGA
Found at i:6640409 original size:28 final size:28
Alignment explanation
Indices: 6640365--6640435 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
6640355 CACAATCAGG
*
6640365 GATACTCCAACCCCGTTATTTTTGAAGA
1 GATACTCCAACCCCGTTATTTTCGAAGA
* * *
6640393 GATACTCCAACCTCGTTATTTTCGAGGG
1 GATACTCCAACCCCGTTATTTTCGAAGA
6640421 GATACTCCAACCCCG
1 GATACTCCAACCCCG
6640436 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
GATACTCCAACCCCGTTATTTTCGAAGA
Found at i:6640422 original size:107 final size:106
Alignment explanation
Indices: 6640285--6640510 Score: 296
Period size: 107 Copynumber: 2.1 Consensus size: 106
6640275 TTCACAATCG
* * * * * *
6640285 GAGATACTCCAA-CTTGTTATTTTCGAGGGGATGCTCTAACGCCGGTTTTA-TTTCTAAAATACC
1 GAGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACC
6640348 GATTTTTCACAATCAGG-GATACTCCAACCCCGTTATTTTTGAA
65 GATTTTTCACAATC-GGTGATACTCCAACCCCGTTA-TTTTGAA
*
6640391 GAGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCG
1 GAGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCG
* * *
6640456 ATTTTTTACAATCGGTGATACTCCAACCCTGTTATTTTGAG
66 ATTTTTCACAATCGGTGATACTCCAACCCCGTTATTTTGAA
* *
6640497 GGGATACTCTAACC
1 GAGATACTCCAACC
6640511 CCAGTTTTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
106 32 0.30
107 69 0.66
108 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (106 bp):
GAGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCG
ATTTTTCACAATCGGTGATACTCCAACCCCGTTATTTTGAA
Found at i:6640482 original size:79 final size:76
Alignment explanation
Indices: 6640393--6640589 Score: 254
Period size: 78 Copynumber: 2.5 Consensus size: 76
6640383 TTTTTGAAGA
*
6640393 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTTATTT-TCAAAACATCG
1 GATACTCCAACC-CGTTATTTT-GAGGGGATACTCCAACCCCAG-TTTTATTTCT-AAAACACCG
*
6640456 ATTTTTTACAATCGG
62 ATTTTTCACAATCGG
*
6640471 TGATACTCCAACCCTGTTATTTTGAGGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGAT
1 -GATACTCCAACCC-GTTATTTTGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCGAT
*
6640536 TTTTCACCATCGG
64 TTTTCACAATCGG
*
6640549 GAATACTCCAACCGCGTTATTTTTTAGGGGATACTCCAACC
1 G-ATACTCCAACC-CGTTA-TTTTGAGGGGATACTCCAACC
6640590 TCGTTATTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
77 1 0.01
78 63 0.59
79 42 0.40
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (76 bp):
GATACTCCAACCCGTTATTTTGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCGATTT
TTCACAATCGG
Found at i:6640520 original size:185 final size:185
Alignment explanation
Indices: 6640208--6640691 Score: 672
Period size: 185 Copynumber: 2.6 Consensus size: 185
6640198 CACCATCGGG
* * *
6640208 GATACTCCAACCTCGTTATTTCCGATGGGATACTCCAACCTCGATTTTATTTTTC-AAACA-CTA
1 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTA-TTTTCAAAACATC-G
* * * *
6640271 ATTTTTCACAATCGGAGATACTCCAACTTGTTATTTTCGAGGGGATGCTCTAACGCCGGTTTTAT
64 ATTTTTCACAATCGGAGATACTCCAACCTGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTAT
*
6640336 TTCTAAAATACCGATTTTTCACAATCAGGG-ATACTCCAACCCCGTTATTTTTGAAGA
129 TTCTAAAACACCGATTTTTCACAATC-GGGAATACTCCAACCCCGTTATTTTTGAAGA
*
6640393 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGAT
1 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACATCGAT
* *
6640458 TTTTTACAATCGGTGATACTCCAACCCTGTTATTTT-GAGGGGATACTCTAACCCCAGTTTTATT
66 TTTTCACAATCGGAGATACTCCAA-CCTGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTATT
* * * * *
6640522 TCTAAAACACCGATTTTTCACCATCGGGAATACTCCAACCGCGTTATTTTTTAGGG
130 TCTAAAACACCGATTTTTCACAATCGGGAATACTCCAACCCCGTTATTTTTGAAGA
* * *
6640578 GATACTCCAACCTCGTTATTTTTGAGGGGATACTCAAACCTCGGTTTTA-TTTCTAAAACATCGA
1 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTC-AAAACATCGA
* * * *
6640642 TTTTTCATAGTCGGGGATATTCCAACCTCGTTATTTTCGAGGGGATACTC
65 TTTTTCACAATCGGAGATACTCCAACCT-GTTATTTTCGAGGGGATACTC
6640692 CAAACCCGTT
Statistics
Matches: 267, Mismatches: 25, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
184 15 0.06
185 229 0.86
186 23 0.09
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (185 bp):
GATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACATCGAT
TTTTCACAATCGGAGATACTCCAACCTGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTATTT
CTAAAACACCGATTTTTCACAATCGGGAATACTCCAACCCCGTTATTTTTGAAGA
Found at i:6640618 original size:28 final size:28
Alignment explanation
Indices: 6640551--6640620 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
6640541 ACCATCGGGA
* *
6640551 ATACTCCAACCGCGTTATTTTTTAGGGG
1 ATACTCCAACCTCGTTATTTTTGAGGGG
6640579 ATACTCCAACCTCGTTATTTTTGAGGGG
1 ATACTCCAACCTCGTTATTTTTGAGGGG
*
6640607 ATACTCAAACCTCG
1 ATACTCCAACCTCG
6640621 GTTTTATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (28 bp):
ATACTCCAACCTCGTTATTTTTGAGGGG
Found at i:6640666 original size:107 final size:106
Alignment explanation
Indices: 6640472--6640694 Score: 315
Period size: 107 Copynumber: 2.1 Consensus size: 106
6640462 TACAATCGGT
*
6640472 GATACTCCAACCCTGTTATTTTGAGGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGATT
1 GATACTCCAACCCTGTTATTTTGAGGGGATACTCAAACCCCAGTTTTATTTCTAAAACACCGATT
**
6640537 TTTCACCATCGGGAATACTCCAACCGCGTTATTTTTTAGGG
66 TTTCACCATCGGGAATACTCCAACCGCGTTATTTTCGAGGG
* * *
6640578 GATACTCCAA-CCTCGTTATTTTTGAGGGGATACTCAAACCTCGGTTTTATTTCTAAAACATCGA
1 GATACTCCAACCCT-GTTA-TTTTGAGGGGATACTCAAACCCCAGTTTTATTTCTAAAACACCGA
* * * *
6640642 TTTTTCA-TAGTCGGGGATATTCCAACCTCGTTATTTTCGAGGG
64 TTTTTCACCA-TCGGGAATACTCCAACCGCGTTATTTTCGAGGG
6640685 GATACTCCAA
1 GATACTCCAA
6640695 ACCCGTTTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
105 3 0.03
106 15 0.14
107 86 0.83
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (106 bp):
GATACTCCAACCCTGTTATTTTGAGGGGATACTCAAACCCCAGTTTTATTTCTAAAACACCGATT
TTTCACCATCGGGAATACTCCAACCGCGTTATTTTCGAGGG
Found at i:6640745 original size:79 final size:78
Alignment explanation
Indices: 6640578--6640747 Score: 193
Period size: 79 Copynumber: 2.2 Consensus size: 78
6640568 TTTTTTAGGG
* * * **
6640578 GATACTCCAACCTCGTTATTTTTGAGGGGATACTCAAACCTCGGTTTTATTTCTAAAACATCGAT
1 GATACTCCAACCTCGTTATTTTCGAGGGGATACTCAAACCTCGGTTTTATCTCCAAAACATAAAT
*
6640643 TTTTCATAGTCGGG
66 TTTTCA-AGTCGGA
* * *
6640657 GATATTCCAACCTCGTTATTTTCGAGGGGATACTCCAAACC-CGTTTTTATCTCCAAAATATTAA
1 GATACTCCAACCTCGTTATTTTCGAGGGGATACT-CAAACCTCGGTTTTATCTCCAAAACA-TAA
6640721 ATTTTTC-A-TCGGA
64 ATTTTTCAAGTCGGA
6640734 GATGTACTCCAACC
1 GA--TACTCCAACC
6640748 ATGTACCCCG
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
77 6 0.08
78 1 0.01
79 56 0.73
80 14 0.18
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (78 bp):
GATACTCCAACCTCGTTATTTTCGAGGGGATACTCAAACCTCGGTTTTATCTCCAAAACATAAAT
TTTTCAAGTCGGA
Found at i:6642946 original size:16 final size:15
Alignment explanation
Indices: 6642921--6642958 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6642911 AATCACGTAA
6642921 ATTT-TTATTTTCTAT
1 ATTTATTATTTT-TAT
6642936 ATTTATTATTTTTAT
1 ATTTATTATTTTTAT
6642951 AGTTTATT
1 A-TTTATT
6642959 TCTTATCGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTATTATTTTTAT
Found at i:6644184 original size:5 final size:5
Alignment explanation
Indices: 6644162--6644347 Score: 112
Period size: 5 Copynumber: 36.6 Consensus size: 5
6644152 TATTAATCAC
* * * * *
6644162 AATAT AATTAT TATAT AATAT AAAAA AATTAA AATAT AATATT AAAAAT
1 AATAT AA-TAT AATAT AATAT AATAT AA-TAT AATAT AATA-T -AATAT
* ** *
6644211 AATACA AATAT AATAT AATAT AGATAT TTTAA AATAT -ATAT AATAT AA-AT
1 AATA-T AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AATAT
* * *
6644261 TAT-T AATAT AA-AT AATAT GAATAC AATAT AATAT AA-AT ATTAT AATAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATAT
* * * * *
6644309 ATTAA AATTT ATATAT AAAAT ATTAT AATAT AATAT AAT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AAT
6644348 TACATACTAC
Statistics
Matches: 136, Mismatches: 32, Indels: 26
0.70 0.16 0.13
Matches are distributed among these distances:
4 17 0.12
5 90 0.66
6 26 0.19
7 3 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:6644199 original size:23 final size:21
Alignment explanation
Indices: 6644174--6644228 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
6644164 TATAATTATT
6644174 ATATAATATAAAAA-AATTAAA
1 ATATAATATAAAAATAA-TAAA
6644195 ATATAATATTAAAAATAATACAA
1 ATATAATA-TAAAAATAATA-AA
6644218 ATATAATATAA
1 ATATAATATAA
6644229 TATAGATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.26
22 11 0.35
23 12 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATATAATATAAAAATAATAAA
Found at i:6644214 original size:12 final size:13
Alignment explanation
Indices: 6644189--6644347 Score: 55
Period size: 13 Copynumber: 12.0 Consensus size: 13
6644179 ATATAAAAAA
6644189 ATTAAAATATAAT
1 ATTAAAATATAAT
6644202 ATTAAAA-ATAAT
1 ATTAAAATATAAT
*
6644214 A--CAAATATAAT
1 ATTAAAATATAAT
* *
6644225 A-TAATATAGATAT
1 ATTAAAATATA-AT
*
6644238 TTTAAAATATATAT
1 ATTAAAATATA-AT
*
6644252 AATATAAATTATTAAT
1 -AT-TAAAATA-TAAT
* *
6644268 ATAAATAATATGA-
1 ATTAA-AATATAAT
*
6644281 A-TACAATATAAT
1 ATTAAAATATAAT
6644293 A-TAAATATTATAATAT
1 ATTAAA-A-TAT-A-AT
*
6644309 ATTAAAAT-TTAT
1 ATTAAAATATAAT
*
6644321 ATATAAAATATTAT
1 AT-TAAAATATAAT
* *
6644335 AATATAATATAAT
1 ATTAAAATATAAT
6644348 TACATACTAC
Statistics
Matches: 110, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
10 3 0.03
11 12 0.11
12 20 0.18
13 26 0.24
14 23 0.21
15 8 0.07
16 12 0.11
17 6 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (13 bp):
ATTAAAATATAAT
Found at i:6644237 original size:16 final size:15
Alignment explanation
Indices: 6644162--6644347 Score: 112
Period size: 16 Copynumber: 12.2 Consensus size: 15
6644152 TATTAATCAC
*
6644162 AATATAATTATTATAT
1 AATATAA-TATAATAT
* * *
6644178 AATATAAAAAAATTAA
1 AATATAATATAA-TAT
*
6644194 AATATAATATTAAAAAT
1 AATATAATA-T-AATAT
*
6644211 AATACAAATATAATAT
1 AATA-TAATATAATAT
** *
6644227 AATATAGATATTTTAA
1 AATATA-ATATAATAT
6644243 AATAT-ATATAATAT
1 AATATAATATAATAT
*
6644257 AA-ATTAT-TAATAT
1 AATATAATATAATAT
*
6644270 AA-ATAATATGAATAC
1 AATATAATAT-AATAT
6644285 AATATAATATAA-AT
1 AATATAATATAATAT
* * *
6644299 ATTATAATATATTAA
1 AATATAATATAATAT
* *
6644314 AATTTATATATAAAAT
1 AATATA-ATATAATAT
*
6644330 ATTATAATATAATAT
1 AATATAATATAATAT
6644345 AAT
1 AAT
6644348 TACATACTAC
Statistics
Matches: 127, Mismatches: 32, Indels: 23
0.70 0.18 0.13
Matches are distributed among these distances:
13 14 0.11
14 22 0.17
15 26 0.20
16 53 0.42
17 6 0.05
18 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:6648264 original size:23 final size:21
Alignment explanation
Indices: 6648226--6648269 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
6648216 TTTTATTAAT
* *
6648226 TTATATATTTTGAATATATAA
1 TTATATATTTTAAATAAATAA
6648247 TTATATATTTTATAAATAAATAA
1 TTATATA-TTT-TAAATAAATAA
6648270 AAGTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATATATTTTAAATAAATAA
Found at i:6648265 original size:19 final size:20
Alignment explanation
Indices: 6648226--6648265 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
6648216 TTTTATTAAT
*
6648226 TTATATATTTTGAATATATAA
1 TTATATATTTT-AATAAATAA
6648247 TTATATATTTT-ATAAATAA
1 TTATATATTTTAATAAATAA
6648266 ATAAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTATATATTTTAATAAATAA
Found at i:6648680 original size:2 final size:2
Alignment explanation
Indices: 6648675--6648718 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
6648665 TTTTTGTATT
* *
6648675 TA TA TA TA TA TA TA T- TA TA GA T- TA TA AA 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
6648715 TA TA
1 TA TA
6648719 AAGACGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6648731 original size:28 final size:28
Alignment explanation
Indices: 6648675--6648732 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
6648665 TTTTTGTATT
* * *
6648675 TATATATATATATATTATAGATTATAAA
1 TATATATATATATATTAAAGAGTAAAAA
6648703 TATATATATATATA-TAAAGACGTAAAAA
1 TATATATATATATATTAAAGA-GTAAAAA
6648731 TA
1 TA
6648733 ATTGTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (28 bp):
TATATATATATATATTAAAGAGTAAAAA
Found at i:6649437 original size:19 final size:20
Alignment explanation
Indices: 6649413--6649450 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6649403 CATTTTAAAG
*
6649413 AATT-AAATTTTAATATTTA
1 AATTAAAATTTAAATATTTA
6649432 AATTAAAATTTAAATATTT
1 AATTAAAATTTAAATATTT
6649451 TAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTAAAATTTAAATATTTA
Found at i:6650779 original size:13 final size:14
Alignment explanation
Indices: 6650753--6650782 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6650743 AAAAAAGAAT
6650753 AATTAAAGATAAAA
1 AATTAAAGATAAAA
6650767 AATTAAA-ATAAAA
1 AATTAAAGATAAAA
6650780 AAT
1 AAT
6650783 CGTACAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AATTAAAGATAAAA
Found at i:6650990 original size:5 final size:5
Alignment explanation
Indices: 6650980--6651128 Score: 52
Period size: 5 Copynumber: 30.8 Consensus size: 5
6650970 ATTTACATAT
*
6650980 TTATA TTATA TTATA TTTTATA CTATAA TTATA TT-TAA TT-TA TTAATA
1 TTATA TTATA TTATA --TTATA TTAT-A TTATA TTAT-A TTATA TT-ATA
* * * * * *
6651028 TT-TA TATAAA TTTTA ATATA TTA-A TAATT TTA-A TTTTA TTA-A TT-T-
1 TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * *
6651073 TTATA -TAT- TTATA TTAT- TTTTA TAATA TAATA -TATT TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
6651119 TTATAA TTAT
1 TTAT-A TTAT
6651129 GTTTAATTTA
Statistics
Matches: 106, Mismatches: 20, Indels: 35
0.66 0.12 0.22
Matches are distributed among these distances:
3 2 0.02
4 27 0.25
5 57 0.54
6 15 0.14
7 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:6651001 original size:17 final size:17
Alignment explanation
Indices: 6650979--6651123 Score: 91
Period size: 17 Copynumber: 8.9 Consensus size: 17
6650969 AATTTACATA
6650979 TTTATATTATATTATAT
1 TTTATATTATATTATAT
*
6650996 TTTATACTATAATTATA-
1 TTTATATTAT-ATTATAT
6651013 TTTA-ATT-TATTA-A-
1 TTTATATTATATTATAT
*
6651026 --TAT-TTATA-TAAAT
1 TTTATATTATATTATAT
6651039 TTTA-A-TATATTAATAAT
1 TTTATATTATATT-AT-AT
* *
6651056 TTTA-ATTTTATTAATTT
1 TTTATATTATATT-ATAT
6651073 TTATATATTTATATTAT-T
1 TT-TATA-TTATATTATAT
* *
6651091 TTTATAATATAATATAT
1 TTTATATTATATTATAT
6651108 TTTATATTATATTATA
1 TTTATATTATATTATA
6651124 ATTATGTTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
11 6 0.06
12 3 0.03
13 1 0.01
14 8 0.08
15 4 0.04
16 10 0.10
17 42 0.41
18 19 0.19
19 3 0.03
20 6 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATTATATTATAT
Found at i:6651030 original size:15 final size:15
Alignment explanation
Indices: 6651010--6651075 Score: 50
Period size: 18 Copynumber: 4.5 Consensus size: 15
6651000 TACTATAATT
6651010 ATATTTAATTTATTA
1 ATATTTAATTTATTA
*
6651025 ATATTT-A--TATAA
1 ATATTTAATTTATTA
*
6651037 AT-TTTAATATATTA
1 ATATTTAATTTATTA
6651051 ATAATTTTAATTTTATTA
1 AT-A-TTTAA-TTTATTA
*
6651069 ATTTTTA
1 ATATTTA
6651076 TATATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
11 3 0.08
12 7 0.17
14 7 0.17
15 6 0.15
16 4 0.10
17 5 0.12
18 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTAATTTATTA
Found at i:6651043 original size:18 final size:18
Alignment explanation
Indices: 6651022--6651086 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
6651012 ATTTAATTTA
6651022 TTAATATTTATATAAATT
1 TTAATATTTATATAAATT
6651040 TTAATATATTA-AT-AATT
1 TTAATAT-TTATATAAATT
*
6651057 TTAAT-TTTAT-TAATTT
1 TTAATATTTATATAAATT
6651073 TTATATATTTATAT
1 TTA-ATATTTATAT
6651087 TATTTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.10
16 7 0.17
17 11 0.28
18 14 0.35
19 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTTATATAAATT
Found at i:6651081 original size:52 final size:52
Alignment explanation
Indices: 6651005--6651121 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 52
6650995 TTTTATACTA
6651005 TAATTATATTTAATTTATTAATATTTATATAAATTTTAAT-ATATTAATA-ATTT
1 TAATTATA-TTAATTTATTAATATTTATAT-AATTTTAATAATA-TAATATATTT
* * *
6651058 TAATTTTATTAATTT-TTATATATTTATATTATTTTTATAATATAATATATTT
1 TAATTATATTAATTTATTA-ATATTTATATAATTTTAATAATATAATATATTT
6651110 TATATTATATTA
1 TA-ATTATATTA
6651122 TAATTATGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 15 0.27
52 26 0.46
53 15 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (52 bp):
TAATTATATTAATTTATTAATATTTATATAATTTTAATAATATAATATATTT
Found at i:6651139 original size:22 final size:21
Alignment explanation
Indices: 6651082--6651142 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
6651072 TTTATATATT
*
6651082 TATATTATT-TTTATAATATAA
1 TATATT-TTATTTATATTATAA
6651103 TATATTTTATATTATATTATAA
1 TATATTTTAT-TTATATTATAA
6651125 T-TATGTTTAATTTATATT
1 TATAT-TTT-ATTTATATT
6651143 TATATTTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 2 0.06
21 10 0.29
22 21 0.60
23 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATATTTTATTTATATTATAA
Found at i:6652411 original size:18 final size:21
Alignment explanation
Indices: 6652384--6652455 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
6652374 AAAAATTTTG
* *
6652384 ATAATGATAAAATTAATTGTT
1 ATAATAATAAAATTAATTATT
6652405 ATAATAATAAAATTAATTATT
1 ATAATAATAAAATTAATTATT
*
6652426 ATAATAA-AAAATAAAATTATT
1 ATAATAATAAAAT-TAATTATT
6652447 AATAA-AATA
1 -ATAATAATA
6652456 TACGTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.11
21 35 0.78
22 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAATAATAAAATTAATTATT
Found at i:6654087 original size:9 final size:9
Alignment explanation
Indices: 6654030--6654089 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
6654020 GTAAAATTAA
6654030 ATATATTTTT
1 ATAT-TTTTT
*
6654040 ATATTATTT
1 ATATTTTTT
6654049 A-ATTTATTT
1 ATATTT-TTT
6654058 A-ATTTTATT
1 ATATTTT-TT
*
6654067 ATCATATTTT
1 AT-ATTTTTT
6654077 ATATTTTTT
1 ATATTTTTT
6654086 ATAT
1 ATAT
6654090 AAATAATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
8 4 0.10
9 26 0.62
10 8 0.19
11 4 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
ATATTTTTT
Found at i:6654271 original size:2 final size:2
Alignment explanation
Indices: 6654264--6654288 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6654254 TTACTAAGTC
6654264 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6654289 GATAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6655560 original size:18 final size:19
Alignment explanation
Indices: 6655537--6655572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6655527 AAATTTATTT
6655537 TTTAAC-TTAATATTTTTA
1 TTTAACTTTAATATTTTTA
6655555 TTTAACTTTAATATTTTT
1 TTTAACTTTAATATTTTT
6655573 TCCAGATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAACTTTAATATTTTTA
Found at i:6657634 original size:21 final size:21
Alignment explanation
Indices: 6657583--6657642 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
6657573 CAATTTTGAT
* * *
6657583 ATAA-TAAAATAATATTAAAT
1 ATAATTAAAATAAAATCAAAC
*
6657603 AT-ATAAAAATAAAATCAAAC
1 ATAATTAAAATAAAATCAAAC
*
6657623 ATAATTAAAATATAATCAAA
1 ATAATTAAAATAAAATCAAA
6657643 ATACAGATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.03
20 16 0.50
21 15 0.47
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAATTAAAATAAAATCAAAC
Found at i:6658250 original size:25 final size:25
Alignment explanation
Indices: 6658188--6658251 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
6658178 AATTATGATA
* *
6658188 TTAATAATATTTATAAAATATAAAAT
1 TTAATTATATTTAT-GAATATAAAAT
* *
6658214 TTATTTATATTTATGAATATATAAT
1 TTAATTATATTTATGAATATAAAAT
6658239 TTAAATTA-ATTTA
1 TT-AATTATATTTA
6658252 AGTTTGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAATTATATTTATGAATATAAAAT
Found at i:6658310 original size:34 final size:35
Alignment explanation
Indices: 6658272--6658356 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 35
6658262 TATCATATTT
* * * *
6658272 TTTAATATATTTTTTAAAAATT-AATTTTTATTAA
1 TTTAATATATTTTTTAAAAATTAAAATATAAATAA
* **
6658306 TTTAATAT-TTTATTAAATTTTAAAATATAAATAA
1 TTTAATATATTTTTTAAAAATTAAAATATAAATAA
6658340 TTTAATATATTTTTTAA
1 TTTAATATATTTTTTAA
6658357 TATATATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 10 0.24
34 24 0.59
35 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTAATATATTTTTTAAAAATTAAAATATAAATAA
Found at i:6658316 original size:16 final size:15
Alignment explanation
Indices: 6658292--6658321 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6658282 TTTTTAAAAA
6658292 TTAATTTTTATTAAT
1 TTAATTTTTATTAAT
6658307 TTAATATTTTATTAA
1 TTAAT-TTTTATTAA
6658322 ATTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTTTTATTAAT
Found at i:6658324 original size:17 final size:17
Alignment explanation
Indices: 6658272--6658325 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
6658262 TATCATATTT
*
6658272 TTTAATATATTTTTTAAAA
1 TTTAATAT-TTTATT-AAA
*
6658291 ATTAAT-TTTTATT-AA
1 TTTAATATTTTATTAAA
6658306 TTTAATATTTTATTAAA
1 TTTAATATTTTATTAAA
6658323 TTT
1 TTT
6658326 TAAAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 10 0.33
18 1 0.03
19 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATATTTTATTAAA
Found at i:6658406 original size:25 final size:26
Alignment explanation
Indices: 6658371--6658462 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 26
6658361 TATTATAACA
6658371 ATATATATTTTATAT-AAAAAATTAT
1 ATATATATTTTATATAAAAAAATTAT
*
6658396 ATATATTTTTTATATAAAAAAATTAT
1 ATATATATTTTATATAAAAAAATTAT
* * *
6658422 GTAATATATATAATA-AATATAAAATTA-
1 AT-ATATATTTTATATAA-A-AAAATTAT
*
6658449 ATATATATTATATA
1 ATATATATTTTATA
6658463 ATTATAGAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
25 14 0.26
26 22 0.41
27 11 0.20
28 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
ATATATATTTTATATAAAAAAATTAT
Found at i:6660564 original size:19 final size:20
Alignment explanation
Indices: 6660540--6660590 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
6660530 TTTTTAATTG
6660540 AAAAATAAGTTTG-ATAAAA
1 AAAAATAAGTTTGTATAAAA
* *
6660559 AAAAATAAATTTGTTTAAAA
1 AAAAATAAGTTTGTATAAAA
* *
6660579 ATAACTAAGTTT
1 AAAAATAAGTTT
6660591 TGACTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAATAAGTTTGTATAAAA
Found at i:6661071 original size:24 final size:22
Alignment explanation
Indices: 6661026--6661072 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
6661016 TTAAAATATT
**
6661026 ATTTTTATAATAATATTTATAA
1 ATTTTTATAATAATATAAATAA
6661048 ATTTTTATAATTAAATATAAATAA
1 ATTTTTATAA-T-AATATAAATAA
6661072 A
1 A
6661073 AAAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTTATAATAATATAAATAA
Found at i:6662131 original size:11 final size:10
Alignment explanation
Indices: 6662113--6662167 Score: 67
Period size: 10 Copynumber: 5.3 Consensus size: 10
6662103 AGTGATATAT
6662113 ATTTTTTAAA
1 ATTTTTTAAA
6662123 ATGTTTTT-AA
1 AT-TTTTTAAA
6662133 ATTTTTTAATA
1 ATTTTTTAA-A
6662144 TATTTTTTAAA
1 -ATTTTTTAAA
*
6662155 TTTTTTTAAA
1 ATTTTTTAAA
6662165 ATT
1 ATT
6662168 AAATATGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.13
10 18 0.46
11 7 0.18
12 9 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:6662150 original size:21 final size:20
Alignment explanation
Indices: 6662113--6662166 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
6662103 AGTGATATAT
6662113 ATTTTTTAAAATGTTTTTAA
1 ATTTTTTAAAATGTTTTTAA
6662133 ATTTTTTAATATAT-TTTTTAA
1 ATTTTTTAA-A-ATGTTTTTAA
6662154 ATTTTTTTAAAAT
1 A-TTTTTTAAAAT
6662167 TAAATATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.35
21 10 0.32
22 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTTTAAAATGTTTTTAA
Found at i:6666109 original size:25 final size:24
Alignment explanation
Indices: 6666070--6666123 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
6666060 TGGTCCACTC
** *
6666070 TAAAATTTTCTAAAATTTTTAATA
1 TAAAATTTTCTAAAAAATTTAAAA
*
6666094 TAAAATTTTTTAAAAAAATTTAAAA
1 TAAAATTTTCT-AAAAAATTTAAAA
6666119 TAAAA
1 TAAAA
6666124 GTTTAAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATTTTCTAAAAAATTTAAAA
Found at i:6666396 original size:2 final size:2
Alignment explanation
Indices: 6666389--6666435 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
6666379 TAAGAGCAGC
* *
6666389 GT GT GT GT GT GT GT GT GC GT GC GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6666431 GT GT G
1 GT GT G
6666436 AGAGAGAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.04, G:0.51, T:0.45
Consensus pattern (2 bp):
GT
Found at i:6671237 original size:14 final size:14
Alignment explanation
Indices: 6671220--6671254 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6671210 TGAATTTTAA
*
6671220 ATTTAAATATTATT
1 ATTTAAAAATTATT
6671234 ATTTAAAAATTATT
1 ATTTAAAAATTATT
*
6671248 ATATAAA
1 ATTTAAA
6671255 GACATCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAAAAATTATT
Found at i:6671967 original size:20 final size:20
Alignment explanation
Indices: 6671942--6671990 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
6671932 TGTGAAACTA
6671942 TTTTTTAATTTGATAT-TTGT
1 TTTTTTAATTT-ATATATTGT
*
6671962 TTTTTT-ATTTATTTATTGT
1 TTTTTTAATTTATATATTGT
6671981 TTTATTTAAT
1 TTT-TTTAAT
6671991 ATTTTTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 9 0.36
21 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTTTTAATTTATATATTGT
Found at i:6674689 original size:16 final size:16
Alignment explanation
Indices: 6674662--6674716 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
6674652 AAATATGATA
6674662 ATTTTATATATTATATT
1 ATTTT-TATATTATATT
6674679 ATTTTTATATTATATT
1 ATTTTTATATTATATT
6674695 ATATATTTAT-TT-TATT
1 AT-T-TTTATATTATATT
6674711 -TTTTTA
1 ATTTTTA
6674717 ATGAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.11
14 1 0.03
15 1 0.03
16 17 0.47
17 8 0.22
18 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTATATTATATT
Found at i:6675219 original size:27 final size:29
Alignment explanation
Indices: 6675086--6675245 Score: 100
Period size: 32 Copynumber: 5.4 Consensus size: 29
6675076 AATAATTGTT
** *
6675086 AAATATATT-AAATTA-AAATATAC-ATA
1 AAATATATTAAAATTATATTTATACTAAA
*
6675112 AAAT-TATTAAAATTATATTTATATTAAATAATA
1 AAATATATTAAAATTATA-TT-TA-T-ACTAA-A
**
6675145 AAATATAAATTAAAA-TATATTTATGTTAAA
1 AAATAT--ATTAAAATTATATTTATACTAAA
6675175 ATAATAATTATCTAAAATT-TATTTATACTAAA
1 A-AAT-A-TAT-TAAAATTATATTTATACTAAA
*
6675207 AAATA-ATTAAAATTATATTTATATTAAA
1 AAATATATTAAAATTATATTTATACTAAA
*
6675235 TAATATATTAA
1 AAATATATTAA
6675246 TATAATTAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
25 4 0.04
26 10 0.09
27 8 0.08
28 18 0.17
29 7 0.07
30 4 0.04
31 12 0.11
32 20 0.19
33 9 0.08
34 3 0.03
35 4 0.04
36 7 0.07
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATATATTAAAATTATATTTATACTAAA
Found at i:6675239 original size:28 final size:29
Alignment explanation
Indices: 6675145--6675245 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 29
6675135 TTAAATAATA
* *
6675145 AAAT-ATAAATTAAAA-TATATTTATGTT
1 AAATAATATATTAAAATTATATTTATATT
*
6675172 AAAATAATAATTATCTAAAATT-TATTTATACT
1 -AAATAAT-A-TAT-TAAAATTATATTTATATT
*
6675204 AAAAAATA-ATTAAAATTATATTTATATT
1 AAATAATATATTAAAATTATATTTATATT
6675232 AAATAATATATTAA
1 AAATAATATATTAA
6675246 TATAATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.12
28 22 0.37
29 7 0.12
30 2 0.03
31 8 0.13
32 13 0.22
33 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (29 bp):
AAATAATATATTAAAATTATATTTATATT
Found at i:6675255 original size:21 final size:18
Alignment explanation
Indices: 6675209--6675256 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
6675199 ATACTAAAAA
*
6675209 ATAATTAAAATTATATTT
1 ATAATTAAAAATATATTT
6675227 AT-ATTAAATAATATATTAAT
1 ATAATTAAA-AATATATT--T
6675247 ATAATTAAAA
1 ATAATTAAAA
6675257 TAAATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
20 4 0.16
21 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAAAAATATATTT
Found at i:6675268 original size:14 final size:15
Alignment explanation
Indices: 6675244--6675281 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
6675234 ATAATATATT
6675244 AATATAATTAAAATA
1 AATATAATTAAAATA
6675259 AATA-AATTAAAATTTA
1 AATATAATTAAAA--TA
6675275 AATATAA
1 AATATAA
6675282 AAAATTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 6 0.30
17 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATAATTAAAATA
Found at i:6676067 original size:17 final size:17
Alignment explanation
Indices: 6676045--6676078 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6676035 ACTAGACCCA
6676045 TTCAACTTTGAAGTGGG
1 TTCAACTTTGAAGTGGG
6676062 TTCAACTTTGAAGTGGG
1 TTCAACTTTGAAGTGGG
6676079 CCACGATTTG
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:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (17 bp):
TTCAACTTTGAAGTGGG
Found at i:6686012 original size:21 final size:21
Alignment explanation
Indices: 6685988--6686034 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6685978 AAATGAAAAG
6685988 AAAAAGTGCAAAAAC-AAAATAA
1 AAAAAG-G-AAAAACAAAAATAA
*
6686010 AAAAAGGAACAACAAAAATAA
1 AAAAAGGAAAAACAAAAATAA
6686031 AAAA
1 AAAA
6686035 TGAGGACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (21 bp):
AAAAAGGAAAAACAAAAATAA
Found at i:6686291 original size:9 final size:9
Alignment explanation
Indices: 6686277--6686302 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6686267 CCCAATCCTA
6686277 AAAAAAAAC
1 AAAAAAAAC
6686286 AAAAAAAAC
1 AAAAAAAAC
6686295 AAAAAAAA
1 AAAAAAAA
6686303 AAACCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:6687389 original size:27 final size:27
Alignment explanation
Indices: 6687358--6688096 Score: 1127
Period size: 27 Copynumber: 27.0 Consensus size: 27
6687348 GTGACATTTT
* *
6687358 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
6687386 TTTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687413 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
6687441 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687468 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
6687495 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687522 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687549 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
6687577 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
6687605 CTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
6687633 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687660 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
6687687 CTTTTAAGTCCACAACTTTGTGGCATGC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
6687715 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
6687742 CTTTTAAGTCCACAACTCTGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687769 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
6687796 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687823 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687850 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
6687878 CTTTTAAGACTACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687905 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
6687932 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
6687960 ATTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6687987 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
6688015 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
6688042 CTTTTAAGTCCACAACTCCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
6688069 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
6688096 C
1 C
6688097 ATTCCAAAGC
Statistics
Matches: 651, Mismatches: 54, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
27 446 0.69
28 205 0.31
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:6687458 original size:82 final size:81
Alignment explanation
Indices: 6687358--6688096 Score: 1129
Period size: 82 Copynumber: 9.0 Consensus size: 81
6687348 GTGACATTTT
* * * *
6687358 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCATAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
6687423 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
6687441 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
6687506 ACAACTTCGTGGCACC
66 ACAACTCCGTGGCACC
*
6687522 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
6687587 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
*
6687605 CTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCTACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
6687670 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
** *
6687687 CTTTTAAGTCCACAACTTTGTGGCATGCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* **
6687752 CACAACTCTGTGGCATT
65 CACAACTCCGTGGCACC
6687769 CTTTTAAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
6687833 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * * *
6687850 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACTACAACTCTGTAGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
6687915 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
6687932 CTTTTAAGTCCATAACTCCGTGGCATCTATTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
6687997 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * * *
6688015 CTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCATGGCATCCTTTTAAATCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
6688080 ACAACTCTGTGGCACC
66 ACAACTCCGTGGCACC
6688096 C
1 C
6688097 ATTCCAAAGC
Statistics
Matches: 605, Mismatches: 42, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
80 2 0.00
81 168 0.28
82 302 0.50
83 109 0.18
84 24 0.04
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:6688603 original size:32 final size:32
Alignment explanation
Indices: 6688079--6688589 Score: 844
Period size: 32 Copynumber: 16.0 Consensus size: 32
6688069 CTTTTAAATC
* * *
6688079 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
6688110 CACAAGTCGGTGGCAACCTATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
6688142 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688174 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688206 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688238 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
6688270 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688302 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
6688334 CACAAGTCCGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688366 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
6688398 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
6688430 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
6688462 CACAAGTCCGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
6688494 CATAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
6688526 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
6688558 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
6688590 TGTAAATCAG
Statistics
Matches: 453, Mismatches: 26, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
31 12 0.03
32 441 0.97
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:6689171 original size:20 final size:20
Alignment explanation
Indices: 6689146--6689197 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
6689136 TACCTTGATG
*
6689146 TATCGATACATTTTTCAATA
1 TATCGATACATTTATCAATA
* * *
6689166 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATA
6689186 TATCGATACATT
1 TATCGATACATT
6689198 ATGTCTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTATCAATA
Found at i:6690144 original size:23 final size:23
Alignment explanation
Indices: 6690114--6690162 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
6690104 TGACCATGCA
6690114 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
6690137 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
6690160 TTT
1 TTT
6690163 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTTTATTATGTTTCATGCATT
Found at i:6690169 original size:20 final size:21
Alignment explanation
Indices: 6690108--6690162 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 21
6690098 AGCCTTTGAC
6690108 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
6690129 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTATTATGTTT
6690152 CATGCATTTTT
1 CATGCATTTTT
6690163 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:6697434 original size:12 final size:12
Alignment explanation
Indices: 6697417--6697460 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 12
6697407 TTACATGAGA
6697417 AAAAATTTAATT
1 AAAAATTTAATT
6697429 AAAAATTTAATCAT
1 AAAAATTTAAT--T
6697443 ATAAAATTATAATT
1 A-AAAATT-TAATT
6697457 AAAA
1 AAAA
6697461 TATCATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.39
13 3 0.11
14 4 0.14
15 6 0.21
16 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAATTTAATT
Found at i:6697437 original size:28 final size:29
Alignment explanation
Indices: 6697398--6697477 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 29
6697388 CAAGGAGTTT
* *
6697398 ATTAAAATTTTACATGAGAAAAAATT-TA
1 ATTAAAAATTTACATAAGAAAAAATTATA
* * *
6697426 ATTAAAAATTTA-ATCATATAAAATTATA
1 ATTAAAAATTTACATAAGAAAAAATTATA
*
6697454 ATT-AAAATAT-CATAAGAAAAAATT
1 ATTAAAAATTTACATAAGAAAAAATT
6697478 GAAATGAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTAAAAATTTACATAAGAAAAAATTATA
Found at i:6699784 original size:28 final size:29
Alignment explanation
Indices: 6699729--6699787 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6699719 ATATGCATGC
* *
6699729 AAAATGACTTAGATGGAACCAAAAACTTA
1 AAAATAACTTAGATGAAACCAAAAACTTA
*
6699758 AAAATAACTTAGATGAAACC-AGAACTTA
1 AAAATAACTTAGATGAAACCAAAAACTTA
6699786 AA
1 AA
6699788 GAAATGTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAATAACTTAGATGAAACCAAAAACTTA
Found at i:6700029 original size:60 final size:60
Alignment explanation
Indices: 6699951--6700202 Score: 224
Period size: 60 Copynumber: 4.2 Consensus size: 60
6699941 TGTAACCAAG
* * * * * *
6699951 ACTTCACGAAATGACCTAGATAAAACTAGAAACCTAAACAATGACTTGGGCGAAACTAAA
1 ACTTAACGAAATGGCCTAGATGAAACTAAAAACCTAAACAATGACTTGAGCAAAACTAAA
* * * *
6700011 ACTTAACGAAATGGCCTAGATGAAACCAAAAACTTAAACAATGACTTGAGCAAAACCAAG
1 ACTTAACGAAATGGCCTAGATGAAACTAAAAACCTAAACAATGACTTGAGCAAAACTAAA
* * * * * *
6700071 ACTTGAC-AAGATGGCCTAGAGGAAACTACAAATCTAAACAATGACTTGAGCGAAA-TCAAG
1 ACTTAACGAA-ATGGCCTAGATGAAACTAAAAACCTAAACAATGACTTGAGCAAAACT-AAA
* * * * * * *
6700131 TCTCAACAAAATGGCCTAGACGAAACTATAAACTTAGAA-AATAACTTG-GACAAAACTAAA
1 ACTTAACGAAATGGCCTAGATGAAACTAAAAACCTA-AACAATGACTTGAG-CAAAACTAAA
*
6700191 ACTTAAAGAAAT
1 ACTTAACGAAAT
6700203 AATTTGGATG
Statistics
Matches: 154, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
59 3 0.02
60 146 0.95
61 5 0.03
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (60 bp):
ACTTAACGAAATGGCCTAGATGAAACTAAAAACCTAAACAATGACTTGAGCAAAACTAAA
Found at i:6700143 original size:120 final size:120
Alignment explanation
Indices: 6699944--6700166 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 120
6699934 ACTTGTGTGT
* * *
6699944 AACCAAGACTTCACGAAATGACCTAGATAAAACTAGAAACCTAAACAATGACTTGGGCGAAACTA
1 AACCAAGACTTCACGAAATGACCTAGAGAAAACTACAAACCTAAACAATGACTTGAGCGAAACTA
* * *
6700009 AAACTTAACGAAATGGCCTAGATGAAACCAAAAACTTAAACAATGACTTGAGCAA
66 AAACTCAACAAAATGGCCTAGACGAAACCAAAAACTTAAACAATGACTTGAGCAA
* * * *
6700064 AACCAAGACTTGAC-AAGATGGCCTAGAGGAAACTACAAATCTAAACAATGACTTGAGCGAAA-T
1 AACCAAGACTTCACGAA-ATGACCTAGAGAAAACTACAAACCTAAACAATGACTTGAGCGAAACT
** * *
6700127 CAAGTCTCAACAAAATGGCCTAGACGAAACTATAAACTTA
65 -AAAACTCAACAAAATGGCCTAGACGAAACCAAAAACTTA
6700167 GAAAATAACT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
119 3 0.03
120 84 0.97
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (120 bp):
AACCAAGACTTCACGAAATGACCTAGAGAAAACTACAAACCTAAACAATGACTTGAGCGAAACTA
AAACTCAACAAAATGGCCTAGACGAAACCAAAAACTTAAACAATGACTTGAGCAA
Found at i:6700187 original size:30 final size:30
Alignment explanation
Indices: 6700153--6700210 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
6700143 GGCCTAGACG
*
6700153 AAACTATAAACTTAGA-AAATAACTTGGACA
1 AAACTA-AAACTTAAAGAAATAACTTGGACA
*
6700183 AAACTAAAACTTAAAGAAATAATTTGGA
1 AAACTAAAACTTAAAGAAATAACTTGGA
6700211 TGAAACCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (30 bp):
AAACTAAAACTTAAAGAAATAACTTGGACA
Found at i:6701551 original size:17 final size:17
Alignment explanation
Indices: 6701529--6701572 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6701519 AAATATGATA
*
6701529 TAAAATATAAATAATAT
1 TAAAATATAAACAATAT
**
6701546 TAAAATACGAACAATAT
1 TAAAATATAAACAATAT
6701563 TAAAATATAA
1 TAAAATATAA
6701573 TATGGATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATATAAACAATAT
Found at i:6701616 original size:19 final size:19
Alignment explanation
Indices: 6701592--6701648 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
6701582 TTAATGTATC
6701592 AAAATTTAAATAAATATAT
1 AAAATTTAAATAAATATAT
*
6701611 AAAATTTTAA-AAATAATTAT
1 AAAATTTAAATAAAT-A-TAT
* * *
6701631 AATATGTAAATATATATA
1 AAAATTTAAATAAATATA
6701649 AATACATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 11 0.37
21 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTTAAATAAATATAT
Found at i:6701892 original size:2 final size:2
Alignment explanation
Indices: 6701885--6701926 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6701875 TGGAGAAATG
6701885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6701927 TGTTTTCCGA
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):
AT
Found at i:6702046 original size:17 final size:18
Alignment explanation
Indices: 6702019--6702064 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
6702009 TAGAACTGAG
*
6702019 TTTTGATTTTTACTTTTT
1 TTTTTATTTTTACTTTTT
6702037 TTTTTATTTTTACTTTTT
1 TTTTTATTTTTACTTTTT
*
6702055 TTTTTGTTTT
1 TTTTTATTTT
6702065 AGTTCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.83
Consensus pattern (18 bp):
TTTTTATTTTTACTTTTT
Found at i:6702461 original size:19 final size:19
Alignment explanation
Indices: 6702410--6702464 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
6702400 ATACAATTAT
6702410 AAAAATT-TAAAAAA-T--
1 AAAAATTATAAAAAATTCA
*
6702425 AAAAATTATTAAAAATTCA
1 AAAAATTATAAAAAATTCA
6702444 AAAAATTATAAAAAATTCA
1 AAAAATTATAAAAAATTCA
6702463 AA
1 AA
6702465 GAATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 1 0.03
19 20 0.59
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAAAAATTCA
Found at i:6702835 original size:19 final size:20
Alignment explanation
Indices: 6702811--6702848 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6702801 TTTTAAAAAA
*
6702811 TTTTT-AATTTTAATTTAAT
1 TTTTTAAATTTAAATTTAAT
6702830 TTTTTAAATTTAAATTTAA
1 TTTTTAAATTTAAATTTAA
6702849 ATTTGATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAAATTTAAATTTAAT
Found at i:6703240 original size:3 final size:3
Alignment explanation
Indices: 6703234--6703276 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
6703224 ATACTTTATT
* *
6703234 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTT ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6703277 AATTTTGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:6703281 original size:12 final size:12
Alignment explanation
Indices: 6703231--6703280 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
6703221 TGCATACTTT
6703231 ATTATAATAATA
1 ATTATAATAATA
*
6703243 ATAATAATAATA
1 ATTATAATAATA
*
6703255 ATAATAATAATA
1 ATTATAATAATA
*
6703267 TTTATAATAA-A
1 ATTATAATAATA
6703278 ATT
1 ATT
6703281 TTGAATTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 3 0.09
12 31 0.91
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATAATAATA
Found at i:6703469 original size:20 final size:20
Alignment explanation
Indices: 6703444--6703486 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
6703434 TCTGTGCATG
*
6703444 AAATTTACTTATTT-TGAAGT
1 AAATTTACTT-TTTAAGAAGT
6703464 AAATTTACTTTTTAAGAAGT
1 AAATTTACTTTTTAAGAAGT
6703484 AAA
1 AAA
6703487 CTAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (20 bp):
AAATTTACTTTTTAAGAAGT
Found at i:6704203 original size:15 final size:16
Alignment explanation
Indices: 6704178--6704207 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6704168 GAGAGAACAA
6704178 AAAAAATTTAAAAATT
1 AAAAAATTTAAAAATT
6704194 AAAAAA-TTAAAAAT
1 AAAAAATTTAAAAAT
6704208 ATTGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATTTAAAAATT
Found at i:6707691 original size:29 final size:28
Alignment explanation
Indices: 6707645--6707700 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
6707635 GGATCTGTTC
6707645 TTTGCAATAGATAACATATGAATTTTATT
1 TTTGCAATAGATAACATAT-AATTTTATT
*
6707674 TTTGCAATTAG-TAGCATATAATTTTAT
1 TTTGCAA-TAGATAACATATAATTTTAT
6707701 GTTGCTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 14 0.56
30 3 0.12
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (28 bp):
TTTGCAATAGATAACATATAATTTTATT
Found at i:6708766 original size:2 final size:2
Alignment explanation
Indices: 6708761--6708799 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6708751 GTTTCTTTTT
6708761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6708800 CAATTACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6709109 original size:79 final size:80
Alignment explanation
Indices: 6708977--6709125 Score: 203
Period size: 79 Copynumber: 1.9 Consensus size: 80
6708967 ATCAAATGTA
* * *
6708977 AAGAGTATAATATACATCTTACCAAGTTATTATCATGAGCATTGGATCCACATCAAATCTAAAAT
1 AAGAGTATAACATACATCTTACCAAGTTATTATCATGAGCATCGGATCCACATCAAATCTAAAAC
6709042 CCTTAAGAAAAATTG
66 CCTTAAGAAAAATTG
* * * * *
6709057 AAGAGTATAACATAGATCTTA-CAAGTTTTTATCAT-AGGCCTCGTATCCACATCTAATCTAAAA
1 AAGAGTATAACATACATCTTACCAAGTTATTATCATGA-GCATCGGATCCACATCAAATCTAAAA
6709120 CCCTTA
65 CCCTTA
6709126 TTCTAATCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.02
79 40 0.67
80 19 0.32
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (80 bp):
AAGAGTATAACATACATCTTACCAAGTTATTATCATGAGCATCGGATCCACATCAAATCTAAAAC
CCTTAAGAAAAATTG
Found at i:6714144 original size:2 final size:2
Alignment explanation
Indices: 6714137--6714182 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
6714127 GTTTAATTTA
* *
6714137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6714179 AT AT
1 AT AT
6714183 TTGTCAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6714343 original size:11 final size:11
Alignment explanation
Indices: 6714315--6714370 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
6714305 ATTAGGTTCA
6714315 ATAATATAAAAT
1 ATAATAT-AAAT
*
6714327 AAAATATAAAT
1 ATAATATAAAT
6714338 ATAATATATTTAAT
1 ATAATATA---AAT
*
6714352 AT-ATATAAAA
1 ATAATATAAAT
6714362 ATAATATAA
1 ATAATATAA
6714371 TAATTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.11
11 17 0.46
12 6 0.16
13 5 0.14
14 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:6714380 original size:29 final size:32
Alignment explanation
Indices: 6714315--6714390 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 32
6714305 ATTAGGTTCA
*
6714315 ATAATATAAAATAAAATATAAATATAATATATT
1 ATAATAT-ATATAAAATATAAATATAATATATT
6714348 -TAATATATATAAAA-AT-AATATAATA-ATT
1 ATAATATATATAAAATATAAATATAATATATT
*
6714376 ATAATATATTTAAAA
1 ATAATATATATAAAA
6714391 CAATTAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 3 0.08
29 22 0.55
30 2 0.05
31 7 0.17
32 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
ATAATATATATAAAATATAAATATAATATATT
Found at i:6714382 original size:38 final size:35
Alignment explanation
Indices: 6714314--6714388 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 35
6714304 AATTAGGTTC
6714314 AATAATATAAAATAAAATATAAATATAATATATTT
1 AATAATATAAAATAAAATATAAATATAATATATTT
* *
6714349 AATATATATAAAAATAATATAATAATTATAATATATTT
1 AATA-ATAT-AAAATAAAAT-ATAAATATAATATATTT
6714387 AA
1 AA
6714389 AACAATTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 4 0.11
36 4 0.11
37 9 0.26
38 18 0.51
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (35 bp):
AATAATATAAAATAAAATATAAATATAATATATTT
Found at i:6716052 original size:21 final size:22
Alignment explanation
Indices: 6716014--6716055 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6716004 TGATACTACT
* *
6716014 TTTTTTTTAAGGATAAATTATC
1 TTTTTTTAAAAGATAAATTATC
6716036 TTTTTTTAAAAGA-AAATTAT
1 TTTTTTTAAAAGATAAATTAT
6716056 TCAAGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTTTTAAAAGATAAATTATC
Found at i:6716739 original size:57 final size:57
Alignment explanation
Indices: 6716624--6716740 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 57
6716614 TAAGCCAAAA
* ** *
6716624 AAATGAAGATATTTTAATAATTAAACCAAAATTTGACAAATATTAATTTCATATATAG
1 AAATGAAGATATTTTAATAATTAAA-CAAAATGTGACAAATATTAATTAAATAAATAG
* *
6716682 AAATGAAGATATTTTTAATATTTTAAA-AAAA-GTGACTAATATTAATTAAATAAATAG
1 AAATGAAGATA-TTTTAATA-ATTAAACAAAATGTGACAAATATTAATTAAATAAATAG
6716739 AA
1 AA
6716741 TCCTAGCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
57 23 0.45
58 15 0.29
59 8 0.16
60 5 0.10
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (57 bp):
AAATGAAGATATTTTAATAATTAAACAAAATGTGACAAATATTAATTAAATAAATAG
Found at i:6716968 original size:15 final size:17
Alignment explanation
Indices: 6716938--6716975 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
6716928 TTTAATATGT
6716938 ATTTGAATTAAAATATA
1 ATTTGAATTAAAATATA
6716955 ATTT-AATT-AAATATA
1 ATTTGAATTAAAATATA
6716970 ATTTGA
1 ATTTGA
6716976 TAGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTTGAATTAAAATATA
Found at i:6716984 original size:21 final size:22
Alignment explanation
Indices: 6716958--6717007 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6716948 AAATATAATT
* * *
6716958 TAATTAAATATAA-TTTGATAG
1 TAATTAAAGATAACTTTAATAC
6716979 TAATTAAAGATAACTTTAATAC
1 TAATTAAAGATAACTTTAATAC
6717001 TAATTAA
1 TAATTAA
6717008 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (22 bp):
TAATTAAAGATAACTTTAATAC
Found at i:6718688 original size:21 final size:19
Alignment explanation
Indices: 6718647--6718718 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
6718637 ATATTATTGA
6718647 ATTTAAATTTAAATAATAAT
1 ATTTAAATTT-AATAATAAT
6718667 ATTTAAATTTAATCAGATAAT
1 ATTTAAATTTAAT-A-ATAAT
** *
6718688 AAATAAATTT-AT-ATATT
1 ATTTAAATTTAATAATAAT
*
6718705 A-TTAAAATTAATAA
1 ATTTAAATTTAATAA
6718719 CAGAAATTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.14
17 7 0.16
18 1 0.02
19 3 0.07
20 13 0.30
21 13 0.30
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
ATTTAAATTTAATAATAAT
Found at i:6718763 original size:20 final size:20
Alignment explanation
Indices: 6718738--6718779 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
6718728 GATTCATTAC
6718738 AATCACTAACATATACACGT
1 AATCACTAACATATACACGT
6718758 AATCACTAACATATACACGT
1 AATCACTAACATATACACGT
6718778 AA
1 AA
6718780 AGAGCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (20 bp):
AATCACTAACATATACACGT
Found at i:6720760 original size:2 final size:2
Alignment explanation
Indices: 6720753--6720779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6720743 GTGGACGTGG
6720753 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 A
6720780 AATAAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6722246 original size:24 final size:24
Alignment explanation
Indices: 6722219--6722264 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6722209 GCTTGAATTA
6722219 TAAAAATTTATTTT-TGTATTTATT
1 TAAAAATTTATTTTAT-TATTTATT
*
6722243 TAAAATTTTATTTTATTATTTA
1 TAAAAATTTATTTTATTATTTA
6722265 ATAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TAAAAATTTATTTTATTATTTATT
Found at i:6723091 original size:19 final size:19
Alignment explanation
Indices: 6723067--6723133 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
6723057 TTTAATAATT
6723067 TATATTATATAAATTTTTA
1 TATATTATATAAATTTTTA
* *
6723086 TATATTA-ATATATTTATA
1 TATATTATATAAATTTTTA
* * *
6723104 TAATATTTTAATTATTTTTTA
1 T-ATATTAT-ATAAATTTTTA
6723125 -ATATTATAT
1 TATATTATAT
6723134 TATGCTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
18 12 0.32
19 18 0.49
21 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTATATAAATTTTTA
Found at i:6723119 original size:28 final size:27
Alignment explanation
Indices: 6723067--6723119 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
6723057 TTTAATAATT
*
6723067 TATATTATATAAATTTTTATATATTAA
1 TATATTATATAAATTTTAATATATTAA
6723094 TATATTTATATAATATTTTAAT-TATT
1 TATA-TTATATAA-ATTTTAATATATT
6723120 TTTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATTATATAAATTTTAATATATTAA
Found at i:6727307 original size:2 final size:2
Alignment explanation
Indices: 6727300--6727334 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6727290 AAATTTTCCT
6727300 TC TC TC TC 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 TC TC TC TC T
6727335 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.