Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 10 of 292
Found at i:2791505 original size:14 final size:14
Alignment explanation
Indices: 2791453--2791515 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
2791443 TTTTGAGCCC
* *
2791453 TAAATCTTAAGCCC
1 TAAATCTTAAACCT
* **
2791467 TAAGTCTTAAGTCT
1 TAAATCTTAAACCT
*
2791481 TAAACCTTAAACCT
1 TAAATCTTAAACCT
*
2791495 TAAATCTTAAATCT
1 TAAATCTTAAACCT
2791509 TAAATCT
1 TAAATCT
2791516 ATATCCTAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (14 bp):
TAAATCTTAAACCT
Found at i:2792514 original size:3 final size:3
Alignment explanation
Indices: 2792502--2792530 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2792492 CCCCTTTAAC
2792502 AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2792531 GCAGTCACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2793870 original size:12 final size:11
Alignment explanation
Indices: 2793839--2793869 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2793829 CTGTTAAAAG
2793839 GGGTTTTTTAA
1 GGGTTTTTTAA
2793850 GGGTTTTTTAA
1 GGGTTTTTTAA
2793861 GGGTTTTTT
1 GGGTTTTTT
2793870 TTTCAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (11 bp):
GGGTTTTTTAA
Found at i:2794245 original size:21 final size:22
Alignment explanation
Indices: 2794220--2794267 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2794210 AACATTCTGC
* *
2794220 AAATTTAT-AAATTGTTTTTTG
1 AAATTTATAAAAATGTTTTTTA
2794241 AAA-TTATAAAAATGTTTTTTA
1 AAATTTATAAAAATGTTTTTTA
2794262 AAATTT
1 AAATTT
2794268 TAATTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
AAATTTATAAAAATGTTTTTTA
Found at i:2796366 original size:41 final size:41
Alignment explanation
Indices: 2796309--2796391 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
2796299 CCTGGCGCAT
*
2796309 AATTTCTCATATCAAACACTTATGAAATTACACAAATTTAA
1 AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
* *
2796350 AATTTCTCATGTCAAACACTTAAGGAATTACACAAATTTAA
1 AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
2796391 A
1 A
2796392 GGGGAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.33
Consensus pattern (41 bp):
AATTTCTCATATCAAACACTTAAGAAATTACACAAATTTAA
Found at i:2797275 original size:96 final size:96
Alignment explanation
Indices: 2797098--2797292 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
2797088 CCATATTTTT
* ** * * ** *
2797098 TGGTACACAAACTCCATGGTGATCACTATCAACATGATCACCGACTCTCCCTGCTAGTGGGATCA
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCAACAACTCTCCCAACTAGTGAGATCA
*
2797163 ACGGATCATGGCTTAATGGTAGAATATGAGA
66 ACGGATAATGGCTTAATGGTAGAATATGAGA
* * *
2797194 TGGTACACAAGCTCCATGGTGATCACTACCAACACAATCAACAACTC-CCACAATTGGTGAGATC
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCAACAACTCTCC-CAACTAGTGAGATC
* * *
2797258 AAGGGATAATGGTTTAATGGTAGAATATGATA
65 AACGGATAATGGCTTAATGGTAGAATATGAGA
2797290 TGG
1 TGG
2797293 AAGCTGCATC
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 2 0.02
96 81 0.98
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (96 bp):
TGGTACACAAACTCCATGGTGATCACTACCAACACAATCAACAACTCTCCCAACTAGTGAGATCA
ACGGATAATGGCTTAATGGTAGAATATGAGA
Found at i:2798435 original size:133 final size:131
Alignment explanation
Indices: 2798282--2798659 Score: 407
Period size: 133 Copynumber: 2.8 Consensus size: 131
2798272 TTTTAAATTG
*
2798282 AATATTTTGACTATTTTAATTTTAAAGATAAAATATCT-TTTATCCTTTCATAAAATTTTAAAAC
1 AATATTTTGA-TTTTTTAATTTTAAAGATAAAATAT-TATTTATCCTTTCATAAAATTTTAAAAC
*
2798346 ATATTACTTATCCTTTCATAAAATTTTAAAACTTTAACTATTTAAATATTAAAGATAAATAATAT
64 ATATTATTTAT-CTTTCATAAAATTTTAAAA-TTTAACTATTTAAATATTAAAGATAAATAATAT
2798411 CTT-A
127 CTTAA
* * *
2798415 AATATTTTGATTGTTTTAATTTT-AAGAATAAAATATTATTTATCCTTTAATAAAATTTAAAAAA
1 AATATTTTGATT-TTTTAATTTTAAAG-ATAAAATATTATTTATCCTTTCATAAAATTTTAAAAC
* *
2798479 ATATTATTTATCTATTCATAAAA-TTT----TTTAAC-AGTTAAAATATTAAGGATAAATAATAT
64 ATATTATTTATCT-TTCATAAAATTTTAAAATTTAACTA-TTTAAATATTAAAGATAAATAATAT
*
2798538 TTTAA
127 CTTAA
* * * *
2798543 AATATTTTGACTTTTTTAATTTGAATGATAAAATATTATTATTTATCATTTCATCAAATTTTAGA
1 AATATTTTGA-TTTTTTAATTTTAAAGAT-AAA-A-TATTATTTATCCTTTCATAAAATTTTA-A
* * * *
2798608 AAC-TATTATTTCTGTTTTCTTAAAATTTTCAAAATTTAACTGTTTAAATATT
61 AACATATTATTTAT-CTTTCATAAAATTTT-AAAATTTAACTATTTAAATATT
2798660 TTAAATATTT
Statistics
Matches: 205, Mismatches: 20, Indels: 36
0.79 0.08 0.14
Matches are distributed among these distances:
126 1 0.00
127 31 0.15
128 22 0.11
129 7 0.03
130 1 0.00
131 40 0.20
132 17 0.08
133 71 0.35
137 15 0.07
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (131 bp):
AATATTTTGATTTTTTAATTTTAAAGATAAAATATTATTTATCCTTTCATAAAATTTTAAAACAT
ATTATTTATCTTTCATAAAATTTTAAAATTTAACTATTTAAATATTAAAGATAAATAATATCTTA
A
Found at i:2798482 original size:32 final size:32
Alignment explanation
Indices: 2798444--2798504 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2798434 TTTTAAGAAT
2798444 AAAATATTATTTATCCT-TTAATAAAATTTAAA
1 AAAATATTATTTAT-CTATTAATAAAATTTAAA
*
2798476 AAAATATTATTTATCTATTCATAAAATTT
1 AAAATATTATTTATCTATTAATAAAATTT
2798505 TTTAACAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAATATTATTTATCTATTAATAAAATTTAAA
Found at i:2801176 original size:15 final size:15
Alignment explanation
Indices: 2801156--2801189 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2801146 CCGTAAAAAT
* *
2801156 AAATAAATATAATAA
1 AAATAAAAAAAATAA
2801171 AAATAAAAAAAATAA
1 AAATAAAAAAAATAA
2801186 AAAT
1 AAAT
2801190 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAAAAAAATAA
Found at i:2802579 original size:12 final size:12
Alignment explanation
Indices: 2802562--2802627 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
2802552 TTTTTATTTA
*
2802562 TATATTATTCAT
1 TATATTATACAT
**
2802574 TATATTAT-TTT
1 TATATTATACAT
2802585 TATTATTATACAT
1 TA-TATTATACAT
* *
2802598 TTTATTTATAAAT
1 TATA-TTATACAT
*
2802611 TTTATTATACAT
1 TATATTATACAT
2802623 TATAT
1 TATAT
2802628 GTTTTACTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
11 3 0.07
12 27 0.63
13 13 0.30
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATTATACAT
Found at i:2802606 original size:25 final size:25
Alignment explanation
Indices: 2802549--2802623 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
2802539 ATAATATATA
*
2802549 TTATTT-TTATTTATATATTATTCATT
1 TTATTTATT-TTTAT-TATTATACATT
*
2802575 ATA-TTATTTTTATTATTATACATT
1 TTATTTATTTTTATTATTATACATT
**
2802599 TTATTTATAAATT-TTATTATACATT
1 TTATTTAT-TTTTATTATTATACATT
2802624 ATATGTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
24 12 0.29
25 23 0.56
26 6 0.15
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATTTATTTTTATTATTATACATT
Found at i:2802801 original size:22 final size:21
Alignment explanation
Indices: 2802776--2802816 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2802766 AGTTATCATA
* *
2802776 TTATTATATTTCATTATATTTT
1 TTATTACATATCA-TATATTTT
2802798 TTATTACATATCATATATT
1 TTATTACATATCATATATT
2802817 ATTATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTACATATCATATATTTT
Found at i:2802861 original size:7 final size:7
Alignment explanation
Indices: 2802847--2802882 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
2802837 TTATCTTCCT
2802847 TTTATTA
1 TTTATTA
*
2802854 TATATTA
1 TTTATTA
2802861 TTTCATTA
1 TTT-ATTA
2802869 TTTATTA
1 TTTATTA
2802876 TTTATTA
1 TTTATTA
2802883 GTATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:2802874 original size:15 final size:14
Alignment explanation
Indices: 2802847--2802887 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
2802837 TTATCTTCCT
2802847 TTTATTATATATTA
1 TTTATTATATATTA
*
2802861 TTTCATTATTTATTA
1 TTT-ATTATATATTA
2802876 TTTATTAGTATA
1 TTTATTA-TATA
2802888 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATTATATATTA
Found at i:2815046 original size:44 final size:44
Alignment explanation
Indices: 2814595--2815057 Score: 532
Period size: 44 Copynumber: 10.5 Consensus size: 44
2814585 GAGACAATAT
* * *
2814595 AGATCGAAAATAGCAGATTTGGCGTCTCTATATTGTCAGAAAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * * * *
2814639 AAATCGAAAAGAACAGATTTGGTGTCTCTGTATTATCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * ** *
2814683 AGATCGAACATAGAAGATTTAACGTCTCTGTATTATCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* *
2814727 AGATCGAAGATAGCAGATTTGACGTCTCTGCATTGTCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
2814771 AGATCGAAGAGAGCAGATTTGACGTCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
**
2814815 AGATCGAAGATAGCAGATTTGGCACCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
** *
2814859 AGATCGAAGATAGCAGATTTGGCACCTCTGTATTGTCAGAGAGT
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
2814903 AGATCGAAAATAGC-GAATTTGGCGTCTCTGTATTATCTGAGAGC
1 AGATCGAAGATAGCAG-ATTTGGCGTCTCTGTATTGTCAGAGAGC
* * ** *
2814947 AGATCGAAAATAACAGATTTGGTATCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * ** * *
2814991 AGATCAAAGATATCAGATTCAGCGTCTCTGTATTGTCAGAAAGT
1 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * *
2815035 AGGTCGGAGATAACAAATTTGGC
1 AGATCGAAGATAGCAGATTTGGC
2815058 ATTCTTGAGT
Statistics
Matches: 359, Mismatches: 58, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
43 1 0.00
44 357 0.99
45 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (44 bp):
AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
Found at i:2815287 original size:19 final size:17
Alignment explanation
Indices: 2815263--2815300 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
2815253 CCGGGCCATT
2815263 AAAAATAAATAAATATAAA
1 AAAAATAAA-AAA-ATAAA
2815282 AAAAATAAAAAAATAAA
1 AAAAATAAAAAAATAAA
2815299 AA
1 AA
2815301 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAAATAAA
Found at i:2816685 original size:18 final size:18
Alignment explanation
Indices: 2816651--2816703 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2816641 TACAAAATAA
*
2816651 TATATATTATT-TTTTATT
1 TATATATTATTATTATA-T
2816669 TATATATTATTCATTATAT
1 TATATATTATT-ATTATAT
*
2816688 TAT-TTTTATTATTATA
1 TATATATTATTATTATA
2816704 CATTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 6 0.19
18 17 0.55
19 4 0.13
20 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATATTATTATTATAT
Found at i:2816715 original size:25 final size:25
Alignment explanation
Indices: 2816657--2816732 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
2816647 ATAATATATA
* *
2816657 TTATTTTTTATTTATATATTATTCATT
1 TTATTTATT-TTTAT-TATTATACATT
*
2816684 ATA-TTATTTTTATTATTATACATT
1 TTATTTATTTTTATTATTATACATT
***
2816708 TTATTTATAAATATTATTATACATT
1 TTATTTATTTTTATTATTATACATT
2816733 ATATGTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.29
25 23 0.56
26 4 0.10
27 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATTTATTTTTATTATTATACATT
Found at i:2816716 original size:74 final size:77
Alignment explanation
Indices: 2816608--2816776 Score: 177
Period size: 74 Copynumber: 2.2 Consensus size: 77
2816598 ATTAAATACC
* *
2816608 TTATA-TATTATTTATTTTTATAAATATTAGTTATACAA-AATAATATATATTAT-T-TTTTA-T
1 TTATATTATT-TTTATTATTATAAATATTAGTTATA-AATAATAATATACATTATATGTTTTACT
*
2816668 TTATATATTATTCA
64 ATATATATTATTCA
* * * * *
2816682 TTATATTATTTTTATTATTATACATTTTATTTATAAATATTATTATACATTATATGTTTTACTAT
1 TTATATTATTTTTATTATTATAAATATTAGTTATAAATAATAATATACATTATATGTTTTACTAT
*
2816747 ATATATTATTCC
66 ATATATTATTCA
** *
2816759 TTGCATTTTTTTTATTAT
1 TTATATTATTTTTATTAT
2816777 AAATTATGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
73 2 0.03
74 38 0.49
75 5 0.06
76 5 0.06
77 28 0.36
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (77 bp):
TTATATTATTTTTATTATTATAAATATTAGTTATAAATAATAATATACATTATATGTTTTACTAT
ATATATTATTCA
Found at i:2816979 original size:7 final size:7
Alignment explanation
Indices: 2816965--2817000 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
2816955 TTATCTTCCT
2816965 TTTATTA
1 TTTATTA
*
2816972 TATATTA
1 TTTATTA
2816979 TTTCATTA
1 TTT-ATTA
2816987 TTTATTA
1 TTTATTA
2816994 TTTATTA
1 TTTATTA
2817001 GTATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:2816992 original size:15 final size:14
Alignment explanation
Indices: 2816965--2817005 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
2816955 TTATCTTCCT
2816965 TTTATTATATATTA
1 TTTATTATATATTA
*
2816979 TTTCATTATTTATTA
1 TTT-ATTATATATTA
2816994 TTTATTAGTATA
1 TTTATTA-TATA
2817006 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATTATATATTA
Found at i:2820907 original size:21 final size:21
Alignment explanation
Indices: 2820860--2820909 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2820850 TATGAGCTCC
* *
2820860 TTTATGTTTTGTTTTTCCAAA
1 TTTATTTTTTGTTTATCCAAA
2820881 TTTATTTTTTGTATTAT-CAAA
1 TTTATTTTTTGT-TTATCCAAA
2820902 TTTATTTT
1 TTTATTTT
2820910 AATAAAACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (21 bp):
TTTATTTTTTGTTTATCCAAA
Found at i:2821001 original size:27 final size:27
Alignment explanation
Indices: 2820970--2821041 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
2820960 AATTTATACC
* * * *
2820970 CTAAATCATAAGTCTTAAGTTTTAACT
1 CTAAATCATAAATCTTAAATCTTAACA
*
2820997 CTAAATCCTAAATCTTAAATCTTAACA
1 CTAAATCATAAATCTTAAATCTTAACA
*
2821024 CTAAA-CTTTAAATCTTAA
1 CTAAATC-ATAAATCTTAA
2821042 CCTTTAAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (27 bp):
CTAAATCATAAATCTTAAATCTTAACA
Found at i:2824774 original size:16 final size:16
Alignment explanation
Indices: 2824750--2824787 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2824740 TGGATTTAAT
2824750 TTAGAACTCTAAACGA
1 TTAGAACTCTAAACGA
* *
2824766 TTAGGACTCTAAATGA
1 TTAGAACTCTAAACGA
2824782 TTAGAA
1 TTAGAA
2824788 TGGAACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAGAACTCTAAACGA
Found at i:2825167 original size:27 final size:26
Alignment explanation
Indices: 2825137--2825187 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2825127 AAAATTTATT
*
2825137 AAAACTCTTATAAAAAAAAACTCAATA
1 AAAACTCTT-GAAAAAAAAACTCAATA
* *
2825164 AAAATTCTTGAAAAGAAAACTCAA
1 AAAACTCTTGAAAAAAAAACTCAA
2825188 AGAGAATCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAACTCTTGAAAAAAAAACTCAATA
Found at i:2826940 original size:14 final size:14
Alignment explanation
Indices: 2826919--2826967 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2826909 TGTTCAAGAG
2826919 TTAAGGTTTATGAT
1 TTAAGGTTTATGAT
* *
2826933 TTAGGGTTCATG-T
1 TTAAGGTTTATGAT
2826946 TTAAGGTTTGA-GAT
1 TTAAGGTTT-ATGAT
2826960 TTAAGGTT
1 TTAAGGTT
2826968 AGAGGTTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (14 bp):
TTAAGGTTTATGAT
Found at i:2826993 original size:34 final size:34
Alignment explanation
Indices: 2826950--2827019 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
2826940 TCATGTTTAA
2826950 GGTTTGAGATTTAAGGTTAGAGGTTAGGGGTTTG
1 GGTTTGAGATTTAAGGTTAGAGGTTAGGGGTTTG
*
2826984 GGTTTGAGATTTAAGGTTAGAGGTTTGGGGTTTG
1 GGTTTGAGATTTAAGGTTAGAGGTTAGGGGTTTG
2827018 GG
1 GG
2827020 GTTTTAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.39
Consensus pattern (34 bp):
GGTTTGAGATTTAAGGTTAGAGGTTAGGGGTTTG
Found at i:2827028 original size:21 final size:21
Alignment explanation
Indices: 2827004--2827044 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2826994 TTAAGGTTAG
*
2827004 AGGTTTGGGGTTTGGGGTTTT
1 AGGTTTGGGATTTGGGGTTTT
* *
2827025 AGGTTTTGGATTTTGGGTTT
1 AGGTTTGGGATTTGGGGTTT
2827045 ATGGTTATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.41, T:0.51
Consensus pattern (21 bp):
AGGTTTGGGATTTGGGGTTTT
Found at i:2827029 original size:14 final size:14
Alignment explanation
Indices: 2827012--2827114 Score: 61
Period size: 14 Copynumber: 7.5 Consensus size: 14
2827002 AGAGGTTTGG
*
2827012 GGTTTGGGGTTTTA
1 GGTTTTGGGTTTTA
* *
2827026 GGTTTTGGATTTTG
1 GGTTTTGGGTTTTA
*
2827040 GGTTTAT-GGTTAT-
1 GGTTT-TGGGTTTTA
*
2827053 GGTTTTGAGTTTTA
1 GGTTTTGGGTTTTA
* *
2827067 GGTTTTGAGTTTGA
1 GGTTTTGGGTTTTA
* *
2827081 GG--TCGGGTTTAA
1 GGTTTTGGGTTTTA
* *
2827093 TGTTTTAGGGTTTAA
1 GGTTTT-GGGTTTTA
2827108 GGTTTTG
1 GGTTTTG
2827115 TATTTCAAGT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
12 9 0.13
13 9 0.13
14 37 0.54
15 14 0.20
ACGTcount: A:0.13, C:0.01, G:0.35, T:0.51
Consensus pattern (14 bp):
GGTTTTGGGTTTTA
Found at i:2827153 original size:28 final size:28
Alignment explanation
Indices: 2827122--2827175 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2827112 TTGTATTTCA
* * * *
2827122 AGTCTTGGGTTTTCGATTTTGAGTTTTG
1 AGTCTAGGGTTTACAATTTAGAGTTTTG
2827150 AGTCTAGGGTTTACAATTTAGAGTTT
1 AGTCTAGGGTTTACAATTTAGAGTTT
2827176 AGTGTTTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.19, C:0.07, G:0.26, T:0.48
Consensus pattern (28 bp):
AGTCTAGGGTTTACAATTTAGAGTTTTG
Found at i:2827230 original size:21 final size:21
Alignment explanation
Indices: 2827170--2827259 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 21
2827160 TTACAATTTA
* *
2827170 GAGTTTAGTGTTT-AAGGTTTA
1 GAGTTTTGTGTTTCAA-GTTTC
* * * *
2827191 GAATTTTGGGCTTCGAGTTTC
1 GAGTTTTGTGTTTCAAGTTTC
2827212 GAGTTTTGTGTTTCAAGTTTC
1 GAGTTTTGTGTTTCAAGTTTC
* * * * *
2827233 AAGCTTTGAGTTTTAGGTTTC
1 GAGTTTTGTGTTTCAAGTTTC
2827254 GAGTTT
1 GAGTTT
2827260 ATTTTTAGAT
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 50 0.98
22 1 0.02
ACGTcount: A:0.18, C:0.08, G:0.27, T:0.48
Consensus pattern (21 bp):
GAGTTTTGTGTTTCAAGTTTC
Found at i:2827908 original size:14 final size:14
Alignment explanation
Indices: 2827891--2827957 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
2827881 TAGAGTTTAA
2827891 GGTTCAAGGTTCAG
1 GGTTCAAGGTTCAG
* *
2827905 GGTTCAGGGTTCAT
1 GGTTCAAGGTTCAG
* * *
2827919 GGTTAAAAGTTTAG
1 GGTTCAAGGTTCAG
* *
2827933 GGCTT-AAGGCTAAG
1 GG-TTCAAGGTTCAG
2827947 GGTTCAAGGTT
1 GGTTCAAGGTT
2827958 TAAAGTTTAG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
13 2 0.05
14 36 0.90
15 2 0.05
ACGTcount: A:0.24, C:0.10, G:0.34, T:0.31
Consensus pattern (14 bp):
GGTTCAAGGTTCAG
Found at i:2829863 original size:26 final size:26
Alignment explanation
Indices: 2829794--2829872 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
2829784 GCCCCACCTA
2829794 TATTTTTAAAATATATATTATTTTTAATTT
1 TATTTTTAAAA-AT-T-TTATTTTT-ATTT
* * *
2829824 AATTTGTAATAATTTTATTTATT-TTT
1 TATTTTTAAAAATTTTATTT-TTATTT
*
2829850 TATTTTTAAAAATTTTATATTTA
1 TATTTTTAAAAATTTTATTTTTA
2829873 GTTATCTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
25 2 0.05
26 19 0.47
27 6 0.15
28 3 0.08
29 2 0.05
30 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TATTTTTAAAAATTTTATTTTTATTT
Found at i:2830851 original size:5 final size:5
Alignment explanation
Indices: 2830841--2830873 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2830831 GTTTAATCAT
2830841 TTTAA TTTAA TTTAA TTTAA TTTAA TTT-A TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
2830874 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:2830985 original size:27 final size:27
Alignment explanation
Indices: 2830928--2830985 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2830918 TTTATAATTT
* ***
2830928 TTATTTTAAAATGAAAAAAAATTATTT
1 TTATTTAAAAATGAAAAAAAATTAAAA
*
2830955 TTATTTAAAAATGAAAAAAATTTAAAA
1 TTATTTAAAAATGAAAAAAAATTAAAA
2830982 TTAT
1 TTAT
2830986 ATATTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TTATTTAAAAATGAAAAAAAATTAAAA
Found at i:2834389 original size:47 final size:47
Alignment explanation
Indices: 2834318--2834436 Score: 132
Period size: 47 Copynumber: 2.5 Consensus size: 47
2834308 CCTCGAGTCA
** * *
2834318 ATGAGGCACTAAAAGTGTCGTACTGTTACT-ATTACTTCGGTTTAATCCG
1 ATGAGGCACT--AAGTACCGTACTGTTACTGATTACTTCGG-CTAAGCCG
* * *
2834367 ATGAGGTACTGAGTACCGTACTGTTACTGTTTACTTCGGCTAAGCCG
1 ATGAGGCACTAAGTACCGTACTGTTACTGATTACTTCGGCTAAGCCG
*
2834414 ATGAGGCACTAAGTGCCGTACTG
1 ATGAGGCACTAAGTACCGTACTG
2834437 GTGTGTTGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 41 0.69
48 9 0.15
49 9 0.15
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (47 bp):
ATGAGGCACTAAGTACCGTACTGTTACTGATTACTTCGGCTAAGCCG
Found at i:2838416 original size:17 final size:17
Alignment explanation
Indices: 2838394--2838445 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2838384 GTTTTCATAT
2838394 TATTTTATTACATATTA
1 TATTTTATTACATATTA
* * *
2838411 TATTTTACTCCATATGA
1 TATTTTATTACATATTA
*
2838428 TA-TTT-TTATATATTA
1 TATTTTATTACATATTA
2838443 TAT
1 TAT
2838446 ACATTTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTATTACATATTA
Found at i:2838445 original size:15 final size:15
Alignment explanation
Indices: 2838351--2838445 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 15
2838341 CTTATATACA
2838351 TTTTATATATTTCACTAT
1 TTTTATATA-TT-A-TAT
*
2838369 ATTTATATATTAT-T
1 TTTTATATATTATAT
2838383 TGTTT-TCATATTAT-T
1 T-TTTAT-ATATTATAT
*
2838398 TTATTACATATTATA-
1 TT-TTATATATTATAT
*
2838413 TTTTACTCCATATGATAT
1 TTTTA-T--ATATTATAT
2838431 TTTTATATATTATAT
1 TTTTATATATTATAT
2838446 ACATTTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 6 0.10
15 32 0.52
16 1 0.02
17 10 0.16
18 13 0.21
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTATATATTATAT
Found at i:2838467 original size:32 final size:32
Alignment explanation
Indices: 2838388--2838469 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 32
2838378 TTATTTGTTT
*
2838388 TCATAT-TATTTTATTACATATTATATTTTAC
1 TCATATATATTTTATTACATATTACATTTTAC
*
2838419 TCCATATGATATTTTTATATA-TTATATACATTTTA-
1 T-CATAT-ATA-TTTTAT-TACATAT-TACATTTTAC
2838454 TCATATATATTTTATT
1 TCATATATATTTTATT
2838470 TTATTTATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
31 2 0.05
32 11 0.26
33 3 0.07
34 7 0.16
35 10 0.23
36 10 0.23
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (32 bp):
TCATATATATTTTATTACATATTACATTTTAC
Found at i:2838651 original size:48 final size:49
Alignment explanation
Indices: 2838598--2838700 Score: 190
Period size: 48 Copynumber: 2.1 Consensus size: 49
2838588 ATTATGTACA
*
2838598 TTCTTAAATTATTTTTATAAGTATAATAGCAATATTTAATACATTA-TT
1 TTCTTAAATTATTTTTATAAGTATAATAGAAATATTTAATACATTATTT
2838646 TTCTTAAATTATTTTTATAAGTATAATAGAAATATTTAATACATTATTT
1 TTCTTAAATTATTTTTATAAGTATAATAGAAATATTTAATACATTATTT
2838695 TTCTTA
1 TTCTTA
2838701 CATATTAAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 45 0.85
49 8 0.15
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (49 bp):
TTCTTAAATTATTTTTATAAGTATAATAGAAATATTTAATACATTATTT
Found at i:2842720 original size:29 final size:28
Alignment explanation
Indices: 2842667--2842729 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
2842657 CCAAAAAAGG
* *
2842667 TAAAAA-GATAAATTATATTATTTTAGTT
1 TAAAAATGAAAAATTATATTATTTTA-TA
*
2842695 TAAAAATGAAAAATTTTAATTA-TTTATA
1 TAAAAATGAAAAATTAT-ATTATTTTATA
2842723 TAAAAAT
1 TAAAAAT
2842730 AATATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 14 0.47
29 12 0.40
30 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
TAAAAATGAAAAATTATATTATTTTATA
Found at i:2842745 original size:15 final size:16
Alignment explanation
Indices: 2842718--2842768 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
2842708 TTTTAATTAT
*
2842718 TTATATAAAAATAATA
1 TTATATAATAATAATA
2842734 TT-TATAATAATACAT-
1 TTATATAATAATA-ATA
2842749 TTATATAAT-ATAATA
1 TTATATAATAATAATA
2842764 TTATA
1 TTATA
2842769 GGCTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.06
15 19 0.61
16 10 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATATAATAATAATA
Found at i:2842757 original size:16 final size:15
Alignment explanation
Indices: 2842711--2842768 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
2842701 TGAAAAATTT
*
2842711 TAATTATTTATATAA
1 TAATAATTTATATAA
*
2842726 AAATAATATT-TATAA
1 TAATAAT-TTATATAA
2842741 TAATACATTTATATAA
1 TAATA-ATTTATATAA
2842757 T-ATAATATTATA
1 TAATAAT-TTATA
2842769 GGCTATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.06
15 24 0.67
16 10 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAATTTATATAA
Found at i:2845515 original size:14 final size:15
Alignment explanation
Indices: 2845498--2845530 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2845488 TTTAGATTCA
2845498 TTTTAAAT-ATAATT
1 TTTTAAATCATAATT
2845512 TTTTAAATCATAATT
1 TTTTAAATCATAATT
2845527 TTTT
1 TTTT
2845531 TAAACATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAAATCATAATT
Found at i:2845736 original size:2 final size:2
Alignment explanation
Indices: 2845729--2845791 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
2845719 TAATTGGTGT
* * * * *
2845729 AG AG AG AG AG GG AG AG AG AG AG AG AG -G GG GG GG GG 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
*
2845770 AG AG AG AG AG AG GG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
2845792 CCCTTTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2845766 original size:23 final size:23
Alignment explanation
Indices: 2845729--2845791 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
2845719 TAATTGGTGT
*
2845729 AGAGAGA-GAGGGAGAGAGAGAG
1 AGAGAGAGGGGGGAGAGAGAGAG
* *
2845751 AGAGGGGGGGGGGAGAGAGAGAG
1 AGAGAGAGGGGGGAGAGAGAGAG
*
2845774 AGAGAGAGGGAGGAGAGA
1 AGAGAGAGGGGGGAGAGA
2845792 CCCTTTTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (23 bp):
AGAGAGAGGGGGGAGAGAGAGAG
Found at i:2847543 original size:2 final size:2
Alignment explanation
Indices: 2847536--2847572 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2847526 TTTGAATTAT
2847536 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 T
2847573 GTGAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2855310 original size:2 final size:2
Alignment explanation
Indices: 2855303--2855327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2855293 ACTTTGAAAC
2855303 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
2855328 ACATAAAATT
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:2855381 original size:9 final size:9
Alignment explanation
Indices: 2855363--2855397 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2855353 CACGATTTAC
2855363 AAAA-AAAA
1 AAAAGAAAA
2855371 AAAAGAAAA
1 AAAAGAAAA
2855380 AAAAGAAAAA
1 AAAAG-AAAA
2855390 AAAAGAAA
1 AAAAGAAA
2855398 TTAAGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 4 0.16
9 12 0.48
10 9 0.36
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:2855381 original size:10 final size:10
Alignment explanation
Indices: 2855366--2855397 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2855356 GATTTACAAA
2855366 AAAAAAAAAG
1 AAAAAAAAAG
2855376 -AAAAAAAAG
1 AAAAAAAAAG
2855385 AAAAAAAAAG
1 AAAAAAAAAG
2855395 AAA
1 AAA
2855398 TTAAGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2856463 original size:14 final size:15
Alignment explanation
Indices: 2856437--2856477 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
2856427 ATGGGATGAA
*
2856437 AATAAATTTTTAATT
1 AATAAAATTTTAATT
2856452 AA-AAAATTTTAATT
1 AATAAAATTTTAATT
2856466 AATTAAAATTTT
1 AA-TAAAATTTT
2856478 CAAACCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 13 0.57
15 2 0.09
16 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAAAATTTTAATT
Found at i:2865473 original size:23 final size:23
Alignment explanation
Indices: 2865447--2865491 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2865437 TATATAATAA
* *
2865447 ATATATATTTTTTATTTTTAATC
1 ATATATATATTTTAATTTTAATC
*
2865470 ATATTTATATTTTAATTTTAAT
1 ATATATATATTTTAATTTTAAT
2865492 TTTAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATATATATTTTAATTTTAATC
Found at i:2865559 original size:40 final size:40
Alignment explanation
Indices: 2865507--2865592 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
2865497 TATAATCAAT
*
2865507 TTTTATTATATTTTTAATTTGTGTATTGTTTTAAGAATTG
1 TTTTAATATATTTTTAATTTGTGTATTGTTTTAAGAATTG
* * * * *
2865547 TTTTAATATATTTTTTATTTGTTTCTTGTTTTAATATTTG
1 TTTTAATATATTTTTAATTTGTGTATTGTTTTAAGAATTG
2865587 TTTTAA
1 TTTTAA
2865593 ATGTATTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.66
Consensus pattern (40 bp):
TTTTAATATATTTTTAATTTGTGTATTGTTTTAAGAATTG
Found at i:2866470 original size:18 final size:18
Alignment explanation
Indices: 2866433--2866486 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
2866423 ATAATAAAAT
*
2866433 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
2866452 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
2866470 AAGTTCCAAA-ATTTATA
1 AA-TTCAAAATATTTATA
2866487 TATTTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:2867464 original size:18 final size:18
Alignment explanation
Indices: 2867441--2867475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2867431 ACAAAACTTC
*
2867441 AAAAAAAATTAAGAAATA
1 AAAAAAAATTAAAAAATA
*
2867459 AAAAAAATTTAAAAAAT
1 AAAAAAAATTAAAAAAT
2867476 TGTTTGGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAAAAAATTAAAAAATA
Found at i:2867539 original size:21 final size:19
Alignment explanation
Indices: 2867499--2867544 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
2867489 AGGTTTTTTT
2867499 TTTTA-GAAAATTTTAGAA
1 TTTTATGAAAATTTTAGAA
*
2867517 TTTTATGAAAACTTTTAATAA
1 TTTTATGAAAA-TTTT-AGAA
2867538 TTTTATG
1 TTTTATG
2867545 GTATTTTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 4 0.17
21 10 0.42
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (19 bp):
TTTTATGAAAATTTTAGAA
Found at i:2868936 original size:3 final size:3
Alignment explanation
Indices: 2868928--2868967 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2868918 TATCATTTCC
*
2868928 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2868968 ACTTATACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2869184 original size:19 final size:18
Alignment explanation
Indices: 2869150--2869187 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2869140 TTATTACTAC
*
2869150 TATTGTCACTGTTATTAT
1 TATTATCACTGTTATTAT
2869168 TATTATCACTCGTTATTAT
1 TATTATCACT-GTTATTAT
2869187 T
1 T
2869188 TTCATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (18 bp):
TATTATCACTGTTATTAT
Found at i:2869214 original size:14 final size:15
Alignment explanation
Indices: 2869195--2869235 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2869185 ATTTTCATAA
2869195 CTATTATTTA-TACT
1 CTATTATTTATTACT
2869209 CTATTA-TTATTACT
1 CTATTATTTATTACT
2869223 -TATTATTTTATTA
1 CTATTA-TTTATTA
2869236 TTGTTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 10 0.42
15 6 0.25
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTATTTATTACT
Found at i:2869214 original size:45 final size:44
Alignment explanation
Indices: 2869165--2869276 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 44
2869155 TCACTGTTAT
*
2869165 TATTATTATCACTCGTTATTATTTTCATAACTATTAT-TTATACT-C
1 TATTATTATCACTC-TTATTATTTT-ATAACTATTATCTAATA-TAC
* * * *
2869210 TATTATTATTA--CTTATTATTTTATTATTGTTATCTAATATAC
1 TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
*
2869252 TATTATTATCACTATTATTATTTTA
1 TATTATTATCACTCTTATTATTTTA
2869277 CTATTGTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 9 0.16
42 25 0.45
43 1 0.02
44 11 0.20
45 10 0.18
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (44 bp):
TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
Found at i:2869556 original size:3 final size:3
Alignment explanation
Indices: 2869210--2869547 Score: 144
Period size: 3 Copynumber: 109.7 Consensus size: 3
2869200 ATTTATACTC
* * *
2869210 TAT TAT TAT TACT TAT TAT T-T TAT TAT TGT TAT CTAA TA- TAC TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * *
2869255 TAT TAT CAC TAT TAT TAT T-T TAC TAT TGT AACT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * *
2869300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- AACT AAT TAAT T-T CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT
* * * *
2869345 T-T TAAT TGT TAT TA- TAC TAT ATACT TCCCT T-T CTAT GT-T TAT TCGCT
1 TAT T-AT TAT TAT TAT TAT TAT -TA-T T--AT TAT -TAT -TAT TAT T--AT
* * *
2869392 TAT TAC T-T TAT TACT AAT TAACT TAACT TAT TAAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TA-T TAT T-A-T T-A-T TAT T-AT TAT TAT TAT TAT
* * * * * * * *
2869439 TAT TAT CAA TGT TGT TAT TAC T-T TAC TAT TGT GTGT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
2869483 TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2869528 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
2869548 GCTATTATTT
Statistics
Matches: 258, Mismatches: 45, Indels: 64
0.70 0.12 0.17
Matches are distributed among these distances:
2 20 0.08
3 195 0.76
4 31 0.12
5 12 0.05
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:2869852 original size:9 final size:9
Alignment explanation
Indices: 2869838--2869873 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2869828 TTACATAATA
2869838 TTTATTATT
1 TTTATTATT
*
2869847 TTTATTATC
1 TTTATTATT
2869856 TTTATTATT
1 TTTATTATT
*
2869865 ATTATTATT
1 TTTATTATT
2869874 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTATT
Found at i:2869861 original size:18 final size:18
Alignment explanation
Indices: 2869838--2869872 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2869828 TTACATAATA
*
2869838 TTTATTATTTTTATTATC
1 TTTATTATTATTATTATC
2869856 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
2869873 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTATTATTATC
Found at i:2874434 original size:16 final size:16
Alignment explanation
Indices: 2874413--2874445 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2874403 ATATTTTGGC
2874413 ATATAATCTCATGCTT
1 ATATAATCTCATGCTT
2874429 ATATAATCTCATGCTT
1 ATATAATCTCATGCTT
2874445 A
1 A
2874446 CAATATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATAATCTCATGCTT
Found at i:2875550 original size:33 final size:33
Alignment explanation
Indices: 2875508--2875573 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2875498 TGATGATTCG
*
2875508 TTGCTCTCTAAATAATCTGATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
*
2875541 TTGCTCTCTACATAATCTAATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
2875574 CGTGTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
Found at i:2877475 original size:3 final size:3
Alignment explanation
Indices: 2877467--2877534 Score: 127
Period size: 3 Copynumber: 22.3 Consensus size: 3
2877457 AAAGGTTTAG
2877467 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
2877513 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
2877535 TATTCAAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2880887 original size:34 final size:34
Alignment explanation
Indices: 2880845--2880939 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 34
2880835 TTGTTTGCAT
2880845 ACTG-TACTGAAAAGGGCTCAGGCCCAGACTGTC-
1 ACTGTTACTGAAAAGGGCTCAGGCCCAGACTG-CG
* *
2880878 ACTGTTACTGAAATGGGCTCAGGCCAAGACTGCG
1 ACTGTTACTGAAAAGGGCTCAGGCCCAGACTGCG
* *
2880912 ACTATTACTGAAAAAGGGGCTAAGGCCC
1 ACTGTTACTG-AAAA-GGGCTCAGGCCC
2880940 CTAACTGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
33 5 0.10
34 34 0.65
35 3 0.06
36 10 0.19
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.19
Consensus pattern (34 bp):
ACTGTTACTGAAAAGGGCTCAGGCCCAGACTGCG
Found at i:2889396 original size:9 final size:9
Alignment explanation
Indices: 2889360--2889465 Score: 56
Period size: 9 Copynumber: 11.4 Consensus size: 9
2889350 TTCTTTTCCC
2889360 TTTTTATT-
1 TTTTTATTA
*
2889368 TATTTATTA
1 TTTTTATTA
*
2889377 TTCTTATTTA
1 TTTTTA-TTA
2889387 TTTTTATTA
1 TTTTTATTA
*
2889396 TATTTATTA
1 TTTTTATTA
2889405 TCCTTTT-TT-
1 T--TTTTATTA
*
2889414 TTGTATTTTTA
1 TT-T-TTATTA
* *
2889425 TTTTTTTTG
1 TTTTTATTA
*
2889434 TTCTTATTA
1 TTTTTATTA
*
2889443 TGTTTATTA
1 TTTTTATTA
*
2889452 TTTATTCTTA
1 TTT-TTATTA
2889462 TTTT
1 TTTT
2889466 AGCTATCGTA
Statistics
Matches: 75, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.01
8 8 0.11
9 40 0.53
10 21 0.28
11 5 0.07
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTTATTA
Found at i:2889411 original size:21 final size:20
Alignment explanation
Indices: 2889387--2889425 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2889377 TTCTTATTTA
2889387 TTTTTATTATATTTATTATCC
1 TTTTTATTATATTT-TTATCC
* *
2889408 TTTTTTTTGTATTTTTAT
1 TTTTTATTATATTTTTAT
2889426 TTTTTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTATTATATTTTTATCC
Found at i:2889449 original size:47 final size:48
Alignment explanation
Indices: 2889358--2889452 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 48
2889348 TTTTCTTTTC
*
2889358 CCTTTTTATTTATTTATTATTCTTATTTATTTTTATTATATTTATTAT
1 CCTTTTTATTTATTTATTATTCTTATTTATTCTTATTATATTTATTAT
* * * *
2889406 CCTTTTTTTTGTATTT-TTATT-TTTTTTGTTCTTATTATGTTTATTAT
1 CCTTTTTATT-TATTTATTATTCTTATTTATTCTTATTATATTTATTAT
2889453 TTATTCTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 22 0.54
48 14 0.34
49 5 0.12
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (48 bp):
CCTTTTTATTTATTTATTATTCTTATTTATTCTTATTATATTTATTAT
Found at i:2892005 original size:34 final size:34
Alignment explanation
Indices: 2891932--2892009 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
2891922 AGTGACAGTC
*
2891932 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAG
1 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
* * *
2891966 TAGTATTATTGTGGGCCTTAGCCCAT-TACAGTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATAT-CAGTAA
2892000 CAGTATCAGT
1 CAGTATCAGT
2892010 AATGCAACAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 1 0.03
34 35 0.97
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
Found at i:2892069 original size:22 final size:23
Alignment explanation
Indices: 2892029--2892071 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2892019 GAAGTCCTAC
2892029 CCGTCCATCCTCTACACTCCACT
1 CCGTCCATCCTCTACACTCCACT
2892052 CCGTCCATCCT-TACACTCCA
1 CCGTCCATCCTCTACACTCCA
2892072 TGTAGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.19, C:0.51, G:0.05, T:0.26
Consensus pattern (23 bp):
CCGTCCATCCTCTACACTCCACT
Found at i:2903567 original size:43 final size:43
Alignment explanation
Indices: 2903474--2903594 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
2903464 CGAGATGTGA
* * **
2903474 TTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGC
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
*
2903517 TTACGTGTAAGACCATGTCTGGGATATTGGCATCGT-TAAT-C
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
* * * *
2903558 AATTTCGTGTAAGACCCTGTCTAGGACAGTGGCATCG
1 --TTACGTGTAAGACCATGTCTGGGACATTGGCATCG
2903595 ATATGTAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 2 0.03
43 63 0.95
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
Found at i:2920465 original size:13 final size:13
Alignment explanation
Indices: 2920447--2920472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2920437 GCAGGGGAGA
2920447 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
2920460 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
2920473 GGGGAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:2933271 original size:10 final size:10
Alignment explanation
Indices: 2933258--2933354 Score: 50
Period size: 10 Copynumber: 10.2 Consensus size: 10
2933248 TAAATAATGA
2933258 AATAATATAT
1 AATAATATAT
*
2933268 AATAA-A-AA
1 AATAATATAT
*
2933276 AGATAATATAGGG
1 A-ATAATATA--T
2933289 AATAATATAT
1 AATAATATAT
2933299 AAT-A-ATAT
1 AATAATATAT
* *
2933307 -ATGATATGT
1 AATAATATAT
2933316 AATAATATAT
1 AATAATATAT
2933326 -AT-ATATA-
1 AATAATATAT
*
2933333 AATAAAATAT
1 AATAATATAT
2933343 AATGAA-ATAT
1 AAT-AATATAT
2933353 AA
1 AA
2933355 ATGATGTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
7 2 0.03
8 14 0.21
9 15 0.22
10 25 0.37
11 3 0.04
12 8 0.12
13 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (10 bp):
AATAATATAT
Found at i:2933318 original size:17 final size:16
Alignment explanation
Indices: 2933293--2933343 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
2933283 ATAGGGAATA
2933293 ATATATAATAATATAT
1 ATATATAATAATATAT
*
2933309 GATATGTAATAATATAT
1 -ATATATAATAATATAT
*
2933326 ATATATAAATAAAATAT
1 ATATAT-AATAATATAT
2933343 A
1 A
2933344 ATGAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
ATATATAATAATATAT
Found at i:2938169 original size:5 final size:5
Alignment explanation
Indices: 2938159--2938185 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2938149 AATTTGTGTG
2938159 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
2938186 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2943226 original size:14 final size:15
Alignment explanation
Indices: 2943209--2943246 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
2943199 GCTTAGATAT
2943209 GATATG-CAATCTTA
1 GATATGACAATCTTA
2943223 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
2943240 GATATGA
1 GATATGA
2943247 TTGCAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:2943285 original size:17 final size:19
Alignment explanation
Indices: 2943188--2943278 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
2943178 ATAATCTTCA
*
2943188 ATGATATGCAAGCTTAGAT
1 ATGATATGCAATCTTAGAT
2943207 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2943226 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
2943243 ATGAT-TGCAATCTTATAT
1 ATGATATGCAATCTTAGAT
2943261 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
2943279 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 15 0.23
19 35 0.53
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2943589 original size:17 final size:18
Alignment explanation
Indices: 2943567--2943601 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2943557 TGTTTCCCAG
*
2943567 ATTTTTTA-TATATTTTA
1 ATTTTTTACTAAATTTTA
2943584 ATTTTTTACTAAATTTTA
1 ATTTTTTACTAAATTTTA
2943602 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTACTAAATTTTA
Found at i:2952150 original size:44 final size:44
Alignment explanation
Indices: 2952013--2952324 Score: 306
Period size: 44 Copynumber: 7.1 Consensus size: 44
2952003 GATCCAAGAT
* * *
2952013 GATTTGGCATCTCTGTATTGTCAGAGAACAAATC-AAGA-AACA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * * **
2952055 GATTTGACATTTCTGTATTAGACAGGGAGCAGATTGAAGATAGCA
1 GATTTGGCATCTCTGTATT-GTCAGAGAGCAGATCAAAGATAGCA
** * * * *
2952100 GATTTGGTGTCTCTGTATTGTTAGAGAGCTGATCGAAGATAGCC
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
2952144 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
**
2952188 GATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * * * *
2952232 AATTTGGCATCTCTGTACTGTCAGAGAACAAATCGAAGA-AACA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* ** * * *
2952275 TATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATT-GTCAGAGAGCAGATC-AA-AGATAGCA
2952322 GAT
1 GAT
2952325 CTGACCTTCA
Statistics
Matches: 217, Mismatches: 46, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
42 17 0.08
43 28 0.13
44 146 0.67
45 19 0.09
46 2 0.01
47 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
Found at i:2952508 original size:77 final size:78
Alignment explanation
Indices: 2952276--2952568 Score: 473
Period size: 78 Copynumber: 3.8 Consensus size: 78
2952266 GAAGAAACAT
** * *
2952276 ATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
*
2952341 CAGATCCAAGATA
66 CAGATCCAAGATG
* * *
2952354 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGTAGATTTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
2952419 CAGATCCAAGATG
66 CAGATCCAAGATG
* *
2952432 ATTTGGCATCTCTGTATTAGACGGGG-GCAGATCAAAGACATAACAGAT-TGGACCTTCATTGAA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
2952495 GCAGATCCAAGATG
65 GCAGATCCAAGATG
2952509 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
2952569 GTGTTTACAT
Statistics
Matches: 198, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
76 1 0.01
77 71 0.36
78 125 0.63
79 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (78 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
CAGATCCAAGATG
Found at i:2952706 original size:44 final size:45
Alignment explanation
Indices: 2952508--2952781 Score: 277
Period size: 45 Copynumber: 6.1 Consensus size: 45
2952498 GATCCAAGAT
*
2952508 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAACA
* * * * * * * * *
2952555 GATCTGACCT-TCATGTGTTTACATC--GAAGTAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAACA
* * *
2952600 GATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* *
2952645 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* *
2952689 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAATATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
* * * * *
2952734 GATTTGGCGTCTCTGTATTAGATGGGGAGTAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
2952779 GAT
1 GAT
2952782 ATCGTCTTCC
Statistics
Matches: 185, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
43 1 0.01
44 44 0.24
45 110 0.59
46 4 0.02
47 21 0.11
48 4 0.02
49 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
Found at i:2952749 original size:89 final size:90
Alignment explanation
Indices: 2952585--2952781 Score: 272
Period size: 89 Copynumber: 2.2 Consensus size: 90
2952575 ACATCGAAGT
* *
2952585 AGATCCAAGAT-GACAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGGAGATAACAGATT
1 AGATCAAAGATAG-CAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATT
2952649 TGGCATCTCTGTATTAGACGGGGAGC
65 TGGCATCTCTGTATTAGACGGGGAGC
** * * * *
2952675 AGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAATATAACAGATTT
1 AGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATTT
* * *
2952739 GGCGTCTCTGTATTAGATGGGGAGT
66 GGCATCTCTGTATTAGACGGGGAGC
2952764 AGATCAAAGATAGCAGAT
1 AGATCAAAGATAGCAGAT
2952782 ATCGTCTTCC
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 77 0.83
90 16 0.17
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (90 bp):
AGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGAAGATAACAGATTT
GGCATCTCTGTATTAGACGGGGAGC
Found at i:2952775 original size:134 final size:136
Alignment explanation
Indices: 2952508--2952781 Score: 306
Period size: 134 Copynumber: 2.0 Consensus size: 136
2952498 GATCCAAGAT
*
2952508 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA-ATAGCAGATCTGACCTTCATGTGA
* * **
2952573 TTACATCGAAGTAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCGGA
65 TTACATCGAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCAAA
2952638 GATAACA
130 GATAACA
* * * *
2952645 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAG-A-AGCAGATTTGGCGTCTC-TGT-A
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAGATCTGACCT-TCATGTGA
* * * * * * * * *
2952706 TTAGA-CGGGGAGCAGATCGAATATAACAGATTTGGCGTCTCTGTATTAGATGGGGAGTAGATCA
65 TTACATC--GAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCA
*
2952770 AAGATAGCA
128 AAGATAACA
2952779 GAT
1 GAT
2952782 ATCGTCTTCC
Statistics
Matches: 115, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
132 1 0.01
133 4 0.03
134 69 0.60
135 3 0.03
137 38 0.33
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (136 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAATAGCAGATCTGACCTTCATGTGAT
TACATCGAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTATTAGACGAGGAGCAAATCAAAG
ATAACA
Found at i:2953154 original size:19 final size:19
Alignment explanation
Indices: 2953130--2953238 Score: 190
Period size: 19 Copynumber: 5.9 Consensus size: 19
2953120 ATAATCTTCA
2953130 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2953149 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2953168 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2953186 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2953203 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2953221 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
2953239 AGATATGATT
Statistics
Matches: 86, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.19
18 34 0.40
19 36 0.42
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2953203 original size:35 final size:36
Alignment explanation
Indices: 2953130--2953238 Score: 184
Period size: 35 Copynumber: 3.0 Consensus size: 36
2953120 ATAATCTTCA
2953130 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATA-GCAATCTTAGAT
2953168 ATGATTGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATAGCAATCTTAGAT
2953203 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
1 ATGATTGCAATCTTAGATATGATA-GCAATCTTAGA
2953239 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
35 35 0.51
37 29 0.42
38 5 0.07
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (36 bp):
ATGATTGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:2953264 original size:22 final size:22
Alignment explanation
Indices: 2953130--2953261 Score: 104
Period size: 18 Copynumber: 6.8 Consensus size: 22
2953120 ATAATCTTCA
2953130 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2953149 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2953168 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2953186 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2953203 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
2953221 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
2953243 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
2953262 GATTTAATTT
Statistics
Matches: 103, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.16
18 34 0.33
19 33 0.32
22 8 0.08
23 12 0.12
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:2953551 original size:17 final size:17
Alignment explanation
Indices: 2953527--2953561 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2953517 TGTTTCCCAG
*
2953527 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
2953545 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
2953562 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:2957432 original size:19 final size:18
Alignment explanation
Indices: 2957408--2957467 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
2957398 TATACATTGT
2957408 AATATATATAAAAAATATG
1 AATATA-ATAAAAAATATG
* *
2957427 AATATAATATAATATATG
1 AATATAATAAAAAATATG
*
2957445 TAATATAATATAATAATAT-
1 -AATATAATA-AAAAATATG
2957464 AATA
1 AATA
2957468 ATATAACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 14 0.41
19 15 0.44
20 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AATATAATAAAAAATATG
Found at i:2957437 original size:5 final size:5
Alignment explanation
Indices: 2957407--2957473 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
2957397 ATATACATTG
* *
2957407 TAATA T-ATA TAA-A AAATA TGAATA TAATA TAATA T-ATG TAATA TAATA
1 TAATA TAATA TAATA TAATA T-AATA TAATA TAATA TAATA TAATA TAATA
2957455 TAATA -ATATAA TAATA TAA
1 TAATA TA-AT-A TAATA TAA
2957474 CATTAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 11 0.22
5 31 0.61
6 8 0.16
7 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:2957450 original size:14 final size:13
Alignment explanation
Indices: 2957427--2957473 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
2957417 AAAAAATATG
2957427 AATATAATATAAT
1 AATATAATATAAT
*
2957440 ATATGTAATATAAT
1 A-ATATAATATAAT
2957454 -ATAATAATATAAT
1 AAT-ATAATATAAT
2957467 AATATAA
1 AATATAA
2957474 CATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 2 0.07
13 14 0.48
14 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:2957462 original size:8 final size:8
Alignment explanation
Indices: 2957430--2957473 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
2957420 AAATATGAAT
2957430 ATAATATA
1 ATAATATA
*
2957438 ATATATGTAA
1 ATA-ATAT-A
2957448 TATAATATA
1 -ATAATATA
2957457 ATAATATA
1 ATAATATA
2957465 ATAATATA
1 ATAATATA
2957473 A
1 A
2957474 CATTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 20 0.65
9 4 0.13
10 4 0.13
11 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:2957684 original size:3 final size:3
Alignment explanation
Indices: 2957670--2957704 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2957660 AAGCATGAAC
* *
2957670 TAA TAT TAA TAA TAA TAA TAA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2957705 TTATTATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2957847 original size:3 final size:3
Alignment explanation
Indices: 2957810--2957888 Score: 63
Period size: 3 Copynumber: 26.3 Consensus size: 3
2957800 TTATACGTAC
* * * *
2957810 ATA ATA A-A ATA TATA CTA ATA CATG ATA GTA ATA ATA ATA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
2957856 ATA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2957889 CAAGGATATT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.07
3 49 0.84
4 5 0.09
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2957857 original size:9 final size:9
Alignment explanation
Indices: 2957817--2957879 Score: 74
Period size: 9 Copynumber: 6.8 Consensus size: 9
2957807 TACATAATAA
2957817 AATATATACT
1 AATA-ATACT
2957827 AATACATGA-T
1 AATA-AT-ACT
* *
2957837 AGTAATAAT
1 AATAATACT
2957846 AATAATACT
1 AATAATACT
2957855 AATAATACT
1 AATAATACT
2957864 AATAATACT
1 AATAATACT
2957873 AATAATA
1 AATAATA
2957880 TAAAAATAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
8 1 0.02
9 35 0.74
10 10 0.21
11 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (9 bp):
AATAATACT
Found at i:2961868 original size:10 final size:9
Alignment explanation
Indices: 2961842--2961872 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2961832 TTATGTGTTC
2961842 TTTATTTTA
1 TTTATTTTA
2961851 TTTATTTTA
1 TTTATTTTA
2961860 TTATATTTTA
1 TT-TATTTTA
2961870 TTT
1 TTT
2961873 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2966126 original size:5 final size:5
Alignment explanation
Indices: 2966107--2966138 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
2966097 AAACTCCATC
2966107 TATTT TATATT TATTT TATTT TATTT TATTT T
1 TATTT TAT-TT TATTT TATTT TATTT TATTT T
2966139 CACATTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:2973593 original size:40 final size:40
Alignment explanation
Indices: 2973534--2973719 Score: 261
Period size: 39 Copynumber: 4.7 Consensus size: 40
2973524 TCGTTCAAAC
* * *** * *
2973534 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
2973574 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
* *
2973614 GCCTTC-GGACTTAGCCCGGATATCATAACTCGCACGATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
2973653 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
2973692 GCCTTCGGG-CTTAGCCCGGATATCACAA
1 GCCTTCGGGACTTAGCCCGGATATCACAA
2973720 TTCTCACATT
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 92 0.70
40 40 0.30
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
Found at i:2980806 original size:40 final size:40
Alignment explanation
Indices: 2980747--2980940 Score: 259
Period size: 39 Copynumber: 4.9 Consensus size: 40
2980737 TCGTTCAAAC
* * *** * *
2980747 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
2980787 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
* *
2980827 GCCTTC-GGACTTAGCCCGGATATCATAACTCGCACGATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
2980866 GCCTTCAGG-CTTAGCCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
2980905 GCCTTCGGG-CTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACA
2980941 TTCATACACA
Statistics
Matches: 138, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 98 0.71
40 40 0.29
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
Found at i:2982786 original size:21 final size:21
Alignment explanation
Indices: 2982762--2982866 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 21
2982752 TAAAATGATA
2982762 TATATATATATTATTTTTATT
1 TATATATATATTATTTTTATT
*
2982783 TATATATTATCCATTATTTTATATC
1 TATATA-TAT--ATTATTTT-TATT
*
2982808 TAT-TAT-TATTTATTTTTAAAT
1 TATATATATA-TTATTTTT-ATT
* *
2982829 TATATGTA-ATTAAATTTTATT
1 TATATATATATT-ATTTTTATT
2982850 ATATTATATGATATTAT
1 -TA-TATAT-ATATTAT
2982867 ATTATTCGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 23
0.67 0.09 0.24
Matches are distributed among these distances:
20 2 0.03
21 21 0.33
22 14 0.22
23 5 0.08
24 12 0.19
25 9 0.14
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (21 bp):
TATATATATATTATTTTTATT
Found at i:2982788 original size:17 final size:17
Alignment explanation
Indices: 2982766--2982969 Score: 75
Period size: 17 Copynumber: 11.8 Consensus size: 17
2982756 ATGATATATA
*
2982766 TATATATTATTTTTATT
1 TATATATTATTATTATT
*
2982783 TATATATTATCCATTATTT
1 TATATATTAT-TATTA-TT
2982802 TATATCTATTATTATTTATT
1 TATA--TATTATTA-TTATT
* * *
2982822 TTTAAATTA-TATGTAAT
1 TATATATTATTAT-TATT
* *
2982839 TAAATTTTATTA-TATT
1 TATATATTATTATTATT
2982855 ATATGATATTA-TATTATT
1 -TAT-ATATTATTATTATT
*
2982873 CGATATAGTATATGTATTA-T
1 -TATATA-T-TAT-TATTATT
*
2982893 TA-ATATT-TTATTAAT
1 TATATATTATTATTATT
* * * *
2982908 TAAATATT-TTCTAATG
1 TATATATTATTATTATT
*
2982924 TATGTATTATTATTATT
1 TATATATTATTATTATT
* * *
2982941 T-TTTGTTATTAATA-T
1 TATATATTATTATTATT
2982956 TATTATATTATTAT
1 TA-TATATTATTAT
2982970 ATGCTTCCTA
Statistics
Matches: 137, Mismatches: 31, Indels: 38
0.67 0.15 0.18
Matches are distributed among these distances:
14 5 0.04
15 6 0.04
16 30 0.22
17 42 0.31
18 24 0.18
19 9 0.07
20 7 0.05
21 14 0.10
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TATATATTATTATTATT
Found at i:2982814 original size:24 final size:24
Alignment explanation
Indices: 2982771--2982816 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2982761 ATATATATAT
*
2982771 ATTATTTTTATTTATATATTATCC
1 ATTATTTTTATCTATATATTATCC
2982795 ATTATTTTATATCTAT-TATTAT
1 ATTATTTT-TATCTATATATTAT
2982817 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTATTTTTATCTATATATTATCC
Found at i:2982854 original size:5 final size:5
Alignment explanation
Indices: 2982762--2982871 Score: 59
Period size: 5 Copynumber: 21.6 Consensus size: 5
2982752 TAAAATGATA
* *
2982762 TATAT ATATAT TAT-T TTTAT T-TA- TATAT TATCCAT TATTT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TAT--AT TATAT TATAT
* * * *
2982807 CTATTAT TAT-T TATTTT TAAAT TATAT GTA-AT TAAAT TTTAT TATAT
1 -TA-TAT TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TATAT
*
2982854 TATAT GATAT TATAT TAT
1 TATAT TATAT TATAT TAT
2982872 TCGATATAGT
Statistics
Matches: 82, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
3 1 0.01
4 12 0.15
5 47 0.57
6 14 0.17
7 8 0.10
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:2988430 original size:799 final size:799
Alignment explanation
Indices: 2986888--2988482 Score: 2861
Period size: 799 Copynumber: 2.0 Consensus size: 799
2986878 TTTTCCGTAT
*
2986888 TGTTCAGCCTCAACGCTTGCACCCATCCCAGCTCCGGAGAGTTGATTTCCTGAAATAATAAATTG
1 TGTTCAGCCTCAACGCTTGCACCCATCCCAGCTCCAGAGAGTTGATTTCCTGAAATAATAAATTG
*
2986953 ATTAAAATATAATTTGAAAAGTATAATGAAAAATAATCTCATGCAGAGCTTCGGGAAAACAAATT
66 ATTAAAATATAATTCGAAAAGTATAATGAAAAATAATCTCATGCAGAGCTTCGGGAAAACAAATT
*
2987018 TAGTTACCAAATTCATAAGAATCAACTTTGTATCCCCTGGAAATAGTATACTTCATGAAGTCCCT
131 TAGTTACCAAATTCATAAGAATCAACTTTGTATCCCCTGGAAATAGTATACTTCATGAAATCCCT
* *
2987083 TGCATTGTGCGATTGCCAATCGCCAACCCAAAGACCCTTTTCGATTTGTGACTGATTTCTTCCGA
196 TGCATTGTGCGATTGCCAATCGCCAACCCAAAGACCCTTTTCGATTTGTGACCGATTTCTTCCAA
* * *
2987148 GAAGAGCATTCAACCCGAACGTAACCTTTACTCTTAAAAATGTCATATTAATAAAGTCAATGTCT
261 GAACAGCATTCAACCCGAACGTAACCTTTACTATTAAAAATGTCATATCAATAAAGTCAATGTCT
**
2987213 TTACTAAGAAAAAAAATGGAATGTTTAATTATTTTTTGGAATAAATAGAAATACCAACCCAGTTT
326 TTACTAAGAAAAAAAATGGAATGTTTAATTATTTTTCAGAATAAATAGAAATACCAACCCAGTTT
* * *
2987278 GATTGAAAATTTTATTGGGTTCGTCCCATCTTTCCATTGGAAGGCATCCCTCAGAGAATCCAAAT
391 GATTGAAAAATTTATTGAGTTCGTCCCATCTTTCCATGGGAAGGCATCCCTCAGAGAATCCAAAT
* *
2987343 AAACTATCTTCATTTTTCATGAAATTGGGGCAATTCTTAACTCCTCCTACTCTGTACACCACTTG
456 AAACTATCTTCATTTTTCATGAAATTAGGGCAATTCTTAACTCCTCCTACTCCGTACACCACTTG
2987408 ATCTTGCAACGACCCACCAACTTTGATTCTTAAAGGATTGAATACTGAAAGTAATTTCAAAAATT
521 ATCTTGCAACGACCCACCAACTTTGATTCTTAAAGGATTGAATACTGAAAGTAATTTCAAAAATT
*
2987473 AGTCCGAAATTGTTCTTACCAGCTTTGAACCAAGTTTAGTCCAACTCGTTCACGCAACCACTCTT
586 AGTCCGAAATTGTTCTTACCAGCTTTGAACCAAGTTTAGTCCAACTCGTTCACACAACCACTCTT
* *
2987538 ACGAGGTGGCTTTTAACAGTATCCGAATCGCAATATTTGCAATCTCTTTTGGACTACCATGGATG
651 ACGAGGTAGCTTTTAACAGTATCCAAATCGCAATATTTGCAATCTCTTTTGGACTACCATGGATG
*
2987603 AATTAATGATAGGGACATGTAATATTATATACGTAGAACTCACCTTTTATTGCATTTATTAGACC
716 AATTAATGATAGGGACATGTAATATTATATACGTAGAACTCACCTTTTATTGCATTTATCAGACC
2987668 CTTCTTTTTCAAATCCTAC
781 CTTCTTTTTCAAATCCTAC
* *
2987687 TGTTTAGCCTCAACGCTTGCACCCATCCCAGCTCTAGAGAGTTGATTTCCTGAAATAATAAATTG
1 TGTTCAGCCTCAACGCTTGCACCCATCCCAGCTCCAGAGAGTTGATTTCCTGAAATAATAAATTG
2987752 ATTAAAATATAATTCGAAAAGTATAATGAAAAATAATCTCATGCAGAGCTTCGGGAAAACAAATT
66 ATTAAAATATAATTCGAAAAGTATAATGAAAAATAATCTCATGCAGAGCTTCGGGAAAACAAATT
* *
2987817 TAGTTACCAAATTCATAAGAATCTACTTTGTATCCCTTGGAAATAGTATACTTCATGAAATCCCT
131 TAGTTACCAAATTCATAAGAATCAACTTTGTATCCCCTGGAAATAGTATACTTCATGAAATCCCT
*
2987882 TGCATTTTGCGATTGCCAATCGCCAACCCAAAGACCCTTTTCGATTTGTGACCGATTTCTTCCAA
196 TGCATTGTGCGATTGCCAATCGCCAACCCAAAGACCCTTTTCGATTTGTGACCGATTTCTTCCAA
*
2987947 GAACAGCATTCAACCCGAACGTAACCTTTACTATTCAAAATGTCATATCAATAAAGTCAATGTCT
261 GAACAGCATTCAACCCGAACGTAACCTTTACTATTAAAAATGTCATATCAATAAAGTCAATGTCT
*
2988012 TTACTAAGAGAAAAAAATGGAATGTTTAATTATTTTTCAGAATAAATAGAACTACCAACCCAGTT
326 TTACTAAGA-AAAAAAATGGAATGTTTAATTATTTTTCAGAATAAATAGAAATACCAACCCAGTT
*
2988077 TGATTGAAAAATTTATTGAGTTCGTCCCATCTTTCCATGGGAAGGCATCCCTGAGAGAAT-CAGA
390 TGATTGAAAAATTTATTGAGTTCGTCCCATCTTTCCATGGGAAGGCATCCCTCAGAGAATCCA-A
*
2988141 ATAAACTATCTTCA-TTTTCATGAAATTAGGGCAATTCTTAACTCCTTCTACTCCGTACACCACT
454 ATAAACTATCTTCATTTTTCATGAAATTAGGGCAATTCTTAACTCCTCCTACTCCGTACACCACT
*
2988205 TGATCTTGCAACGACCCACCAACTTTGATTCTTAAAGGATTGAATGCTGAAAGTAATTTCAAAAA
519 TGATCTTGCAACGACCCACCAACTTTGATTCTTAAAGGATTGAATACTGAAAGTAATTTCAAAAA
**
2988270 TTAGTTTGAAATTGTTCTTACCAGCTTTGAACCAAGTTTAGTCCAACTCGTTCACACAACCACTC
584 TTAGTCCGAAATTGTTCTTACCAGCTTTGAACCAAGTTTAGTCCAACTCGTTCACACAACCACTC
*
2988335 TTACGAGGTAGCTTTTAACAGTATCCAAATTGCAATATTTGCAATCTCTTTTGGACTACCATGGA
649 TTACGAGGTAGCTTTTAACAGTATCCAAATCGCAATATTTGCAATCTCTTTTGGACTACCATGGA
2988400 TGAATTAATGATAGGGACATGTAATATTATATACGTAGAACTCACCTTTTATTGCATTTATCAGA
714 TGAATTAATGATAGGGACATGTAATATTATATACGTAGAACTCACCTTTTATTGCATTTATCAGA
*
2988465 CCCTTTTTTTTCAAATCC
779 CCCTTCTTTTTCAAATCC
2988483 AACAAAAAAC
Statistics
Matches: 761, Mismatches: 33, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
799 638 0.84
800 123 0.16
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (799 bp):
TGTTCAGCCTCAACGCTTGCACCCATCCCAGCTCCAGAGAGTTGATTTCCTGAAATAATAAATTG
ATTAAAATATAATTCGAAAAGTATAATGAAAAATAATCTCATGCAGAGCTTCGGGAAAACAAATT
TAGTTACCAAATTCATAAGAATCAACTTTGTATCCCCTGGAAATAGTATACTTCATGAAATCCCT
TGCATTGTGCGATTGCCAATCGCCAACCCAAAGACCCTTTTCGATTTGTGACCGATTTCTTCCAA
GAACAGCATTCAACCCGAACGTAACCTTTACTATTAAAAATGTCATATCAATAAAGTCAATGTCT
TTACTAAGAAAAAAAATGGAATGTTTAATTATTTTTCAGAATAAATAGAAATACCAACCCAGTTT
GATTGAAAAATTTATTGAGTTCGTCCCATCTTTCCATGGGAAGGCATCCCTCAGAGAATCCAAAT
AAACTATCTTCATTTTTCATGAAATTAGGGCAATTCTTAACTCCTCCTACTCCGTACACCACTTG
ATCTTGCAACGACCCACCAACTTTGATTCTTAAAGGATTGAATACTGAAAGTAATTTCAAAAATT
AGTCCGAAATTGTTCTTACCAGCTTTGAACCAAGTTTAGTCCAACTCGTTCACACAACCACTCTT
ACGAGGTAGCTTTTAACAGTATCCAAATCGCAATATTTGCAATCTCTTTTGGACTACCATGGATG
AATTAATGATAGGGACATGTAATATTATATACGTAGAACTCACCTTTTATTGCATTTATCAGACC
CTTCTTTTTCAAATCCTAC
Found at i:2994184 original size:22 final size:22
Alignment explanation
Indices: 2994159--2994202 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2994149 ACAACCGGAG
2994159 GCTGGAACTTTCCCATAAGAAT
1 GCTGGAACTTTCCCATAAGAAT
2994181 GCTGGAACTTTCCCATAAGAAT
1 GCTGGAACTTTCCCATAAGAAT
2994203 TTATTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (22 bp):
GCTGGAACTTTCCCATAAGAAT
Found at i:3045389 original size:21 final size:23
Alignment explanation
Indices: 3045345--3045407 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
3045335 ATAGTTAACT
3045345 TTTAATAA-AATATATAAAAAGA
1 TTTAATAATAATATATAAAAAGA
* *
3045367 -TTAATAATAATA-ATATAATGA
1 TTTAATAATAATATATAAAAAGA
3045388 TTTAA-AATAA-ATAGTAAAAA
1 TTTAATAATAATATA-TAAAAA
3045408 AAATAGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 20 0.61
22 12 0.36
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TTTAATAATAATATATAAAAAGA
Found at i:3049275 original size:21 final size:21
Alignment explanation
Indices: 3049242--3049283 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3049232 TTCTTGAAAT
*
3049242 AAATTCAAAAAATTAGGAAAAA
1 AAATTCAAAAAATCA-GAAAAA
*
3049264 AAATT-AACAAATCAGAAAAA
1 AAATTCAAAAAATCAGAAAAA
3049284 TATGGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATTCAAAAAATCAGAAAAA
Found at i:3050418 original size:34 final size:33
Alignment explanation
Indices: 3050358--3050730 Score: 410
Period size: 34 Copynumber: 11.1 Consensus size: 33
3050348 AGAAAGTAAC
* * * *
3050358 ATGCAAACCCTATTTTATATTA-TATGACTTAGT
1 ATGCGAACCCCATGTTATA-TAGTATGACATAGT
* *
3050391 ATGTGAGCCCCATTGTTATATAGTATGACATAGT
1 ATGCGAACCCCA-TGTTATATAGTATGACATAGT
*
3050425 ATAC-AACCCCTCATGTTATATAGTATGACATAGT
1 ATGCGAA-CCC-CATGTTATATAGTATGACATAGT
* *
3050459 ATGTGAACCCCCATGTTATATAGTATGACATAGC
1 ATGCGAA-CCCCATGTTATATAGTATGACATAGT
* *
3050493 ATG-GAACCCCATGTCATATAGAATGACATAGT
1 ATGCGAACCCCATGTTATATAGTATGACATAGT
* *
3050525 ATGCAAACCCCCATGTTATATCGTATGACATAGT
1 ATGCGAA-CCCCATGTTATATAGTATGACATAGT
* **
3050559 ATGCAAACCCTCACATTATATAGTATGACATAGT
1 ATGCGAACCC-CATGTTATATAGTATGACATAGT
* *
3050593 ATGCAAACTCCCATGTTATATAGAATGACATAGT
1 ATGCGAAC-CCCATGTTATATAGTATGACATAGT
* * *
3050627 ATACGAGCCCTCATGTTATATAGTATGACAAAGT
1 ATGCGAACCC-CATGTTATATAGTATGACATAGT
*
3050661 ATGTGAACCCCAATGTTATATAGTATGACATAGT
1 ATGCGAACCCC-ATGTTATATAGTATGACATAGT
**
3050695 ATGCGAACACCCACATTATATAGTATGACATAGT
1 ATGCGAAC-CCCATGTTATATAGTATGACATAGT
3050729 AT
1 AT
3050731 ATGAACCTGA
Statistics
Matches: 291, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
32 26 0.09
33 22 0.08
34 230 0.79
35 13 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
ATGCGAACCCCATGTTATATAGTATGACATAGT
Found at i:3052333 original size:15 final size:15
Alignment explanation
Indices: 3052308--3052374 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 15
3052298 ATGTGATTTA
*
3052308 ATATGTGCAAACCCT
1 ATATGTACAAACCCT
* *
3052323 ATATATACAAACCTT
1 ATATGTACAAACCCT
* *
3052338 ATATGTGCAAACCTT
1 ATATGTACAAACCCT
*
3052353 TTATGTACAAACCCT
1 ATATGTACAAACCCT
3052368 ATATGTA
1 ATATGTA
3052375 AACTTGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (15 bp):
ATATGTACAAACCCT
Found at i:3052343 original size:30 final size:30
Alignment explanation
Indices: 3052308--3052373 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3052298 ATGTGATTTA
*
3052308 ATATGTGCAAACCCTATATATACAAACCTT
1 ATATGTGCAAACCCTATATATACAAACCCT
* * *
3052338 ATATGTGCAAACCTTTTATGTACAAACCCT
1 ATATGTGCAAACCCTATATATACAAACCCT
3052368 ATATGT
1 ATATGT
3052374 AAACTTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (30 bp):
ATATGTGCAAACCCTATATATACAAACCCT
Found at i:3052386 original size:28 final size:29
Alignment explanation
Indices: 3052308--3052387 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
3052298 ATGTGATTTA
* * * *
3052308 ATATGTGCAAACCCTATATATACAAACCTT
1 ATATGT-CAAACCTTTTATGTACAAACCCT
3052338 ATATGTGCAAACCTTTTATGTACAAACCCT
1 ATATGT-CAAACCTTTTATGTACAAACCCT
3052368 ATATGT-AAA-CTTGTTATGTA
1 ATATGTCAAACCTT-TTATGTA
3052388 TGTGTTAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 3 0.07
28 10 0.22
30 32 0.71
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (29 bp):
ATATGTCAAACCTTTTATGTACAAACCCT
Found at i:3058348 original size:5 final size:5
Alignment explanation
Indices: 3058338--3058401 Score: 110
Period size: 5 Copynumber: 12.8 Consensus size: 5
3058328 CTTATACTCG
*
3058338 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA TTATA
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA
*
3058388 ATATA CTATA CTAT
1 CTATA CTATA CTAT
3058402 TCCTTGGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (5 bp):
CTATA
Found at i:3060707 original size:8 final size:8
Alignment explanation
Indices: 3060694--3060719 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3060684 CTTATACGAA
3060694 ATCACATT
1 ATCACATT
3060702 ATCACATT
1 ATCACATT
3060710 ATCACATT
1 ATCACATT
3060718 AT
1 AT
3060720 ACCGATGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (8 bp):
ATCACATT
Found at i:3060760 original size:61 final size:63
Alignment explanation
Indices: 3060648--3060770 Score: 171
Period size: 61 Copynumber: 2.0 Consensus size: 63
3060638 CTTACACGGT
*
3060648 TCACATATCATACCGAAGCCATATCCCAGACATGGTCTTATACGAAATCACATTATCACATTA
1 TCACATATCATACCGAAGCCATAGCCCAGACATGGTCTTATACGAAATCACATTATCACATTA
* * * *
3060711 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATATGGAGTCACATTATCACATT
1 TCACATATCATACCGAAGCCATAGCCCAGAC-ATGGTCTTATACGAAATCACATTATCACATT
3060771 GCACCGATGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 1 0.02
61 46 0.85
62 1 0.02
63 6 0.11
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (63 bp):
TCACATATCATACCGAAGCCATAGCCCAGACATGGTCTTATACGAAATCACATTATCACATTA
Found at i:3063361 original size:7 final size:7
Alignment explanation
Indices: 3063349--3063389 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
3063339 AGTTCTTTTC
3063349 TTTTCTT
1 TTTTCTT
3063356 TTTTCTT
1 TTTTCTT
3063363 TTTTC-T
1 TTTTCTT
3063369 TTTTCTT
1 TTTTCTT
*
3063376 TTTTATT
1 TTTTCTT
*
3063383 ATTTCTT
1 TTTTCTT
3063390 ACCCCTACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:3063368 original size:14 final size:14
Alignment explanation
Indices: 3063349--3063389 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
3063339 AGTTCTTTTC
3063349 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
3063363 TTTTC-TTTTTCTT
1 TTTTCTTTTTTCTT
* *
3063376 TTTTATTATTTCTT
1 TTTTCTTTTTTCTT
3063390 ACCCCTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:3063374 original size:20 final size:20
Alignment explanation
Indices: 3063344--3063389 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3063334 TCCTTAGTTC
*
3063344 TTTTC-TTTTCTTTTTTCTT
1 TTTTCTTTTTCTTTTTTATT
3063363 TTTTCTTTTTCTTTTTTATT
1 TTTTCTTTTTCTTTTTTATT
*
3063383 ATTTCTT
1 TTTTCTT
3063390 ACCCCTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTTTATT
Found at i:3064567 original size:22 final size:23
Alignment explanation
Indices: 3064516--3064567 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
3064506 TCTTAAGCTT
*
3064516 TATTTT-CATGGTTGCCTTAGTTT
1 TATTTTCCATGGTTG-CTTAGTTG
3064539 TCA-TTTCCATGGTTG-TTAGTTG
1 T-ATTTTCCATGGTTGCTTAGTTG
3064561 TATTTTC
1 TATTTTC
3064568 ATTATGGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 11 0.44
23 4 0.16
24 9 0.36
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.56
Consensus pattern (23 bp):
TATTTTCCATGGTTGCTTAGTTG
Found at i:3066298 original size:44 final size:44
Alignment explanation
Indices: 3066249--3066337 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
3066239 GTTTTTAAAA
*
3066249 CTTAATGTTATGCAAGCAATTCATGCAAATTAGAATAAAAAATC
1 CTTAATGTTATGCAAGCAATTCATGCAAATCAGAATAAAAAATC
3066293 CTTAATGTTATGCAAGCAATTCATGCAAATCAGAATAAAAAATC
1 CTTAATGTTATGCAAGCAATTCATGCAAATCAGAATAAAAAATC
3066337 C
1 C
3066338 CCAACGTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (44 bp):
CTTAATGTTATGCAAGCAATTCATGCAAATCAGAATAAAAAATC
Done.