Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 211 of 226
Found at i:66441513 original size:11 final size:11
Alignment explanation
Indices: 66441482--66441515 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
66441472 GTCACAAGTG
66441482 AATTAATTCACA
1 AATTAATTCA-A
*
66441494 AATTGATTCAA
1 AATTAATTCAA
66441505 AATTAATTCAA
1 AATTAATTCAA
66441516 CTTGGGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:66443897 original size:2 final size:2
Alignment explanation
Indices: 66443890--66443916 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66443880 TTATAAAAAG
66443890 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
66443917 ACTGTATCCG
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:66446685 original size:2 final size:2
Alignment explanation
Indices: 66446678--66446708 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66446668 AGAATCTTAC
66446678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66446709 CGCATCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66450728 original size:23 final size:23
Alignment explanation
Indices: 66450702--66450755 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
66450692 TTTAAAAAAT
*
66450702 TATAAAGA-TATAAATTTATAATA
1 TATAAA-ATTATAAATTAATAATA
*
66450725 TATAAAATTTTAAATTAATAATA
1 TATAAAATTATAAATTAATAATA
66450748 -ATAAAATT
1 TATAAAATT
66450756 GTACTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TATAAAATTATAAATTAATAATA
Found at i:66450764 original size:22 final size:23
Alignment explanation
Indices: 66450712--66450758 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
66450702 TATAAAGATA
* *
66450712 TAAATTTATAATATATAAAATTT
1 TAAATTAATAATATATAAAATTG
66450735 TAAATTAATAATA-ATAAAATTG
1 TAAATTAATAATATATAAAATTG
66450757 TA
1 TA
66450759 CTTTAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTAATAATATATAAAATTG
Found at i:66450795 original size:31 final size:32
Alignment explanation
Indices: 66450731--66450813 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 32
66450721 AATATATAAA
*
66450731 ATTTTAAATTAATAATAATAAAATTGTACTTTAA-
1 ATTTTAAA--AATAATAA-AAAATTGTAATTTAAT
66450765 ACTTCTTAAAAATAATAAAAAA-T-TAATTTAAT
1 A-TT-TTAAAAATAATAAAAAATTGTAATTTAAT
*
66450797 ATTTTAAAAATTATAAA
1 ATTTTAAAAATAATAAA
66450814 TATATAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
30 13 0.30
31 9 0.20
32 2 0.05
33 4 0.09
34 9 0.20
35 2 0.05
36 5 0.11
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (32 bp):
ATTTTAAAAATAATAAAAAATTGTAATTTAAT
Found at i:66450831 original size:17 final size:18
Alignment explanation
Indices: 66450806--66450842 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
66450796 TATTTTAAAA
66450806 ATTATAAATATATA-AATT
1 ATTATAAATA-ATACAATT
66450824 ATTA-AAATAATACAATT
1 ATTATAAATAATACAATT
66450841 AT
1 AT
66450843 ATTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 11 0.61
18 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATACAATT
Found at i:66455999 original size:46 final size:46
Alignment explanation
Indices: 66455947--66456057 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
66455937 TTCAAACCAC
* * * *
66455947 AATTAGTACTACATAACATTA-AATTAATAATATTATCCAAGTGCAT
1 AATTAGTACTACACAACATGATAACT-ACAATATTATCCAAGTGCAT
* * *
66455993 AATTAGTAGTACACCACATGATGACTACAATATTATCCAAGTGCAT
1 AATTAGTACTACACAACATGATAACTACAATATTATCCAAGTGCAT
* *
66456039 ATTTAGTACTACACCACAT
1 AATTAGTACTACACAACAT
66456058 AATTGATAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 53 0.96
47 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (46 bp):
AATTAGTACTACACAACATGATAACTACAATATTATCCAAGTGCAT
Found at i:66468000 original size:26 final size:26
Alignment explanation
Indices: 66467964--66468015 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
66467954 TTACTAAGTT
66467964 TACTTAAACTTATAAGCTTCCTGCTC
1 TACTTAAACTTATAAGCTTCCTGCTC
66467990 TACTTAAACTTATAAGCTTCCTGCTC
1 TACTTAAACTTATAAGCTTCCTGCTC
66468016 AAATTGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (26 bp):
TACTTAAACTTATAAGCTTCCTGCTC
Found at i:66477849 original size:6 final size:6
Alignment explanation
Indices: 66477838--66477864 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
66477828 TGATATTTTT
66477838 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
66477865 GAATAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:66477881 original size:25 final size:24
Alignment explanation
Indices: 66477844--66477912 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
66477834 TTTTAAATTA
* *
66477844 AAATTAAAATTAAAATTAAAAGAAT
1 AAATT-AAATTAAAATTAAAAAAAC
*
66477869 AGAATTAAATTAAACTGTAAAAAAAC
1 A-AATTAAATTAAAAT-TAAAAAAAC
66477895 AAATTAAATT-AAATTAAA
1 AAATTAAATTAAAATTAAA
66477913 TTAAAACTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 4 0.11
24 3 0.08
25 19 0.50
26 12 0.32
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (24 bp):
AAATTAAATTAAAATTAAAAAAAC
Found at i:66480571 original size:31 final size:30
Alignment explanation
Indices: 66480527--66480595 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
66480517 AACGGTTGGT
* *
66480527 GACCAAAAGAGAAAACTTCAAATATTTGGGC
1 GACCAAAAGAGAAAA-GTCAAATAGTTGGGC
* *
66480558 GACC-AAAGAAGAAAAGTCAAGTAGTTGGGT
1 GACCAAAAG-AGAAAAGTCAAATAGTTGGGC
66480588 GACCAAAA
1 GACCAAAA
66480596 AATAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.16
Consensus pattern (30 bp):
GACCAAAAGAGAAAAGTCAAATAGTTGGGC
Found at i:66484429 original size:21 final size:21
Alignment explanation
Indices: 66484387--66484432 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
66484377 CTTGTACAAA
*
66484387 GTATTGATATCTTTGTAATAG
1 GTATTGATATCTGTGTAATAG
*
66484408 GTATTGATAT-TGTGTTATTAG
1 GTATTGATATCTGTG-TAATAG
66484429 GTAT
1 GTAT
66484433 CGATGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (21 bp):
GTATTGATATCTGTGTAATAG
Found at i:66486779 original size:40 final size:40
Alignment explanation
Indices: 66486724--66486940 Score: 353
Period size: 40 Copynumber: 5.4 Consensus size: 40
66486714 AGGCTTGTGC
66486724 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
**
66486764 CTAGCAGGCTTAATGCCGGTGAAATATTCAGGTTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
66486804 CTAGCAGGCTTAATGCCAGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
66486844 CTAGCAGGCTTAATGCCAGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
66486884 CTAGCAGACTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
66486924 CTAGCAGGCTTCATGCC
1 CTAGCAGGCTTAATGCC
66486941 AATGTACGGT
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 167 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:66489244 original size:52 final size:52
Alignment explanation
Indices: 66489173--66489422 Score: 473
Period size: 52 Copynumber: 4.8 Consensus size: 52
66489163 ATCAAGTGAC
66489173 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
66489225 AAAGTGATAATTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
66489277 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
66489329 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
**
66489381 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAG
66489423 AAACAAAGTG
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 194 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:66489447 original size:37 final size:37
Alignment explanation
Indices: 66489403--66489511 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
66489393 GATAGCTTTA
66489403 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
66489440 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
66489477 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
66489512 ATCATACGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 54 0.77
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:66496723 original size:22 final size:22
Alignment explanation
Indices: 66496698--66496749 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
66496688 AGAAAAATCA
66496698 AGACAAAGA-CGTGC-CAAAAGGC
1 AGACAAA-ACCGTGCACAAAA-GC
66496720 AGACAAAACCGTGCTACAAAAGC
1 AGACAAAACCGTGC-ACAAAAGC
66496743 AGACAAA
1 AGACAAA
66496750 TTAAAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
23 9 0.33
24 5 0.19
ACGTcount: A:0.50, C:0.23, G:0.21, T:0.06
Consensus pattern (22 bp):
AGACAAAACCGTGCACAAAAGC
Found at i:66497101 original size:2 final size:2
Alignment explanation
Indices: 66497094--66497122 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66497084 TTACAATTTT
66497094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66497123 TACACAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66497516 original size:46 final size:46
Alignment explanation
Indices: 66497447--66497585 Score: 244
Period size: 46 Copynumber: 3.0 Consensus size: 46
66497437 TTTTGGTGAT
* *
66497447 AATGACCTTT-TATTTTTCGTCAATGGAATTCCCAAAATAGCCTAAA
1 AATGA-CTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
66497493 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
1 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
66497539 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
1 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
66497585 A
1 A
66497586 TACAATTGAA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.04
46 86 0.96
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (46 bp):
AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAA
Found at i:66497640 original size:64 final size:62
Alignment explanation
Indices: 66497539--66497669 Score: 244
Period size: 64 Copynumber: 2.1 Consensus size: 62
66497529 ATAGCTTAAA
66497539 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAAATACAATTGAATGCTTCC
1 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTT-AAA-ACAATTGAATGCTTCC
66497603 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAAACAATTGAATGCTTCC
1 AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAAACAATTGAATGCTTCC
66497665 AATGA
1 AATGA
66497670 GGATTTGGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 21 0.31
63 3 0.04
64 43 0.64
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (62 bp):
AATGACTTTCTATTTTTCATCAATGGAATTCCCAAAATAGCTTAAAACAATTGAATGCTTCC
Found at i:66499626 original size:30 final size:31
Alignment explanation
Indices: 66499563--66499633 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
66499553 ATTTTAAATT
* *
66499563 AATAAAAATAAATTTATATTTTATCCCTTAAA
1 AATAATAA-AAATTTATATTTAATCCCTTAAA
* *
66499595 AATAATAAAAATTTA-ATTTAATTCTTTAAA
1 AATAATAAAAATTTATATTTAATCCCTTAAA
*
66499625 AATTATAAA
1 AATAATAAA
66499634 GATATAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 20 0.59
31 7 0.21
32 7 0.21
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (31 bp):
AATAATAAAAATTTATATTTAATCCCTTAAA
Found at i:66499728 original size:94 final size:93
Alignment explanation
Indices: 66499614--66499808 Score: 291
Period size: 94 Copynumber: 2.1 Consensus size: 93
66499604 AATTTAATTT
* * * * *
66499614 AATTCTTTAAAAATTATAAAGATATAAGCTACTAAAATAATTACATTACATTTTTATTATCGTAA
1 AATTTTTTAAAAATTATAAAGATATAAGCTACTAAAATAATAAAATTACATTTTTACTATAGTAA
66499679 AAATTATAATTTAATTTCGGCCCCTTAA
66 AAATTATAATTTAATTTCGGCCCCTTAA
* * *
66499707 AATTTTTTAAAAAATTATAAAGATATAAGCTATTAAAATGATAAAATTATATTTTTACTATAGTA
1 AATTTTTT-AAAAATTATAAAGATATAAGCTACTAAAATAATAAAATTACATTTTTACTATAGTA
* *
66499772 AAAATTATAATTTAATTTTGGCGCCTTAA
65 AAAATTATAATTTAATTTCGGCCCCTTAA
66499801 AATTTTTT
1 AATTTTTT
66499809 CTTGCTTCGC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 7 0.08
94 84 0.92
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (93 bp):
AATTTTTTAAAAATTATAAAGATATAAGCTACTAAAATAATAAAATTACATTTTTACTATAGTAA
AAATTATAATTTAATTTCGGCCCCTTAA
Found at i:66501417 original size:9 final size:9
Alignment explanation
Indices: 66501391--66501424 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
66501381 ATTACTTGGG
66501391 TAAAAAATA
1 TAAAAAATA
66501400 -AAAATAATA
1 TAAAA-AATA
66501409 TAAAAAATA
1 TAAAAAATA
66501418 TAAAAAA
1 TAAAAAA
66501425 ATTTGGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.17
9 15 0.65
10 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAAAAATA
Found at i:66503550 original size:100 final size:99
Alignment explanation
Indices: 66503361--66503550 Score: 213
Period size: 100 Copynumber: 1.9 Consensus size: 99
66503351 TAATATATAC
* * * *
66503361 ATAATAATATATAAAAAATTGAAACAAACGAAATATATAAAGTAGGGTTTTTTTAAAAGAAAATA
1 ATAATAATATATAAAAAATTGAAACAAACAAAATAAATAAAATAGGG-TTTCTTAAAAGAAAATA
* *
66503426 ATTATATATATATATATAGGAATAAGTAAAAATAG
65 ATTATATATATATATAGAGAAATAAGTAAAAATAG
* * **
66503461 ATAATAATATATACAAAAGTTGAAATAAACAAAATAAATTAAAATAGGG-TTCTTAAAA-AATCT
1 ATAATAATATATA-AAAAATTGAAACAAACAAAATAAA-TAAAATAGGGTTTCTTAAAAGAAAAT
* * *
66503524 AAATTATATGTATGTATAGATAAATAA
64 -AATTATATATATATATAGAGAAATAA
66503551 AAGGTATAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
99 3 0.04
100 42 0.57
101 20 0.27
102 9 0.12
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (99 bp):
ATAATAATATATAAAAAATTGAAACAAACAAAATAAATAAAATAGGGTTTCTTAAAAGAAAATAA
TTATATATATATATAGAGAAATAAGTAAAAATAG
Found at i:66504646 original size:22 final size:22
Alignment explanation
Indices: 66504616--66504659 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
66504606 AAACAATGTA
*
66504616 TTTCGTTTTTCT-CTTATTTCTT
1 TTTCGTTTTGCTGC-TATTTCTT
*
66504638 TTTCTTTTTGCTGCTATTTCTT
1 TTTCGTTTTGCTGCTATTTCTT
66504660 CGCTGCTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.05, C:0.18, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTCGTTTTGCTGCTATTTCTT
Found at i:66505401 original size:100 final size:100
Alignment explanation
Indices: 66505227--66505854 Score: 959
Period size: 100 Copynumber: 6.3 Consensus size: 100
66505217 CTTTTGGAAA
*** * * * * * *
66505227 GTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
* * * * *
66505292 GTGACTTTAATCTGTTCCACGGCACCGCCAGGGAA
66 GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
* *
66505327 GTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
* *
66505392 GTGGTTTTAATCTGCTCCACTGCACCGCCAGGGAG
66 GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
* *
66505427 GTAAGATTCGCTGCTGTAGCTTTAATCTTCTTTAACCGCAATGTCAGGGAGGCAAGATTCACCAT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCT-TTTAACCGCAATGTCAGGGAGGCAAGATTCACCGT
* *
66505492 TGTGGCTTTAATCTACTCCGCTGCACCGCCTGGGAG
65 TGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
* *
66505528 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAAACGCAATGTCAGGGAGGCAAGATTAACCGTT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
*
66505593 GTGGCTTTAATCTGCTCCACTGCACTGCCTGGGAG
66 GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
*
66505628 GTAAGATTCGTTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
* *
66505693 GTGGCTTTAATCTGCTCCACTGCACTGCTTGGGAG
66 GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
* *
66505728 GTAAGATTTGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTTAGGGAGGCAAGATTCACCGTT
1 GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
* *
66505793 GTGGCTTTAATCTGCTCCACTGCACTGCTTGGGAG
66 GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
66505828 GTAAGATTCGCTGCTGTAGCTTTAATC
1 GTAAGATTCGCTGCTGTAGCTTTAATC
66505855 AAGATTCACC
Statistics
Matches: 494, Mismatches: 33, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
100 400 0.81
101 94 0.19
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (100 bp):
GTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
GTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAG
Found at i:66505827 original size:50 final size:50
Alignment explanation
Indices: 66505272--66505854 Score: 331
Period size: 50 Copynumber: 11.6 Consensus size: 50
66505262 TGCAATGTCG
* * * * * *
66505272 GGGAAGCAAGATTCACCGATGT-GACTTTAATCTGTTCCACGGCACCGCCA
1 GGGAGGCAAGATTCACCGTTGTAG-CTTTAATCTGCTCCACTGCACTGCTA
* * * * ** ** * *
66505322 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACCGCAATG-TCA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCT-A
* * * *
66505372 GGGAGGCAAGATTCACCGTTGTGGTTTTAATCTGCTCCACTGCACCGCCA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCTA
* * * * * ** * *
66505422 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCTTCTTTAACCGCAATG-TCA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGC-TCCACTGCACTGCT-A
* * * * *
66505473 GGGAGGCAAGATTCACCATTGTGGCTTTAATCTACTCCGCTGCACCGCCT-
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTG-CTA
* * * * ** ** *
66505523 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATCCTTTTAAAC-GCAATG-TCA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAAT-CTGCTCCACTGCACTGCT-A
* *
66505573 GGGAGGCAAGATTAACCGTTGTGGCTTTAATCTGCTCCACTGCACTGCCT-
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTG-CTA
* *** * * ** * *
66505623 GGGAGGTAAGATTCGTTGCTGTAGCTTTAATCCT-TTTAACCGCAATG-TCA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAAT-CTGCTCCACTGCACTGCT-A
* *
66505673 GGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGCTCCACTGCACTGCTT
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCTA
* ** * * * ** * * *
66505723 GGGAGGTAAGATTTGCTGCTGTAGCTTTAATCCT-TTTAACCGCAATGTTA
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAAT-CTGCTCCACTGCACTGCTA
* *
66505773 GGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGCTCCACTGCACTGCTT
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCTA
* * * *
66505823 GGGAGGTAAGATTCGCTGCTGTAGCTTTAATC
1 GGGAGGCAAGATTCACCGTTGTAGCTTTAATC
66505855 AAGATTCACC
Statistics
Matches: 383, Mismatches: 130, Indels: 40
0.69 0.24 0.07
Matches are distributed among these distances:
48 2 0.01
49 9 0.02
50 324 0.85
51 46 0.12
52 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (50 bp):
GGGAGGCAAGATTCACCGTTGTAGCTTTAATCTGCTCCACTGCACTGCTA
Found at i:66505858 original size:25 final size:25
Alignment explanation
Indices: 66505830--66505879 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
66505820 CTTGGGAGGT
* *
66505830 AAGATTCGCTGCTGTAGCTTTAATC
1 AAGATTCACCGCTGTAGCTTTAATC
* *
66505855 AAGATTCACCGTTGTGGCTTTAATC
1 AAGATTCACCGCTGTAGCTTTAATC
66505880 TGCTCCACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (25 bp):
AAGATTCACCGCTGTAGCTTTAATC
Found at i:66511413 original size:52 final size:52
Alignment explanation
Indices: 66511341--66511538 Score: 369
Period size: 52 Copynumber: 3.8 Consensus size: 52
66511331 ATCAAGTGAC
*
66511341 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
66511393 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
66511445 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
**
66511497 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAG
66511539 AAACAAAGTG
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 143 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:66511563 original size:37 final size:37
Alignment explanation
Indices: 66511519--66511627 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
66511509 GATAGCTTTA
66511519 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
66511556 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
66511593 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
66511628 ATCATACGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 54 0.77
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:66518840 original size:22 final size:22
Alignment explanation
Indices: 66518815--66518866 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
66518805 AGAAAAATCA
66518815 AGACAAAGA-CGTGC-CAAAAGGC
1 AGACAAA-ACCGTGCACAAAA-GC
66518837 AGACAAAACCGTGCTACAAAAGC
1 AGACAAAACCGTGC-ACAAAAGC
66518860 AGACAAA
1 AGACAAA
66518867 TTAAAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.04
22 12 0.44
23 9 0.33
24 5 0.19
ACGTcount: A:0.50, C:0.23, G:0.21, T:0.06
Consensus pattern (22 bp):
AGACAAAACCGTGCACAAAAGC
Found at i:66522060 original size:30 final size:31
Alignment explanation
Indices: 66521997--66522067 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
66521987 ATTTTAAATT
* *
66521997 AATAAAAATAAATTTATATTTTATCTCTTAAA
1 AATAATAA-AAATTTATATTTAATCTCTTAAA
66522029 AATAATAAAAATTTA-ATTTAAT-TCTTTAAA
1 AATAATAAAAATTTATATTTAATCTC-TTAAA
*
66522059 AATTATAAA
1 AATAATAAA
66522068 GATATAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 7 0.20
32 7 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (31 bp):
AATAATAAAAATTTATATTTAATCTCTTAAA
Found at i:66527642 original size:20 final size:20
Alignment explanation
Indices: 66527617--66527655 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
66527607 TTCAGTTGTA
*
66527617 AGTTTCTGTTGTAAGCTGTT
1 AGTTTCAGTTGTAAGCTGTT
66527637 AGTTTCAGTTGTAAGCTGT
1 AGTTTCAGTTGTAAGCTGT
66527656 CAGTGGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (20 bp):
AGTTTCAGTTGTAAGCTGTT
Found at i:66532287 original size:20 final size:20
Alignment explanation
Indices: 66532262--66532300 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
66532252 TTCAGTTGTA
*
66532262 AGTTTCTGTTGTAAGCTGTT
1 AGTTTCAGTTGTAAGCTGTT
66532282 AGTTTCAGTTGTAAGCTGT
1 AGTTTCAGTTGTAAGCTGT
66532301 CAGTGGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (20 bp):
AGTTTCAGTTGTAAGCTGTT
Found at i:66534969 original size:24 final size:24
Alignment explanation
Indices: 66534942--66535002 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
66534932 ATAATTTTAA
*
66534942 AATTTTAATTTTAATTAATACAAT
1 AATTTTAATTTTAATTAATAAAAT
* * *
66534966 AATTGTAAATTTTATTTATTAAAAT
1 AATT-TTAATTTTAATTAATAAAAT
* *
66534991 AATGTTATTTTT
1 AATTTTAATTTT
66535003 TAAGTATCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
AATTTTAATTTTAATTAATAAAAT
Found at i:66535266 original size:19 final size:18
Alignment explanation
Indices: 66535242--66535324 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 18
66535232 TCCTAATTCT
66535242 ATTTTTATAATTTATTTGA
1 ATTTTTATAATTT-TTTGA
66535261 ATTTTTATTAAGTTTTTAT-A
1 ATTTTTA-TAA-TTTTT-TGA
* *
66535281 ATATTTATATATTTTTAGA
1 ATTTTTATA-ATTTTTTGA
*
66535300 ATTTTTAATGAATTTTAT-A
1 ATTTTT-AT-AATTTTTTGA
66535319 ATTTTT
1 ATTTTT
66535325 TAAAGTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
19 27 0.52
20 20 0.38
21 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
ATTTTTATAATTTTTTGA
Found at i:66535377 original size:17 final size:17
Alignment explanation
Indices: 66535339--66535378 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
66535329 GTTTATATAA
66535339 GATTTTAATATTTTCAT
1 GATTTTAATATTTTCAT
* *
66535356 AATTTTAATATTTTTAT
1 GATTTTAATATTTTCAT
66535373 GATTTT
1 GATTTT
66535379 TATTTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
GATTTTAATATTTTCAT
Found at i:66536061 original size:47 final size:47
Alignment explanation
Indices: 66536010--66536108 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
66536000 AGTAGATAGC
66536010 TACTTATAACTTAATATGGAAAATATTATGTTGATTTTTCAAAACCT
1 TACTTATAACTTAATATGGAAAATATTATGTTGATTTTTCAAAACCT
66536057 TACTTATAACTTAATATGGAAAATATTATGTTGATTTTTCAAAACCT
1 TACTTATAACTTAATATGGAAAATATTATGTTGATTTTTCAAAACCT
66536104 TACTT
1 TACTT
66536109 TTGAAATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (47 bp):
TACTTATAACTTAATATGGAAAATATTATGTTGATTTTTCAAAACCT
Found at i:66542817 original size:21 final size:21
Alignment explanation
Indices: 66542787--66542840 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
66542777 TAAAAAAATT
**
66542787 TATAAAAAAAAAC-TAAAGGA
1 TATAAAAAAAAACTTAAAAAA
*
66542807 TATATAAAAAAACTTAAAAAA
1 TATAAAAAAAAACTTAAAAAA
66542828 TATAAAAAAAAAC
1 TATAAAAAAAAAC
66542841 CCCTAAACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.19
Consensus pattern (21 bp):
TATAAAAAAAAACTTAAAAAA
Found at i:66543182 original size:13 final size:13
Alignment explanation
Indices: 66543164--66543191 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
66543154 GTGTTTGGAA
66543164 TTGGACACACCGT
1 TTGGACACACCGT
66543177 TTGGACACACCGT
1 TTGGACACACCGT
66543190 TT
1 TT
66543192 TGTGGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (13 bp):
TTGGACACACCGT
Found at i:66543201 original size:21 final size:21
Alignment explanation
Indices: 66543175--66543244 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
66543165 TGGACACACC
66543175 GTTTGGACACACCGTTTTGTG
1 GTTTGGACACACCGTTTTGTG
*
66543196 GTTTGGACACAGCTC-TTTTACATG
1 GTTTGGACACA-C-CGTTTT--GTG
*
66543220 GCTTGGACACACCGTTTTGTG
1 GTTTGGACACACCGTTTTGTG
66543241 GTTT
1 GTTT
66543245 TGCCCAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 16 0.40
22 6 0.15
23 6 0.15
24 12 0.30
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.39
Consensus pattern (21 bp):
GTTTGGACACACCGTTTTGTG
Found at i:66543564 original size:34 final size:33
Alignment explanation
Indices: 66543515--66543658 Score: 116
Period size: 34 Copynumber: 4.3 Consensus size: 33
66543505 AAATACATGT
* *
66543515 TAAGCAAGTTTATTGCTA-CTATAATGATCTGTTA
1 TAAGCATG-TTATTGCTACCTAT-ATGATCTATTA
66543549 TAAGCATGTTAATTGCTACCT-TATTGATCTATTA
1 TAAGCATGTT-ATTGCTACCTATA-TGATCTATTA
* * * * *
66543583 TAAGCATGATATATGCTA-CTGTATCAACTTTCTA
1 TAAGCATGTTAT-TGCTACCTATATGATCTAT-TA
* *
66543617 TAAGAATGTTATTGCTATCGTAT-TGATCTATTA
1 TAAGCATGTTATTGCTA-CCTATATGATCTATTA
66543650 TAAGCATGT
1 TAAGCATGT
66543659 CATGTTGCAT
Statistics
Matches: 88, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
33 27 0.31
34 57 0.65
35 4 0.05
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (33 bp):
TAAGCATGTTATTGCTACCTATATGATCTATTA
Found at i:66543827 original size:49 final size:49
Alignment explanation
Indices: 66543724--66543891 Score: 192
Period size: 49 Copynumber: 3.4 Consensus size: 49
66543714 TTTGCAACGA
* ** * * * *
66543724 CAGTGGTTTATCCACAATGTATTTTAGTTAGCAGTTTGTCTGCAATGAC
1 CAGTGGTTCATCCACAACATATTTTAGTCAGTAGTTTATCTGCAATAAC
* * * *
66543773 TAGTGGTTCATCCACAACATATTTTAGTCGGTAATTTATCTGAAATAAC
1 CAGTGGTTCATCCACAACATATTTTAGTCAGTAGTTTATCTGCAATAAC
* * * *
66543822 CAGTGGTTCATTCACAACATATTTCAGTCAATAGTTTATCTGCAACAAC
1 CAGTGGTTCATCCACAACATATTTTAGTCAGTAGTTTATCTGCAATAAC
*
66543871 CAGTGGTTCATCCATAACATA
1 CAGTGGTTCATCCACAACATA
66543892 CTAGCAACTT
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 98 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (49 bp):
CAGTGGTTCATCCACAACATATTTTAGTCAGTAGTTTATCTGCAATAAC
Found at i:66544651 original size:30 final size:31
Alignment explanation
Indices: 66544617--66544676 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
66544607 AAACCATTTA
66544617 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
* *
66544647 TTTTCCCCTAAAATTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAATTTTTACTCCCTTCCCA
66544677 TTCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTTACTCCCTTCCCAC
Found at i:66551670 original size:3 final size:3
Alignment explanation
Indices: 66551662--66551714 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
66551652 TACAAAAGTG
66551662 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
66551710 ATA AT
1 ATA AT
66551715 CCAGATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:66551813 original size:13 final size:13
Alignment explanation
Indices: 66551745--66551819 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 13
66551735 AGATAGAAAT
66551745 AAATAAAT-ATTA
1 AAATAAATAATTA
*
66551757 AAATGACATAA-TA
1 AAAT-AAATAATTA
66551770 AAATAAATATATTTA
1 AAATAAATA-A-TTA
* *
66551785 AAAT-ATTTA-TA
1 AAATAAATAATTA
66551796 TAAATAAATAATTA
1 -AAATAAATAATTA
66551810 AAAT-AATAAT
1 AAATAAATAAT
66551820 AATGCAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
11 2 0.04
12 18 0.37
13 18 0.37
14 5 0.10
15 6 0.12
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (13 bp):
AAATAAATAATTA
Found at i:66555747 original size:18 final size:18
Alignment explanation
Indices: 66555707--66555748 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
66555697 AGGTATCTGA
* *
66555707 ATTTGGTATATTATATTT
1 ATTTGGTATACTAAATTT
66555725 ATTTGGTATACCTAAATTT
1 ATTTGGTATA-CTAAATTT
66555744 -TTTGG
1 ATTTGG
66555749 ACCTAACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (18 bp):
ATTTGGTATACTAAATTT
Found at i:66556046 original size:2 final size:2
Alignment explanation
Indices: 66556039--66556070 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
66556029 GGTTAGATTT
66556039 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
66556071 AAGAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66556809 original size:3 final size:3
Alignment explanation
Indices: 66556801--66556850 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
66556791 AGATTAGTTT
66556801 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
66556849 AT
1 AT
66556851 TTAGATATCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:66557628 original size:10 final size:9
Alignment explanation
Indices: 66557597--66557626 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
66557587 TTAAACAAAT
66557597 AATATAATA
1 AATATAATA
66557606 AATATCAATA
1 AATAT-AATA
66557616 AATATAATA
1 AATATAATA
66557625 AA
1 AA
66557627 ATTCGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATAATA
Found at i:66557894 original size:21 final size:21
Alignment explanation
Indices: 66557790--66557891 Score: 123
Period size: 21 Copynumber: 4.9 Consensus size: 21
66557780 TTTGACGCTG
*
66557790 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
66557811 CTCTACTTCCCTCGCTTTAGC
1 CTCTACTTCCCTCGCTGCAGC
*
66557832 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* * *
66557853 CTGTACTTCTCTCGCTGCCGC
1 CTCTACTTCCCTCGCTGCAGC
* *
66557874 CTCTACTTCTCTTGCTGC
1 CTCTACTTCCCTCGCTGC
66557892 CGCATCTGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.06, C:0.44, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:66563415 original size:16 final size:16
Alignment explanation
Indices: 66563394--66563426 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
66563384 ACTAAGCTAC
66563394 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
66563410 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
66563426 G
1 G
66563427 GCAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:66563474 original size:9 final size:9
Alignment explanation
Indices: 66563462--66564294 Score: 157
Period size: 9 Copynumber: 98.8 Consensus size: 9
66563452 CAAATTATGC
66563462 TATGTAAGT
1 TATGTAAGT
*
66563471 TATGTATGT
1 TATGTAAGT
** *
66563480 CGTATAAGT
1 TATGTAAGT
66563489 TATGTAAG-
1 TATGTAAGT
66563497 T-TGTAAGT
1 TATGTAAGT
66563505 TATGTAAGT
1 TATGTAAGT
*
66563514 TAT-TTA-T
1 TATGTAAGT
* *
66563521 TATGAAAAT
1 TATGTAAGT
*
66563530 TAAGTAAGT
1 TATGTAAGT
*
66563539 TATGTAATT
1 TATGTAAGT
*
66563548 TACG-AA-T
1 TATGTAAGT
* **
66563555 AAT-TAAAA
1 TATGTAAGT
*
66563563 AATTGTAAGT
1 TA-TGTAAGT
66563573 TATGTAAG-
1 TATGTAAGT
66563581 T-TGTAAGT
1 TATGTAAGT
66563589 TATGTAAG-
1 TATGTAAGT
66563597 T-TGTAAGT
1 TATGTAAGT
*
66563605 TATGTATA-A
1 TATGTA-AGT
*
66563614 CAT-TAA-T
1 TATGTAAGT
**
66563621 TAACTAAGT
1 TATGTAAGT
*
66563630 TATGTAATT
1 TATGTAAGT
*
66563639 TATGTATA-A
1 TATGTA-AGT
66563648 TACTGATTAA-T
1 TA-TG--TAAGT
**
66563659 TAACTAAGT
1 TATGTAAGT
*
66563668 TATGTAATT
1 TATGTAAGT
66563677 TATGT-A--
1 TATGTAAGT
*
66563683 TAT-TAACT
1 TATGTAAGT
*
66563691 AAT-TAAGT
1 TATGTAAGT
**
66563699 TATGTATTT
1 TATGTAAGT
66563708 TATG-AA-T
1 TATGTAAGT
* **
66563715 AAT-TAAAAA
1 TATGT-AAGT
*
66563724 AATGTAAGT
1 TATGTAAGT
66563733 TATGTAAGT
1 TATGTAAGT
*
66563742 TATTTAAG-
1 TATGTAAGT
66563750 T-TGTAAG-
1 TATGTAAGT
66563757 T-TGTAAGT
1 TATGTAAGT
66563765 TATGTAAG-
1 TATGTAAGT
66563773 T-TGTAAG-
1 TATGTAAGT
66563780 T-TGTAAGT
1 TATGTAAGT
66563788 TATGTAAG-
1 TATGTAAGT
*
66563796 T-TGTACGT
1 TATGTAAGT
*
66563804 TATGTATA-A
1 TATGTA-AGT
66563813 TAT-TAA-T
1 TATGTAAGT
**
66563820 TAACTAAGT
1 TATGTAAGT
*
66563829 TATGTAATT
1 TATGTAAGT
*
66563838 TATGTATCACAT
1 TATGTA--A-GT
66563850 TAATGTAAGT
1 T-ATGTAAGT
**
66563860 TATGTAACA
1 TATGTAAGT
66563869 TATGTAA--
1 TATGTAAGT
66563876 TAT-TAA-T
1 TATGTAAGT
**
66563883 TAACTAAGT
1 TATGTAAGT
*
66563892 TATGTAATT
1 TATGTAAGT
*
66563901 TATGTATCATAT
1 TATGTA--A-GT
66563913 TAATGTAAGT
1 T-ATGTAAGT
**
66563923 TATGTAACA
1 TATGTAAGT
66563932 TATGTAA--
1 TATGTAAGT
66563939 TAT-TAA-T
1 TATGTAAGT
**
66563946 TAACTAAGT
1 TATGTAAGT
*
66563955 TATGTAACT
1 TATGTAAGT
66563964 TATGTATA-T
1 TATGTA-AGT
66563973 TAAT-TAA-T
1 T-ATGTAAGT
*
66563981 TAATGTAACT
1 T-ATGTAAGT
66563991 TATGT-A--
1 TATGTAAGT
66563997 TAT-TAA-T
1 TATGTAAGT
66564004 TAAT-TAAGT
1 T-ATGTAAGT
* *
66564013 TTTGTAACT
1 TATGTAAGT
66564022 TATGT-A--
1 TATGTAAGT
66564028 TAT-TAA-T
1 TATGTAAGT
**
66564035 TAACTAAGT
1 TATGTAAGT
*
66564044 TATGTAATT
1 TATGTAAGT
66564053 TATGT-A--
1 TATGTAAGT
*
66564059 TAT-TAACT
1 TATGTAAGT
*
66564067 AAT-TAAGT
1 TATGTAAGT
66564075 TATGT--GT
1 TATGTAAGT
66564082 GT-TGTAAG-
1 -TATGTAAGT
66564090 T-TGTAAGT
1 TATGTAAGT
66564098 TATGTAAG-
1 TATGTAAGT
66564106 T-TGTAAG-
1 TATGTAAGT
66564113 T-TGTAAG-
1 TATGTAAGT
66564120 T-TGTAAGT
1 TATGTAAGT
66564128 TA--TAAGT
1 TATGTAAGT
66564135 TATGTAAGT
1 TATGTAAGT
66564144 TA--TAAGT
1 TATGTAAGT
66564151 TATGTAAG-
1 TATGTAAGT
66564159 T-TGTAAGT
1 TATGTAAGT
*
66564167 TATGTATA-A
1 TATGTA-AGT
66564176 TAT-TAA-T
1 TATGTAAGT
**
66564183 TAACTAAGT
1 TATGTAAGT
*
66564192 TATGTAATT
1 TATGTAAGT
*
66564201 TATGTATCACAT
1 TATGTA--A-GT
66564213 TAATGTAAGT
1 T-ATGTAAGT
**
66564223 TATGTAACA
1 TATGTAAGT
*
66564232 TATGTATA-A
1 TATGTA-AGT
66564241 TAT-TAA-T
1 TATGTAAGT
**
66564248 TAACTAAGT
1 TATGTAAGT
*
66564257 TATGTAATT
1 TATGTAAGT
*
66564266 TATGTATCATAT
1 TATGTA--A-GT
66564278 TAATGTAAGT
1 T-ATGTAAGT
66564288 TATGTAA
1 TATGTAA
66564295 CTTACGCATC
Statistics
Matches: 627, Mismatches: 102, Indels: 190
0.68 0.11 0.21
Matches are distributed among these distances:
5 4 0.01
6 22 0.04
7 135 0.22
8 92 0.15
9 309 0.49
10 24 0.04
11 11 0.02
12 10 0.02
13 20 0.03
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (9 bp):
TATGTAAGT
Found at i:66563502 original size:34 final size:31
Alignment explanation
Indices: 66563464--66563611 Score: 93
Period size: 34 Copynumber: 4.5 Consensus size: 31
66563454 AATTATGCTA
* *
66563464 TGTAAGTTATGTATGTCGTATAAGTTATGTAAGT
1 TGTAAGTTATGTATGT--TATAA-TTATGAAAAT
* *
66563498 TGTAAGTTATGTAAGTTATTTATTATGAAAAT
1 TGTAAGTTATGTATGTTA-TAATTATGAAAAT
*
66563530 TAAGTAAGTTATGTAAT-TTACGAATAATTA-AAAAAT
1 T--GTAAGTTATGT-ATGTT----ATAATTATGAAAAT
* * * *
66563566 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TGTAAGTTATGTATGTTATAA-TTATGAAAAT
66563598 TGTAAGTTATGTAT
1 TGTAAGTTATGTAT
66563612 AACATTAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
30 3 0.03
31 3 0.03
32 27 0.30
33 3 0.03
34 41 0.46
35 1 0.01
36 6 0.07
37 5 0.06
38 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (31 bp):
TGTAAGTTATGTATGTTATAATTATGAAAAT
Found at i:66563505 original size:16 final size:16
Alignment explanation
Indices: 66563464--66563610 Score: 102
Period size: 16 Copynumber: 8.8 Consensus size: 16
66563454 AATTATGCTA
*
66563464 TGTAAGTTATGTATGT
1 TGTAAGTTATGTAAGT
*
66563480 CGTATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
66563498 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
66563514 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
66563530 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
** *
66563548 TACGAATAA-TTA-AAAAAT
1 T--G--TAAGTTATGTAAGT
66563566 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
66563582 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
66563598 TGTAAGTTATGTA
1 TGTAAGTTATGTA
66563611 TAACATTAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 58 0.56
17 5 0.05
18 29 0.28
19 3 0.03
20 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:66563698 original size:31 final size:31
Alignment explanation
Indices: 66563653--66564079 Score: 319
Period size: 31 Copynumber: 13.6 Consensus size: 31
66563643 TATAATACTG
*
66563653 ATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* * *
66563684 ATTAACTAATTAAGTTATGTATTTTATGAAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
** * *
66563715 AATTAAAAAAATGTAAGTTATGTAAGTTATTTA-
1 -ATT-AATTAAT-TAAGTTATGTAATTTATGTAT
* *
66563748 AGTTGTAAGTT--GTAAGTTATGTAAGTTGTAAGT-T
1 A--T-TAA-TTAATTAAGTTATGTAA-TT-TATGTAT
* **
66563782 -GTAAGTT-ATGTAAG-T-TGTACGTTATGTATAAT
1 ATTAA-TTAAT-TAAGTTATGTAATTTATG--T-AT
*
66563814 ATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* **
66563845 CA--CATTAATGTAAGTTATGTAACATATGTAAT
1 -ATTAATTAAT-TAAGTTATGTAATTTATGT-AT
*
66563877 ATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
**
66563908 CA-T-ATTAATGTAAGTTATGTAACATATGTAAT
1 -ATTAATTAAT-TAAGTTATGTAATTTATGT-AT
* *
66563940 ATTAATTAACTAAGTTATGTAACTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
*
66563971 ATTAATTAATT-A---ATGTAACTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* *
66563998 ATTAATTAATTAAGTTTTGTAACTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
*
66564029 ATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
*
66564060 ATTAACTAATTAAGTTATGT
1 ATTAATTAATTAAGTTATGT
66564080 GTGTTGTAAG
Statistics
Matches: 317, Mismatches: 45, Indels: 68
0.74 0.10 0.16
Matches are distributed among these distances:
27 26 0.08
28 4 0.01
29 1 0.00
30 22 0.07
31 141 0.44
32 70 0.22
33 21 0.07
34 31 0.10
35 1 0.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTAATTAATTAAGTTATGTAATTTATGTAT
Found at i:66563720 original size:63 final size:62
Alignment explanation
Indices: 66563653--66564298 Score: 353
Period size: 63 Copynumber: 10.4 Consensus size: 62
66563643 TATAATACTG
* * * * *
66563653 ATTAATTAACTAAGTTATGTAATTTATGTATATTAACTAATTAAGTTATGTATTTTATGAAT
1 ATTAATTAAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTAT
** * * *
66563715 AATTAAAAAAATGTAAGTTATGTAAGTTATTTA-AGTTGTAAGTT--GTAAGTTATGTAAGTTGT
1 -ATT-AATTAA-GTAAGTTATGTAACTTATGTATA--T-TAA-TTAATTAAGTTATGTAA-TT-T
*
66563777 AAGT-T
57 ATGTAT
* * *
66563782 -GTAAGTTATGTAAG-T-TGT-ACGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGT
1 ATTAA-TTAAGTAAGTTATGTAAC-TTATG--T-ATATTAATTAATTAAGTTATGTAATTTATGT
66563843 AT
61 AT
* * *
66563845 CA--CATTAATGTAAGTTATGTAACATATGTAATATTAATTAACTAAGTTATGTAATTTATGTAT
1 -ATTAATTAA-GTAAGTTATGTAACTTATGT-ATATTAATTAATTAAGTTATGTAATTTATGTAT
* * *
66563908 CA-T-ATTAATGTAAGTTATGTAACATATGTAATATTAATTAACTAAGTTATGTAACTTATGTAT
1 -ATTAATTAA-GTAAGTTATGTAACTTATGT-ATATTAATTAATTAAGTTATGTAATTTATGTAT
* * *
66563971 ATTAATTAA-T---TAATGTAACTTATGTATATTAATTAATTAAGTTTTGTAACTTATGTAT
1 ATTAATTAAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTAT
* * * * *
66564029 ATTAATTAACTAAGTTATGTAATTTATGTATATTAACTAATTAAGTTATGT-GTGT-TGTA-
1 ATTAATTAAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTAT
* *
66564088 AGTTGTAAGTTATGTAAG-T-TGTAA-GT-TGTA-AGTTGTAAGTT-A-TAAGTTATGTAAGTTA
1 A--T-TAA-TTAAGTAAGTTATGTAACTTATGTATA--T-TAA-TTAATTAAGTTATGTAA-TT-
*
66564146 TAAGT-T
56 TATGTAT
*
66564152 ATGTAAGTT--GTAAGTTATGT-A--TA---ATATTAATTAACTAAGTTATGTAATTTATGTAT
1 AT-TAA-TTAAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTAT
* * *
66564208 CA--CATTAATGTAAGTTATGTAACATATGTATAATATTAATTAACTAAGTTATGTAATTTATGT
1 -ATTAATTAA-GTAAGTTATGTAACTTATG--T-ATATTAATTAATTAAGTTATGTAATTTATGT
66564271 AT
61 AT
66564273 CA-T-ATTAATGTAAGTTATGTAACTTA
1 -ATTAATTAA-GTAAGTTATGTAACTTA
66564299 CGCATCGAGA
Statistics
Matches: 476, Mismatches: 43, Indels: 126
0.74 0.07 0.20
Matches are distributed among these distances:
53 2 0.00
54 1 0.00
55 6 0.01
56 18 0.04
57 15 0.03
58 42 0.09
59 22 0.05
60 22 0.05
61 14 0.03
62 68 0.14
63 121 0.25
64 35 0.07
65 85 0.18
66 15 0.03
67 6 0.01
68 4 0.01
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (62 bp):
ATTAATTAAGTAAGTTATGTAACTTATGTATATTAATTAATTAAGTTATGTAATTTATGTAT
Found at i:66563756 original size:16 final size:16
Alignment explanation
Indices: 66563725--66563809 Score: 88
Period size: 16 Copynumber: 5.3 Consensus size: 16
66563715 AATTAAAAAA
66563725 ATGTAAGTTATGTAAGTT
1 ATGTAAG-T-TGTAAGTT
*
66563743 ATTTAAGTTGTAAG-T
1 ATGTAAGTTGTAAGTT
66563758 -TGTAAGTTATGTAAG-T
1 ATGTAAG-T-TGTAAGTT
66563774 -TGTAAGTTGTAAGTT
1 ATGTAAGTTGTAAGTT
*
66563789 ATGTAAGTTGTACGTT
1 ATGTAAGTTGTAAGTT
66563805 ATGTA
1 ATGTA
66563810 TAATATTAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.18
15 4 0.07
16 38 0.63
17 1 0.02
18 6 0.10
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.45
Consensus pattern (16 bp):
ATGTAAGTTGTAAGTT
Found at i:66563758 original size:7 final size:7
Alignment explanation
Indices: 66563746--66563800 Score: 74
Period size: 7 Copynumber: 7.3 Consensus size: 7
66563736 GTAAGTTATT
66563746 TAAGTTG
1 TAAGTTG
66563753 TAAGTTG
1 TAAGTTG
66563760 TAAGTTATG
1 TAAG-T-TG
66563769 TAAGTTG
1 TAAGTTG
66563776 TAAGTTG
1 TAAGTTG
66563783 TAAGTTATG
1 TAAG-T-TG
66563792 TAAGTTG
1 TAAGTTG
66563799 TA
1 TA
66563801 CGTTATGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
7 28 0.64
8 4 0.09
9 12 0.27
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (7 bp):
TAAGTTG
Found at i:66563765 original size:23 final size:23
Alignment explanation
Indices: 66563727--66563809 Score: 66
Period size: 23 Copynumber: 3.5 Consensus size: 23
66563717 TTAAAAAAAT
*
66563727 GTAAGTTATGTAAGTTATTTAAGTT
1 GTAAGTTATGTAAG-T-TGTAAGTT
66563752 GTAAG-T-TGTAAGTTATGTAAGTT
1 GTAAGTTATGTAAG-T-TGTAAGTT
66563775 GTAAG-T-TGTAAGTTATGTAAGTT
1 GTAAGTTATGTAAG-T-TGTAAGTT
*
66563798 GTACGTTATGTA
1 GTAAGTTATGTA
66563810 TAATATTAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
23 43 0.80
24 2 0.04
25 9 0.17
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.45
Consensus pattern (23 bp):
GTAAGTTATGTAAGTTGTAAGTT
Found at i:66563866 original size:72 final size:63
Alignment explanation
Indices: 66563810--66564295 Score: 459
Period size: 63 Copynumber: 7.9 Consensus size: 63
66563800 ACGTTATGTA
66563810 TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
1 TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
*
66563873 TAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACATATG
1 TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
* *
66563936 TAATATTAATTAACTAAGTTATGTAACTTATGTAT---ATTAAT-TAA-TTAATGTAACTTATG
1 TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTT-ATGTAACATATG
* * * * * **
66563995 T-ATATTAATTAATTAAGTTTTGTAACTTATGTAT-ATTAATTAA-CTAAGTTATGTAATTTATG
1 TAATATTAATTAACTAAGTTATGTAATTTATGTATCA--CATTAATGTAAGTTATGTAACATATG
* * ** * * *
66564057 T-ATATTAACTAATTAAGTTATGTGTGTTGTAAGT-TGTA-AGTT-ATGTAAG-T-TGTAA-GT-
1 TAATATTAATTAACTAAGTTATGT-AATT-TATGTAT-CACA-TTAATGTAAGTTATGTAACATA
66564114 TG
62 TG
* * **
66564116 TAAGT-TGTAAGTT-A-TAAGTTATGTAAGTTA--TA--A-GTT-ATGTAAG-T-TGTAAGTTAT
1 TAA-TAT-TAA-TTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATAT
66564170 G
63 G
66564171 TATAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
1 --TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
*
66564236 TATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAAC
1 --TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAAC
66564296 TTACGCATCG
Statistics
Matches: 365, Mismatches: 25, Indels: 64
0.80 0.06 0.14
Matches are distributed among these distances:
53 15 0.04
54 2 0.01
55 4 0.01
56 6 0.02
57 19 0.05
58 35 0.10
59 21 0.06
60 19 0.05
61 11 0.03
62 46 0.13
63 113 0.31
64 5 0.01
65 69 0.19
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (63 bp):
TAATATTAATTAACTAAGTTATGTAATTTATGTATCACATTAATGTAAGTTATGTAACATATG
Found at i:66563895 original size:23 final size:21
Alignment explanation
Indices: 66563810--66563969 Score: 74
Period size: 22 Copynumber: 7.6 Consensus size: 21
66563800 ACGTTATGTA
66563810 TAATATTAAT-TAACTAAGTTATG
1 TAATATT-ATGTAAC-AA-TTATG
*
66563833 TAAT-TTATGTATCACATTAATG
1 TAATATTATGTAACA-ATT-ATG
*
66563855 TAA-GTTATGTAAC-A-TATG
1 TAATATTATGTAACAATTATG
66563873 TAATATTAAT-TAACTAAGTTATG
1 TAATATT-ATGTAAC-AA-TTATG
*
66563896 TAAT-TTATGTATCATATTAATG
1 TAATATTATGTAACA-ATT-ATG
*
66563918 TAA-GTTATGTAAC-A-TATG
1 TAATATTATGTAACAATTATG
66563936 TAATATTAAT-TAACTAAGTTATG
1 TAATATT-ATGTAAC-AA-TTATG
*
66563959 TAA-CTTATGTA
1 TAATATTATGTA
66563970 TATTAATTAA
Statistics
Matches: 109, Mismatches: 7, Indels: 43
0.69 0.04 0.27
Matches are distributed among these distances:
18 12 0.11
19 14 0.13
20 6 0.06
21 14 0.13
22 44 0.40
23 19 0.17
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.44
Consensus pattern (21 bp):
TAATATTATGTAACAATTATG
Found at i:66563925 original size:22 final size:22
Alignment explanation
Indices: 66563830--66563939 Score: 81
Period size: 22 Copynumber: 5.1 Consensus size: 22
66563820 TAACTAAGTT
* * *
66563830 ATGTAATTTATGTATCACATTA
1 ATGTAAGTTATGTAACATATTA
66563852 ATGTAAGTTATGTAACATATGTA
1 ATGTAAGTTATGTAACATAT-TA
66563875 A--T-A-TTAAT-TAAC-TAAGTT-
1 ATGTAAGTT-ATGTAACAT-A-TTA
* *
66563893 ATGTAATTTATGTATCATATTA
1 ATGTAAGTTATGTAACATATTA
66563915 ATGTAAGTTATGTAACATATGTA
1 ATGTAAGTTATGTAACATAT-TA
66563938 AT
1 AT
66563940 ATTAATTAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
18 2 0.03
19 8 0.11
20 5 0.07
21 6 0.09
22 41 0.59
23 8 0.11
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ATGTAAGTTATGTAACATATTA
Found at i:66564094 original size:7 final size:7
Alignment explanation
Indices: 66564082--66564167 Score: 100
Period size: 7 Copynumber: 11.4 Consensus size: 7
66564072 AGTTATGTGT
66564082 GTTGTAA
1 GTTGTAA
66564089 GTTGTAA
1 GTTGTAA
66564096 GTTATGTAA
1 G-T-TGTAA
66564105 GTTGTAA
1 GTTGTAA
66564112 GTTGTAA
1 GTTGTAA
66564119 GTTGTAA
1 GTTGTAA
*
66564126 GTTATAA
1 GTTGTAA
66564133 GTTATGTAA
1 G-T-TGTAA
*
66564142 GTTATAA
1 GTTGTAA
66564149 GTTATGTAA
1 G-T-TGTAA
66564158 GTTGTAA
1 GTTGTAA
66564165 GTT
1 GTT
66564168 ATGTATAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
7 47 0.68
8 6 0.09
9 16 0.23
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (7 bp):
GTTGTAA
Found at i:66564098 original size:23 final size:23
Alignment explanation
Indices: 66564070--66564172 Score: 115
Period size: 23 Copynumber: 4.5 Consensus size: 23
66564060 ATTAACTAAT
**
66564070 TAAGTTATGTGTGTTGTAAGTTG
1 TAAGTTATGTAAGTTGTAAGTTG
66564093 TAAGTTATGTAAGTTGTAAGTTG
1 TAAGTTATGTAAGTTGTAAGTTG
*
66564116 TAAG-T-TGTAAGTTATAAGTTATG
1 TAAGTTATGTAAGTTGTAAG-T-TG
66564139 TAAGTTA--TAAGTTATGTAAGTTG
1 TAAGTTATGTAAG-T-TGTAAGTTG
66564162 TAAGTTATGTA
1 TAAGTTATGTA
66564173 TAATATTAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
21 12 0.18
22 2 0.03
23 44 0.65
24 3 0.04
25 7 0.10
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (23 bp):
TAAGTTATGTAAGTTGTAAGTTG
Found at i:66564103 original size:16 final size:16
Alignment explanation
Indices: 66564084--66564172 Score: 115
Period size: 16 Copynumber: 5.2 Consensus size: 16
66564074 TTATGTGTGT
66564084 TGTAAGTTGTAAGTTA
1 TGTAAGTTGTAAGTTA
66564100 TGTAAGTTGTAAGTTGTAA
1 TGTAAGTTGTAAG-T-T-A
*
66564119 GTTGTAAGTTATAAGTTA
1 --TGTAAGTTGTAAGTTA
*
66564137 TGTAAGTTATAAGTTA
1 TGTAAGTTGTAAGTTA
66564153 TGTAAGTTGTAAGTTA
1 TGTAAGTTGTAAGTTA
66564169 TGTA
1 TGTA
66564173 TAATATTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
16 48 0.73
17 1 0.02
18 2 0.03
19 2 0.03
20 1 0.02
21 12 0.18
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (16 bp):
TGTAAGTTGTAAGTTA
Found at i:66564204 original size:34 final size:34
Alignment explanation
Indices: 66564160--66564281 Score: 160
Period size: 34 Copynumber: 3.7 Consensus size: 34
66564150 TTATGTAAGT
*
66564160 TGTAAGTTATGTATAATATTAATTAACTAAGTTA
1 TGTAATTTATGTATAATATTAATTAACTAAGTTA
* * *
66564194 TGTAATTTATGTATCACATTAA-T--GTAAGTTA
1 TGTAATTTATGTATAATATTAATTAACTAAGTTA
**
66564225 TGTAACATATGTATAATATTAATTAACTAAGTTA
1 TGTAATTTATGTATAATATTAATTAACTAAGTTA
*
66564259 TGTAATTTATGTATCATATTAAT
1 TGTAATTTATGTATAATATTAAT
66564282 GTAAGTTATG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
31 25 0.34
32 1 0.01
33 1 0.01
34 46 0.63
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (34 bp):
TGTAATTTATGTATAATATTAATTAACTAAGTTA
Found at i:66564225 original size:31 final size:31
Alignment explanation
Indices: 66564152--66564294 Score: 146
Period size: 34 Copynumber: 4.5 Consensus size: 31
66564142 GTTATAAGTT
* *
66564152 ATGTAAG-T-TGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTAATTTATGTATCATATTA
* *
66564181 ATTAACTAAGTTATGTAATTTATGTATCACATTA
1 A-T--GTAAGTTATGTAATTTATGTATCATATTA
** *
66564215 ATGTAAGTTATGTAACATATGTATAATATTA
1 ATGTAAGTTATGTAATTTATGTATCATATTA
*
66564246 ATTAACTAAGTTATGTAATTTATGTATCATATTA
1 A-T--GTAAGTTATGTAATTTATGTATCATATTA
66564280 ATGTAAGTTATGTAA
1 ATGTAAGTTATGTAA
66564295 CTTACGCATC
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 37 0.40
32 5 0.05
33 3 0.03
34 45 0.49
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (31 bp):
ATGTAAGTTATGTAATTTATGTATCATATTA
Found at i:66569207 original size:41 final size:40
Alignment explanation
Indices: 66569143--66569424 Score: 208
Period size: 41 Copynumber: 6.9 Consensus size: 40
66569133 ATTTGTTACT
* * *
66569143 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTCAATAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTCAA-GC
* * * * *
66569184 ATTAGCGGCGCTTAGATACAAACGCCGCTGAA-GACAAGAGA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTC-A-AGC
* * * ** * * *
66569225 ATTAGTGACGCTCAGTTAGAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT-CAAGC
* * **
66569266 ATTGGCGGCGCTT-GTATAAAAACGCCGCTAAAGACCCCAAGC
1 ATTAGCGGCGCTTAG-ACAAAAACGCCGCTAAAG--GTCAAGC
* * ** *
66569308 ATTAGCGGCGCATAGAAAAAAACGCCGCTAAATATCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT-CAAGC
* * *
66569349 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACTCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG-GTCAAGC
*
66569390 ATTAGCGGCGCTTAGACAAAAACGACGCTAAAGGT
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGT
66569425 TTAAAAAATC
Statistics
Matches: 191, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
40 4 0.02
41 152 0.80
42 33 0.17
43 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTCAAGC
Found at i:66569346 original size:83 final size:82
Alignment explanation
Indices: 66569244--66569422 Score: 252
Period size: 83 Copynumber: 2.2 Consensus size: 82
66569234 GCTCAGTTAG
* * *
66569244 AAACGCCGCTAAAGATCCGAGCATTGGCGGCGC-TTGTATAAAAACGCCGCTAAAGACCCCAAGC
1 AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAG-ACAAAAACGCCGCTAAAGA-CCCAAGC
66569308 ATTAGCGGCGCATAGAAAA
64 ATTAGCGGCGCATAGAAAA
* * *
66569327 AAACGCCGCTAAATATCCGAGCATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACTCGAGCAT
1 AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACCCAAGCAT
* *
66569392 TAGCGGCGCTTAGACAA
66 TAGCGGCGCATAGAAAA
*
66569409 AAACGACGCTAAAG
1 AAACGCCGCTAAAG
66569423 GTTTAAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
82 34 0.40
83 49 0.58
84 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.14
Consensus pattern (82 bp):
AAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACCCAAGCAT
TAGCGGCGCATAGAAAA
Found at i:66569549 original size:40 final size:40
Alignment explanation
Indices: 66569480--66569578 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
66569470 GGTGCTTTAT
* * **
66569480 ATAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTCGGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTT-GGG
* *
66569520 AT-AATCGCCGCTGATGCTCTACCTTTAGCGGCGCTTTGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTGGG
*
66569559 CTAAATCGCCGCTAATGCTC
1 ATAAATCGCCGCTAATGCTC
66569579 GATTTGTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 15 0.31
40 34 0.69
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (40 bp):
ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTGGG
Found at i:66581800 original size:19 final size:19
Alignment explanation
Indices: 66581776--66581881 Score: 64
Period size: 17 Copynumber: 5.7 Consensus size: 19
66581766 CAACTTTTTC
66581776 TTTTTTTGAAAACACAAAT
1 TTTTTTTGAAAACACAAAT
*
66581795 TTTTTTT-AAAATACAAGA-
1 TTTTTTTGAAAACACAA-AT
* * * *
66581813 -ATTTTAG-AAACACGATT
1 TTTTTTTGAAAACACAAAT
*
66581830 TTTTTTTTAAAACACGAAA-
1 TTTTTTTGAAAACAC-AAAT
*
66581849 -ATTTTT-AAAACACAAAAT
1 TTTTTTTGAAAACAC-AAAT
66581867 TTGTTTTTGAAAACA
1 TT-TTTTTGAAAACA
66581882 TAAAAATTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
17 20 0.32
18 17 0.27
19 14 0.22
20 6 0.10
21 6 0.10
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (19 bp):
TTTTTTTGAAAACACAAAT
Found at i:66581865 original size:16 final size:17
Alignment explanation
Indices: 66581833--66581868 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
66581823 CACGATTTTT
66581833 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
66581850 TTTTTAAAACAC-AAAA
1 TTTTTAAAACACGAAAA
66581866 TTT
1 TTT
66581869 GTTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:66581890 original size:22 final size:20
Alignment explanation
Indices: 66581850--66581890 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
66581840 AACACGAAAA
*
66581850 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
66581870 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
66581891 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:66581988 original size:17 final size:17
Alignment explanation
Indices: 66581902--66582093 Score: 82
Period size: 17 Copynumber: 10.5 Consensus size: 17
66581892 GATAAAAAAC
*
66581902 GAAACACGAGGATTTTTTT
1 GAAACACGA-GA-ATTTTT
* * *
66581921 GAAACATGAAAATTTAT
1 GAAACACGAGAATTTTT
66581938 GAAACACG-GTCAATTTTTT
1 GAAACACGAG--AA-TTTTT
* *
66581957 GAAAACACAAAAATTTTT
1 G-AAACACGAGAATTTTT
*
66581975 GAAAGACGAGAATTTTTT
1 GAAACACGAGAA-TTTTT
** * *
66581993 TTAACACGAAAATTTAT
1 GAAACACGAGAATTTTT
66582010 GAAACACG-GAAATCTTTTTT
1 GAAACACGAG-AA---TTTTT
* * *
66582030 GAAAAGAAGAAAATTTTT
1 G-AAACACGAGAATTTTT
* *
66582048 AAAATACGAGAATTTTT
1 GAAACACGAGAATTTTT
*
66582065 GAAAACACGGGAAATTTTTT
1 G-AAACACGAG-AA-TTTTT
66582085 GAAACACGA
1 GAAACACGA
66582094 TTTTTTTAAG
Statistics
Matches: 126, Mismatches: 32, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
17 44 0.35
18 34 0.27
19 24 0.19
20 17 0.13
21 7 0.06
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (17 bp):
GAAACACGAGAATTTTT
Found at i:66581990 original size:73 final size:72
Alignment explanation
Indices: 66581902--66582092 Score: 206
Period size: 73 Copynumber: 2.6 Consensus size: 72
66581892 GATAAAAAAC
* * *
66581902 GAAACACGAGGATTTTTTTGAAACATGAAAATTTATGAAACACGGTCAA-TTTTTTGAAAACACA
1 GAAACACGAGAATTTTTTT-AAACACGAAAATTTATGAAACACGG-AAACTTTTTTGAAAACA-A
66581966 -AAAATTTTT
63 GAAAATTTTT
* * *
66581975 GAAAGACGAGAATTTTTTTTAACACGAAAATTTATGAAACACGGAAATCTTTTTTGAAAAGAAGA
1 GAAACACGAGAATTTTTTTAAACACGAAAATTTATGAAACACGGAAA-CTTTTTTGAAAACAAGA
66582040 AAATTTTT
65 AAATTTTT
* * ** * *
66582048 AAAATACGAGAATTTTTGAAAACACGGGAAATTTTTTGAAACACG
1 GAAACACGAGAATTTTTTTAAACAC--GAAAATTTATGAAACACG
66582093 ATTTTTTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
71 2 0.02
72 24 0.24
73 58 0.58
75 16 0.16
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (72 bp):
GAAACACGAGAATTTTTTTAAACACGAAAATTTATGAAACACGGAAACTTTTTTGAAAACAAGAA
AATTTTT
Found at i:66581991 original size:18 final size:18
Alignment explanation
Indices: 66581902--66582093 Score: 94
Period size: 18 Copynumber: 10.5 Consensus size: 18
66581892 GATAAAAAAC
*
66581902 GAAACACGAGGATTTTTTT
1 GAAACACGA-GAATTTTTT
* * *
66581921 GAAACATGA-AAATTTAT
1 GAAACACGAGAATTTTTT
66581938 GAAACACG-GTCAATTTTTT
1 GAAACACGAG--AATTTTTT
* *
66581957 GAAAACAC-AAAAATTTTT
1 G-AAACACGAGAATTTTTT
*
66581975 GAAAGACGAGAATTTTTT
1 GAAACACGAGAATTTTTT
** * *
66581993 TTAACACGA-AAATTTAT
1 GAAACACGAGAATTTTTT
66582010 GAAACACG-GAAATCTTTTTT
1 GAAACACGAG-AA--TTTTTT
*
66582030 GAAA-A-GAAGAAAATTTTT
1 GAAACACG-AG-AATTTTTT
* *
66582048 AAAATACGAGAA-TTTTT
1 GAAACACGAGAATTTTTT
*
66582065 GAAAACACGGGAAATTTTTT
1 G-AAACACGAG-AATTTTTT
66582085 GAAACACGA
1 GAAACACGA
66582094 TTTTTTTAAG
Statistics
Matches: 129, Mismatches: 27, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
17 34 0.26
18 42 0.33
19 28 0.22
20 25 0.19
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
GAAACACGAGAATTTTTT
Found at i:66581999 original size:35 final size:35
Alignment explanation
Indices: 66581902--66582064 Score: 118
Period size: 36 Copynumber: 4.5 Consensus size: 35
66581892 GATAAAAAAC
* *
66581902 GAAACACGAGGATTTTTTTGAA-ACATGAAAATTTAT
1 GAAACACGAGAATTTTTTTGAACACA--AAAATTTTT
66581938 GAAACACG-GTCAA-TTTTTTGAAAACACAAAAATTTTT
1 GAAACACGAG--AATTTTTTTG--AACACAAAAATTTTT
* * * *
66581975 GAAAGACGAGAATTTTTTTTAACACGAAAATTTAT
1 GAAACACGAGAATTTTTTTGAACACAAAAATTTTT
* *
66582010 GAAACACG-GAAATCTTTTTTGAAAAGAAGAAAATTTTT
1 GAAACACGAG-AAT-TTTTTTGAACA-CA-AAAATTTTT
* *
66582048 AAAATACGAGAATTTTT
1 GAAACACGAGAATTTTT
66582065 GAAAACACGG
Statistics
Matches: 101, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
34 1 0.01
35 24 0.24
36 26 0.26
37 26 0.26
38 20 0.20
39 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (35 bp):
GAAACACGAGAATTTTTTTGAACACAAAAATTTTT
Found at i:66582082 original size:19 final size:19
Alignment explanation
Indices: 66581952--66582093 Score: 88
Period size: 17 Copynumber: 7.8 Consensus size: 19
66581942 CACGGTCAAT
*
66581952 TTTTTGAAAACAC-AAAAA
1 TTTTTGAAAACACGAGAAA
*
66581970 TTTTTG-AAAGACGAG-AA
1 TTTTTGAAAACACGAGAAA
***
66581987 TTTTTTTTAACACGA-AAA
1 TTTTTGAAAACACGAGAAA
*
66582005 TTTATG-AAACACG-GAAA
1 TTTTTGAAAACACGAGAAA
* *
66582022 TCTTTTTTGAAAAGAAGA-AAA
1 ---TTTTTGAAAACACGAGAAA
*
66582043 TTTTT-AAAATACGAG-AA
1 TTTTTGAAAACACGAGAAA
*
66582060 TTTTTGAAAACACGGGAAA
1 TTTTTGAAAACACGAGAAA
66582079 TTTTTTG-AAACACGA
1 -TTTTTGAAAACACGA
66582094 TTTTTTTAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
17 35 0.37
18 32 0.34
19 9 0.09
20 11 0.12
21 8 0.08
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.32
Consensus pattern (19 bp):
TTTTTGAAAACACGAGAAA
Found at i:66582566 original size:5 final size:5
Alignment explanation
Indices: 66582556--66582605 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
66582546 AAACTCCATT
* *
66582556 TTTTC TTTTC TTTTC TTTT- TTTTC TCTTC -TTTC TTGTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
66582605 T
1 T
66582606 GGCCTGCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 7 0.18
5 26 0.68
6 5 0.13
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:66582729 original size:19 final size:18
Alignment explanation
Indices: 66582705--66582746 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
66582695 TGCTTTAAAG
* *
66582705 CTGCTGGGCTGTTTTTTTT
1 CTGCTGGCCT-TTGTTTTT
66582724 CTGCT-GCCTTTGTTTTT
1 CTGCTGGCCTTTGTTTTT
66582741 CTGCTG
1 CTGCTG
66582747 CTCCTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 12 0.60
18 3 0.15
19 5 0.25
ACGTcount: A:0.00, C:0.21, G:0.24, T:0.55
Consensus pattern (18 bp):
CTGCTGGCCTTTGTTTTT
Found at i:66582739 original size:20 final size:19
Alignment explanation
Indices: 66582714--66582762 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
66582704 GCTGCTGGGC
66582714 TGTTTTTTTTCTGCTGCCTT
1 TGTTTTTTTTCTGCT-CCTT
* *
66582734 TGTTTTTCTGCTGCTCCTT
1 TGTTTTTTTTCTGCTCCTT
66582753 T-TTCTTTTTT
1 TGTT-TTTTTT
66582763 TTTCCTGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 13 0.54
ACGTcount: A:0.00, C:0.20, G:0.12, T:0.67
Consensus pattern (19 bp):
TGTTTTTTTTCTGCTCCTT
Found at i:66582930 original size:6 final size:6
Alignment explanation
Indices: 66582919--66583006 Score: 70
Period size: 6 Copynumber: 13.8 Consensus size: 6
66582909 AAAAAATATA
*
66582919 TTTCTT TTTCTT TTTCTT TTT-TT TTCTCTT TTTCTT TCTTCTT CTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTTCTT T-TTCTT TTTCTT
* * * *
66582968 CTTCTT CCTTCTT TCCTTCTCT TTTCTT CTTCTT CTTCT
1 TTTCTT -TTTCTT T--TTCT-T TTTCTT TTTCTT TTTCT
66583007 CTGTTCGGCC
Statistics
Matches: 72, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
5 4 0.06
6 43 0.60
7 19 0.26
8 4 0.06
9 2 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTCTT
Found at i:66582960 original size:3 final size:3
Alignment explanation
Indices: 66582954--66583006 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
66582944 CTCTTTTTCT
*
66582954 TTC TTC TTC TTC TTC TTC TTCC TTC TT- TCC TTC -TC TT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC
66582997 TTC TTC TTC T
1 TTC TTC TTC T
66583007 CTGTTCGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 5 0.11
3 36 0.82
4 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:66583136 original size:11 final size:11
Alignment explanation
Indices: 66583107--66583137 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
66583097 CTCCCCTCTC
*
66583107 TTCTTTTCCTT
1 TTCTTTTTCTT
66583118 TTCTTTTTCTT
1 TTCTTTTTCTT
66583129 TTCTTTTTC
1 TTCTTTTTC
66583138 GACACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:66583620 original size:30 final size:29
Alignment explanation
Indices: 66583538--66583636 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
66583528 CTTCTGGGGC
*
66583538 CAAAATATAATTTT-GAGAAAATTTAGGGAT
1 CAAAATATAATTTTAG-GAAAGTTTAGGG-T
* * * *
66583568 CAAAATGTAACTTCA-AAAAGTTTACGGGT
1 CAAAATATAATTTTAGGAAAGTTTA-GGGT
66583597 CAAAATATAATTTTAGGAAAGTTTAGGGT
1 CAAAATATAATTTTAGGAAAGTTTAGGGT
* *
66583626 TAAAATGTAAT
1 CAAAATATAAT
66583637 CTCAAAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
29 33 0.60
30 22 0.40
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.32
Consensus pattern (29 bp):
CAAAATATAATTTTAGGAAAGTTTAGGGT
Found at i:66583661 original size:59 final size:59
Alignment explanation
Indices: 66583538--66583669 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 59
66583528 CTTCTGGGGC
66583538 CAAAATATAATTTTGAGAAAATTTAGGGATCAAAATGTAACTTCAAAAAGTTTACGGGT
1 CAAAATATAATTTTGAGAAAATTTAGGGATCAAAATGTAACTTCAAAAAGTTTACGGGT
* * * *
66583597 CAAAATATAATTTT-AGGAAAGTTTAGGG-TTAAAATGTAA-TCTCAAAAATTTTAGGGGT
1 CAAAATATAATTTTGA-GAAAATTTAGGGATCAAAATGTAACT-TCAAAAAGTTTACGGGT
*
66583655 CAAAAATGTAATTTT
1 C-AAAATATAATTTT
66583670 TCATTTTTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
57 1 0.02
58 27 0.42
59 37 0.57
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (59 bp):
CAAAATATAATTTTGAGAAAATTTAGGGATCAAAATGTAACTTCAAAAAGTTTACGGGT
Found at i:66583663 original size:30 final size:29
Alignment explanation
Indices: 66583555--66583666 Score: 104
Period size: 29 Copynumber: 3.9 Consensus size: 29
66583545 TAATTTTGAG
*
66583555 AAAA-TTTAGGGATCAAAATGTAA-CTTCA
1 AAAAGTTTAGGGGTCAAAATGTAATC-TCA
* * * *
66583583 AAAAGTTTACGGGTCAAAATATAATTTTA
1 AAAAGTTTAGGGGTCAAAATGTAATCTCA
* *
66583612 GGAAAGTTTA-GGGTTAAAATGTAATCTCA
1 -AAAAGTTTAGGGGTCAAAATGTAATCTCA
*
66583641 AAAATTTTAGGGGTCAAAAATGTAAT
1 AAAAGTTTAGGGGTC-AAAATGTAAT
66583667 TTTTCATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.17
29 37 0.56
30 18 0.27
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (29 bp):
AAAAGTTTAGGGGTCAAAATGTAATCTCA
Found at i:66589782 original size:10 final size:10
Alignment explanation
Indices: 66589739--66589844 Score: 64
Period size: 10 Copynumber: 10.9 Consensus size: 10
66589729 CCTAATTCTA
66589739 TTTTTATAATT
1 TTTTTATAA-T
66589750 TTTTTATAAT
1 TTTTTATAAT
*
66589760 TTATTT-GAA-
1 TT-TTTATAAT
66589769 TTTTTATAAT
1 TTTTTATAAT
66589779 TTTTTATAA-
1 TTTTTATAAT
* *
66589788 TATTTA-GAT
1 TTTTTATAAT
*
66589797 ATTTTTAGAAT
1 -TTTTTATAAT
*
66589808 TTTTAATGAA-
1 TTTTTAT-AAT
66589818 -TTTTATAAT
1 TTTTTATAAT
*
66589827 TTTTT-TAAG
1 TTTTTATAAT
*
66589836 TTTATATAA
1 TTTTTATAA
66589845 GATTTTAATA
Statistics
Matches: 74, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
8 6 0.08
9 21 0.28
10 31 0.42
11 16 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:66589782 original size:29 final size:31
Alignment explanation
Indices: 66589737--66589820 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 31
66589727 CACCTAATTC
66589737 TATTTTTATAATTTTTTTATAATTTATTT-GA
1 TATTTTTATAA-TTTTTTATAATTTATTTAGA
66589768 -ATTTTTATAATTTTTTATAA--TATTTAGA
1 TATTTTTATAATTTTTTATAATTTATTTAGA
* *
66589796 TATTTTTAGAATTTTTAATGAATTT
1 TATTTTTATAATTTTTTAT-AATTT
66589821 TATAATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
27 5 0.11
28 2 0.04
29 26 0.57
30 12 0.26
32 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (31 bp):
TATTTTTATAATTTTTTATAATTTATTTAGA
Found at i:66589793 original size:19 final size:18
Alignment explanation
Indices: 66589740--66589841 Score: 64
Period size: 19 Copynumber: 5.4 Consensus size: 18
66589730 CTAATTCTAT
66589740 TTTTATAATTTTTTTATAA
1 TTTTATAA-TTTTTTATAA
*
66589759 TTTATTTGAA-TTTTTATAA
1 TTT-TAT-AATTTTTTATAA
** *
66589778 TTTTTTATAATATTTAGATAT
1 --TTTTATAAT-TTTTTATAA
* *
66589799 TTTTAGAATTTTTAATGAA
1 TTTTATAATTTTTTAT-AA
66589818 TTTTATAATTTTTT-TAA
1 TTTTATAATTTTTTATAA
*
66589835 GTTTATA
1 TTTTATA
66589842 TAAGATTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
17 8 0.12
18 6 0.09
19 35 0.55
20 4 0.06
21 11 0.17
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTTATAA
Found at i:66589822 original size:29 final size:28
Alignment explanation
Indices: 66589738--66589830 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
66589728 ACCTAATTCT
* *
66589738 ATTTTTATAATTTTTTTATAATTTATTT-GA
1 ATTTTTAGAA-TTTTTAATAA--TATTTAGA
* *
66589768 ATTTTTATAATTTTTTATAATATTTAGA
1 ATTTTTAGAATTTTTAATAATATTTAGA
*
66589796 TATTTTTAGAATTTTTAATGAAT-TTTATA
1 -ATTTTTAGAATTTTTAAT-AATATTTAGA
66589825 ATTTTT
1 ATTTTT
66589831 TTAAGTTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.09
28 8 0.14
29 31 0.54
30 13 0.23
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
ATTTTTAGAATTTTTAATAATATTTAGA
Found at i:66590574 original size:6 final size:7
Alignment explanation
Indices: 66590554--66590578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
66590544 TTCTCATTTT
66590554 ATTAAAA
1 ATTAAAA
66590561 ATTAAAA
1 ATTAAAA
66590568 ATTAAAA
1 ATTAAAA
66590575 ATTA
1 ATTA
66590579 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:66591959 original size:376 final size:376
Alignment explanation
Indices: 66591263--66592015 Score: 1427
Period size: 376 Copynumber: 2.0 Consensus size: 376
66591253 TCAAAAAAAT
66591263 TATCGTTTTCGTAAAAACCCCTTTTACCAATCTTTATGCTAGAAAACCAAAATAAAAATCCAAAA
1 TATCGTTTTCGTAAAAACCCCTTTTACCAATCTTTATGCTAGAAAACCAAAATAAAAATCCAAAA
66591328 CCAAAAATAGTCCGAAGAGTCTAAATTAGAAAAAACTCCCAAAACCAAAACATAAAGTCAAATTC
66 CCAAAAATAGTCCGAAGAGTCTAAATTAGAAAAAACTCCCAAAACCAAAACATAAAGTCAAATTC
*
66591393 AATCACATGACAAAACAGATACAGACATAAGTCTTTTACAGAATCAGATTCATAACCGAGTCGTA
131 AATCACATGACAAAACAGATACAGACATAAGTCTTTTACAGAATCAGATTCATAACAGAGTCGTA
66591458 TAGATACAAATATGCATGGTCCTACCCCCATCCTTACACACCAACTCTGACCATCCCAACAAACC
196 TAGATACAAATATGCATGGTCCTACCCCCATCCTTACACACCAACTCTGACCATCCCAACAAACC
*
66591523 ATGTGGGTTATTAAACACCCACCCAGCCTTACACACCGCATAGTGTCCATACCGCACTTTCCAGA
261 ATGTGGGATATTAAACACCCACCCAGCCTTACACACCGCATAGTGTCCATACCGCACTTTCCAGA
66591588 ATAATCGCAGCAGTGCTGCCAGAATATTAACAAGATATCGCCTCACACAGA
326 ATAATCGCAGCAGTGCTGCCAGAATATTAACAAGATATCGCCTCACACAGA
*
66591639 TATCGTTTTCGTAAAAACCCCTTTTACCAGTCTTTATGCTAGAAAACCAAAATAAAAATCCAAAA
1 TATCGTTTTCGTAAAAACCCCTTTTACCAATCTTTATGCTAGAAAACCAAAATAAAAATCCAAAA
66591704 CCAAAAATAGTCCGAAGAGTCTAAATTAGAAAAAACTCCCAAAACCAAAACATAAAGTCAAATTC
66 CCAAAAATAGTCCGAAGAGTCTAAATTAGAAAAAACTCCCAAAACCAAAACATAAAGTCAAATTC
**
66591769 AATCACATGACAAAACAGATGTAGACATAAGTCTTTTACAGAATCAGATTCATAACAGAGTCGTA
131 AATCACATGACAAAACAGATACAGACATAAGTCTTTTACAGAATCAGATTCATAACAGAGTCGTA
66591834 TAGATACAAATATGCATGGTCCTACCCCCATCCTTACACACCAACTCTGACCATCCCAACAAACC
196 TAGATACAAATATGCATGGTCCTACCCCCATCCTTACACACCAACTCTGACCATCCCAACAAACC
*
66591899 ATGTGGGATATTAAACACCCACCCAGCCTTACACACCGCATAGTGTCCATA-CGACACTTTCTAG
261 ATGTGGGATATTAAACACCCACCCAGCCTTACACACCGCATAGTGTCCATACCG-CACTTTCCAG
*
66591963 AATAATCGCAGCAGTGCTGCCAGAATATTAACTAGATATCGCCTCACACAGA
325 AATAATCGCAGCAGTGCTGCCAGAATATTAACAAGATATCGCCTCACACAGA
66592015 T
1 T
66592016 TACTTCCTCC
Statistics
Matches: 369, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
375 2 0.01
376 367 0.99
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (376 bp):
TATCGTTTTCGTAAAAACCCCTTTTACCAATCTTTATGCTAGAAAACCAAAATAAAAATCCAAAA
CCAAAAATAGTCCGAAGAGTCTAAATTAGAAAAAACTCCCAAAACCAAAACATAAAGTCAAATTC
AATCACATGACAAAACAGATACAGACATAAGTCTTTTACAGAATCAGATTCATAACAGAGTCGTA
TAGATACAAATATGCATGGTCCTACCCCCATCCTTACACACCAACTCTGACCATCCCAACAAACC
ATGTGGGATATTAAACACCCACCCAGCCTTACACACCGCATAGTGTCCATACCGCACTTTCCAGA
ATAATCGCAGCAGTGCTGCCAGAATATTAACAAGATATCGCCTCACACAGA
Found at i:66594718 original size:2 final size:2
Alignment explanation
Indices: 66594711--66594743 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66594701 ATTTCATGTT
66594711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66594744 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66602424 original size:129 final size:129
Alignment explanation
Indices: 66602258--66602540 Score: 458
Period size: 129 Copynumber: 2.2 Consensus size: 129
66602248 TTGTTCCACT
* * * *
66602258 GTAATCTCAGGGAAACAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCT
1 GTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT
* *
66602323 TCATTTTAATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAACTTCAATCTGCTCTGCC
66 TCATTTTAATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAACTTCAATCCGCTCCGCC
*
66602387 GTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT
1 GTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT
* * * * *
66602452 TCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCT
66 TCATTTTAATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAACTTCAATCCGCTCCGCC
66602516 GTAATCTCAGGGAGATAAGATCTGA
1 GTAATCTCAGGGAGATAAGATCTGA
66602541 AATTCTTCAG
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 142 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (129 bp):
GTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT
TCATTTTAATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAACTTCAATCCGCTCCGCC
Found at i:66602568 original size:175 final size:174
Alignment explanation
Indices: 66602387--66603061 Score: 1100
Period size: 175 Copynumber: 3.9 Consensus size: 174
66602377 CTGCTCTGCC
* * ***
66602387 GTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT
1 GTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT
* * *
66602452 TCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTG
66 T-ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
*
66602517 TAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTGTTCTACT
130 TAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTGTTCCACT
*
66602562 GTAATCTCAGGGAAATAAGACTTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCAT
1 GTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-T
* *
66602627 TTATTTGAATCCGCTCCACTGTAATCCCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
65 TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
66602692 TAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTGTTCCACT
130 TAATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTGTTCCACT
* * * *
66602737 GTTATCTTAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTTAGAGAGATAAAATCCT
1 GTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CT
*
66602802 TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCATCAATCTGCTCCGCTG
65 TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
66602867 TAATCTCAGGGAGATAAGATCTGAAATTCTTC-GATCTGTTCCACT
130 TAATCTCAGGGAGATAAGATCTGAAATTCTTCAG-TCTGTTCCACT
*
66602912 GTAATCTCAGGGGAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT
1 GTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CT
** *
66602977 TGGTTTTAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
65 TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTG
*
66603042 TAATATCAGGGAGATAAGAT
130 TAATCTCAGGGAGATAAGAT
66603062 TTTTGGCTTC
Statistics
Matches: 467, Mismatches: 30, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
174 1 0.00
175 462 0.99
176 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (174 bp):
GTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTT
TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCTTCAATCTGCTCCGCTGT
AATCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTGTTCCACT
Found at i:66602615 original size:304 final size:304
Alignment explanation
Indices: 66602111--66602715 Score: 951
Period size: 304 Copynumber: 2.0 Consensus size: 304
66602101 AACCTGATGT
* * *
66602111 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATTTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
* *
66602176 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATT
66 AGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
** * *
66602241 CTTTGGTTTGTTCCACTGTAATCTCAGGGAAACAAGACCTGACACGATCTACTCTGCTGTAACTT
131 CTTCAGTCTGTTCCACTGTAATCTCAGGGAAACAAGACCTGACACGATCTACTCTACTGTAACTT
* * *
66602306 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAAC
196 CAGAGAGATAAGATCATTCATTTGAATCCACTCCACTATAATCCCAAGAAGATAGGATTACTAAC
*
66602371 TTCAATCTGCTCTGCCGTAATCTCAGGGAGATAAGATCTGACAC
261 TTCAATCTGCTCCGCCGTAATCTCAGGGAGATAAGATCTGACAC
66602415 GATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTTTCATTTTAATCCACTCCACTGTAATCT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT-ATTTTAATCCACTCCACTGTAATCT
66602479 CAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
65 CAGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
* * * ***
66602544 TCTTCAGTCTGTTCTACTGTAATCTCAGGGAAATAAGACTTGGTGCGATCTACTCTACTGTAACT
130 TCTTCAGTCTGTTCCACTGTAATCTCAGGGAAACAAGACCTGACACGATCTACTCTACTGTAACT
* * * * * * *
66602609 TCAGAGAGATAAGATCATTTATTTGAATCCGCTCCACTGTAATCCCAGGGAGATAGGATTATTAG
195 TCAGAGAGATAAGATCATTCATTTGAATCCACTCCACTATAATCCCAAGAAGATAGGATTACTAA
*
66602674 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
260 CTTCAATCTGCTCCGCCGTAATCTCAGGGAGATAAGATCTGA
66602716 AATTCTTCAG
Statistics
Matches: 273, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
303 4 0.01
304 269 0.99
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (304 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
AGGGAGATAGGATTACTAGCTTCAATCCGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT
CTTCAGTCTGTTCCACTGTAATCTCAGGGAAACAAGACCTGACACGATCTACTCTACTGTAACTT
CAGAGAGATAAGATCATTCATTTGAATCCACTCCACTATAATCCCAAGAAGATAGGATTACTAAC
TTCAATCTGCTCCGCCGTAATCTCAGGGAGATAAGATCTGACAC
Found at i:66603071 original size:44 final size:44
Alignment explanation
Indices: 66602155--66603077 Score: 322
Period size: 44 Copynumber: 21.1 Consensus size: 44
66602145 CCTTTGTTTT
* * * * *
66602155 AATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* *
66602199 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATT--CTTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T---ATTGGCTTC
** * * * * ** * *
66602245 GGTTTGTTCCACTGTAATCTCAGGGAAACAAGA--CCTGAC-AC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* * ** * ** *** *
66602286 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTCATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTATTGGCTTC
** * * * * * **
66602330 AATCCACTCCACTATAATCTCAAGAAGATAGGATTACTAACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
** * * * *
66602374 AATCTGCTCTGCCGTAATCTCAGGGAGATAAGA-T-CTGAC-AC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* * * * *** *
66602415 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCT-TTCATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-TATTGGCTTC
** * * *
66602459 AATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* *
66602503 AATCCGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT--CTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T---ATTGGCTTC
* * * * * *
66602549 AGTCTGTTCTACTGTAATCTCAGGGAAATAAGA--CTTGG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* * * * * *** *
66602590 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTG
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTATTGGCTTC
* * * *
66602634 AATCCGCTCCACTGTAATCCCAGGGAGATAGGATTATTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
*
66602678 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT--CTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T---ATTGGCTTC
* * * * * ** *
66602724 AGTCTGTTCCACTGTTATCTTAGGGAAATAAGA--CCTGG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* * * * * * ** *** *
66602765 GATCTACTCTACTGTAA-CTTTAGAGAGATAAAATCCTTTATTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTATTGGCTTC
* * * *
66602809 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTATTAGCATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
*
66602853 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATT--CTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T---ATTGGCTTC
* * ** *
66602899 GATCTGTTCCACTGTAATCTCAGGG-GAATAAGA--CCTGG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAG-ATAAGATTATTGGCTTC
* * * * ** * *
66602940 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTGGTTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTATTGGCTTC
* * * *
66602984 AATCCGCTCTACTGTAATCTCAGGGAGATAGGATTATTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
* * *
66603028 AATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTTTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
66603072 AATCTG
1 AATCTG
66603078 ATGCGATCTA
Statistics
Matches: 639, Mismatches: 188, Indels: 104
0.69 0.20 0.11
Matches are distributed among these distances:
40 10 0.02
41 127 0.20
42 6 0.01
43 16 0.03
44 338 0.53
45 10 0.02
46 122 0.19
48 10 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTATTGGCTTC
Found at i:66603127 original size:54 final size:52
Alignment explanation
Indices: 66603029--66603272 Score: 125
Period size: 54 Copynumber: 4.9 Consensus size: 52
66603019 ATTAGCTTCA
* **
66603029 ATCTGCTCCGCTGTAA-TATCAGGGAGATAAGAT-TTTTGGCTTCAATCTGATGCG
1 ATCTACTCCGCTGTAACT-TCAGGGAGATAAGATCTTTT-ATTTCAATCTG-T-CG
* *
66603083 ATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAA--T-TCG
1 ATCTACTCCGCTGTAACTTCAGGGAGATAAGATCTTTTATTTCAATCTGTCG
* * *
66603132 -----CTCCACTGTAACTTCAGGGAGATAGGA-----TAGTGTC--T-T-T-G
1 ATCTACTCCGCTGTAACTTCAGGGAGATAAGATCTTTTA-TTTCAATCTGTCG
* * *** *
66603170 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTG
1 ATCTACTCCGCTGTAACT-TCAGGGAGATAAGATCTTTTATTTCAATCTG-T-CG
* *
66603224 ATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCTG
1 ATCTACTCCGCTGTAACTTCAGGGAGATAAGATCTTTTATTTCAATCTG
66603273 CTCCACTGTA
Statistics
Matches: 144, Mismatches: 23, Indels: 46
0.68 0.11 0.22
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 3 0.02
42 1 0.01
43 23 0.16
44 23 0.16
47 2 0.01
49 3 0.02
50 2 0.01
52 2 0.01
54 74 0.51
55 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (52 bp):
ATCTACTCCGCTGTAACTTCAGGGAGATAAGATCTTTTATTTCAATCTGTCG
Found at i:66603345 original size:141 final size:141
Alignment explanation
Indices: 66602937--66603324 Score: 575
Period size: 141 Copynumber: 2.7 Consensus size: 141
66602927 TAAGACCTGG
* * * ** * * *
66602937 TGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCTACTGTAA-
1 TGCGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCTGCTCCACTGTAAC
* ** * *
66603001 TCTCAGGGAGATAGGATTATTAG-CTTCAATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTT
66 T-TCAGGGAGATAGGA-TAGT-GTCTTTGATCTGCTCCGCTGTAATATCAGGGAGATAAGATCTC
66603065 TGGCTTCAATCTGA
128 TGGCTTCAATCTGA
66603079 TGCGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAAT-TCGCTCCACTGTAA
1 TGCGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCT-GCTCCACTGTAA
*
66603143 CTTCAGGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTG
65 CTTCAGGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATATCAGGGAGATAAGATCTCTG
66603208 GCTTCAATCTGA
130 GCTTCAATCTGA
*
66603220 TGTGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCTGCTCCACTGTAAC
1 TGCGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCTGCTCCACTGTAAC
*
66603285 TTCAGGGAGATAGGATAGTGTCTTTGATCTGCTTCGCTGT
66 TTCAGGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGT
66603325 CAATGCAGGA
Statistics
Matches: 226, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
140 1 0.00
141 154 0.68
142 70 0.31
143 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (141 bp):
TGCGATCTACTCTGCTGTAACTTCAGTGAGATAAGATCTTTTATTTCAATCTGCTCCACTGTAAC
TTCAGGGAGATAGGATAGTGTCTTTGATCTGCTCCGCTGTAATATCAGGGAGATAAGATCTCTGG
CTTCAATCTGA
Found at i:66603396 original size:43 final size:43
Alignment explanation
Indices: 66603348--66603485 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 43
66603338 CAAGATCTTT
66603348 TGTCTTCAACCAGCTCCATCACAATCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCATCACAATCGAGAGAGGCAAGGTTTG
* * ** ** * *
66603391 TGTCTTCGACCTGCTTCGTTGTCAAT-GCAG-GAAGGCAAGATCTTT
1 TGTCTTCAACCAGC-TCCATCACAATCG-AGAG-AGGCAAGGT-TTG
* * *
66603436 TATCTTCAACCAGCTCCATCATAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCATCACAATCGAGAGAGGCAAGGTTTG
66603479 TGTCTTC
1 TGTCTTC
66603486 GATCTGCGTC
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
43 22 0.32
44 32 0.46
45 15 0.22
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCCATCACAATCGAGAGAGGCAAGGTTTG
Found at i:66603405 original size:88 final size:88
Alignment explanation
Indices: 66603302--66603531 Score: 370
Period size: 88 Copynumber: 2.6 Consensus size: 88
66603292 AGATAGGATA
* *
66603302 GTGTCTTTGATCTGCTTCGCTGTCAATGCAGGAAAGCAAGATCTTTTGTCTTCAACCAGCTCCAT
1 GTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCAT
*
66603367 CACAATCGAGAGAGGCAAGGTTT
66 CACAACCGAGAGAGGCAAGGTTT
* * *
66603390 GTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTTTTATCTTCAACCAGCTCCAT
1 GTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCAT
*
66603455 CATAACCGAGAGAGGCAAGGTTT
66 CACAACCGAGAGAGGCAAGGTTT
* * *
66603478 GTGTCTTCGATCTGCGTCGCTGTCAATGCAGGAAGGCAAAATCTGTTGTCTTCA
1 GTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCA
66603532 CTGATCTGTT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 129 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
GTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCAT
CACAACCGAGAGAGGCAAGGTTT
Found at i:66603427 original size:44 final size:44
Alignment explanation
Indices: 66603379--66603516 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
66603369 CAATCGAGAG
66603379 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGA
* * * * * * * ** *
66603423 AGGCAAGATCTTTTATCTTCAACCAGCTCCATCAT-AA--CCGAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGTTGTCAATGCAG-GA
* * *
66603466 GAGGCAAGGTTTGTGTCTTCGATCTGCGTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGA
66603511 AGGCAA
1 AGGCAA
66603517 AATCTGTTGT
Statistics
Matches: 65, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
42 2 0.03
43 16 0.25
44 26 0.40
45 19 0.29
46 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGA
Found at i:66604737 original size:8 final size:8
Alignment explanation
Indices: 66604726--66604768 Score: 70
Period size: 8 Copynumber: 5.4 Consensus size: 8
66604716 CCATTTTTAC
66604726 TTTTTCAT
1 TTTTTCAT
66604734 TTTTTCAT
1 TTTTTCAT
66604742 TTTTTCA-
1 TTTTTCAT
66604749 TTTTTCATT
1 TTTTTCA-T
66604758 TTTTTCAT
1 TTTTTCAT
66604766 TTT
1 TTT
66604769 CATCATCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.21
8 19 0.58
9 7 0.21
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:66604744 original size:15 final size:15
Alignment explanation
Indices: 66604717--66604768 Score: 70
Period size: 16 Copynumber: 3.4 Consensus size: 15
66604707 TTAGCCTCTC
*
66604717 CATTTTT-ACTTTTT
1 CATTTTTCATTTTTT
66604731 CATTTTTTCATTTTTT
1 CA-TTTTTCATTTTTT
66604747 CATTTTTCATTTTTTT
1 CATTTTTCA-TTTTTT
66604763 CATTTT
1 CATTTT
66604769 CATCATCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
14 2 0.06
15 12 0.35
16 20 0.59
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
CATTTTTCATTTTTT
Found at i:66605567 original size:7 final size:7
Alignment explanation
Indices: 66605549--66605636 Score: 99
Period size: 7 Copynumber: 12.4 Consensus size: 7
66605539 TTATTTTGAC
66605549 TTTGATTT
1 TTTGA-TT
66605557 TTTGATT
1 TTTGATT
66605564 TTTGATT
1 TTTGATT
66605571 TTTGATT
1 TTTGATT
66605578 TTTGATT
1 TTTGATT
66605585 TTTG-TT
1 TTTGATT
*
66605591 TTTGTTTT
1 TTTG-ATT
66605599 TTTGATT
1 TTTGATT
66605606 TTTG-TT
1 TTTGATT
*
66605612 TTTGTTTT
1 TTTG-ATT
*
66605620 TTTGTTT
1 TTTGATT
*
66605627 TTTTATT
1 TTTGATT
66605634 TTT
1 TTT
66605637 TTTTTAGTCT
Statistics
Matches: 73, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
6 12 0.16
7 44 0.60
8 17 0.23
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.80
Consensus pattern (7 bp):
TTTGATT
Found at i:66605635 original size:21 final size:21
Alignment explanation
Indices: 66605531--66605641 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
66605521 TTTTTCTTCT
* * *
66605531 TTTTTTTCTTATTTTGACTTTG
1 TTTTTTTGTT-TTTTTATTTTG
* * *
66605553 ATTTTTTGATTTTTGATTTT-
1 TTTTTTTGTTTTTTTATTTTG
* *
66605573 TGATTTTTGATTTTTGT-TTTTG
1 T-TTTTTTG-TTTTTTTATTTTG
*
66605595 TTTTTTTGATTTTTGT-TTTTG
1 TTTTTTTG-TTTTTTTATTTTG
66605616 TTTTTTTGTTTTTTTATTTT-
1 TTTTTTTGTTTTTTTATTTTG
66605636 TTTTTT
1 TTTTTT
66605642 AGTCTGAACT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
20 12 0.16
21 50 0.68
22 12 0.16
ACGTcount: A:0.08, C:0.02, G:0.11, T:0.79
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTATTTTG
Found at i:66605638 original size:8 final size:8
Alignment explanation
Indices: 66605589--66605638 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
66605579 TTGATTTTTG
66605589 TTTTTGTT
1 TTTTTGTT
*
66605597 TTTTTG-A
1 TTTTTGTT
66605604 TTTTTG--
1 TTTTTGTT
66605610 TTTTTGTT
1 TTTTTGTT
66605618 TTTTTGTT
1 TTTTTGTT
*
66605626 TTTTTATT
1 TTTTTGTT
66605634 TTTTT
1 TTTTT
66605639 TTTAGTCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 26 0.68
ACGTcount: A:0.04, C:0.00, G:0.10, T:0.86
Consensus pattern (8 bp):
TTTTTGTT
Found at i:66605727 original size:14 final size:14
Alignment explanation
Indices: 66605705--66605735 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66605695 CATGTTATTC
*
66605705 TAAAGTCTTCCACA
1 TAAAATCTTCCACA
66605719 TAAAATCTTCCACA
1 TAAAATCTTCCACA
66605733 TAA
1 TAA
66605736 GTCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAAATCTTCCACA
Found at i:66608159 original size:19 final size:20
Alignment explanation
Indices: 66608130--66608181 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
66608120 CACTTCGTGA
* *
66608130 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
66608149 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
66608169 AAATG-AATGCAAA
1 AAATGTAATGCAAA
66608182 AAAGAGACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:66610730 original size:3 final size:3
Alignment explanation
Indices: 66610722--66610753 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
66610712 TATATAAAAG
66610722 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
66610754 TGAAATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:66612057 original size:18 final size:18
Alignment explanation
Indices: 66612017--66612058 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
66612007 AGGTATCTGA
* *
66612017 ATTTGGTATCTTATATTT
1 ATTTGGTATCCTAAATTT
66612035 ATTTGGTATACCTAAATTT
1 ATTTGGTAT-CCTAAATTT
66612054 -TTTGG
1 ATTTGG
66612059 ACCTAACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (18 bp):
ATTTGGTATCCTAAATTT
Found at i:66618227 original size:16 final size:15
Alignment explanation
Indices: 66618180--66618227 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
66618170 AAATTTTACA
*
66618180 AAAAAATATTATCAT
1 AAAAAATATTATTAT
66618195 ATAAAAATAATTAATTAT
1 A-AAAAAT-ATT-ATTAT
66618213 AAAAAATCATTATTA
1 AAAAAAT-ATTATTA
66618228 ATTGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 1 0.04
16 10 0.36
17 12 0.43
18 5 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATATTATTAT
Found at i:66618248 original size:15 final size:16
Alignment explanation
Indices: 66618228--66618257 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66618218 ATCATTATTA
66618228 ATTGAT-ATAAATTCT
1 ATTGATAATAAATTCT
66618243 ATTGATAATAAATTC
1 ATTGATAATAAATTC
66618258 CATTTATGTA
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTGATAATAAATTCT
Found at i:66618446 original size:18 final size:18
Alignment explanation
Indices: 66618415--66618462 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
66618405 TGCCGTTCGT
*
66618415 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
66618432 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
66618451 TTTCAAAACGTT
1 TTTCAAAACGTT
66618463 TTTTTATAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:66621673 original size:31 final size:31
Alignment explanation
Indices: 66621611--66621673 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
66621601 GAGCAAGAAT
* * *
66621611 AAAGATAAGATAAATAAAAAAAAATTTATAA
1 AAAGATAAGATAAACAAAAAAAAACTAATAA
*
66621642 AAAGAGTAA-ATAAACAAATAAAAACTAATAA
1 AAAGA-TAAGATAAACAAAAAAAAACTAATAA
66621673 A
1 A
66621674 GAGTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAGATAAGATAAACAAAAAAAAACTAATAA
Found at i:66622889 original size:28 final size:29
Alignment explanation
Indices: 66622875--66622980 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
66622865 AAATTTGGGC
*
66622875 TCAAAATGTAATTTTAAGAAAGTTTATGG
1 TCAAAATGTAATTTTAAGAAAGTTTAGGG
* *
66622904 TCAAAATGTAATTTTAAAAAAGTTAGAGGGG
1 TCAAAATGTAATTTTAAGAAAGTT-TA-GGG
* * *
66622935 TTAAAATGTAACTTTAAGAAA-TTTGAGAG
1 TCAAAATGTAATTTTAAGAAAGTTT-AGGG
*
66622964 TCAAATTGTAATTTTAA
1 TCAAAATGTAATTTTAA
66622981 ATTTTCTGGA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
29 39 0.62
30 4 0.06
31 20 0.32
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (29 bp):
TCAAAATGTAATTTTAAGAAAGTTTAGGG
Found at i:66624065 original size:34 final size:34
Alignment explanation
Indices: 66624016--66624091 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
66624006 AAATACATGT
* * *
66624016 TAAGCAAGTTTATTGCTA-CTATAATGATCTGTTA
1 TAAGCATGTTAATTGCTACCT-TAATGATCTATTA
*
66624050 TAAGCATGTTAATTGCTACCTTATTGATCTATTA
1 TAAGCATGTTAATTGCTACCTTAATGATCTATTA
66624084 TAAGCATG
1 TAAGCATG
66624092 ATATATGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (34 bp):
TAAGCATGTTAATTGCTACCTTAATGATCTATTA
Found at i:66624101 original size:34 final size:33
Alignment explanation
Indices: 66624029--66624158 Score: 104
Period size: 34 Copynumber: 3.8 Consensus size: 33
66624019 GCAAGTTTAT
* * *
66624029 TGCTACTATAATGATCTGTTATAAGCATGTTA-A
1 TGCTACT-TATTGATCTATTATAAGCATGATATA
66624062 TTGCTACCTTATTGATCTATTATAAGCATGATATA
1 -TGCTA-CTTATTGATCTATTATAAGCATGATATA
* * * *
66624097 TGCTACTGTATCGA-CTTTCTATAAGAATGCTAT-
1 TGCTACT-TATTGATCTAT-TATAAGCATGATATA
**
66624130 TGCTATCGAATTGATCTATTATAAGCATG
1 TGCTA-CTTATTGATCTATTATAAGCATG
66624159 TCATGTTGCA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
33 23 0.29
34 52 0.67
35 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TGCTACTTATTGATCTATTATAAGCATGATATA
Done.