Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 7 of 103
Found at i:2669588 original size:21 final size:21
Alignment explanation
Indices: 2669544--2669589 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2669534 ACACAATTAA
2669544 AAGCACAATAATGTTCCAAATTC
1 AAGCACAATAATGTT-C-AATTC
2669567 AAGCACAATAATGTAT-AATTC
1 AAGCACAATAATGT-TCAATTC
2669588 AA
1 AA
2669590 CTACATTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
23 14 0.64
24 1 0.05
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (21 bp):
AAGCACAATAATGTTCAATTC
Found at i:2670229 original size:16 final size:17
Alignment explanation
Indices: 2670208--2670243 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2670198 TGTGGAAGGC
*
2670208 AAAAGAACAAAAAAA-G
1 AAAAGAAAAAAAAAACG
2670224 AAAAGAAAAAAAAAACG
1 AAAAGAAAAAAAAAACG
2670241 AAA
1 AAA
2670244 TGGGAGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAACG
Found at i:2677116 original size:22 final size:22
Alignment explanation
Indices: 2677083--2677125 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2677073 AACCTGATAT
*
2677083 GCCTCCACTTCTGCGTCGTTCC
1 GCCTCCACTTCTGCATCGTTCC
*
2677105 GCCTCC-CTTTCTTCATCGTTC
1 GCCTCCAC-TTCTGCATCGTTC
2677126 GCTTTTGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.05, C:0.44, G:0.14, T:0.37
Consensus pattern (22 bp):
GCCTCCACTTCTGCATCGTTCC
Found at i:2680889 original size:30 final size:30
Alignment explanation
Indices: 2680822--2680880 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
2680812 TTCAATGCAG
2680822 CTCTTATATTTTTATTTTAAATCAAATAAA
1 CTCTTATATTTTTATTTTAAATCAAATAAA
2680852 CTCTTATATTTTTATTTTAAATCAAATAA
1 CTCTTATATTTTTATTTTAAATCAAATAA
2680881 GTGTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (30 bp):
CTCTTATATTTTTATTTTAAATCAAATAAA
Found at i:2682749 original size:264 final size:265
Alignment explanation
Indices: 2682247--2682776 Score: 782
Period size: 264 Copynumber: 2.0 Consensus size: 265
2682237 GGTCTCTAAT
* * *
2682247 GTCTGTCTATTTGTCCTAATTTCTTGTTTCAATCCGTGAATTAATTGTTGGAAAATCACAACGTG
1 GTCTGTCCATTTGTCCTAATTTCTTGTTTCAATCCATAAATTAATTGTTGGAAAATCACAACGTG
* * ** *
2682312 AAGCTGCAGTGACCACAAAGAAATAGAAAAAAGTTTGAAGATAATCAGAAAACCATATTCATACT
66 AAGCTACAGTGAACACAAAGAAATAGAAAAAAGTAGGAAGAAAATCAGAAAACCATATTCATACT
* **
2682377 GTAAATTTCTAGCGTTCTAACTTCCAAATCATGAAAAATTGCTTGCTTATGTACACATATTACAT
131 GCAAATTTCTAGCACTCTAACTTCCAAATCATGAAAAATTGCTTGCTTATGTACACATATTACAT
* ** *
2682442 CTTCAGTCATGTGACATTGAGAAAGCTTAATTTGGGTTTGTTTGTTGCATGGCTGTGATTCTTAG
196 CTTCACTCAAATGACATTGAAAAAGCTTAATTTGGGTTTGTTTGTTGCATGGCTGTGATTCTTAG
2682507 TCGTA
261 TCGTA
* * *
2682512 GTCTGTCCATTTGTCTTAAATTT-TTGTTTCAATCCATAAATTAATTGTTGGAAATTCACAATGT
1 GTCTGTCCATTTGTCCT-AATTTCTTGTTTCAATCCATAAATTAATTGTTGGAAAATCACAACGT
2682576 GAA-CTTACAGTGAACACAAAGAAA-A-AAAAAAGTAGGAAGAAAATCAGAAAACCATATTCATA
65 GAAGC-TACAGTGAACACAAAGAAATAGAAAAAAGTAGGAAGAAAATCAGAAAACCATATTCATA
* *
2682638 CTGCAAATTTCTATCACTCTAAACTTCCAAATCATGAAAAATTGCTTGC-TATTTACACATATTA
129 CTGCAAATTTCTAGCACTCT-AACTTCCAAATCATGAAAAATTGCTTGCTTATGTACACATATTA
* * *
2682702 CATCTTCAACTCAAATGACATTGAAAAAGCTTACTTTGGGTTTGTTTGTTGCATGGCTGTTATTG
193 CATCTTC-ACTCAAATGACATTGAAAAAGCTTAATTTGGGTTTGTTTGTTGCATGGCTGTGATTC
2682767 TTAGTCGTA
257 TTAGTCGTA
2682776 G
1 G
2682777 AACATTCGTT
Statistics
Matches: 238, Mismatches: 23, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
263 71 0.30
264 90 0.38
265 72 0.30
266 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (265 bp):
GTCTGTCCATTTGTCCTAATTTCTTGTTTCAATCCATAAATTAATTGTTGGAAAATCACAACGTG
AAGCTACAGTGAACACAAAGAAATAGAAAAAAGTAGGAAGAAAATCAGAAAACCATATTCATACT
GCAAATTTCTAGCACTCTAACTTCCAAATCATGAAAAATTGCTTGCTTATGTACACATATTACAT
CTTCACTCAAATGACATTGAAAAAGCTTAATTTGGGTTTGTTTGTTGCATGGCTGTGATTCTTAG
TCGTA
Found at i:2686776 original size:35 final size:35
Alignment explanation
Indices: 2686730--2686799 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2686720 TCCTCACCTC
2686730 TTGCTCTACCTCATTCACTTTGTACTCTTTCAGGT
1 TTGCTCTACCTCATTCACTTTGTACTCTTTCAGGT
2686765 TTGCTCTACCTCATTCACTTTGTACTCTTTCAGGT
1 TTGCTCTACCTCATTCACTTTGTACTCTTTCAGGT
2686800 GTTTCCTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.29, G:0.11, T:0.46
Consensus pattern (35 bp):
TTGCTCTACCTCATTCACTTTGTACTCTTTCAGGT
Found at i:2688700 original size:228 final size:227
Alignment explanation
Indices: 2688205--2689341 Score: 1139
Period size: 228 Copynumber: 5.0 Consensus size: 227
2688195 TCACTGCCCA
* * * * * * * *
2688205 CCACGGAGACGAAGGACAAGGTGGAGGGTAGACT-CTTTCTGAATGTTATAATCAGCTAAAGTCC
1 CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTT-TGGATGTTATAATCAGCCAAGGTAC
* * * * * * * *
2688269 TCCCATCCTCCAA-TTGCTTCCCGGCAAAGATAAGCCTTTGCTGATCTGGG-GGGATTCCTTCCT
65 GCCCGTCCT-CAAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTC-GGGTGGGATCCCTTCCT
* * * * * * * * * * * * * *
2688332 TATCCTGAATCTTTGCCTTGACATTATCGATTGTATCCGAACTTTCCACCTCCAAGGTGATTGTT
128 TGTCTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGA-TGGT
* * * * *
2688397 TTTCCAGTCAAGGTCTTGACAAAAATCTGCATTCCT
192 TTTCCGGTCAAGGTTTTGACAAAGATCTGCATACCG
* ** ** * * * * * * * * *
2688433 CCACGAAGCCTCAAAACAAGATGAAGGGTTGATTCCTTTTGTATGTTGTAATCAGCCAAGGTCCT
1 CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATGTTATAATCAGCCAAGGTACG
* * * ** * * * *
2688498 CCCGTCCTCAAGCTGCTTCCCAGCGAAGATCAATCGTTGTTGGTCTGGTGGGATCCCTTCCTTAT
66 CCCGTCCTCAAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGT
* * * * * * * *
2688563 CTTGGATCTTGGCCTTAACGTTATCAATCGTGTCCGAGCTCTCGACCTCCAGGGTTATAGTCTTT
131 CTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGATGGT-TTT
* * * *
2688628 CCTGTCAAGGTTTTGACAAAGATTTGCATGCCT
195 CCGGTCAAGGTTTTGACAAAGATCTGCATACCG
* * * * *
2688661 CCACGGAGCCTGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATATTATAATCAGCCAAAGTACG
1 CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATGTTATAATCAGCCAAGGTACG
* * ** * * * *
2688726 GCCGTCCTCCAGCTGTTTCCCGGCGAAGATGAGCCGCTGTTGGTCGGGAGGGATGCCTTCTTTGT
66 CCCGTCCTCAAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGT
* * *
2688791 CCTGGATTTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACTTCGAGGGTGATGGTTTTG
131 CTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGATGGTTTT-
* *
2688856 CCGGTCAAAGTTTTGACAAAGATTTGCATACCG
195 CCGGTCAAGGTTTTGACAAAGATCTGCATACCG
* * * *
2688889 CCACGAAGACGGAGGACCAGGTGGAGAGTTGACTCCTTCTGGATGTTATAATCCGCCAAGGTACG
1 CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATGTTATAATCAGCCAAGGTACG
* * *
2688954 ACCGTCTTCGAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGT
66 CCCGTCCTCAAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGT
* *
2689019 CTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCCACTTCGAGGGTGATGGTTTTA
131 CTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGATGGTTTT-
*
2689084 CCGGTCAAGGTTTTGACGAAGATCTGCATACCG
195 CCGGTCAAGGTTTTGACAAAGATCTGCATACCG
* * * *
2689117 CCACGAAGACGGAGGACCAGGTGGAGAGTCGACTCCTTCTGGATGTTGTAATCCGCCAAGGTACG
1 CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATGTTATAATCAGCCAAGGTACG
* * *
2689182 GCCGTCTTCGAGCTGTTTGCCAC-GCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTT
66 CCCGTCCTCAAGCTGTTT-CC-CGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTT
* * * *
2689246 GTCTTGGATCTTGGCCTTAACGTTGTCGATGGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCT
129 GTCTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGATGGT-T
* * * *
2689311 TGCCGGTCAGGGTTTTCACGAAGATCTGCAT
193 TTCCGGTCAAGGTTTTGACAAAGATCTGCAT
2689342 CTTCTAAAAG
Statistics
Matches: 775, Mismatches: 126, Indels: 15
0.85 0.14 0.02
Matches are distributed among these distances:
227 10 0.01
228 631 0.81
229 131 0.17
230 3 0.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.29
Consensus pattern (227 bp):
CCACGAAGACGGAGGACAAGGTGGAGAGTCGACTCCTTTTGGATGTTATAATCAGCCAAGGTACG
CCCGTCCTCAAGCTGTTTCCCGGCGAAGATGAGCCTTTGCTGGTCGGGTGGGATCCCTTCCTTGT
CTTGGATCTTGGCCTTGACGTTGTCGATCGTGTCGGAACTCTCGACCTCGAGGGTGATGGTTTTC
CGGTCAAGGTTTTGACAAAGATCTGCATACCG
Found at i:2698637 original size:18 final size:18
Alignment explanation
Indices: 2698616--2698652 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2698606 AATTTACTAG
2698616 ATTTAATATT-TTTAAAAA
1 ATTTAA-ATTATTTAAAAA
2698634 ATTTAAATTATTTAAAAA
1 ATTTAAATTATTTAAAAA
2698652 A
1 A
2698653 ATTCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAATTATTTAAAAA
Found at i:2705031 original size:109 final size:108
Alignment explanation
Indices: 2704895--2705105 Score: 314
Period size: 109 Copynumber: 1.9 Consensus size: 108
2704885 TATAAGAAAT
* * *
2704895 TTTGTGTAAATTTAAATAAAAGGTAAATTGAATAAGAGTTAAATAATTTTAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAACAAAAGGTAAATTGAATAAGAGTTAAATAATTTCAAAAGAATGTGTA-T
* *
2704960 TTGTAAATTGTGAAAGTTGTAACTAAATCAGCATATTTTGCTAA
65 TTATAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAA
* * * * *
2705004 TTTGAGTAAGTTTAAACAAAAGTTAAATTGAGTAAGATTTGAATAATTTCAAAAGAATGTGTATT
1 TTTGAGTAAATTTAAACAAAAGGTAAATTGAATAAGAGTTAAATAATTTCAAAAGAATGTGTATT
*
2705069 TATAAATTGTGAAAGTTGTAACTAAATTAACATATTT
66 TATAAATTGTGAAAGTTGTAACTAAATCAACATATTT
2705106 AATTATTTTA
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 36 0.40
109 55 0.60
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (108 bp):
TTTGAGTAAATTTAAACAAAAGGTAAATTGAATAAGAGTTAAATAATTTCAAAAGAATGTGTATT
TATAAATTGTGAAAGTTGTAACTAAATCAACATATTTTGCTAA
Found at i:2706795 original size:32 final size:30
Alignment explanation
Indices: 2706750--2706849 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 30
2706740 AGTCAAAATC
*
2706750 ATTTATTTGACTTAAAATGAAAAAATATAAAA
1 ATTTATTTAACTTAAAAT--AAAAATATAAAA
2706782 ATTTATTTAACTTAAAATAAAAATAT-AAA
1 ATTTATTTAACTTAAAATAAAAATATAAAA
* * *
2706811 ACTTAGTTAAACGT--AATAAAAATATAAAA
1 ATTTA-TTTAACTTAAAATAAAAATATAAAA
2706840 ATTTATTTAA
1 ATTTATTTAA
2706850 AATTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 15 0.25
29 14 0.23
30 14 0.23
32 17 0.28
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (30 bp):
ATTTATTTAACTTAAAATAAAAATATAAAA
Found at i:2706849 original size:29 final size:30
Alignment explanation
Indices: 2706770--2706850 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 30
2706760 CTTAAAATGA
*
2706770 AAAAATATAAAAATTTATTT-AACTTAAAAT
1 AAAAATATAAAAATTTATTTAAACGT-AAAT
* *
2706800 AAAAATAT-AAAACTTAGTTAAACGT-AAT
1 AAAAATATAAAAATTTATTTAAACGTAAAT
2706828 AAAAATATAAAAATTTATTTAAA
1 AAAAATATAAAAATTTATTTAAA
2706851 ATTTTTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.25
29 21 0.48
30 12 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAATATAAAAATTTATTTAAACGTAAAT
Found at i:2708524 original size:2 final size:2
Alignment explanation
Indices: 2708517--2708541 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2708507 CAAAAAGGTG
2708517 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2708542 CATTTGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2713963 original size:2 final size:2
Alignment explanation
Indices: 2713956--2713999 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2713946 TCTGAGCAGG
2713956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2713998 AT
1 AT
2714000 TACATATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2715980 original size:78 final size:80
Alignment explanation
Indices: 2715851--2716059 Score: 314
Period size: 78 Copynumber: 2.6 Consensus size: 80
2715841 AGGCATGAGA
* *
2715851 ATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTAAATACCATCAAGGTCTAT
1 ATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTAAATACCATCAAGGTCCAC
*
2715916 GTGATAGGT-GG-AC
66 GTGATAAGTGGGAAC
* *
2715929 ATGTGACATTCCTATTATACATTAAGGTATAATGATGCTAATATGTAAATACCATCAAGGTCCAC
1 ATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTAAATACCATCAAGGTCCAC
2715994 GTGATAAGTGGGCAAC
66 GTGATAAGTGGG-AAC
* * * *
2716010 ATGTGGCATTCCTATTGTACATGAAGGTATAATGGTGCCAATATATAAAT
1 ATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTAAAT
2716060 TAAACATCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
78 69 0.59
79 2 0.02
81 46 0.39
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (80 bp):
ATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTAAATACCATCAAGGTCCAC
GTGATAAGTGGGAAC
Found at i:2723020 original size:2 final size:2
Alignment explanation
Indices: 2723013--2723056 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2723003 AGTTGGATCC
2723013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2723055 AT
1 AT
2723057 TCAATTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2725571 original size:2 final size:2
Alignment explanation
Indices: 2725508--2725551 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2725498 TCCTATCACT
* *
2725508 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2725550 TC
1 TC
2725552 GGGAACCCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:2729348 original size:19 final size:21
Alignment explanation
Indices: 2729311--2729349 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2729301 CCTTTGCACG
*
2729311 TCTCTAATTTGTTTTCTTTTC
1 TCTCTAATTTGTTTGCTTTTC
2729332 TCTCT-ATTT-TTTGCTTTT
1 TCTCTAATTTGTTTGCTTTT
2729350 TTGGTTTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.69
Consensus pattern (21 bp):
TCTCTAATTTGTTTGCTTTTC
Found at i:2730561 original size:2 final size:2
Alignment explanation
Indices: 2730554--2730580 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2730544 CTGCACAAAA
2730554 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2730581 TGTGCAATGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2735313 original size:1 final size:1
Alignment explanation
Indices: 2735309--2735397 Score: 79
Period size: 1 Copynumber: 89.0 Consensus size: 1
2735299 TGTCCTCCTT
* * ***** * *
2735309 CCCCCCCCCCCCCCCCCCCCCCACTCCCCCCCCNNNNNCCCTCCCCGCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *
2735374 CCCCCCCCCGCTCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCC
2735398 TTTTTCTTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.88, G:0.02, T:0.03
Consensus pattern (1 bp):
C
Found at i:2738553 original size:19 final size:19
Alignment explanation
Indices: 2738517--2738553 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2738507 ATACATGCAT
* *
2738517 AAACGTAAATGAACACAAA
1 AAACGTAAAGGAAAACAAA
2738536 AAACGTAAAGGAAAACAA
1 AAACGTAAAGGAAAACAA
2738554 TCTTGTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.14, G:0.14, T:0.08
Consensus pattern (19 bp):
AAACGTAAAGGAAAACAAA
Found at i:2760264 original size:18 final size:18
Alignment explanation
Indices: 2760241--2760280 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2760231 AGGCAAATTA
2760241 AAAGT-GATAAGACAAAAG
1 AAAGTGGATAA-ACAAAAG
*
2760259 AAAGTGGATAAAGAAAAG
1 AAAGTGGATAAACAAAAG
2760277 AAAG
1 AAAG
2760281 GCAACAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.03, G:0.25, T:0.10
Consensus pattern (18 bp):
AAAGTGGATAAACAAAAG
Found at i:2765509 original size:17 final size:18
Alignment explanation
Indices: 2765487--2765527 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2765477 TTTTATTAGT
2765487 TATTTTTT-ACTTTTATA
1 TATTTTTTAACTTTTATA
*
2765504 TATTTTTTAATTTTTATA
1 TATTTTTTAACTTTTATA
2765522 TATTTT
1 TATTTT
2765528 AAATATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTTTTAACTTTTATA
Found at i:2765528 original size:16 final size:17
Alignment explanation
Indices: 2765491--2765529 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2765481 ATTAGTTATT
* *
2765491 TTTTACTTTTATATATT
1 TTTTAATTTTATATATA
2765508 TTTTAATTTT-TATATA
1 TTTTAATTTTATATATA
2765524 TTTTAA
1 TTTTAA
2765530 ATATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATTTTATATATA
Found at i:2768351 original size:22 final size:22
Alignment explanation
Indices: 2768309--2768351 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2768299 AATTAATTAT
*
2768309 TTATCATTAATCAAATCATCAC
1 TTATCATTAATCAAATAATCAC
*
2768331 TTATCA-TATATCATATAATCA
1 TTATCATTA-ATCAAATAATCA
2768352 TTTTATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATCATTAATCAAATAATCAC
Found at i:2768731 original size:25 final size:25
Alignment explanation
Indices: 2768672--2768737 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2768662 AATGTTTATT
* *
2768672 TAATTTAATTTTCAAATATATTATAA
1 TAATTTTATTTT-AAATATATAATAA
* *
2768698 AAATATTATTTT-AATATAATAATAA
1 TAATTTTATTTTAAATAT-ATAATAA
2768723 TAATTTTATTTTAAA
1 TAATTTTATTTTAAA
2768738 GTGGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 5 0.16
25 16 0.50
26 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATTTTATTTTAAATATATAATAA
Found at i:2770287 original size:54 final size:51
Alignment explanation
Indices: 2770205--2770306 Score: 159
Period size: 54 Copynumber: 1.9 Consensus size: 51
2770195 GTAACATAAA
2770205 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGGGGGGGCAAAGTTCAAGGGTT
1 CATCTTACTTCTGGAATTGAGCTTTTCT---GGGGGGGGCAAAGTTCAAGGGTT
* *
2770259 CATCTTTCTTCTGGAATTGAGCTTTTCTGGGGGTGGCAAAGTTCAAGG
1 CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGGGGCAAAGTTCAAGG
2770307 TTTCCCAGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 19 0.41
54 27 0.59
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (51 bp):
CATCTTACTTCTGGAATTGAGCTTTTCTGGGGGGGGCAAAGTTCAAGGGTT
Found at i:2774236 original size:1 final size:1
Alignment explanation
Indices: 2774230--2774259 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2774220 CCCTCGGACA
2774230 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2774260 AATTGTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2786244 original size:35 final size:35
Alignment explanation
Indices: 2786196--2786262 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2786186 TCTTCCTTGC
*
2786196 TTCACTTGCTGCTCTAGCCGGTGATCGTCTATTAG
1 TTCACTTACTGCTCTAGCCGGTGATCGTCTATTAG
*
2786231 TTCACTTATTGCTCTAGCCGGTGATCGTCTAT
1 TTCACTTACTGCTCTAGCCGGTGATCGTCTAT
2786263 CAGAATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (35 bp):
TTCACTTACTGCTCTAGCCGGTGATCGTCTATTAG
Found at i:2788399 original size:20 final size:20
Alignment explanation
Indices: 2788361--2788408 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2788351 TTCATTTTTT
2788361 AAAATTAT-CATTTTAAATA
1 AAAATTATACATTTTAAATA
* *
2788380 AAAATTATAGATTTTCAATA
1 AAAATTATACATTTTAAATA
*
2788400 ACAATTATA
1 AAAATTATA
2788409 AATTAAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAATTATACATTTTAAATA
Found at i:2792372 original size:36 final size:36
Alignment explanation
Indices: 2792332--2792423 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 36
2792322 AACGAAGATT
* * *
2792332 AAATCATGTACGGTGTCGAAGTTGCTGACA-AAAAAA
1 AAATCACGTACGGTGTCGAAGCTACTGA-AGAAAAAA
* * * *
2792368 AAATCACGTATGATGTTGAAGCTACTGAAGAAAAAT
1 AAATCACGTACGGTGTCGAAGCTACTGAAGAAAAAA
*
2792404 AAATCACGTACGGTGCCGAA
1 AAATCACGTACGGTGTCGAA
2792424 ACTATCGACG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
35 1 0.02
36 43 0.98
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (36 bp):
AAATCACGTACGGTGTCGAAGCTACTGAAGAAAAAA
Found at i:2794753 original size:16 final size:16
Alignment explanation
Indices: 2794714--2794776 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 16
2794704 TTTAAAATCT
* *
2794714 ATAATTATAAAA-ATA
1 ATAATAATAAAATAAA
*
2794729 ATTATAATAAAATAAA
1 ATAATAATAAAATAAA
* *
2794745 ATAATAATAACATCAA
1 ATAATAATAAAATAAA
*
2794761 AT-ATAACAAAATAAA
1 ATAATAATAAAATAAA
2794776 A
1 A
2794777 GTTCAAAGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 21 0.55
16 17 0.45
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATAATAAAATAAA
Found at i:2795488 original size:27 final size:27
Alignment explanation
Indices: 2795436--2795488 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2795426 TTGTTGCTTG
* *
2795436 ATATTTTTTAAATGTTATCTGGCTCAC
1 ATATTTGTTAAATGTTATCTGACTCAC
*
2795463 ATATTTGTTAAATGTTATTTGACTCA
1 ATATTTGTTAAATGTTATCTGACTCA
2795489 GCATCTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (27 bp):
ATATTTGTTAAATGTTATCTGACTCAC
Found at i:2795652 original size:25 final size:25
Alignment explanation
Indices: 2795605--2795653 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2795595 ACCAAGCCTC
*
2795605 TCCTCTAAAGCTTCTTTATATACTT
1 TCCTCTAAAGCTTCTTTACATACTT
* *
2795630 TCCTCTAAAGCTTTTTTGCATACT
1 TCCTCTAAAGCTTCTTTACATACT
2795654 CTTTCCTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.06, T:0.47
Consensus pattern (25 bp):
TCCTCTAAAGCTTCTTTACATACTT
Found at i:2801947 original size:27 final size:27
Alignment explanation
Indices: 2801917--2801969 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2801907 CTGTTGCATA
* *
2801917 ATATTTCTTAAACGTTGTTTGACTCAG
1 ATATTTCTTAAACGGTATTTGACTCAG
*
2801944 ATATTTGTTAAACGGTATTTGACTCA
1 ATATTTCTTAAACGGTATTTGACTCA
2801970 ACATCTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (27 bp):
ATATTTCTTAAACGGTATTTGACTCAG
Found at i:2802011 original size:11 final size:11
Alignment explanation
Indices: 2801997--2802022 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2801987 ATTTTTTCAC
2801997 TGATTTTATGT
1 TGATTTTATGT
2802008 TGATTTTATGT
1 TGATTTTATGT
2802019 TGAT
1 TGAT
2802023 ATTCTGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (11 bp):
TGATTTTATGT
Found at i:2809666 original size:19 final size:19
Alignment explanation
Indices: 2809642--2809679 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2809632 AATTAGTATT
2809642 AGAATCAGCTCTAAGGTAC
1 AGAATCAGCTCTAAGGTAC
* *
2809661 AGAATCGGCTCTAGGGTAC
1 AGAATCAGCTCTAAGGTAC
2809680 TAACGATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (19 bp):
AGAATCAGCTCTAAGGTAC
Found at i:2811112 original size:15 final size:15
Alignment explanation
Indices: 2811094--2811126 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2811084 TAATGTTACA
2811094 AAAATTA-TAACTTAT
1 AAAATTATTAA-TTAT
2811109 AAAATTATTAATTAT
1 AAAATTATTAATTAT
2811124 AAA
1 AAA
2811127 TATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:2812720 original size:22 final size:22
Alignment explanation
Indices: 2812682--2812724 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2812672 TTGAGACATT
*
2812682 GCGTGATTGATTTTTATGTATA
1 GCGTGATTGATTGTTATGTATA
2812704 GCGTGACTTG-TTGTTATGTAT
1 GCGTGA-TTGATTGTTATGTAT
2812725 TGCACGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.19, C:0.07, G:0.26, T:0.49
Consensus pattern (22 bp):
GCGTGATTGATTGTTATGTATA
Found at i:2816593 original size:21 final size:19
Alignment explanation
Indices: 2816567--2816617 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2816557 TAAACTCTCA
*
2816567 ATATATTTCTTAATATATAAT
1 ATATATTT-TTAA-ATAAAAT
2816588 ATATATTTTTAAATAAAAT
1 ATATATTTTTAAATAAAAT
*
2816607 ATACATTTTTA
1 ATATATTTTTA
2816618 TATTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.57
20 4 0.14
21 8 0.29
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTTTTAAATAAAAT
Found at i:2818229 original size:17 final size:16
Alignment explanation
Indices: 2818196--2818242 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2818186 CTTATCTCAA
*
2818196 TTAACTTTACATTTTTT
1 TTAA-TTTATATTTTTT
2818213 TTAATTTATATTATTTT
1 TTAATTTATATT-TTTT
*
2818230 TTTATTTATATTT
1 TTAATTTATATTT
2818243 GTTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAATTTATATTTTTT
Found at i:2818231 original size:18 final size:17
Alignment explanation
Indices: 2818208--2818241 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
2818198 AACTTTACAT
2818208 TTTTTTTAATTTATATTA
1 TTTTTTT-ATTTATATTA
2818226 TTTTTTTATTTATATT
1 TTTTTTTATTTATATT
2818242 TGTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTTATATTA
Found at i:2818237 original size:22 final size:22
Alignment explanation
Indices: 2818207--2818270 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
2818197 TAACTTTACA
2818207 TTTTT-TTTA-ATTTATATTATT
1 TTTTTATTTATATTTAT-TTATT
*
2818228 TTTTTATTTATATTTGTTTATT
1 TTTTTATTTATATTTATTTATT
*
2818250 TTTTTCATTTCTATTCTATTT
1 TTTTT-ATTTATATT-TATTT
2818271 GTTCATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.14
22 14 0.39
23 13 0.36
24 4 0.11
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTATTTATATTTATTTATT
Found at i:2818433 original size:14 final size:15
Alignment explanation
Indices: 2818405--2818441 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2818395 TTTATATTAC
2818405 ATAAATTTAATTTTT
1 ATAAATTTAATTTTT
*
2818420 ATAATTTTAATTTTT
1 ATAAATTTAATTTTT
*
2818435 AAAAATT
1 ATAAATT
2818442 AATAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAAATTTAATTTTT
Found at i:2835502 original size:30 final size:29
Alignment explanation
Indices: 2835446--2835506 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
2835436 TTTAATTTTT
* *
2835446 TTAATTTATAAATTTATGTTATTAATTGAA
1 TTAATTTATAAATTTATATTAATAATT-AA
2835476 TTAATTTATAAA-TTATAATTAATAATTAA
1 TTAATTTATAAATTTAT-ATTAATAATTAA
2835505 TT
1 TT
2835507 TATAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TTAATTTATAAATTTATATTAATAATTAA
Found at i:2838528 original size:15 final size:15
Alignment explanation
Indices: 2838508--2838538 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2838498 GTTCTCAATG
2838508 TACTTTATTATTCAT
1 TACTTTATTATTCAT
*
2838523 TACTTTATTGTTCAT
1 TACTTTATTATTCAT
2838538 T
1 T
2838539 CTAACAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
TACTTTATTATTCAT
Found at i:2839070 original size:19 final size:20
Alignment explanation
Indices: 2839046--2839085 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2839036 AACTTATTTG
2839046 ATTTAAATAAAAAT-ATAAA
1 ATTTAAATAAAAATAATAAA
* *
2839065 ATTTAATTAAACATAATAAA
1 ATTTAAATAAAAATAATAAA
2839085 A
1 A
2839086 AAATAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAATAAAAATAATAAA
Found at i:2841950 original size:7 final size:7
Alignment explanation
Indices: 2841932--2841963 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2841922 AAAAAGGATC
2841932 TCTGCTTT
1 TCTGC-TT
2841940 TCTGCTT
1 TCTGCTT
2841947 TCTGCTT
1 TCTGCTT
2841954 TCTGCTT
1 TCTGCTT
2841961 TCT
1 TCT
2841964 TAGTTTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.00, C:0.28, G:0.12, T:0.59
Consensus pattern (7 bp):
TCTGCTT
Found at i:2843799 original size:75 final size:77
Alignment explanation
Indices: 2843631--2843801 Score: 181
Period size: 78 Copynumber: 2.2 Consensus size: 77
2843621 CAGAAGATAA
* * * *
2843631 ATTCTCTTGAGAAACATTCTCGTCTTCTTTGGTTTCAACAGCAGGAGTATCCACACTGGGGGAAG
1 ATTCTCTTGAGAAAGATTCTCCTCTTCTTTGGTTTCAACAGCAGGAGGATCCACACT-GGCGAAG
*
2843696 GAGGGAGAGATGT
65 GAGGAAGAGATGT
* * * * *
2843709 GTTCTCCTG-GAAAAGA-TCTTCACTC-TCTTTGGTTTCAACAGCTGGAGGATCCGC-CT-TCGA
1 ATTCTCTTGAG-AAAGATTC-TC-CTCTTCTTTGGTTTCAACAGCAGGAGGATCCACACTGGCGA
2843769 AGGAGGAAGAGATGT
63 AGGAGGAAGAGATGT
2843784 ATTCTCTTGAGAAAGATT
1 ATTCTCTTGAGAAAGATT
2843802 ATCCATATCT
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
75 28 0.37
76 2 0.03
77 5 0.07
78 39 0.51
79 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (77 bp):
ATTCTCTTGAGAAAGATTCTCCTCTTCTTTGGTTTCAACAGCAGGAGGATCCACACTGGCGAAGG
AGGAAGAGATGT
Found at i:2863087 original size:40 final size:39
Alignment explanation
Indices: 2863042--2863153 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 39
2863032 TTTTAAAGGA
*
2863042 AAAAAATTAAAATAAAGTATATAATATAAGAAATTATATT
1 AAAAAATAAAAATAAA-TATATAATATAAGAAATTATATT
*
2863082 AAAAAATAAAAAT-AA-A-AT-ATATAAG--ATTATAAT
1 AAAAAATAAAAATAAATATATAATATAAGAAATTATATT
* *
2863115 AAAAAATAAAAATAAAATATATAACAT-TGAAATTATATT
1 AAAAAATAAAAAT-AAATATATAATATAAGAAATTATATT
2863154 TAAGAGATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
33 20 0.33
35 9 0.15
36 3 0.05
37 4 0.07
38 3 0.05
39 9 0.15
40 12 0.20
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (39 bp):
AAAAAATAAAAATAAATATATAATATAAGAAATTATATT
Found at i:2863111 original size:33 final size:34
Alignment explanation
Indices: 2863065--2863138 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
2863055 AAAGTATATA
*
2863065 ATATAAGAAATTATATTAAAAAATAAAAATAAAAT
1 ATATAAG-AATTATAATAAAAAATAAAAATAAAAT
2863100 ATATAAG-ATTATAATAAAAAATAAAAATAAAAT
1 ATATAAGAATTATAATAAAAAATAAAAATAAAAT
2863133 ATATAA
1 ATATAA
2863139 CATTGAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 31 0.82
35 7 0.18
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (34 bp):
ATATAAGAATTATAATAAAAAATAAAAATAAAAT
Found at i:2863334 original size:23 final size:22
Alignment explanation
Indices: 2863282--2863335 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
2863272 CAAATACTAT
2863282 AATATTATCTTTTCTATATTAA
1 AATATTATCTTTTCTATATTAA
*
2863304 AATAATTATCTTATT-TATATATTA
1 AAT-ATTATCTT-TTCTATAT-TAA
2863328 AATATTAT
1 AATATTAT
2863336 AATATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 3 0.11
23 18 0.64
24 7 0.25
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTATCTTTTCTATATTAA
Found at i:2863341 original size:23 final size:25
Alignment explanation
Indices: 2863296--2863341 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
2863286 TTATCTTTTC
**
2863296 TATATTAAAATAATTATCTTATTTA
1 TATATTAAAATAATTATAATATTTA
2863321 TATATT-AAAT-ATTATAATATT
1 TATATTAAAATAATTATAATATT
2863342 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 4 0.21
25 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTAAAATAATTATAATATTTA
Found at i:2875301 original size:16 final size:18
Alignment explanation
Indices: 2875277--2875313 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2875267 AAAGGGCCCC
2875277 TTTTCTTTT-ATTT-TTA
1 TTTTCTTTTAATTTCTTA
*
2875293 TTTTTTTTTAATTTCTTA
1 TTTTCTTTTAATTTCTTA
2875311 TTT
1 TTT
2875314 GATTGTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTTTAATTTCTTA
Found at i:2887594 original size:3 final size:3
Alignment explanation
Indices: 2887586--2887614 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2887576 TATACAATAC
2887586 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2887615 AATATGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2894064 original size:26 final size:26
Alignment explanation
Indices: 2894034--2894089 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
2894024 TCATTCTTCT
*
2894034 TTTTCTTTGGTAACTTGTCCATTCCA
1 TTTTCCTTGGTAACTTGTCCATTCCA
2894060 TTTTCCTTGGTAACTTGTCCATTCCA
1 TTTTCCTTGGTAACTTGTCCATTCCA
2894086 TTTT
1 TTTT
2894090 AAAACTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (26 bp):
TTTTCCTTGGTAACTTGTCCATTCCA
Found at i:2901134 original size:104 final size:103
Alignment explanation
Indices: 2901008--2901215 Score: 353
Period size: 104 Copynumber: 2.0 Consensus size: 103
2900998 AAATTATAGG
*
2901008 TTAAATTATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATATTATAAAATC
1 TTAAAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATATTATAAAATC
2901073 TAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATA
66 TAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATA
* * * *
2901111 TNTAAAATATTTTATATCGAAGTTTGTATAAATAATAATTAATTATAAATAATATGTTATAAAAT
1 T-TAAAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATATTATAAAAT
*
2901176 TTAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATA
65 CTAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATA
2901215 T
1 T
2901216 AAATAAATTC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 1 0.01
104 97 0.99
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (103 bp):
TTAAAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATATTATAAAATC
TAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATA
Found at i:2901404 original size:319 final size:320
Alignment explanation
Indices: 2900798--2901430 Score: 902
Period size: 319 Copynumber: 2.0 Consensus size: 320
2900788 TGTTGTAATG
*
2900798 TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTTTAAAATCTAAAGTGA
1 TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGA
* * *
2900863 TAGCTAATAAACTTGTTAAGTATAATCATATAAATAAAGTTTATTATAAGTTGTAGTAATGTTTA
66 TAACTAATAAACTTGTTAAGTATAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGTTAA
* *
2900928 TGCATAAATTAAATATATGTGTATATAATATATTACTTTATTATATATATATATATATAATTAAT
131 TGCATAAATTAAATATA-GTGAATATAATATATCACTTTATTATATATATATATATATAATTAAT
* *
2900993 GATACAAATTATAGGTTAAATTATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACA
195 GACACAAATTAGAGGTTAAATTATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACA
* *
2901058 ATATATTATAAAATCTAAGGTGATAACTAATAAAGTTAGTAAGTGTAATCATATNTAAAATA
260 ATATATTATAAAATCTAAGATGATAACTAATAAAGCTAGTAAGTGTAATCATAT-TAAAATA
* * * * *
2901120 TTTTATATCGAAGTTTGTATAAATAATAATTAATTATAAATAATATGTTATAAAATTTAAGGTGA
1 TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGA
* * *
2901185 TAACTAATAAAGTTAG-TAAGTGTAATCATATAAATAAA-TTCTTTTATAAGTTATAGTAATGCT
66 TAACTAATAAACTT-GTTAAGTATAATCATATAAATAAAGTT-TATTATAAGTTATAGTAATG-T
* * *
2901248 TAAT-TATAAATTAAATATA-T-AATATAATATATCACTTTATTTTATATTTATATATGA-AATT
128 TAATGCATAAATTAAATATAGTGAATATAATATATCACTTTATTATATATATATATAT-ATAATT
* * * * *
2901309 AATGACATAACTTAGATGTTATAA-TGTTTTATATCAAAGTTTGTATAAATAATAGCTAATTATA
192 AATGACACAAATTAGAGGTTA-AATTATTTTATATCAAAGTTTGTATAAATAATAACTAATTATA
* *
2901373 AACAATATGTTATAAAATCTAAGATGATAACTAATAAAGCTATTAAGTGTAATCATAT
256 AACAATATATTATAAAATCTAAGATGATAACTAATAAAGCTAGTAAGTGTAATCATAT
2901431 AAATAAAATT
Statistics
Matches: 278, Mismatches: 28, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
319 143 0.51
320 4 0.01
321 2 0.01
322 124 0.45
323 5 0.02
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (320 bp):
TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAAGTGA
TAACTAATAAACTTGTTAAGTATAATCATATAAATAAAGTTTATTATAAGTTATAGTAATGTTAA
TGCATAAATTAAATATAGTGAATATAATATATCACTTTATTATATATATATATATATAATTAATG
ACACAAATTAGAGGTTAAATTATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAA
TATATTATAAAATCTAAGATGATAACTAATAAAGCTAGTAAGTGTAATCATATTAAAATA
Found at i:2920853 original size:26 final size:26
Alignment explanation
Indices: 2920823--2920872 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2920813 AGTGTAATCA
* *
2920823 CTTAAAGTAAATTAAAATAGATTTAT
1 CTTAAAATAAATCAAAATAGATTTAT
*
2920849 CTTAAAATAAATCAGAATAGATTT
1 CTTAAAATAAATCAAAATAGATTT
2920873 TAATAAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (26 bp):
CTTAAAATAAATCAAAATAGATTTAT
Found at i:2927657 original size:39 final size:39
Alignment explanation
Indices: 2927600--2927848 Score: 309
Period size: 39 Copynumber: 6.4 Consensus size: 39
2927590 TATCATTGGA
* *
2927600 ATTGTTCTCTGCTAGATCCCAATCATGGTTTTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * * *
2927639 GTTGTTCTCTACTGGATCCGTATCATGTTTTTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * *
2927678 ATTGTTCTTTGCTGGATCCCAATCATGATTTTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * * * *
2927717 GTTGTTCTCTACTGGATCCGTATCATGTTTTTCTAATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * * *
2927756 AGTGTTTTCTGCTGGGTCCTTATCATGGTTTTCTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
* * *
2927795 ATTGTTCTTTGCTAGATCCCTATCATGGTTTTTTGATGT
1 ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
2927834 ATTGTTCTCTGCTGG
1 ATTGTTCTCTGCTGG
2927849 GAGCTTCTTT
Statistics
Matches: 174, Mismatches: 36, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 174 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (39 bp):
ATTGTTCTCTGCTGGATCCCTATCATGGTTTTCTGATGT
Found at i:2927849 original size:78 final size:78
Alignment explanation
Indices: 2927600--2927848 Score: 356
Period size: 78 Copynumber: 3.2 Consensus size: 78
2927590 TATCATTGGA
*
2927600 ATTGTTCTCTGCTAGATCCCAATCATGGTTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
1 ATTGTTCTCTGCTGGATCCCAATCATGGTTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
2927665 GTTTTTCTGATGT
66 GTTTTTCTGATGT
* *
2927678 ATTGTTCTTTGCTGGATCCCAATCATGATTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
1 ATTGTTCTCTGCTGGATCCCAATCATGGTTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
*
2927743 GTTTTTCTAATGT
66 GTTTTTCTGATGT
* * * ** * * * * *
2927756 AGTGTTTTCTGCTGGGTCCTTATCATGGTTTTCTGATGTATTGTTCTTTGCTAGATCCCTATCAT
1 ATTGTTCTCTGCTGGATCCCAATCATGGTTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
2927821 GGTTTTT-TGATGT
66 -GTTTTTCTGATGT
2927834 ATTGTTCTCTGCTGG
1 ATTGTTCTCTGCTGG
2927849 GAGCTTCTTT
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 145 0.96
79 6 0.04
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (78 bp):
ATTGTTCTCTGCTGGATCCCAATCATGGTTTTCTGATGTGTTGTTCTCTACTGGATCCGTATCAT
GTTTTTCTGATGT
Found at i:2928647 original size:53 final size:53
Alignment explanation
Indices: 2928567--2928673 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
2928557 TCACATATTA
* *
2928567 AAAGGTTATATGTGTCTCTATTTTATACTTTTTAGCTGCACATTTTATATGCT
1 AAAGGTTATATGTGTCTATATTTTATACTTTTTAACTGCACATTTTATATGCT
*
2928620 AAAGGTTATATGTGTTTATATTTTATACTTTTTAACTGCACATTTTATATGCT
1 AAAGGTTATATGTGTCTATATTTTATACTTTTTAACTGCACATTTTATATGCT
2928673 A
1 A
2928674 CCATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (53 bp):
AAAGGTTATATGTGTCTATATTTTATACTTTTTAACTGCACATTTTATATGCT
Found at i:2930023 original size:2 final size:2
Alignment explanation
Indices: 2929974--2930004 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2929964 ATAATAATCG
2929974 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2930005 GCATGCGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2933912 original size:17 final size:16
Alignment explanation
Indices: 2933876--2933918 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
2933866 TCCATTGGAG
*
2933876 CTTTTTCTTTCTTTCTT
1 CTTTTT-TTTCTTTCCT
2933893 CTTTTTTTTCTTTCCCT
1 CTTTTTTTTCTTT-CCT
2933910 CTTTGTTTT
1 CTTT-TTTT
2933919 GATTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 12 0.52
18 4 0.17
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (16 bp):
CTTTTTTTTCTTTCCT
Found at i:2952498 original size:18 final size:18
Alignment explanation
Indices: 2952477--2952512 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2952467 TAAAATTTTG
2952477 ATTAATAATAATTAATTA
1 ATTAATAATAATTAATTA
* *
2952495 ATTATTAATTATTAATTA
1 ATTAATAATAATTAATTA
2952513 TAAAAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATAATAATTAATTA
Found at i:2953145 original size:19 final size:19
Alignment explanation
Indices: 2953121--2953165 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2953111 GCTAACGTGG
*
2953121 CACAATTTACTAGCATGGT
1 CACAATCTACTAGCATGGT
2953140 CACAATCTACTAGCATGGT
1 CACAATCTACTAGCATGGT
2953159 CACAATC
1 CACAATC
2953166 AAATGGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (19 bp):
CACAATCTACTAGCATGGT
Found at i:2957914 original size:2 final size:2
Alignment explanation
Indices: 2957874--2957898 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2957864 CACCCCTCCT
2957874 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2957899 TGAAACTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2971991 original size:17 final size:19
Alignment explanation
Indices: 2971949--2971992 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2971939 TTAACTATTG
2971949 ATAATAAATTAATAATTAATT
1 ATAA-AAATTAAT-ATTAATT
2971970 ATAAAAATTAAT-TTAATT
1 ATAAAAATTAATATTAATT
2971988 -TAAAA
1 ATAAAA
2971993 TAAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
20 8 0.35
21 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAAATTAATATTAATT
Found at i:2972578 original size:17 final size:18
Alignment explanation
Indices: 2972545--2972579 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2972535 TATAGTTTTT
2972545 AATTAATTCAATTATAAA
1 AATTAATTCAATTATAAA
*
2972563 AATTAA-TCATTTATAAA
1 AATTAATTCAATTATAAA
2972580 CAAGAGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAATTCAATTATAAA
Found at i:2982647 original size:25 final size:27
Alignment explanation
Indices: 2982599--2982659 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
2982589 TAAATTATTT
* *
2982599 TAAAAAATTAATTAGAATCGATCAATTA
1 TAAAAAA-TAATTAGAATCAATCAAATA
2982627 TAAAAAA-AATT-GAATCAATCAAATA
1 TAAAAAATAATTAGAATCAATCAAATA
*
2982652 TATAAAAT
1 TAAAAAAT
2982660 TGATTCAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 18 0.62
26 4 0.14
28 7 0.24
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (27 bp):
TAAAAAATAATTAGAATCAATCAAATA
Found at i:2982809 original size:20 final size:20
Alignment explanation
Indices: 2982784--2982851 Score: 84
Period size: 20 Copynumber: 3.3 Consensus size: 20
2982774 TTATAAAAAT
2982784 ATATATTATATATAAATTTAA
1 ATATATTATATATAAATTT-A
2982805 TATATATTATATATAAATTTA
1 -ATATATTATATATAAATTTA
* *
2982826 AAATAATATATATAAATATT-
1 ATATATTATATATAAAT-TTA
2982846 ATATAT
1 ATATAT
2982852 GTACTTAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.46
21 3 0.07
22 19 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATTATATATAAATTTA
Found at i:2982809 original size:22 final size:22
Alignment explanation
Indices: 2982781--2982851 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
2982771 TAATTATAAA
2982781 AATATATATTATATATAAATTT
1 AATATATATTATATATAAATTT
2982803 AATATATATTATATATAAATTT
1 AATATATATTATATATAAATTT
*
2982825 AA-A-ATAATATATATAAATATT
1 AATATATATTATATATAAAT-TT
2982846 -ATATAT
1 AATATAT
2982852 GTACTTAGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
20 15 0.33
21 4 0.09
22 26 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATATATTATATATAAATTT
Found at i:2989510 original size:234 final size:234
Alignment explanation
Indices: 2989100--2989563 Score: 775
Period size: 234 Copynumber: 2.0 Consensus size: 234
2989090 TCCTTGAAAG
* *
2989100 AGTTGCTCTTTCTAAGGACACTGCATCTGTTTCGTCACTTTCTTCATCGGGCTGGGTAGCATTGG
1 AGTTGCTCTTTCTAAGGACACTGCATCTGTTTCATCACTATCTTCATCGGGCTGGGTAGCATTGG
**
2989165 TAGTTTTCACAAGGTCATTGCCTGTAACCATTGCATTACATTGGGCTTGGGGAACTTCAGAAGGC
66 TAGTAGTCACAAGGTCATTGCCTGTAACCATTGCATTACATTGGGCTTGGGGAACTTCAGAAGGC
** *
2989230 TCTGTTACAAAATCAGTAGCCGGCAGTCTAACAGGACTTCGGTGGTGTCGAGAATCTGATATAAG
131 TCTGCAACAAAATCAGTAGCCGGCAGTCTAACAGGACTTCGGTGGTGTCGAGAATCTAATATAAG
*
2989295 GGCATGATCTTTTGGTTGATCACTGGGACTACCAAAAAC
196 GGCATGATCTTTTGGTTGATCACAGGGACTACCAAAAAC
* *
2989334 AGTTGCTCTTTCTAAGGTCACTGCATCTGTTTCATCACTATCTTCATTGGGCTGGGTAGCATTGG
1 AGTTGCTCTTTCTAAGGACACTGCATCTGTTTCATCACTATCTTCATCGGGCTGGGTAGCATTGG
* * *
2989399 TTGTAGTCACAAGGTCATTGCCTGTAACTATTTCATTACATTGGGCTTGGGGAACTTCAGAAGGC
66 TAGTAGTCACAAGGTCATTGCCTGTAACCATTGCATTACATTGGGCTTGGGGAACTTCAGAAGGC
* * * *
2989464 TCTGCAATAAAATCAGTGGTCGGCAGTCTAACAGGACTTTGGTGGTGTCGAGAATCTAATATAAG
131 TCTGCAACAAAATCAGTAGCCGGCAGTCTAACAGGACTTCGGTGGTGTCGAGAATCTAATATAAG
2989529 GGCATGATCTTTTGGTTGATCACAGGGACTACCAA
196 GGCATGATCTTTTGGTTGATCACAGGGACTACCAA
2989564 CCTTAAAATG
Statistics
Matches: 213, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
234 213 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (234 bp):
AGTTGCTCTTTCTAAGGACACTGCATCTGTTTCATCACTATCTTCATCGGGCTGGGTAGCATTGG
TAGTAGTCACAAGGTCATTGCCTGTAACCATTGCATTACATTGGGCTTGGGGAACTTCAGAAGGC
TCTGCAACAAAATCAGTAGCCGGCAGTCTAACAGGACTTCGGTGGTGTCGAGAATCTAATATAAG
GGCATGATCTTTTGGTTGATCACAGGGACTACCAAAAAC
Found at i:3005458 original size:31 final size:32
Alignment explanation
Indices: 3005422--3005499 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
3005412 CAATTTGTTT
3005422 TTCAATTTAGTCCCTAATCACTACA-A-TTTTA
1 TTCAATTTAGTCCCTAAT-ACTACATATTTTTA
* *
3005453 TTCAATTTAGTCCAT-ATACTATATATTTTTA
1 TTCAATTTAGTCCCTAATACTACATATTTTTA
*
3005484 TTTAATTTAGTCCCTA
1 TTCAATTTAGTCCCTA
3005500 TAACGTGACA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.12
30 3 0.08
31 32 0.80
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (32 bp):
TTCAATTTAGTCCCTAATACTACATATTTTTA
Found at i:3008906 original size:18 final size:18
Alignment explanation
Indices: 3008880--3008914 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3008870 TTATTCAAAT
*
3008880 GTGATTATTCAAATTAAA
1 GTGAGTATTCAAATTAAA
*
3008898 GTGAGTATTTAAATTAA
1 GTGAGTATTCAAATTAA
3008915 GTATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
GTGAGTATTCAAATTAAA
Found at i:3011734 original size:13 final size:13
Alignment explanation
Indices: 3011716--3011742 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3011706 GCACTTCTTA
3011716 ATCTTTGGAATTG
1 ATCTTTGGAATTG
3011729 ATCTTTGGAATTG
1 ATCTTTGGAATTG
3011742 A
1 A
3011743 AAATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
ATCTTTGGAATTG
Found at i:3015090 original size:15 final size:15
Alignment explanation
Indices: 3015070--3015103 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3015060 CCCTTTCGCA
* *
3015070 TTCCTCTTCCTTTCT
1 TTCCTCCTCCTCTCT
3015085 TTCCTCCTCCTCTCT
1 TTCCTCCTCCTCTCT
3015100 TTCC
1 TTCC
3015104 GTTCCTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCCTCCTCCTCTCT
Found at i:3024499 original size:2 final size:2
Alignment explanation
Indices: 3024494--3024552 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
3024484 TTGTGTGATT
3024494 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3024536 TA TA TN T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3024553 GGTTAATTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3037650 original size:62 final size:62
Alignment explanation
Indices: 3037570--3037755 Score: 300
Period size: 62 Copynumber: 3.0 Consensus size: 62
3037560 TTTGTTAATT
* * *
3037570 ATTGGTTTTACTTCATTAAACATGAATTAAATACATGAAAAGCAAATTCCTTGAATGGAATC
1 ATTGGTTTTACTTTATTAAACATGAATTAAATACATGAAAAACATATTCCTTGAATGGAATC
* *
3037632 ATTGGTTTTACTTTATTAAACATGAACTAAATACATGAAAAACATATTCCCTGAATGGAATC
1 ATTGGTTTTACTTTATTAAACATGAATTAAATACATGAAAAACATATTCCTTGAATGGAATC
* * *
3037694 ATTGGTTTTACTATACTAAACATGAATTAAAGACATGAAAAACATATTCCTTGAATGGAATC
1 ATTGGTTTTACTTTATTAAACATGAATTAAATACATGAAAAACATATTCCTTGAATGGAATC
3037756 TGGCCTTTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 114 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (62 bp):
ATTGGTTTTACTTTATTAAACATGAATTAAATACATGAAAAACATATTCCTTGAATGGAATC
Found at i:3053957 original size:10 final size:8
Alignment explanation
Indices: 3053905--3053937 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
3053895 TTATTTAGAA
3053905 AACTTTTT
1 AACTTTTT
3053913 AACTTTTT
1 AACTTTTT
3053921 AACTTTTT
1 AACTTTTT
3053929 AACTTTTT
1 AACTTTTT
3053937 A
1 A
3053938 GAACTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (8 bp):
AACTTTTT
Found at i:3053968 original size:10 final size:9
Alignment explanation
Indices: 3053905--3053969 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 9
3053895 TTATTTAGAA
3053905 AACT-TTTT
1 AACTATTTT
3053913 AACT-TTTT
1 AACTATTTT
3053921 AACT-TTTT
1 AACTATTTT
3053929 AACT-TTTT
1 AACTATTTT
3053937 AGAACTAATTTT
1 --AACT-ATTTT
3053949 AATCTATTTT
1 AA-CTATTTT
3053959 AACTAGTTTT
1 AACTA-TTTT
3053969 A
1 A
3053970 GTTTTTTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
8 24 0.47
9 3 0.06
10 18 0.35
11 2 0.04
12 4 0.08
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (9 bp):
AACTATTTT
Found at i:3059724 original size:27 final size:29
Alignment explanation
Indices: 3059693--3059763 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
3059683 AATTATAAAA
*
3059693 AAATATTTTATTTAAA-ATAA-AAAATAT
1 AAATATTTTATTTAAATATAATAAAAGAT
* * *
3059720 AAATA-CTTAATTAAATTTAATAAAAGAT
1 AAATATTTTATTTAAATATAATAAAAGAT
3059748 AAA-ATTTTATTTAAAT
1 AAATATTTTATTTAAAT
3059764 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 8 0.23
27 9 0.26
28 18 0.51
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
AAATATTTTATTTAAATATAATAAAAGAT
Found at i:3060542 original size:13 final size:13
Alignment explanation
Indices: 3060524--3060549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3060514 GTTATAATAA
3060524 ATGATAATATGAT
1 ATGATAATATGAT
3060537 ATGATAATATGAT
1 ATGATAATATGAT
3060550 TGTGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGATAATATGAT
Found at i:3074844 original size:2 final size:2
Alignment explanation
Indices: 3074837--3074913 Score: 136
Period size: 2 Copynumber: 38.0 Consensus size: 2
3074827 ATTATGATTG
3074837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3074879 AT AT AT AT AN AT AT AT ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
3074914 CTAGCTACAT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 70 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3082659 original size:14 final size:15
Alignment explanation
Indices: 3082640--3082668 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3082630 GATATTGTTG
3082640 TTTTATTA-TAATTT
1 TTTTATTATTAATTT
3082654 TTTTATTATTAATTT
1 TTTTATTATTAATTT
3082669 AAAATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTATTAATTT
Found at i:3082724 original size:20 final size:21
Alignment explanation
Indices: 3082688--3082727 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3082678 ATAATGAAGT
*
3082688 TGTATTTTATTTTTAATTATA
1 TGTATTTTATATTTAATTATA
3082709 TGTATTTTA-ATTTAATTAT
1 TGTATTTTATATTTAATTAT
3082728 GTTTATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TGTATTTTATATTTAATTATA
Found at i:3083566 original size:3 final size:3
Alignment explanation
Indices: 3083558--3083583 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3083548 AATAGGTTAG
3083558 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3083584 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3090150 original size:2 final size:2
Alignment explanation
Indices: 3090143--3090218 Score: 127
Period size: 2 Copynumber: 38.0 Consensus size: 2
3090133 ATGGTTACAA
*
3090143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NCT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
3090185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3090219 TGATAATACC
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.01
2 68 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3099350 original size:18 final size:17
Alignment explanation
Indices: 3099327--3099360 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3099317 GTTATAAGGA
3099327 TTAAATTAAAATAAATTT
1 TTAAATTAAAA-AAATTT
3099345 TTAAATTAAAAAAATT
1 TTAAATTAAAAAAATT
3099361 AAAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTAAAAAAATTT
Found at i:3100541 original size:29 final size:29
Alignment explanation
Indices: 3100500--3100580 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
3100490 GAACGCATAA
**
3100500 TATTTTAAAAAATTTAAATAAATTATTAT
1 TATTTTATTAAATTTAAATAAATTATTAT
* * *
3100529 TATTTTATTAAATTTAATTAATTTTTTAT
1 TATTTTATTAAATTTAAATAAATTATTAT
* *
3100558 AATTTTATTTTAATTTAAATAAA
1 TATTTTA-TTAAATTTAAATAAA
3100581 CTCTTATAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTTTATTAAATTTAAATAAATTATTAT
Found at i:3100704 original size:18 final size:18
Alignment explanation
Indices: 3100683--3100720 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3100673 ATAATGAATG
*
3100683 ATGATGTGA-TATATTTAT
1 ATGATATGATTATA-TTAT
3100701 ATGATATGATTATATTAT
1 ATGATATGATTATATTAT
3100719 AT
1 AT
3100721 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (18 bp):
ATGATATGATTATATTAT
Found at i:3111742 original size:1 final size:1
Alignment explanation
Indices: 3111733--3111793 Score: 104
Period size: 1 Copynumber: 61.0 Consensus size: 1
3111723 TACTTTGAAG
* *
3111733 AAAAGAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3111794 CACTAATAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.97, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:3115688 original size:89 final size:90
Alignment explanation
Indices: 3115535--3115715 Score: 303
Period size: 89 Copynumber: 2.0 Consensus size: 90
3115525 ATAAAGGAAA
*
3115535 TCCATAGCACAAGAATGATACAGACATATAAAATATAGATTTTTTTTTTTCAAAATTATAGGTAT
1 TCCATAGCACAAAAATGATA-AGACATATAAAATATAGATTTTTTTTTTTCAAAATTATAGGTAT
*
3115600 TGGTAATTTCTTCATACATACTCATT
65 TGGTAACTTCTTCATACATACTCATT
*
3115626 TCCATAGGACAAAAATGAT-AGACACT-TAAAATATAGATTTTTTTTTTTCAAAATTATAGGTAT
1 TCCATAGCACAAAAATGATAAGACA-TATAAAATATAGATTTTTTTTTTTCAAAATTATAGGTAT
3115689 TGGTAACTTCTTCATACATACTCATT
65 TGGTAACTTCTTCATACATACTCATT
3115715 T
1 T
3115716 ACATTATAAA
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
89 68 0.79
90 1 0.01
91 17 0.20
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (90 bp):
TCCATAGCACAAAAATGATAAGACATATAAAATATAGATTTTTTTTTTTCAAAATTATAGGTATT
GGTAACTTCTTCATACATACTCATT
Found at i:3119125 original size:24 final size:23
Alignment explanation
Indices: 3119072--3119133 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
3119062 AAATTGTTAT
3119072 ATTTTTATT-TTAAATTAAATAA
1 ATTTTTATTATTAAATTAAATAA
*
3119094 ATTTTTATTATTAATGATT-AATTA
1 ATTTTTATTATTAA--ATTAAATAA
3119118 ATTTTTATTAATTAAA
1 ATTTTTATT-ATTAAA
3119134 ATATTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 9 0.26
23 5 0.14
24 13 0.37
25 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTTATTATTAAATTAAATAA
Found at i:3119261 original size:33 final size:33
Alignment explanation
Indices: 3119213--3119300 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
3119203 TGATCATTTT
* * *
3119213 ATTATATTAAATTAATATATTAAGTTATTATTA
1 ATTATAATAAATTAATATATCAAGTTATTATCA
* *
3119246 ATTGTAATAAATTAATATATCAATTTATTATCA
1 ATTATAATAAATTAATATATCAAGTTATTATCA
* *
3119279 ATTATGATATATTAATATATCA
1 ATTATAATAAATTAATATATCA
3119301 GTAATGATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
ATTATAATAAATTAATATATCAAGTTATTATCA
Found at i:3119375 original size:30 final size:29
Alignment explanation
Indices: 3119340--3119443 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
3119330 AATTATTAGT
3119340 AATA-AAAATTTATTTGATTGAAAATAAA
1 AATATAAAATTTATTTGATTGAAAATAAA
* *
3119368 AATATAAAAATTTGTTTGATTAAAAATAAA
1 AATAT-AAAATTTATTTGATTGAAAATAAA
* * * * *
3119398 AATATGAAATTGGA-TTAAATG-TAATAAA
1 AATATAAAATT-TATTTGATTGAAAATAAA
3119426 AATATAAAATTTATTTGA
1 AATATAAAATTTATTTGA
3119444 AATTTTTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.02
28 23 0.38
29 9 0.15
30 27 0.45
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.37
Consensus pattern (29 bp):
AATATAAAATTTATTTGATTGAAAATAAA
Found at i:3123147 original size:32 final size:32
Alignment explanation
Indices: 3123104--3123169 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3123094 CATTTCTCAG
*
3123104 TTGTTGTACTCAAAAATGGTGAGCCCAAGAAA
1 TTGTTGAACTCAAAAATGGTGAGCCCAAGAAA
3123136 TTGTTGAACTCAAAAATGGTGAGCCCAAGAAA
1 TTGTTGAACTCAAAAATGGTGAGCCCAAGAAA
3123168 TT
1 TT
3123170 CTTTGTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (32 bp):
TTGTTGAACTCAAAAATGGTGAGCCCAAGAAA
Found at i:3123168 original size:16 final size:16
Alignment explanation
Indices: 3123117--3123168 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3123107 TTGTACTCAA
3123117 AAATGGTGAGCCCAAG
1 AAATGGTGAGCCCAAG
* * *
3123133 AAATTGTTGAACTCAA-
1 AAA-TGGTGAGCCCAAG
3123149 AAATGGTGAGCCCAAG
1 AAATGGTGAGCCCAAG
3123165 AAAT
1 AAAT
3123169 TCTTTGTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 9 0.32
16 10 0.36
17 9 0.32
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (16 bp):
AAATGGTGAGCCCAAG
Found at i:3146181 original size:30 final size:31
Alignment explanation
Indices: 3146145--3146217 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 31
3146135 TTTTGTCATT
3146145 TTTTATTATTTAATTAT-TATTTTC-ATTTTA
1 TTTTATTATTT-ATTATATATTTTCTATTTTA
3146175 TTTTATT-TTTATTATCATATTTTCTATTTTA
1 TTTTATTATTTATTAT-ATATTTTCTATTTTA
3146206 TTTCTAATTATT
1 TTT-T-ATTATT
3146218 ATTTTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 5 0.14
29 3 0.08
30 14 0.38
31 9 0.24
32 1 0.03
33 3 0.08
34 2 0.05
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (31 bp):
TTTTATTATTTATTATATATTTTCTATTTTA
Found at i:3146186 original size:22 final size:22
Alignment explanation
Indices: 3146150--3146226 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
3146140 TCATTTTTTA
* *
3146150 TTATTTAATTATTATTTTCATT
1 TTATTTTATTTTTATTTTCATT
* *
3146172 TTATTTTATTTTTATTATCATA
1 TTATTTTATTTTTATTTTCATT
* *
3146194 TT-TTCTA-TTTTATTTCTAATT
1 TTATTTTATTTTTATTT-TCATT
3146215 ATTATTTT-TTTT
1 -TTATTTTATTTT
3146227 ATACTTTATG
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 7 0.17
21 7 0.17
22 22 0.52
23 6 0.14
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTTATTTTTATTTTCATT
Found at i:3146475 original size:14 final size:13
Alignment explanation
Indices: 3146434--3146489 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
3146424 ATTCAAATTA
3146434 TTAT-TATTATTT
1 TTATCTATTATTT
*
3146446 TTATC-ATCATTTT
1 TTATCTATTA-TTT
3146459 TTATCTATTATTAT
1 TTATCTATTATT-T
*
3146473 TTATTTATTATTT
1 TTATCTATTATTT
3146486 TTAT
1 TTAT
3146490 TGAGTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 15 0.41
14 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATCTATTATTT
Found at i:3146926 original size:2 final size:2
Alignment explanation
Indices: 3146919--3146972 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
3146909 TTTATCTCTT
*
3146919 TA TA TA TA TA TA TA TA TA TG TGA TA TA TA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
3146960 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3146973 TTTATCCTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3148350 original size:22 final size:21
Alignment explanation
Indices: 3148306--3148351 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3148296 TATTACTTTA
3148306 TTATATATATATATATATATT
1 TTATATATATATATATATATT
* * *
3148327 TTATCATATATTTATTTATTTT
1 TTAT-ATATATATATATATATT
3148349 TTA
1 TTA
3148352 AACACAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATATATATATATATATT
Found at i:3150524 original size:21 final size:21
Alignment explanation
Indices: 3150499--3150540 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3150489 GCTCTTGATG
3150499 CAACAA-TCCTTGATGAAGACC
1 CAACAACT-CTTGATGAAGACC
3150520 CAACAACTCTTGATGAAGACC
1 CAACAACTCTTGATGAAGACC
3150541 TAGGCAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (21 bp):
CAACAACTCTTGATGAAGACC
Found at i:3150623 original size:26 final size:26
Alignment explanation
Indices: 3150593--3150644 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3150583 TTAGATGCAT
* *
3150593 TAAATTGCATATTTAATTTAAATTAC
1 TAAATTGCATAATTAATGTAAATTAC
*
3150619 TAAATTGCATAATTAATGTAGATTAC
1 TAAATTGCATAATTAATGTAAATTAC
3150645 CTTTCTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAATTGCATAATTAATGTAAATTAC
Found at i:3154788 original size:2 final size:2
Alignment explanation
Indices: 3154781--3154814 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3154771 ATGTCTTTTA
3154781 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
3154815 ATGTGTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3154865 original size:14 final size:14
Alignment explanation
Indices: 3154848--3154874 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3154838 ATTACCATTA
3154848 TATATATACTTTAG
1 TATATATACTTTAG
3154862 TATATATACTTTA
1 TATATATACTTTA
3154875 AATGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (14 bp):
TATATATACTTTAG
Found at i:3155618 original size:159 final size:158
Alignment explanation
Indices: 3155330--3155624 Score: 382
Period size: 159 Copynumber: 1.9 Consensus size: 158
3155320 TACGGCCTTG
* *
3155330 GATTCGGATAATTAAGTACTCATGAAGAGCTTTTAATAATTTTTTAACATAATCTAATTTTTAAA
1 GATTCGGATAATTAAGTACCCATGAAGAGATTTTAATAATTTTTTAACATAATCTAATTTTTAAA
* * * * * *
3155395 TAGATTCGGGTAATTATCGAGTAGTGGGTATATATTAGGGTTCGGGTTAAGATAATAAATTTTAA
66 GAGATTCGGGTAATTATCGAGAAGTGGATATATATCAGAGTTCAGGTTAAGATAATAAATTTTAA
3155460 AAATATGTGAGATACGGGTGCGAATTCA
131 AAATATGTGAGATACGGGTGCGAATTCA
* ** *
3155488 GATTCGGGTAATTGAA-TACCCATGAAGAGTATTTTAATAATTTTTTTGCATAA-CTGGATTTTT
1 GATTCGGATAATT-AAGTACCCATGAAGAG-ATTTTAATAATTTTTTAACATAATCT-AATTTTT
* * *
3155551 AAACGAG-TTCGGGTAATTATC-AGAAAGTGGATATCTATCAGAGTTTAGGTTAAGATAGTAAAT
63 AAA-GAGATTCGGGTAATTATCGAG-AAGTGGATATATATCAGAGTTCAGGTTAAGATAATAAAT
3155614 TTTAAAAATAT
126 TTTAAAAATAT
3155625 TCGGATAGTT
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
158 28 0.24
159 87 0.74
160 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (158 bp):
GATTCGGATAATTAAGTACCCATGAAGAGATTTTAATAATTTTTTAACATAATCTAATTTTTAAA
GAGATTCGGGTAATTATCGAGAAGTGGATATATATCAGAGTTCAGGTTAAGATAATAAATTTTAA
AAATATGTGAGATACGGGTGCGAATTCA
Found at i:3158901 original size:24 final size:24
Alignment explanation
Indices: 3158869--3158916 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3158859 TTAAATTAAT
*
3158869 TCTTCCCATCGCACCTTCGTATCC
1 TCTTCCCATAGCACCTTCGTATCC
*
3158893 TCTTCCCATAGCGCCTTCGTATCC
1 TCTTCCCATAGCACCTTCGTATCC
3158917 CCCTCGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.44, G:0.10, T:0.33
Consensus pattern (24 bp):
TCTTCCCATAGCACCTTCGTATCC
Found at i:3159062 original size:18 final size:18
Alignment explanation
Indices: 3159039--3159073 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3159029 TTAATACAGT
*
3159039 TAAACCTCTGTAAAGTAG
1 TAAACCTCTATAAAGTAG
3159057 TAAACCTCTATAAAGTA
1 TAAACCTCTATAAAGTA
3159074 ATACTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAACCTCTATAAAGTAG
Found at i:3159159 original size:20 final size:20
Alignment explanation
Indices: 3159093--3159198 Score: 79
Period size: 20 Copynumber: 5.2 Consensus size: 20
3159083 GATAATGAAA
*
3159093 ATTTATTAATTAATTAAAAT
1 ATTTATTAATTTATTAAAAT
** *
3159113 A-TTATTTAATCAATAAATTAAT
1 ATTTA-TTAATTTATTAA--AAT
3159135 AATTTATTAATTTATTAAAAT
1 -ATTTATTAATTTATTAAAAT
* * *
3159156 ATTTTTTATTTTTTTAAAAT
1 ATTTATTAATTTATTAAAAT
* * *
3159176 ATTTTTTATTTTTTTAAAAT
1 ATTTATTAATTTATTAAAAT
3159196 ATT
1 ATT
3159199 AAGCTTAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.04
20 51 0.70
21 3 0.04
22 3 0.04
23 10 0.14
24 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATTAATTTATTAAAAT
Found at i:3159166 original size:19 final size:20
Alignment explanation
Indices: 3159149--3159198 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3159139 TATTAATTTA
3159149 TTAAAATATTTTTTATTTTT
1 TTAAAATATTTTTTATTTTT
3159169 TTAAAATATTTTTTATTTTT
1 TTAAAATATTTTTTATTTTT
3159189 TTAAAATATT
1 TTAAAATATT
3159199 AAGCTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAAAATATTTTTTATTTTT
Found at i:3165114 original size:186 final size:186
Alignment explanation
Indices: 3164782--3165167 Score: 488
Period size: 186 Copynumber: 2.1 Consensus size: 186
3164772 TCTGTCTTGA
* *
3164782 CTTTTTCTTCTGACCCATATCTTTCCTTTCCACTAGTCAACTTGTCAACCTTACTTTTAGATTTC
1 CTTTTGCTT-TGACCCATATCTTTCCTTTCCACTAGTCAACTTGTCAACCCTACTTTTAGATTTC
* * * * * * * **
3164847 TCCCTCTAACAAGACTTTATTAGATTGTAAACAATCTCCTATAAAACCTTGGTAAAATCTTGAAT
65 TCCCTATAACAAGACTCTATCAAACTATAAACAATCTCATATAAAACCTTGGTAAAATCCCGAAT
* * *
3164912 TTTCTTCTCATTGTCGTACATCCATTTTGCCCTTCTTCTTCGACTTTAATTCAAATT
130 TTTCTTCTCATTGTCGTACATCCATTCTGCCCTTCTCCTTCAACTTTAATTCAAATT
3164969 CTTTTGCTTTGACCCATATCTTTCCTTTCCACTAGTCAACTTGTCAACCCTACTTTTA-ACTTTC
1 CTTTTGCTTTGACCCATATCTTTCCTTTCCACTAGTCAACTTGTCAACCCTACTTTTAGA-TTTC
* * * *** * *
3165033 TTCTTATGATTGGACTCTATCAAACTATAAACAATCTCATCTAAAACCTTGGTATAATCCCGAAT
65 TCCCTATAACAAGACTCTATCAAACTATAAACAATCTCATATAAAACCTTGGTAAAATCCCGAAT
* * * *
3165098 TTTCTTTTTC-TTGTCGTGCATTCATTCTGCCCTTCTCCTTCAACTTTAATTCAATTT
130 TTTC-TTCTCATTGTCGTACATCCATTCTGCCCTTCTCCTTCAACTTTAATTCAAATT
*
3165155 CTTCTGCTTTGAC
1 CTTTTGCTTTGAC
3165168 ATCTTTCTTA
Statistics
Matches: 170, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
185 1 0.01
186 157 0.92
187 12 0.07
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.43
Consensus pattern (186 bp):
CTTTTGCTTTGACCCATATCTTTCCTTTCCACTAGTCAACTTGTCAACCCTACTTTTAGATTTCT
CCCTATAACAAGACTCTATCAAACTATAAACAATCTCATATAAAACCTTGGTAAAATCCCGAATT
TTCTTCTCATTGTCGTACATCCATTCTGCCCTTCTCCTTCAACTTTAATTCAAATT
Found at i:3166161 original size:27 final size:26
Alignment explanation
Indices: 3166012--3166183 Score: 107
Period size: 27 Copynumber: 6.5 Consensus size: 26
3166002 ATGTTTTTGT
* * **
3166012 GCTTGAAACACCCTTGGGCGCTTCTGC
1 GCTTGGAACACCCTTGGGC-ATTCCAC
* ***
3166039 GCTTGGAACACCCCTGAGAGC-TTTTGC
1 GCTTGGAACACCCTTG-G-GCATTCCAC
*
3166066 GCTTGAAACACCCTTGGG-ATTCCAC
1 GCTTGGAACACCCTTGGGCATTCCAC
* * * * *
3166091 GCTTAGAATACCCGTGGACACTTCTAC
1 GCTTGGAACACCCTTGGGCA-TTCCAC
*
3166118 GCTTGGAACACCTTTGGGCATTTCCAC
1 GCTTGGAACACCCTTGGGCA-TTCCAC
* *
3166145 GTTTGGAACACCCTTGGGTGC-TTCTAC
1 GCTTGGAACACCCTT-GG-GCATTCCAC
3166172 GCTTGGAACACC
1 GCTTGGAACACC
3166184 TGTACGCACT
Statistics
Matches: 113, Mismatches: 25, Indels: 14
0.74 0.16 0.09
Matches are distributed among these distances:
25 17 0.15
26 2 0.02
27 87 0.77
28 3 0.03
29 4 0.04
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (26 bp):
GCTTGGAACACCCTTGGGCATTCCAC
Found at i:3166173 original size:54 final size:52
Alignment explanation
Indices: 3166038--3166184 Score: 152
Period size: 54 Copynumber: 2.8 Consensus size: 52
3166028 GGCGCTTCTG
* * * * *
3166038 CGCTTGGAACACCCCTGAGAGCTTTTGCGCTTGAAACACCCTTGGGATTCCA
1 CGCTTGGAACACCCCTGGGAGCTTCTACGCTTGGAACACCTTTGGGATTCCA
* * * *
3166090 CGCTTAGAATACCCGT-GGACACTTCTACGCTTGGAACACCTTTGGGCATTTCCA
1 CGCTTGGAACACCCCTGGGA-GCTTCTACGCTTGGAACACCTTTGGG-A-TTCCA
* * *
3166144 CGTTTGGAACACCCTTGGGTGCTTCTACGCTTGGAACACCT
1 CGCTTGGAACACCCCTGGGAGCTTCTACGCTTGGAACACCT
3166185 GTACGCACTT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
51 2 0.03
52 34 0.45
53 1 0.01
54 37 0.49
55 2 0.03
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.27
Consensus pattern (52 bp):
CGCTTGGAACACCCCTGGGAGCTTCTACGCTTGGAACACCTTTGGGATTCCA
Found at i:3166195 original size:27 final size:26
Alignment explanation
Indices: 3166012--3166242 Score: 103
Period size: 27 Copynumber: 8.7 Consensus size: 26
3166002 ATGTTTTTGT
* * *
3166012 GCTTGAAACACCCTTGGGCGCTTCTGC
1 GCTTGGAACA-CCTTGGGCACTTCTAC
* * * *
3166039 GCTTGGAACACCCCTGAG-AGCTTTTGC
1 GCTTGGAACA-CCTTGGGCA-CTTCTAC
* *
3166066 GCTTGAAACACCCTTGGG-A-TTCCAC
1 GCTTGGAACA-CCTTGGGCACTTCTAC
* * * *
3166091 GCTTAGAATACCCGTGGACACTTCTAC
1 GCTTGGAACA-CCTTGGGCACTTCTAC
* *
3166118 GCTTGGAACACCTTTGGGCATTTCCAC
1 GCTTGGAACACC-TTGGGCACTTCTAC
* **
3166145 GTTTGGAACACCCTTGGGTGCTTCTAC
1 GCTTGGAACA-CCTTGGGCACTTCTAC
**
3166172 GCTTGGAACACCTGTACGCACTTCTA-
1 GCTTGGAACACCT-TGGGCACTTCTAC
* * ** * *
3166198 ACTTGGGACACCTTTGGG-GTTTCCAT
1 GCTTGGAACACC-TTGGGCACTTCTAC
3166224 GCTTGGAACACTCTTGGGC
1 GCTTGGAACAC-CTTGGGC
3166243 GCTTTTGTGC
Statistics
Matches: 152, Mismatches: 42, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
25 20 0.13
26 32 0.21
27 98 0.64
28 2 0.01
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.28
Consensus pattern (26 bp):
GCTTGGAACACCTTGGGCACTTCTAC
Found at i:3166261 original size:79 final size:81
Alignment explanation
Indices: 3166109--3166262 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 81
3166099 TACCCGTGGA
* * *
3166109 CACTTCTACGCTTGGAACACCTTTGGGCATTTCCACGTTTGGAACACCCTTGGGTGCTTCTACGC
1 CACTTCTACACTTGGAACACCTTTGGGCATTTCCACGCTTGGAACACCCTTGGGCGCTTCTACGC
* *
3166174 TTGGAACACCTGTACG
66 GTGAAACACCTGTACG
* * * * * **
3166190 CACTTCTA-ACTTGGGACACCTTTGGG-GTTTCCATGCTTGGAACACTCTTGGGCGCTTTTGTGC
1 CACTTCTACACTTGGAACACCTTTGGGCATTTCCACGCTTGGAACACCCTTGGGCGCTTCTACGC
3166253 GTGAAACACC
66 GTGAAACACC
3166263 CCTGGACGCT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 37 0.61
80 16 0.26
81 8 0.13
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (81 bp):
CACTTCTACACTTGGAACACCTTTGGGCATTTCCACGCTTGGAACACCCTTGGGCGCTTCTACGC
GTGAAACACCTGTACG
Found at i:3166287 original size:27 final size:27
Alignment explanation
Indices: 3166223--3166289 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
3166213 GGGGTTTCCA
* * *
3166223 TGCTTGGAACACTCTTGGGCGCTTTTG
1 TGCTTGGAACACCCCTGGACGCTTTTG
* *
3166250 TGCGTGAAACACCCCTGGACGCTTTTG
1 TGCTTGGAACACCCCTGGACGCTTTTG
*
3166277 TGTTTGGAACACC
1 TGCTTGGAACACC
3166290 TCTAGTGCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (27 bp):
TGCTTGGAACACCCCTGGACGCTTTTG
Found at i:3175071 original size:36 final size:36
Alignment explanation
Indices: 3175024--3175098 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
3175014 GTCTTAACGA
* * * *
3175024 CTTGATCTTGATCACGAGCTAGATTTGATATCCTCG
1 CTTGATCTTGATCACAAACTAGACTTAATATCCTCG
* *
3175060 CTTGATTTTGATCACAAACTAGACTTAATATCTTCG
1 CTTGATCTTGATCACAAACTAGACTTAATATCCTCG
3175096 CTT
1 CTT
3175099 CAAGAGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
CTTGATCTTGATCACAAACTAGACTTAATATCCTCG
Found at i:3175182 original size:12 final size:12
Alignment explanation
Indices: 3175165--3175191 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3175155 GCTTGATTTT
3175165 GATCACGGACTA
1 GATCACGGACTA
3175177 GATCACGGACTA
1 GATCACGGACTA
3175189 GAT
1 GAT
3175192 TTGATATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (12 bp):
GATCACGGACTA
Found at i:3177170 original size:19 final size:18
Alignment explanation
Indices: 3177146--3177183 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3177136 TAAATATTAA
3177146 ATATTAAATATTATAATTT
1 ATATTAAA-ATTATAATTT
*
3177165 ATATTAAAATTTTAATTT
1 ATATTAAAATTATAATTT
3177183 A
1 A
3177184 ATTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAAATTATAATTT
Done.