Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_pilon, whole genome shotgun sequence
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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2543358 original size:22 final size:24
Alignment explanation
Indices: 2543311--2543357 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2543301 TAATAATAAT
2543311 ATAATATAATAATATTAAAACAAA
1 ATAATATAATAATATTAAAACAAA
2543335 ATAATAATAATAA-A-TAAAACAAA
1 ATAAT-ATAATAATATTAAAACAAA
2543358 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
ATAATATAATAATATTAAAACAAA
Found at i:2543933 original size:113 final size:113
Alignment explanation
Indices: 2543808--2545353 Score: 2060
Period size: 113 Copynumber: 13.7 Consensus size: 113
2543798 TAATTCGAGC
* * *
2543808 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * * *
2543873 GCCCTGGCAATGCT-AGTCCATCGAATGATAAATTCAAGCGAAAA-GTTG
66 TACCTGGAAATGCTGA-TCCATCGAATGATGAATTCGAGC-AAAAGGTTG
*
2543921 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTACAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2543986 GACCTGGTAAA-GTTGATCCATC-AAGTGATGAATTCGAGCAAAAAGTTA
66 TACCTGG-AAATGCTGATCCATCGAA-TGATGAATTCGAGCAAAAGGTTG
*
2544034 AACAAGGTT-TTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AACAA-GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * *
2544098 CTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTG
65 CTACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* *
2544147 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2544212 T-CTCTGGAAAAT-CTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTG
66 TAC-CTGG-AAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* *
2544260 AACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
2544325 GACCTGGTAAA-GTTGATCCATC-AAGTGATGAATTCGAGCAAAAAGTTG
66 TACCTGG-AAATGCTGATCCATCGAA-TGATGAATTCGAGCAAAAGGTTG
* *
2544373 AACAAGTTTTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * * *
2544438 TACCTGGTAATGATGATCTATTGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
** *
2544486 AACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * *
2544551 T-CTCTGGAAAAGCTGATCCAGCGAGTGATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* *
2544599 AACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCTGATGAGTTCTTCTCATTATGAACT-
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * *
2544663 TTCTCTGGAAATGCCGATCCATC-AAGTAATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAA-TGATGAATTCGAGCAAAAGGTTG
* *
2544712 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2544777 TACCTGGAAATGCTGATCCATC-AAGTAATGGATTTGAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAA-TGATGAATTCGAGCAAAAGGTTG
* * *
2544825 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2544890 TACCTGGTAATGATGATCCATCGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* *
2544938 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2545003 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* * *
2545051 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * **
2545116 TACCTGGTAATGATGATCCATCGAATGATGAATTCAAATAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
* *
2545164 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
2545229 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
*
2545277 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
2545342 TACCTAGAAATG
66 TACCTGGAAATG
2545354 TTTTAAGAAA
Statistics
Matches: 1273, Mismatches: 136, Indels: 48
0.87 0.09 0.03
Matches are distributed among these distances:
112 19 0.01
113 1234 0.97
114 20 0.02
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TACCTGGAAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTG
Found at i:2544210 original size:339 final size:339
Alignment explanation
Indices: 2543696--2545346 Score: 2309
Period size: 339 Copynumber: 4.9 Consensus size: 339
2543686 AGAATCATGC
* *
2543696 AAAAGATTGAACAAG-TTCTTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAATTCTTCTCA
1 AAAAG-TTGAACAAGCTT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * * *
2543760 TTATGAACTCT-CTTTGGAAAAGTTGATCCATCGAGTGAT-AATT----C--GA-G--CAACAAG
64 TTATGAACTCTAC-CTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAA
* * * ** *
2543814 TTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCCCTG
128 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTG
* * ** ** *
2543879 GCAATGCT-AGTCCATCGAATGATAAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGA
193 GAAATGCTGA-TCCATCGAGTGATGGATTTGAGC-AAAAGGTTGAACAAGCTCTTCTCATTATGA
* *
2543942 ACTTCTTCTTCCTTCTACAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGTTGATCCAT
256 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGCTGATCCAT
2544007 CAAGTGATGAATTCGAGCA
321 CAAGTGATGAATTCGAGCA
* * *
2544026 AAAAGTTAAACAAGGTTTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2544091 ATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAATTC
66 ATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAATTC
2544156 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGG-A
*
2544221 AAT-CTGATCCATCGAGTGATGGATTTGAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTT
195 AATGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
* *
2544285 CTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGTTGATCCATCAAG
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGCTGATCCATCAAG
2544350 TGATGAATTCGAGCA
325 TGATGAATTCGAGCA
* *
2544365 AAAAGTTGAACAAGTTTTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2544430 ATGAACTCTACCTGGTAATGATGATCTATTGAATGATGAATTCAAACAAAAGGTTGAACAAAATC
66 ATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAATTC
2544495 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
* * *
2544560 AAGCTGATCCAGCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGATCTTCTCATTATGAACTTC
196 ATGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* ** *
2544625 TTCTTCCTTCTTCTGATGAGTTCTTCTCATTATGAACT-TTCTCTGG-AAATGCCGATCCATCAA
261 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CTGGTAAA-GCTGATCCATCAA
* * *
2544688 GTAATGGATTTGAGCA
324 GTGATGAATTCGAGCA
* * *
2544704 AAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * ** **
2544769 ATGAACTCTACCTGGAAATGCTGATCCA-TCAAGTAATGGATTTGAACAAAAGGTTGAACAAGCT
66 ATGAACTCTACCTGGTAATGATGATCCATTGAA-TGATGAATTCAAACAAAAGGTTGAACAAATT
* * *
2544833 CTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTAT-CTCTGG
* * * * ** * **
2544897 TAATGATGATCCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
194 AAATGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
*
2544962 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT--ATCTCTGGAAAAGCTGATCCATC
259 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA-C-CTGGTAAAGCTGATCCATC
* * *
2545025 GAGTGATGGATTTGAGCA
322 AAGTGATGAATTCGAGCA
* * * *
2545043 AAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATT
1 AAAAGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2545108 ATGAACTCTACCTGGTAATGATGATCCATCGAATGATGAATTCAAATAAAAGGTTGAACAAATTC
66 ATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAATTC
2545173 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
*
2545238 AAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
196 ATGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
2545303 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
261 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCT
2545347 AGAAATGTTT
Statistics
Matches: 1191, Mismatches: 104, Indels: 43
0.89 0.08 0.03
Matches are distributed among these distances:
329 82 0.07
330 12 0.01
334 1 0.00
336 1 0.00
337 1 0.00
338 15 0.01
339 1067 0.90
340 11 0.01
341 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (339 bp):
AAAAGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTGGAA
ATGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGCTGATCCATCAAGT
GATGAATTCGAGCA
Found at i:2547794 original size:35 final size:35
Alignment explanation
Indices: 2547734--2547800 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2547724 TCTTGTTGAG
2547734 ATGAGCCTCCAAGAATGCCCAAATATTCATATTGTT
1 ATGAGCCTCCAAGAATGCCCAAATATTC-TATTGTT
* *
2547770 ATGAGCCTTCAA-AATGCCCCAATATTCTATT
1 ATGAGCCTCCAAGAATGCCCAAATATTCTATT
2547801 TTTGGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 11 0.38
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (35 bp):
ATGAGCCTCCAAGAATGCCCAAATATTCTATTGTT
Found at i:2551043 original size:14 final size:13
Alignment explanation
Indices: 2551013--2551083 Score: 54
Period size: 14 Copynumber: 5.2 Consensus size: 13
2551003 ATTTCTCCCC
*
2551013 TTTTTCTTTTTC-
1 TTTTTTTTTTTCT
*
2551025 CTTTTTTTTTTCAT
1 TTTTTTTTTTTC-T
*
2551039 TTTTTCATTTTATCT
1 TTTTT--TTTTTTCT
*
2551054 TTTTCTTTCTTTCT
1 TTTT-TTTTTTTCT
2551068 TTTTTTTTCTTTCT
1 TTTTTTTT-TTTCT
2551082 TT
1 TT
2551084 GCTGGATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 10 0.22
13 3 0.07
14 21 0.46
15 5 0.11
16 7 0.15
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:2554771 original size:14 final size:14
Alignment explanation
Indices: 2554752--2554787 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2554742 AAGATGCCAG
2554752 ATGTAAATATGCAA
1 ATGTAAATATGCAA
* *
2554766 ATGTAAAAATGTAA
1 ATGTAAATATGCAA
2554780 ATGTAAAT
1 ATGTAAAT
2554788 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (14 bp):
ATGTAAATATGCAA
Found at i:2556440 original size:28 final size:26
Alignment explanation
Indices: 2556385--2556442 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
2556375 AAACATTAAT
*
2556385 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
2556411 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
2556439 AAAA
1 AAAA
2556443 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:2556917 original size:45 final size:48
Alignment explanation
Indices: 2556867--2556956 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
2556857 AATTGTCTCT
*
2556867 TATTA-TTAGAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATCC
1 TATTATTTA-AAATTATAATAATGAAAAATATATATTAATTTATAATCC
*
2556912 TATTATTTTAAAATTATAATTATGAAAAATATATATTAATTTATA
1 TATTA-TTTAAAATTATAATAATGAAAAATATATATTAATTTATA
2556957 TATTTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 5 0.13
46 6 0.16
47 5 0.13
48 12 0.32
49 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (48 bp):
TATTATTTAAAATTATAATAATGAAAAATATATATTAATTTATAATCC
Found at i:2556958 original size:29 final size:29
Alignment explanation
Indices: 2556926--2556983 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2556916 ATTTTAAAAT
*
2556926 TATAATTATGAAAAATATATATTAATTTA
1 TATAATTATAAAAAATATATATTAATTTA
* * *
2556955 TATATTTATAAAAAATATTTATTTATTTA
1 TATAATTATAAAAAATATATATTAATTTA
2556984 GAAATATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATAATTATAAAAAATATATATTAATTTA
Found at i:2558693 original size:3 final size:3
Alignment explanation
Indices: 2558685--2558755 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
2558675 GGCCTGTTTG
* * *
2558685 TAA TAA TAA TAA TTA T-T TAT TTAA TAA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
2558728 TAA TAT TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2558756 ATAAAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 9 0.16
3 46 0.81
4 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2558729 original size:13 final size:14
Alignment explanation
Indices: 2558706--2558759 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
2558696 ATTATTTATT
2558706 TAATAATAATAATA
1 TAATAATAATAATA
2558720 TAAT-ATAATAATA
1 TAATAATAATAATA
* *
2558733 T--TAA-AACAAAA
1 TAATAATAATAATA
2558744 TAATAATAATAA-A
1 TAATAATAATAATA
2558757 TAA
1 TAA
2558760 AAAAATGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.21
12 1 0.03
13 17 0.52
14 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:2558729 original size:16 final size:16
Alignment explanation
Indices: 2558708--2558752 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2558698 TATTTATTTA
* *
2558708 ATAATAATAATATAAT
1 ATAATAATAATAAAAC
*
2558724 ATAATAATATTAAAAC
1 ATAATAATAATAAAAC
*
2558740 AAAATAATAATAA
1 ATAATAATAATAA
2558753 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATAATAATAAAAC
Found at i:2558762 original size:19 final size:20
Alignment explanation
Indices: 2558706--2558762 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
2558696 ATTATTTATT
* *
2558706 TAATAATAAT-AATATAATA
1 TAATAATAATAAATACAAAA
*
2558725 TAATAATATTAAA-ACAAAA
1 TAATAATAATAAATACAAAA
2558744 TAATAATAATAAATA-AAAA
1 TAATAATAATAAATACAAAA
2558763 AATGAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 29 0.91
20 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATAATAATAAATACAAAA
Found at i:2560213 original size:5 final size:5
Alignment explanation
Indices: 2560192--2560230 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
2560182 CTAAGAAAGC
2560192 TAAAA TTAAAA TAAAAA TAAAAA TAAAA TAAAA TAAAA T
1 TAAAA -TAAAA T-AAAA T-AAAA TAAAA TAAAA TAAAA T
2560231 CTTAATTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 16 0.50
6 16 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:2568611 original size:45 final size:44
Alignment explanation
Indices: 2568586--2569221 Score: 691
Period size: 45 Copynumber: 14.1 Consensus size: 44
2568576 TATTATTTTT
* * *
2568586 ATTTATGGCATCCTTTCATGCCTTTAATGCACAATTGTGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* *
2568631 ATTTATGGCATCCTTTAATGCCTTTAATGCATCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* *
2568676 ATTTACGACATCCTTTCATGCCTTTAATGCA-ACGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATA-GTTAT-CATTTC
* * * * *
2568721 ATTTATGACATCATTTCATGCCTTTAATGTATCGTTATGAATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* * **
2568766 ATTTATGGCATCATTTCATGCCTTTAATACACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
*
2568811 ATTTATGGCATCCTTTCATGACTTTAATGCACT-GTTATACATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCA-TAGTTAT-CATTTC
* * * * *
2568856 ATTTATGGCATCTTTTCATGCCTTTAATGTACAATTGTGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
*
2568901 ATTTATGGCATCCTTTCATGCCTTTAATGCATCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* **
2568946 ATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* * **
2568991 ATTTATGACATCCTTTCATGCCTTCAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* * **
2569036 ATTTATGGCATCATTTCATGCCTTTAATACACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* ** *
2569081 ATTTATGGCATCCTTTCATGACTTTAATGCACCGCTATACATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* * * **
2569126 ATTTATGGCTTTCTTTTATGCCTTTAATGCACCGTTATACATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
* * **
2569171 ATTTATGACATCCTTTAATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTAT-CATTTC
2569216 ATTTAT
1 ATTTAT
2569222 CTAATGAAAA
Statistics
Matches: 528, Mismatches: 59, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
45 528 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (44 bp):
ATTTATGGCATCCTTTCATGCCTTTAATGCATAGTTATCATTTC
Found at i:2568717 original size:90 final size:90
Alignment explanation
Indices: 2568586--2569221 Score: 930
Period size: 90 Copynumber: 7.1 Consensus size: 90
2568576 TATTATTTTT
** * *
2568586 ATTTATGGCATCCTTTCATGCCTTTAATGCACAATTGTGCATTTCATTTATGGCATCCTTTAATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
*
2568651 CCTTTAATGCATCGTTATGCATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* * * * *
2568676 ATTTACGACATCCTTTCATGCCTTTAATGCAACGTTATGCATTTCATTTATGACATCATTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
* * *
2568741 CCTTTAATGTATCGTTATGAATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* *
2568766 ATTTATGGCATCATTTCATGCCTTTAATACACCGTTATGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
* * *
2568831 ACTTTAATGCACTGTTATACATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* * ** *
2568856 ATTTATGGCATCTTTTCATGCCTTTAATGTACAATTGTGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
*
2568921 CCTTTAATGCATCGTTATGCATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* *
2568946 ATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
*
2569011 CCTTCAATGCACCGTTATGCATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* *
2569036 ATTTATGGCATCATTTCATGCCTTTAATACACCGTTATGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
* * *
2569101 ACTTTAATGCACCGCTATACATTTC
66 CCTTTAATGCACCGTTATGCATTTC
* * * * * *
2569126 ATTTATGGCTTTCTTTTATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCCTTTAATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
2569191 CCTTTAATGCACCGTTATGCATTTC
66 CCTTTAATGCACCGTTATGCATTTC
2569216 ATTTAT
1 ATTTAT
2569222 CTAATGAAAA
Statistics
Matches: 484, Mismatches: 62, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 484 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (90 bp):
ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG
CCTTTAATGCACCGTTATGCATTTC
Found at i:2568804 original size:135 final size:134
Alignment explanation
Indices: 2568586--2569221 Score: 896
Period size: 135 Copynumber: 4.7 Consensus size: 134
2568576 TATTATTTTT
* * *
2568586 ATTTATGGCATCCTTTCATGCCTTTAATGCACAATTGTGCATTTCATTTATGGCATCCTTTAATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCAC-GTTATGCATTTCATTTATGGCATCCTTTCATG
* * * *
2568651 CCTTTAATGCATCGTTATGCATTTCATTTACGACATCCTTTCATGCCTTTAATGCAACGTTATGC
65 CCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGACTTTAATGCAACGTTATAC
2568716 ATTTC
130 ATTTC
* * * * *
2568721 ATTTATGACATCATTTCATGCCTTTAATGTATCGTTATGAATTTCATTTATGGCATCATTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTATGGCATCCTTTCATG
* *
2568786 CCTTTAATACACCGTTATGCATTTCATTTATGGCATCCTTTCATGACTTTAATGC-ACTGTTATA
65 CCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGACTTTAATGCAAC-GTTATA
2568850 CATTTC
129 CATTTC
* * * *
2568856 ATTTATGGCATCTTTTCATGCCTTTAATGTACAATTGTGCATTTCATTTATGGCATCCTTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCAC-GTTATGCATTTCATTTATGGCATCCTTTCATG
* * * *
2568921 CCTTTAATGCATCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
65 CCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGACTTTAATGCAACGTTATAC
2568986 ATTTC
130 ATTTC
* * *
2568991 ATTTATGACATCCTTTCATGCCTTCAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTATGGCATCCTTTCATG
* * * *
2569056 CCTTTAATACACCGTTATGCATTTCATTTATGGCATCCTTTCATGACTTTAATGCACCGCTATAC
65 CCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGACTTTAATGCAACGTTATAC
2569121 ATTTC
130 ATTTC
* * * * * *
2569126 ATTTATGGCTTTCTTTTATGCCTTTAATGCACCGTTATACATTTCATTTATGACATCCTTTAATG
1 ATTTATGGCATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTATGGCATCCTTTCATG
2569191 CCTTTAATGCACCGTTATGCATTTCATTTAT
65 CCTTTAATGCACCGTTATGCATTTCATTTAT
2569222 CTAATGAAAA
Statistics
Matches: 447, Mismatches: 49, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
134 3 0.01
135 441 0.99
136 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (134 bp):
ATTTATGGCATCCTTTCATGCCTTTAATGCACGTTATGCATTTCATTTATGGCATCCTTTCATGC
CTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGACTTTAATGCAACGTTATACA
TTTC
Found at i:2569667 original size:20 final size:20
Alignment explanation
Indices: 2569642--2569690 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2569632 TCATGGTATT
2569642 GATACTTTTCTCTTAATATC
1 GATACTTTTCTCTTAATATC
* *
2569662 GATACTTTTCTCTTAGTATT
1 GATACTTTTCTCTTAATATC
2569682 GATACTTTT
1 GATACTTTT
2569691 ATACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.53
Consensus pattern (20 bp):
GATACTTTTCTCTTAATATC
Found at i:2580356 original size:5 final size:5
Alignment explanation
Indices: 2580346--2580424 Score: 65
Period size: 5 Copynumber: 15.8 Consensus size: 5
2580336 TCTGATCTAT
** *
2580346 TTTTA TTTTA TTTTA TTACA TTTT- TATTTA TTTTTA TTTTA TTCTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA -TTTTA TTTTA TTTTA TTTTA
* *
2580396 TTTTA TTTGGA -TTAA TTTTA TTTTA TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTT
2580425 CTCTGAAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
4 5 0.08
5 48 0.81
6 5 0.08
7 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:2583320 original size:17 final size:17
Alignment explanation
Indices: 2583295--2583328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2583285 CTTTATCCCA
*
2583295 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
2583312 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
2583329 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:2583727 original size:22 final size:23
Alignment explanation
Indices: 2583699--2583753 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
2583689 CTCAAAATCT
2583699 AAAGAAAATTGCTC-AAAATTGA
1 AAAGAAAATTGCTCAAAAATTGA
*
2583721 AAAGAAAATTGTTCAAAAATTGA
1 AAAGAAAATTGCTCAAAAATTGA
2583744 AAAGAAAATT
1 AAAGAAAATT
2583754 TCTCTTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (23 bp):
AAAGAAAATTGCTCAAAAATTGA
Found at i:2587536 original size:23 final size:23
Alignment explanation
Indices: 2587477--2587545 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
2587467 CACCAAAGTG
* * *
2587477 CCACATAGATTTTTCCCGAAAGA
1 CCACATAGATTTGTCCTGAATGA
* * * *
2587500 CCGCGTACAATTGTCCTGAATGA
1 CCACATAGATTTGTCCTGAATGA
2587523 CCACATAGATTTGT-CTCGAATGA
1 CCACATAGATTTGTCCT-GAATGA
2587546 TCGCGTAGAA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (23 bp):
CCACATAGATTTGTCCTGAATGA
Found at i:2588752 original size:13 final size:13
Alignment explanation
Indices: 2588727--2588764 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2588717 GTCATAAATC
2588727 TATGACA-ACATT
1 TATGACACACATT
2588739 TATGACACACATT
1 TATGACACACATT
*
2588752 TATGACGCACATT
1 TATGACACACATT
2588765 AATGGCGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (13 bp):
TATGACACACATT
Found at i:2588880 original size:85 final size:84
Alignment explanation
Indices: 2588782--2588949 Score: 223
Period size: 85 Copynumber: 2.0 Consensus size: 84
2588772 TTCATTAAGT
* *
2588782 GTCATTAAAGCCCCCGTCATAAAT-TAAGAC-GACACATATTTGTGCGTCATAAATTTATGACAC
1 GTCATTAAAGCCCCCATCATAAATCT--G-CTGACACACATTTGTGCGTCATAAATTTATGACAC
*
2588845 GCATGTATGACTTACATTGCAC
63 CCATGTATGACTTACATTGCAC
* * * *
2588867 GTCATTGAAGCCCCCATCATAAATCTGCTTGATATACATTTGTGTGTCATAAATTTATGACACCC
1 GTCATTAAAGCCCCCATCATAAATCTGC-TGACACACATTTGTGCGTCATAAATTTATGACACCC
2588932 ATGTATGACTTACATTGC
65 ATGTATGACTTACATTGC
2588950 GTGTCTTGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
83 1 0.01
84 1 0.01
85 70 0.96
86 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (84 bp):
GTCATTAAAGCCCCCATCATAAATCTGCTGACACACATTTGTGCGTCATAAATTTATGACACCCA
TGTATGACTTACATTGCAC
Found at i:2589025 original size:2 final size:2
Alignment explanation
Indices: 2589018--2589088 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
2589008 TTTCGTAAAT
*
2589018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA 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
*
2589060 TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2589089 TGTAGATTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2595315 original size:15 final size:15
Alignment explanation
Indices: 2595295--2595345 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
2595285 TTTTTTTCTC
2595295 CTTCTTTGACGTTTT
1 CTTCTTTGACGTTTT
**
2595310 CTTCTTTGGTGTTTT
1 CTTCTTTGACGTTTT
* *
2595325 CTTCTTAGACGTTAT
1 CTTCTTTGACGTTTT
2595340 CTTCTT
1 CTTCTT
2595346 ACCCCCATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.20, G:0.14, T:0.59
Consensus pattern (15 bp):
CTTCTTTGACGTTTT
Found at i:2599448 original size:54 final size:54
Alignment explanation
Indices: 2599212--2599448 Score: 316
Period size: 54 Copynumber: 4.4 Consensus size: 54
2599202 GATATGTAAG
* * *
2599212 TCACAAACTCATTATGAATTCCATGGGTTGCACACATAGTG-CTTATACGATAAT
1 TCACAAACTTATTATGAATTTCATGGGTTGCACACATAGTGTC-GATACGATAAT
* *
2599266 TCACAAA-TTAATTATGAATTCCATGGGTTGCACACATAGTGTCGATACGGTAAT
1 TCACAAACTT-ATTATGAATTTCATGGGTTGCACACATAGTGTCGATACGATAAT
** *
2599320 TCATGAACTTATTATGAATTTCATGGGTTGCACACATAGTGTCGATACGGTAAT
1 TCACAAACTTATTATGAATTTCATGGGTTGCACACATAGTGTCGATACGATAAT
** * * * *
2599374 TCACAAACTCGTTATGAATTTCGTGGGTTGTACACATAGTATCGATATGATAAT
1 TCACAAACTTATTATGAATTTCATGGGTTGCACACATAGTGTCGATACGATAAT
2599428 TCACAAACTTATTATGAATTT
1 TCACAAACTTATTATGAATTT
2599449 TGTGATGATA
Statistics
Matches: 163, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 159 0.98
55 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (54 bp):
TCACAAACTTATTATGAATTTCATGGGTTGCACACATAGTGTCGATACGATAAT
Found at i:2600412 original size:20 final size:21
Alignment explanation
Indices: 2600369--2600412 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2600359 AAACTAACTT
** *
2600369 ACATCCACAAATCTCCTTATA
1 ACATCCACAAATCTCCAAAGA
2600390 ACATCCA-AAATCTCCAAAGA
1 ACATCCACAAATCTCCAAAGA
2600410 ACA
1 ACA
2600413 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.20
Consensus pattern (21 bp):
ACATCCACAAATCTCCAAAGA
Found at i:2606455 original size:54 final size:54
Alignment explanation
Indices: 2606373--2606649 Score: 328
Period size: 54 Copynumber: 5.2 Consensus size: 54
2606363 ATTATATCTA
* * * * *
2606373 AGTGTCGATATGGAAAGTCACAAACTCATTATGAATTCCATAGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* * *
2606427 AGTGTTGATACGGTAATTCACAAACTCATTATGAATT-TGTTGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* * * * ** *
2606480 AGTGTCGATATGATAATTCAAAAACTTATTATGAATTATGTGGGTTACACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
*
2606534 AGTGTCGATACGGTAATTCACAAACACATTATGAATTCCGTGGGTTGCACACAT
1 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
* * * *
2606588 ATTG-CTGAT--GGTAATTCACAAACTTATTATGAATTTCGTGGGTTGCACACCT
1 AGTGTC-GATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
*
2606640 AGTGCCGATA
1 AGTGTCGATA
2606650 GTACACATAG
Statistics
Matches: 191, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
52 45 0.24
53 47 0.25
54 99 0.52
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
Found at i:2606564 original size:107 final size:107
Alignment explanation
Indices: 2606373--2606649 Score: 339
Period size: 107 Copynumber: 2.6 Consensus size: 107
2606363 ATTATATCTA
* * ** * *
2606373 AGTGTCGATATGGA-AAGTCACAAACTCATTATGAATTCCATAGGTTGCACACATAGTGTTGATA
1 AGTGTCGATAT-GATAATTCACAAACTTATTATGAATT-TGTGGGTTGCACACATAGTGTCGATA
* * *
2606437 CGGTAATTCACAAACTCATTATGAATT-TGTTGGTTGCACACAT
64 CGGTAATTCACAAACACATTATGAATTCCGTGGGTTGCACACAT
* *
2606480 AGTGTCGATATGATAATTCAAAAACTTATTATGAATTATGTGGGTTACACACATAGTGTCGATAC
1 AGTGTCGATATGATAATTCACAAACTTATTATGAATT-TGTGGGTTGCACACATAGTGTCGATAC
2606545 GGTAATTCACAAACACATTATGAATTCCGTGGGTTGCACACAT
65 GGTAATTCACAAACACATTATGAATTCCGTGGGTTGCACACAT
* * * *
2606588 A-T-T-GCTGATGGTAATTCACAAACTTATTATGAATTTCGTGGGTTGCACACCTAGTGCCGATA
1 AGTGTCGAT-ATGATAATTCACAAACTTATTATGAATTT-GTGGGTTGCACACATAGTGTCGATA
2606650 GTACACATAG
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
105 3 0.02
106 51 0.34
107 79 0.53
108 15 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (107 bp):
AGTGTCGATATGATAATTCACAAACTTATTATGAATTTGTGGGTTGCACACATAGTGTCGATACG
GTAATTCACAAACACATTATGAATTCCGTGGGTTGCACACAT
Found at i:2613370 original size:38 final size:37
Alignment explanation
Indices: 2613232--2613570 Score: 339
Period size: 37 Copynumber: 8.9 Consensus size: 37
2613222 AATAATATAG
* * ** *
2613232 TATAGTTTTTGAAAATATTTTCGAAAA-ACGTATAACA
1 TATAG-TTTTGAAAACATTTTTGAAAATATATATAATA
* *
2613269 TATAGTTTTAAGAAACCATTTTTTGAAAACATATATAATA
1 TATAGTTTT--GAAAACA-TTTTTGAAAATATATATAATA
*
2613309 TATAGTTTTGAAAACATTCTTGAAAATATATATAATA
1 TATAGTTTTGAAAACATTTTTGAAAATATATATAATA
*
2613346 TATAGTTTTTAAAAACATTTTTGAAAATATATATAATA
1 TATAG-TTTTGAAAACATTTTTGAAAATATATATAATA
2613384 TATAGTTTTGAAAACATTTTTGAAAATATATATAATA
1 TATAGTTTTGAAAACATTTTTGAAAATATATATAATA
* * *
2613421 TATAGTTTTTTAAAACCTTTTAGAAAATATATATTGTATATAATA
1 TATAG-TTTTGAAAACATTTTTG--AA-A-ATA---TATATAATA
* *
2613466 TATAGTTTTTGAAAACCTTTTTGAAAATACATAT--TA
1 TATAG-TTTTGAAAACATTTTTGAAAATATATATAATA
*
2613502 TATAGTTTTGGAAACAATTTTTGAAAATATATAT--TA
1 TATAGTTTTGAAAAC-ATTTTTGAAAATATATATAATA
* **
2613538 TATAG-TTTGAAAATAAATTTGAAAATATATATA
1 TATAGTTTTGAAAACATTTTTGAAAATATATATA
2613571 TAGTTTTGAA
Statistics
Matches: 262, Mismatches: 25, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
34 16 0.06
35 16 0.06
36 34 0.13
37 65 0.25
38 64 0.24
39 9 0.03
40 18 0.07
41 4 0.02
42 4 0.02
43 2 0.01
45 30 0.11
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (37 bp):
TATAGTTTTGAAAACATTTTTGAAAATATATATAATA
Found at i:2613378 original size:75 final size:73
Alignment explanation
Indices: 2613232--2613570 Score: 330
Period size: 75 Copynumber: 4.5 Consensus size: 73
2613222 AATAATATAG
* ** *
2613232 TATAGTTTTTGAAAATATTTTCGAAAA-ACGTATAACATATAGTTTTAAGAAACCATTTTTTGAA
1 TATAG-TTTTGAAAACATTTT-GAAAATATATATAATATATAGTTTTAA-AAA-CA-TTTTTGAA
*
2613296 AACATATATAATA
61 AATATATATAATA
2613309 TATAGTTTTGAAAACATTCTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTTGAAAAT
1 TATAGTTTTGAAAACATT-TTGAAAATATATATAATATATAG-TTTTAAAAACATTTTTGAAAAT
2613374 ATATATAATA
64 ATATATAATA
* * *
2613384 TATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTTTAAAACCTTTTAGAAAAT
1 TATAGTTTTGAAAACA-TTTTGAAAATATATATAATATATAG-TTTTAAAAACATTTTTG--AA-
2613449 ATATATTGTATATAATA
61 A-ATA---TATATAATA
* * **
2613466 TATAGTTTTTGAAAACCTTTTTGAAAATACATAT--TATATAGTTTTGGAAACAATTTTTGAAAA
1 TATAG-TTTTGAAAA-CATTTTGAAAATATATATAATATATAGTTTTAAAAAC-ATTTTTGAAAA
2613529 TATATAT--TA
63 TATATATAATA
* *
2613538 TATAG-TTTGAAAATAAATTTGAAAATATATATA
1 TATAGTTTTGAAAA-CATTTTGAAAATATATATA
2613571 TAGTTTTGAA
Statistics
Matches: 228, Mismatches: 19, Indels: 36
0.81 0.07 0.13
Matches are distributed among these distances:
70 22 0.10
72 7 0.03
74 5 0.02
75 74 0.32
76 21 0.09
77 27 0.12
78 8 0.04
79 5 0.02
80 8 0.04
81 12 0.05
82 14 0.06
83 24 0.11
84 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (73 bp):
TATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTTGAAAATAT
ATATAATA
Found at i:2613464 original size:45 final size:45
Alignment explanation
Indices: 2613410--2613505 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
2613400 TTTTTGAAAA
* *
2613410 TATATATAATATATAGTTTTTTAAAACCTTTTAGAAAATATATAT
1 TATATATAATATATAGTTTTTGAAAACCTTTTAGAAAATACATAT
* *
2613455 TGTATATAATATATAGTTTTTGAAAACCTTTTTGAAAATACATAT
1 TATATATAATATATAGTTTTTGAAAACCTTTTAGAAAATACATAT
2613500 TATATA
1 TATATA
2613506 GTTTTGGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (45 bp):
TATATATAATATATAGTTTTTGAAAACCTTTTAGAAAATACATAT
Found at i:2613534 original size:83 final size:81
Alignment explanation
Indices: 2613375--2613541 Score: 230
Period size: 81 Copynumber: 2.0 Consensus size: 81
2613365 TTTGAAAATA
* ** *
2613375 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTTTAAAACCTT
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATACATAT-ATATATAGTTTTGGAAAAACTT
2613440 TTAGAAAATATATATTG
65 TTAGAAAATATATATTG
*
2613457 TATATAATATATAGTTTTTGAAAACCTTTTTGAAAATACATAT-TATATAGTTTTGGAAACAA-T
1 TATATAATATATAG-TTTTGAAAACATTTTTGAAAATACATATATATATAGTTTTGGAAA-AACT
* *
2613520 TTTTGAAAATATATATTA
64 TTTAGAAAATATATATTG
2613538 TATA
1 TATA
2613542 GTTTGAAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 35 0.46
82 15 0.20
83 26 0.34
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (81 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATACATATATATATAGTTTTGGAAAAACTTT
TAGAAAATATATATTG
Found at i:2613571 original size:36 final size:36
Alignment explanation
Indices: 2613457--2613597 Score: 141
Period size: 36 Copynumber: 4.0 Consensus size: 36
2613447 ATATATATTG
* * *
2613457 TATATAATATATAGTTTTTGAAAAC-CTTTTTGAAAA
1 TATATATTATATAG-TTTTGAAAACAATATTTGAAAA
* * *
2613493 TACATATTATATAGTTTTGGAAACAATTTTTGAAAA
1 TATATATTATATAGTTTTGAAAACAATATTTGAAAA
*
2613529 TATATATTATATAG-TTTGAAAATAA-ATTTG-AAA
1 TATATATTATATAGTTTTGAAAACAATATTTGAAAA
*
2613562 -ATATA-TATATAGTTTTGAAAAAAAAATATTTGAAAA
1 TATATATTATATAGTTTTG--AAAACAATATTTGAAAA
2613598 CATTTTGAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
31 7 0.08
32 9 0.10
33 3 0.03
34 10 0.11
35 23 0.26
36 38 0.42
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (36 bp):
TATATATTATATAGTTTTGAAAACAATATTTGAAAA
Found at i:2613633 original size:36 final size:37
Alignment explanation
Indices: 2613589--2613661 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
2613579 AAAAAAAAAT
*
2613589 ATTTGAAAACATTTTGAAA-ATATATATA-ATATATA
1 ATTTGAAAACATTTTCAAATATATATATATATATATA
2613624 ATTTAGAAAACATTTTCAAATATATATATATATATATA
1 ATTT-GAAAACATTTTCAAATATATATATATATATATA
2613662 TAATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 4 0.12
36 14 0.41
37 9 0.26
38 7 0.21
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (37 bp):
ATTTGAAAACATTTTCAAATATATATATATATATATA
Found at i:2613639 original size:117 final size:117
Alignment explanation
Indices: 2613239--2613659 Score: 325
Period size: 115 Copynumber: 3.6 Consensus size: 117
2613229 TAGTATAGTT
* ** * * *
2613239 TTTGAAAATATTTTCGAAAA-ACGTATAACATATAGTTTTAAGAAACCATTTTTTGAAAACATAT
1 TTTGAAAACATTTT-GAAAATATATATAATATATAGTTTT--GAAAACA-TTTTTGAAAATATAT
* * * * * *
2613303 ATAATATATAGTTTTG-AAAACATTCTTGAAAATATATA---TA-AT---ATATAGTT
62 AT-ATATATAGTTTTGAAAAAAATT-TAGAAAATATATATTGTATATAAAAAAAAATA
*
2613353 TTTAAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATA
1 TTTGAAAACA-TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATAT-
* *** * * * * *
2613418 ATATATAGTTTTTTAAAACCTTTTAGAAAATATATATTGTATATAATATATAGTT
64 ATATATAG-TTTTGAAAAAAATTTAGAAAATATATATTGTATATAAAAAAAAATA
* * *
2613473 TTTGAAAACCTTTTTGAAAATACATAT--TATATAGTTTTGGAAACAATTTTTGAAAATATATAT
1 TTTGAAAA-CATTTTGAAAATATATATAATATATAGTTTTGAAAAC-ATTTTTGAAAATATATAT
*
2613536 -TATATAG-TTTGAAAATAAATTT-GAAAATATATATATAGT-TTTGAAAAAAAAATA
64 ATATATAGTTTTGAAAA-AAATTTAGAAAATATATAT-T-GTATAT-AAAAAAAAATA
* * *
2613590 TTTGAAAACATTTTGAAAATATATATAATATATAATTTAGAAAACA-TTTTCAAATATATATATA
1 TTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAA-ATATATATA
2613654 TATATA
65 TATATA
2613660 TATAATATGA
Statistics
Matches: 255, Mismatches: 31, Indels: 38
0.79 0.10 0.12
Matches are distributed among these distances:
112 25 0.10
113 22 0.09
114 19 0.07
115 39 0.15
116 31 0.12
117 34 0.13
118 36 0.14
119 18 0.07
120 30 0.12
121 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (117 bp):
TTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAT
ATATAGTTTTGAAAAAAATTTAGAAAATATATATTGTATATAAAAAAAAATA
Found at i:2613724 original size:4 final size:4
Alignment explanation
Indices: 2613715--2613746 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2613705 TCATTTACAT
2613715 TTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2613747 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 22 0.85
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2613753 original size:14 final size:14
Alignment explanation
Indices: 2613715--2613746 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2613705 TCATTTACAT
2613715 TTTATTTA--TTTA
1 TTTATTTATTTTTA
2613727 TTTATTTATTTTTA
1 TTTATTTATTTTTA
2613741 TTTATT
1 TTTATT
2613747 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
14 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:2613756 original size:18 final size:18
Alignment explanation
Indices: 2613714--2613756 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2613704 TTCATTTACA
*
2613714 TTTTATTTATTTATTTAT
1 TTTTTTTTATTTATTTAT
* *
2613732 TTATTTTTATTTA-TTCT
1 TTTTTTTTATTTATTTAT
2613749 TTTTTTTT
1 TTTTTTTT
2613757 CTTTTTTAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTTATTTATTTAT
Found at i:2613960 original size:15 final size:15
Alignment explanation
Indices: 2613942--2613971 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2613932 TATTTATTTC
2613942 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2613957 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2613972 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:2615896 original size:18 final size:18
Alignment explanation
Indices: 2615873--2615912 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2615863 TTCCTTCAAG
2615873 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
2615891 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
2615909 TCTG
1 TCTG
2615913 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:2616440 original size:8 final size:8
Alignment explanation
Indices: 2616427--2616465 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2616417 GAACATTTCA
*
2616427 TGCATTCT
1 TGCATTTT
2616435 TGCA-TTT
1 TGCATTTT
2616442 TGCATTTT
1 TGCATTTT
*
2616450 TGCCTTTT
1 TGCATTTT
2616458 TGCATTTT
1 TGCATTTT
2616466 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:2617596 original size:9 final size:8
Alignment explanation
Indices: 2617582--2617633 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
2617572 AAAAAAGGCA
2617582 AAAAAAAG
1 AAAAAAAG
*
2617590 AAGAAAA-
1 AAAAAAAG
2617597 AAAAAAAG
1 AAAAAAAG
*
2617605 CAAAAAAG
1 AAAAAAAG
2617613 AACAAAAAG
1 AA-AAAAAG
2617622 -AAAAAAG
1 AAAAAAAG
2617629 AAAAA
1 AAAAA
2617634 GGGACAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 12 0.32
8 19 0.51
9 6 0.16
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2617599 original size:24 final size:25
Alignment explanation
Indices: 2617567--2617628 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2617557 AGATTCAATC
* *
2617567 AGAATAAAAAAGGCAAAAAA-AAGA
1 AGAAAAAAAAAGGCAAAAAAGAACA
*
2617591 AGAAAAAAAAAAAGCAAAAAAGAACA
1 AG-AAAAAAAAAGGCAAAAAAGAACA
2617617 A-AAAGAAAAAAG
1 AGAAA-AAAAAAG
2617629 AAAAAGGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 5 0.16
25 22 0.71
26 4 0.13
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (25 bp):
AGAAAAAAAAAGGCAAAAAAGAACA
Found at i:2617602 original size:16 final size:16
Alignment explanation
Indices: 2617581--2617634 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
2617571 TAAAAAAGGC
2617581 AAAAAAAAGAAG-AAA
1 AAAAAAAAGAAGAAAA
*
2617596 AAAAAAAAGCA-AAAA
1 AAAAAAAAGAAGAAAA
* *
2617611 AGAACAAA-AAGAAAA
1 AAAAAAAAGAAGAAAA
*
2617626 AAGAAAAAG
1 AAAAAAAAG
2617635 GGACAAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAGAAAA
Found at i:2617609 original size:23 final size:23
Alignment explanation
Indices: 2617583--2617644 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2617573 AAAAAGGCAA
*
2617583 AAAAAAGAAGAAAAA-AAAAAAG
1 AAAAAAGAACAAAAAGAAAAAAG
2617605 CAAAAAAGAACAAAAAGAAAAAAG
1 -AAAAAAGAACAAAAAGAAAAAAG
* *
2617629 AAAAAGGGACAAAAAG
1 AAAAAAGAACAAAAAG
2617645 CACATGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 28 0.80
24 7 0.20
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAACAAAAAGAAAAAAG
Found at i:2619331 original size:22 final size:22
Alignment explanation
Indices: 2619300--2619368 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
2619290 AAACATTTCC
2619300 CTTGAAATAAATTTTCGTCTCT
1 CTTGAAATAAATTTTCGTCTCT
*
2619322 CTTGAGAT-AA--TT--TC-C-
1 CTTGAAATAAATTTTCGTCTCT
2619337 CTTGAAATAAATTTTCGTCTCT
1 CTTGAAATAAATTTTCGTCTCT
*
2619359 CTTGAGATAA
1 CTTGAAATAA
2619369 TTTCCCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 3 0.08
22 16 0.43
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
CTTGAAATAAATTTTCGTCTCT
Found at i:2619431 original size:36 final size:36
Alignment explanation
Indices: 2619294--2619489 Score: 302
Period size: 37 Copynumber: 5.4 Consensus size: 36
2619284 CATTGAAAAC
*
2619294 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACA
*
2619331 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACA
*
2619368 ATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACA
* *
2619405 GTTTCCCTTGAAATAAATTTTATCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
2619441 TTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
2619477 GTTTCCCTTGAAA
1 ATTTCCCTTGAAA
2619490 CAAAATATTT
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
36 67 0.45
37 76 0.51
38 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (36 bp):
ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
Found at i:2619612 original size:36 final size:36
Alignment explanation
Indices: 2619513--2619628 Score: 94
Period size: 36 Copynumber: 3.2 Consensus size: 36
2619503 TATGTTTTCT
* * **
2619513 TTGAAACAAATTTCGT-TCCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCT-CTCTTGAGACAGTTTCCC
* * *
2619549 TTGGAACTAAGTTTTTGTCTCTC--GAGACAGTTTCTC
1 TTGAAAC-AA-ATTTTGTCTCTCTTGAGACAGTTTCCC
* * *
2619585 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
2619621 TTGAAACA
1 TTGAAACA
2619629 CAAAATCTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
34 10 0.15
35 2 0.03
36 44 0.67
37 2 0.03
38 7 0.11
39 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
Found at i:2620413 original size:105 final size:105
Alignment explanation
Indices: 2620231--2620738 Score: 801
Period size: 105 Copynumber: 4.9 Consensus size: 105
2620221 AAATACTTGG
*
2620231 AGTTCAACTTCACGACGAAGGGTCCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
2620296 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
2620336 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
*
2620401 TCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
2620441 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAAACTTCCCAATCTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
2620506 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
**
2620546 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
* *
2620606 TCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * * * * * ** *
2620646 AGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAACAATTTCCCGGTTCCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
* *
2620711 TCAACTTCACGACGGAGGATATTGGACT
66 TCAACTTCACAACGAAGGATATTGGACT
2620739 TGGAACAATG
Statistics
Matches: 375, Mismatches: 23, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
100 84 0.22
101 3 0.01
102 3 0.01
103 3 0.01
104 2 0.01
105 280 0.75
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
Found at i:2621330 original size:34 final size:34
Alignment explanation
Indices: 2621283--2621374 Score: 125
Period size: 34 Copynumber: 2.7 Consensus size: 34
2621273 TTTCGTCCTA
* *
2621283 CTAGGATTGAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATA-AATTT
*
2621318 -TAGGATTCAAACTCCT-AAAATAGGATAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAATTT
2621350 GCTAGGATTCAAACTCCTAAAAATA
1 -CTAGGATTCAAACTCCTAAAAATA
2621375 ATAGAGTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.08
33 10 0.20
34 31 0.61
35 6 0.12
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (34 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAATTT
Found at i:2621714 original size:24 final size:23
Alignment explanation
Indices: 2621685--2621739 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
2621675 TTTCATGTAA
*
2621685 TATTTTTTACATTT-TATGTATTT
1 TATTTTTTAC-TTTATATATATTT
*
2621708 TCTTTTTTACTTTAGTATATATTT
1 TATTTTTTACTTTA-TATATATTT
2621732 TATTTTTT
1 TATTTTTT
2621740 TTAGATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 9 0.33
24 15 0.56
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTTTTTACTTTATATATATTT
Found at i:2621801 original size:13 final size:13
Alignment explanation
Indices: 2621783--2621807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2621773 GTTTTTAATT
2621783 TATATATATATTA
1 TATATATATATTA
2621796 TATATATATATT
1 TATATATATATT
2621808 TACTTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATATTA
Found at i:2621832 original size:29 final size:29
Alignment explanation
Indices: 2621791--2621858 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 29
2621781 TTTATATATA
*
2621791 TATTATATATATATATTTACTTTTTATTTTTT
1 TATT-TATATATATA-TTA-TTTTTACTTTTT
2621823 TATTTATATATATATTATTTTTACTTTTT
1 TATTTATATATATATTATTTTTACTTTTT
2621852 TATTTAT
1 TATTTAT
2621859 TTGTTTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 18 0.51
30 3 0.09
31 10 0.29
32 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (29 bp):
TATTTATATATATATTATTTTTACTTTTT
Found at i:2622017 original size:15 final size:15
Alignment explanation
Indices: 2621999--2622028 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2621989 TTATTATTTC
2621999 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2622014 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2622029 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:2622617 original size:70 final size:70
Alignment explanation
Indices: 2622494--2622839 Score: 247
Period size: 70 Copynumber: 4.9 Consensus size: 70
2622484 AATAATATAG
* * *
2622494 TATAGTTTTGAAAATATTTTCGAAAACGTATA-ACATATAG--TTTAAGAACCATTTTTTGAAAA
1 TATAGTTTTGAAAACATTTT-GAAAA--TATATATATATAGTTTTTAA-AAACATTTTTTGAAAA
2622556 CATATAA-A
62 CATATAATA
*
2622564 TATAGTTTTGAAAACATTCTTGAAAATATATATATATAGTTTTTAAAAACA-TTTTTGAAAATAT
1 TATAGTTTTGAAAACATT-TTGAAAATATATATATATAGTTTTTAAAAACATTTTTTGAAAACAT
2622628 ATAATA
65 ATAATA
* ****
2622634 TATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTAGAAAATAT
1 TATAGTTTTGAAAACATTTTG-AAA-ATATAT-ATATATAGTTTTTAAAAACATTTTTTGAA-A-
*
2622699 ATTGTATATAATA
61 A---CATATAATA
* * * ** *
2622712 TATAGTTTTTGAAACCTTTTTG-AAA-ATACATATATAG-TTTTGGAAACAATTTTTG--AA-A-
1 TATAG-TTTTGAAAACATTTTGAAAATATATATATATAGTTTTTAAAAACATTTTTTGAAAACAT
2622770 AT-ATA
65 ATAATA
* * *
2622775 T-TAGTTTTGAAAATAAATTTTG-AAATATAT-TATATAGTTTTGAAAAAAAATATTTTTGAAAA
1 TATAGTTTTG-AAA-ACATTTTGAAAATATATATATATAGTTTT-TAAAAACAT-TTTTTGAAAA
2622837 CAT
62 CAT
2622840 TTTGAAAAAT
Statistics
Matches: 223, Mismatches: 28, Indels: 50
0.74 0.09 0.17
Matches are distributed among these distances:
61 5 0.02
62 6 0.03
63 19 0.09
64 8 0.04
65 5 0.02
66 6 0.03
68 6 0.03
69 28 0.13
70 49 0.22
71 13 0.06
72 19 0.09
73 15 0.07
74 9 0.04
75 4 0.02
76 1 0.00
77 2 0.01
78 14 0.06
79 14 0.06
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (70 bp):
TATAGTTTTGAAAACATTTTGAAAATATATATATATAGTTTTTAAAAACATTTTTTGAAAACATA
TAATA
Found at i:2622707 original size:35 final size:34
Alignment explanation
Indices: 2622489--2622777 Score: 196
Period size: 35 Copynumber: 8.1 Consensus size: 34
2622479 TATATAATAA
* **
2622489 TATAGTATAGTTTTGAAAATATTTTCGAAAACGTAT
1 TATA-TATAGTTTTGAAAACATTTT-GAAAATATAT
* * *
2622525 AACATATAG-TTT-AAGAACCATTTTTTGAAAACATA-
1 TATATATAGTTTTGAA-AA-CA--TTTTGAAAATATAT
*
2622560 TAAATATAGTTTTGAAAACATTCTTGAAAATATA-
1 TATATATAGTTTTGAAAACATT-TTGAAAATATAT
*
2622594 TATATATAGTTTTTAAAAACATTTTTGAAAATATAT
1 TATATATAG-TTTTGAAAACA-TTTTGAAAATATAT
*
2622630 AATATATAGTTTTGAAAACATTTTGAAAATATAT
1 TATATATAGTTTTGAAAACATTTTGAAAATATAT
* *
2622664 ATAATATATAGTTTTTTAAAACATTTAGAAAATATATTGTAT
1 -T-ATATATAG-TTTTGAAAACATTTTG-AAA-ATA---TAT
* *
2622706 ATAATATATAGTTTTTGAAACCTTTTTG-AAA-ATA-
1 -T-ATATATAG-TTTTGAAAACATTTTGAAAATATAT
* *
2622740 CATATATAGTTTTGGAAACAATTTTTGAAAATATAT
1 TATATATAGTTTTGAAAAC-A-TTTTGAAAATATAT
2622776 TA
1 TA
2622778 GTTTTGAAAA
Statistics
Matches: 207, Mismatches: 23, Indels: 46
0.75 0.08 0.17
Matches are distributed among these distances:
31 8 0.04
32 8 0.04
33 9 0.04
34 40 0.19
35 51 0.25
36 34 0.16
37 20 0.10
38 4 0.02
39 4 0.02
40 2 0.01
42 27 0.13
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (34 bp):
TATATATAGTTTTGAAAACATTTTGAAAATATAT
Found at i:2622745 original size:32 final size:31
Alignment explanation
Indices: 2622709--2622819 Score: 113
Period size: 32 Copynumber: 3.5 Consensus size: 31
2622699 ATTGTATATA
*
2622709 ATATATAGTTTTTGAAAC-CTTTTTGAAAAT
1 ATATATAGTTTTTGAAACAATTTTTGAAAAT
*
2622739 ACATATATAGTTTTGGAAACAATTTTTGAAAAT
1 --ATATATAGTTTTTGAAACAATTTTTGAAAAT
* *
2622772 ATAT-TAG-TTTTGAAAATAAATTTTGAAATAT
1 ATATATAGTTTTTG-AAACAATTTTTGAAA-AT
2622803 ATTATATAG-TTTTGAAA
1 A-TATATAGTTTTTGAAA
2622820 AAAAATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.06
30 16 0.23
31 7 0.10
32 23 0.33
33 19 0.28
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (31 bp):
ATATATAGTTTTTGAAACAATTTTTGAAAAT
Found at i:2622784 original size:17 final size:17
Alignment explanation
Indices: 2622762--2622820 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
2622752 TGGAAACAAT
2622762 TTTTGAAAATATATTAG
1 TTTTGAAAATATATTAG
2622779 TTTTGAAAATA-A--A-
1 TTTTGAAAATATATTAG
2622792 TTTTGAAATATATTATATAG
1 TTTTGAAA-ATA-TAT-TAG
2622812 TTTTGAAAA
1 TTTTGAAAA
2622821 AAAATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 8 0.23
14 4 0.11
16 2 0.06
17 11 0.31
19 2 0.06
20 8 0.23
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTTGAAAATATATTAG
Found at i:2622818 original size:33 final size:31
Alignment explanation
Indices: 2622729--2622825 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 31
2622719 TTTGAAACCT
* * *
2622729 TTTTGAAAATACATATATAGTTTTGGAAACAAT
1 TTTTGAAAAT--ATATATAGTTTTGAAAAAAAA
*
2622762 TTTTGAAAATATAT-TAGTTTTGAAAATAAA
1 TTTTGAAAATATATATAGTTTTGAAAAAAAA
2622792 TTTTGAAATATATTATATAGTTTTGAAAAAAAA
1 TTTTGAAA-ATA-TATATAGTTTTGAAAAAAAA
2622825 T
1 T
2622826 ATTTTTGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 21 0.37
31 7 0.12
32 3 0.05
33 26 0.46
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTTGAAAATATATATAGTTTTGAAAAAAAA
Found at i:2624212 original size:20 final size:20
Alignment explanation
Indices: 2624168--2624454 Score: 200
Period size: 20 Copynumber: 14.2 Consensus size: 20
2624158 AATGACCAAC
* **
2624168 AAAATCACAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
*
2624187 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2624207 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2624227 -AAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2624246 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2624267 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2624288 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
2624309 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
2624330 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2624352 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2624372 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
2624390 GAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2624412 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* *
2624430 AAAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2624450 AAAAT
1 AAAAT
2624455 GAGTAAATTC
Statistics
Matches: 220, Mismatches: 29, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.00
18 6 0.03
19 29 0.13
20 139 0.63
21 13 0.06
22 32 0.15
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2624232 original size:19 final size:20
Alignment explanation
Indices: 2624205--2624257 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
2624195 AACGCGATTT
* *
2624205 AGAAAATCGCAACGTTGAAA
1 AGAAAATCGCAACGGTCAAA
2624225 AG-AAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTCAAA
2624244 AGAAAATCGCAACG
1 AGAAAATCGCAACG
2624258 CGATATTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTCAAA
Found at i:2624365 original size:40 final size:39
Alignment explanation
Indices: 2624168--2624454 Score: 234
Period size: 40 Copynumber: 7.1 Consensus size: 39
2624158 AATGACCAAC
* *
2624168 AAAATCACAACGCGATATCAA-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCAAGAATCGCAACGCGATTCAG
* *
2624207 AAAATCGCAACGTTGA--AAAGAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACG-CGATTCAAG-AATCGCAACGCGATTC---AG
* *
2624246 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATT-CAAGAATCGCAACGCGATTCAG
* *
2624288 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TT-CAAGAATCGCAACGCGATTCAG
2624330 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAAGAATCGCAACGCGATT-CAG
*
2624370 AGAATCGCAACGCGATT-AAGGAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATTCAA-G-AATCGCAACGCGATT-CAG
* *
2624410 AGAATCGCAACGCGATT-AAGAAAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAAG--AATCGCAACGCGATTCAG
2624450 AAAAT
1 AAAAT
2624455 GAGTAAATTC
Statistics
Matches: 212, Mismatches: 15, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
36 1 0.00
37 2 0.01
38 4 0.02
39 39 0.18
40 97 0.46
41 2 0.01
42 62 0.29
43 4 0.02
45 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (39 bp):
AAAATCGCAACGCGATTCAAGAATCGCAACGCGATTCAG
Found at i:2624398 original size:60 final size:60
Alignment explanation
Indices: 2624170--2624454 Score: 241
Period size: 60 Copynumber: 4.7 Consensus size: 60
2624160 TGACCAACAA
* * **
2624170 AATCACAACGCGATAT-CAA-AATCGCAACGCGATTTAGAAAATCGCAA--CG-TTGAAAAG
1 AATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CCAAG
* *** * *
2624227 AAATCGCAACG-G--TCAAAAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT-AAG
1 -AATCGCAACGCGATTC-CAAG--AATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCCA-
2624288 AG
59 AG
* *
2624290 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
*
2624352 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGGAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
* *
2624412 AATCGCAACGCGATT--AAGAAAATCGCAATGCGATTCAGAAAAT
1 AATCGCAACGCGATTCCAAG--AATCGCAACGCGATTAAGAAAAT
2624455 GAGTAAATTC
Statistics
Matches: 191, Mismatches: 17, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
54 1 0.01
56 2 0.01
57 1 0.01
58 12 0.06
59 14 0.07
60 83 0.43
61 8 0.04
62 41 0.21
63 9 0.05
64 15 0.08
66 3 0.02
67 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
Found at i:2624561 original size:6 final size:6
Alignment explanation
Indices: 2624550--2624612 Score: 84
Period size: 6 Copynumber: 11.5 Consensus size: 6
2624540 GACACGTATT
2624550 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-C-
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2624595 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
2624613 CGAGACGGCG
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.07
5 19 0.34
6 33 0.59
ACGTcount: A:0.29, C:0.56, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2625101 original size:6 final size:6
Alignment explanation
Indices: 2625090--2625140 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
2625080 GTCTCGGGTC
2625090 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2625138 GGT
1 GGT
2625141 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2625306 original size:22 final size:20
Alignment explanation
Indices: 2625236--2625373 Score: 167
Period size: 20 Copynumber: 6.8 Consensus size: 20
2625226 CTCATTTTCT
*
2625236 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2625256 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
2625277 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2625296 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
2625318 G-ATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
2625337 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
2625357 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
2625374 CTTCTTTTCA
Statistics
Matches: 104, Mismatches: 3, Indels: 20
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.07
19 15 0.14
20 41 0.39
21 4 0.04
22 37 0.36
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:2625342 original size:61 final size:62
Alignment explanation
Indices: 2625238--2625373 Score: 247
Period size: 61 Copynumber: 2.2 Consensus size: 62
2625228 CATTTTCTGA
* *
2625238 ATCGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
2625300 ATCGCGTTGCGATTCTTGG-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
2625361 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
2625374 CTTCTTTTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 54 0.75
62 18 0.25
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (62 bp):
ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:2625391 original size:42 final size:39
Alignment explanation
Indices: 2625238--2625378 Score: 108
Period size: 42 Copynumber: 3.5 Consensus size: 39
2625228 CATTTTCTGA
* * * *
2625238 ATCGCATTGCGATTCTT-GGAATCGCGTTGCGATTTTCTT-A
1 ATCGCGTTGCGA-TCTTCTGAATCACGTTGCGA--TTCTTGG
* *
2625278 ATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGG
1 ATCGCGTTGCGA-TCTTCTG-A-ATCACGTTGCGATTCTTGG
* *
2625319 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATCTTCTGAATCACGTTGCGATTCTT-G--G
2625361 ATCGCGTTGCGATCTTCT
1 ATCGCGTTGCGATCTTCT
2625379 TTTCAACGTT
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
39 17 0.19
40 28 0.31
41 14 0.16
42 30 0.34
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.37
Consensus pattern (39 bp):
ATCGCGTTGCGATCTTCTGAATCACGTTGCGATTCTTGG
Found at i:2625530 original size:12 final size:13
Alignment explanation
Indices: 2625507--2625536 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2625497 TATTATTACC
2625507 ATTTTCATTTTTT
1 ATTTTCATTTTTT
2625520 ATTTT-ATTTTTT
1 ATTTTCATTTTTT
2625532 ATTTT
1 ATTTT
2625537 TTTATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTCATTTTTT
Found at i:2631890 original size:178 final size:175
Alignment explanation
Indices: 2631587--2631916 Score: 462
Period size: 178 Copynumber: 1.9 Consensus size: 175
2631577 CCCAGCCTAT
* * * * *
2631587 TACAATATAGCTCAAGGCGAGAAGGGCTATCTGTTAACCAAAAGTGTCGAGTTCGATTCCATTCA
1 TACAACATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
* * * *
2631652 GCTCGATAACATATCAACTGCTTGGTAGCAACAAGGAACTACTTTCCGATTGAAGTTTAAACTGA
66 GCTCGATAACATATCAACCGCATGGTAGCAACAAGAAACTACTTTCCGATTGAAGTTTAAACCGA
*
2631717 GGTCTTTTAAGTCAAGAGGAAGATCTGGGGTAATCTCTCAGCTTAG
131 GGTC-TTTAAGTCAAGACGAAGATCTGGGGTAATCTCTCAGCTTAG
* *
2631763 TACAACATAGCTCAAGGCGAGAAGAGTTATTTGTCAACAAAAAAACTGTCGAGTTCGATTCCATT
1 TACAACATAGCTCAAGGCGAGAAGAGCTATCTGTCAAC--AAAAACTGTCGAGTTCGATTCCATT
* * * * * *
2631828 TAGCTTGATGACATATCAACCGCATGGTAGCAGCAAGAAACTACTTTTCGGTTGAAGTTTAAACC
64 CAGCTCGATAACATATCAACCGCATGGTAGCAACAAGAAACTACTTTCCGATTGAAGTTTAAACC
*
2631893 GAGGTCTTTATGTCAAGACGAAGA
129 GAGGTCTTTAAGTCAAGACGAAGA
2631917 CATGGGTTAG
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
176 33 0.25
177 16 0.12
178 84 0.63
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (175 bp):
TACAACATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACTGTCGAGTTCGATTCCATTCA
GCTCGATAACATATCAACCGCATGGTAGCAACAAGAAACTACTTTCCGATTGAAGTTTAAACCGA
GGTCTTTAAGTCAAGACGAAGATCTGGGGTAATCTCTCAGCTTAG
Found at i:2632527 original size:38 final size:36
Alignment explanation
Indices: 2632428--2632882 Score: 282
Period size: 37 Copynumber: 12.7 Consensus size: 36
2632418 TCTGAGTTAT
*
2632428 ATATATAATATAGTATATTTTGAAAATATTTTCGAAAA
1 ATATATAATATA-TA-ATTTTGAAAACATTTTCGAAAA
* * *
2632466 ATGTATAACA-A-AATTTTTAGAAAACATTTTTTGAAAA
1 ATATATAATATATAA-TTTT-GAAAACA-TTTTCGAAAA
*
2632503 CATATATAATATATAGTTTTG-AAA-A---T------
1 -ATATATAATATATAATTTTGAAAACATTTTCGAAAA
* *
2632529 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1 ATATATAATATATAATTTTGAAAACATTTTCGAAAA
* * **
2632565 TATATATAATATACAGTTTTGAAAACATTTTTAAAAA
1 -ATATATAATATATAATTTTGAAAACATTTTCGAAAA
* * * *
2632602 TATATATAATACATAGTTTTTGAAAACATTTTTGAAACT
1 -ATATATAATATATA-ATTTTGAAAACATTTTCGAAA-A
* *
2632641 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1 ATATATAATATATAATTTTGAAAACATTTTCGAAAA
* * *
2632677 TATATATAATATATAGTTTTTTAAAACATTTTTG-AAA
1 -ATATATAATATATA-ATTTTGAAAACATTTTCGAAAA
* * *
2632714 ATATATATTATATAGTTTTGAAAATATTTT-GAAATA
1 ATATATAATATATAATTTTGAAAACATTTTCGAAA-A
* * * *
2632750 TATATATAATATATAGTTTTTAAAAACCTTTTTG-AAA
1 -ATATATAATATATA-ATTTTGAAAACATTTTCGAAAA
* * * *
2632787 ATACATATTATATAGTTTTGAAAATAACTTTT-G-AAA
1 ATATATAATATATAATTTTGAAAA-CA-TTTTCGAAAA
* * * *
2632823 ATATATATTATATAGTTTTGAAAATAATTTTTG-AAA
1 ATATATAATATATAATTTTGAAAA-CATTTTCGAAAA
* *
2632859 ATATATATTATATAGTTTTGAAAA
1 ATATATAATATATAATTTTGAAAA
2632883 ATTATTTTTG
Statistics
Matches: 352, Mismatches: 35, Indels: 62
0.78 0.08 0.14
Matches are distributed among these distances:
25 20 0.06
26 3 0.01
27 1 0.00
30 1 0.00
32 1 0.00
34 2 0.01
35 32 0.09
36 91 0.26
37 115 0.33
38 79 0.22
39 6 0.02
40 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATATAATATATAATTTTGAAAACATTTTCGAAAA
Found at i:2632539 original size:23 final size:25
Alignment explanation
Indices: 2632494--2632555 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
2632484 AGAAAACATT
2632494 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
2632519 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
2632544 TTTTGAAAACAT
1 TTTTGAAAACAT
2632556 TTTTGAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:2632560 original size:37 final size:37
Alignment explanation
Indices: 2632519--2632896 Score: 504
Period size: 37 Copynumber: 10.2 Consensus size: 37
2632509 TAATATATAG
2632519 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
*
2632556 TTTTGAAAATATATATAATATACAGTTTTGAAAACAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
* *
2632593 TTTTAAAAATATATATAATACATAGTTTTTGAAAACAT
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACAT
*
2632631 TTTTGAAACTATATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
*
2632668 TTTTGAAAATATATATAATATATAGTTTTTTAAAACAT
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACAT
*
2632706 TTTTGAAAATATATAT--TATATAGTTTTGAAAATA-
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
* *
2632740 TTTTGAAATATATATATAATATATAGTTTTTAAAAACCT
1 TTTTGAAA-ATATATATAATATATAG-TTTTGAAAACAT
* * *
2632779 TTTTGAAAATACATAT--TATATAGTTTTGAAAATAAC
1 TTTTGAAAATATATATAATATATAGTTTTGAAAA-CAT
*
2632815 TTTTGAAAATATATAT--TATATAGTTTTGAAAATAAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAA-CAT
*
2632851 TTTTGAAAATATATAT--TATATAGTTTTGAAAAATTAT
1 TTTTGAAAATATATATAATATATAGTTTTG-AAAA-CAT
2632888 TTTTGAAAA
1 TTTTGAAAA
2632897 CATTTTGAAA
Statistics
Matches: 310, Mismatches: 22, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
34 8 0.03
35 25 0.08
36 76 0.25
37 117 0.38
38 76 0.25
39 8 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACAT
Found at i:2632639 original size:11 final size:12
Alignment explanation
Indices: 2632544--2632638 Score: 50
Period size: 12 Copynumber: 7.7 Consensus size: 12
2632534 TAATATATAG
2632544 TTTTGAAAACAT
1 TTTTGAAAACAT
*
2632556 TTTTGAAAATAT
1 TTTTGAAAACAT
* * *
2632568 ATAT-AATATACAG
1 TTTTGAA-A-ACAT
2632581 TTTTGAAAACAT
1 TTTTGAAAACAT
* *
2632593 TTTTAAAAATAT
1 TTTTGAAAACAT
* * *
2632605 ATAT-AATACATAGT
1 TTTTGAA-A-ACA-T
2632619 TTTTGAAAACAT
1 TTTTGAAAACAT
2632631 TTTTGAAA
1 TTTTGAAA
2632639 CTATATATAA
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
11 4 0.07
12 39 0.64
13 10 0.16
14 6 0.10
15 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:2632732 original size:73 final size:73
Alignment explanation
Indices: 2632519--2632896 Score: 523
Period size: 73 Copynumber: 5.1 Consensus size: 73
2632509 TAATATATAG
*
2632519 TTTTGAAAATATATATAATATATAG-TTTTGAAAACATTTTTGAAAATATATATAATATACAGTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATAT--TATATAGTT
2632583 TTGAAAACAT
64 TTGAAAACAT
* * *
2632593 TTTTAAAAATATATATAATACATAGTTTTTGAAAACATTTTTGAAACTATATATAATATATAGTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAA--ATATATATTATATAGTT
2632658 TTGAAAACAT
64 TTGAAAACAT
*
2632668 TTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATATTATATAGTTTT
*
2632733 GAAAATA-
66 GAAAACAT
* * *
2632740 TTTTGAAATATATATATAATATATAGTTTTTAAAAACCTTTTTGAAAATACATATTATATAGTTT
1 TTTTGAAA-ATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATATTATATAGTTT
* *
2632805 TGAAAATAAC
65 TGAAAA-CAT
*
2632815 TTTTGAAAATATATAT--TATATAG-TTTTGAAAATAATTTTTGAAAATATATATTATATAGTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAA-CATTTTTGAAAATATATATTATATAGTTT
*
2632877 TGAAAAATTAT
65 TG-AAAA-CAT
2632888 TTTTGAAAA
1 TTTTGAAAA
2632897 CATTTTGAAA
Statistics
Matches: 277, Mismatches: 19, Indels: 17
0.88 0.06 0.05
Matches are distributed among these distances:
71 8 0.03
72 43 0.16
73 98 0.35
74 32 0.12
75 89 0.32
77 7 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (73 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAATATATATTATATAGTTTT
GAAAACAT
Found at i:2632999 original size:38 final size:37
Alignment explanation
Indices: 2632910--2633014 Score: 97
Period size: 38 Copynumber: 2.8 Consensus size: 37
2632900 TTTGAAAATG
* *
2632910 TTTTGAAATATATATATAATATATAATTTAGAAAACA
1 TTTTCAAAAATATATATAATATATAATTTAGAAAACA
* *
2632947 -TTTCAAATATATATATATAATATATGATTTTAG-AACCA
1 TTTTCAAA-A-ATATATATAATATAT-AATTTAGAAAACA
* * *
2632985 TTTTTTAAAAATATATGTAATATGTAATTT
1 -TTTTCAAAAATATATATAATATATAATTT
2633015 TCATTTACAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
36 6 0.11
37 4 0.07
38 32 0.58
39 7 0.13
40 6 0.11
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAATATATATAATATATAATTTAGAAAACA
Found at i:2633034 original size:4 final size:4
Alignment explanation
Indices: 2633025--2633057 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2633015 TCATTTACAT
2633025 TTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2633058 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:2633052 original size:18 final size:17
Alignment explanation
Indices: 2633029--2633075 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
2633019 TTACATTTTA
2633029 TTTATTTATTTATTTATT
1 TTTATTTATTT-TTTATT
*
2633047 TTTATTTATTTTTTCTT
1 TTTATTTATTTTTTATT
*
2633064 TTT-TTTCTTTTT
1 TTTATTTATTTTT
2633076 CTAGGGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
18 11 0.41
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTATTTATTTTTTATT
Found at i:2633052 original size:22 final size:20
Alignment explanation
Indices: 2633024--2633069 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
2633014 TTCATTTACA
2633024 TTTTATTTATTTATTTATTTAT
1 TTTTATTTATTT-TTTATTT-T
*
2633046 TTTTATTTATTTTTTCTTTT
1 TTTTATTTATTTTTTATTTT
2633066 TTTT
1 TTTT
2633070 CTTTTTCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTATTTATTTTTTATTTT
Found at i:2633069 original size:11 final size:11
Alignment explanation
Indices: 2633024--2633069 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
2633014 TTCATTTACA
2633024 TTTTATTTATT
1 TTTTATTTATT
2633035 TATTTATTTA-T
1 T-TTTATTTATT
2633046 TTTTATTTATT
1 TTTTATTTATT
*
2633057 TTTTCTTT-TT
1 TTTTATTTATT
2633067 TTT
1 TTT
2633070 CTTTTTCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 13 0.41
11 11 0.34
12 8 0.25
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:2634279 original size:15 final size:15
Alignment explanation
Indices: 2634261--2634292 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2634251 TTTTTAGAAA
2634261 TTAACATTTTTTATT
1 TTAACATTTTTTATT
*
2634276 TTAACATTTTTTCTT
1 TTAACATTTTTTATT
2634291 TT
1 TT
2634293 TATTTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAACATTTTTTATT
Found at i:2634348 original size:6 final size:6
Alignment explanation
Indices: 2634339--2634376 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
2634329 CTTTTTTAAT
2634339 TTTTTA -TTTTA TTTTTTA TTTTT- TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTT
2634377 CTTAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.34
6 14 0.48
7 5 0.17
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:2634354 original size:12 final size:12
Alignment explanation
Indices: 2634332--2634376 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
2634322 TTATTACCTT
2634332 TTTTAATTTTTTA
1 TTTT-ATTTTTTA
2634345 TTTTATTTTTTA
1 TTTTATTTTTTA
2634357 TTTT-TTTTTTA
1 TTTTATTTTTTA
2634368 TTTTTATTT
1 -TTTTATTT
2634377 CTTAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.23
12 16 0.53
13 7 0.23
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:2634364 original size:11 final size:11
Alignment explanation
Indices: 2634338--2634372 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
2634328 CCTTTTTTAA
2634338 TTTTTTATTTT
1 TTTTTTATTTT
2634349 ATTTTTTATTTT
1 -TTTTTTATTTT
2634361 TTTTTTATTTT
1 TTTTTTATTTT
2634372 T
1 T
2634373 ATTTCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:2634385 original size:18 final size:18
Alignment explanation
Indices: 2634339--2634376 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2634329 CTTTTTTAAT
2634339 TTTTTATTTTATTTTTTA
1 TTTTTATTTTATTTTTTA
*
2634357 TTTTTTTTTTA-TTTTTA
1 TTTTTATTTTATTTTTTA
2634374 TTT
1 TTT
2634377 CTTAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTATTTTATTTTTTA
Found at i:2636888 original size:10 final size:9
Alignment explanation
Indices: 2636863--2636892 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2636853 AACATAATCA
2636863 TTCCTTTCC
1 TTCCTTTCC
2636872 TTCCTTTCC
1 TTCCTTTCC
2636881 TATCCTTTCC
1 T-TCCTTTCC
2636891 TT
1 TT
2636893 TCTGCCTCTC
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:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (9 bp):
TTCCTTTCC
Found at i:2641150 original size:24 final size:20
Alignment explanation
Indices: 2641099--2641157 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 20
2641089 TTCCCTTTGA
2641099 AGTGTATCGGTACACACTAT
1 AGTGTATCGGTACACACTAT
* *
2641119 AGGGTATCGGTACATCCCTTCACT
1 AGTGTATCGGTACA-CAC-T-A-T
2641143 AGTGTATCGGTACAC
1 AGTGTATCGGTACAC
2641158 TGCCTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.41
21 2 0.06
22 1 0.03
23 2 0.06
24 14 0.44
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (20 bp):
AGTGTATCGGTACACACTAT
Found at i:2642818 original size:41 final size:41
Alignment explanation
Indices: 2642773--2643008 Score: 329
Period size: 41 Copynumber: 5.9 Consensus size: 41
2642763 CAATCCAATT
* * *
2642773 CAATTCAATCATGCCAATATACAATAGTTCACCATTCGATC
1 CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
*
2642814 CAATTCAACCATGACAGTATGC-A-A--T-ACCATTCGATC
1 CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
* * *
2642850 CAATTCAACCATGATAATATGCAATAGTTCACTATTTGATC
1 CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
* *
2642891 CAATTCAACCATGACAATATGCAATATTTCACCATTTGATC
1 CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
* **
2642932 CAATTCAACCATGACAATATGCAATAATTCAATATTCGATC
1 CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
2642973 CAATTCAACCATGACAATATGCAATAGTTCACCATT
1 CAATTCAACCATGACAATATGCAATAGTTCACCATT
2643009 TAACTTGATT
Statistics
Matches: 172, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
36 31 0.18
37 2 0.01
38 1 0.01
39 1 0.01
40 2 0.01
41 135 0.78
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (41 bp):
CAATTCAACCATGACAATATGCAATAGTTCACCATTCGATC
Found at i:2642860 original size:18 final size:18
Alignment explanation
Indices: 2642803--2642861 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
2642793 ACAATAGTTC
2642803 ACCATTCGATCCAATTCA
1 ACCATTCGATCCAATTCA
* *
2642821 ACCATGACAGTATGCAA-T--
1 ACCAT-TC-G-ATCCAATTCA
2642839 ACCATTCGATCCAATTCA
1 ACCATTCGATCCAATTCA
2642857 ACCAT
1 ACCAT
2642862 GATAATATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 5 0.16
16 2 0.06
17 1 0.03
18 15 0.48
19 1 0.03
20 2 0.06
21 5 0.16
ACGTcount: A:0.36, C:0.31, G:0.08, T:0.25
Consensus pattern (18 bp):
ACCATTCGATCCAATTCA
Found at i:2645318 original size:77 final size:78
Alignment explanation
Indices: 2644990--2645316 Score: 265
Period size: 77 Copynumber: 4.2 Consensus size: 78
2644980 AAGAAATACG
* * * * * * *** *
2644990 GTTGCGCCTAAAAATGTCATGGTTCACAAAAAAATAGATTGTAATCT-GGAATGTTAATATTTTT
1 GTTGCGCCTAAGAATATCATGATTCACTAAGAAATAGGTTACGATCTAGAAATGTTAATATTTTT
2645054 ATTAATAAAAT-A
66 ATTAATAAAATGA
* * * * *
2645066 GGTTGCGCCTAAGAACATCATGGTTCACTAAGAATTAGG-TAGCGATCTGTAATGTAATGTAAAT
1 -GTTGCGCCTAAGAATATCATGATTCACTAAGAAATAGGTTA-CGATC--T-A-GAAATGTTAAT
* *
2645130 ATTTTT-TTAGTAAAATAA
60 ATTTTTATTAATAAAATGA
* * * ** *
2645148 GTTGGGCCTAAGAATATC-TTAGTTCATTAAGAAATATATTGCGATCT-GAAATGTTAATATTTT
1 GTTGCGCCTAAGAATATCATGA-TTCACTAAGAAATAGGTTACGATCTAGAAATGTTAATATTTT
* *
2645211 TATTAAGAAAATGG
65 TATTAATAAAATGA
* * *
2645225 GTTGTGCCCAAGAATGTCATGATTCACTAAGAAATAGGTTACGATCTAG-AATGTTAATATTTTT
1 GTTGCGCCTAAGAATATCATGATTCACTAAGAAATAGGTTACGATCTAGAAATGTTAATATTTTT
*
2645289 TTTAATAAAATGA
66 ATTAATAAAATGA
2645302 GTTGCGCAC-AAGAAT
1 GTTGCGC-CTAAGAAT
2645317 GTTAACCTTA
Statistics
Matches: 197, Mismatches: 40, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
76 16 0.08
77 115 0.58
78 4 0.02
79 2 0.01
80 1 0.01
81 42 0.21
82 17 0.09
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (78 bp):
GTTGCGCCTAAGAATATCATGATTCACTAAGAAATAGGTTACGATCTAGAAATGTTAATATTTTT
ATTAATAAAATGA
Found at i:2645363 original size:36 final size:38
Alignment explanation
Indices: 2645316--2645407 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 38
2645306 CGCACAAGAA
*
2645316 TGTTAACCTTAACATTCCA-A-ATCAACTATTATAATT
1 TGTTAACCTTAACATTACAGAGATCAACTATTATAATT
* *
2645352 TGTTAACCTTAACATTATATGAGGTCAACTATTATAATT
1 TGTTAACCTTAACATTACA-GAGATCAACTATTATAATT
2645391 TGTTAACCTTAACATTA
1 TGTTAACCTTAACATTA
2645408 AACTCATCTC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.34
38 1 0.02
39 32 0.64
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (38 bp):
TGTTAACCTTAACATTACAGAGATCAACTATTATAATT
Found at i:2646239 original size:60 final size:59
Alignment explanation
Indices: 2646138--2646264 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 59
2646128 AAAACTATAC
* * ** *
2646138 ATACTTTCGAATTTAAAAAATGAAAAATGATATTTTAACTTTCTCATATAAAAGTATCG
1 ATACTTTTGAATTTAAAAAATAAAAAATGATATTTTAACTTTCGAATATAAAAATATCG
* *
2646197 ATACTTTTGAATTTAAAAAATAAAAAAATGATATTTTAACTTTCGAATTTAAAAATATTG
1 ATACTTTTGAATTTAAAAAAT-AAAAAATGATATTTTAACTTTCGAATATAAAAATATCG
2646257 ATACTTTT
1 ATACTTTT
2646265 AAAAAAGTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
59 20 0.33
60 40 0.67
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (59 bp):
ATACTTTTGAATTTAAAAAATAAAAAATGATATTTTAACTTTCGAATATAAAAATATCG
Found at i:2646267 original size:18 final size:20
Alignment explanation
Indices: 2646247--2646283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2646237 TTTCGAATTT
*
2646247 AAAAA-TATTGATACTTTTA
1 AAAAAGTATCGATACTTTTA
2646266 AAAAAGTATCGATACTTT
1 AAAAAGTATCGATACTTT
2646284 GCAATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (20 bp):
AAAAAGTATCGATACTTTTA
Found at i:2646407 original size:20 final size:21
Alignment explanation
Indices: 2646382--2646431 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
2646372 CTTTTAAATT
2646382 TAAAAGTATCGATAATTTT-A
1 TAAAAGTATCGATAATTTTGA
* *
2646402 TAAAAGCATCGATACTTTTGA
1 TAAAAGTATCGATAATTTTGA
2646423 -AAAAGTATC
1 TAAAAGTATC
2646432 AATATTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
TAAAAGTATCGATAATTTTGA
Found at i:2653626 original size:17 final size:18
Alignment explanation
Indices: 2653604--2653637 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2653594 TTGAAAGGTC
2653604 TGGAA-TAAATAATAAGT
1 TGGAATTAAATAATAAGT
2653621 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
2653638 ACAGAATGGA
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:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:2657089 original size:28 final size:28
Alignment explanation
Indices: 2657058--2657123 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2657048 AATATTAATG
*
2657058 TAATAATTTTATTTTAAT-AGTATAATAA
1 TAATAATTTTAATTTAATAAGTA-AATAA
*
2657086 TAAT-ATTCTTAATTTAATAAGTAATTAA
1 TAATAATT-TTAATTTAATAAGTAAATAA
*
2657114 TAATATTTTT
1 TAATAATTTT
2657124 CAATAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.09
28 23 0.72
29 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
TAATAATTTTAATTTAATAAGTAAATAA
Found at i:2657287 original size:22 final size:21
Alignment explanation
Indices: 2657262--2657320 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
2657252 ATAAATAATA
2657262 TTAAATAAATTATTATAGTATT
1 TTAAATAAATTATTATA-TATT
*
2657284 TT-AAGAAATATATTAT-TATT
1 TTAAATAAAT-TATTATATATT
*
2657304 TTAATATATATT-TTATA
1 TTAA-ATAAATTATTATA
2657321 ATAAATCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
20 10 0.33
21 8 0.27
22 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAATAAATTATTATATATT
Found at i:2658756 original size:24 final size:24
Alignment explanation
Indices: 2658714--2658786 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
2658704 TTTTAAAATT
*
2658714 TTATTAATTTAATTTAATATATAAAA
1 TTATTAA--TAATTAAATATATAAAA
* *
2658740 TTATTAATAATTAAATATGTAATA
1 TTATTAATAATTAAATATATAAAA
* *
2658764 TTATT-ATATATAAAATAAATAAA
1 TTATTAATA-ATTAAATATATAAA
2658787 TGTAACCGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.08
24 29 0.74
26 7 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
TTATTAATAATTAAATATATAAAA
Found at i:2659309 original size:3 final size:3
Alignment explanation
Indices: 2659301--2659345 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
2659291 TTTCGGCAGC
*
2659301 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2659346 GCAACGACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2660781 original size:2 final size:2
Alignment explanation
Indices: 2660776--2660863 Score: 162
Period size: 2 Copynumber: 45.0 Consensus size: 2
2660766 GCGCGCCTAC
2660776 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
2660818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2660859 -T AT AT
1 AT AT AT
2660864 TAAGTTATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 82 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2664650 original size:56 final size:56
Alignment explanation
Indices: 2664542--2664655 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 56
2664532 CTTGGGTCCG
* * * * * * ** *
2664542 AGACATTGATGCAAGTTTTCGACAGGGAGGTTCAAGATAGAGTTTTGGGCTTGTCA
1 AGACATTGATGCAAGTGTCCGACAAGAAGGGTCAAGATAGAGTGTCAGGCTTGCCA
* *
2664598 AGACATTGGTGCAAGTGTCCGACAAGAAGGGTCAAGATAGAGTGTCATGCTTGCCA
1 AGACATTGATGCAAGTGTCCGACAAGAAGGGTCAAGATAGAGTGTCAGGCTTGCCA
2664654 AG
1 AG
2664656 GCCACCAGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (56 bp):
AGACATTGATGCAAGTGTCCGACAAGAAGGGTCAAGATAGAGTGTCAGGCTTGCCA
Found at i:2672919 original size:6 final size:6
Alignment explanation
Indices: 2672908--2672935 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2672898 ATGCTTGATC
2672908 AAATAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAAT
2672936 TTAACGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:2686047 original size:39 final size:39
Alignment explanation
Indices: 2686004--2686114 Score: 222
Period size: 39 Copynumber: 2.8 Consensus size: 39
2685994 AGCAGTAAAT
2686004 TATTTGATTTAGTAGTTTATATTAACTATAACTCTCTCC
1 TATTTGATTTAGTAGTTTATATTAACTATAACTCTCTCC
2686043 TATTTGATTTAGTAGTTTATATTAACTATAACTCTCTCC
1 TATTTGATTTAGTAGTTTATATTAACTATAACTCTCTCC
2686082 TATTTGATTTAGTAGTTTATATTAACTATAACT
1 TATTTGATTTAGTAGTTTATATTAACTATAACT
2686115 TCATCCTTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.50
Consensus pattern (39 bp):
TATTTGATTTAGTAGTTTATATTAACTATAACTCTCTCC
Found at i:2688703 original size:39 final size:39
Alignment explanation
Indices: 2688656--2688739 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
2688646 TTCATTTAAA
* *
2688656 AGTTTAGATTAATTAGAACTATATC-CTATTTGATTTAGT
1 AGTTTAGATTAAGTAGAACCATATCAC-ATTTGATTTAGT
*
2688695 AGTTTAGATTAAGTAGAACCCTATCACATTTGATTTAGT
1 AGTTTAGATTAAGTAGAACCATATCACATTTGATTTAGT
2688734 AGTTTA
1 AGTTTA
2688740 TATGAACTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (39 bp):
AGTTTAGATTAAGTAGAACCATATCACATTTGATTTAGT
Found at i:2690185 original size:18 final size:18
Alignment explanation
Indices: 2690162--2690215 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
2690152 TCTTTCTTCT
2690162 CCCATTTGCAAGAACGAA
1 CCCATTTGCAAGAACGAA
2690180 CCCATTTGCAAGAACGAA
1 CCCATTTGCAAGAACGAA
2690198 CCCATTTGCAAGAACGAA
1 CCCATTTGCAAGAACGAA
2690216 GGTGGAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (18 bp):
CCCATTTGCAAGAACGAA
Found at i:2693039 original size:15 final size:13
Alignment explanation
Indices: 2693017--2693052 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
2693007 ATCAAACAAG
2693017 AAAAAAGATTAAGA
1 AAAAAAGATTAA-A
2693031 AAAAGAAGATTAAA
1 AAAA-AAGATTAAA
2693045 AAAAAAGA
1 AAAAAAGA
2693053 CAAACAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (13 bp):
AAAAAAGATTAAA
Found at i:2694515 original size:15 final size:14
Alignment explanation
Indices: 2694486--2694523 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
2694476 GATTTTGAGA
2694486 TTTTGAAA-TCAAG
1 TTTTGAAATTCAAG
2694499 TTTTGAAATTACAAG
1 TTTTGAAATT-CAAG
2694514 TTTTGAAATT
1 TTTTGAAATT
2694524 TGAAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (14 bp):
TTTTGAAATTCAAG
Found at i:2696661 original size:20 final size:20
Alignment explanation
Indices: 2696624--2696662 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2696614 AGATTGAGTG
* * *
2696624 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
2696644 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2696663 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:2702456 original size:20 final size:20
Alignment explanation
Indices: 2702431--2702481 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2702421 TTGAGCGTGG
2702431 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
2702451 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
*
2702471 GAGGAATCGGT
1 GGGGAATCGGT
2702482 TCCCTAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:2706545 original size:30 final size:31
Alignment explanation
Indices: 2706485--2706549 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2706475 GGAAACATCT
*
2706485 GATCTAATACATAACATGGCATACCATTATA
1 GATCTAATACATAACATGACATACCATTATA
*
2706516 GATCTAATGCATAACATGACATA-CATTATA
1 GATCTAATACATAACATGACATACCATTATA
2706546 GATC
1 GATC
2706550 CTATTTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (31 bp):
GATCTAATACATAACATGACATACCATTATA
Found at i:2720363 original size:20 final size:21
Alignment explanation
Indices: 2720334--2720373 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2720324 TGATGTGCTA
2720334 TGTTGTAAATTAATGTTAGAG
1 TGTTGTAAATTAATGTTAGAG
*
2720355 TGTTG-AAATTGATGTTAGA
1 TGTTGTAAATTAATGTTAGA
2720374 AAGTGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (21 bp):
TGTTGTAAATTAATGTTAGAG
Found at i:2725132 original size:21 final size:21
Alignment explanation
Indices: 2725102--2725143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2725092 AGATCTCTCA
2725102 TTTCCTTTCTTTATT-TTCCT
1 TTTCCTTTCTTTATTCTTCCT
*
2725122 TTTCCATTTCTTTTTTCTTCCT
1 TTTCC-TTTCTTTATTCTTCCT
2725144 CCTCAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCCTTTCTTTATTCTTCCT
Found at i:2725635 original size:20 final size:20
Alignment explanation
Indices: 2725599--2725636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2725589 AGGGTTCAAG
*
2725599 TATCGATACTGGATGAATAA
1 TATCGATACTAGATGAATAA
*
2725619 TATCGATACTAGTTGAAT
1 TATCGATACTAGATGAAT
2725637 TGGGGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATACTAGATGAATAA
Found at i:2726931 original size:32 final size:32
Alignment explanation
Indices: 2726831--2726932 Score: 150
Period size: 32 Copynumber: 3.2 Consensus size: 32
2726821 CAGATACTAG
* *
2726831 TCAGGTTTGCATTCAGATAATACATAATATGT
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
* * *
2726863 TCAAGTTTGCATTTAGATAATGCACAATATGA
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
*
2726895 TCAGGTTTGCATTCATATAATGCACAATATGT
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
2726927 TCAGGT
1 TCAGGT
2726933 CATACGTGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TCAGGTTTGCATTCAGATAATGCACAATATGT
Found at i:2729336 original size:45 final size:44
Alignment explanation
Indices: 2729232--2729530 Score: 330
Period size: 45 Copynumber: 6.6 Consensus size: 44
2729222 ATACTTTATT
* * * * * *
2729232 TTCATTTGTAGCATCATTTCATGCTTATAATTCACCGTTATACA
1 TTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * * *
2729276 TTTTCATTTATGGCATCCTTTTATGCCAATAATGCACCATTATGCGG
1 --TTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGC-A
* * *
2729323 TTCATTTAAGGCATCCTTTCATGCCGATAATGCAACGTTATGCA
1 TTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* * *
2729367 TCTCATTTATGGTATTCTTTCATGCCTATAATGCACTGTTATGCA
1 T-TCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
**
2729412 TT-ATATATATGATATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTCAT-T-TATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
*
2729457 TTACATATATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TT-CATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
* *
2729502 TTACATATATGGCATCATTTCATGCCTAT
1 TT-CATTTATGGCATCCTTTCATGCCTAT
2729531 TCCTACTCTA
Statistics
Matches: 218, Mismatches: 29, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.01
44 3 0.01
45 177 0.81
46 34 0.16
47 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (44 bp):
TTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
Found at i:2729465 original size:24 final size:24
Alignment explanation
Indices: 2729438--2729510 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
2729428 CTTTCATGCC
2729438 TATAATGCACCGTTATGCATTACA
1 TATAATGCACCGTTATGCATTACA
* *
2729462 TAT-ATGGCATCC-TT-T-CA-TGCC
1 TATAAT-GCA-CCGTTATGCATTACA
2729483 TATAATGCACCGTTATGCATTACA
1 TATAATGCACCGTTATGCATTACA
2729507 TATA
1 TATA
2729511 TGGCATCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 5 0.13
23 5 0.13
24 14 0.37
25 2 0.05
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (24 bp):
TATAATGCACCGTTATGCATTACA
Found at i:2729486 original size:21 final size:21
Alignment explanation
Indices: 2729462--2729530 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
2729452 ATGCATTACA
2729462 TATATGGCATCCTTTCATGCC
1 TATATGGCATCCTTTCATGCC
* *
2729483 TATAAT-GCA-CCGTTATGCATTACA
1 TAT-ATGGCATCC-TT-T-CA-TGCC
*
2729507 TATATGGCATCATTTCATGCC
1 TATATGGCATCCTTTCATGCC
2729528 TAT
1 TAT
2729531 TCCTACTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 5 0.14
23 5 0.14
24 10 0.28
25 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (21 bp):
TATATGGCATCCTTTCATGCC
Found at i:2729988 original size:53 final size:52
Alignment explanation
Indices: 2729930--2730189 Score: 175
Period size: 53 Copynumber: 5.2 Consensus size: 52
2729920 TTTTTATACT
*
2729930 ATGGTATCGACACTCCTTTTCAGTATCGATACCATTTCTATATTCTGTAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATT-TGTAATCC
* *
2729983 ATGGTATCGATACCTTTCTTTT-AGTATCGATA-C--TTCTATA----T-AT-T
1 ATGGTATCGATA-C-TCCTTTTCAGTATCGATACCATTTCTATATTTGTAATCC
* *
2730027 ATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATTTTGTAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATA-TTTGTAATCC
*
2730080 ATGGTATCGATA--CCTTTCTCTTAGTATCGATA-CA--TCTATA----T-AT-T
1 ATGGTATCGATACTCCTTT-TC--AGTATCGATACCATTTCTATATTTGTAATCC
* * * * * * *
2730124 ATGGAACCGATACTCCCTTTCAATATCGATGCCATTTCTACATTCTGGAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATT-TGTAATCC
*
2730177 CTGGTATCGATAC
1 ATGGTATCGATAC
2730190 CTTTCTCTTA
Statistics
Matches: 158, Mismatches: 21, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
42 5 0.03
43 19 0.12
44 24 0.15
45 6 0.04
46 18 0.11
51 18 0.11
52 6 0.04
53 35 0.22
54 21 0.13
55 6 0.04
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (52 bp):
ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATTTGTAATCC
Done.