Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 165 of 198
Found at i:51894083 original size:128 final size:128
Alignment explanation
Indices: 51893855--51894361 Score: 789
Period size: 128 Copynumber: 4.0 Consensus size: 128
51893845 TAGCCTTATC
* * * * * * *
51893855 TCCCTGAACAGTAGTGGAGTAGGTGGGAAACTGAAGATCTTGTCTCCCTAAGCAGTAGTGGAGTA
1 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGAAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
*
51893920 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCCACAAGTCCTATG
66 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* * * *
51893983 TCCCTAACCAACAGTGGAATAGGTTGGAAATTGCAGATCTTGTCTCCCTAAGCAGTACCGGAGCA
1 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGAAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* *
51894048 GATCGAAGACGGCGAGTCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCATATG
66 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* * * *
51894111 TCCCTGACCAGCAGTGGAATAGGTTAGAAATTGAAGATCTTGTCTCCCTAAGTAATATCGGAGCA
1 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGAAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
51894176 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
66 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* * **
51894239 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTGGCTCCCTAAGCAGTAGTAGAGCA
1 TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGAAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* * *
51894304 GATCGAAGACAGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTC
66 GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTC
51894362 ATTTCTCTCT
Statistics
Matches: 345, Mismatches: 34, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 345 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (128 bp):
TCCCTGACCAGCAGTGGAATAGGTTGGAAATTGAAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
GATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
Found at i:51894538 original size:130 final size:129
Alignment explanation
Indices: 51894302--51894540 Score: 304
Period size: 130 Copynumber: 1.8 Consensus size: 129
51894292 AGTAGTAGAG
* * * * *
51894302 CAGATCGAAGACAGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACGAGTCATTTC
1 CAGATCGAAGACAGCGAATCTTATCTTCAAGCGTAAGGAAGCAGATTTAAGCCACAAATCATATC
* **
51894367 TCTCTAAGGTTGCAGTGGAGCAGACTAAGTAAGCAGGTCTTATCCCGACTGAAGTTGCAGTGGGA
66 TCTCTAAGGTTGCAGTGGAGCAGACTAAG-AAACAAATCTTATCCCGACTGAAGTTGCAGTGGGA
* *
51894432 CAGATCGAAGAC-GACGAATCTTATCTTCAAGCGTAAGGAAGCAGATTTCAGCCACAAATCCTAT
1 CAGATCGAAGACAG-CGAATCTTATCTTCAAGCGTAAGGAAGCAGATTTAAGCCACAAATCATAT
* *
51894496 CTCTCTGAA-GTTGCAGTGGAGCGGATTAA-AACCACAAATCTTATC
65 CTCTCT-AAGGTTGCAGTGGAGCAGACTAAGAA--ACAAATCTTATC
51894541 TCTTTGAAGT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
128 2 0.02
129 1 0.01
130 88 0.95
131 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (129 bp):
CAGATCGAAGACAGCGAATCTTATCTTCAAGCGTAAGGAAGCAGATTTAAGCCACAAATCATATC
TCTCTAAGGTTGCAGTGGAGCAGACTAAGAAACAAATCTTATCCCGACTGAAGTTGCAGTGGGA
Found at i:51894645 original size:44 final size:44
Alignment explanation
Indices: 51894591--51894689 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
51894581 CTTCCTGAGA
* *
51894591 TTGCAGTGGAGCAGATTGAAGCCGATA-ATCCTATCTCCCAGAAG
1 TTGCAGTGGAGCAGATTAAAG-CAATAGATCCTATCTCCCAGAAG
* * * *
51894635 TTGTAGTGGAGCGGATTAAAGTAATAGATCCTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCAATAGATCCTATCTCCCAGAAG
51894679 TTGCAGTGGAG
1 TTGCAGTGGAG
51894690 GGATCAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 3 0.06
44 44 0.94
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (44 bp):
TTGCAGTGGAGCAGATTAAAGCAATAGATCCTATCTCCCAGAAG
Found at i:51895849 original size:13 final size:13
Alignment explanation
Indices: 51895814--51895839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51895804 GAGAGGGGGC
51895814 GTTTATTTTTTAT
1 GTTTATTTTTTAT
51895827 GTTTATTTTTTAT
1 GTTTATTTTTTAT
51895840 TTTCGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTATTTTTTAT
Found at i:51896341 original size:3 final size:3
Alignment explanation
Indices: 51896298--51896326 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
51896288 TAATATTAAT
51896298 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
51896327 TGTTGTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:51898925 original size:11 final size:11
Alignment explanation
Indices: 51898898--51898947 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
51898888 AAATAAATCC
51898898 TTTCTCT-AAT
1 TTTCTCTCAAT
*
51898908 ATTCTCTCAAT
1 TTTCTCTCAAT
51898919 TTTCTCTCAAT
1 TTTCTCTCAAT
* * *
51898930 TTCCTCTAAAA
1 TTTCTCTCAAT
51898941 TTTCTCT
1 TTTCTCT
51898948 TAAATCCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 6 0.18
11 27 0.82
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTCTCTCAAT
Found at i:51899007 original size:28 final size:27
Alignment explanation
Indices: 51898958--51899015 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
51898948 TAAATCCCTA
* **
51898958 TTTAAAATAACTTTAATTTTTTAATTATT
1 TTTAAAATAAATTTAAAATTTT-ATT-TT
51898987 TTTAAAA-AAATTTAAAATTTTATTTT
1 TTTAAAATAAATTTAAAATTTTATTTT
51899013 TTT
1 TTT
51899016 GATTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 3 0.12
28 11 0.42
29 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTAAAATAAATTTAAAATTTTATTTT
Found at i:51900820 original size:18 final size:18
Alignment explanation
Indices: 51900797--51900834 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
51900787 TGCCAAGTGC
* *
51900797 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
51900815 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
51900833 GT
1 GT
51900835 TTCCGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:51904727 original size:126 final size:126
Alignment explanation
Indices: 51904492--51904776 Score: 498
Period size: 126 Copynumber: 2.3 Consensus size: 126
51904482 GTGGGAGCTC
* *
51904492 TTTTCAGGAGCTACTATAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGTACTTCTGCTGACA
1 TTTTCAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACA
*
51904557 AAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTTCTCAAAAACGTCTACTCGAAATTATT
66 AAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATT
51904618 TTTTCAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACA
1 TTTTCAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACA
* * *
51904683 AAGCATCCTGCTTAAAGTGTTTTTGACATTGTTTGCTCAGAAACGTCTACTCGAAATTATT
66 AAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATT
* *
51904744 TTTTTAGGAGCTACTGTAGCAAAAGTGCGTCCA
1 TTTTCAGGAGCTACTGTAGCAAAAGCGCGTCCA
51904777 ACCCTAATCT
Statistics
Matches: 151, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 151 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
TTTTCAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACA
AAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAAAAACGTCTACTCGAAATTATT
Found at i:51907277 original size:2 final size:2
Alignment explanation
Indices: 51907226--51907259 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
51907216 ATAACTTATT
*
51907226 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51907260 CTTATATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51907439 original size:13 final size:13
Alignment explanation
Indices: 51907421--51907480 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
51907411 ATTCATATAC
*
51907421 ATATATATTTTTT
1 ATATATATATTTT
51907434 ATATATATATTTT
1 ATATATATATTTT
* * *
51907447 ACAATTTATATATAT
1 A-TATATATAT-TTT
*
51907462 ACATATATATTTT
1 ATATATATATTTT
51907475 -TATATA
1 ATATATA
51907481 CTTTATAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
12 5 0.14
13 15 0.41
14 14 0.38
15 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATATATATTTT
Found at i:51907491 original size:18 final size:20
Alignment explanation
Indices: 51907431--51907491 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
51907421 ATATATATTT
* *
51907431 TTTATATATATATTTTACAA
1 TTTATATATATACTTTATAA
*
51907451 TTTATATATATAC-ATATATA
1 TTTATATATATACTTTATA-A
51907471 TTT-T-TATATACTTTATAA
1 TTTATATATATACTTTATAA
51907489 TTT
1 TTT
51907492 CCATATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 11 0.31
19 8 0.23
20 16 0.46
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATATATATACTTTATAA
Found at i:51907504 original size:40 final size:40
Alignment explanation
Indices: 51907385--51907510 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
51907375 ATACCCTTTT
*
51907385 TACATATATATTTTCT-TAT-TTTTATAA-TTCATATACA
1 TACATATATATTTTATATATATTTTATAATTTCATATACA
* * * *
51907422 TATATAT-TTTTTATATATATATTTTACAATTT-ATATATA
1 TACATATATATTT-TATATATATTTTATAATTTCATATACA
* *
51907461 TACATATATATTTT-TATATACTTTATAATTTCCATATGCA
1 TACATATATATTTTATATATATTTTATAATTT-CATATACA
51907501 TACATATATA
1 TACATATATA
51907511 CATATTTATA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
36 4 0.06
37 8 0.11
38 18 0.25
39 20 0.28
40 21 0.30
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (40 bp):
TACATATATATTTTATATATATTTTATAATTTCATATACA
Found at i:51920819 original size:48 final size:48
Alignment explanation
Indices: 51920748--51920939 Score: 348
Period size: 48 Copynumber: 4.0 Consensus size: 48
51920738 CAAAATTATT
* *
51920748 TTGGACCTGGTCAAAATGCAAAAGACTTTGGTCAAAATTGGTGTGCTG
1 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
51920796 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
1 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
* *
51920844 TTGGACCTGGTCAAAATGCAAAAGACTTTGGTCAAAATTGGGGTACTG
1 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
51920892 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
1 TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
51920940 AAGCAGGCTA
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 138 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (48 bp):
TTGGACCTGGTCAAAATGCAAAAGAATTTGGTCAAAATTGGGGTGCTG
Found at i:51927039 original size:15 final size:16
Alignment explanation
Indices: 51927011--51927040 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51927001 TTATCATTAT
51927011 TATAAAAATATTTAAC
1 TATAAAAATATTTAAC
51927027 TATAAAAAT-TTTAA
1 TATAAAAATATTTAA
51927041 ATAATTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAAAATATTTAAC
Found at i:51927331 original size:21 final size:21
Alignment explanation
Indices: 51927293--51927343 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
51927283 CATTATTTCT
*
51927293 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* ** *
51927314 AATCTCACTGCTTTAGTAACT
1 AATCTCACCGCTACAGTAACC
51927335 AATCTCACC
1 AATCTCACC
51927344 ATCACCGCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.29
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:51928856 original size:20 final size:20
Alignment explanation
Indices: 51928818--51928856 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
51928808 GATAATTTAA
*
51928818 TTTTGTATATATAATTAATT
1 TTTTGTATATATAAGTAATT
* *
51928838 TTTTTTATATGTAAGTAAT
1 TTTTGTATATATAAGTAAT
51928857 GCAAATTTTG
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:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTGTATATATAAGTAATT
Found at i:51930555 original size:7 final size:7
Alignment explanation
Indices: 51930545--51930574 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
51930535 AAAATAAAGG
51930545 TTTGATC
1 TTTGATC
51930552 TTTGATC
1 TTTGATC
51930559 TTTGATC
1 TTTGATC
51930566 TTTGATC
1 TTTGATC
51930573 TT
1 TT
51930575 CGCTTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (7 bp):
TTTGATC
Found at i:51932733 original size:27 final size:29
Alignment explanation
Indices: 51932694--51932756 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
51932684 ACCATTAAGA
*
51932694 ATAATAGAAAATATAAATT-T-TAAA-AAT
1 ATAATATAAAATA-AAATTATATAAATAAT
*
51932721 ATAATATATAATAAAATTATATAAATAAT
1 ATAATATAAAATAAAATTATATAAATAAT
*
51932750 TTAATAT
1 ATAATAT
51932757 TTGTAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 12 0.40
28 4 0.13
29 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
ATAATATAAAATAAAATTATATAAATAAT
Found at i:51932748 original size:17 final size:17
Alignment explanation
Indices: 51932693--51932749 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 17
51932683 CACCATTAAG
*
51932693 AATAATAGAAA-ATATA
1 AATAATAAAAATATATA
**
51932709 AATTTTAAAAATATAATA
1 AATAATAAAAATAT-ATA
* *
51932727 TATAATAAAATTATATA
1 AATAATAAAAATATATA
51932744 AATAAT
1 AATAAT
51932750 TTAATATTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 8 0.26
17 10 0.32
18 13 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATAATAAAAATATATA
Found at i:51934868 original size:22 final size:22
Alignment explanation
Indices: 51934825--51934869 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
51934815 TTAGATATAG
* *
51934825 ATTTTAATTATGTATAATTTTT
1 ATTTTAATTATGTAGAAGTTTT
* *
51934847 ATTTTTATTATTTAGAAGTTTT
1 ATTTTAATTATGTAGAAGTTTT
51934869 A
1 A
51934870 AGCTTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATGTAGAAGTTTT
Found at i:51938293 original size:19 final size:20
Alignment explanation
Indices: 51938269--51938306 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
51938259 TGTTCTAGAA
*
51938269 TTTCTTTTTA-ATTTTTAAC
1 TTTCTTTATATATTTTTAAC
51938288 TTTCTTTATATATTTTTAA
1 TTTCTTTATATATTTTTAA
51938307 AATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTTTATATATTTTTAAC
Found at i:51938314 original size:19 final size:20
Alignment explanation
Indices: 51938292--51938331 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
51938282 TTTAACTTTC
*
51938292 TTTATATAT-TTTTAAAATT
1 TTTATAAATATTTTAAAATT
51938311 TTTATAAATATTTTAAAATT
1 TTTATAAATATTTTAAAATT
51938331 T
1 T
51938332 AAAAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATAAATATTTTAAAATT
Found at i:51938324 original size:11 final size:9
Alignment explanation
Indices: 51938299--51938372 Score: 51
Period size: 11 Copynumber: 7.7 Consensus size: 9
51938289 TTCTTTATAT
51938299 ATTTTTAAA
1 ATTTTTAAA
51938308 ATTTTTATAA
1 ATTTTTA-AA
51938318 ATATTTTAAA
1 AT-TTTTAAA
*
51938328 A-TTTAAAA
1 ATTTTTAAA
*
51938336 ATTAGTTTGAA
1 ATT--TTTAAA
* *
51938347 CTTTTGAAA
1 ATTTTTAAA
51938356 ATTATTTTAAA
1 A-T-TTTTAAA
51938367 ATTTTT
1 ATTTTT
51938373 TTTAAAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
8 7 0.14
9 16 0.32
10 9 0.18
11 18 0.36
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:51938371 original size:20 final size:20
Alignment explanation
Indices: 51938301--51938371 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
51938291 CTTTATATAT
*
51938301 TTTTAAAATTTTTATAAA-TA
1 TTTTAAAA-TTTTAAAAATTA
51938321 TTTTAAAA-TTTAAAAATTA
1 TTTTAAAATTTTAAAAATTA
* * * *
51938340 GTTTGAACTTTTGAAAATTA
1 TTTTAAAATTTTAAAAATTA
51938360 TTTTAAAATTTT
1 TTTTAAAATTTT
51938372 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 27 0.66
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTAAAATTTTAAAAATTA
Found at i:51938375 original size:12 final size:12
Alignment explanation
Indices: 51938360--51938384 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51938350 TTGAAAATTA
51938360 TTTTAAAATTTT
1 TTTTAAAATTTT
51938372 TTTTAAAATTTT
1 TTTTAAAATTTT
51938384 T
1 T
51938385 GTTGAGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:51940136 original size:17 final size:17
Alignment explanation
Indices: 51940114--51940156 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
51940104 TATAAAGATA
*
51940114 AATATTAGATTAAATTT
1 AATATTAAATTAAATTT
51940131 AATATTAAATTAAATTT
1 AATATTAAATTAAATTT
51940148 AATATTAAA
1 AATATTAAA
51940157 GTAATTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATATTAAATTAAATTT
Found at i:51947248 original size:66 final size:69
Alignment explanation
Indices: 51947088--51947336 Score: 243
Period size: 66 Copynumber: 3.5 Consensus size: 69
51947078 GTTAAAAGTG
* * *
51947088 ATTAAATTTAATCATATTTCAACTCTTTAAACTTTGCGATAAATATTAGATTAAATTTAACATTA
1 ATTAAATTTAATCATAATTCAACTCTCTAAACTCT-CGATAAATATTAGATTAAATTTAACATTA
51947153 AAGCA
65 AAGCA
* * * *
51947158 ATTAAATTTAATCATAGTTGAACTCTCTAAACTCT-G-TAAATATTAGATTAAATTTAATATTCA
1 ATTAAATTTAATCATAATTCAACTCTCTAAACTCTCGATAAATATTAGATTAAATTTAACATTAA
51947221 A-CA
66 AGCA
* * * *
51947224 ATTAAGTTTAATCATAATTCAACTCTCTAAACTCTCCTTATATAAACATAAATATTGGAGTAAAT
1 ATTAAATTTAATCATAATTCAACTCTCTAAACTCT-C---------GATAAATATTAGATTAAAT
* *
51947289 TTAATATTAAAGTA
56 TTAACATTAAAGCA
* *
51947303 ATTAAGTTTAATCATAATTGAACTCTCTAAACTC
1 ATTAAATTTAATCATAATTCAACTCTCTAAACTC
51947337 CACCTATATA
Statistics
Matches: 151, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
66 34 0.23
67 26 0.17
68 1 0.01
70 31 0.21
78 25 0.17
79 34 0.23
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (69 bp):
ATTAAATTTAATCATAATTCAACTCTCTAAACTCTCGATAAATATTAGATTAAATTTAACATTAA
AGCA
Found at i:51947407 original size:82 final size:79
Alignment explanation
Indices: 51947194--51947431 Score: 329
Period size: 82 Copynumber: 3.0 Consensus size: 79
51947184 CTAAACTCTG
* * *
51947194 TAAATATTAGATTAAATTTAATATTCAA-CAATTAAGTTTAATCATAATTCAACTCTCTAAACTC
1 TAAATATTAGATTAAATTTAATATTAAAGTAATTAAGTTTAATCATAATTGAACTCTCTAAACTC
* *
51947258 TC-CTTATATAAACA
66 -CACCTATATAAAGA
* *
51947272 TAAATATTGGAGTAAATTTAATATTAAAGTAATTAAGTTTAATCATAATTGAACTCTCTAAACTC
1 TAAATATTAGATTAAATTTAATATTAAAGTAATTAAGTTTAATCATAATTGAACTCTCTAAACTC
51947337 CACCTATATAAAGA
66 CACCTATATAAAGA
* **
51947351 TAAATATTAATAGATTAAATTTAATATTAAAGTAATTAAGTTTAATTATAGGTGAACTCTCTAAA
1 TAAATA-T--TAGATTAAATTTAATATTAAAGTAATTAAGTTTAATCATAATTGAACTCTCTAAA
51947416 CT-CACCTATATAAAGA
63 CTCCACCTATATAAAGA
51947432 GTCTTGGGTC
Statistics
Matches: 143, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
78 26 0.18
79 50 0.35
80 1 0.01
81 14 0.10
82 52 0.36
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (79 bp):
TAAATATTAGATTAAATTTAATATTAAAGTAATTAAGTTTAATCATAATTGAACTCTCTAAACTC
CACCTATATAAAGA
Found at i:51958981 original size:22 final size:22
Alignment explanation
Indices: 51958953--51959105 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
51958943 TTTATTGTTC
*
51958953 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
51958975 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
51958997 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
51959019 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
51959041 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
51959063 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
51959085 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
51959106 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:51962339 original size:93 final size:92
Alignment explanation
Indices: 51962116--51962401 Score: 547
Period size: 93 Copynumber: 3.1 Consensus size: 92
51962106 GTTTAAAAGC
*
51962116 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAAAAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
51962181 TTACTATTTTTTTAA-ATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
51962207 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
51962272 TTACTATTTTTTTTAATATTATACATAT
66 TTACTA-TTTTTTTAATATTATACATAT
51962300 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
1 ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
51962365 TTACTATTTTTTTAATATTATACATAT
66 TTACTATTTTTTTAATATTATACATAT
51962392 ATTCATTTAC
1 ATTCATTTAC
51962402 ATAACACATA
Statistics
Matches: 192, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
91 70 0.36
92 40 0.21
93 82 0.43
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (92 bp):
ATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTA
TTACTATTTTTTTAATATTATACATAT
Found at i:51965213 original size:66 final size:65
Alignment explanation
Indices: 51965106--51965276 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
51965096 GAGCAAATTA
* * * *
51965106 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
51965170 G
65 G
* *
51965171 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
51965236 G
65 G
* ** * *
51965237 CAGCAGCTTAAAGCAGATGTGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
51965277 CGGCAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:51965273 original size:21 final size:21
Alignment explanation
Indices: 51965247--51965355 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
51965237 CAGCAGCTTA
* *
51965247 AAGCAGATGTGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
51965268 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * * *
51965289 AAGTACAGGCTGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* *** *
51965310 AAGTAGAGGCTAAAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
* * *
51965331 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
51965352 AAGC
1 AAGC
51965356 CGAGCAGCGT
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.41, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:51965722 original size:43 final size:43
Alignment explanation
Indices: 51965675--51966002 Score: 209
Period size: 43 Copynumber: 7.7 Consensus size: 43
51965665 CAAATTTTGT
* *
51965675 GGCGTTTTTGGAAAAAGCGCCACTAAAGATCATGGTCTTTAGC
1 GGCGTTTTTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
* * * * *
51965718 GGCGTTTGTAGG-GAAAGCGCCGCTAAAGATTAGGTTCTTTAGT
1 GGCGTTT-TTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
** * * * * *
51965761 GGCGTTTGAAGG-GAAAGCGCCGCTAAAGATTAAGTTCTTTAGT
1 GGCGTTT-TTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
* ** *
51965804 GGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTTTAGC
1 GGCGTTTTTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
* *** *
51965847 GGCGCTTGTCCCAAAAA-CACCGCTAAAGATCAGGGTCTTTAGC
1 GGCG-TTTTTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
** * * * *** *
51965890 GGCACTTCT--ACTAAAGCGCCGCTAAAGGTCTTAGTCTTCAGC
1 GGCGTTTTTGGA-AAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
* ** * *
51965932 GGCGTTTGTGCTAGAAGCGCCACTAAAGATCAGGGTCTTTAGC
1 GGCGTTTTTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
** *
51965975 GGCGATTTTTTTAAAAA-CGTCGCTAAAG
1 GGCG-TTTTTGGAAAAAGCGCCGCTAAAG
51966003 TTAGCGGCGC
Statistics
Matches: 220, Mismatches: 57, Indels: 16
0.75 0.19 0.05
Matches are distributed among these distances:
40 1 0.00
41 3 0.01
42 29 0.13
43 172 0.78
44 15 0.07
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (43 bp):
GGCGTTTTTGGAAAAAGCGCCGCTAAAGATCAGGGTCTTTAGC
Found at i:51965821 original size:86 final size:86
Alignment explanation
Indices: 51965688--51965978 Score: 239
Period size: 86 Copynumber: 3.4 Consensus size: 86
51965678 GTTTTTGGAA
* * * *
51965688 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTAGGGAAAGCGCCGCTAAAGATTAGGT
1 AAAGCGCCACTAAAGATCAAGGTCTTTAGCGGCGTTTGTAGGCAAAGCGCCGCTAAAGATCAGGG
*
51965753 TCTTTAGTGGCGTTTGAAGGG
66 TCTTTAGCGGCGTTTGAAGGG
* * * * *
51965774 AAAGCGCCGCTAAAGATTAAGTTCTTTAGTGGCGTTTGT-GGTCAAAGCGCCGCTATAGATCAGG
1 AAAGCGCCACTAAAGATCAAGGTCTTTAGCGGCGTTTGTAGG-CAAAGCGCCGCTAAAGATCAGG
* *****
51965838 GTCTTTAGCGGCGCTTGTCCCA
65 GTCTTTAGCGGCGTTTGAAGGG
* * * * ** * * ***
51965860 AAAACACCGCTAAAGATCAGGGTCTTTAGCGGCACTTCTA--CTAAAGCGCCGCTAAAGGTCTTA
1 AAAGCGCCACTAAAGATCAAGGTCTTTAGCGGCGTTTGTAGGC-AAAGCGCCGCTAAAGATCAGG
* * **
51965923 GTCTTCAGCGGCGTTTG-TGCT
65 GTCTTTAGCGGCGTTTGAAGGG
*
51965944 AGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCG
1 A-AAGCGCCACTAAAGATCAAGGTCTTTAGCGGCG
51965979 ATTTTTTTAA
Statistics
Matches: 162, Mismatches: 39, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
84 3 0.02
85 62 0.38
86 97 0.60
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (86 bp):
AAAGCGCCACTAAAGATCAAGGTCTTTAGCGGCGTTTGTAGGCAAAGCGCCGCTAAAGATCAGGG
TCTTTAGCGGCGTTTGAAGGG
Found at i:51965963 original size:128 final size:129
Alignment explanation
Indices: 51965688--51965978 Score: 327
Period size: 129 Copynumber: 2.3 Consensus size: 129
51965678 GTTTTTGGAA
* * *** * * * *
51965688 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTAGGGAAAGCGCCGCTAAAGATTAGGT
1 AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGCTTGTACCAAAAACACCGCTAAAGATCAGGG
* ** * * * * *
51965753 TCTTTAGTGGCGTTTGAAGGGAAAGCGCCGCTAAAGATTAAGTTCTTTAGTGGCGTTTGTGGTC
66 TCTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGATTAAGTTCTTCAGCGGCGTTTGTGCTC
* * *
51965817 AAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGCTTGTCCCAAAAACACCGCTAAAGATCAGGG
1 AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGCTTGTACCAAAAACACCGCTAAAGATCAGGG
* * * *
51965882 TCTTTAGCGGCACTTCTA-CTAAAGCGCCGCTAAAGGTCTTAG-TCTTCAGCGGCGTTTGTGCT-
66 TCTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGAT-TAAGTTCTTCAGCGGCGTTTGTGCTC
51965944 AGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCG
1 A-AAGCGCCACTAAAGATCAGGGTCTTTAGCGGCG
51965979 ATTTTTTTAA
Statistics
Matches: 134, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
127 1 0.01
128 64 0.48
129 69 0.51
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (129 bp):
AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGCTTGTACCAAAAACACCGCTAAAGATCAGGG
TCTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGATTAAGTTCTTCAGCGGCGTTTGTGCTC
Found at i:51965991 original size:128 final size:128
Alignment explanation
Indices: 51965688--51966002 Score: 312
Period size: 128 Copynumber: 2.4 Consensus size: 128
51965678 GTTTTTGGAA
* *** * * *
51965688 AAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTAGGGAAAGCGCCGCTAAAGATTAGGT
1 AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGTTT-TACCAAAAACGCCGCTAAAGATCAGGG
* ** * * * * *
51965753 TCTTTAGTGGCGTTTGAAGGGAAAGCGCCGCTAAAGATTAAGTTCTTTAGTGGCGTTTGTGGTC
65 TCTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGATTAAGTTCTTCAGCGGCGTTTGTGCTC
* * * * *
51965817 AAAGCGCCGCTATAGATCAGGGTCTTTAGCGGCGCTTGTCCCAAAAACACCGCTAAAGATCAGGG
1 AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCG-TTTTACCAAAAACGCCGCTAAAGATCAGGG
* * * *
51965882 TCTTTAGCGGCACTTCTA-CTAAAGCGCCGCTAAAGGTCTTAG-TCTTCAGCGGCGTTTGTGCT-
65 TCTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGAT-TAAGTTCTTCAGCGGCGTTTGTGCTC
*** *
51965944 AGAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGATTTTTTTAAAAACGTCGCTAAAG
1 A-AAGCGCCACTAAAGATCAGGGTCTTTAGCGGCG-TTTTACCAAAAACGCCGCTAAAG
51966003 TTAGCGGCGC
Statistics
Matches: 150, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
127 1 0.01
128 81 0.54
129 66 0.44
130 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (128 bp):
AAAGCGCCACTAAAGATCAGGGTCTTTAGCGGCGTTTTACCAAAAACGCCGCTAAAGATCAGGGT
CTTTAGCGGCACTTCAAGCGAAAGCGCCGCTAAAGATTAAGTTCTTCAGCGGCGTTTGTGCTC
Found at i:51966102 original size:22 final size:22
Alignment explanation
Indices: 51966074--51966116 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51966064 CTGCGGCGCT
*
51966074 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
51966096 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
51966117 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:51967632 original size:489 final size:489
Alignment explanation
Indices: 51966702--51967654 Score: 1681
Period size: 489 Copynumber: 1.9 Consensus size: 489
51966692 AATATTTCAC
*
51966702 TTATTTTTAATATTAAAAATTGGTCCATGTATATCAGCATGTGGTACATATAGCAAGTCACATGT
1 TTATTTTTAATATTAAAAACTGGTCCATGTATATCAGCATGTGGTACATATAGCAAGTCACATGT
*
51966767 CAGTGTCCTATTATTCTGTCAGTCACGCCACTTTTTACTAGTACAAAAGGATGAAATTTTTAACA
66 CAGTGTCCTATTATTCTGTCAGTCACGCCACTTTTTACTAGTACAAAAGAATGAAATTTTTAACA
* *
51966832 AAAACGACCAATTTACACTTTGATCCAACGTATAGGGACTATTTTACTCATCAAACAAAATACAA
131 AAAAAGACCAATTTACACTTTGATCCAACGTATAGAGACTATTTTACTCATCAAACAAAATACAA
* *
51966897 TTCGACTGTTAATACAATAACATTTATAATACTTTTACCATCAAACATGTAAAAACACAACGATC
196 TCCGACTCTTAATACAATAACATTTATAATACTTTTACCATCAAACATGTAAAAACACAACGATC
51966962 AAATTAAATTTCAGAAAGTTATGTGTTTCTATTAACACCTCATTATGCATAAAATAATTAAATAT
261 AAATTAAATTTCAGAAAGTTATGTGTTTCTATTAACACCTCATTATGCATAAAATAATTAAATAT
*
51967027 TTAAAATTTGATCCGAAATTAATAATTAAATTGATAAAATAGTGGTAACGCGTTGCATTGCCGTT
326 TTAAAATTTGATCCGAAATTAATAATTAAATTGATAAAATAGGGGTAACGCGTTGCATTGCCGTT
*
51967092 GAGCTGCTTATAGCTGTCCTCAACCGCAAACCAAGTGGAAGAAAATTAGAAGATGATGTAATTTG
391 GAGCTGCTTATAGCTGTCCTCAACCGCAAACCAAGTGGAAGAAAATTAGAAGAAGATGTAATTTG
51967157 TAAACAAATCAGACATACTGTAAAAAAATTTCTT
456 TAAACAAATCAGACATACTGTAAAAAAATTTCTT
* *
51967191 TTATTTTTAATATTAAAAACTGGTCCATGTATATCAGCATGTGGTACATATGGCAAGTCACGTGT
1 TTATTTTTAATATTAAAAACTGGTCCATGTATATCAGCATGTGGTACATATAGCAAGTCACATGT
*
51967256 TAGTGTCCTATTATTCTGTCAGTCACGCCACTTTTTACTAGTACAAAAGAATGAAATTTTTAACA
66 CAGTGTCCTATTATTCTGTCAGTCACGCCACTTTTTACTAGTACAAAAGAATGAAATTTTTAACA
* * ** *
51967321 AAAAAGACCAATTTACACTTTGATCCAACGTGTAGAGACTATTTTGCTCATCGGACAAAATAGAA
131 AAAAAGACCAATTTACACTTTGATCCAACGTATAGAGACTATTTTACTCATCAAACAAAATACAA
* * *
51967386 TCCGACTCTTAATACAATAACATTTATAGTACTTTTACCATCTAACATGTAAAAACACAATGATC
196 TCCGACTCTTAATACAATAACATTTATAATACTTTTACCATCAAACATGTAAAAACACAACGATC
*
51967451 AAATTAAATTTCAGAAAGTTATTTGTTTCTATTAACACCTCATTATGCATAAAATAATTAAATAT
261 AAATTAAATTTCAGAAAGTTATGTGTTTCTATTAACACCTCATTATGCATAAAATAATTAAATAT
*
51967516 TTAAAATTTGATCCGAAATTAATAATTAAATTGATAAAATTGGGGTAACGCGTTGCATTGCCGTT
326 TTAAAATTTGATCCGAAATTAATAATTAAATTGATAAAATAGGGGTAACGCGTTGCATTGCCGTT
* * *
51967581 GAGCTGCTTATAGCTGTCCTCAACCGCAAACCAAGTGGCAGAAATTTAGAAGAAGATGTGATTTG
391 GAGCTGCTTATAGCTGTCCTCAACCGCAAACCAAGTGGAAGAAAATTAGAAGAAGATGTAATTTG
*
51967646 TAAAGAAAT
456 TAAACAAAT
51967655 AGTCGTGAAA
Statistics
Matches: 439, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
489 439 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (489 bp):
TTATTTTTAATATTAAAAACTGGTCCATGTATATCAGCATGTGGTACATATAGCAAGTCACATGT
CAGTGTCCTATTATTCTGTCAGTCACGCCACTTTTTACTAGTACAAAAGAATGAAATTTTTAACA
AAAAAGACCAATTTACACTTTGATCCAACGTATAGAGACTATTTTACTCATCAAACAAAATACAA
TCCGACTCTTAATACAATAACATTTATAATACTTTTACCATCAAACATGTAAAAACACAACGATC
AAATTAAATTTCAGAAAGTTATGTGTTTCTATTAACACCTCATTATGCATAAAATAATTAAATAT
TTAAAATTTGATCCGAAATTAATAATTAAATTGATAAAATAGGGGTAACGCGTTGCATTGCCGTT
GAGCTGCTTATAGCTGTCCTCAACCGCAAACCAAGTGGAAGAAAATTAGAAGAAGATGTAATTTG
TAAACAAATCAGACATACTGTAAAAAAATTTCTT
Found at i:51969452 original size:22 final size:22
Alignment explanation
Indices: 51969424--51969471 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
51969414 CTCTCCAATC
51969424 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
51969446 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
51969468 CTCT
1 CTCT
51969472 GAAACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:51969510 original size:51 final size:51
Alignment explanation
Indices: 51969446--51969558 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
51969436 TTCCAAAATT
*
51969446 CTCTCAATTTCCTTCCAAAATTCTCTGAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
* *
51969497 CTCTCAATTTCCTTCGAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
51969548 CCCTCAATTTC
1 CTCTCAATTTC
51969559 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:51969698 original size:25 final size:26
Alignment explanation
Indices: 51969666--51969738 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 26
51969656 ATGGTAAGTA
51969666 TTAA-ATTTAATT-TTTATTTATTAT
1 TTAAGATTTAATTATTTATTTATTAT
* *
51969690 TTAAGATTT-TTTATTTATGTATT-T
1 TTAAGATTTAATTATTTATTTATTAT
*
51969714 TT-AGA--TAATTATTAATTTATTAT
1 TTAAGATTTAATTATTTATTTATTAT
51969737 TT
1 TT
51969739 GTTATAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 1 0.03
22 11 0.28
23 6 0.15
24 9 0.22
25 13 0.32
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
TTAAGATTTAATTATTTATTTATTAT
Found at i:51970686 original size:7 final size:7
Alignment explanation
Indices: 51970674--51970698 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51970664 AGTCGATTGA
51970674 TATTTAG
1 TATTTAG
51970681 TATTTAG
1 TATTTAG
51970688 TATTTAG
1 TATTTAG
51970695 TATT
1 TATT
51970699 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:51971376 original size:18 final size:18
Alignment explanation
Indices: 51971350--51971384 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51971340 AGGTGTGTTT
* *
51971350 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
51971368 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
51971385 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:51971622 original size:132 final size:132
Alignment explanation
Indices: 51971385--51971623 Score: 372
Period size: 132 Copynumber: 1.8 Consensus size: 132
51971375 CTTACATGTA
*
51971385 TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCCGGTTCAGCTTCATTTCCTGTGATGC
1 TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCCGGTTCAACTTCATTTCCTGTGATGC
51971450 CGAGCGGACAGTCGATATCTACGCCAACGGCGCAAGAGGGATTGCAAGGTGAGCCGTCGGAGAGC
66 CGAGCGGACAGTCGATATCTACGCCAACGGCGCAAGAGGGATTGCAAGGTGAGCCGTCGGAGAGC
51971515 TC
131 TC
* * * *
51971517 TCCTTTTCTGAATATTATGGCAGGTTGGAGCCAAATGCCTGGTTCAAC-TCTATTTCCTGTTATG
1 TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCCGGTTCAACTTC-ATTTCCTGTGATG
* * * * *
51971581 TCGAGCGGACCGTCGATATCTAGGCCAGCGGCGCAGGAGGGAT
65 CCGAGCGGACAGTCGATATCTACGCCAACGGCGCAAGAGGGAT
51971624 CGCAGATGCC
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.02
132 94 0.98
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (132 bp):
TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCCGGTTCAACTTCATTTCCTGTGATGC
CGAGCGGACAGTCGATATCTACGCCAACGGCGCAAGAGGGATTGCAAGGTGAGCCGTCGGAGAGC
TC
Found at i:51973877 original size:125 final size:125
Alignment explanation
Indices: 51973651--51973877 Score: 402
Period size: 125 Copynumber: 1.8 Consensus size: 125
51973641 CCCAAACTTG
51973651 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
* * *
51973716 TAGAAGCGATTTTATACTATTTACTCAGAAATGTCAAACAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACAATTTACACAGAAACGTCAAACAAAAATTATTTCTTACATGAC
*
51973776 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
51973841 TAGAAGCGATTTTATACAATTTGA-ACAGAAACGTCAA
66 TAGAAGCGATTTTATACAATTT-ACACAGAAACGTCAA
51973878 CTCGAAATAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
125 96 0.99
126 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
TAGAAGCGATTTTATACAATTTACACAGAAACGTCAAACAAAAATTATTTCTTACATGAC
Found at i:51974713 original size:153 final size:151
Alignment explanation
Indices: 51974472--51974811 Score: 524
Period size: 153 Copynumber: 2.2 Consensus size: 151
51974462 TTTTTTATTG
* *
51974472 AAAGTAATAAAATCCGGAAAAAAAATACGAATAAA--GGGTCGAAATAAGAGTTTTTAAAATTTA
1 AAAGTAATAAAATCTGG-AAAAAAATACGAATAAAGGGGGCCGAAATAAGAGTTTTTAAAATTTA
*
51974535 TTTAAAACACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
65 TTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
*
51974600 ATTAGAAAATAGTATATTTTTT
130 ATTAAAAAATAGTATATTTTTT
* * * *
51974622 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGGGCCGAAATAAGGGTTTTTTTAAATTT
1 AAAGTAATAAAATCT-GGAAAAAAATACGAATAAAGGGGGCCGAAATAAGAG-TTTTTAAAATTT
* *
51974687 ATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTGCTGAAATAATGTAAAATAATAA
64 ATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
*
51974752 AATTAAAAAATAGTATTTTTTTT
129 AATTAAAAAATAGTATATTTTTT
51974775 AAA-TAATAAAATCTGAGAAAAAAATACGAATAAAGGG
1 AAAGTAATAAAATCTG-GAAAAAAATACGAATAAAGGG
51974812 TTGAAATACG
Statistics
Matches: 172, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
150 29 0.17
151 3 0.02
152 43 0.25
153 97 0.56
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (151 bp):
AAAGTAATAAAATCTGGAAAAAAATACGAATAAAGGGGGCCGAAATAAGAGTTTTTAAAATTTAT
TTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
TTAAAAAATAGTATATTTTTT
Found at i:51974989 original size:2 final size:2
Alignment explanation
Indices: 51974977--51975015 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
51974967 AATTACCTCC
*
51974977 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51975016 TAAAACGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:51979661 original size:138 final size:138
Alignment explanation
Indices: 51979498--51979917 Score: 675
Period size: 138 Copynumber: 3.1 Consensus size: 138
51979488 ACATAGATAA
* *
51979498 AATTAATATATTAATTTGATTCATACAAGATATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATA
* *
51979563 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTATTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
51979628 AAGAATAT
131 AAGAATAT
* **
51979636 AATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATA
* * * *
51979701 TGAACAGTTGTATTAATCAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG-
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
51979765 AAGAAATAT
131 AAG-AATAT
51979774 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-TCGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACT-GAATTTATTAAT
* * *
51979838 ATAAATAATTATATTAATTAATTTCGGTCAAAATATAAAAGATATGGAAATTAATATTCTTTTGG
65 ATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
51979903 AAA-AATAT
130 AAAGAATAT
51979911 AATTAAT
1 AATTAAT
51979918 TTGTTCTAAC
Statistics
Matches: 258, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
137 15 0.06
138 241 0.93
139 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:51979979 original size:75 final size:75
Alignment explanation
Indices: 51979891--51980037 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 75
51979881 ATGGAAATTA
*
51979891 ATATTCTTTTGGAAA-AATATAATTAATTTGTTCTAACTTTCCATTTGTCTTCTCTATTAATAAG
1 ATATTCTTTTGGAAAGAATATAATT-ATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAG
51979955 GGAATAATGAT
65 GGAATAATGAT
* *
51979966 ATATTCTTTTGGAAAGAATATAATTCTTTTTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
51980031 GAATAAT
66 GAATAAT
51980038 CTTGGTTTTC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 59 0.87
76 9 0.13
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTATTTGTTCTAACTTTCAATTTGTCTTCTCTATTAATAAGG
GAATAATGAT
Found at i:51984932 original size:27 final size:27
Alignment explanation
Indices: 51984891--51984970 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
51984881 ACTCCCTGGG
*
51984891 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
51984918 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
51984945 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
51984971 CTCGTGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.30, T:0.14
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:51987522 original size:27 final size:27
Alignment explanation
Indices: 51987416--51987511 Score: 174
Period size: 27 Copynumber: 3.6 Consensus size: 27
51987406 ATAACACGAG
51987416 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
51987443 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
**
51987470 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGAACCCTTGTT
51987497 TGGTGCCGCCAACAG
1 TGGTGCCGCCAACAG
51987512 TGTTCCCTTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGAACCCTTGTT
Found at i:51987611 original size:27 final size:26
Alignment explanation
Indices: 51987579--51987646 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 26
51987569 TTTTTTTTTG
51987579 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAATT-T
51987606 ATATATTTTGGTAAATAAAAAAATTT
1 ATATATTTTGGTAAATAAAAAAATTT
*
51987632 ATAACATTTTGGTAA
1 AT-ATATTTTGGTAA
51987647 TTTTTAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 3 0.08
27 36 0.92
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (26 bp):
ATATATTTTGGTAAATAAAAAAATTT
Found at i:51989145 original size:2 final size:2
Alignment explanation
Indices: 51989138--51989164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51989128 TAAAAACTTA
51989138 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
51989165 AAATCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52006608 original size:17 final size:17
Alignment explanation
Indices: 52006588--52006660 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
52006578 ACTATAGATA
*
52006588 AATATTAATTTAATATT
1 AATATTAATTAAATATT
52006605 AATATCTAGA-TAAATATT
1 AATAT-TA-ATTAAATATT
52006623 AA-ATTAAATTAAATATT
1 AATATT-AATTAAATATT
*
52006640 AA-ATTTATTAAA-A-T
1 AATATTAATTAAATATT
52006654 AATATTA
1 AATATTA
52006661 TCTTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 3 0.06
15 4 0.08
16 8 0.17
17 21 0.44
18 11 0.23
19 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
AATATTAATTAAATATT
Found at i:52013773 original size:24 final size:25
Alignment explanation
Indices: 52013718--52013773 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
52013708 TCATATCTTT
* * *
52013718 GAAGTTATTGTGTATTATTATTCTA
1 GAAGTTATTATGCATTATTACTCTA
*
52013743 -AAATTATTATGCATTATTACT-TA
1 GAAGTTATTATGCATTATTACTCTA
52013766 GAAGTTAT
1 GAAGTTAT
52013774 GCTATATTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (25 bp):
GAAGTTATTATGCATTATTACTCTA
Found at i:52014490 original size:22 final size:22
Alignment explanation
Indices: 52014462--52014506 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52014452 GGTGTTTAGG
52014462 AATTTTAAGAAATTGAACCCTA
1 AATTTTAAGAAATTGAACCCTA
52014484 AATTTTAAGAAATTGAACCCTA
1 AATTTTAAGAAATTGAACCCTA
52014506 A
1 A
52014507 CTTACTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (22 bp):
AATTTTAAGAAATTGAACCCTA
Found at i:52015458 original size:2 final size:2
Alignment explanation
Indices: 52015451--52015489 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
52015441 TAAAAATTAT
52015451 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52015490 CNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52018782 original size:15 final size:15
Alignment explanation
Indices: 52018743--52018782 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
52018733 TCTCTTATTC
* *
52018743 ACAAAGAATAATGAA
1 ACAATGAATGATGAA
52018758 ACAATGAATGATGAA
1 ACAATGAATGATGAA
52018773 ACAATGAATG
1 ACAATGAATG
52018783 GAGTGAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (15 bp):
ACAATGAATGATGAA
Found at i:52027457 original size:18 final size:18
Alignment explanation
Indices: 52027436--52027474 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52027426 AAATAAAAGA
52027436 ATAAAAA-TTTAAAAAACT
1 ATAAAAATTTTAAAAAA-T
52027454 ATAAAAATTTTAAAAAAT
1 ATAAAAATTTTAAAAAAT
52027472 ATA
1 ATA
52027475 TATCCTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATTTTAAAAAAT
Found at i:52028095 original size:17 final size:17
Alignment explanation
Indices: 52028048--52028096 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
52028038 CTCTTTTCTG
52028048 ATTTTTATTT-TTTTAT
1 ATTTTTATTTATTTTAT
*
52028064 ATTTTTA-TAACTTTTGA-
1 ATTTTTATTTA-TTTT-AT
52028081 ATTTTTATTTATTTTA
1 ATTTTTATTTATTTTA
52028097 AAAAAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 1 0.04
16 8 0.30
17 15 0.56
18 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTTATTTATTTTAT
Found at i:52030622 original size:10 final size:10
Alignment explanation
Indices: 52030576--52030627 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
52030566 TGCCCATTTT
52030576 TATTTTAAAA
1 TATTTTAAAA
52030586 T-TTTTAAAA
1 TATTTTAAAA
* **
52030595 AATTAAAAAAA
1 TATT-TTAAAA
52030606 TATTTTTAAAA
1 TA-TTTTAAAA
52030617 TATTTTAAAA
1 TATTTTAAAA
52030627 T
1 T
52030628 TAAAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
9 8 0.24
10 12 0.36
11 11 0.33
12 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:52030641 original size:8 final size:9
Alignment explanation
Indices: 52030623--52030744 Score: 50
Period size: 9 Copynumber: 12.6 Consensus size: 9
52030613 AAAATATTTT
52030623 AAAATTAAA
1 AAAATTAAA
52030632 AAAATTAAA
1 AAAATTAAA
**
52030641 AAAGTATT-TT
1 AAA--ATTAAA
52030651 AAAATTAAA
1 AAAATTAAA
*
52030660 AAAACTAAAA
1 AAAA-TTAAA
52030670 AAAGTATTTTAAA
1 AAA--A--TTAAA
* **
52030683 AATATTTTA
1 AAAATTAAA
*
52030692 AAATTTAAA
1 AAAATTAAA
52030701 AAAATTAAA
1 AAAATTAAA
52030710 AAAGTATGTAAA
1 AAA--AT-TAAA
**
52030722 AAATATT-TT
1 AAA-ATTAAA
52030731 AAAATTAAA
1 AAAATTAAA
52030740 AAAAT
1 AAAAT
52030745 AAATATATTT
Statistics
Matches: 83, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
8 6 0.07
9 43 0.52
10 11 0.13
11 9 0.11
12 8 0.10
13 6 0.07
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:52030648 original size:28 final size:29
Alignment explanation
Indices: 52030613--52030683 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
52030603 AAATATTTTT
*
52030613 AAAA-TATTTTAAAATTAAAAAAA-TTAA
1 AAAAGTATTTTAAAATTAAAAAAACTAAA
52030640 AAAAGTATTTTAAAATTAAAAAAACTAAA
1 AAAAGTATTTTAAAATTAAAAAAACTAAA
52030669 AAAAGTATTTTAAAA
1 AAAAGTATTTTAAAA
52030684 ATATTTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 4 0.10
28 19 0.46
29 18 0.44
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAGTATTTTAAAATTAAAAAAACTAAA
Found at i:52030686 original size:68 final size:69
Alignment explanation
Indices: 52030576--52030716 Score: 223
Period size: 69 Copynumber: 2.0 Consensus size: 69
52030566 TGCCCATTTT
* * *
52030576 TATTTTAAAATTTTTAAAAAATTAAAAAAATATTTTTAAAATATTTTAAAA-TTAAAAAAATTAA
1 TATTTTAAAA-TTTAAAAAAACTAAAAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
52030640 AAAAG
65 AAAAG
52030645 TATTTTAAAA-TTAAAAAAACTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
1 TATTTTAAAATTTAAAAAAACTAAAAAAA-TATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
52030709 AAAAG
65 AAAAG
52030714 TAT
1 TAT
52030717 GTAAAAAATA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
67 16 0.24
68 20 0.30
69 31 0.46
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (69 bp):
TATTTTAAAATTTAAAAAAACTAAAAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
AAAG
Found at i:52030693 original size:40 final size:39
Alignment explanation
Indices: 52030637--52030747 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 39
52030627 TTAAAAAAAT
*
52030637 TAAAAAAGTATTTTAAAATTAAAAAAACTAAAAAAAGTATT
1 TAAAAAA-TATTTTAAAATTAAAAAAA-TAAAAAAAGTATG
* *
52030678 TTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAGTATG
1 TAAAAAATATTTTAAAA-TTAAAAAAATAAAAAAAGTATG
52030718 TAAAAAATATTTTAAAATTAAAAAAATAAA
1 TAAAAAATATTTTAAAATTAAAAAAATAAA
52030748 TATATTTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 12 0.19
40 37 0.58
41 15 0.23
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (39 bp):
TAAAAAATATTTTAAAATTAAAAAAATAAAAAAAGTATG
Found at i:52030722 original size:68 final size:67
Alignment explanation
Indices: 52030591--52030722 Score: 212
Period size: 68 Copynumber: 2.0 Consensus size: 67
52030581 TAAAATTTTT
* * *
52030591 AAAAAATTAAAAAAATATTTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAT
1 AAAAAACTAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTGTAAAAT
52030656 TA
66 TA
52030658 AAAAAACTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAGTA-TGTAAA
1 AAAAAACTAAAAAAA-TATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAGTATTGTAAA
52030722 A
64 A
52030723 AATATTTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
67 14 0.23
68 26 0.43
69 20 0.33
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (67 bp):
AAAAAACTAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTGTAAAAT
TA
Found at i:52042853 original size:21 final size:21
Alignment explanation
Indices: 52042803--52042860 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
52042793 TGTTGCTCTC
52042803 ATGAGCTTCAG-TTAACTCAT
1 ATGAGCTTCAGTTTAACTCAT
* * *
52042823 ATGAGTTTCAGTTTAGCTCTT
1 ATGAGCTTCAGTTTAACTCAT
*
52042844 TTGAGCTTCAGTTTAAC
1 ATGAGCTTCAGTTTAAC
52042861 CCTAATAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (21 bp):
ATGAGCTTCAGTTTAACTCAT
Found at i:52042878 original size:42 final size:42
Alignment explanation
Indices: 52042804--52042905 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
52042794 GTTGCTCTCA
* * *
52042804 TGAGCTTCAGTTAACTC-ATATGAGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGTTAACCCTATATAAGTTTCAGTTTAGCTCTTC
*
52042845 TGAGCTTCAGTTTAACCCTA-ATAAGTTTTAGTTTAGCTCTTC
1 TGAGCTTCAG-TTAACCCTATATAAGTTTCAGTTTAGCTCTTC
*
52042887 TAAGCTTCAGATTAACCCT
1 TGAGCTTCAG-TTAACCCT
52042906 TATGGGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 10 0.19
42 42 0.79
43 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (42 bp):
TGAGCTTCAGTTAACCCTATATAAGTTTCAGTTTAGCTCTTC
Found at i:52043973 original size:5 final size:5
Alignment explanation
Indices: 52043963--52044009 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
52043953 TGAAGTTTTC
* *
52043963 TCGAA TCGAA TCGAG T-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGA-A TCGAA -TCGAA TCGAA TCGAA TCGAA T
52044010 ATATTTGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:52044389 original size:17 final size:16
Alignment explanation
Indices: 52044351--52044391 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
52044341 CAATTTTAAT
*
52044351 ATAAATATTCAATATG
1 ATAAATATTCAATAAG
52044367 ACTAAATGATTCAATAAG
1 A-TAAAT-ATTCAATAAG
52044385 ATAAATA
1 ATAAATA
52044392 ATATAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 10 0.45
18 10 0.45
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (16 bp):
ATAAATATTCAATAAG
Found at i:52044825 original size:9 final size:9
Alignment explanation
Indices: 52044811--52044835 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52044801 TATAGTTTGA
52044811 TATTCGAAT
1 TATTCGAAT
52044820 TATTCGAAT
1 TATTCGAAT
52044829 TATTCGA
1 TATTCGA
52044836 GTCGAATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52046863 original size:22 final size:22
Alignment explanation
Indices: 52046821--52046866 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52046811 AAGAAATGGT
*
52046821 ATGAAATGAGTAATAGTTATGA
1 ATGAAATGAGTAATAGATATGA
*
52046843 ATGAAATTGAGTAGT-GATATGA
1 ATGAAA-TGAGTAATAGATATGA
52046865 AT
1 AT
52046867 TGAACTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (22 bp):
ATGAAATGAGTAATAGATATGA
Found at i:52050581 original size:18 final size:19
Alignment explanation
Indices: 52050547--52050584 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
52050537 TACTGAAACT
52050547 TTAGGCTTATGTATCGATAC
1 TTAGGCTTA-GTATCGATAC
52050567 TTAGGCTTA-TATCGATAC
1 TTAGGCTTAGTATCGATAC
52050585 CTACCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (19 bp):
TTAGGCTTAGTATCGATAC
Found at i:52056363 original size:16 final size:17
Alignment explanation
Indices: 52056335--52056369 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
52056325 AAATTTTTTC
52056335 TATTTTCTTATGGAAAA
1 TATTTTCTTATGGAAAA
52056352 TATTTT-TTATGGAAAA
1 TATTTTCTTATGGAAAA
52056368 TA
1 TA
52056370 AAAAAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
TATTTTCTTATGGAAAA
Found at i:52058225 original size:23 final size:22
Alignment explanation
Indices: 52058193--52058240 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
52058183 AGTATTTTTA
*
52058193 TTTTTATTTTAAGAATTTAATT
1 TTTTTATTTTAAGAATTTAAAT
* *
52058215 TTTTTATTTTTTAGATTTTAAAT
1 TTTTTA-TTTTAAGAATTTAAAT
52058238 TTT
1 TTT
52058241 AGGTTGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTTATTTTAAGAATTTAAAT
Found at i:52059590 original size:24 final size:24
Alignment explanation
Indices: 52059571--52059615 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
52059561 CATATATTTC
52059571 TGTTTTAT-AATATTTTTATAGTT
1 TGTTTTATGAATATTTTTATAGTT
*
52059594 TGTTTTATGTATA-TTTTATAGT
1 TGTTTTATGAATATTTTTATAGT
52059616 CCAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (24 bp):
TGTTTTATGAATATTTTTATAGTT
Found at i:52059765 original size:14 final size:14
Alignment explanation
Indices: 52059748--52059791 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
52059738 TACTAATATA
*
52059748 TATTTACTTTTTTT
1 TATTTACATTTTTT
* *
52059762 TATTTACCTTTATT
1 TATTTACATTTTTT
*
52059776 TATTTCCATTTTTT
1 TATTTACATTTTTT
52059790 TA
1 TA
52059792 GATACCTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTACATTTTTT
Found at i:52062412 original size:12 final size:13
Alignment explanation
Indices: 52062390--52062418 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52062380 GAAACTTTCA
52062390 ATATATTATATTT
1 ATATATTATATTT
52062403 ATAT-TTATATTT
1 ATATATTATATTT
52062415 ATAT
1 ATAT
52062419 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATATTATATTT
Found at i:52066712 original size:34 final size:34
Alignment explanation
Indices: 52066637--52066704 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
52066627 AAGTTTTTAT
* * *
52066637 AATATATATACGTACATATTTTTTAATTTGTATA
1 AATATATACACATACATATTTTTTAATCTGTATA
*
52066671 AATATATACACATACATATTTTTTTATCT-TATA
1 AATATATACACATACATATTTTTTAATCTGTATA
52066704 A
1 A
52066705 TTTATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (34 bp):
AATATATACACATACATATTTTTTAATCTGTATA
Found at i:52066768 original size:12 final size:12
Alignment explanation
Indices: 52066751--52066779 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
52066741 TTTTATAATC
52066751 TTATTAAATTCT
1 TTATTAAATTCT
52066763 TTATTAAATTCT
1 TTATTAAATTCT
52066775 TTATT
1 TTATT
52066780 TACATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTAAATTCT
Found at i:52067226 original size:72 final size:72
Alignment explanation
Indices: 52067113--52067252 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 72
52067103 TTTCAAACTT
* * *
52067113 AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGTGTCCTAACTTACTGGACATGATTCTTTT
1 AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTTT
52067178 TTTTCTC
66 TTTTCTC
* * * * *
52067185 AAGTTTTAAACGATCTCGGGAATTAAGAAA-AGATTGCGTCCTAACTTTCTGGGCATGATCCCTT
1 AAGTTTTAAACGACCTCGAGAATTAA-AAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTT
52067249 TTTT
65 TTTT
52067253 AAATCTGAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 56 0.95
73 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (72 bp):
AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTTT
TTTTCTC
Found at i:52068691 original size:142 final size:142
Alignment explanation
Indices: 52068435--52068714 Score: 515
Period size: 142 Copynumber: 2.0 Consensus size: 142
52068425 AAAACGTGAT
*
52068435 AAGAGAAGGATGATAGTTTAATGGAGGACTACACGACTATTACTCCAATGCCCTAGGATTCAAGA
1 AAGAGAAGGATGACAGTTTAATGGAGGACTACACGACTATTACTCCAATGCCCTAGGATTCAAGA
* *
52068500 TGACAAAGATTATTCAAGAGTCGCTGAACTTTCTTAAAGAGAAGCCAACGAGCATCACGATGATG
66 TGACAAAGATTATTCAAGAGTCACTGAACTTTCTTAAAAAGAAGCCAACGAGCATCACGATGATG
52068565 AATGAGCAACGA
131 AATGAGCAACGA
*
52068577 AAGAGAAGGATGACAGTTTAATGGAGGACTACACGACTATTACTCCATTGCCCTAGGATTCAAGA
1 AAGAGAAGGATGACAGTTTAATGGAGGACTACACGACTATTACTCCAATGCCCTAGGATTCAAGA
*
52068642 TGACAAAGATTATTCAAGAGTCACTGAACTTTCTTAAAAAGAAGCCAACGAGCATCGCGATGATG
66 TGACAAAGATTATTCAAGAGTCACTGAACTTTCTTAAAAAGAAGCCAACGAGCATCACGATGATG
52068707 AATGAGCA
131 AATGAGCA
52068715 GCGAGTCGCG
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (142 bp):
AAGAGAAGGATGACAGTTTAATGGAGGACTACACGACTATTACTCCAATGCCCTAGGATTCAAGA
TGACAAAGATTATTCAAGAGTCACTGAACTTTCTTAAAAAGAAGCCAACGAGCATCACGATGATG
AATGAGCAACGA
Found at i:52070305 original size:32 final size:32
Alignment explanation
Indices: 52070268--52070346 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
52070258 TTGAGCCAAT
*
52070268 ATTCTTTCATTCTTTACAAATAATTATTGTTG
1 ATTCTTTCATTCTTTACAAATAATTATTGTCG
52070300 ATTCTTTCATTCTTTACAAATAATTATTGTCG
1 ATTCTTTCATTCTTTACAAATAATTATTGTCG
52070332 ATTCTTTCATTCTTT
1 ATTCTTTCATTCTTT
52070347 TAGATTTCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.54
Consensus pattern (32 bp):
ATTCTTTCATTCTTTACAAATAATTATTGTCG
Found at i:52071311 original size:19 final size:19
Alignment explanation
Indices: 52071287--52071331 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
52071277 TATATTTAAA
*
52071287 AAAAAAGAAGGAAAGGAAAAG
1 AAAAAAGAA--AAAGAAAAAG
52071308 AAAAAAGAAAAAGAAAAAG
1 AAAAAAGAAAAAGAAAAAG
52071327 AAAAA
1 AAAAA
52071332 GGAGAGGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.61
21 9 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAGAAAAAG
Found at i:52071315 original size:7 final size:6
Alignment explanation
Indices: 52071284--52071332 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
52071274 AAATATATTT
*
52071284 AAAA-A AAAAGA AGGAAAGG AAAAGAA AAAAGA AAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA A--AAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAG
52071333 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.11
6 24 0.63
7 5 0.13
8 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:52072717 original size:44 final size:44
Alignment explanation
Indices: 52072654--52073005 Score: 334
Period size: 44 Copynumber: 7.9 Consensus size: 44
52072644 ACAACAGATT
* *
52072654 TTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACACCAGCC
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTC
* * * * * *
52072698 TTGCCTTCCTATACTGACAGCGGAGTA-AACTGAAGATAACAGATC
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-TC
* * *
52072743 TTGCCTTCCTGTACTGATAGTGAAGCAGATCGAAGACACCAGTT
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTC
* * * * * *
52072787 TTTCCTTCCTGTACTAACAGC-AGAGTAGA-CTAAAGATAACAGATC
1 TTGCCTTCCTGTACTGACAGCGA-AGCAGATC-GAAGACACCAG-TC
* * * *
52072832 TTTCCTTCCTATAATGACAGCGAAGCAGATCGAAGACACCAGCC
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTC
* * * *
52072876 TTGCCTTCCTATACTGACAGCGGAGCAGA-CTGAAGATAGCAGATC
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-TC
* * * *
52072921 TTGCCTTCCTGTACTGACAGCGAAGCATATCGAAAACACTAGCC
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTC
* *
52072965 TTGCCTTTCTGTACTGACAGCGAAGCAAATCGAAGACACCA
1 TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
52073006 TAGTTTGCAG
Statistics
Matches: 245, Mismatches: 52, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
43 4 0.02
44 138 0.56
45 98 0.40
46 5 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (44 bp):
TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTC
Found at i:52072751 original size:89 final size:89
Alignment explanation
Indices: 52072627--52072986 Score: 495
Period size: 89 Copynumber: 4.0 Consensus size: 89
52072617 CTAAAATTAT
* * * *
52072627 AGCGGAGTAGACTAAAAACAACAGATTTTGCCTTCCTGTACTGACAGCGAAGCAGATTGAAGACA
1 AGCGGAGTAGACTAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA
52072692 CCAGCCTTGCCTTCCTATACTGAC
66 CCAGCCTTGCCTTCCTATACTGAC
* * * *
52072716 AGCGGAGTAAACTGAAGATAACAGATCTTGCCTTCCTGTACTGATAGTGAAGCAGATCGAAGACA
1 AGCGGAGTAGACTAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA
** * * *
52072781 CCAGTTTTTCCTTCCTGTACTAAC
66 CCAGCCTTGCCTTCCTATACTGAC
* * * *
52072805 AGCAGAGTAGACTAAAGATAACAGATCTTTCCTTCCTATAATGACAGCGAAGCAGATCGAAGACA
1 AGCGGAGTAGACTAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA
52072870 CCAGCCTTGCCTTCCTATACTGAC
66 CCAGCCTTGCCTTCCTATACTGAC
* * * * *
52072894 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCATATCGAAAACA
1 AGCGGAGTAGACTAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA
* * *
52072959 CTAGCCTTGCCTTTCTGTACTGAC
66 CCAGCCTTGCCTTCCTATACTGAC
52072983 AGCG
1 AGCG
52072987 AAGCAAATCG
Statistics
Matches: 233, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 233 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (89 bp):
AGCGGAGTAGACTAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA
CCAGCCTTGCCTTCCTATACTGAC
Found at i:52073275 original size:100 final size:100
Alignment explanation
Indices: 52073023--52073433 Score: 531
Period size: 100 Copynumber: 4.1 Consensus size: 100
52073013 CAGCAGAGTG
*
52073023 GATTGAAGCTACAACAACGAATCTTACTTCCCA-GGCGGTGCAGTGGAACAGATCGAAGCTACAA
1 GATTGAAGCTACAACAACGAATCTTACTT-CCATGGCGGTGCAGTGGAACAGATTGAAGCTACAA
* * *
52073087 CGGCAAATCTTGCTTCCCAGACATTGCAATT-AAAA
65 CAGCGAATCTTGCTTCCCCGACATTGCAATTAAAAA
* * * * *
52073122 GATTGAGGCCACAACAACGAATCTTACTTTCC-TGGCAGTGTAGTGGAACAGATTGAAACTACAA
1 GATTGAAGCTACAACAACGAATCTTAC-TTCCATGGCGGTGCAGTGGAACAGATTGAAGCTACAA
* *
52073186 CGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAA
65 CAGCGAATCTTGCTTCCCCGACATTGCAATTAAAAA
* ** * * * * *
52073222 GATTGAAACTACAACGGCGAATCTTACTTCCATGGCGGTGTAATAGAGCAGATTGAGGCTACAAC
1 GATTGAAGCTACAACAACGAATCTTACTTCCATGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
* *
52073287 AGTGAATCTTGCTTCCCCGACATCGCAATTAAAAA
66 AGCGAATCTTGCTTCCCCGACATTGCAATTAAAAA
* *** * *
52073322 GATTGAAGCCACAATGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACGGATTGAAGCTACAAC
1 GATTGAAGCTACAACAACGAATCTTACTTCCATGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
*
52073387 AGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAA
66 AGCGAATCTTGCTTCCCCGACATTGCAATTAAAAA
52073422 GATTGAAGCTAC
1 GATTGAAGCTAC
52073434 TAATCTTATT
Statistics
Matches: 272, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
99 86 0.32
100 186 0.68
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (100 bp):
GATTGAAGCTACAACAACGAATCTTACTTCCATGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
AGCGAATCTTGCTTCCCCGACATTGCAATTAAAAA
Found at i:52073414 original size:50 final size:50
Alignment explanation
Indices: 52073023--52073433 Score: 277
Period size: 50 Copynumber: 8.2 Consensus size: 50
52073013 CAGCAGAGTG
* * * * * *
52073023 GATTGAAGCTACAACAACGAATCTTACTTCCCAGGCGGTGCAGTGGAACA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * * * * * *
52073073 GATCGAAGCTACAACGGCAAATCTTGCTTCCCAGACATTGCAAT-TAAAA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * * * * * * * *
52073122 GATTGAGGCCACAACAACGAATCTTACTTTCCTGGCAGTGTAGTGGAACA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * * * * **
52073172 GATTGAAACTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * ** * * * * **
52073222 GATTGAAACTACAACGGCGAATCTTACTTCCATGGCGGTGTAATAGAGCA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * * **
52073272 GATTGAGGCTACAACAGTGAATCTTGCTTCCCCGACA-TCGCAATTAAAAA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGT-GCAATGGAAAA
* ** * * * * **
52073322 GATTGAAGCCACAATGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACG
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
* * * **
52073372 GATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAA
1 GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
52073422 GATTGAAGCTAC
1 GATTGAAGCTAC
52073434 TAATCTTATT
Statistics
Matches: 264, Mismatches: 94, Indels: 6
0.73 0.26 0.02
Matches are distributed among these distances:
49 35 0.13
50 228 0.86
51 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (50 bp):
GATTGAAGCTACAACAGCGAATCTTACTTCCCCGACAGTGCAATGGAAAA
Found at i:52073600 original size:44 final size:44
Alignment explanation
Indices: 52073421--52073608 Score: 180
Period size: 44 Copynumber: 4.1 Consensus size: 44
52073411 GCAGTTAAAA
* *
52073421 AGATTGAAGCTACTAATCTTATTTCCCTGAAGTTGCAGTGGAGC
1 AGATTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
* * ** * * *
52073465 AGGTTAAAAATAAACCAATCTTATCTACCTGAAGTTGCAGTGGAGC
1 AGATTGAAGCT--ACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
** *
52073511 AGATTGAAGATCGGCTGTAAAT-CTCATCTCCCTGAAGTTGTAGTGGAGC
1 AGATTGAAG--CTAC--T-AATCCT-ATCTCCCTGAAGTTGCAGTGGAGC
*
52073560 AGATTGAAGCTACTAATCCTATCTCCCTGAAATTGCAGTGGAGC
1 AGATTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
52073604 AGATT
1 AGATT
52073609 CAAATGATAA
Statistics
Matches: 114, Mismatches: 21, Indels: 18
0.75 0.14 0.12
Matches are distributed among these distances:
44 37 0.32
45 3 0.03
46 37 0.32
47 2 0.02
48 1 0.01
49 34 0.30
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AGATTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGC
Found at i:52074298 original size:20 final size:21
Alignment explanation
Indices: 52074250--52074298 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
52074240 TTTAAAGGTG
52074250 ATTGTTGTCATTTTTTACTCTT
1 ATTGTT-TCATTTTTTACTCTT
*
52074272 ATT-TTTCATTTTTTTCT-TT
1 ATTGTTTCATTTTTTACTCTT
*
52074291 CTTGTTTC
1 ATTGTTTC
52074299 GAAATAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 15 0.62
21 2 0.08
22 3 0.12
ACGTcount: A:0.10, C:0.14, G:0.06, T:0.69
Consensus pattern (21 bp):
ATTGTTTCATTTTTTACTCTT
Found at i:52075237 original size:34 final size:33
Alignment explanation
Indices: 52075165--52075237 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 33
52075155 GAATAAGTTT
* * *
52075165 TTAT-AATATATATACGTACATATTTTTTAATT
1 TTATAAATATATACACATACATATTTTTTAATC
*
52075197 TGTATAAATATATACACATACATATTTTTTTTATC
1 T-TATAAATATATACACATACATA-TTTTTTAATC
52075232 TTATAA
1 TTATAA
52075238 TTTATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 1 0.03
33 3 0.09
34 21 0.62
35 9 0.26
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (33 bp):
TTATAAATATATACACATACATATTTTTTAATC
Found at i:52075758 original size:72 final size:72
Alignment explanation
Indices: 52075645--52075784 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 72
52075635 TTTCAAACTT
* * *
52075645 AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGTGTCCTAACTTACTGGACATGATTCTTTT
1 AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTTT
52075710 TTTTCTC
66 TTTTCTC
* * * *
52075717 AAGTTTTAAACGATCTCGGGAATTAAGAAA-AGATTGCGTCCTAACTTACTGGGCATGATCCCTT
1 AAGTTTTAAACGACCTCGAGAATTAA-AAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTT
52075781 TTTT
65 TTTT
52075785 AAATCTGAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 57 0.95
73 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (72 bp):
AAGTTTTAAACGACCTCGAGAATTAAAAAGAGATCGCGTCCTAACTTACTGGACATGATCCCTTT
TTTTCTC
Found at i:52079349 original size:29 final size:29
Alignment explanation
Indices: 52079312--52079379 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
52079302 ATAAAAAATA
* *
52079312 TATTTAATTACATTGAATCAAAGTTCATG
1 TATTAAATTACATTGAATCAAAATTCATG
* *
52079341 TATTAAATTGTACATTGGATCAAAATTCGTG
1 TATTAAA-T-TACATTGAATCAAAATTCATG
52079372 TA-TAAATT
1 TATTAAATT
52079380 TAAAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 7 0.21
30 5 0.15
31 20 0.61
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (29 bp):
TATTAAATTACATTGAATCAAAATTCATG
Found at i:52079363 original size:31 final size:30
Alignment explanation
Indices: 52079320--52079379 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
52079310 TATATTTAAT
*
52079320 TACATTGAATCAAAGTTCATGTATTAAATTG
1 TACATTGAATCAAAATTCATGTA-TAAATTG
* *
52079351 TACATTGGATCAAAATTCGTGTATAAATT
1 TACATTGAATCAAAATTCATGTATAAATT
52079380 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (30 bp):
TACATTGAATCAAAATTCATGTATAAATTG
Found at i:52079671 original size:20 final size:20
Alignment explanation
Indices: 52079637--52079690 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
52079627 CACATATTTT
52079637 AATAATTTT-AAAAAAGTAA
1 AATAATTTTAAAAAAAGTAA
52079656 AATAATTTTAAAAAAAGTAA
1 AATAATTTTAAAAAAAGTAA
52079676 AATAATTTTAAAAAA
1 AATAATTTTAAAAAA
52079691 TTATATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 9 0.26
20 25 0.74
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AATAATTTTAAAAAAAGTAA
Found at i:52079822 original size:21 final size:21
Alignment explanation
Indices: 52079798--52079849 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
52079788 CCATTGTTTT
* *
52079798 TAATCTCACCGTTACAGTATC
1 TAATCTCACCGCTACAGTAAC
*
52079819 TAATCTCACTGCTACAGTAAC
1 TAATCTCACCGCTACAGTAAC
52079840 TAATCTCACC
1 TAATCTCACC
52079850 ACCACCGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (21 bp):
TAATCTCACCGCTACAGTAAC
Found at i:52084977 original size:26 final size:26
Alignment explanation
Indices: 52084941--52084995 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
52084931 AATTTTTAAC
*
52084941 TTATATATTTTTATATTTTAGAT-TTT
1 TTATATATTTTTAT-TTTTAAATATTT
52084967 TTATATATTTTTATTTTTAAATATTT
1 TTATATATTTTTATTTTTAAATATTT
52084993 TTA
1 TTA
52084996 AAAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATATATTTTTATTTTTAAATATTT
Found at i:52084983 original size:16 final size:16
Alignment explanation
Indices: 52084946--52084995 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
52084936 TTAACTTATA
*
52084946 TATTTTTATAT-TTTA
1 TATTTTTATATATTTT
*
52084961 GATTTTTTATATATTTT
1 TA-TTTTTATATATTTT
*
52084978 TATTTTTAAATATTTT
1 TATTTTTATATATTTT
52084994 TA
1 TA
52084996 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 1 0.03
16 24 0.83
17 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TATTTTTATATATTTT
Found at i:52095214 original size:2 final size:2
Alignment explanation
Indices: 52095209--52095242 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
52095199 ATATATGGTC
* *
52095209 AT AT AT AT AT AT AT AA AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52095243 CCTTTACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:52099048 original size:18 final size:16
Alignment explanation
Indices: 52099019--52099055 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
52099009 AAAATATATG
52099019 AAAAAATTTAAAAATT
1 AAAAAATTTAAAAATT
52099035 AAAAAATTCATAAAAATT
1 AAAAAATT--TAAAAATT
52099053 AAA
1 AAA
52099056 GAAAATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATTTAAAAATT
Found at i:52101803 original size:31 final size:31
Alignment explanation
Indices: 52101768--52101835 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
52101758 TAATAATATG
*
52101768 GTGACTTAAATAAAAAAAATTGAATAGTTTA
1 GTGACTTAAATAAAAAAAATTGAATAGTTCA
* ***
52101799 GTGACTTAAATGAAAATTTTTGAATAGTTCA
1 GTGACTTAAATAAAAAAAATTGAATAGTTCA
52101830 GTGACT
1 GTGACT
52101836 ATTTTTAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (31 bp):
GTGACTTAAATAAAAAAAATTGAATAGTTCA
Found at i:52105198 original size:3 final size:3
Alignment explanation
Indices: 52105128--52105179 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
52105118 AGAATAAAAC
* * *
52105128 TAA TAA TAA TTAA TAG TAG TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52105174 TAA TAA
1 TAA TAA
52105180 ATGATGAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52108336 original size:179 final size:178
Alignment explanation
Indices: 52108077--52108539 Score: 620
Period size: 179 Copynumber: 2.6 Consensus size: 178
52108067 TACTATCTTC
* * * *
52108077 AGTCTGCTCCGCTGCAAACTCAGGGAGGTCAGACTTGTGTCTTCAATCTACTTCACTGCCAGTAC
1 AGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACTTGTGTCTTCGATCTACTTCGCTACCAGTAC
* * * * *
52108142 ATGAAGACAAGATCTGTTACTTTTAGTCTGCTCCGCTGTAAACTTAGGGAGATCAGGCTTGTGTC
66 AGGAAGACCAGATCTGTTGCTTTTAGTCTGCTCCGCTGTAAACTCAGAGAGATCAGGCTTGTGTC
* * ** * *
52108207 TTTGATCTGCTTCACTGTCGGTATAGGAAGACTAGATCTATTGTTTTTT
131 TTCGATCTGCTTCACTGCCGGTATAAAAAGACAAGATCTATTG-CTTTT
* * * * * *
52108256 TGTCTGCTTCACTGCAAACTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTACCGGTAC
1 AGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACTTGTGTCTTCGATCTACTTCGCTACCAGTAC
* * * *
52108321 AGGAAGACCAGATCTGCTGCTTTTAGTCTGCTCCGCTGCAAACTCAGAGAGGTCAGGCTTGTTTC
66 AGGAAGACCAGATCTGTTGCTTTTAGTCTGCTCCGCTGTAAACTCAGAGAGATCAGGCTTGTGTC
* *
52108386 TTCGATCTGCTTCGCTGCCGGTATAAAAAGACAAGATCTGTTGCTTTT
131 TTCGATCTGCTTCACTGCCGGTATAAAAAGACAAGATCTATTGCTTTT
* * * *
52108434 AGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACTTGTGTCTTTGATCTACTTTGCTACCCGTAT
1 AGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACTTGTGTCTTCGATCTACTTCGCTACCAGTAC
* *
52108499 AGGAAGACCAGATCTGTTGCTTTTAGTCTACTCCTCTGTAA
66 AGGAAGACCAGATCTGTTGCTTTTAGTCTGCTCCGCTGTAA
52108540 TTTCTGAGAG
Statistics
Matches: 244, Mismatches: 40, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
178 97 0.40
179 147 0.60
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (178 bp):
AGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACTTGTGTCTTCGATCTACTTCGCTACCAGTAC
AGGAAGACCAGATCTGTTGCTTTTAGTCTGCTCCGCTGTAAACTCAGAGAGATCAGGCTTGTGTC
TTCGATCTGCTTCACTGCCGGTATAAAAAGACAAGATCTATTGCTTTT
Found at i:52108501 original size:268 final size:268
Alignment explanation
Indices: 52108006--52108522 Score: 687
Period size: 268 Copynumber: 1.9 Consensus size: 268
52107996 TCCGCTACTG
* *
52108006 CTCAGGGAGATAAGGCTAGTGCTTTCAATATGCTTCACTGCCAGTACAGGAAGACAATATCTACT
1 CTCAGGGAGATAAGGCTAGTGCTTTCAATATGCTTCACTACCAGTACAGGAAGACAAGATCTACT
*
52108071 ATCTTCAGTCTGCTCCGCTGCAAACTCAGGGAGGTCAGACTTGTGTCTTCAATCTACTTCACTGC
66 ATCTTCAGTCTGCTCCGCTGCAAACTCAGAGAGGTCAGACTTGTGTCTTCAATCTACTTCACTGC
** * * *
52108136 CAGTACATGAAGACAAGATCTGTTACTTTTAGTCTGCTCCGCTGTAAACTTAGGGAGATCAGGCT
131 CAGTACAAAAAGACAAGATCTGTTACTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACT
* ** * * *
52108201 TGTGTCTTTGATCTGCTTCACTGTCGGTATAGGAAGACTAGATCTATTGTTTTTTTGTCTGCTTC
196 TGTGTCTTTGATCTACTTCACTACCCGTATAGGAAGACCAGATCTATTGCTTTTTTGTCTGCTTC
52108266 ACTGCAAA
261 ACTGCAAA
* * * * * * * *
52108274 CTCAGGGAGATCAGGCTTGTG-TCTTCGATCTGCTTCGCTACCGGTACAGGAAGACCAGATCTGC
1 CTCAGGGAGATAAGGCTAGTGCT-TTCAATATGCTTCACTACCAGTACAGGAAGACAAGATCTAC
* * * * * * *
52108338 T-GCTTTTAGTCTGCTCCGCTGCAAACTCAGAGAGGTCAGGCTTGTTTCTTCGATCTGCTTCGCT
65 TATC-TTCAGTCTGCTCCGCTGCAAACTCAGAGAGGTCAGACTTGTGTCTTCAATCTACTTCACT
* * *
52108402 GCCGGTATAAAAAGACAAGATCTGTTGCTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGATCAGA
129 GCCAGTACAAAAAGACAAGATCTGTTACTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGATCAGA
** *
52108467 CTTGTGTCTTTGATCTACTTTGCTACCCGTATAGGAAGACCAGATCTGTTGCTTTT
194 CTTGTGTCTTTGATCTACTTCACTACCCGTATAGGAAGACCAGATCTATTGCTTTT
52108523 AGTCTACTCC
Statistics
Matches: 212, Mismatches: 35, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
267 2 0.01
268 210 0.99
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (268 bp):
CTCAGGGAGATAAGGCTAGTGCTTTCAATATGCTTCACTACCAGTACAGGAAGACAAGATCTACT
ATCTTCAGTCTGCTCCGCTGCAAACTCAGAGAGGTCAGACTTGTGTCTTCAATCTACTTCACTGC
CAGTACAAAAAGACAAGATCTGTTACTTTTAGTCTGCTCCGCTGCAAACTCAGGGAGATCAGACT
TGTGTCTTTGATCTACTTCACTACCCGTATAGGAAGACCAGATCTATTGCTTTTTTGTCTGCTTC
ACTGCAAA
Found at i:52108559 original size:89 final size:89
Alignment explanation
Indices: 52108006--52108532 Score: 574
Period size: 89 Copynumber: 5.9 Consensus size: 89
52107996 TCCGCTACTG
* * * * * * * * *
52108006 CTCAGGGAGATAAGGCTAGTG-CTTTCAATATGCTTCACTGCCAGTACAGGAAGACAATATCTAC
1 CTCAGGGAGATCAGGCTTGTGTC-TTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCT-G
*
52108070 TAT-C-TTCAGTCTGCTCCGCTGCAAA
64 T-TGCTTTTAGTCTGCTCCGCTGCAAA
* * * * * * * *
52108095 CTCAGGGAGGTCAGACTTGTGTCTTCAATCTACTTCACTGCCAGTACATGAAGACAAGATCTGTT
1 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
* *
52108160 ACTTTTAGTCTGCTCCGCTGTAAA
66 GCTTTTAGTCTGCTCCGCTGCAAA
* * * * * *
52108184 CTTAGGGAGATCAGGCTTGTGTCTTTGATCTGCTTCACTGTCGGTATAGGAAGACTAGATCTATT
1 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
* * * *
52108249 GTTTTTTTGTCTGCTTCACTGCAAA
66 G-CTTTTAGTCTGCTCCGCTGCAAA
* * * *
52108274 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTACCGGTACAGGAAGACCAGATCTGCT
1 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
52108339 GCTTTTAGTCTGCTCCGCTGCAAA
66 GCTTTTAGTCTGCTCCGCTGCAAA
* * * **
52108363 CTCAGAGAGGTCAGGCTTGTTTCTTCGATCTGCTTCGCTGCCGGTATAAAAAGACAAGATCTGTT
1 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
52108428 GCTTTTAGTCTGCTCCGCTGCAAA
66 GCTTTTAGTCTGCTCCGCTGCAAA
* * * * * * *
52108452 CTCAGGGAGATCAGACTTGTGTCTTTGATCTACTTTGCTACCCGTATAGGAAGACCAGATCTGTT
1 CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
*
52108517 GCTTTTAGTCTACTCC
66 GCTTTTAGTCTGCTCC
52108533 TCTGTAATTT
Statistics
Matches: 370, Mismatches: 64, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
87 1 0.00
88 2 0.01
89 291 0.79
90 76 0.21
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (89 bp):
CTCAGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTT
GCTTTTAGTCTGCTCCGCTGCAAA
Found at i:52108748 original size:16 final size:15
Alignment explanation
Indices: 52108723--52108760 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
52108713 TAACTAGGTG
52108723 TGTATGAATGATATT
1 TGTATGAATGATATT
52108738 TGTATTGAATGATATT
1 TGTA-TGAATGATATT
*
52108754 TGCATGA
1 TGTATGA
52108761 GTGTAGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:52109587 original size:93 final size:93
Alignment explanation
Indices: 52109428--52109714 Score: 484
Period size: 93 Copynumber: 3.0 Consensus size: 93
52109418 GAAAAATGCT
52109428 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
52109493 TATGATAGCAAATTTTGCTAAGATAAGA
66 TATGATAGCAAATTTTGCTAAGATAAGA
*
52109521 TGAAAAAGATTATCACAATGGACAAAAAGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
52109586 TATGATAGCAAATTTTGCTAAGATAAGA
66 TATGATAGCAAATTTTGCTAAGATAAGA
* * * * *
52109614 TGAAAAAGATTATCACAATGGATAATATGAAATTTTATTAAGAACAAGGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
52109679 TAATCAAGATAGCAAATTTTGCTAAGATAAGA
66 T-AT---GATAGCAAATTTTGCTAAGATAAGA
52109711 TGAA
1 TGAA
52109715 TAAGTTGAAA
Statistics
Matches: 183, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
93 152 0.83
94 2 0.01
97 29 0.16
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (93 bp):
TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
TATGATAGCAAATTTTGCTAAGATAAGA
Found at i:52113885 original size:440 final size:432
Alignment explanation
Indices: 52113045--52113896 Score: 1018
Period size: 440 Copynumber: 1.9 Consensus size: 432
52113035 GGGGTTGAAG
* * * *
52113045 TGGTTCTACCTAGGGTGGGCTCCTAAGGTCCTCTATATGTGGTTTGGTTCTAAAGAAAGGGTACA
1 TGGTTCTACCTAGGGTAGGCTCCTAAGGTCATCTATATGCGGTTCGGTTCTAAAGAAAGGGTACA
* * * *
52113110 TGAACCAGTAGATTCCTCGATCCTCACCCATATAGGCTCATATGGACTGAGTTCGGTTCAGGGGA
66 TGAACCAGCAGATTCCTCGATCCTCACCCATATAGGCTCATACGGACCGAGTTCAGTTCAGGGGA
* *
52113175 ATACATTTTCCTATGGCTGCAAGGAGATGAAAATCTCACGAAGACATAGGTACAGATGTATCCCG
131 ATACATTTCCCTATGGCTGC-AGGAGATGAAAATCTCACGAAAACATAGGTACAGATGTATCCCG
52113240 AAAGTGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGTAGCTTCTCACTCCCACTT
195 AAAGTGATCCACTATCCTG-ACGGAGGTGAAAACCTCACGAAGGAGTAGCTTCTCACTCCCACTT
* * * *
52113305 AAAAGGGTGTAACCAAGCGATTATGTAATGCAATATGCAGAAACATATAAAAAAATTCAAACCAA
259 AAAAGGGTATAACCAAGCGATCATGCAATGCAATACGCAGAAACATATAAAAAAATTCAAACCAA
* * ** * * *
52113370 TAGAGTAATTACAAACCGAAGTAATGAAAATCATAACAAAACGGATGAAATACAACAAAATAATT
324 CACAACAATTACAAACCGAAGTAATGAAAATCATAACAAAACGAATGAAATACAACAAAAGAATC
52113435 GTAAATTTAAACCAAGTTTTCGGGTGACCTCTAGGCATTCGATA
389 GTAAATTTAAACCAAGTTTTCGGGTGACCTCTAGGCATTCGATA
* *
52113479 TGGTTCTACCTAGGGTAGGCTTCTAAGGCTCAT-TATATGCGGTTCGGTTCTAAAGTAAGGGTAC
1 TGGTTCTACCTAGGGTAGGCTCCTAAGG-TCATCTATATGCGGTTCGGTTCTAAAGAAAGGGTAC
* * * *
52113543 CTGAACTAGCAGATTCCTCGATTCTCACCCATTATAGGCTCATACGGGCCGAGTTCAATTCAGTT
65 ATGAACCAGCAGATTCCTCGATCCTCACCCA-TATAGGCTCATACGGACCGAG-----TTCAGTT
*
52113608 CAGGGGAATACATTTCCCTATGGCCATGC-GGAGATGAAAATCTCACGAAAACATAGGTACGGAT
124 CAGGGGAATACATTTCCCTATGG-C-TGCAGGAGATGAAAATCTCACGAAAACATAGGTACAGAT
* * * * *
52113672 GTATCTCGAAAGTGATTCACTATCCCATG-CGGAGGTGAAAACTTCACGAAGGCGTAGTTTCTCA
187 GTATCCCGAAAGTGATCCACTAT-CC-TGACGGAGGTGAAAACCTCACGAAGGAGTAGCTTCTCA
* * * * * * * * *
52113736 CTCCCACTTAAAATGGTATGACCGAGTGGTCATGCAATGCAATGCGCAG-AA-ATATAACCAGAC
250 CTCCCACTTAAAAGGGTATAACCAAGCGATCATGCAATGCAATACGCAGAAACATATAA-AAAAA
* * * * * *
52113799 TT-AAACTAACACAACGATTATAAATCAC-AA-TGATGAAAATCGTAATAAAGACGAATGAAAAT
314 TTCAAACCAACACAACAATTACAAA-C-CGAAGTAATGAAAATCATAACAAA-ACGAATG-AAAT
* * * *
52113861 GCAACGAAAGGATCGTATATTTAAACCAAGTTTTCG
375 ACAACAAAAGAATCGTAAATTTAAACCAAGTTTTCG
52113897 ATTTTTGACA
Statistics
Matches: 350, Mismatches: 52, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
434 81 0.23
435 21 0.06
438 37 0.11
439 15 0.04
440 188 0.54
441 3 0.01
442 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (432 bp):
TGGTTCTACCTAGGGTAGGCTCCTAAGGTCATCTATATGCGGTTCGGTTCTAAAGAAAGGGTACA
TGAACCAGCAGATTCCTCGATCCTCACCCATATAGGCTCATACGGACCGAGTTCAGTTCAGGGGA
ATACATTTCCCTATGGCTGCAGGAGATGAAAATCTCACGAAAACATAGGTACAGATGTATCCCGA
AAGTGATCCACTATCCTGACGGAGGTGAAAACCTCACGAAGGAGTAGCTTCTCACTCCCACTTAA
AAGGGTATAACCAAGCGATCATGCAATGCAATACGCAGAAACATATAAAAAAATTCAAACCAACA
CAACAATTACAAACCGAAGTAATGAAAATCATAACAAAACGAATGAAATACAACAAAAGAATCGT
AAATTTAAACCAAGTTTTCGGGTGACCTCTAGGCATTCGATA
Found at i:52115430 original size:3 final size:3
Alignment explanation
Indices: 52115348--52115411 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
52115338 AAAATAAAAC
*
52115348 TAA TAA TAA TTAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
52115394 TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
52115412 ATGATGAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52118241 original size:41 final size:40
Alignment explanation
Indices: 52118187--52118418 Score: 198
Period size: 41 Copynumber: 5.7 Consensus size: 40
52118177 GTTTTAAAAA
** * * *
52118187 AAAAGCGTTGCTAATTCCCAGATCTTTAGCAGCGATTTTGT
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG-TTTTGT
* * * *
52118228 AAAAGCGCCGCTAATGTTAATATCTTTAGCGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCG-TTTTGT
* *
52118269 AAAAGCGCCGGTAATGCTCAGATATTTAGCGGCGTTTCTGT
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTT-TGT
* * **
52118310 AGAAGCGCCGCTAATGCTCAGATCTTTATCTACGTTTT-T
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTGT
* * * * *
52118349 CCAAAATCGCCTC-GATGCTCAAATCTTTAGCGGCGTTTATAT
1 --AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTT-TGT
* *
52118391 AAAAGCGCTGCTAACGCTCAGATCTTTA
1 AAAAGCGCCGCTAATGCTCAGATCTTTA
52118419 ATTATACTTC
Statistics
Matches: 149, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
39 1 0.01
40 32 0.21
41 115 0.77
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTGT
Found at i:52118335 original size:82 final size:80
Alignment explanation
Indices: 52118205--52118418 Score: 223
Period size: 82 Copynumber: 2.6 Consensus size: 80
52118195 TGCTAATTCC
* * * * * **
52118205 CAGATCTTTAGCAGCGATTTTGTAAAAGCGCCGCTAATGTTAATATCTTTAGCGGCGTTTTTGGA
1 CAGATCTTTAGCGGCG-TTTTGTAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTCCA
52118270 AAAGCGCCGGT-AATGCT
65 AAAGCGCC--TCAATGCT
* * * *
52118287 CAGATATTTAGCGGCGTTTCTGTAGAAGCGCCGCTAATGCTCAGATCTTTATCTACGTTTTTCCA
1 CAGATCTTTAGCGGCGTTT-TGTAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTCCA
* *
52118352 AAATCGCCTCGATGCT
65 AAAGCGCCTCAATGCT
* * * *
52118368 CAAATCTTTAGCGGCGTTTATATAAAAGCGCTGCTAACGCTCAGATCTTTA
1 CAGATCTTTAGCGGCGTTT-TGTAAAAGCGCCGCTAATGCTCAGATCTTTA
52118419 ATTATACTTC
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 52 0.47
82 57 0.52
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (80 bp):
CAGATCTTTAGCGGCGTTTTGTAAAAGCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTCCAA
AAGCGCCTCAATGCT
Found at i:52118714 original size:43 final size:42
Alignment explanation
Indices: 52118667--52118912 Score: 174
Period size: 43 Copynumber: 5.8 Consensus size: 42
52118657 AGAGAAAAAA
* *
52118667 GCCGCTAACGATCAGGGTCTTTAGCGACGTTTTCTGGAGAAGC
1 GCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTT-TGGAGAAGC
* * *
52118710 GCCGCTAAAGATCAGGGTGTTTAGCGGCGATTGTTGGAGTAGC
1 GCCGCTAAAGATCAGGGTCTTTAGCGGCG-TTTTTGGAGAAGC
* ** *
52118753 GCCGCTAAAGGTCATTGTCTTTAGCGGCGTTTGTTTGG-TAAGC
1 GCCGCTAAAGATCAGGGTCTTTAGCGGCG-TT-TTTGGAGAAGC
* * * * ** * *
52118796 ACCACTAAAG-CCATGACCTTTAGCGGCGTTTGTGGTAAAAGC
1 GCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGG-AGAAGC
* * * * *
52118838 GCCGCTAAAGACCA-TGACTTTTAGCGGCGTTTGTGGTGAAAGC
1 GCCGCTAAAGATCAGGGTC-TTTAGCGGCGTTTTTGGAG-AAGC
* ***
52118881 GCCGCTAAAGGTTTTGGTCTTTAGCGGCGTTT
1 GCCGCTAAAGATCAGGGTCTTTAGCGGCGTTT
52118913 ATTTCTAAAA
Statistics
Matches: 161, Mismatches: 34, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
40 4 0.02
41 2 0.01
42 27 0.17
43 119 0.74
44 9 0.06
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (42 bp):
GCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGGAGAAGC
Found at i:52119035 original size:22 final size:22
Alignment explanation
Indices: 52118993--52119035 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52118983 TTGCGACGCT
* *
52118993 AAAAAGCGCCGCTGAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
52119015 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
52119036 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.23, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:52126776 original size:18 final size:17
Alignment explanation
Indices: 52126743--52126781 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52126733 TTTTATAAAT
52126743 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52126761 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52126778 TGTG
1 TGTG
52126782 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52126899 original size:8 final size:8
Alignment explanation
Indices: 52126886--52126914 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52126876 CACTAGAGAC
52126886 CAGTGTTA
1 CAGTGTTA
52126894 CAGTGTTA
1 CAGTGTTA
52126902 CAGTGTTA
1 CAGTGTTA
52126910 CAGTG
1 CAGTG
52126915 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:52127028 original size:23 final size:23
Alignment explanation
Indices: 52127001--52127076 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
52126991 AGTGTTATTG
52127001 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52127024 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52127047 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52127070 ATCAGTG
1 ATCAGTG
52127077 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52132190 original size:2 final size:2
Alignment explanation
Indices: 52132183--52132257 Score: 101
Period size: 2 Copynumber: 41.0 Consensus size: 2
52132173 ACCCTAAAAT
52132183 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG -G AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52132222 -G AG AG AG AG -G AG -G AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52132258 GAGGAGGAGG
Statistics
Matches: 66, Mismatches: 0, Indels: 14
0.82 0.00 0.17
Matches are distributed among these distances:
1 7 0.11
2 59 0.89
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52132216 original size:3 final size:3
Alignment explanation
Indices: 52132208--52132350 Score: 204
Period size: 3 Copynumber: 47.0 Consensus size: 3
52132198 GAGAGAGAGA
52132208 GAG GAG GA- GAG GAG GA- GAG AGAG GAG GAG AGAG AGAG GA- GAG AGAG
1 GAG GAG GAG GAG GAG GAG GAG -GAG GAG GAG -GAG -GAG GAG GAG -GAG
52132254 AGAG GAG GAG GAG GAG GAG GAG GAGG GAG GAG GAG GAG GAG GAG GAG
1 -GAG GAG GAG GAG GAG GAG GAG GA-G GAG GAG GAG GAG GAG GAG GAG
52132301 GAG GAG GAG GAG GAG GAG GAG GA- GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
52132348 GAG
1 GAG
52132351 AGGGAAAGGG
Statistics
Matches: 132, Mismatches: 0, Indels: 16
0.89 0.00 0.11
Matches are distributed among these distances:
2 8 0.06
3 104 0.79
4 20 0.15
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
GAG
Done.