Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015058.1 Kokia drynarioides strain JFW-HI SEQ_130102, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 830620
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 706 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:380143 original size:18 final size:18
Alignment explanation
Indices: 380116--380150 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
380106 ATTGTTCCCA
*
380116 TCCTCGTCCTCATCCTCG
1 TCCTCATCCTCATCCTCG
*
380134 TCCTCATCCTCGTCCTC
1 TCCTCATCCTCATCCTC
380151 AACCAACTTT
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:0.06, C:0.51, G:0.09, T:0.34
Consensus pattern (18 bp):
TCCTCATCCTCATCCTCG
Found at i:388037 original size:22 final size:22
Alignment explanation
Indices: 388012--388053 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
388002 TTTTTTGTTT
*
388012 TACTATTATTTTGTTATTATAG
1 TACTACTATTTTGTTATTATAG
*
388034 TACTACTATTTTGTTGTTAT
1 TACTACTATTTTGTTATTAT
388054 TATTCAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (22 bp):
TACTACTATTTTGTTATTATAG
Found at i:388094 original size:12 final size:12
Alignment explanation
Indices: 388077--388102 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
388067 TATACTTTTT
388077 ATTTTATTATTA
1 ATTTTATTATTA
388089 ATTTTATTATTA
1 ATTTTATTATTA
388101 AT
1 AT
388103 ATAGAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTATTATTA
Found at i:390866 original size:9 final size:9
Alignment explanation
Indices: 390852--390878 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
390842 TATTTGATTT
390852 AAATCAATC
1 AAATCAATC
390861 AAATCAATC
1 AAATCAATC
390870 AAATCAATC
1 AAATCAATC
390879 GAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATCAATC
Found at i:395813 original size:4 final size:4
Alignment explanation
Indices: 395806--395837 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
395796 GTGTGTATGT
395806 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
395838 TGATCCTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:396694 original size:19 final size:20
Alignment explanation
Indices: 396650--396694 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
396640 TCTTAAATTA
*
396650 TAATTATTTTTAAATTTTTAT
1 TAATTA-TTTCAAATTTTTAT
396671 T--TTATTTCAAATTTTT-T
1 TAATTATTTCAAATTTTTAT
396688 TAATTAT
1 TAATTAT
396695 AAATATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 2 0.10
18 11 0.52
19 7 0.33
21 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TAATTATTTCAAATTTTTAT
Found at i:402695 original size:25 final size:26
Alignment explanation
Indices: 402655--402711 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
402645 CTTAAATCAT
402655 ATTTTTCGAAAGTATTTTATCACAAC
1 ATTTTTCGAAAGTATTTTATCACAAC
* *
402681 ATTTTTC-AAATTATTTTATCACGAC
1 ATTTTTCGAAAGTATTTTATCACAAC
402706 ATTTTT
1 ATTTTT
402712 AAAAAACCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTTTTCGAAAGTATTTTATCACAAC
Found at i:407900 original size:42 final size:42
Alignment explanation
Indices: 407840--407956 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
407830 CGCTTTACTT
*
407840 AGTTTAATTTT-TGAATTCGAAGTAAGGTTAATAGTATGTTTC
1 AGTTTAATTTTCTG-ATTCGAAGTAAGATTAATAGTATGTTTC
* * **
407882 AGTTTACTTTTCTGATTCGGAGTAAGATTCTTAGTATGTTTC
1 AGTTTAATTTTCTGATTCGAAGTAAGATTAATAGTATGTTTC
*
407924 AGTTTAATTTTCGGATT-GCAAGTAAGATTAATA
1 AGTTTAATTTTCTGATTCG-AAGTAAGATTAATA
407957 ATGTGTGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.02
42 60 0.95
43 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (42 bp):
AGTTTAATTTTCTGATTCGAAGTAAGATTAATAGTATGTTTC
Found at i:408166 original size:42 final size:42
Alignment explanation
Indices: 408107--408189 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
408097 CTTAGTTCAA
* * *
408107 TTTTTTGATTCGAAGTAAGATTAATAGTATGTTTCAGTTTAC
1 TTTTTGGATCCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
* *
408149 TTTTTGGATCCGAAGTAAGATTTAGAGTATGTTTCGGTTTA
1 TTTTTGGATCCGAAGTAAGATTAAGAGTATGTTTCAGTTTA
408190 TATTTGATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (42 bp):
TTTTTGGATCCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
Found at i:408408 original size:97 final size:97
Alignment explanation
Indices: 408274--408450 Score: 275
Period size: 97 Copynumber: 1.8 Consensus size: 97
408264 GATTCATGAA
* ** * * *
408274 TCATGATATGTTCTTTTGTTTGATTAAGTTATGTCGTAGCTT-TTCATTTCTACATTTCCTCTTT
1 TCATGATATGTTCTTTTGTTTGATTAAATTACCTCGTAG-TTCTACATTTCTACATTTCCGCCTT
408338 ACTTAGTTTAATTTTTTTAATTTGTTGTAAGAT
65 ACTTAGTTTAATTTTTTTAATTTGTTGTAAGAT
408371 TCATGATATGTTCTTTTGTTTGATTAAATTACCTCGTAGTTCTACATTTCTACATTTCCGCCTTA
1 TCATGATATGTTCTTTTGTTTGATTAAATTACCTCGTAGTTCTACATTTCTACATTTCCGCCTTA
*
408436 CTTGGTTTAATTTTT
66 CTTAGTTTAATTTTT
408451 GAATACATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 2 0.03
97 70 0.97
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (97 bp):
TCATGATATGTTCTTTTGTTTGATTAAATTACCTCGTAGTTCTACATTTCTACATTTCCGCCTTA
CTTAGTTTAATTTTTTTAATTTGTTGTAAGAT
Found at i:413182 original size:19 final size:20
Alignment explanation
Indices: 413160--413197 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
413150 TGATTTTTAG
*
413160 TACCCTTTT-TTATTTCTAT
1 TACCATTTTCTTATTTCTAT
*
413179 TACCATTTTCTTTTTTCTA
1 TACCATTTTCTTATTTCTA
413198 AATCCAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (20 bp):
TACCATTTTCTTATTTCTAT
Found at i:416889 original size:20 final size:21
Alignment explanation
Indices: 416853--416896 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
416843 CAAATAAATA
416853 TATTTTATTACTTAATT-TAT
1 TATTTTATTACTTAATTATAT
*
416873 TATTTTATT-TTTAAATTATAT
1 TATTTTATTACTT-AATTATAT
416894 TAT
1 TAT
416897 GAGATTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTATTACTTAATTATAT
Found at i:421954 original size:20 final size:20
Alignment explanation
Indices: 421937--421978 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
421927 AAATTTAACT
421937 TAATAAAATTAAAATTAAAA
1 TAATAAAATTAAAATTAAAA
421957 TAATAAAAATTTAAATATTAAA
1 TAAT-AAAA-TTAAA-ATTAAA
421979 GAATTTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 5 0.26
23 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATAAAATTAAAATTAAAA
Found at i:421983 original size:16 final size:15
Alignment explanation
Indices: 421947--421985 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
421937 TAATAAAATT
*
421947 AAAATTAAAATAATA
1 AAAATTTAAATAATA
*
421962 AAAATTTAAATATTA
1 AAAATTTAAATAATA
421977 AAGAATTTA
1 AA-AATTTA
421986 CCATTAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATTTAAATAATA
Found at i:422712 original size:22 final size:22
Alignment explanation
Indices: 422668--422712 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
422658 AATATTACAA
*
422668 AAATTAAAAAAAAACTACTTAT
1 AAATTAAAAAAAAACTAATTAT
*
422690 AAATTAAATAAAAA-TAATATAT
1 AAATTAAAAAAAAACTAAT-TAT
422712 A
1 A
422713 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTAAAAAAAAACTAATTAT
Found at i:431705 original size:26 final size:26
Alignment explanation
Indices: 431673--431730 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 26
431663 AGTGTACTTT
*
431673 TCTCTTCCATTCCTCTCCTCAAAT-TCA
1 TCTCTT-C-TTCCTCTCCACAAATCTCA
*
431700 -CTCTTCTTTCTCTCCACAAATCTCA
1 TCTCTTCTTCCTCTCCACAAATCTCA
431725 TCTCTT
1 TCTCTT
431731 TGACTCTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 13 0.48
25 4 0.15
26 10 0.37
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (26 bp):
TCTCTTCTTCCTCTCCACAAATCTCA
Found at i:439985 original size:33 final size:33
Alignment explanation
Indices: 439943--440009 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
439933 GTCAAATATA
439943 AATATTGGTTTTTTACAATTTTATATATAAAAT
1 AATATTGGTTTTTTACAATTTTATATATAAAAT
*
439976 AATATTGGTTTTTTATAATTTTATATATAAAAT
1 AATATTGGTTTTTTACAATTTTATATATAAAAT
440009 A
1 A
440010 TTGATTTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (33 bp):
AATATTGGTTTTTTACAATTTTATATATAAAAT
Found at i:441127 original size:24 final size:24
Alignment explanation
Indices: 441100--441146 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
441090 CTGCAGCAGT
* * *
441100 TGCAGTGGCAGCGGCGGCAGCTGC
1 TGCAGCGGCAGCAGAGGCAGCTGC
*
441124 TGCAGCGGCGGCAGAGGCAGCTG
1 TGCAGCGGCAGCAGAGGCAGCTG
441147 GACTTGCACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.47, T:0.11
Consensus pattern (24 bp):
TGCAGCGGCAGCAGAGGCAGCTGC
Found at i:452429 original size:38 final size:40
Alignment explanation
Indices: 452359--452438 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 40
452349 ATTTTTGGCC
* *
452359 TTCATTTTTTTGCTATTTTTAGCCTGTCATC-T-TAGGTT
1 TTCATTTTTTTGCTATTTTTACCCTGTAATCTTGTAGGTT
*
452397 TTCATTTTTTTGTTATTTTTAACCCT-TAATCTTGTAGGTT
1 TTCATTTTTTTGCTATTTTT-ACCCTGTAATCTTGTAGGTT
452437 TT
1 TT
452439 GTCAAAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 23 0.64
39 5 0.14
40 8 0.22
ACGTcount: A:0.15, C:0.14, G:0.11, T:0.60
Consensus pattern (40 bp):
TTCATTTTTTTGCTATTTTTACCCTGTAATCTTGTAGGTT
Found at i:462622 original size:14 final size:14
Alignment explanation
Indices: 462587--462624 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
462577 ACGAGACATT
462587 TTAATATTT-AAAA
1 TTAATATTTAAAAA
*
462600 TTATTATTTAAAAA
1 TTAATATTTAAAAA
*
462614 TTAAAATTTAA
1 TTAATATTTAA
462625 TTAATAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:474263 original size:15 final size:15
Alignment explanation
Indices: 474243--474291 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
474233 TTTATTTTTA
474243 TATAAAAATTAAATT
1 TATAAAAATTAAATT
**
474258 TATAAAAA-TAAAAA
1 TATAAAAATTAAATT
*
474272 TATAGAAATTAAATT
1 TATAAAAATTAAATT
474287 T-TAAA
1 TATAAA
474292 TTTGCAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TATAAAAATTAAATT
Found at i:474824 original size:16 final size:17
Alignment explanation
Indices: 474803--474848 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
474793 GGAGAAGCAG
474803 AAGAAAATAAAAAAT-A
1 AAGAAAATAAAAAATAA
**
474819 AAGAAAA-AAAAGTTAA
1 AAGAAAATAAAAAATAA
*
474835 AAGAACATAAAAAA
1 AAGAAAATAAAAAA
474849 AAATTAAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (17 bp):
AAGAAAATAAAAAATAA
Found at i:475147 original size:20 final size:20
Alignment explanation
Indices: 475106--475147 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
475096 TAATAATTAC
**
475106 TAAATCAAATTAAACTTTTT
1 TAAATCAAATTAAACTAATT
475126 TAAATCAAAATTAAA-TAATT
1 TAAATC-AAATTAAACTAATT
475146 TA
1 TA
475148 CAACCAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATCAAATTAAACTAATT
Found at i:486405 original size:13 final size:11
Alignment explanation
Indices: 486380--486413 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
486370 ACGACGTGCC
486380 AAATTTTTAAT
1 AAATTTTTAAT
486391 AAAATTTTGTAAT
1 -AAATTTT-TAAT
486404 AAATTTTTAA
1 AAATTTTTAA
486414 ATTAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 14 0.67
13 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AAATTTTTAAT
Found at i:486889 original size:17 final size:17
Alignment explanation
Indices: 486867--486912 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
486857 GAAATACAAG
486867 TTTTTAAATTTTATTAT
1 TTTTTAAATTTTATTAT
* * *
486884 TTTTTAAAATATGTTAT
1 TTTTTAAATTTTATTAT
486901 TTTTT-AATTTTA
1 TTTTTAAATTTTA
486913 AATATATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTAAATTTTATTAT
Found at i:487886 original size:13 final size:13
Alignment explanation
Indices: 487856--487957 Score: 50
Period size: 13 Copynumber: 7.5 Consensus size: 13
487846 TCCGTTCATT
487856 TTATTTTTTTA-A
1 TTATTTTTTTATA
487868 TT-TTTTTTTATA
1 TTATTTTTTTATA
*
487880 TTATTTTAAGTTAATA
1 TTATTTT---TTTATA
*
487896 TTGAATATTTTTATA
1 TT--ATTTTTTTATA
487911 TT-TTTTATTTAT-
1 TTATTTT-TTTATA
*
487923 TGAATTTTTTTATA
1 T-TATTTTTTTATA
* * *
487937 TAATTATCTTATCA
1 TTATTTTTTTAT-A
487951 TTATTTT
1 TTATTTT
487958 AATATTTACA
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
11 8 0.12
12 9 0.13
13 23 0.33
14 11 0.16
15 7 0.10
16 7 0.10
18 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:487948 original size:26 final size:26
Alignment explanation
Indices: 487894--487948 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
487884 TTTAAGTTAA
**
487894 TATTGAATATTTTTATATTTTTTATT
1 TATTGAATATTTTTATATTAATTATT
*
487920 TATTGAATTTTTTTATA-TAATTATCT
1 TATTGAATATTTTTATATTAATTAT-T
487946 TAT
1 TAT
487949 CATTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
TATTGAATATTTTTATATTAATTATT
Found at i:498800 original size:3 final size:3
Alignment explanation
Indices: 498792--498822 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
498782 TTTGGGTGTT
498792 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
498823 ATGAAGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:502634 original size:5 final size:5
Alignment explanation
Indices: 502624--502651 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
502614 CTCTAAGTAC
502624 ACTAG ACTAG ACTAG ACTAG ACTAG ACT
1 ACTAG ACTAG ACTAG ACTAG ACTAG ACT
502652 CTTAGTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (5 bp):
ACTAG
Found at i:516074 original size:24 final size:24
Alignment explanation
Indices: 516013--516075 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
516003 TAGAGTAATA
* * *
516013 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
516037 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
516061 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
516076 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:517196 original size:31 final size:30
Alignment explanation
Indices: 517155--517214 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
517145 AAAGATAAAA
*
517155 ATTATTAAAATA-ATAATAGTATATTTTTACT
1 ATTATAAAAATATATAATA-TA-ATTTTTACT
517186 ATTATAAAAATATATAATATAATTTTTAC
1 ATTATAAAAATATATAATATAATTTTTAC
517215 CTAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 13 0.48
32 6 0.22
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTATAAAAATATATAATATAATTTTTACT
Found at i:519746 original size:15 final size:14
Alignment explanation
Indices: 519716--519742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
519706 AATATATGTT
519716 TTTTTAAATATTTA
1 TTTTTAAATATTTA
519730 TTTTTAAATATTT
1 TTTTTAAATATTT
519743 TATTATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTAAATATTTA
Found at i:521494 original size:25 final size:25
Alignment explanation
Indices: 521447--521494 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
521437 TGATAATCAT
* * **
521447 AAAAATAATAATTATAATTATTTCG
1 AAAAATAAAAATTACAAAAATTTCG
521472 AAAAATAAAAATTACAAAAATTT
1 AAAAATAAAAATTACAAAAATTT
521495 ATTCTACCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAATAAAAATTACAAAAATTTCG
Found at i:522496 original size:17 final size:17
Alignment explanation
Indices: 522474--522507 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
522464 AGCTACCATC
522474 CTCTAAAATACTTGTGT
1 CTCTAAAATACTTGTGT
*
522491 CTCTAAAATATTTGTGT
1 CTCTAAAATACTTGTGT
522508 TAATTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (17 bp):
CTCTAAAATACTTGTGT
Found at i:523530 original size:33 final size:31
Alignment explanation
Indices: 523464--523578 Score: 124
Period size: 33 Copynumber: 3.6 Consensus size: 31
523454 TTAATATAAT
*
523464 ATTTGGTACTTGAACTTGATATTTTTTTT-TA
1 ATTTGGTAC-TAAACTTGATATTTTTTTTCTA
* ** *
523495 ATTTGGCACCTAAACTTTTTTTTTTTTTGTCTA
1 ATTTGGTA-CTAAACTTGATATTTTTTT-TCTA
*
523528 ATTTGGTACTCAAACTTGATATTTTTTTCCTA
1 ATTTGGTACT-AAACTTGATATTTTTTTTCTA
523560 ATTTGGTATCTAAACTTGA
1 ATTTGGTA-CTAAACTTGA
523579 AGTGTCAAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
31 21 0.30
32 23 0.33
33 25 0.36
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.53
Consensus pattern (31 bp):
ATTTGGTACTAAACTTGATATTTTTTTTCTA
Found at i:523553 original size:32 final size:32
Alignment explanation
Indices: 523464--523578 Score: 121
Period size: 32 Copynumber: 3.6 Consensus size: 32
523454 TTAATATAAT
* *
523464 ATTTGGTACT-TGAACTTGATATTTTTTTTTA
1 ATTTGGTACTCTAAACTTGATATTTTTTTCTA
* ** *
523495 ATTTGGCAC-CTAAACTTTTTTTTTTTTTGTCTA
1 ATTTGGTACTCTAAAC-TTGATATTTTTT-TCTA
523528 ATTTGGTACTC-AAACTTGATATTTTTTTCCTA
1 ATTTGGTACTCTAAACTTGATATTTTTTT-CTA
523560 ATTTGGTA-TCTAAACTTGA
1 ATTTGGTACTCTAAACTTGA
523579 AGTGTCAAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
31 15 0.22
32 37 0.54
33 15 0.22
34 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTGGTACTCTAAACTTGATATTTTTTTCTA
Found at i:532114 original size:21 final size:21
Alignment explanation
Indices: 532090--532142 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
532080 TTTTAATTTT
532090 TTAA-ATTTAAATTATTTCAAA
1 TTAATATTTAAATTA-TTCAAA
*
532111 TTAATTTTTAAATTATTCAAA
1 TTAATATTTAAATTATTCAAA
532132 TTGAGATATTT
1 TT-A-ATATTT
532143 CAAACCCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.44
22 10 0.37
23 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (21 bp):
TTAATATTTAAATTATTCAAA
Found at i:548464 original size:25 final size:25
Alignment explanation
Indices: 548436--548495 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
548426 TTAAGATGAC
548436 AATATAAATAATT-TTAATAAATAAA
1 AATATAAATAATTATTAA-AAATAAA
*
548461 AATATATAA-AATTATTAAATATAAA
1 AATATA-AATAATTATTAAAAATAAA
548486 AATA-AAATAA
1 AATATAAATAA
548496 ATCTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.06
24 3 0.10
25 20 0.65
26 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AATATAAATAATTATTAAAAATAAA
Found at i:549691 original size:17 final size:17
Alignment explanation
Indices: 549669--549703 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
549659 AATATACTTC
549669 ATGATTT-TTTAGTTTTT
1 ATGATTTATTTA-TTTTT
549686 ATGATTTATTTATTTTT
1 ATGATTTATTTATTTTT
549703 A
1 A
549704 AATATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (17 bp):
ATGATTTATTTATTTTT
Found at i:550551 original size:16 final size:16
Alignment explanation
Indices: 550530--550562 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
550520 CCCGGCAGCG
*
550530 ACAAAATTAAAATAAA
1 ACAAAAATAAAATAAA
550546 ACAAAAATAAAATAAA
1 ACAAAAATAAAATAAA
550562 A
1 A
550563 TATTAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
ACAAAAATAAAATAAA
Found at i:557868 original size:17 final size:18
Alignment explanation
Indices: 557848--557889 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
557838 AAAAACACAA
557848 AAAAATTAAAATATTT-T
1 AAAAATTAAAATATTTAT
*
557865 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
557883 AAAAATT
1 AAAAATT
557890 TCAACATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:558198 original size:21 final size:21
Alignment explanation
Indices: 558163--558208 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
558153 AAAAAGTAGG
558163 AAATATTTTTAATAA-TTTTT
1 AAATATTTTTAATAATTTTTT
*
558183 AAATATTTTTTTATAATTTTTT
1 AAATA-TTTTTAATAATTTTTT
558205 AAAT
1 AAAT
558209 TTTAAGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AAATATTTTTAATAATTTTTT
Found at i:565004 original size:30 final size:31
Alignment explanation
Indices: 564968--565027 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
564958 ATATTATAGT
*
564968 CTCTTTA-AAATGATAAAATTTTAATTTAGG
1 CTCTTTATAAATGATAAAATTTTAAATTAGG
* *
564998 CTCTTTATAATTTATAAAATTTTAAATTAG
1 CTCTTTATAAATGATAAAATTTTAAATTAG
565028 TAATGGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
CTCTTTATAAATGATAAAATTTTAAATTAGG
Found at i:572531 original size:14 final size:15
Alignment explanation
Indices: 572507--572550 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
572497 TGATTATATA
572507 TAAAATATTAAAAAT
1 TAAAATATTAAAAAT
*
572522 TAAAAT-TTAAAAAA
1 TAAAATATTAAAAAT
* *
572536 AAAAAAATTAAAAAT
1 TAAAATATTAAAAAT
572551 GTAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAATATTAAAAAT
Found at i:573320 original size:24 final size:23
Alignment explanation
Indices: 573280--573325 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
573270 ATATAGAATT
573280 TTTTATTTTTTAAATAAATTTTAA
1 TTTTATTTTTTAAAT-AATTTTAA
*
573304 TTTTAGTTTTTT-TATAATTTTA
1 TTTTA-TTTTTTAAATAATTTTA
573326 TACAGAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATTTTTTAAATAATTTTAA
Found at i:581390 original size:2 final size:2
Alignment explanation
Indices: 581383--581417 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
581373 TCATCTCTTT
581383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
581418 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:589692 original size:23 final size:23
Alignment explanation
Indices: 589660--589732 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
589650 AAACTAGTGC
* *
589660 GCCCTTTGTTTAGCACTGTGTGT
1 GCCCTCTGTTTAGCACTTTGTGT
*
589683 GCCCTCTGTTATTAGCATTTTGTGT
1 GCCCTCTG-T-TTAGCACTTTGTGT
*
589708 GCCCTCTGATTAGCACTTTGTGT
1 GCCCTCTGTTTAGCACTTTGTGT
589731 GC
1 GC
589733 TCTGTTACAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 22 0.51
24 1 0.02
25 20 0.47
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
GCCCTCTGTTTAGCACTTTGTGT
Found at i:589697 original size:25 final size:25
Alignment explanation
Indices: 589669--589739 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
589659 CGCCCTTTGT
*
589669 TTAGCACTGTGTGTGCCCTCTGTTA
1 TTAGCACTTTGTGTGCCCTCTGTTA
*
589694 TTAGCATTTTGTGTGCCCTCTG--A
1 TTAGCACTTTGTGTGCCCTCTGTTA
589717 TTAGCACTTTGTGTG--CTCTGTTA
1 TTAGCACTTTGTGTGCCCTCTGTTA
589740 CACAGCACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.12
23 16 0.39
25 20 0.49
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (25 bp):
TTAGCACTTTGTGTGCCCTCTGTTA
Found at i:594659 original size:29 final size:30
Alignment explanation
Indices: 594601--594662 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
594591 ATTCATATTA
*
594601 TTATTGATGAAATTATAATTTTATAGAATT
1 TTATTGATGAAATTATAATTTTATAAAATT
* *
594631 TTATTTATGAATTTAT-ATTTTA-ACAAATT
1 TTATTGATGAAATTATAATTTTATA-AAATT
594660 TTA
1 TTA
594663 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 13 0.46
30 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (30 bp):
TTATTGATGAAATTATAATTTTATAAAATT
Found at i:595112 original size:7 final size:7
Alignment explanation
Indices: 595100--595130 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
595090 ATAAAGATAC
595100 CAAATTT
1 CAAATTT
595107 CAAATTT
1 CAAATTT
595114 CAAATTT
1 CAAATTT
595121 CAAATTT
1 CAAATTT
595128 CAA
1 CAA
595131 CAGTTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (7 bp):
CAAATTT
Found at i:596770 original size:30 final size:29
Alignment explanation
Indices: 596734--596792 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
596724 TCATTTTGAC
* **
596734 TTTTTTTAAAAAATTGATGGTCAAATTTAA
1 TTTTTTT-AAAAATTAAAAGTCAAATTTAA
596764 TTTTTTTAAAAATTAAAAGTCAAATTTAA
1 TTTTTTTAAAAATTAAAAGTCAAATTTAA
596793 CTTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
TTTTTTTAAAAATTAAAAGTCAAATTTAA
Found at i:604622 original size:110 final size:110
Alignment explanation
Indices: 604429--604647 Score: 341
Period size: 110 Copynumber: 2.0 Consensus size: 110
604419 TGTTTGTTTG
* * * **
604429 AGTTGATGGTGATGCGGTACCGTTTAAAAATCCACACATTCTATTTTTTATGTGGGGAGTGCACC
1 AGTTGATGGTGATGCGGTACCGCTCAAAAATCCACACATTCCATTTCCTATGTGGGGAGTGCACC
*
604494 ATCACCTTAGAAGATGTTGCATTGCAACTTGAGCT-CTCAGTTCAC
66 ATCACCTTAGAAGATGTTGCATTGCAACTCGAGCTCCT-AGTTCAC
* * *
604539 AGTTGATGGTGATGCGGTACCGCTCAGAGATCCACGCATTCCATTTCCTATGTGGGGAGTGCACC
1 AGTTGATGGTGATGCGGTACCGCTCAAAAATCCACACATTCCATTTCCTATGTGGGGAGTGCACC
604604 ATCACCTTAGAAGATGTTGCATTGCAACTCGAGCTCCTAGTTCA
66 ATCACCTTAGAAGATGTTGCATTGCAACTCGAGCTCCTAGTTCA
604648 TAATGGTTAT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 97 0.98
111 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (110 bp):
AGTTGATGGTGATGCGGTACCGCTCAAAAATCCACACATTCCATTTCCTATGTGGGGAGTGCACC
ATCACCTTAGAAGATGTTGCATTGCAACTCGAGCTCCTAGTTCAC
Found at i:606168 original size:28 final size:28
Alignment explanation
Indices: 606113--606171 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
606103 AGTAAAAAAT
* * *
606113 AATTATTTTTTATTTTAAAATATTTTAA
1 AATTATTTTTTAATATAAAATATATTAA
606141 AATTATTTTTTAAATATAAAAT-TATTAA
1 AATTATTTTTT-AATATAAAATATATTAA
606169 AAT
1 AAT
606172 CATCATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATTATTTTTTAATATAAAATATATTAA
Found at i:606864 original size:12 final size:13
Alignment explanation
Indices: 606840--606869 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
606830 ACCCTAAACA
606840 AAAGGGAAAGGGG
1 AAAGGGAAAGGGG
606853 AAAGGG-AAGGGG
1 AAAGGGAAAGGGG
606865 AAAGG
1 AAAGG
606870 TAACAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (13 bp):
AAAGGGAAAGGGG
Found at i:606936 original size:11 final size:10
Alignment explanation
Indices: 606909--606985 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 10
606899 ATGATGATTT
606909 AATAATTTT-
1 AATAATTTTA
606918 -AT-ATTTTA
1 AATAATTTTA
606926 AATTAATTTTAA
1 AA-TAATTTT-A
*
606938 AATAGTTTT-
1 AATAATTTTA
606947 AATAATTTT-
1 AATAATTTTA
*
606956 -AT-ATTTAAA
1 AATAATTT-TA
606965 AATAATTTT-
1 AATAATTTTA
606974 AATAATTTTA
1 AATAATTTTA
606984 AA
1 AA
606986 ATTATTTGCT
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
7 9 0.17
8 4 0.07
9 18 0.33
10 5 0.09
11 15 0.28
12 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (10 bp):
AATAATTTTA
Found at i:606961 original size:27 final size:27
Alignment explanation
Indices: 606931--606983 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
606921 TTTTAAATTA
* *
606931 ATTTTAAAATAGTTTTAATAATTTTAT
1 ATTTAAAAATAATTTTAATAATTTTAT
606958 ATTTAAAAATAATTTTAATAATTTTA
1 ATTTAAAAATAATTTTAATAATTTTA
606984 AAATTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTAAAAATAATTTTAATAATTTTAT
Found at i:607310 original size:23 final size:23
Alignment explanation
Indices: 607267--607310 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
607257 GAAATTAAAT
* *
607267 TATAATTTTTATAATAGTAAAAA
1 TATAATTTTTAAAAGAGTAAAAA
*
607290 TATAATTTTTAAAAGATTAAA
1 TATAATTTTTAAAAGAGTAAA
607311 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TATAATTTTTAAAAGAGTAAAAA
Found at i:610443 original size:6 final size:6
Alignment explanation
Indices: 610432--610459 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
610422 GTTCTTTGAT
610432 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
610460 TCTGTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:613363 original size:23 final size:23
Alignment explanation
Indices: 613335--613383 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
613325 TAAAATAACG
* * *
613335 AAATTACATTTTTACTATAATAA
1 AAATTACAGTTTAACTACAATAA
*
613358 AAATTACAGTTTAACTCCAATAA
1 AAATTACAGTTTAACTACAATAA
613381 AAA
1 AAA
613384 AAAACATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATTACAGTTTAACTACAATAA
Found at i:647617 original size:26 final size:27
Alignment explanation
Indices: 647546--647617 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
647536 AATGTTATTA
**
647546 AATTATATATTATTT-TTATTAAGTTAT
1 AATTA-ATATTATTTATTATTAAAATAT
* * *
647573 ATTTAATAATAATTA-TATTAAAATAT
1 AATTAATATTATTTATTATTAAAATAT
647599 AATTAA-ATTATTTATTATT
1 AATTAATATTATTTATTATT
647618 TTTTTATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 6 0.17
26 25 0.71
27 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTAATATTATTTATTATTAAAATAT
Found at i:647638 original size:60 final size:59
Alignment explanation
Indices: 647521--647646 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 59
647511 AATTCATAAA
* * * *
647521 AATAATCATATTAAGAATGTTATTAAATTATATATTATTTTTATTAAGTTATATTTAAT
1 AATAATTATATTAAGAATATAATTAAATTATATATTATTTTTATTAAATTATATTTAAT
*
647580 AATAATTATATTAA-AATATAATTAAATTATTTATTATTTTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAGAATATAATTAAATTATATATTA--TTTTTATTAAATTATATTTAAT
*
647640 ACTAATT
1 AATAATT
647647 CTATCAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 19 0.32
59 13 0.22
60 27 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (59 bp):
AATAATTATATTAAGAATATAATTAAATTATATATTATTTTTATTAAATTATATTTAAT
Found at i:648467 original size:21 final size:23
Alignment explanation
Indices: 648441--648486 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
648431 CATCGCGCAC
*
648441 AGCTTTTTCGA-CC-AAATCTGG
1 AGCTTTTTCAATCCAAAATCTGG
648462 AGCTTTTTCAATCCAAAATCTGG
1 AGCTTTTTCAATCCAAAATCTGG
648485 AG
1 AG
648487 ATCTGATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (23 bp):
AGCTTTTTCAATCCAAAATCTGG
Found at i:658613 original size:25 final size:24
Alignment explanation
Indices: 658549--658613 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
658539 GGGTTTACTC
*
658549 ATTATTTTTCATAAATATAAATAA
1 ATTATTTTTTATAAATATAAATAA
658573 ATTCATTGTTTT-TAAATATAGATATAA
1 ATT-ATT-TTTTATAAATATA-A-ATAA
658600 A-TATTTTTTATAAA
1 ATTATTTTTTATAAA
658614 GAGAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 7 0.20
25 18 0.51
26 5 0.14
27 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (24 bp):
ATTATTTTTTATAAATATAAATAA
Found at i:669889 original size:30 final size:29
Alignment explanation
Indices: 669855--669911 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
669845 TGTCATGCAT
*
669855 GAATTTTGATTTTATGCAATTTTATATATA
1 GAATTTTGATTTAATGCAATTTT-TATATA
* *
669885 GAATTTTGGTTTAATTCAATTTTTATA
1 GAATTTTGATTTAATGCAATTTTTATA
669912 AATCTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (29 bp):
GAATTTTGATTTAATGCAATTTTTATATA
Found at i:676618 original size:2 final size:2
Alignment explanation
Indices: 676611--676638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
676601 TCGATCTTTC
676611 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
676639 GTTCTTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:692017 original size:48 final size:47
Alignment explanation
Indices: 691946--692042 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 47
691936 TAAGGAAGGT
*
691946 TAGAAAATTTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGAC
1 TAGAAAATTTTAAGGATTAAATAGTAAAGGAGAG-AAATATAGGGGAC
691994 TAGAAAATTTTAAGGATTAAATAGTAAAGGAGAGAAATATAGGGGAC
1 TAGAAAATTTTAAGGATTAAATAGTAAAGGAGAGAAATATAGGGGAC
692041 TA
1 TA
692043 AATAACGAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 14 0.29
48 34 0.71
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (47 bp):
TAGAAAATTTTAAGGATTAAATAGTAAAGGAGAGAAATATAGGGGAC
Found at i:693603 original size:23 final size:23
Alignment explanation
Indices: 693573--693658 Score: 120
Period size: 23 Copynumber: 3.8 Consensus size: 23
693563 AATAGTATTG
693573 TGTGTGCTCTCTGATTAGCACTT
1 TGTGTGCTCTCTGATTAGCACTT
* *
693596 TGTGTGCTCTCTGATCAGTACTT
1 TGTGTGCTCTCTGATTAGCACTT
* * *
693619 TGTGTACTCTCTGTTTAGCACTG
1 TGTGTGCTCTCTGATTAGCACTT
693642 TGTGTGCTCTCTG-TTAG
1 TGTGTGCTCTCTGATTAG
693659 TTCTTTAGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 4 0.07
23 51 0.93
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
TGTGTGCTCTCTGATTAGCACTT
Found at i:693671 original size:44 final size:46
Alignment explanation
Indices: 693579--693678 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
693569 ATTGTGTGTG
* * *
693579 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTTGAGTA
* *
693625 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTAGTTCTTT-AGTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTTGAGTA
*
693669 CTCTTTGTTT
1 CTCTCTGTTT
693679 GTTTCGTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 12 0.25
45 8 0.17
46 28 0.58
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (46 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATCAGTACTTTGAGTA
Found at i:694768 original size:19 final size:18
Alignment explanation
Indices: 694758--694793 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
694748 ATAAAATTTT
694758 TAAATAATTATTAAAACTA
1 TAAATAATTA-TAAAACTA
*
694777 TCAATAATTATAAAACT
1 TAAATAATTATAAAACT
694794 TATATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATAATTATAAAACTA
Found at i:695219 original size:5 final size:5
Alignment explanation
Indices: 695204--695234 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
695194 GACAAGAAGA
695204 TTCCAC TTCCC TTCCC TTCCC TTCCC TTCCC
1 TTCC-C TTCCC TTCCC TTCCC TTCCC TTCCC
695235 CTGCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.03, C:0.58, G:0.00, T:0.39
Consensus pattern (5 bp):
TTCCC
Found at i:695435 original size:18 final size:18
Alignment explanation
Indices: 695412--695447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
695402 TGTCACATTT
695412 GATATTTATATTTTTATA
1 GATATTTATATTTTTATA
695430 GATATTTATATTTTTATA
1 GATATTTATATTTTTATA
695448 AAATATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
GATATTTATATTTTTATA
Found at i:698091 original size:21 final size:23
Alignment explanation
Indices: 698051--698092 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
698041 AATTTAATTT
*
698051 AATATTTTAAGTATTTTTCATAC
1 AATATTTTAAGTAGTTTTCATAC
698074 AATATTTTAA-T-GTTTTCAT
1 AATATTTTAAGTAGTTTTCAT
698093 TTCCTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (23 bp):
AATATTTTAAGTAGTTTTCATAC
Found at i:699931 original size:14 final size:14
Alignment explanation
Indices: 699912--699944 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
699902 TACAATATCC
699912 AAATAATAACAATA
1 AAATAATAACAATA
699926 AAATAATAACAATA
1 AAATAATAACAATA
*
699940 TAATA
1 AAATA
699945 GCAAAACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:702030 original size:26 final size:26
Alignment explanation
Indices: 701983--702032 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
701973 TTTTTGAATT
*
701983 TTTTTTTTTAAATGCATTCATTTTAA
1 TTTTTTTTTAAATGAATTCATTTTAA
*
702009 TTTTTTTTTAGAT-AATTACATTTT
1 TTTTTTTTTAAATGAATT-CATTTT
702033 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTTTTTTAAATGAATTCATTTTAA
Found at i:703798 original size:29 final size:31
Alignment explanation
Indices: 703766--703829 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
703756 AATAGTTTAG
703766 GTATCACATTAGATATTTT-T-AAAGTACAT
1 GTATCACATTAGATATTTTATGAAAGTACAT
* *
703795 GTATCACATTGGATATTTTATGAAAGTATAT
1 GTATCACATTAGATATTTTATGAAAGTACAT
703826 GTAT
1 GTAT
703830 AATAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 18 0.58
30 1 0.03
31 12 0.39
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (31 bp):
GTATCACATTAGATATTTTATGAAAGTACAT
Found at i:704408 original size:2 final size:2
Alignment explanation
Indices: 704367--704423 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
704357 CCAATTAAAC
* * *
704367 AT AT -T AT AT AA AT AT AC AT -T AT A- AT CAT A- AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
704406 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
704424 GCAATTACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
1 4 0.09
2 38 0.86
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:704745 original size:34 final size:34
Alignment explanation
Indices: 704707--704774 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
704697 AAGCTTTAAA
704707 ATTTTATCTAAAATGGAAATCAAATATTATGTTT
1 ATTTTATCTAAAATGGAAATCAAATATTATGTTT
*
704741 ATTTTATCTAAAATGGCAATCAAATATTATGTTT
1 ATTTTATCTAAAATGGAAATCAAATATTATGTTT
704775 TTTACATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (34 bp):
ATTTTATCTAAAATGGAAATCAAATATTATGTTT
Found at i:704787 original size:34 final size:34
Alignment explanation
Indices: 704707--704787 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
704697 AAGCTTTAAA
*
704707 ATTTTATCTAAAATGGAAATCAAATATTATGTTT
1 ATTTCATCTAAAATGGAAATCAAATATTATGTTT
* *
704741 ATTTTATCTAAAATGGCAATCAAATATTATGTTT
1 ATTTCATCTAAAATGGAAATCAAATATTATGTTT
*
704775 -TTTACATGTAAAA
1 ATTT-CATCTAAAA
704788 GATGCGTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.07
34 40 0.93
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (34 bp):
ATTTCATCTAAAATGGAAATCAAATATTATGTTT
Found at i:713589 original size:22 final size:20
Alignment explanation
Indices: 713535--713589 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
713525 TTTATGTGTC
*
713535 AATACTATATATTATAAAAAT
1 AATA-TATATATTATAAAAAA
713556 AATATACT-TATTCATAAAAAA
1 AATATA-TATATT-ATAAAAAA
713577 AATTATATATATT
1 AA-TATATATATT
713590 TTTTATCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 6 0.21
21 15 0.52
22 8 0.28
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATATATATTATAAAAAA
Found at i:713823 original size:24 final size:26
Alignment explanation
Indices: 713773--713823 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
713763 TTAACTTAGC
**
713773 ATAAGTTTCTTCAAAATTAAATTTAT
1 ATAAGTTTCTTCAAAATTAAAGCTAT
*
713799 ATAAGTTT-TT-ATAATTAAAGCTAT
1 ATAAGTTTCTTCAAAATTAAAGCTAT
713823 A
1 A
713824 GATTATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 8 0.36
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (26 bp):
ATAAGTTTCTTCAAAATTAAAGCTAT
Found at i:728241 original size:21 final size:21
Alignment explanation
Indices: 728217--728258 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
728207 CAAATGACAC
728217 ACAGCCCTAATTAACGAGGCT
1 ACAGCCCTAATTAACGAGGCT
*
728238 ACAGCCCTAGTTAACGAGGCT
1 ACAGCCCTAATTAACGAGGCT
728259 GTGATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (21 bp):
ACAGCCCTAATTAACGAGGCT
Found at i:739219 original size:20 final size:20
Alignment explanation
Indices: 739194--739236 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
739184 GAGATGAAAG
*
739194 TATGACTGGTTTGAGGTTGA
1 TATGACTAGTTTGAGGTTGA
739214 TATGACTAGTTTGAGGTTGA
1 TATGACTAGTTTGAGGTTGA
739234 TAT
1 TAT
739237 TGAGACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (20 bp):
TATGACTAGTTTGAGGTTGA
Found at i:744837 original size:9 final size:9
Alignment explanation
Indices: 744812--744855 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
744802 AATTATTCTC
744812 TTAATTTTT
1 TTAATTTTT
*
744821 GTT-TTTTTT
1 -TTAATTTTT
744830 TTAATTTTT
1 TTAATTTTT
*
744839 TTAATTTAT
1 TTAATTTTT
744848 TTAATTTT
1 TTAATTTT
744856 AATTGAACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 25 0.86
10 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTAATTTTT
Found at i:756427 original size:7 final size:7
Alignment explanation
Indices: 756417--756445 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
756407 ATAATCTATT
756417 ATCTTCA
1 ATCTTCA
756424 ATCTTCA
1 ATCTTCA
756431 ATCTTCA
1 ATCTTCA
756438 ATCTTCA
1 ATCTTCA
756445 A
1 A
756446 AGAGATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (7 bp):
ATCTTCA
Found at i:757052 original size:2 final size:2
Alignment explanation
Indices: 757045--757081 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
757035 CAACAAGCCC
757045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
757082 CAAAAGAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:760770 original size:3 final size:3
Alignment explanation
Indices: 760762--760793 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
760752 TTGTCCATGT
760762 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
760794 GGAAGCAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:761831 original size:31 final size:30
Alignment explanation
Indices: 761768--761840 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
761758 TTATATATAT
*
761768 AAACTTTAATTTAGTGCAATTATACATGTG
1 AAACTTTAATTTAGTGCAAATATACATGTG
* * *
761798 AAA-TTCTAATTGTAGTTCAAATATATATTTG
1 AAACTT-TAATT-TAGTGCAAATATACATGTG
761829 AAACTTTAATTT
1 AAACTTTAATTT
761841 TGATTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.06
30 9 0.25
31 23 0.64
32 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (30 bp):
AAACTTTAATTTAGTGCAAATATACATGTG
Found at i:762060 original size:31 final size:29
Alignment explanation
Indices: 761982--762062 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
761972 GAATTGGATC
*
761982 AAATCACAATTTCATGTATAAAATTACACA
1 AAATCA-AAGTTCATGTATAAAATTACACA
* *
762012 AAATCAAAGGTCATGTATACAATTACACA
1 AAATCAAAGTTCATGTATAAAATTACACA
*
762041 TTAAA-CTATAGTTCATGTATAA
1 --AAATC-AAAGTTCATGTATAA
762063 TTTTGAGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 20 0.48
30 7 0.17
31 15 0.36
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTACACA
Found at i:762540 original size:29 final size:30
Alignment explanation
Indices: 762476--762542 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
762466 TTTAAGAATA
* * *
762476 TTTTTAAAAAAAATTTGAAATTTTTTATTG
1 TTTTTAAAAAAAATATCAAATTTTTAATTG
** *
762506 AATTTAAAAAAAA-ATCAAATTTTTAATTT
1 TTTTTAAAAAAAATATCAAATTTTTAATTG
762535 TTTTTAAA
1 TTTTTAAA
762543 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTTTAAAAAAAATATCAAATTTTTAATTG
Found at i:766900 original size:21 final size:21
Alignment explanation
Indices: 766845--766900 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
766835 GCCAAATTGG
*
766845 AATAGAGTTAACATTTATTGTTT
1 AATAGAGTT-A-ATTTATTATTT
* *
766868 AA-AAAATATAATTTATTATTT
1 AATAGAGT-TAATTTATTATTT
766889 AATAGAGTTAAT
1 AATAGAGTTAAT
766901 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
21 16 0.62
22 7 0.27
23 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
AATAGAGTTAATTTATTATTT
Found at i:784205 original size:17 final size:16
Alignment explanation
Indices: 784183--784214 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
784173 ATTTATTCAA
784183 TTAATTAAATTAATTTC
1 TTAATTAAA-TAATTTC
784200 TTAATTAAATAATTT
1 TTAATTAAATAATTT
784215 TTTCAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:790597 original size:3 final size:3
Alignment explanation
Indices: 790589--790613 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
790579 AGTAAAAATC
790589 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
790614 ATTTAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:796555 original size:2 final size:2
Alignment explanation
Indices: 796550--796580 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
796540 TTAATTAATT
*
796550 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
796581 TTAAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:796650 original size:37 final size:38
Alignment explanation
Indices: 796565--796651 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
796555 ATATATATAT
* *
796565 ATATATATATAAATATTTAAACATAATATAATTTAATGC
1 ATATATATA-AAAGATTTAAACATAATATAATTTAATAC
* **
796604 ATATATATAAAAGATTTACACATAATATGTTTTAATAC
1 ATATATATAAAAGATTTAAACATAATATAATTTAATAC
*
796642 AT-TGTATAAA
1 ATATATATAAA
796652 CATATCGTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 7 0.17
38 26 0.62
39 9 0.21
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (38 bp):
ATATATATAAAAGATTTAAACATAATATAATTTAATAC
Found at i:796831 original size:11 final size:11
Alignment explanation
Indices: 796808--796837 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
796798 CTCTCCTAAA
796808 ATAAATCAAATT
1 ATAAAT-AAATT
796820 ATAAATAAATT
1 ATAAATAAATT
796831 ATAAATA
1 ATAAATA
796838 TTATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAATAAATT
Found at i:797556 original size:27 final size:29
Alignment explanation
Indices: 797509--797562 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
797499 TTTTTTATTT
797509 TATTAATTTATTTATAAATTAA-AAAATA
1 TATTAATTTATTTATAAATTAAGAAAATA
797537 TATTAATATT-TTT-TAAATTAAGAAAA
1 TATTAAT-TTATTTATAAATTAAGAAAA
797563 AAGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.33
28 14 0.58
29 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TATTAATTTATTTATAAATTAAGAAAATA
Found at i:802899 original size:6 final size:6
Alignment explanation
Indices: 802890--802923 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
802880 AAAAAGAAAA
802890 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA
802924 AATTTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:802905 original size:18 final size:18
Alignment explanation
Indices: 802884--802925 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
802874 GGAAAGAAAA
802884 AGAAAAAGAAGGAGAAGG
1 AGAAAAAGAAGGAGAAGG
**
802902 AGAAGGAGAAGGAGAAGG
1 AGAAAAAGAAGGAGAAGG
802920 AGAAAA
1 AGAAAA
802926 TTTTGAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAGGAGAAGG
Found at i:810096 original size:7 final size:7
Alignment explanation
Indices: 810084--810117 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
810074 ATATATTTTA
810084 ATCCGCC
1 ATCCGCC
810091 ATCCGCC
1 ATCCGCC
810098 ATCCGCC
1 ATCCGCC
810105 ATCCGCC
1 ATCCGCC
810112 ATCCGC
1 ATCCGC
810118 TACTAATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (7 bp):
ATCCGCC
Found at i:811182 original size:15 final size:15
Alignment explanation
Indices: 811135--811182 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
811125 GTTTTTCGGA
811135 TTACATTTTAATTAT
1 TTACATTTTAATTAT
* * *
811150 TTATATTTAAAATA-
1 TTACATTTTAATTAT
*
811164 TTACATTTTAGTTAT
1 TTACATTTTAATTAT
811179 TTAC
1 TTAC
811183 GTTATCGTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (15 bp):
TTACATTTTAATTAT
Found at i:821248 original size:149 final size:149
Alignment explanation
Indices: 820978--821277 Score: 449
Period size: 149 Copynumber: 2.0 Consensus size: 149
820968 CATTTAAATC
820978 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCAACACATATAGCAACTAGCAAG
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCAACACATATAGCAACTAGCAAG
* * * **
821043 TTTGAAGGGAGTGCTCAAAGAACTATACATCTGCAGAAGTCATTTATAGATATCAAATCTTGCAA
66 TGTGAAAGGAGTGCTCAAAAAACTATACATCTGCAGAAACCATTTATAGATATCAAATCTTGCAA
* *
821108 TAAATTTTCCTCAAATTAT
131 TAAATTTACATCAAATTAT
* *
821127 AAAGGGAATTTATGAGGAAGACTTCCAACATTACCATTAATGC-ACTGCATATAGCAACTAGCAA
1 AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCAAC-ACATATAGCAACTAGCAA
* * **
821191 GTGTGAAAGTAGTTCTCAAAAAACTATGTATCTGCAGAAACCATTTATAGATATCAAATCTTGCA
65 GTGTGAAAGGAGTGCTCAAAAAACTATACATCTGCAGAAACCATTTATAGATATCAAATCTTGCA
* *
821256 ATAAGTTTACATCAATTTAT
130 ATAAATTTACATCAAATTAT
821276 AA
1 AA
821278 CTGTAATCCC
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 2 0.01
149 133 0.99
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (149 bp):
AAAGGGAATTTATGAGGAAGACTTCCAACATGACCATTAATGCAACACATATAGCAACTAGCAAG
TGTGAAAGGAGTGCTCAAAAAACTATACATCTGCAGAAACCATTTATAGATATCAAATCTTGCAA
TAAATTTACATCAAATTAT
Found at i:822147 original size:53 final size:52
Alignment explanation
Indices: 822006--822162 Score: 228
Period size: 53 Copynumber: 3.0 Consensus size: 52
821996 CAATTAGATA
*
822006 TGCCATGAGCATTGATAACAATACATATAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATGTAACAGTGTAACTATATCCATAAGC
*
822058 TGCCATGA--ATTGATAACAATACATAGTAACAGTGTAACTATATCAATAAGC
1 TGCCATGAGCATTGATAACAATACAT-GTAACAGTGTAACTATATCCATAAGC
* * * *
822109 TGTCATGAGCATTGATAACAACACATGGTAACAATGTAACCATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACAT-GTAACAGTGTAACTATATCCATAAGC
822162 T
1 T
822163 ATGTAATCAA
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
50 16 0.17
51 31 0.33
52 8 0.09
53 39 0.41
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (52 bp):
TGCCATGAGCATTGATAACAATACATGTAACAGTGTAACTATATCCATAAGC
Found at i:824085 original size:14 final size:15
Alignment explanation
Indices: 824050--824087 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
824040 TTTAATATAA
824050 ATTTTAAATATAATT
1 ATTTTAAATATAATT
824065 -TTGTTAAA-ATAATT
1 ATT-TTAAATATAATT
824079 ATTTTAAAT
1 ATTTTAAAT
824088 TTAACTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTTAAATATAATT
Found at i:824722 original size:18 final size:18
Alignment explanation
Indices: 824683--824724 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
824673 AGAAAGAGAC
* *
824683 ATATTTTGTGATTTTTTT
1 ATATTTTGTAATTTTTTA
824701 ATATTTT-TAATTTATTTA
1 ATATTTTGTAATTT-TTTA
824719 ATATTT
1 ATATTT
824725 AAATGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
ATATTTTGTAATTTTTTA
Found at i:830422 original size:6 final size:6
Alignment explanation
Indices: 830411--830435 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
830401 TTGTAATGTT
830411 TTTGTC TTTGTC TTTGTC TTTGTC T
1 TTTGTC TTTGTC TTTGTC TTTGTC T
830436 GATGGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTGTC
Found at i:830597 original size:25 final size:25
Alignment explanation
Indices: 830568--830615 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
830558 CTGCAATAAG
*
830568 GTGAAATTTAGAAGATA-AGAACTAA
1 GTGAAAGTTA-AAGATATAGAACTAA
*
830593 GTGAAAGTTACAGATATAGAACT
1 GTGAAAGTTAAAGATATAGAACT
830616 TCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (25 bp):
GTGAAAGTTAAAGATATAGAACTAA
Done.