Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 2 of 20
Found at i:469458 original size:31 final size:31
Alignment explanation
Indices: 469423--469531 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
469413 AGAAAGAAAT
* *
469423 AAATGTT-TTCACATGCTATGCATGCCAAGTC
1 AAATGTTGTT-ACATGCTATGCATACCAAGTA
* *
469454 AAATGTTGTTACATGTTATGCATATCAAGTA
1 AAATGTTGTTACATGCTATGCATACCAAGTA
* * * * *
469485 AAATGTTGTTACACGTTAAGCATATCAAGTG
1 AAATGTTGTTACATGCTATGCATACCAAGTA
*
469516 AAATGTTGTTTCATGC
1 AAATGTTGTTACATGC
469532 CAATGCTAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
31 65 0.97
32 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (31 bp):
AAATGTTGTTACATGCTATGCATACCAAGTA
Found at i:470220 original size:23 final size:23
Alignment explanation
Indices: 470191--470253 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
470181 TTATATTTTA
*
470191 AACCATGACGTGTCACATATT-C
1 AACCATGACGTGTCACACATTCC
* *
470213 AAGCCATGCCGTCTCACACATTCC
1 AA-CCATGACGTGTCACACATTCC
*
470237 CACCATGACGTGTCACA
1 AACCATGACGTGTCACA
470254 AACTCTAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.22
Consensus pattern (23 bp):
AACCATGACGTGTCACACATTCC
Found at i:470426 original size:23 final size:22
Alignment explanation
Indices: 470373--470427 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
470363 GTGTCACAGC
470373 CATGTCACATATGCTCACCATG
1 CATGTCACATATGCTCACCATG
* *
470395 C-TGTCTCACATATTCTCACTATGG
1 CATG--TCACATATGCTCACCAT-G
470419 CATGTCACA
1 CATGTCACA
470428 AACTCTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.07
22 1 0.04
23 20 0.74
24 2 0.07
25 2 0.07
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (22 bp):
CATGTCACATATGCTCACCATG
Found at i:470565 original size:23 final size:23
Alignment explanation
Indices: 470539--470583 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
470529 AAACTCTGAA
* *
470539 CCCTACCGTGTCACAGATTCTTT
1 CCCTACCATGTCACAAATTCTTT
**
470562 CCCTGGCATGTCACAAATTCTT
1 CCCTACCATGTCACAAATTCTT
470584 AATCTTGCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (23 bp):
CCCTACCATGTCACAAATTCTTT
Found at i:470680 original size:23 final size:23
Alignment explanation
Indices: 470634--470681 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
470624 GCCATCTCGT
* * **
470634 ATATTCTCACCATGGCGTGTCAC
1 ATATTCACACCATGACGTCCCAC
470657 ATATTCACACCATGACGTCCCAC
1 ATATTCACACCATGACGTCCCAC
470680 AT
1 AT
470682 TCTCAAACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (23 bp):
ATATTCACACCATGACGTCCCAC
Found at i:470847 original size:23 final size:23
Alignment explanation
Indices: 470820--470886 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
470810 CTCACTATAA
*
470820 CATGTCACACATTCCCGCCAT-G
1 CATGTCACACATTCCCACCATGG
*
470842 CTATGTCACACATTCCTACCATGG
1 C-ATGTCACACATTCCCACCATGG
*
470866 CGTGTCACACATTCCCACCAT
1 CATGTCACACATTCCCACCAT
470887 ACCGTTTCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
22 1 0.03
23 36 0.92
24 2 0.05
ACGTcount: A:0.24, C:0.39, G:0.12, T:0.25
Consensus pattern (23 bp):
CATGTCACACATTCCCACCATGG
Found at i:470896 original size:23 final size:23
Alignment explanation
Indices: 470822--470897 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
470812 CACTATAACA
* **
470822 TGTCACACATTCCCGCCATGCTA
1 TGTCACACATTCCCACCATGCCG
* *
470845 TGTCACACATTCCTACCATGGCG
1 TGTCACACATTCCCACCATGCCG
*
470868 TGTCACACATTCCCACCATACCG
1 TGTCACACATTCCCACCATGCCG
*
470891 TTTCACA
1 TGTCACA
470898 AACTCTAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.24, C:0.38, G:0.12, T:0.26
Consensus pattern (23 bp):
TGTCACACATTCCCACCATGCCG
Found at i:476261 original size:2 final size:2
Alignment explanation
Indices: 476256--476283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
476246 TCAAATATCG
476256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
476284 GATAATAGTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:477369 original size:6 final size:6
Alignment explanation
Indices: 477358--477383 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
477348 TTACTGAGTA
477358 GTGAAT GTGAAT GTGAAT GTGAAT GT
1 GTGAAT GTGAAT GTGAAT GTGAAT GT
477384 TCCTCAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (6 bp):
GTGAAT
Found at i:482788 original size:22 final size:22
Alignment explanation
Indices: 482762--482811 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
482752 GTAAATTTAG
* *
482762 TTAATGATCAGT-AAACTAAATA
1 TTAATAATCAGTGAAA-TAAAGA
*
482784 TTAATAATTAGTGAAATAAAGA
1 TTAATAATCAGTGAAATAAAGA
482806 TTAATA
1 TTAATA
482812 TTACATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (22 bp):
TTAATAATCAGTGAAATAAAGA
Found at i:491278 original size:13 final size:13
Alignment explanation
Indices: 491260--491284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
491250 GTCGAAAATG
491260 CAAAAAATAACCC
1 CAAAAAATAACCC
491273 CAAAAAATAACC
1 CAAAAAATAACC
491285 AGGCTGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAAAATAACCC
Found at i:497818 original size:34 final size:34
Alignment explanation
Indices: 497775--497849 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
497765 TTTGTGGTTC
497775 CTCCATGATAGGCTTGTTTTGCCTACATGTAAAG
1 CTCCATGATAGGCTTGTTTTGCCTACATGTAAAG
497809 CTCCATGATAGGCTTGTTTTGCCTACATGTAAAG
1 CTCCATGATAGGCTTGTTTTGCCTACATGTAAAG
497843 CTCCATG
1 CTCCATG
497850 TCATATGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (34 bp):
CTCCATGATAGGCTTGTTTTGCCTACATGTAAAG
Found at i:501542 original size:23 final size:24
Alignment explanation
Indices: 501516--501569 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
501506 CTAAAAAATT
501516 AAATATTTA-TCAATTA-TAATATA
1 AAATATTTATTC-ATTATTAATATA
**
501539 AAATAAATATTCATTATTAATATA
1 AAATATTTATTCATTATTAATATA
501563 AAATATT
1 AAATATT
501570 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATTTATTCATTATTAATATA
Found at i:502664 original size:241 final size:242
Alignment explanation
Indices: 501899--502883 Score: 1309
Period size: 240 Copynumber: 4.0 Consensus size: 242
501889 NNNNNNNNNN
*
501899 ACGTCAAGGCTTTTTCACGTCAATTTTGAATTATAATTAGTTATCCTTATTATTCCTAATTTAAA
1 ACGTCAAAGCTTTTTCACGTCAATTTTGAATTATAATTAGTTAT-C---TT-TT--T-ATTTAAA
* *
501964 AATTAAAATTTTTATATCGTTAAACATTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTT
58 AATTAAAATTTTTATATCGTTAAACACTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTG
********** * * *
502029 NNNNNNNNNNCATTGTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACGGTTACGTTAAGA
123 ATTAAATTTACAATGTTTTTACTTAATTGACTTCTTACGTTAACTCTCACACGCTTACGTTAAGA
* * *
502094 TTTAAAATTTAGTTATTCCACATTTACAAACTTTTACGTCAATTCTTACAGTTTT
188 TTTAAAATTTAGTTATTCCACCTTTACAAGCTTTTACATCAATTCTTACAGTTTT
* *
502149 ACGT-TAAGACTTTTTCACGTCAATTTTGAATTATAATTAGTTATC-CTTTATTTAAAAATTAAA
1 ACGTCAAAG-CTTTTTCACGTCAATTTTGAATTATAATTAGTTATCTTTTTATTTAAAAATTAAA
* * * *
502212 AATTTTATATCGTTAAACACTTTCAGCTCAAGAATATAAATTTAAATATTTACTTTTGATTTAAT
65 ATTTTTATATCGTTAAACACTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTGATTAAAT
* * *
502277 TTACAAT-ATTTTACTTAATTTACTTCTTACGTTAACTCTCCCACGCTTACGTTAAGATTTAAAA
130 TTACAATGTTTTTACTTAATTGACTTCTTACGTTAACTCTCACACGCTTACGTTAAGATTTAAAA
* * *
502341 TTTAGTTATTCTACCTTTATAATCTTTTACATCAATTCTTACAGTTTT
195 TTTAGTTATTCCACCTTTACAAGCTTTTACATCAATTCTTACAGTTTT
* *
502389 ACGTCAAGGTTTTTTCACGTCAATTTTGAATTATAATTAGTTATC-TTTTATTTAAAAATTAAAA
1 ACGTCAAAGCTTTTTCACGTCAATTTTGAATTATAATTAGTTATCTTTTTATTTAAAAATTAAAA
502453 TTTTTATATCGTTAAACACTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTGATTAAATT
66 TTTTTATATCGTTAAACACTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTGATTAAATT
* * *
502518 TACATTGTTTTTACTTAATTGACTTCTTACGTTAACACTCACATGCTTACGTTAAGATTTAAAAT
131 TACAATGTTTTTACTTAATTGACTTCTTACGTTAACTCTCACACGCTTACGTTAAGATTTAAAAT
* *
502583 TTAGTTATTCCACCTTTACAAGCTTTTACGTCCATTCTTACAGTTTT
196 TTAGTTATTCCACCTTTACAAGCTTTTACATCAATTCTTACAGTTTT
*
502630 ACGTCAAAGCTTTTTCACATCAATTTTGAATTATAATTAGTTTTATCTTTATTATTCTTAATTTA
1 ACGTCAAAGCTTTTTCACGTCAATTTTGAATTATAATTAG--TTATCTTT-TTA-T-TT-A---A
*
502695 CAAATTAAAATTTTTATATCGTTAAACAC-TTCA-ACCTGAGAATATAAATTTAAATATTTACTT
57 -AAATTAAAATTTTTATATCGTTAAACACTTTCAGCCCT-AGAATATAAATTTAAATATTTACTT
* * * * * *
502758 TTCATTAAATTTATAATATTTTTACTTAATTGACTTGTTTCGTTAACTCTTACACGCTTACGTTA
120 TTGATTAAATTTACAATGTTTTTACTTAATTGACTTCTTACGTTAACTCTCACACGCTTACGTTA
* *
502823 AGATTTAAAATTTAGTTATTTCACCTTTACAAGTTTTTACATCAATTCTTACAG-TTT
185 AGATTTAAAATTTAGTTATTCCACCTTTACAAGCTTTTACATCAATTCTTACAGTTTT
502880 ACGT
1 ACGT
502884 TAATGATTTT
Statistics
Matches: 655, Mismatches: 65, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
240 218 0.33
241 204 0.31
242 1 0.00
243 5 0.01
244 4 0.01
245 3 0.00
246 1 0.00
247 2 0.00
248 1 0.00
249 3 0.00
250 49 0.07
251 136 0.21
252 28 0.04
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.45
Consensus pattern (242 bp):
ACGTCAAAGCTTTTTCACGTCAATTTTGAATTATAATTAGTTATCTTTTTATTTAAAAATTAAAA
TTTTTATATCGTTAAACACTTTCAGCCCTAGAATATAAATTTAAATATTTACTTTTGATTAAATT
TACAATGTTTTTACTTAATTGACTTCTTACGTTAACTCTCACACGCTTACGTTAAGATTTAAAAT
TTAGTTATTCCACCTTTACAAGCTTTTACATCAATTCTTACAGTTTT
Found at i:507125 original size:62 final size:61
Alignment explanation
Indices: 507059--507223 Score: 163
Period size: 62 Copynumber: 2.7 Consensus size: 61
507049 CACTGCAGTA
* * *
507059 CCACACTCCCAGCACTGCAGCACTATCACTCTTCACCAAGCAGCACTTT-TCGAGCTGTAGCG
1 CCACACTCCCA-CGCTGCAGCACTATCACCCTTCACCAAGCAGCACTTTCT-GAGCTGCAGCG
* ** * * * *
507121 CCACACTCCCTACGCTGCAACGTTGTCCCCCTTCACCAAGTAGCACTTTCTGCGCTGCAGCG
1 CCACACTCCC-ACGCTGCAGCACTATCACCCTTCACCAAGCAGCACTTTCTGAGCTGCAGCG
* * *
507183 CCACACTCCCAACGCTGCAGCGCTGTC-CCCTTCATCAAGCA
1 CCACACTCCC-ACGCTGCAGCACTATCACCCTTCACCAAGCA
507224 ATAGCATCAA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
61 12 0.14
62 72 0.84
63 2 0.02
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (61 bp):
CCACACTCCCACGCTGCAGCACTATCACCCTTCACCAAGCAGCACTTTCTGAGCTGCAGCG
Found at i:507397 original size:62 final size:62
Alignment explanation
Indices: 507254--507465 Score: 232
Period size: 62 Copynumber: 3.5 Consensus size: 62
507244 CCACACTCTT
* * * * ** *
507254 AGCGTTGTCCCCCTTCACTAAGCAGCACTTTTCGCACTGCA-CGCCACACTTCCAGTGCTGT
1 AGCGCTGTCCCCCTTCACCAAGCAGCACTTTTCGCGCTGCAGCGCCACACTCCCAACGCTGC
* * * * *
507315 AGTGCTATCCCGCTTCACCAAGCAGCACTTTTCGCGCTGTAGCACCACACTCCCAACGCTGC
1 AGCGCTGTCCCCCTTCACCAAGCAGCACTTTTCGCGCTGCAGCGCCACACTCCCAACGCTGC
* * * * **
507377 AGCGCTGTCCCCCTTCACCAAGTATCACTTTTCACGCTGCAGCGTCACACTCCCAACATTGC
1 AGCGCTGTCCCCCTTCACCAAGCAGCACTTTTCGCGCTGCAGCGCCACACTCCCAACGCTGC
*
507439 AACGCTGT--CCCTTCACCAAGCAGCACT
1 AGCGCTGTCCCCCTTCACCAAGCAGCACT
507466 CCCAGGGCAG
Statistics
Matches: 124, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
60 17 0.14
61 34 0.27
62 73 0.59
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.23
Consensus pattern (62 bp):
AGCGCTGTCCCCCTTCACCAAGCAGCACTTTTCGCGCTGCAGCGCCACACTCCCAACGCTGC
Found at i:507871 original size:20 final size:22
Alignment explanation
Indices: 507846--507885 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
507836 ATTTATAAAA
507846 TAAATTAT-TA-ATTACATAGT
1 TAAATTATATATATTACATAGT
507866 TAAATTATATATATTACATA
1 TAAATTATATATATTACATA
507886 AGTGAACGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (22 bp):
TAAATTATATATATTACATAGT
Found at i:511867 original size:97 final size:96
Alignment explanation
Indices: 511572--511962 Score: 493
Period size: 96 Copynumber: 4.1 Consensus size: 96
511562 AAGCTAGCGA
* * *
511572 AAAC-CTCATACTCTCGTTGCTTCTCTTTTTCTTTCATCTTTTGACTATTTTTATCATTCTCCAA
1 AAACTCTCATACTCTCGTTGCTTCTCTTTTTCTTTCAGCTTTTGACTATTTTTATCATACTTCAA
* *
511636 TAATTCTTTCAACTTTTCAATTTCACACTTC
66 CAATTCCTTCAACTTTTCAATTTCACACTTC
* * * * * *
511667 AAACTCTCACACTCTTGTTGTTTCTCTTTTTCTTTCAGCTTTTGATTATTTTTATCATAATTTAA
1 AAACTCTCATACTCTCGTTGCTTCTCTTTTTCTTTCAGCTTTTGACTATTTTTATCATACTTCAA
511732 CAA-TCTCTTCAACTTTTCAATTTCACACTTC
66 CAATTC-CTTCAACTTTTCAATTTCACACTTC
* * * *
511763 AAACTCTCATACTCCCATTGTTTCTCTTTTTCTTTCAACTTTTGACTATTTTTTATCATACTTCA
1 AAACTCTCATACTCTCGTTGCTTCTCTTTTTCTTTCAGCTTTTGACTA-TTTTTATCATACTTCA
*
511828 ATAATTCCTTCAAC-TTTCAAATTTCACACTTC
65 ACAATTCCTTCAACTTTTC-AATTTCACACTTC
* * * * *
511860 GAACTCTCATACTCTTGTTGCTTCTGTTTTTCTTTCAGCTTTTGATTATTTTTATTATAC-TCAA
1 AAACTCTCATACTCTCGTTGCTTCTCTTTTTCTTTCAGCTTTTGACTATTTTTATCATACTTC-A
* * * *
511924 ACAATCCCTTTAACATTTCAATTTCATACTTC
65 ACAATTCCTTCAACTTTTCAATTTCACACTTC
511956 AAACTCT
1 AAACTCT
511963 TAATTTCACT
Statistics
Matches: 255, Mismatches: 34, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
95 8 0.03
96 164 0.64
97 81 0.32
98 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.04, T:0.49
Consensus pattern (96 bp):
AAACTCTCATACTCTCGTTGCTTCTCTTTTTCTTTCAGCTTTTGACTATTTTTATCATACTTCAA
CAATTCCTTCAACTTTTCAATTTCACACTTC
Found at i:511904 original size:193 final size:192
Alignment explanation
Indices: 511572--511962 Score: 579
Period size: 193 Copynumber: 2.0 Consensus size: 192
511562 AAGCTAGCGA
* * * *
511572 AAAC-CTCATACTCTCGTTGCTTCTCTTTTTCTTTCATCTTTTGACTATTTTTATCATTCTCCAA
1 AAACTCTCATACTCCCATTGCTTCTCTTTTTCTTTCAACTTTTGACTATTTTTATCATACTCCAA
* *
511636 TAATTCTTTCAACTTTTCAATTTCACACTTCAAACTCTCACACTCTTGTTGTTTCTCTTTTTCTT
66 TAATTCCTTCAACTTTTCAATTTCACACTTCAAACTCTCACACTCTTGTTGCTTCTCTTTTTCTT
** * *
511701 TCAGCTTTTGATTATTTTTATCATAATTTAACAATCTCTTCAACTTTTCAATTTCACACTTC
131 TCAGCTTTTGATTATTTTTATCATAATCAAACAATCCCTTCAACATTTCAATTTCACACTTC
* *
511763 AAACTCTCATACTCCCATTGTTTCTCTTTTTCTTTCAACTTTTGACTATTTTTTATCATACTTCA
1 AAACTCTCATACTCCCATTGCTTCTCTTTTTCTTTCAACTTTTGACTA-TTTTTATCATACTCCA
* * *
511828 ATAATTCCTTCAAC-TTTCAAATTTCACACTTCGAACTCTCATACTCTTGTTGCTTCTGTTTTTC
65 ATAATTCCTTCAACTTTTC-AATTTCACACTTCAAACTCTCACACTCTTGTTGCTTCTCTTTTTC
* * * *
511892 TTTCAGCTTTTGATTATTTTTATTATACTCAAACAATCCCTTTAACATTTCAATTTCATACTTC
129 TTTCAGCTTTTGATTATTTTTATCATAATCAAACAATCCCTTCAACATTTCAATTTCACACTTC
511956 AAACTCT
1 AAACTCT
511963 TAATTTCACT
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
191 4 0.02
192 43 0.24
193 131 0.74
ACGTcount: A:0.23, C:0.24, G:0.04, T:0.49
Consensus pattern (192 bp):
AAACTCTCATACTCCCATTGCTTCTCTTTTTCTTTCAACTTTTGACTATTTTTATCATACTCCAA
TAATTCCTTCAACTTTTCAATTTCACACTTCAAACTCTCACACTCTTGTTGCTTCTCTTTTTCTT
TCAGCTTTTGATTATTTTTATCATAATCAAACAATCCCTTCAACATTTCAATTTCACACTTC
Found at i:513358 original size:19 final size:18
Alignment explanation
Indices: 513322--513358 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
513312 ATTTATTTAT
*
513322 AAATTTTTTAAATAATTA
1 AAATTTTTTAAAAAATTA
513340 AAATTTTTTAAAAATATTA
1 AAATTTTTTAAAAA-ATTA
513359 TGTGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTTTTTAAAAAATTA
Found at i:515228 original size:23 final size:23
Alignment explanation
Indices: 515198--515244 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
515188 AATATACTGG
515198 AGTAAACTCTTGAATCTTTATTA
1 AGTAAACTCTTGAATCTTTATTA
515221 AGTAAACTCTTGAATCTTTATTA
1 AGTAAACTCTTGAATCTTTATTA
515244 A
1 A
515245 CAAAATCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
AGTAAACTCTTGAATCTTTATTA
Found at i:516124 original size:443 final size:428
Alignment explanation
Indices: 514964--516191 Score: 1497
Period size: 443 Copynumber: 2.8 Consensus size: 428
514954 CGTTCACAAA
* * * *
514964 AAGCATGCTTGACTTTAAGTGTCTCTTTGGTTCTTTTAGTTTTTAATTTCTTTTGTTAGCTATTC
1 AAGCATGCTTGACTTTAAGTCTCCCTTCGGTTCTTTTAGTTTTTAATTTCTTTTGTTAACTATTC
* * * * * * *
515029 TTTTAATAATAAAAAAGGACAATTTCAACTCTGTTTACCAGAATAAAAAAATTAAGTAACATATT
66 TTTTAACAATAAAAAAGGACAATTTCAGCTCTGTTGACAAGAAT-AAAAAAGTAAATAATATATT
* * * *
515094 TGCACAACTTTTATTGAAGATGGAAGTGAAGAAACTTGGACCTTTGTTTTTTATATTAGTTATGA
130 TGCACAACTTTTATAGAAGATGAAAGTGAAGAAACTTGGACCTTTGTTTATGATATTAGTTATGA
* * * * *
515159 TAATGCTTGATCTTTGGAACGTATCAGGCAATATACTGGAGTAAACTCTTGAATCTTTATTAAGT
195 TAATGTTTGATCTTTGGAACATATTAGGCGATATAGTGGAGTAAA--C-----TC----TT--G-
* *
515224 AAACTCTTGAATCTTTATTAACAAAATCCTTACGTTTTAAGCTTCTTAGATATAATACATAAGGA
246 -AA----TG----TTTATTAACAAAATCCTTATGTTTTAAGCTTCATAGATATAATACATAAGGA
** * * * * *
515289 TTTTCTTTGT-TACCTCTGTACTCCATTAATTATCTTTTAGAAATAAGATGCAAAGCTTCTTTTT
302 TTTTCTTTGTCT-TGTATGTACTCCATTAATTAGCTTTTAGAAATAAGATGCAAAACATCTTTGT
** * * *
515353 TATTTCTAAGATCTTCTAGGCACAGTTAATCTTATTAGTAGAAAAATAACTATATGTTTATAC
366 TATTAATAACATCTTCTAGGCACAGTTAATCTTATCAGTAGAAAAATAAATATATGTTTATAC
* ** * *
515416 AAGCATGCTTGACTTTAAGTGTTTCTTTGGTTCTTTTAGTTTTTAATTTCTTTTGTTAGCTATTC
1 AAGCATGCTTGACTTTAAGTCTCCCTTCGGTTCTTTTAGTTTTTAATTTCTTTTGTTAACTATTC
* *
515481 TTTTAGCAATAAAAAAGGACAATTTCAGCTCTGTTGACAGGAATAAAAAAGTAAATAATATATTT
66 TTTTAACAATAAAAAAGGACAATTTCAGCTCTGTTGACAAGAATAAAAAAGTAAATAATATATTT
* * * *
515546 GCACAACTTTTTTCGAAGATGGAAGTGAAGAAACTTGGACCTTTGTTTATGATGTTAGTTATGAT
131 GCACAACTTTTATAGAAGATGAAAGTGAAGAAACTTGGACCTTTGTTTATGATATTAGTTATGAT
* *
515611 AATGTTTGATCTTTGGAACATATTAGGCTATATAGTGGAGTAAACTCTTGAATGTTTGTTAACAA
196 AATGTTTGATCTTTGGAACATATTAGGCGATATAGTGGAGTAAACTCTTGAATGTTTATTAACAA
*
515676 AATCCTTATGCTTTAAGCTTCATAGATATAATACATAAGGATTTTCTTTGTCTTGTATGTACTCC
261 AATCCTTATGTTTTAAGCTTCATAGATATAATACATAAGGATTTTCTTTGTCTTGTATGTACTCC
*
515741 ATTAATTCGCTTTTAGAAATAAGATGCAAAACATCTTTGTTATTAATAACATCTTCTAGGCACAG
326 ATTAATTAGCTTTTAGAAATAAGATGCAAAACATCTTTGTTATTAATAACATCTTCTAGGCACAG
* *
515806 TTAATGTTGTCAGTAGAAAAATAAATATATGTTTGTACATCTACAC
391 TTAATCTTATCAGTAGAAAAATAAATATATG-TT-T--A--T--AC
*
515852 AAAAAAGCATGCTTGAGTTTAAGTCTCCCTTCGGTTCTTTTAGTTTTTAATTTCTTTTGTTAACT
1 ----AAGCATGCTTGACTTTAAGTCTCCCTTCGGTTCTTTTAGTTTTTAATTTCTTTTGTTAACT
* * * *
515917 ATTCTTTTAATAATAAAAAGGGACAATTTCAGTTCTGTTTACAAGAATAAAAAAAGTAAATAATA
62 ATTCTTTTAACAATAAAAAAGGACAATTTCAGCTCTGTTGACAAGAAT-AAAAAAGTAAATAATA
*
515982 TATTTGCACAAAACTTTTATAGAAGATGAAAGTGTAGAAACTTGGACCTTTGTTTATGATATTAG
126 TATTTGCAC--AACTTTTATAGAAGATGAAAGTGAAGAAACTTGGACCTTTGTTTATGATATTAG
* *
516047 TTATGATAATGTTTGATCTTTGGAACATGTTAGGCGATATAGTTGAGTAAACTCTTGAATGTTTA
189 TTATGATAATGTTTGATCTTTGGAACATATTAGGCGATATAGTGGAGTAAACTCTTGAATGTTTA
* * * *
516112 TTAACAAAATCCTTATGTTTTAAGCTTCGTAGATTTGATACGAT-AGGATTTTTTTTGTCTTGTA
254 TTAACAAAATCCTTATGTTTTAAGCTTCATAGATATAATAC-ATAAGGATTTTCTTTGTCTTGTA
*
516176 TGTACTCCAATAATTA
318 TGTACTCCATTAATTA
516192 TCTCTCAGAA
Statistics
Matches: 692, Mismatches: 67, Indels: 43
0.86 0.08 0.05
Matches are distributed among these distances:
428 151 0.22
429 3 0.00
430 1 0.00
432 3 0.00
434 1 0.00
436 4 0.01
438 1 0.00
440 99 0.14
441 25 0.04
443 180 0.26
444 4 0.01
449 1 0.00
451 117 0.17
452 102 0.15
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (428 bp):
AAGCATGCTTGACTTTAAGTCTCCCTTCGGTTCTTTTAGTTTTTAATTTCTTTTGTTAACTATTC
TTTTAACAATAAAAAAGGACAATTTCAGCTCTGTTGACAAGAATAAAAAAGTAAATAATATATTT
GCACAACTTTTATAGAAGATGAAAGTGAAGAAACTTGGACCTTTGTTTATGATATTAGTTATGAT
AATGTTTGATCTTTGGAACATATTAGGCGATATAGTGGAGTAAACTCTTGAATGTTTATTAACAA
AATCCTTATGTTTTAAGCTTCATAGATATAATACATAAGGATTTTCTTTGTCTTGTATGTACTCC
ATTAATTAGCTTTTAGAAATAAGATGCAAAACATCTTTGTTATTAATAACATCTTCTAGGCACAG
TTAATCTTATCAGTAGAAAAATAAATATATGTTTATAC
Found at i:516548 original size:38 final size:38
Alignment explanation
Indices: 516497--516572 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
516487 AAATTTGGAG
516497 TATGAATCCTTCTGTGTTGCTTTGAAGCACACAGGTTA
1 TATGAATCCTTCTGTGTTGCTTTGAAGCACACAGGTTA
516535 TATGAATCCTTCTGTGTTGCTTTGAAGCACACAGGTTA
1 TATGAATCCTTCTGTGTTGCTTTGAAGCACACAGGTTA
516573 CAAACTCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (38 bp):
TATGAATCCTTCTGTGTTGCTTTGAAGCACACAGGTTA
Found at i:528375 original size:16 final size:16
Alignment explanation
Indices: 528351--528381 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
528341 TCATGTTTAT
*
528351 ATATCTAAAATATTTG
1 ATATATAAAATATTTG
528367 ATATATAAAATATTT
1 ATATATAAAATATTT
528382 AATGCTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATATAAAATATTTG
Found at i:528914 original size:14 final size:15
Alignment explanation
Indices: 528888--528916 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
528878 AATATAGATA
528888 TAAAATAATATTTAT
1 TAAAATAATATTTAT
528903 TAAAAT-ATATTTAT
1 TAAAATAATATTTAT
528917 ATTTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATAATATTTAT
Found at i:533708 original size:2 final size:2
Alignment explanation
Indices: 533701--533742 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
533691 TCCATAAGTG
*
533701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
533743 GTTATAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:542494 original size:10 final size:10
Alignment explanation
Indices: 542479--542521 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
542469 GTTAAGTAAC
542479 ATTTAAAAAA
1 ATTTAAAAAA
**
542489 ATTT-AAATT
1 ATTTAAAAAA
542498 ATTTAAAAAA
1 ATTTAAAAAA
*
542508 ATTTAAATAA
1 ATTTAAAAAA
542518 ATTT
1 ATTT
542522 TTATATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:542503 original size:19 final size:19
Alignment explanation
Indices: 542479--542515 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
542469 GTTAAGTAAC
542479 ATTTAAAAAAATTTAAATT
1 ATTTAAAAAAATTTAAATT
542498 ATTTAAAAAAATTTAAAT
1 ATTTAAAAAAATTTAAAT
542516 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAAAAATTTAAATT
Found at i:542583 original size:30 final size:28
Alignment explanation
Indices: 542510--542604 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 28
542500 TTAAAAAAAT
*
542510 TTAAATAAATTTTTATA-TTTTATTACA
1 TTAAATAAATTTTTATATTTTTATTAAA
* *
542537 TTCAATTAAATATTTATATTTTTATTTTAAA
1 TT-AAATAAATTTTTATATTTTTA--TTAAA
542568 TTAAATAAATTTTTATA-TTTT-TTAAA
1 TTAAATAAATTTTTATATTTTTATTAAA
*
542594 TCAAATAAATT
1 TTAAATAAATT
542605 CATATAACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
26 15 0.26
27 2 0.03
28 13 0.22
29 9 0.16
30 13 0.22
31 6 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
TTAAATAAATTTTTATATTTTTATTAAA
Found at i:542610 original size:26 final size:26
Alignment explanation
Indices: 542561--542610 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
542551 TATATTTTTA
* **
542561 TTTTAAATTAAATAAATTTTTATATT
1 TTTTAAATCAAATAAATTCATATATT
542587 TTTTAAATCAAATAAATTCATATA
1 TTTTAAATCAAATAAATTCATATA
542611 ACTAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTAAATCAAATAAATTCATATATT
Found at i:542773 original size:21 final size:21
Alignment explanation
Indices: 542727--542774 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
542717 TCATAATTAA
*
542727 TAATAAAATAAAATATCAATT
1 TAATATAATAAAATATCAATT
* *
542748 CAATATAATAAAATTAT-TATT
1 TAATATAATAAAA-TATCAATT
542769 TAATAT
1 TAATAT
542775 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATATAATAAAATATCAATT
Found at i:545134 original size:2 final size:2
Alignment explanation
Indices: 545124--545153 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
545114 CGCTCTCTCT
*
545124 CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
545154 TTATGCATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:547533 original size:27 final size:27
Alignment explanation
Indices: 547472--547534 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
547462 AATTGGTATA
*
547472 TAATTTTTTTAATTTAAAAATTAGAGT
1 TAATTTTTTTAATTTAAAAAATAGAGT
547499 TGAA-TTTTTTAATTTAAAATAAATA-AG-
1 T-AATTTTTTTAATTT-AAA-AAATAGAGT
547526 TAATTTTTT
1 TAATTTTTT
547535 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
26 2 0.06
27 18 0.58
28 7 0.23
29 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (27 bp):
TAATTTTTTTAATTTAAAAAATAGAGT
Found at i:551908 original size:22 final size:22
Alignment explanation
Indices: 551854--551898 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
551844 CAGTTACGAA
* *
551854 GAAAAGTGAAAGAAGTAAAAGG
1 GAAAAATGAAAGAAGAAAAAGG
551876 GAAAAATGAAAGAAGAAAAAGG
1 GAAAAATGAAAGAAGAAAAAGG
551898 G
1 G
551899 GAAGAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (22 bp):
GAAAAATGAAAGAAGAAAAAGG
Found at i:551915 original size:14 final size:14
Alignment explanation
Indices: 551876--551915 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
551866 AAGTAAAAGG
*
551876 GAAAAATGAAAGAA
1 GAAAAATGGAAGAA
*
551890 GAAAAAGGGGAAGAA
1 GAAAAA-TGGAAGAA
551905 GAAAAATGGAA
1 GAAAAATGGAA
551916 AAAAGGGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (14 bp):
GAAAAATGGAAGAA
Found at i:551996 original size:16 final size:16
Alignment explanation
Indices: 551975--552006 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
551965 GCAGACTAGC
551975 AATAAAGTGAAAGAGT
1 AATAAAGTGAAAGAGT
551991 AATAAAGTGAAAGAGT
1 AATAAAGTGAAAGAGT
552007 GAAAGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (16 bp):
AATAAAGTGAAAGAGT
Found at i:552008 original size:24 final size:23
Alignment explanation
Indices: 551980--552025 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
551970 CTAGCAATAA
* *
551980 AGTGAAAGAGTAATAAAGTGAAAG
1 AGTGAAAGACTAA-AAAGGGAAAG
552004 AGTGAAAGACTAAAAAGGGAAA
1 AGTGAAAGACTAAAAAGGGAAA
552026 AATGGGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.28, T:0.13
Consensus pattern (23 bp):
AGTGAAAGACTAAAAAGGGAAAG
Found at i:556750 original size:20 final size:20
Alignment explanation
Indices: 556725--556762 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
556715 TTTTCCTCAG
556725 TGCCCTCTTTTTCTCATTAC
1 TGCCCTCTTTTTCTCATTAC
556745 TGCCCTCTTTTTCTCATT
1 TGCCCTCTTTTTCTCATT
556763 CTTCCCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.34, G:0.05, T:0.53
Consensus pattern (20 bp):
TGCCCTCTTTTTCTCATTAC
Found at i:559772 original size:25 final size:25
Alignment explanation
Indices: 559736--559795 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
559726 TCACATGATC
*
559736 ATATTATCATTAACTATAATATATT
1 ATATTATAATTAACTATAATATATT
* * *
559761 ATATTATAATTAATTATATTATTTT
1 ATATTATAATTAACTATAATATATT
559786 A-ATATATAAT
1 ATAT-TATAAT
559796 ATTAACGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTATAATTAACTATAATATATT
Found at i:559927 original size:30 final size:31
Alignment explanation
Indices: 559854--559928 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
559844 ATTGTTAGTG
*
559854 ATAAAAATTTATTTGATTTTAAATAAAAAAT
1 ATAAAAATTTATTTGATTTAAAATAAAAAAT
* *
559885 ATAAAAAATTATTTTATTTAAAAT-AAAAAT
1 ATAAAAATTTATTTGATTTAAAATAAAAAAT
* *
559915 GTAAAAGTTTATTT
1 ATAAAAATTTATTT
559929 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (31 bp):
ATAAAAATTTATTTGATTTAAAATAAAAAAT
Found at i:569284 original size:34 final size:34
Alignment explanation
Indices: 569246--569314 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
569236 AAGCAAGGTC
*
569246 TCTTTTAATAGTGTTTCTGGGTGTGATTTTAAAA
1 TCTTTTAATAGTGTTTCTGGGTGCGATTTTAAAA
* *
569280 TCTTTTAATAGTGTTTCTGTGTGCGATTTTTAAA
1 TCTTTTAATAGTGTTTCTGGGTGCGATTTTAAAA
569314 T
1 T
569315 TAACATATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (34 bp):
TCTTTTAATAGTGTTTCTGGGTGCGATTTTAAAA
Found at i:606585 original size:20 final size:20
Alignment explanation
Indices: 606543--606585 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
606533 TGTATTTACA
* *
606543 AAAAAAAGGTAAATTAGGTT
1 AAAAAAAGGTAAATAAGGAT
* *
606563 AAAAAAAGGTGACTAAGGAT
1 AAAAAAAGGTAAATAAGGAT
606583 AAA
1 AAA
606586 TATAACAAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAAAAAGGTAAATAAGGAT
Found at i:610272 original size:17 final size:18
Alignment explanation
Indices: 610243--610277 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
610233 TATAGATCAT
610243 AACAAACCAAAAAGAAAA
1 AACAAACCAAAAAGAAAA
*
610261 AACAAA-CAAAAATAAAA
1 AACAAACCAAAAAGAAAA
610278 CAAAGTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (18 bp):
AACAAACCAAAAAGAAAA
Found at i:612408 original size:32 final size:32
Alignment explanation
Indices: 612339--612420 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
612329 ACTGAAAATG
* * * *
612339 CTGACGTGGTAATGCCATATCATTTTGAGATG
1 CTGATGTGGTAATGCCATATCACTTTGACATA
*
612371 TTGATGTGGTAATGCCATATCACTTTGACATA
1 CTGATGTGGTAATGCCATATCACTTTGACATA
* *
612403 CTGATGTCGTAGTGCCAT
1 CTGATGTGGTAATGCCAT
612421 GTGGCACTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (32 bp):
CTGATGTGGTAATGCCATATCACTTTGACATA
Found at i:612671 original size:32 final size:32
Alignment explanation
Indices: 612629--612700 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
612619 TTGAAAATGA
* * * *
612629 TGATGAGGCAATGTCATATTACTTTGACATGC
1 TGATGTGGCAACGCCATATCACTTTGACATGC
*
612661 TGATGTGGCAACGCCATATCACTTTGGCATGC
1 TGATGTGGCAACGCCATATCACTTTGACATGC
*
612693 TAATGTGG
1 TGATGTGG
612701 TAGTGCCACG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (32 bp):
TGATGTGGCAACGCCATATCACTTTGACATGC
Found at i:612836 original size:289 final size:289
Alignment explanation
Indices: 612317--612845 Score: 720
Period size: 289 Copynumber: 1.8 Consensus size: 289
612307 GCTAACGTGG
* * * * * * * *
612317 CATGTGAGGTGGACTGAAAATGCTGACGTGGTAATGCCATATCATTTTGAGATGTTGATGTGGTA
1 CATGTGAAGTGGACTGAAAATGATGACGAGGCAATGCCATATCACTTTGACATGCTGATGTGGCA
* * * *
612382 ATGCCATATCACTTTGACATACTGATGTCGTAGTGCCATGTGGCACTAACATGCTAATGTAGTTA
66 ACGCCATATCACTTTGACATACTAATGTCGTAGTGCCACGTGGCACTAACATGCTAATGTAGATA
* * * * *
612447 TGCCATGAGGCATGTCAGCAAGGGCACCATGTGTCAAACTCTTCTTTAACACCCATCCATGTCAT
131 TACCATGAGACATGTCAGCAAGGGCACCACGTGTCAAACTCTCCTTCAACACCCATCCATGTCAT
* *
612512 GCCACATGGCATGTTTAGAGGGTGACACATGGCATGACAAAAGAGAAACACGTGTCTGATATGGC
196 GCCACATGGCATATTCAGAGGGTGACACATGGCATGACAAAAGAGAAACACGTGTCTGATATGGC
612577 ATATGAAGTGATTAGAAATGCTGACATGA
261 ATATGAAGTGATTAGAAATGCTGACATGA
* * * *
612606 CATGTGAAGTGGATTGAAAATGATGATGAGGCAATGTCATATTACTTTGACATGCTGATGTGGCA
1 CATGTGAAGTGGACTGAAAATGATGACGAGGCAATGCCATATCACTTTGACATGCTGATGTGGCA
* * * * *
612671 ACGCCATATCACTTTGGCATGCTAATGTGGTAGTGCCACGTGGCATTAACATGCTGATGTAGATA
66 ACGCCATATCACTTTGACATACTAATGTCGTAGTGCCACGTGGCACTAACATGCTAATGTAGATA
* ** * *
612736 TACCATGTGACATGTC--CAAGAAGGCACCACGTGTCATGCTCTCCTTCATCACCTATCCATGTC
131 TACCATGAGACATGTCAGCAAG--GGCACCACGTGTCAAACTCTCCTTCAACACCCATCCATGTC
*
612799 ATGCCACATGGCATATTCAGAGGGTGACACATGGCATGACAAGAGAG
194 ATGCCACATGGCATATTCAGAGGGTGACACATGGCATGACAAAAGAG
612846 TGACGTGTGT
Statistics
Matches: 204, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
287 4 0.02
289 200 0.98
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (289 bp):
CATGTGAAGTGGACTGAAAATGATGACGAGGCAATGCCATATCACTTTGACATGCTGATGTGGCA
ACGCCATATCACTTTGACATACTAATGTCGTAGTGCCACGTGGCACTAACATGCTAATGTAGATA
TACCATGAGACATGTCAGCAAGGGCACCACGTGTCAAACTCTCCTTCAACACCCATCCATGTCAT
GCCACATGGCATATTCAGAGGGTGACACATGGCATGACAAAAGAGAAACACGTGTCTGATATGGC
ATATGAAGTGATTAGAAATGCTGACATGA
Found at i:613018 original size:21 final size:22
Alignment explanation
Indices: 612985--613029 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
612975 CTTTTGTTTT
*
612985 TTTTTCTTCTTTTCTTTC-CTC
1 TTTTCCTTCTTTTCTTTCTCTC
*
613006 TTTTCCTTTTTTTCTTTCTCTC
1 TTTTCCTTCTTTTCTTTCTCTC
613028 TT
1 TT
613030 CTCTCACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCCTTCTTTTCTTTCTCTC
Found at i:615955 original size:17 final size:18
Alignment explanation
Indices: 615933--615968 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
615923 CTCTGGAAAC
615933 TACTAACAACTAA-CTTT
1 TACTAACAACTAACCTTT
*
615950 TACTAACAAGTAACCTTT
1 TACTAACAACTAACCTTT
615968 T
1 T
615969 TAACTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (18 bp):
TACTAACAACTAACCTTT
Found at i:620874 original size:17 final size:18
Alignment explanation
Indices: 620852--620886 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
620842 TCTGGAAACA
620852 ACTAACAACTAA-CTTTT
1 ACTAACAACTAACCTTTT
*
620869 ACTAACAAGTAACCTTTT
1 ACTAACAACTAACCTTTT
620887 TAACTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (18 bp):
ACTAACAACTAACCTTTT
Found at i:629015 original size:154 final size:155
Alignment explanation
Indices: 628752--629040 Score: 375
Period size: 154 Copynumber: 1.9 Consensus size: 155
628742 TGTGCATTTA
* * * *
628752 CGTGAAAAATTAACAACACATACTTTCTTTCAGCACCTATTCATGTCATGCCACATGGCATGTTC
1 CGTGAAAAATCAACAACACATACTTTCTTTCAGCACCCATCCATATCATGCCACATGGCATGTTC
* ** * ** * *
628817 AGAGGGTGACATGTGATATGACAAGAGAGTGACACATGTCTTTTCTTTGTTTTCTCATAAAA-TA
66 AGAGGATGACACATGACATGACAAGAGAGCAACACATGTCTTTTCATTATTTTCTCA-AAAATTA
628881 TTAAGTACTTAATGAGTGTGTACTTG
130 TTAAGTACTTAATGAGTGTGTACTTG
* * * *
628907 CGTGAGAAATCAACAATACATGCTTT-TTTTAGCACCCATCCATATCATGCCACATGGCATGTTC
1 CGTGAAAAATCAACAACACATACTTTCTTTCAGCACCCATCCATATCATGCCACATGGCATGTTC
* * * *
628971 AGAGGATGACACATGGCATGACAATAGAGCAACACGTGTTTTTTCATTATTTTCTCAAAAATTAT
66 AGAGGATGACACATGACATGACAAGAGAGCAACACATGTCTTTTCATTATTTTCTCAAAAATTAT
629036 TAAGT
131 TAAGT
629041 TTGAGTTTCG
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 4 0.04
154 87 0.77
155 22 0.19
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (155 bp):
CGTGAAAAATCAACAACACATACTTTCTTTCAGCACCCATCCATATCATGCCACATGGCATGTTC
AGAGGATGACACATGACATGACAAGAGAGCAACACATGTCTTTTCATTATTTTCTCAAAAATTAT
TAAGTACTTAATGAGTGTGTACTTG
Found at i:629152 original size:12 final size:11
Alignment explanation
Indices: 629134--629178 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 11
629124 CTTTTGTTTC
629134 TTTTCTTCTTT
1 TTTTCTTCTTT
629145 TATTTCTTCTTT
1 T-TTTCTTCTTT
629157 TTTT-TTCTATT
1 TTTTCTTCT-TT
629168 TTTTCTCTCTT
1 TTTTCT-TCTT
629179 CTCTCACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.13
11 10 0.33
12 13 0.43
13 3 0.10
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTCTTT
Found at i:629164 original size:22 final size:23
Alignment explanation
Indices: 629134--629178 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
629124 CTTTTGTTTC
629134 TTTTCTTCT-TTTATTTCT-TCTT
1 TTTTCTTCTATTT-TTTCTCTCTT
*
629156 TTTTTTTCTATTTTTTCTCTCTT
1 TTTTCTTCTATTTTTTCTCTCTT
629179 CTCTCACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTCTTCTATTTTTTCTCTCTT
Found at i:629400 original size:8 final size:8
Alignment explanation
Indices: 629383--629439 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
629373 GAGCGAAGAG
629383 AAAAGAAAA
1 AAAAG-AAA
*
629392 AAAATAAA
1 AAAAGAAA
629400 AAAAGAAA
1 AAAAGAAA
*
629408 AAGAGGAAA
1 AA-AAGAAA
*
629417 GAAAAGAAG
1 -AAAAGAAA
629426 AAAAGAAA
1 AAAAGAAA
629434 TAAAAG
1 -AAAAG
629440 TAATATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 19 0.49
9 18 0.46
10 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (8 bp):
AAAAGAAA
Found at i:629430 original size:13 final size:12
Alignment explanation
Indices: 629378--629433 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
629368 AAGGCGAGCG
*
629378 AAGAGAAAAGAA
1 AAGAAAAAAGAA
*
629390 AA-AAAATAAAAA
1 AAGAAAA-AAGAA
*
629402 AAGAAAAAGAGGA
1 AAGAAAAA-AGAA
629415 AAGAAAAGAAGAA
1 AAGAAAA-AAGAA
629428 AAGAAA
1 AAGAAA
629434 TAAAAGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 3 0.09
12 9 0.26
13 22 0.63
14 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:629935 original size:31 final size:31
Alignment explanation
Indices: 629900--629974 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
629890 TTAGGACTGT
* *
629900 GCAACGGTCAGTTGGGACCCCCCAACTGACC
1 GCAACCGTCAGTTGGGACCCCCCAACCGACC
* **
629931 GCAACCTTCAGTTGGGACTGCCCAACCGACC
1 GCAACCGTCAGTTGGGACCCCCCAACCGACC
*
629962 GCAACTGTCAGTT
1 GCAACCGTCAGTT
629975 ATTGTAACCG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.23, C:0.36, G:0.24, T:0.17
Consensus pattern (31 bp):
GCAACCGTCAGTTGGGACCCCCCAACCGACC
Found at i:638127 original size:2 final size:2
Alignment explanation
Indices: 638120--638144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
638110 ATTTGATATT
638120 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
638145 AAATACTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:650764 original size:26 final size:26
Alignment explanation
Indices: 650725--650791 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
650715 TCTCATCATC
*
650725 AAAAACCGACCGAAACTGACTTTCTA
1 AAAAACCGACCGAAACCGACTTTCTA
* * *
650751 AAAAATCGATCGAAACCGACTTTTTA
1 AAAAACCGACCGAAACCGACTTTCTA
650777 AAAAACCGACCGAAA
1 AAAAACCGACCGAAA
650792 TCGATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.24, G:0.12, T:0.18
Consensus pattern (26 bp):
AAAAACCGACCGAAACCGACTTTCTA
Found at i:653027 original size:24 final size:24
Alignment explanation
Indices: 652984--653033 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
652974 TATCCAGCAA
652984 AACTAAATGGAAAAAGAAAAACAT
1 AACTAAATGGAAAAAGAAAAACAT
*
653008 AACTCAAATGGAAATA-AAAAACAT
1 AACT-AAATGGAAAAAGAAAAACAT
653032 AA
1 AA
653034 GGCTAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (24 bp):
AACTAAATGGAAAAAGAAAAACAT
Found at i:656576 original size:25 final size:25
Alignment explanation
Indices: 656542--656593 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
656532 AAAATTCCTT
656542 AGTCTTAGTATTGCTATCATTTCGA
1 AGTCTTAGTATTGCTATCATTTCGA
656567 AGTCTTAGTATTGCTATCATTTCGA
1 AGTCTTAGTATTGCTATCATTTCGA
656592 AG
1 AG
656594 CTTTGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (25 bp):
AGTCTTAGTATTGCTATCATTTCGA
Found at i:661843 original size:3 final size:3
Alignment explanation
Indices: 661835--661869 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
661825 TCTTATGTTC
661835 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
661870 TTGAAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:667912 original size:40 final size:40
Alignment explanation
Indices: 667853--667931 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
667843 ACCGCTAGTC
667853 GTGGTGCTCTTGTTAGCTATGCCCATTCACTACTTTCTAT
1 GTGGTGCTCTTGTTAGCTATGCCCATTCACTACTTTCTAT
* *
667893 GTGGTGCTTTTGTTGGCTATGCCCATTCACTACTTTCTA
1 GTGGTGCTCTTGTTAGCTATGCCCATTCACTACTTTCTA
667932 CATAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (40 bp):
GTGGTGCTCTTGTTAGCTATGCCCATTCACTACTTTCTAT
Found at i:676504 original size:19 final size:19
Alignment explanation
Indices: 676477--676513 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
676467 TTATATATGC
* *
676477 AAAATTTTAAAATAAAATA
1 AAAAATTTAAAAAAAAATA
676496 AAAAATTTAAAAAAAAAT
1 AAAAATTTAAAAAAAAAT
676514 TATTCCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATTTAAAAAAAAATA
Found at i:679387 original size:31 final size:32
Alignment explanation
Indices: 679328--679389 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
679318 AATAAATTAA
679328 AATTAATTTATAAAAAATAAATGAAATTTTAT
1 AATTAATTTATAAAAAATAAATGAAATTTTAT
* *
679360 AATTATATTTA-AAAGAATTAATG-AATTTTA
1 AATTA-ATTTATAAAAAATAAATGAAATTTTA
679390 GTAAGTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 7 0.26
32 15 0.56
33 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (32 bp):
AATTAATTTATAAAAAATAAATGAAATTTTAT
Found at i:684199 original size:41 final size:41
Alignment explanation
Indices: 684154--684237 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
684144 TTGTGTGACA
684154 ATACTATTATATTACATATGAGAATGCATTCAAAACAAACC
1 ATACTATTATATTACATATGAGAATGCATTCAAAACAAACC
*
684195 ATACTATTTTATTACATATGAGAATGCATTCAAAACAAACC
1 ATACTATTATATTACATATGAGAATGCATTCAAAACAAACC
684236 AT
1 AT
684238 TTCTACATGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (41 bp):
ATACTATTATATTACATATGAGAATGCATTCAAAACAAACC
Found at i:691804 original size:25 final size:25
Alignment explanation
Indices: 691768--691824 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
691758 AGACTTAGCA
691768 AATCTCATAACTACTTCCTTTTTAT
1 AATCTCATAACTACTTCCTTTTTAT
691793 AATCTCGA-AACTACTTCCTTTTTAT
1 AATCTC-ATAACTACTTCCTTTTTAT
691818 AATCTCA
1 AATCTCA
691825 AAAAATTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.44
Consensus pattern (25 bp):
AATCTCATAACTACTTCCTTTTTAT
Found at i:695560 original size:26 final size:26
Alignment explanation
Indices: 695529--695578 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
695519 CATCTCACAT
* *
695529 TATATATGAATGTGATTATCAAAACC
1 TATATATAAATGTAATTATCAAAACC
695555 TATATATAAATGTAATTATCAAAA
1 TATATATAAATGTAATTATCAAAA
695579 TCTAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
TATATATAAATGTAATTATCAAAACC
Found at i:695931 original size:23 final size:24
Alignment explanation
Indices: 695900--695947 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
695890 ATACTTATTT
* *
695900 ATTTATTTATTCA-CATTAAAATA
1 ATTTATTTAATCACCATGAAAATA
*
695923 ATTTTTTTAATCACCATGAAAATA
1 ATTTATTTAATCACCATGAAAATA
695947 A
1 A
695948 AAAAACAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTATTTAATCACCATGAAAATA
Found at i:701642 original size:30 final size:30
Alignment explanation
Indices: 701599--701694 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
701589 AATCATTAAT
* * * *
701599 TATAAGAGTTTATTTGACTCAAAATAAAAG
1 TATAAGGGCTTATTTGGCTCAAAATAAAAA
701629 TATAAGGGCTTATTTGGCTCAAAATAAAAA
1 TATAAGGGCTTATTTGGCTCAAAATAAAAA
*
701659 TATAAAGGCTTATTTGGCTCAAAATAAAAA
1 TATAAGGGCTTATTTGGCTCAAAATAAAAA
*
701689 TTTAAG
1 TATAAG
701695 AGTTTGATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
TATAAGGGCTTATTTGGCTCAAAATAAAAA
Found at i:714386 original size:22 final size:24
Alignment explanation
Indices: 714361--714414 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
714351 ATAAAAAAAA
* * *
714361 TTAAAATATTTTTTTTAT-TAA-T
1 TTAAAAAATTATTATTATATAATT
714383 TTAAAAAATTATTATTATATAATT
1 TTAAAAAATTATTATTATATAATT
714407 TTAAAAAA
1 TTAAAAAA
714415 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
23 3 0.11
24 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAAAAATTATTATTATATAATT
Found at i:714704 original size:18 final size:19
Alignment explanation
Indices: 714681--714718 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
714671 CATTAACAAT
714681 ATAAAAGATTT-TTTTAAA
1 ATAAAAGATTTATTTTAAA
*
714699 ATAAAATATTTATTTTAAA
1 ATAAAAGATTTATTTTAAA
714718 A
1 A
714719 ACTAATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAAAAGATTTATTTTAAA
Found at i:727708 original size:24 final size:24
Alignment explanation
Indices: 727527--727713 Score: 96
Period size: 24 Copynumber: 7.5 Consensus size: 24
727517 ATACTTGTTG
* *
727527 TAATATATATTGATAAATTAGTGTAT
1 TAATATATATT-ATATA-TAATGTAT
* * *
727553 TAATAAGTATACTATCTATAGTGTAT
1 TAAT-A-TATATTATATATAATGTAT
*
727579 TAAGATATA-TATTATATAATGTA-
1 TAATATATATTA-TATATAATGTAT
* * *
727602 TAACTATAAATAATATATACTGTAT
1 TAA-TATATATTATATATAATGTAT
*
727627 TAATACT-TACTATATATAAT-TAT
1 TAATA-TATATTATATATAATGTAT
* * * *
727650 ATAGTACACGCACTTATATATATTGTAT
1 -TAATATA--TA-TTATATATAATGTAT
*
727678 TGATATATATTATATATAATGTA-
1 TAATATATATTATATATAATGTAT
727701 TAATTATATATTA
1 TAA-TATATATTA
727714 ATGCAATGTT
Statistics
Matches: 122, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
23 10 0.08
24 64 0.52
25 7 0.06
26 16 0.13
27 17 0.14
28 8 0.07
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (24 bp):
TAATATATATTATATATAATGTAT
Found at i:727833 original size:20 final size:20
Alignment explanation
Indices: 727808--727848 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
727798 ACATATTTAC
*
727808 TATATAATAGTATATTGTTA
1 TATATAATAGTAAATTGTTA
727828 TATATAATAGTAAATTGTTA
1 TATATAATAGTAAATTGTTA
727848 T
1 T
727849 TGACTAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TATATAATAGTAAATTGTTA
Found at i:727963 original size:18 final size:18
Alignment explanation
Indices: 727926--728050 Score: 52
Period size: 20 Copynumber: 6.9 Consensus size: 18
727916 CCTAAAAGGA
727926 ATATATATAATATATTGTTAC
1 ATAT-TATAATATA--GTTAC
727947 ATATTATAATATAGTT--
1 ATATTATAATATAGTTAC
727963 A-ATTATTAATATAAGTTAC
1 ATATTA-TAATAT-AGTTAC
* * *
727982 ATTAGTATAAAATA-CTA-
1 A-TATTATAATATAGTTAC
727999 ATA-T-TAATATAAGTTAC
1 ATATTATAATAT-AGTTAC
*
728016 -T-TTAGTAATATAAGTTAT
1 ATATTA-TAATAT-AGTTAC
*
728034 ACTATAATAATATAGTT
1 A-TATTATAATATAGTT
728051 TGTTAATAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
14 5 0.06
15 6 0.07
16 13 0.16
17 5 0.06
18 17 0.21
19 6 0.07
20 21 0.26
21 9 0.11
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATTATAATATAGTTAC
Found at i:727967 original size:15 final size:18
Alignment explanation
Indices: 727949--728032 Score: 72
Period size: 18 Copynumber: 4.9 Consensus size: 18
727939 ATTGTTACAT
727949 ATTA-TAATAT-AGTTA-
1 ATTATTAATATAAGTTAC
727964 ATTATTAATATAAGTTAC
1 ATTATTAATATAAGTTAC
* *
727982 ATTAGT-ATA-AA-ATAC
1 ATTATTAATATAAGTTAC
*
727997 TAATATTAATATAAGTTAC
1 -ATTATTAATATAAGTTAC
* *
728016 TTTAGTAATATAAGTTA
1 ATTATTAATATAAGTTA
728033 TACTATAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 7 0.13
16 12 0.22
17 11 0.20
18 21 0.39
19 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (18 bp):
ATTATTAATATAAGTTAC
Found at i:728044 original size:20 final size:19
Alignment explanation
Indices: 727993--728047 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
727983 TTAGTATAAA
*
727993 ATACTAATATTAATATAAGT
1 ATACT-ATAATAATATAAGT
* *
728013 -TACTTTAGTAATATAAGTT
1 ATACTATAATAATATAAG-T
728032 ATACTATAATAATATA
1 ATACTATAATAATATA
728048 GTTTGTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.38
19 5 0.17
20 13 0.45
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
ATACTATAATAATATAAGT
Found at i:728119 original size:16 final size:17
Alignment explanation
Indices: 728088--728124 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
728078 TACTATAGTC
*
728088 TATAGTACTCTATATTG
1 TATAGTACTATATATTG
728105 TATAG-ACTATATATTG
1 TATAGTACTATATATTG
728121 TATA
1 TATA
728125 TTAGTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (17 bp):
TATAGTACTATATATTG
Found at i:729060 original size:21 final size:21
Alignment explanation
Indices: 729032--729075 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
729022 TATAATTGTT
729032 AAATTTAAA-TTTAAAATAAA
1 AAATTTAAAGTTTAAAATAAA
*
729052 AAATATTAAAGTTTTAATATAAA
1 AAAT-TTAAAG-TTTAAAATAAA
729075 A
1 A
729076 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
23 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTTAAAGTTTAAAATAAA
Found at i:729075 original size:28 final size:27
Alignment explanation
Indices: 729030--729091 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
729020 CTTATAATTG
*
729030 TTAAATTTAAATTTAAAATA-AAAAATA
1 TTAAATTTAAATATAAAATATAAAAA-A
*
729057 TTAAAGTTTTAATATAAAATATAAAAAA
1 TTAAA-TTTAAATATAAAATATAAAAAA
729085 TTAAATT
1 TTAAATT
729092 ACAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.23
28 19 0.61
29 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TTAAATTTAAATATAAAATATAAAAAA
Found at i:729203 original size:17 final size:16
Alignment explanation
Indices: 729181--729231 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
729171 AATGATTTAA
729181 TTATAAATTATTAATAT
1 TTATAAA-TATTAATAT
*
729198 TTATAAACTA-TAAAAT
1 TTATAAA-TATTAATAT
*
729214 TTA-ATATATTAATAT
1 TTATAAATATTAATAT
729229 TTA
1 TTA
729232 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 8 0.28
17 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAAATATTAATAT
Found at i:729723 original size:5 final size:5
Alignment explanation
Indices: 729713--729744 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
729703 AGAGGACAGC
*
729713 CAAGG CAAGG CAAGG CAAGG CAAGG GAAGG CA
1 CAAGG CAAGG CAAGG CAAGG CAAGG CAAGG CA
729745 CCGAGAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.41, C:0.19, G:0.41, T:0.00
Consensus pattern (5 bp):
CAAGG
Found at i:736173 original size:3 final size:3
Alignment explanation
Indices: 736161--736198 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
736151 AATGCACACC
736161 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
736199 AGTAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:744028 original size:197 final size:190
Alignment explanation
Indices: 743693--744072 Score: 503
Period size: 197 Copynumber: 2.0 Consensus size: 190
743683 ATAAAAAGCT
* *
743693 GACAAAGAACACAACGAGCAAAGATCATCCATACTCTATAAACCCTAAAAACACCCTCAATAGAT
1 GACAAAGAACACAACGAGCAAACATCATACATACTCTATAAACCCTAAAAACACCCTCAATAGAT
* * *
743758 CCCTGATGAAATCTGAATAAAATAAACCTATATATTCATGAAGCACAAGGAAAAAACCAATCAAG
66 CCCTGATGAAATCTGAATAAAATAAACCTAGATATTCACGAAGCACAAGGAAAAAACCAACCAAG
* *
743823 AAGATCATTCATCAGAATGAGAAAAACCCTTTAATTATCTCGAACCCTCATTCTGAATCC
131 AAGATCATTCATCAGAATCAGAAAAACCCTTTAATTATCTCAAACCCTCATTCTGAATCC
* * * * *
743883 GACAAAGAACACAAGGAGC-AACTTCATACATTCTCTCTAGACCCTAAAAACACCCTCAATAGAT
1 GACAAAGAACACAACGAGCAAACATCATACATACTCTATAAACCCTAAAAACACCCTCAATAGA-
* * * *
743947 TCCTTGTTCTTG-TGAAAATCTTAATTAAATAACCCTAGATATTCACGAAGCACATGAGAAAAAA
65 TCC-----C-TGATG-AAATCTGAATAAAATAAACCTAGATATTCACGAAGCACAAG-GAAAAAA
* *
744011 CCAACCAAGAAGATCATTCATCAGAATCAGGAAAACCCTTTAATTATCTCAAACCCTTATTC
122 CCAACCAAGAAGATCATTCATCAGAATCAGAAAAACCCTTTAATTATCTCAAACCCTCATTC
744073 AATCTATACC
Statistics
Matches: 163, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
189 38 0.23
190 21 0.13
195 3 0.02
196 37 0.23
197 64 0.39
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (190 bp):
GACAAAGAACACAACGAGCAAACATCATACATACTCTATAAACCCTAAAAACACCCTCAATAGAT
CCCTGATGAAATCTGAATAAAATAAACCTAGATATTCACGAAGCACAAGGAAAAAACCAACCAAG
AAGATCATTCATCAGAATCAGAAAAACCCTTTAATTATCTCAAACCCTCATTCTGAATCC
Found at i:745686 original size:21 final size:21
Alignment explanation
Indices: 745662--745711 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
745652 AATCCATCTC
745662 ACCCAATGGATAAAAGAAAAT
1 ACCCAATGGATAAAAGAAAAT
745683 ACCCAATGGATAAAAGAAAAT
1 ACCCAATGGATAAAAGAAAAT
745704 ACCCAATG
1 ACCCAATG
745712 CATCTTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.54, C:0.18, G:0.14, T:0.14
Consensus pattern (21 bp):
ACCCAATGGATAAAAGAAAAT
Found at i:746170 original size:15 final size:17
Alignment explanation
Indices: 746135--746177 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
746125 AATTAAATTC
*
746135 ATAATTAAGTTAATTAT
1 ATAATTAAGTTAATTAA
746152 ATAATTAA-TT-ATTAA
1 ATAATTAAGTTAATTAA
746167 ATAATTAAGTT
1 ATAATTAAGTT
746178 TTGAGGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
16 4 0.17
17 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATAATTAAGTTAATTAA
Found at i:747200 original size:36 final size:35
Alignment explanation
Indices: 747134--747203 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
747124 AAAACTCCGA
747134 ATTATATATAAAAAATTAATTTAATGTTTATTTTTT
1 ATTATATATAAAAAATT-ATTTAATGTTTATTTTTT
* *
747170 ATTATATTTAAATAAATT-TTTAAATTTTTATTTT
1 ATTATATATAAA-AAATTATTT-AATGTTTATTTT
747204 AAATTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.10
36 22 0.73
37 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
ATTATATATAAAAAATTATTTAATGTTTATTTTTT
Found at i:747459 original size:19 final size:19
Alignment explanation
Indices: 747418--747463 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
747408 ATTACAATTG
*
747418 TTTCCTAATTAATTATCAT
1 TTTCCTAATTAAATATCAT
*
747437 TTTCTTAATTAAAT-TCAT
1 TTTCCTAATTAAATATCAT
747455 CTTTCCTAA
1 -TTTCCTAA
747464 AAAAAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTCCTAATTAAATATCAT
Found at i:753758 original size:10 final size:10
Alignment explanation
Indices: 753743--753802 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
753733 GGAGTTCAAG
753743 GAGAGAGAAA
1 GAGAGAGAAA
*
753753 GAGAGAAAAA
1 GAGAGAGAAA
753763 GAGAGA-AAA
1 GAGAGAGAAA
*
753772 GAAAGAGGAAA
1 GAGAGA-GAAA
*
753783 GAGAAAGAAA
1 GAGAGAGAAA
*
753793 GGGAGAGAAA
1 GAGAGAGAAA
753803 AAGGAGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
9 8 0.19
10 27 0.64
11 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:753782 original size:22 final size:23
Alignment explanation
Indices: 753748--753792 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
753738 TCAAGGAGAG
*
753748 AGAAAGAGAGAAAAAGAGAGAAA
1 AGAAAGAGAGAAAAAGAAAGAAA
*
753771 AGAAAGAG-GAAAGAGAAAGAAA
1 AGAAAGAGAGAAAAAGAAAGAAA
753793 GGGAGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AGAAAGAGAGAAAAAGAAAGAAA
Found at i:753810 original size:30 final size:30
Alignment explanation
Indices: 753744--753812 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
753734 GAGTTCAAGG
753744 AGAGAGAAAGAGAGAAAAAGAGAGAAAAGAA
1 AGAG-GAAAGAGAGAAAAAGAGAGAAAAGAA
*
753775 AGAGGAAAGAGA-AAGAAAGGGAGAGAAA-AA
1 AGAGGAAAGAGAGAA-AAAGAGAGA-AAAGAA
*
753805 GGAGGAAA
1 AGAGGAAA
753813 CTGAGGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 25 0.74
31 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (30 bp):
AGAGGAAAGAGAGAAAAAGAGAGAAAAGAA
Found at i:758081 original size:27 final size:27
Alignment explanation
Indices: 758043--758094 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
758033 CCAAACCAAA
*
758043 AAGAGACTTATTAGCATATTGTTTGCC
1 AAGAGACTTATTAGCATACTGTTTGCC
758070 AAGAGACTTATTAGCATACTGTTTG
1 AAGAGACTTATTAGCATACTGTTTG
758095 AGATGCCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (27 bp):
AAGAGACTTATTAGCATACTGTTTGCC
Found at i:764027 original size:21 final size:21
Alignment explanation
Indices: 764001--764040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
763991 TCTGAGAAGG
*
764001 ATCTATCGATAAATGCATGCC
1 ATCTATCAATAAATGCATGCC
*
764022 ATCTATCAATAGATGCATG
1 ATCTATCAATAAATGCATG
764041 TAAACTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (21 bp):
ATCTATCAATAAATGCATGCC
Found at i:767549 original size:142 final size:142
Alignment explanation
Indices: 767273--767549 Score: 355
Period size: 142 Copynumber: 2.0 Consensus size: 142
767263 CTTGGGTATG
* *
767273 GGTATAACTATTTATAACAACTGGGATATTCTAGAAAGAGGAAAAGAAAAATATCTACTATCACA
1 GGTATAACTATATATAACAAATGGGATATTCTAGAAAGAGGAAAAGAAAAATATCTACTATCACA
* * * *
767338 CTAGAAGCATTTATATGTTACTAGTTTGAACTTTGAGGTATGGGTATAACCATATATCAAAGTAG
66 CTAAAAGCATTTATATGTTACTAATTTGAACTTTGAGCTATGGGTATAACCACATATCAAAGTAG
767403 TCTTTAGATATA
131 TCTTTAGATATA
* * * *
767415 GGTATAATTATATATAACAAATGGGATATTCTAGAAAGAGTAAAA-ACAAAATATCTATTGTCAC
1 GGTATAACTATATATAACAAATGGGATATTCTAGAAAGAGGAAAAGA-AAAATATCTACTATCAC
* * * *
767479 ACTAAAAGCATTTATGTGTT-GTCAATTTGAA-TTGTGAGCTTTGGGTATAATCACATAT-AAAT
65 ACTAAAAGCATTTATATGTTACT-AATTTGAACTT-TGAGCTATGGGTATAACCACATATCAAA-
*
767541 GTATTCTTT
127 GTAGTCTTT
767550 GTGGTATGTT
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
141 7 0.06
142 109 0.94
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (142 bp):
GGTATAACTATATATAACAAATGGGATATTCTAGAAAGAGGAAAAGAAAAATATCTACTATCACA
CTAAAAGCATTTATATGTTACTAATTTGAACTTTGAGCTATGGGTATAACCACATATCAAAGTAG
TCTTTAGATATA
Found at i:770463 original size:79 final size:79
Alignment explanation
Indices: 770320--770475 Score: 224
Period size: 79 Copynumber: 2.0 Consensus size: 79
770310 TATGAGTTAT
* * * *
770320 CCATCTTTCATCCAACAAACTCTATACTACATTTCCAAAACTCAAACATGAGACCTAAGTTCTAA
1 CCATCTTTCATCCAACAAACTCTATACTACATTCCCAAAACCCAAACATAAGACCTAAGATCTAA
770385 TTATTCGGATGTAG
66 TTATTCGGATGTAG
* *
770399 CCATCTTTTATCCAACAAACTCTATCCTACATTCCCAAAACCCAAACATAAGA-CTCAAGATCTA
1 CCATCTTTCATCCAACAAACTCTATACTACATTCCCAAAACCCAAACATAAGACCT-AAGATCTA
* *
770463 ATTGTTGGGATGT
65 ATTATTCGGATGT
770476 TTTAGAGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 2 0.03
79 66 0.97
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.29
Consensus pattern (79 bp):
CCATCTTTCATCCAACAAACTCTATACTACATTCCCAAAACCCAAACATAAGACCTAAGATCTAA
TTATTCGGATGTAG
Found at i:770777 original size:33 final size:34
Alignment explanation
Indices: 770713--770782 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
770703 GAAAGAGGGA
*
770713 AGAGAAAAATATCTAGCAATTGATGTGTCACACT
1 AGAGAAAAATATCTAGCAATTAATGTGTCACACT
770747 AGAGAAAAATATCTAG-AGA-TAATGTGTCACACT
1 AGAGAAAAATATCTAGCA-ATTAATGTGTCACACT
770780 AGA
1 AGA
770783 AGCATTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (34 bp):
AGAGAAAAATATCTAGCAATTAATGTGTCACACT
Found at i:772550 original size:15 final size:16
Alignment explanation
Indices: 772530--772572 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
772520 AACATAAATT
*
772530 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
772545 AAAATAAACTAACTATA
1 AAAAT-AACTAACTATA
*
772562 AAAACAACTAA
1 AAAATAACTAA
772573 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 13 0.54
17 6 0.25
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:792225 original size:18 final size:19
Alignment explanation
Indices: 792202--792240 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
792192 GTGTAAAGGG
792202 TTTTA-TTATAT-TAATTTT
1 TTTTATTTATATAT-ATTTT
792220 TTTTATTTATATATATTTT
1 TTTTATTTATATATATTTT
792239 TT
1 TT
792241 ATAATTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 13 0.68
20 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTATATATATTTT
Found at i:801748 original size:3 final size:3
Alignment explanation
Indices: 801740--801774 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
801730 TGCCCTTTGA
801740 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
801775 GCATTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:808608 original size:13 final size:13
Alignment explanation
Indices: 808590--808615 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
808580 AATTTACGTA
808590 ATTATATTATTAT
1 ATTATATTATTAT
808603 ATTATATTATTAT
1 ATTATATTATTAT
808616 TAATTATGAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:812099 original size:15 final size:16
Alignment explanation
Indices: 812079--812109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
812069 TAAAATATTT
812079 TTATTA-ATTTTAAAA
1 TTATTATATTTTAAAA
812094 TTATTATATTTTAAAA
1 TTATTATATTTTAAAA
812110 AAACTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTATATTTTAAAA
Found at i:812530 original size:25 final size:25
Alignment explanation
Indices: 812485--812533 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
812475 TTTTATTTTA
*
812485 AATTAAATAAGTTTTTATAATCAAT
1 AATTAAATAAGTTATTATAATCAAT
*
812510 AATTAATTAA-TTATTATTAATCAA
1 AATTAAATAAGTTATTA-TAATCAA
812534 AATATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
AATTAAATAAGTTATTATAATCAAT
Found at i:812970 original size:2 final size:2
Alignment explanation
Indices: 812928--812960 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
812918 CCACGAAAGG
*
812928 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
812961 TCTTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:814982 original size:108 final size:108
Alignment explanation
Indices: 814869--815078 Score: 339
Period size: 108 Copynumber: 1.9 Consensus size: 108
814859 TATAAAAAAT
* * * * * *
814869 TTTGAGTAAATTTAAATAAAAAGTAAATTGGGTAAGAGTTGAATAATTTTAAAAGAATGTTTATT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGAGTAAGAATTGAATAATTTCAAAAAAATATGTATT
*
814934 TGTAAATTGTGAAAATTGTAACAAAATTAACATATTTTGCTAA
66 TGTAAATTGTGAAAATTGTAACAAAATCAACATATTTTGCTAA
814977 TTTGAGTAAATTTAAATAAAAAGTAAATTGAGTAAGAATTGAATAATTTCAAAAAAATATGTATT
1 TTTGAGTAAATTTAAATAAAAAGTAAATTGAGTAAGAATTGAATAATTTCAAAAAAATATGTATT
* *
815042 TGTAAATTGTGAAAGTTGTAACTAAATCAACATATTT
66 TGTAAATTGTGAAAATTGTAACAAAATCAACATATTT
815079 AACCATTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 93 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAAGTAAATTGAGTAAGAATTGAATAATTTCAAAAAAATATGTATT
TGTAAATTGTGAAAATTGTAACAAAATCAACATATTTTGCTAA
Found at i:816007 original size:3 final size:3
Alignment explanation
Indices: 815999--816033 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
815989 AAGAGGGATT
*
815999 AAC AAC AAC AAC AAC AAT AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
816034 TAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:816021 original size:18 final size:18
Alignment explanation
Indices: 815998--816036 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
815988 TAAGAGGGAT
815998 TAACAACAACAACAACAA
1 TAACAACAACAACAACAA
816016 TAACAACAACAACAACAA
1 TAACAACAACAACAACAA
816034 TAA
1 TAA
816037 TAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.08
Consensus pattern (18 bp):
TAACAACAACAACAACAA
Found at i:816038 original size:3 final size:3
Alignment explanation
Indices: 816032--816066 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
816022 CAACAACAAC
816032 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
816067 GCATAAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:817681 original size:23 final size:22
Alignment explanation
Indices: 817651--817704 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
817641 TGAAGCAAAC
817651 TACAAATATTAAAAAGACAGTA
1 TACAAATATTAAAAAGACAGTA
817673 TTACAAATATTAAAAAGACAGTA
1 -TACAAATATTAAAAAGACAGTA
817696 TAGCAAATA
1 TA-CAAATA
817705 AAACCAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (22 bp):
TACAAATATTAAAAAGACAGTA
Found at i:817910 original size:24 final size:24
Alignment explanation
Indices: 817882--817936 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
817872 CTGGTGAACG
817882 CTTTTCTCACCCTTAGGCCAGCCA
1 CTTTTCTCACCCTTAGGCCAGCCA
817906 CTTTTCTCACCCTTAGGCCAGCCA
1 CTTTTCTCACCCTTAGGCCAGCCA
817930 CTTTTCT
1 CTTTTCT
817937 TATGATCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.40, G:0.11, T:0.35
Consensus pattern (24 bp):
CTTTTCTCACCCTTAGGCCAGCCA
Found at i:822987 original size:2 final size:2
Alignment explanation
Indices: 822980--823008 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
822970 TGTACATGTA
822980 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
823009 AATTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:824147 original size:33 final size:31
Alignment explanation
Indices: 824073--824154 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 31
824063 CCTACAAACC
**
824073 CTAAAATGTTCCAACAAACATGGTTAACACA
1 CTAAAATGTTCCAACAAACATGGAAAACACA
* * *
824104 TTAAAATGTTCCAACAAACATAATGAAAATACA
1 CTAAAATGTTCCAACAAACAT--GGAAAACACA
*
824137 CTAAAATGTTCCCACAAA
1 CTAAAATGTTCCAACAAA
824155 TATATGCAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 20 0.48
33 22 0.52
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (31 bp):
CTAAAATGTTCCAACAAACATGGAAAACACA
Found at i:829242 original size:18 final size:19
Alignment explanation
Indices: 829218--829265 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
829208 TTTGTTTTCT
829218 ACTCTCTTTCTCT-AAAAA
1 ACTCTCTTTCTCTGAAAAA
* *
829236 TCTCTCTCTCT-TGAAAAA
1 ACTCTCTTTCTCTGAAAAA
829254 ACTCT-TTTCTCT
1 ACTCTCTTTCTCT
829266 TGTTTTGCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.44
Consensus pattern (19 bp):
ACTCTCTTTCTCTGAAAAA
Found at i:835108 original size:76 final size:76
Alignment explanation
Indices: 835028--835173 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
835018 CGTCATATAT
* *
835028 AAAAATATATTAC-ACGTCA-AATTTAGGTTATCT-CACGTCATGTTGAAAAAAAATACTGTTGT
1 AAAAACATATTACAACGTCATAA-TTAGATTAT-TACACGTCATGTT-AAAAAAAATACTGTTGT
835090 TACACGTCGTAGGC
63 TACACGTCGTAGGC
* * * * * *
835104 AAAAACATATTACAATGTTATAATTAGATTGTTACACGTTATGTTAAAAAAAATATTGTTGTTAT
1 AAAAACATATTACAACGTCATAATTAGATTATTACACGTCATGTTAAAAAAAATACTGTTGTTAC
835169 ACGTC
66 ACGTC
835174 ATGTATAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
76 36 0.61
77 21 0.36
78 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (76 bp):
AAAAACATATTACAACGTCATAATTAGATTATTACACGTCATGTTAAAAAAAATACTGTTGTTAC
ACGTCGTAGGC
Found at i:836227 original size:21 final size:21
Alignment explanation
Indices: 836197--836237 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
836187 ATAAAAGTCA
*
836197 ATTTTGAAAAAATATTTTTTT
1 ATTTTGAAAAAATATATTTTT
*
836218 ATTTTTAAAAAATATATTTT
1 ATTTTGAAAAAATATATTTT
836238 ACAACGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTGAAAAAATATATTTTT
Found at i:837079 original size:12 final size:14
Alignment explanation
Indices: 837053--837087 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
837043 TCAAAAAACG
837053 AAATAAAGCATTAA
1 AAATAAAGCATTAA
837067 AAA-AAAG-ATTAA
1 AAATAAAGCATTAA
837079 AAATAAAGC
1 AAATAAAGC
837088 GGTTGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.42
13 8 0.42
14 3 0.16
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (14 bp):
AAATAAAGCATTAA
Found at i:838464 original size:33 final size:34
Alignment explanation
Indices: 838413--838476 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
838403 AATATCACAA
*
838413 ATTATATTAAAGAAATGAAAATAAAATATATAAG
1 ATTATAATAAAGAAATGAAAATAAAATATATAAG
838447 ATTATAAT-AAGAAATGAAAATAAAATATAT
1 ATTATAATAAAGAAATGAAAATAAAATATAT
838477 GACATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (34 bp):
ATTATAATAAAGAAATGAAAATAAAATATATAAG
Found at i:838746 original size:30 final size:30
Alignment explanation
Indices: 838693--838751 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
838683 TTATTTTTCC
* ***
838693 TACAATTATATTACTTTTTATCACATTATT
1 TACAATTATATTACCTACAATCACATTATT
838723 TACAATTATATTACCTACAATCACATTAT
1 TACAATTATATTACCTACAATCACATTAT
838752 ATTGTAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (30 bp):
TACAATTATATTACCTACAATCACATTATT
Found at i:842645 original size:13 final size:13
Alignment explanation
Indices: 842627--842664 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
842617 GTGATGAAAA
842627 GTGATCATATCAC
1 GTGATCATATCAC
842640 GTGATCATATCAC
1 GTGATCATATCAC
842653 GTGATCATATCA
1 GTGATCATATCA
842665 ATATGTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
GTGATCATATCAC
Found at i:845915 original size:16 final size:17
Alignment explanation
Indices: 845884--845918 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
845874 GGTGTGATAA
845884 TATTTTTTAAATAATTT
1 TATTTTTTAAATAATTT
*
845901 TATTTTTTATA-AATTT
1 TATTTTTTAAATAATTT
845917 TA
1 TA
845919 AAAATTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTTAAATAATTT
Found at i:855989 original size:21 final size:22
Alignment explanation
Indices: 855963--856008 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
855953 TATTCTTTAC
*
855963 TTTATTT-TT-AAATTTTATAAT
1 TTTATTTCTTCAAATATTA-AAT
855984 TTTATTTCTTCAAATATTAAAT
1 TTTATTTCTTCAAATATTAAAT
856006 TTT
1 TTT
856009 TCATTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTCTTCAAATATTAAAT
Found at i:857530 original size:29 final size:30
Alignment explanation
Indices: 857482--857544 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
857472 CTATTTTTAT
857482 TTCAAAGACTCAAAGTTTGACCAATCAAAA
1 TTCAAAGACTCAAAGTTTGACCAATCAAAA
* * *
857512 TTCAAAGATTC-AAGTTTGATCAATTAAAA
1 TTCAAAGACTCAAAGTTTGACCAATCAAAA
857541 TTCA
1 TTCA
857545 TCTATGAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (30 bp):
TTCAAAGACTCAAAGTTTGACCAATCAAAA
Found at i:858588 original size:2 final size:2
Alignment explanation
Indices: 858581--858616 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
858571 TATTTTAACA
858581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
858617 GAATTGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.