Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold182
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: 891401
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 40281 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:586978 original size:99 final size:100
Alignment explanation
Indices: 586822--587019 Score: 256
Period size: 99 Copynumber: 2.0 Consensus size: 100
586812 TCACATAATC
* * * **
586822 TATACTATTATTTAAGTGTGTGATTGAGTTAGTATCATAATTTAACGGGACACCAACTGGGTCAA
1 TATACTATTATTTAAGTGTGTGATTGAGTTAGTATCACAAGTCAACGGGACACCAACTCAGTCAA
*
586887 GGAAATTACTAAAATAACATTACATATTTTAAATT
66 GAAAATTACTAAAATAACATTACATATTTTAAATT
* * * * *
586922 TATATTATTTTTTAAGTGTGTGA-TGAGTTGGTGTCACAAGTCAACTTGG-CACCAACTCAGTCA
1 TATACTATTATTTAAGTGTGTGATTGAGTTAGTATCACAAGTCAAC-GGGACACCAACTCAGTCA
* *
586985 AGAAAATTACTAAATTAACTTTACATATTTTAAAT
65 AGAAAATTACTAAAATAACATTACATATTTTAAAT
587020 AAGTTATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
99 61 0.73
100 23 0.27
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (100 bp):
TATACTATTATTTAAGTGTGTGATTGAGTTAGTATCACAAGTCAACGGGACACCAACTCAGTCAA
GAAAATTACTAAAATAACATTACATATTTTAAATT
Found at i:591408 original size:45 final size:45
Alignment explanation
Indices: 591353--591584 Score: 152
Period size: 44 Copynumber: 5.2 Consensus size: 45
591343 TGTCTTCGAT
* * *
591353 CTGCTTCGCTGTCGGTGCAGGAAGGGAAGATCTGCTATTTTTAAC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
**** * * * ** *
591398 CTGCTCCGCTG-CAACCCATGG-AGGCAAGGT-TGGTGTCTTCGAT
1 CTGCTCCGCTGTCGGTGCA-GGAAGGCAAGATCTGGTATTTTTAAC
*
591441 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
**** * * * * ** *
591486 CTGCTCCG-T-TACAACCCAGGGAGGCAAG-GCTGGTGTCTTCGAT
1 CTGCTCCGCTGT-CGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
* * *
591529 CTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAAC
1 CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
591574 CTGCTCCGCTG
1 CTGCTCCGCTG
591585 CAACCTAGGG
Statistics
Matches: 127, Mismatches: 52, Indels: 16
0.65 0.27 0.08
Matches are distributed among these distances:
43 35 0.28
44 47 0.37
45 45 0.35
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (45 bp):
CTGCTCCGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAAC
Found at i:591451 original size:43 final size:42
Alignment explanation
Indices: 591316--591535 Score: 107
Period size: 43 Copynumber: 5.0 Consensus size: 42
591306 NNNNNNNCTC
*
591316 CGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTT
1 CGCTGCAACCCA-GGAGGCAAGGTTGGTGTCTTCGATCTGCTT
**** * * * * * ** * *
591359 CGCTGTCGGTGCAGGAAGGGAAGATCTGCTATTTTTAACCTGCTC
1 CGCTG-CAACCCAGG-AGGCAAGGT-TGGTGTCTTCGATCTGCTT
591404 CGCTGCAACCCATGGAGGCAAGGTTGGTGTCTTCGATCTGCTT
1 CGCTGCAACCCA-GGAGGCAAGGTTGGTGTCTTCGATCTGCTT
**** * * * ** * *
591447 CGCTGTCGGTGCAGGAAGGCAAGATCTGGTATTTTTAACCTGCTC
1 CGCTG-CAACCCAGG-AGGCAAGGT-TGGTGTCTTCGATCTGCTT
* * *
591492 CGTTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTT
1 CGCTGCAACCCA-GGAGGCAAGGTTGGTGTCTTCGATCTGCTT
591535 C
1 C
591536 ACTGTCGGTG
Statistics
Matches: 117, Mismatches: 52, Indels: 16
0.63 0.28 0.09
Matches are distributed among these distances:
43 40 0.34
44 40 0.34
45 37 0.32
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (42 bp):
CGCTGCAACCCAGGAGGCAAGGTTGGTGTCTTCGATCTGCTT
Found at i:591462 original size:88 final size:88
Alignment explanation
Indices: 591313--591738 Score: 645
Period size: 88 Copynumber: 4.8 Consensus size: 88
591303 NNNNNNNNNN
591313 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
1 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
*
591378 GAAGATCTGCTATTTTTAACCTG
66 CAAGATCTGCTATTTTTAACCTG
* *
591401 CTCCGCTGCAACCCATGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
1 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
*
591466 CAAGATCTGGTATTTTTAACCTG
66 CAAGATCTGCTATTTTTAACCTG
* * *
591489 CTCCGTTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGG
1 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
*
591554 CAAGATCTGTTATTTTTAACCTG
66 CAAGATCTGCTATTTTTAACCTG
* * * * * * *
591577 CTCCGCTGCAACCTAGGGAGGCAATGCTAGTGTTTTCGATTTGCTTCGCTGTCAGTGCAGGAATG
1 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
* *
591642 CAAGATCTACTATTTTTAACCTA
66 CAAGATCTGCTATTTTTAACCTG
* * * * *
591665 CTTCGCTACAACCCAAGGAGGCAAGGTTGGTGTCTTCGATCTGCTACGCTGTCGGTGCAGGAAGG
1 CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
*
591730 TAAGATCTG
66 CAAGATCTG
591739 TTATCTTCAC
Statistics
Matches: 301, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 301 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
CTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGG
CAAGATCTGCTATTTTTAACCTG
Found at i:591555 original size:44 final size:44
Alignment explanation
Indices: 591326--591557 Score: 148
Period size: 44 Copynumber: 5.3 Consensus size: 44
591316 CGCTGCAACC
*
591326 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
* * * * * ** * * ****
591370 CAGGAAGGGAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
*
591414 CATGG-AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CA-GGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
* * * ** * * ****
591458 CAGGAAGGCAAGATCTGGTATTTTTAACCTGCTCCG-T-TACAACC
1 CAGGAAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGT-CGGTG
* *
591502 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
591546 CAGGAAGGCAAG
1 CAGGAAGGCAAG
591558 ATCTGTTATT
Statistics
Matches: 126, Mismatches: 54, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
43 35 0.28
44 55 0.44
45 36 0.29
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
Found at i:593281 original size:15 final size:15
Alignment explanation
Indices: 593261--593294 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
593251 TTTTTTAATT
593261 TTTTATTGCGCCATC
1 TTTTATTGCGCCATC
593276 TTTTATTGCGCCATC
1 TTTTATTGCGCCATC
593291 TTTT
1 TTTT
593295 TTTTGGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTTATTGCGCCATC
Found at i:596615 original size:22 final size:23
Alignment explanation
Indices: 596590--596637 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
596580 ATATACATAT
596590 AAATAT-GAAAATATTCATTAAA
1 AAATATAGAAAATATTCATTAAA
*
596612 AAATATAGGAAAATATTCGTTAAA
1 AAATATA-GAAAATATTCATTAAA
596636 AA
1 AA
596638 TAAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
24 17 0.74
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (23 bp):
AAATATAGAAAATATTCATTAAA
Found at i:596695 original size:30 final size:30
Alignment explanation
Indices: 596640--596722 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 30
596630 GTTAAAAATA
* *
596640 AATAAATATATACATGTACATATATAAATGAT
1 AATAATTATATACA--TATATATATAAATGAT
* *
596672 AATAATTATATACATATATATATAGATTAT
1 AATAATTATATACATATATATATAAATGAT
* *
596702 AAAAATAATAATTACATATAT
1 AATAATTAT-A-TACATATAT
596723 TGAAATTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 20 0.47
31 1 0.02
32 22 0.51
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (30 bp):
AATAATTATATACATATATATATAAATGAT
Found at i:596879 original size:17 final size:17
Alignment explanation
Indices: 596857--596900 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
596847 TAGGAAATAA
596857 AAAATGTATATGTATAT
1 AAAATGTATATGTATAT
*
596874 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
596891 -ATATGTATAT
1 AAAATGTATAT
596901 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:596933 original size:60 final size:60
Alignment explanation
Indices: 596814--596936 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
596804 AAAGTAAAAA
* * *
596814 AAAATATAAAAGTATATATATGCATATAAAAGTTAGGAAATAAAAAATGTATATGTATAT
1 AAAATATAAAAGTATATATATGCATATAAAAGTTAGCAAATAAAAAATGAATATATATAT
* * * *
596874 AAAATGTAAATGTATATATATGTATATAAAAGTTATGCAAATAGAATAAT-AATAATATATAT
1 AAAATATAAAAGTATATATATGCATATAAAAGTTA-GCAAATA-AAAAATGAAT-ATATATAT
596936 A
1 A
596937 TATATAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 32 0.60
61 8 0.15
62 13 0.25
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (60 bp):
AAAATATAAAAGTATATATATGCATATAAAAGTTAGCAAATAAAAAATGAATATATATAT
Found at i:597036 original size:3 final size:3
Alignment explanation
Indices: 597028--597069 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
597018 GTATATATAG
* *
597028 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
597070 GAACTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:597452 original size:19 final size:20
Alignment explanation
Indices: 597411--597455 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
597401 AATCATATCT
*
597411 TCTAAGATTGCATAAATCATA
1 TCTAAGATTGCAT-AACCATA
597432 TCTAAGATTGCAT-ACCATA
1 TCTAAGATTGCATAACCATA
597451 TCTAA
1 TCTAA
597456 TATTACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (20 bp):
TCTAAGATTGCATAACCATA
Found at i:597464 original size:19 final size:19
Alignment explanation
Indices: 597428--597464 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
597418 TTGCATAAAT
*
597428 CATATCTAAGATTGCATAC
1 CATATCTAAGATTACATAC
*
597447 CATATCTAATATTACATA
1 CATATCTAAGATTACATA
597465 TCCTTGAAGA
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:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (19 bp):
CATATCTAAGATTACATAC
Found at i:601477 original size:20 final size:20
Alignment explanation
Indices: 601434--601474 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
601424 TTATAAAAAC
*
601434 AATAAATTTAAATAATTATA
1 AATAAAATTAAATAATTATA
*
601454 AATAAAATT-AATCATTATA
1 AATAAAATTAAATAATTATA
601473 AA
1 AA
601475 ATACAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAAATTAAATAATTATA
Found at i:605654 original size:3 final size:3
Alignment explanation
Indices: 605648--605673 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
605638 CCTCCCGACG
605648 ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA AC
605674 GCAAGCAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:609407 original size:27 final size:27
Alignment explanation
Indices: 609339--609408 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
609329 CGCCAATGAG
*
609339 ATTGGCGGCACCAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAATGGTGCCAAAGCC
609366 ATTGGCGGCACCAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTGCCAA-AGCC
609393 ATTGGCGGCACCAATG
1 ATTGGCGGCACCAATG
609409 TTTATTGGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGCC
Found at i:609459 original size:4 final size:4
Alignment explanation
Indices: 609450--609594 Score: 89
Period size: 4 Copynumber: 37.8 Consensus size: 4
609440 GATGGAGAGG
* *
609450 GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA
* * *
609497 GAAGA GAAA AAAA GAAA GAAA GAAA G-AA G-AA GAAAA GGAA -AAG GAGAA
1 GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GA-AA
* *
609545 G-AA -AAA GAAA GAAA GAAG GAAA G-AA -AAA GAAA G-GA GAAGA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA
609589 -AAA GAA
1 GAAA GAA
609595 GAAGAAGAAG
Statistics
Matches: 110, Mismatches: 14, Indels: 34
0.70 0.09 0.22
Matches are distributed among these distances:
3 26 0.24
4 64 0.58
5 19 0.17
6 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:609524 original size:38 final size:38
Alignment explanation
Indices: 609473--609591 Score: 139
Period size: 38 Copynumber: 2.9 Consensus size: 38
609463 AAAGAAAGAA
*
609473 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG
1 AAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG
* *
609511 AAAGAAAGAAAGAAGAAGAAAAGGAAAAGGAGAAGAAAAAG
1 AAAGAAAGAAAGAA-AAGGAAAGGAGAA-GAGAA-AAAAAG
*
609552 AAAGAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAA
1 AAAG--A-AA-GAAAGAAAAGGAAAGGAGAAGAGAAAAAA
609592 GAAGAAGAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
38 13 0.19
39 11 0.16
40 5 0.07
41 10 0.15
42 4 0.06
43 6 0.09
44 12 0.18
45 7 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (38 bp):
AAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG
Found at i:609544 original size:17 final size:16
Alignment explanation
Indices: 609468--609639 Score: 78
Period size: 17 Copynumber: 10.9 Consensus size: 16
609458 GAAAGAAAGA
*
609468 AAGAAAA-AGAAGGA-
1 AAGAAAAGAAAAGGAG
*
609482 AAGAAAAGGAAAGGAG
1 AAGAAAAGAAAAGGAG
609498 AAGAGAAA-AAAA-GA-
1 AAGA-AAAGAAAAGGAG
*
609512 AAG-AAAG-AAAGAAG
1 AAGAAAAGAAAAGGAG
609526 AAGAAAAGGAAAAGGAG
1 AAGAAAA-GAAAAGGAG
*
609543 AAGAAAA-AGAAAGAAAG
1 AAGAAAAGA-AAAG-GAG
* *
609560 AAGGAAAGAAAAAGA-
1 AAGAAAAGAAAAGGAG
*
609575 AAGGAGAAGAGAAAA-AAG
1 AA-GA-AA-AGAAAAGGAG
*
609593 AAGAAGAAGAAGAGG-G
1 AAGAA-AAGAAAAGGAG
* * * *
609609 AAGGAAGGAAAAAGAAA
1 AAGAAAAG-AAAAGGAG
609626 AAGAAAAGAAAAGG
1 AAGAAAAGAAAAGG
609640 TATTTTTTTT
Statistics
Matches: 117, Mismatches: 21, Indels: 38
0.66 0.12 0.22
Matches are distributed among these distances:
12 6 0.05
13 1 0.01
14 13 0.11
15 15 0.13
16 34 0.29
17 39 0.33
18 9 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAGGAG
Found at i:609622 original size:83 final size:83
Alignment explanation
Indices: 609459--609636 Score: 224
Period size: 83 Copynumber: 2.1 Consensus size: 83
609449 GGAAAGAAAG
*
609459 AAAG-AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAAG
1 AAAGAAAAGAAAG-AAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAAG
*
609523 AAGAAGAAAAGGAAAAGGA
65 AAGAAGAAAAGGAAAAGAA
*
609542 GAAGAAAAAGAAAG-AAAGAAGGAAAGAAAAAGAAAGGAGAAGAG-AAAAAAG-AAG-AAG-AAG
1 AAAG-AAAAGAAAGAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAAG
*
609602 AAGAGGGAAGGAAGGAAAAAGAA
65 AAGA-AGAA--AAGG-AAAAGAA
609625 AAAGAAAAGAAA
1 AAAGAAAAGAAA
609637 AGGTATTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
79 7 0.08
80 6 0.07
81 3 0.04
82 19 0.23
83 41 0.49
85 8 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (83 bp):
AAAGAAAAGAAAGAAAAGAAGGAAAGAAAAAGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAAGA
AGAAGAAAAGGAAAAGAA
Found at i:610499 original size:28 final size:26
Alignment explanation
Indices: 610441--610504 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
610431 GTTTGGATAT
*
610441 ATTTTGGTAAATAAAAATATATATAC
1 ATTTTGGTAAATAAAAAAATATATAC
*
610467 TTTTTGGTAAATAAAAAAA-AGTTATAAC
1 ATTTTGGTAAATAAAAAAATA--TAT-AC
610495 ATTTTGGTAA
1 ATTTTGGTAA
610505 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 17 0.53
27 3 0.09
28 11 0.34
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (26 bp):
ATTTTGGTAAATAAAAAAATATATAC
Found at i:614131 original size:3 final size:3
Alignment explanation
Indices: 614125--614189 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
614115 TAATAATAAT
614125 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
614173 AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AA
614190 TAATAATACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:614268 original size:10 final size:10
Alignment explanation
Indices: 614253--614285 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
614243 AGTAAAACAA
614253 AAAATATTAC
1 AAAATATTAC
614263 AAAATA-TAC
1 AAAATATTAC
*
614272 AAAATATTAT
1 AAAATATTAC
614282 AAAA
1 AAAA
614286 AATATCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATTAC
Found at i:614535 original size:21 final size:21
Alignment explanation
Indices: 614511--614551 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
614501 TGTTTTTTTG
*
614511 ATATATTTTGATAAATAAAAT
1 ATATATATTGATAAATAAAAT
614532 ATATATATTGATAAATAAAA
1 ATATATATTGATAAATAAAA
614552 AAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
ATATATATTGATAAATAAAAT
Found at i:618392 original size:2 final size:2
Alignment explanation
Indices: 618385--618415 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
618375 CTAGAAGAAG
618385 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
618416 CTAATCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:622934 original size:33 final size:34
Alignment explanation
Indices: 622895--622966 Score: 137
Period size: 33 Copynumber: 2.1 Consensus size: 34
622885 AAGTTTCATT
622895 AAAAATTAAAAATTGTTTTAGTTCAAAGGGTAA-
1 AAAAATTAAAAATTGTTTTAGTTCAAAGGGTAAG
622928 AAAAATTAAAAATTGTTTTAGTTCAAAGGGTAAG
1 AAAAATTAAAAATTGTTTTAGTTCAAAGGGTAAG
622962 AAAAA
1 AAAAA
622967 GAATTATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 33 0.87
34 5 0.13
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (34 bp):
AAAAATTAAAAATTGTTTTAGTTCAAAGGGTAAG
Found at i:631503 original size:45 final size:46
Alignment explanation
Indices: 631432--631528 Score: 160
Period size: 45 Copynumber: 2.1 Consensus size: 46
631422 AGTGTTATTG
631432 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
* **
631478 TTCAGTGGTAGC-ACGGCTATGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
631523 ATCAGT
1 ATCAGT
631529 TTGGCACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 36 0.77
46 11 0.23
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
Found at i:631504 original size:22 final size:23
Alignment explanation
Indices: 631432--631528 Score: 142
Period size: 23 Copynumber: 4.3 Consensus size: 23
631422 AGTGTTATTG
631432 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
*
631455 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* **
631478 TTCAGTGGTAGC-ACGGCTATGT
1 ATCAGTGGTAGCTACGGCTACAT
*
631500 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
631523 ATCAGT
1 ATCAGT
631529 TTGGCACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 18 0.28
23 46 0.72
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:634778 original size:10 final size:10
Alignment explanation
Indices: 634753--634787 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
634743 AATAAAAATT
634753 ATAATTTTT-
1 ATAATTTTTA
*
634762 ATGATTTTTA
1 ATAATTTTTA
634772 ATAATTTTTA
1 ATAATTTTTA
634782 ATAATT
1 ATAATT
634788 AAAAGGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:635295 original size:26 final size:26
Alignment explanation
Indices: 635260--635309 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
635250 AATATAAAAT
635260 AAATATATAAATA-TATAAAATTTTATA
1 AAATATATAAA-AGTAT-AAATTTTATA
635287 AAATA-ATAAAAGTATAAATTTTA
1 AAATATATAAAAGTATAAATTTTA
635310 ATATCATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.41
26 8 0.36
27 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATATATAAAAGTATAAATTTTATA
Found at i:636704 original size:27 final size:27
Alignment explanation
Indices: 636658--636752 Score: 129
Period size: 27 Copynumber: 3.5 Consensus size: 27
636648 GAGGGTATCT
* *
636658 CATAGGCGGCACCGATGGTGCCATTT-C
1 CATAGGCGGCACCAAAGGTGCC-TTTCC
* *
636685 CATGGGCGGCACCAAAGGTGTCTTTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCC
*
636712 CATAGGCGGCACCGAAGGTGCCTTTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCC
636739 CATAGGCGGCACCA
1 CATAGGCGGCACCA
636753 CTTGTGTCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 3 0.05
27 56 0.95
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.19
Consensus pattern (27 bp):
CATAGGCGGCACCAAAGGTGCCTTTCC
Found at i:643775 original size:24 final size:24
Alignment explanation
Indices: 643731--643777 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
643721 TATTTTATAT
643731 TATTTTATTACATTTTGTTTGAAA
1 TATTTTATTACATTTTGTTTGAAA
643755 TATTTGTATTA-ATTATT-TTTGAA
1 TATTT-TATTACATT-TTGTTTGAA
643778 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (24 bp):
TATTTTATTACATTTTGTTTGAAA
Found at i:643831 original size:88 final size:88
Alignment explanation
Indices: 643733--643904 Score: 317
Period size: 88 Copynumber: 2.0 Consensus size: 88
643723 TTTTATATTA
* *
643733 TTTTATTACATTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTTAAAAAAGTTAGTAAA
1 TTTTAGTACATTTTGTTTGAAATATTTGTATTAATTACTTTTGAATTTTTAAAAAAGTTAGTAAA
*
643798 AGTAAAATACTCTTACTTCTGCT
66 AGTAAAACACTCTTACTTCTGCT
643821 TTTTAGTACATTTTGTTTGAAATATTTGTATTAATTACTTTTGAATTTTTAAAAAAGTTAGTAAA
1 TTTTAGTACATTTTGTTTGAAATATTTGTATTAATTACTTTTGAATTTTTAAAAAAGTTAGTAAA
643886 AGTAAAACACTCTTACTTC
66 AGTAAAACACTCTTACTTC
643905 GGTCATTTGT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (88 bp):
TTTTAGTACATTTTGTTTGAAATATTTGTATTAATTACTTTTGAATTTTTAAAAAAGTTAGTAAA
AGTAAAACACTCTTACTTCTGCT
Found at i:644450 original size:44 final size:44
Alignment explanation
Indices: 644371--644515 Score: 168
Period size: 44 Copynumber: 3.3 Consensus size: 44
644361 TTCCTCCCTT
* *
644371 CTTCTTCTTCTTTCTTTTTTTTCTCTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTCT-TCTTCTCCTTTCCTTTTCTTTC
* *
644416 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCCTTC
1 CTTCTTCTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
* * ** * *
644460 CTTCTTTTTCTTTATTTCCTC-TCTTTTCCTTTTC-TTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
*
644502 TTTCTTCTTCTTTC
1 CTTCTTCTTCTTTC
644516 CCTCTCCTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 18 0.21
43 11 0.13
44 38 0.44
45 20 0.23
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (44 bp):
CTTCTTCTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:644488 original size:28 final size:29
Alignment explanation
Indices: 644457--644514 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
644447 TTCCTTTTCC
644457 TTCCTTCTT-TTTCTTTATTTCCTC-TCTT
1 TTCCTT-TTCTTTCTTTATTTCCTCTTCTT
* *
644485 TTCCTTTTCTTTCTTTCTTTCTTCTTCTT
1 TTCCTTTTCTTTCTTTATTTCCTCTTCTT
644514 T
1 T
644515 CCCTCTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 19 0.73
29 5 0.19
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (29 bp):
TTCCTTTTCTTTCTTTATTTCCTCTTCTT
Found at i:644498 original size:72 final size:77
Alignment explanation
Indices: 644345--644526 Score: 202
Period size: 72 Copynumber: 2.4 Consensus size: 77
644335 AAAAAATTAC
* * * * * * *
644345 CTTTTTTTCTTTTTTCTTCCTCCCTTCTTCTTCTTCTTTCTTTTTTTTCTCTTCTCATTTCCTTT
1 CTTTCTTTCTTTTTTCTTCTTCCCTTCTCCTTCTTCCTTCCTTCTTTTCTCTTCTCATTTCCTTC
644410 TCTTTCCTTCTT
66 TCTTTCCTTCTT
644422 -TTTCTTTCTTTTTTCTTCTTCTCCTT-TCCTT-TTCCTTCCTTCTTTT-TCTT-T-ATTTCC-T
1 CTTTCTTTCTTTTTTCTTCTTC-CCTTCTCCTTCTTCCTTCCTTCTTTTCTCTTCTCATTTCCTT
644480 CTCTTTTCCTT-TT
65 CTC-TTTCCTTCTT
*
644493 CTTTCTTTCTTTCTTCTTCTTTCCC-TCTCCTTCT
1 CTTTCTTTCTTTTTTCTTC-TTCCCTTCTCCTTCT
644527 CTTCCCCCCA
Statistics
Matches: 91, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
71 6 0.07
72 37 0.41
73 5 0.05
74 4 0.04
75 12 0.13
76 23 0.25
77 4 0.04
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (77 bp):
CTTTCTTTCTTTTTTCTTCTTCCCTTCTCCTTCTTCCTTCCTTCTTTTCTCTTCTCATTTCCTTC
TCTTTCCTTCTT
Found at i:644516 original size:38 final size:36
Alignment explanation
Indices: 644411--644521 Score: 113
Period size: 38 Copynumber: 3.0 Consensus size: 36
644401 ATTTCCTTTT
644411 CTTTCCTTCTT-TTTCTTTCTTTTTTCTTC-TT-CTC-
1 CTTTCCTT-TTCTTTCTTTC-TTTTTCTTCTTTCCTCT
* * *
644445 CTTTCCTTTTCCTTCCTTCTTTTTCTTTATTTCCTCT
1 CTTTCCTTTTCTTTCTTTCTTTTTC-TTCTTTCCTCT
644482 CTTTTCCTTTTCTTTCTTTCTTTCTTCTTCTTTCCCTCT
1 C-TTTCCTTTTCTTTCTTTCTTT-TTCTTCTTT-CCTCT
644521 C
1 C
644522 CTTCTCTTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
33 8 0.13
34 16 0.25
35 2 0.03
36 3 0.05
37 1 0.02
38 24 0.38
39 9 0.14
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (36 bp):
CTTTCCTTTTCTTTCTTTCTTTTTCTTCTTTCCTCT
Found at i:644602 original size:27 final size:26
Alignment explanation
Indices: 644570--644636 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
644560 TATGGGCAGT
644570 GCCGCCCATGGGAATGGCACCATCGGG
1 GCCGCCCATGGGAAT-GCACCATCGGG
* * * * *
644597 GTCGCCTATGGGAAATGCACCTTTGGT
1 GCCGCCCATGGG-AATGCACCATCGGG
644624 GCCGCCCATGGGA
1 GCCGCCCATGGGA
644637 TACACTCCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 1 0.03
27 28 0.88
28 3 0.09
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (26 bp):
GCCGCCCATGGGAATGCACCATCGGG
Found at i:644993 original size:24 final size:24
Alignment explanation
Indices: 644948--644999 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
644938 TTTCTAAAAG
***
644948 ATTTAGTATTTATGAGTGTAATAT
1 ATTTAGTATTTATGAACATAATAT
*
644972 ATTTAGTATTTATTAACATAATAT
1 ATTTAGTATTTATGAACATAATAT
644996 ATTT
1 ATTT
645000 GATTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATGAACATAATAT
Found at i:649330 original size:24 final size:24
Alignment explanation
Indices: 649296--649347 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
649286 TTTCTAGAAG
* **
649296 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
649320 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
649344 ATTT
1 ATTT
649348 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:652625 original size:16 final size:17
Alignment explanation
Indices: 652604--652635 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
652594 TAGAATTCAG
652604 TTGAGAAATT-ATTTAA
1 TTGAGAAATTAATTTAA
652620 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
652636 GTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:655663 original size:21 final size:21
Alignment explanation
Indices: 655639--655693 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
655629 CATAAAGGGT
655639 TGAACGGAAGCTCATAGGAGC
1 TGAACGGAAGCTCATAGGAGC
* * *
655660 TGAACGGAAACTCATATGAGT
1 TGAACGGAAGCTCATAGGAGC
* *
655681 TAAACAGAAGCTC
1 TGAACGGAAGCTC
655694 GTGAGAGCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
TGAACGGAAGCTCATAGGAGC
Found at i:655800 original size:25 final size:24
Alignment explanation
Indices: 655761--655808 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
655751 TACTTGGGTA
655761 CATTTTCCATCAATTCATCCTTTG
1 CATTTTCCATCAATTCATCCTTTG
*
655785 CATTTTACCGTCAATTCATCCTTT
1 CATTTT-CCATCAATTCATCCTTT
655809 ACCACAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (24 bp):
CATTTTCCATCAATTCATCCTTTG
Found at i:657299 original size:19 final size:20
Alignment explanation
Indices: 657277--657329 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
657267 TTTCTTTCTT
657277 TTTATTTTTTA-TTTTTAAG
1 TTTATTTTTTAGTTTTTAAG
* *
657296 TTTA-ATTTTAGTTTTTATG
1 TTTATTTTTTAGTTTTTAAG
* *
657315 TTTCTTTTTTTGTTT
1 TTTATTTTTTAGTTT
657330 ACTTTTTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 5 0.19
19 14 0.52
20 8 0.30
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (20 bp):
TTTATTTTTTAGTTTTTAAG
Found at i:657338 original size:13 final size:13
Alignment explanation
Indices: 657302--657339 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
657292 TAAGTTTAAT
* *
657302 TTTAGTTTTTATG
1 TTTACTTTTTTTG
657315 TTT-CTTTTTTTG
1 TTTACTTTTTTTG
657327 TTTACTTTTTTTG
1 TTTACTTTTTTTG
657340 AAACAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.08, C:0.05, G:0.11, T:0.76
Consensus pattern (13 bp):
TTTACTTTTTTTG
Found at i:662732 original size:22 final size:23
Alignment explanation
Indices: 662707--662756 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
662697 AAAAAATTTC
*
662707 TTTAACAAAA-CA-AAATCATTAT
1 TTTAACAAAATAATAAAT-ATTAT
662729 TTTAACAAAATAATAAATATTAT
1 TTTAACAAAATAATAAATATTAT
662752 TTTAA
1 TTTAA
662757 AGATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 11 0.44
24 4 0.16
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAACAAAATAATAAATATTAT
Found at i:665783 original size:44 final size:44
Alignment explanation
Indices: 665714--665813 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
665704 TGTTGTGCTT
** * *
665714 CCACAGCCATTGACAGATTTGATCTGTAATATTTTGTTATGTAC
1 CCACAGCCATTGACAGATTCCATCTGCAACATTTTGTTATGTAC
* * **
665758 CCACAGCCATATG-CAGATTCCATCTGCGACATTTTGTTTTGTGT
1 CCACAGCCAT-TGACAGATTCCATCTGCAACATTTTGTTATGTAC
665802 CCACAGCCATTG
1 CCACAGCCATTG
665814 GCAGTAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.04
44 43 0.91
45 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (44 bp):
CCACAGCCATTGACAGATTCCATCTGCAACATTTTGTTATGTAC
Found at i:668444 original size:227 final size:228
Alignment explanation
Indices: 668038--668492 Score: 894
Period size: 227 Copynumber: 2.0 Consensus size: 228
668028 AATTAATTAA
*
668038 ATAAAATATTAAAATAATTAGAATTAAAAATTTTAGGTTGAGAAATCAAAATTAGGTGTCCGAGA
1 ATAAAAGATTAAAATAATTAGAATTAAAAATTTTAGGTTGAGAAATCAAAATTAGGTGTCCGAGA
668103 ATTAATTTGGTTAAAATAGATTTTTAAAAACGAGGTTTGATTTGAAAATAATTTTGAAATTGGCT
66 ATTAATTTGGTTAAAATAGATTTTTAAAAACGAGGTTTGATTTGAAAATAATTTTGAAATTGGCT
668168 TTCATTGGAAACTAAAGACCAATTTGGAAAATAGAGGAAACTGTAGGTGGTCAAAGGGGCAAATG
131 TTCATTGGAAACTAAAGACCAATTTGGAAAATAGAGGAAACTGTAGGTGGTCAAAGGGGCAAATG
668233 CCCAATTTTTAAATTTTGGTTGGTTATTTAAAC
196 CCCAATTTTTAAATTTTGGTTGGTTATTTAAAC
668266 ATAAAAGATT-AAATAATTAGAATTAAAAATTTTAGGTTGAGAAATCAAAATTAGGTGTCCGAGA
1 ATAAAAGATTAAAATAATTAGAATTAAAAATTTTAGGTTGAGAAATCAAAATTAGGTGTCCGAGA
668330 ATTAATTTGGTTAAAATAGATTTTTAAAAACGAGGTTTGATTTGAAAATAATTTTGAAATTGGCT
66 ATTAATTTGGTTAAAATAGATTTTTAAAAACGAGGTTTGATTTGAAAATAATTTTGAAATTGGCT
668395 TTCATTGGAAACTAAAGACCAATTTGGAAAATAGAGGAAACTGTAGGTGGTCAAAGGGGCAAATG
131 TTCATTGGAAACTAAAGACCAATTTGGAAAATAGAGGAAACTGTAGGTGGTCAAAGGGGCAAATG
668460 CCCAATTTTTAAATTTTGGTTGGTTATTTAAAC
196 CCCAATTTTTAAATTTTGGTTGGTTATTTAAAC
668493 CACCCACCGT
Statistics
Matches: 226, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
227 217 0.96
228 9 0.04
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (228 bp):
ATAAAAGATTAAAATAATTAGAATTAAAAATTTTAGGTTGAGAAATCAAAATTAGGTGTCCGAGA
ATTAATTTGGTTAAAATAGATTTTTAAAAACGAGGTTTGATTTGAAAATAATTTTGAAATTGGCT
TTCATTGGAAACTAAAGACCAATTTGGAAAATAGAGGAAACTGTAGGTGGTCAAAGGGGCAAATG
CCCAATTTTTAAATTTTGGTTGGTTATTTAAAC
Found at i:669062 original size:30 final size:30
Alignment explanation
Indices: 669026--669103 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 30
669016 ATTAGATCTG
669026 TGTAATTAGATAAAATTGATGGTTCAGACT
1 TGTAATTAGATAAAATTGATGGTTCAGACT
669056 TGTAATTAGATGATATTTAAAATTGATGGTTCAGACT
1 TGTAATT--A-G--A--TAAAATTGATGGTTCAGACT
669093 TGTAATTAGAT
1 TGTAATTAGAT
669104 GATATTTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
30 8 0.20
32 2 0.05
33 1 0.02
34 1 0.02
35 2 0.05
37 27 0.66
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (30 bp):
TGTAATTAGATAAAATTGATGGTTCAGACT
Found at i:669067 original size:21 final size:20
Alignment explanation
Indices: 669039--669104 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
669029 AATTAGATAA
669039 AATTGATGGTTCAGACTTGT
1 AATTGATGGTTCAGACTTGT
* * **
669059 AATTAGAT-G---ATATTTAA
1 AATT-GATGGTTCAGACTTGT
669076 AATTGATGGTTCAGACTTGT
1 AATTGATGGTTCAGACTTGT
669096 AATTAGATG
1 AATT-GATG
669105 ATATTTAGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 11
0.63 0.16 0.22
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
20 13 0.41
21 7 0.22
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (20 bp):
AATTGATGGTTCAGACTTGT
Found at i:669086 original size:37 final size:37
Alignment explanation
Indices: 669036--669111 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
669026 TGTAATTAGA
669036 TAAAATTGATGGTTCAGACTTGTAATTAGATGATATT
1 TAAAATTGATGGTTCAGACTTGTAATTAGATGATATT
669073 TAAAATTGATGGTTCAGACTTGTAATTAGATGATATT
1 TAAAATTGATGGTTCAGACTTGTAATTAGATGATATT
669110 TA
1 TA
669112 GGGTGTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (37 bp):
TAAAATTGATGGTTCAGACTTGTAATTAGATGATATT
Found at i:669541 original size:24 final size:23
Alignment explanation
Indices: 669514--669629 Score: 105
Period size: 24 Copynumber: 5.0 Consensus size: 23
669504 TATAACCACT
*
669514 TATCACCTGATACATGTGAACCCC
1 TATCACCAG-TACATGTGAACCCC
* *
669538 TATCACCA-AACATGTGCAAACCCT
1 TATCACCAGTACATGTG--AACCCC
669562 TATCACCAGT-CATGTGTAAACCCC
1 TATCACCAGTACATGTG--AACCCC
669586 TATCACCAGTGACATGTGAA-CCC
1 TATCACCAGT-ACATGTGAACCCC
* *
669609 TATCACC-TTATATGTGAACCC
1 TATCACCAGTACATGTGAACCC
669630 ATCCACCATA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
21 8 0.10
22 10 0.13
23 10 0.13
24 44 0.56
26 6 0.08
ACGTcount: A:0.31, C:0.32, G:0.12, T:0.25
Consensus pattern (23 bp):
TATCACCAGTACATGTGAACCCC
Found at i:669567 original size:48 final size:46
Alignment explanation
Indices: 669507--669629 Score: 128
Period size: 48 Copynumber: 2.6 Consensus size: 46
669497 GTTAGTATAT
669507 AACCACTTATCACCTGATACATGTGAACCCCTATCACCA-AACATGTG
1 AACC-CTTATCACCTG-TACATGTGAACCCCTATCACCAGAACATGTG
* *
669554 CAAACCCTTATCACCAGT-CATGTGTAAACCCCTATCACCAGTGACATGTG
1 --AACCCTTATCACCTGTACATGTG--AACCCCTATCACCAG-AACATGTG
*
669604 AACCC-TATCACCT-TATATGTGAACCC
1 AACCCTTATCACCTGTACATGTGAACCC
669630 ATCCACCATA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
45 5 0.08
46 7 0.11
47 13 0.20
48 29 0.45
49 4 0.06
50 7 0.11
ACGTcount: A:0.32, C:0.33, G:0.11, T:0.24
Consensus pattern (46 bp):
AACCCTTATCACCTGTACATGTGAACCCCTATCACCAGAACATGTG
Found at i:669613 original size:23 final size:24
Alignment explanation
Indices: 669514--669615 Score: 106
Period size: 24 Copynumber: 4.3 Consensus size: 24
669504 TATAACCACT
*
669514 TATCACCTGATACATGTG-AACCCC
1 TATCACCAG-TACATGTGAAACCCC
* *
669538 TATCACCA-AACATGTGCAAACCCT
1 TATCACCAGTACATGTG-AAACCCC
669562 TATCACCAGT-CATGTGTAAACCCC
1 TATCACCAGTACATGTG-AAACCCC
669586 TATCACCAGTGACATGTG-AA-CCC
1 TATCACCAGT-ACATGTGAAACCCC
669609 TATCACC
1 TATCACC
669616 TTATATGTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.10
23 10 0.15
24 44 0.66
26 6 0.09
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.24
Consensus pattern (24 bp):
TATCACCAGTACATGTGAAACCCC
Found at i:669908 original size:22 final size:22
Alignment explanation
Indices: 669883--670001 Score: 125
Period size: 22 Copynumber: 5.3 Consensus size: 22
669873 GTGTGATTGT
669883 CATGTGATATGCGAACTTATGC
1 CATGTGATATGCGAACTTATGC
* * *
669905 CATGTGATATGTGAACCTATGT
1 CATGTGATATGCGAACTTATGC
*
669927 CATGTGATATACGAACTTATGC
1 CATGTGATATGCGAACTTATGC
* *
669949 TAAAGTGATATGCGAA-TATATGC
1 -CATGTGATATGCGAACT-TATGC
*
669972 CATGTGATATGCAAAC-TATGAC
1 CATGTGATATGCGAACTTATG-C
669994 CTATGTGA
1 C-ATGTGA
670002 GCTATGACAT
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
21 4 0.05
22 52 0.66
23 23 0.29
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (22 bp):
CATGTGATATGCGAACTTATGC
Found at i:669976 original size:45 final size:44
Alignment explanation
Indices: 669883--669981 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
669873 GTGTGATTGT
* * * * * *
669883 CATGTGATATGCGAACTTATGCCATGTGATATGTGAACCTATGT
1 CATGTGATATACGAACTTATGCAAAGTGATATGCGAACATATGC
*
669927 CATGTGATATACGAACTTATGCTAAAGTGATATGCGAATATATGC
1 CATGTGATATACGAACTTATGC-AAAGTGATATGCGAACATATGC
669972 CATGTGATAT
1 CATGTGATAT
669982 GCAAACTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 21 0.45
45 26 0.55
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (44 bp):
CATGTGATATACGAACTTATGCAAAGTGATATGCGAACATATGC
Found at i:673164 original size:25 final size:26
Alignment explanation
Indices: 673136--673190 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
673126 TAATAACTTT
673136 ACTTTACATT-AATAAAATTAGCACA
1 ACTTTACATTAAATAAAATTAGCACA
***
673161 ACTTTGTTTTAAAATAAAATTAGCACA
1 ACTTTACATT-AAATAAAATTAGCACA
673188 ACT
1 ACT
673191 CTTTTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
27 18 0.72
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (26 bp):
ACTTTACATTAAATAAAATTAGCACA
Found at i:673181 original size:27 final size:27
Alignment explanation
Indices: 673146--673198 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
673136 ACTTTACATT
673146 AATAAAATTAGCACAACT-TTGTTTTAA
1 AATAAAATTAGCACAACTCTT-TTTTAA
673173 AATAAAATTAGCACAACTCTTTTTTA
1 AATAAAATTAGCACAACTCTTTTTTA
673199 GTCAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (27 bp):
AATAAAATTAGCACAACTCTTTTTTAA
Found at i:674171 original size:5 final size:5
Alignment explanation
Indices: 674161--674192 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
674151 AATATTAGAA
*
674161 TATTT TATTT TATTT TATTT TATTT TAGTT TA
1 TATTT TATTT TATTT TATTT TATTT TATTT TA
674193 CATAATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:676447 original size:91 final size:92
Alignment explanation
Indices: 676335--676517 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 92
676325 CCATTTATAG
676335 TGCTTAGAATATTTGTATTATAATGTAATGTATAATGTATTATTAAAATTTAATAATATCCATAA
1 TGCTTAGAATATTTGTATTATAATGTAATGTATAATGTATTATTAAAATTTAATAATATCCATAA
676400 AGTTTTTTTATGTTGCTATATTAACAA
66 AGTTTTTTTATGTTGCTATATTAACAA
676427 TGCTTAGAAT-TTTGTATTATAATGTAATGTATAATGTATTATTAAAATTTAATAATATCCATAA
1 TGCTTAGAATATTTGTATTATAATGTAATGTATAATGTATTATTAAAATTTAATAATATCCATAA
676491 AGTTTTTTTATGTTGCTATATTAACAA
66 AGTTTTTTTATGTTGCTATATTAACAA
676518 AATTAAACAA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 81 0.89
92 10 0.11
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (92 bp):
TGCTTAGAATATTTGTATTATAATGTAATGTATAATGTATTATTAAAATTTAATAATATCCATAA
AGTTTTTTTATGTTGCTATATTAACAA
Found at i:677866 original size:195 final size:196
Alignment explanation
Indices: 677524--677914 Score: 775
Period size: 195 Copynumber: 2.0 Consensus size: 196
677514 CACTAATTAA
677524 AATTTTAAATTATAAAATATATTATTTATAATTGATTACCAAATAGAATTTGAGTGTTTGATAAA
1 AATTTTAAATTATAAAATATATTATTTATAATTGATTACCAAATAGAATTTGAGTGTTTGATAAA
677589 TAAAAATTTTAAATTATAAAAATTTGCATCCTTAATTTTTTAAATATTTCACTTTATTCTAGATA
66 TAAAAATTTTAAATTATAAAAATTTGCATCCTTAATTTTTTAAATATTTCACTTTATTCTAGATA
677654 AAATTAAATTTTAAACATCATTTTTTATGAAATAATAAAATGTAAAAGTAAATTAATTAAAAGAT
131 AAATTAAATTTTAAACATCATTTTTTATGAAATAATAAAATGTAAAAGTAAATTAATTAAAAGAT
677719 T
196 T
677720 AATTTTAAA-TATAAAATATATTATTTATAATTGATTACCAAATAGAATTTGAGTGTTTGATAAA
1 AATTTTAAATTATAAAATATATTATTTATAATTGATTACCAAATAGAATTTGAGTGTTTGATAAA
677784 TAAAAATTTTAAATTATAAAAATTTGCATCCTTAATTTTTTAAATATTTCACTTTATTCTAGATA
66 TAAAAATTTTAAATTATAAAAATTTGCATCCTTAATTTTTTAAATATTTCACTTTATTCTAGATA
677849 AAATTAAATTTTAAACATCATTTTTTATGAAATAATAAAATGTAAAAGTAAATTAATTAAAAGAT
131 AAATTAAATTTTAAACATCATTTTTTATGAAATAATAAAATGTAAAAGTAAATTAATTAAAAGAT
677914 T
196 T
677915 TTACTTATTT
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 186 0.95
196 9 0.05
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (196 bp):
AATTTTAAATTATAAAATATATTATTTATAATTGATTACCAAATAGAATTTGAGTGTTTGATAAA
TAAAAATTTTAAATTATAAAAATTTGCATCCTTAATTTTTTAAATATTTCACTTTATTCTAGATA
AAATTAAATTTTAAACATCATTTTTTATGAAATAATAAAATGTAAAAGTAAATTAATTAAAAGAT
T
Found at i:687934 original size:29 final size:29
Alignment explanation
Indices: 687899--687968 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
687889 TCAGATTACA
* * *
687899 TTTTAGTCACTTATGTTTAAAATATTATG
1 TTTTAGTCACTTACGTTTAAAATACTACG
* *
687928 TTTTAGTTACTTACGTTTGAAATACTACG
1 TTTTAGTCACTTACGTTTAAAATACTACG
687957 TTTTAGTCACTT
1 TTTTAGTCACTT
687969 GCATTATCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (29 bp):
TTTTAGTCACTTACGTTTAAAATACTACG
Found at i:699697 original size:29 final size:28
Alignment explanation
Indices: 699635--699697 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 28
699625 TGAAAAGTAT
* * *
699635 ATTGATTGAAAAGTAATTAATAGTTTGA
1 ATTGATTGAAAAGTAATTAAAACTATGA
699663 ATTTGATTGGAAAA-TGAATTAAAACTATGA
1 A-TTGATT-GAAAAGT-AATTAAAACTATGA
699693 ATTGA
1 ATTGA
699698 ATAAAGTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 11 0.38
30 17 0.59
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (28 bp):
ATTGATTGAAAAGTAATTAAAACTATGA
Found at i:703278 original size:13 final size:13
Alignment explanation
Indices: 703258--703291 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
703248 GTGTTGACCA
703258 TTTTTTTATT-AT
1 TTTTTTTATTAAT
703270 TTATTTTTATTAAT
1 TT-TTTTTATTAAT
703284 TTTTTTTA
1 TTTTTTTA
703292 ATAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 14 0.70
14 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTATTAAT
Found at i:711574 original size:6 final size:6
Alignment explanation
Indices: 711565--711626 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
711555 AAACAAAAGA
**
711565 AAAATT AAAATGT AACAATT -AAATT AAAAACAA AAATATT AAAATT AAAATT
1 AAAATT AAAAT-T AA-AATT AAAATT -AAAA-TT AAA-ATT AAAATT AAAATT
711617 AAAATT AAAA
1 AAAATT AAAA
711627 AAATGCTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
5 4 0.09
6 25 0.54
7 13 0.28
8 4 0.09
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:711620 original size:20 final size:20
Alignment explanation
Indices: 711565--711621 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
711555 AAACAAAAGA
*
711565 AAAATTAAAATGTAACA-ATT
1 AAAATTAAAAT-TAAAATATT
**
711585 -AAATTAAAAACAAAAATATT
1 AAAATT-AAAATTAAAATATT
711605 AAAATTAAAATTAAAAT
1 AAAATTAAAATTAAAAT
711622 TAAAAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.28
20 16 0.55
21 5 0.17
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAATTAAAATTAAAATATT
Found at i:711626 original size:26 final size:26
Alignment explanation
Indices: 711564--711626 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
711554 CAAACAAAAG
711564 AAAAATTAAAATGTAACAATTAAATT
1 AAAAATTAAAATGTAACAATTAAATT
** *
711590 AAAAACAAAAATATTAA-AATTAAAATT
1 AAAAATTAAAAT-GTAACAATT-AAATT
711617 -AAAATTAAAA
1 AAAAATTAAAA
711627 AAATGCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAAATTAAAATGTAACAATTAAATT
Found at i:711628 original size:20 final size:21
Alignment explanation
Indices: 711565--711620 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
711555 AAACAAAAGA
*
711565 AAAATTAAAATGT-AACA-ATT
1 AAAATTAAAAT-TAAAAATATT
**
711585 -AAATTAAAAACAAAAATATT
1 AAAATTAAAATTAAAAATATT
711605 AAAATTAAAATTAAAA
1 AAAATTAAAATTAAAA
711621 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTAAAATTAAAAATATT
Found at i:713751 original size:31 final size:31
Alignment explanation
Indices: 713715--713776 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
713705 AGATAATTTT
713715 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
*
713746 AAAGAGTTTTGTTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
713777 TAATTTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:714310 original size:12 final size:11
Alignment explanation
Indices: 714295--714335 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
714285 CAGCAAAAAA
714295 AAAAGAAAATGC
1 AAAA-AAAATGC
714307 --AAAAAATGC
1 AAAAAAAATGC
714316 AAAAAAAATCGC
1 AAAAAAAAT-GC
714328 AAAAAAAA
1 AAAAAAAA
714336 AGTTGCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 7 0.27
12 10 0.38
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGC
Found at i:715654 original size:12 final size:12
Alignment explanation
Indices: 715637--715662 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
715627 GGTTCTACTT
715637 CTACTAATCGAG
1 CTACTAATCGAG
715649 CTACTAATCGAG
1 CTACTAATCGAG
715661 CT
1 CT
715663 CCATCTTCTT
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:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (12 bp):
CTACTAATCGAG
Found at i:721723 original size:3 final size:3
Alignment explanation
Indices: 721715--721781 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
721705 TTTTTGTTTG
721715 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
721763 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
721782 ACATGCTAGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:728318 original size:97 final size:93
Alignment explanation
Indices: 728168--728340 Score: 204
Period size: 92 Copynumber: 1.8 Consensus size: 93
728158 CTACAACGTC
* * * **
728168 TTTTTAATTTTTCAAAATAATTATAAAAAATTACTAATTATTTTATTTTATTTTATTTTCGGAGC
1 TTTTTAATTTTCCAAAACAATTATAAAAAATTACTAATTATTTGATTCCA---T-TTTT-GGAGC
728233 ACATGGGCTTGAGTCTGGTATTACAATAATATA
61 ACATGGGCTTGAGTCTGGTATTACAATAATATA
* * * * *
728266 TTTTTAATTTTCCATAACAGTTAT-ACAAATTACTAGTTATTTGATTCCATTTTTGGGGCACATG
1 TTTTTAATTTTCCAAAACAATTATAAAAAATTACTAATTATTTGATTCCATTTTTGGAGCACATG
728330 GGCTTGAGTCT
66 GGCTTGAGTCT
728341 AATGTCAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
92 20 0.31
93 4 0.06
94 1 0.02
97 20 0.31
98 20 0.31
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.46
Consensus pattern (93 bp):
TTTTTAATTTTCCAAAACAATTATAAAAAATTACTAATTATTTGATTCCATTTTTGGAGCACATG
GGCTTGAGTCTGGTATTACAATAATATA
Found at i:730070 original size:14 final size:15
Alignment explanation
Indices: 730051--730080 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
730041 TTTAAAAAAG
730051 TTAAACA-AATTATT
1 TTAAACATAATTATT
730065 TTAAACATAATTATT
1 TTAAACATAATTATT
730080 T
1 T
730081 AATATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAACATAATTATT
Found at i:737520 original size:19 final size:19
Alignment explanation
Indices: 737496--737539 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
737486 TAATTTTTGG
*
737496 AATTTTTATAAA-TATTTTT
1 AATTTTTAAAAATTA-TTTT
737515 AA-TTTTAAAAATTATTTT
1 AATTTTTAAAAATTATTTT
737533 AATTTTT
1 AATTTTT
737540 TTTAGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTAAAAATTATTTT
Found at i:746742 original size:58 final size:57
Alignment explanation
Indices: 746583--746748 Score: 170
Period size: 58 Copynumber: 2.8 Consensus size: 57
746573 ATTTTGAGGT
* * *
746583 TTGAATTTGGTAATTTTTCTCACATTGGGGCTTGAAAATTTTTTGGGTCCAAGTTAGGCC
1 TTGAATTTGGTAATTGTTCCCACATT-GGGCTTG-AAATTTTTTGGGT-CAAGTTAGACC
* ** * * * *
746643 TTGAACTTAATAATTGTTCCCACATAGGGGTCTGAACTTTTTTTGGTCAAGTTAGACC
1 TTGAATTTGGTAATTGTTCCCACATTGGGCT-TGAAATTTTTTGGGTCAAGTTAGACC
* * *
746701 TTGAATTTGGCAAATGTTCCCACATTGGGACTTGAATTTTTTTGGGTC
1 TTGAATTTGGTAATTGTTCCCACATTGGG-CTTGAAATTTTTTGGGTC
746749 CAATTTGGTC
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
58 47 0.55
59 16 0.19
60 22 0.26
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (57 bp):
TTGAATTTGGTAATTGTTCCCACATTGGGCTTGAAATTTTTTGGGTCAAGTTAGACC
Found at i:748281 original size:2 final size:2
Alignment explanation
Indices: 748274--748312 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
748264 CAATATTTAA
*
748274 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
748313 AGGGTATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:751374 original size:88 final size:87
Alignment explanation
Indices: 751238--751426 Score: 245
Period size: 88 Copynumber: 2.2 Consensus size: 87
751228 CAAGAAAAAT
* * * *
751238 AATTAAGTCCCT-CCTTTTTTGCACTCAATTGAGCACGTGAACTTTCAAAAAACATCAAAAAGGC
1 AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
*
751302 CCTCAAACTTCTTCAAAAAAAGC
66 CCTCAAAATTCTTC-AAAAAAGC
* * * * * **
751325 AATTAAGCCCTTACTTTTTTTTCACTCAATTGGGTACTTGAACTCTCAAAATGCATCAAAAAGAC
1 AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
*
751390 CCTCAAAATTTTTCAAAAAAGC
66 CCTCAAAATTCTTCAAAAAAGC
751412 AATTAAGCCCCTACT
1 AATTAAGCCCCTACT
751427 CTTATTAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 32 0.37
88 55 0.63
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (87 bp):
AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
CCTCAAAATTCTTCAAAAAAGC
Found at i:751503 original size:19 final size:18
Alignment explanation
Indices: 751449--751543 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 18
751439 TAGAAAATAA
*
751449 TTATAATAAATGATAAATT
1 TTATAAAAAAT-ATAAATT
* *
751468 TTAGAAAAATTATTAAATT
1 TTATAAAAAATA-TAAATT
751487 TTAATAAAAAATATAAAAAATAT
1 TT-ATAAAAAATAT---AAAT-T
* * *
751510 TTAT-AAAATTGTAAAAT
1 TTATAAAAAATATAAATT
751527 TTATAAAAAATCATAAA
1 TTATAAAAAAT-ATAAA
751544 AAAAATTAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.09
18 9 0.16
19 21 0.36
20 8 0.14
21 6 0.10
22 6 0.10
23 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (18 bp):
TTATAAAAAATATAAATT
Found at i:751770 original size:10 final size:9
Alignment explanation
Indices: 751757--751806 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
751747 CTTTATAAAA
751757 TTTTATAATT
1 TTTTAT-ATT
751767 TTTTATA-T
1 TTTTATATT
*
751775 TTTTATATA
1 TTTTATATT
751784 TTTTATAATT
1 TTTTAT-ATT
751794 TTTTACTATT
1 TTTTA-TATT
751804 TTT
1 TTT
751807 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.23
9 7 0.20
10 19 0.54
11 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:751791 original size:27 final size:28
Alignment explanation
Indices: 751756--751809 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
751746 ACTTTATAAA
751756 ATTTTATAATTTTTTA-TATTTTTATAT
1 ATTTTATAATTTTTTACTATTTTTATAT
751783 ATTTTATAATTTTTTACTATTTTTATA
1 ATTTTATAATTTTTTACTATTTTTATA
751810 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
ATTTTATAATTTTTTACTATTTTTATAT
Found at i:751807 original size:9 final size:8
Alignment explanation
Indices: 751766--751809 Score: 52
Period size: 9 Copynumber: 5.0 Consensus size: 8
751756 ATTTTATAAT
751766 TTTTTATA
1 TTTTTATA
751774 TTTTTATA
1 TTTTTATA
751782 TATTTTATAA
1 T-TTTTAT-A
751792 TTTTTTACTA
1 -TTTTTA-TA
751802 TTTTTATA
1 TTTTTATA
751810 AAAAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 11 0.34
9 12 0.38
10 7 0.22
11 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:752031 original size:88 final size:87
Alignment explanation
Indices: 751895--752083 Score: 245
Period size: 88 Copynumber: 2.2 Consensus size: 87
751885 CAAGAAAAAT
* * * *
751895 AATTAAGTCCCT-CCTTTTTTGCACTCAATTGAGCACGTGAACTTTCAAAAAACATCAAAAAGGC
1 AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
*
751959 CCTCAAACTTCTTCAAAAAAAGC
66 CCTCAAAATTCTTC-AAAAAAGC
* * * * * **
751982 AATTAAGCCCTTACTTTTTTTTCACTCAATTGGGTACTTGAACTCTCAAAATGCATCAAAAAGAC
1 AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
*
752047 CCTCAAAATTTTTCAAAAAAGC
66 CCTCAAAATTCTTCAAAAAAGC
752069 AATTAAGCCCCTACT
1 AATTAAGCCCCTACT
752084 CTTATTAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 32 0.37
88 55 0.63
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (87 bp):
AATTAAGCCCCTACTTTTTTTGCACTCAATTGAGCACGTGAACTCTCAAAAAACATCAAAAAGAC
CCTCAAAATTCTTCAAAAAAGC
Found at i:756542 original size:9 final size:9
Alignment explanation
Indices: 756525--756555 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
756515 TCGAGTTGAT
756525 TCGAATAAC
1 TCGAATAAC
*
756534 TCGATTAAC
1 TCGAATAAC
756543 TCGAATAAC
1 TCGAATAAC
756552 TCGA
1 TCGA
756556 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:758465 original size:4 final size:4
Alignment explanation
Indices: 758456--758506 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
758446 TATTTTGCAA
758456 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
758504 ATA
1 ATA
758507 TATGTTTGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:770106 original size:21 final size:21
Alignment explanation
Indices: 770077--770119 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
770067 AGAATACGCC
770077 AACAAAAGCTCATAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
* *
770098 AACAGAAGCTCGTAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
770119 A
1 A
770120 TCCACCCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTG
Found at i:775261 original size:2 final size:2
Alignment explanation
Indices: 775254--775278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
775244 AACTTAGTTT
775254 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 T
775279 GTACATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:779490 original size:51 final size:47
Alignment explanation
Indices: 779375--779490 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 47
779365 ATCCGATTCG
* *
779375 AAAAAGGAAAAG-GAAAAGAGAGAAAAAATCAAAATCAAAATAATAA
1 AAAAAGAAAAAGAGAAAAGAGAGAAAAAATCAAAATCAAAATAAAAA
** *
779421 AAAAAGAAAAAGAG-AAAGAGA-AATCAATCAAAGTCAAAATAAAAA
1 AAAAAGAAAAAGAGAAAAGAGAGAAAAAATCAAAATCAAAATAAAAA
779466 TATGAAAAGCAAAGAAGAGAAAAGA
1 -A--AAAAG-AAA-AAGAGAAAAGA
779491 AGAGGCTAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
45 20 0.34
46 19 0.33
47 1 0.02
48 5 0.09
49 3 0.05
50 5 0.09
51 5 0.09
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (47 bp):
AAAAAGAAAAAGAGAAAAGAGAGAAAAAATCAAAATCAAAATAAAAA
Found at i:779849 original size:7 final size:7
Alignment explanation
Indices: 779837--779869 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
779827 AAAAAGAGAG
779837 ATGAAAA
1 ATGAAAA
779844 ATG-AAA
1 ATGAAAA
779850 ATG-AAA
1 ATGAAAA
779856 ATGAAAA
1 ATGAAAA
779863 ATGAAAA
1 ATGAAAA
779870 TGGAGAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:779850 original size:6 final size:6
Alignment explanation
Indices: 779841--779871 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
779831 AGAGAGATGA
779841 AAAATG AAAATG AAAATG AAAAATG AAAATG
1 AAAATG AAAATG AAAATG -AAAATG AAAATG
779872 GAGAGGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:779853 original size:13 final size:12
Alignment explanation
Indices: 779841--779871 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
779831 AGAGAGATGA
779841 AAAATGAAAATG
1 AAAATGAAAATG
779853 AAAATGAAAAATG
1 AAAATG-AAAATG
779866 AAAATG
1 AAAATG
779872 GAGAGGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAATGAAAATG
Found at i:781261 original size:98 final size:98
Alignment explanation
Indices: 781092--781458 Score: 571
Period size: 98 Copynumber: 3.9 Consensus size: 98
781082 AGATCAGTGA
*
781092 AGATC-AAAGACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
1 AGATCGAAA-ACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGC
*
781156 CTTCCTGCGTTAACAGCGAAGTTAACAGTGAAGC
65 CTTCCTGCGTTAACAGCGAAGTTAACAGCGAAGC
*
781190 AGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
781255 TTCCTGCGTTAACAGCGAAGTTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGTTAACAGCGAAGC
**
781288 AGATAAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
781353 TT-C--C--T----GC--A-TTAACAGCGAAGC
66 TTCCTGCGTTAACAGCGAAGTTAACAGCGAAGC
*
781374 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCGGATCTTGCC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
*
781439 TTCCTGCATTAACAGCGAAG
66 TTCCTGCGTTAACAGCGAAG
781459 CAGATCGAAA
Statistics
Matches: 247, Mismatches: 9, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
86 77 0.31
87 2 0.01
89 3 0.01
91 1 0.00
93 1 0.00
95 3 0.01
97 2 0.01
98 155 0.63
99 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (98 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGTTAACAGCGAAGC
Found at i:781279 original size:12 final size:12
Alignment explanation
Indices: 781262--781286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
781252 GCCTTCCTGC
781262 GTTAACAGCGAA
1 GTTAACAGCGAA
781274 GTTAACAGCGAA
1 GTTAACAGCGAA
781286 G
1 G
781287 CAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (12 bp):
GTTAACAGCGAA
Found at i:781394 original size:43 final size:43
Alignment explanation
Indices: 781347--781480 Score: 105
Period size: 43 Copynumber: 3.1 Consensus size: 43
781337 AGAAGCAGAT
781347 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
* * * * * * ** ** *
781390 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGAAGCGGA-T
1 CTTGCCTTCC-TGC-ATTAACAGCGAAGCAGATCGAA-AA-CAAAGC
781433 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
781476 CTTGC
1 CTTGC
781481 TTCTCTCGGT
Statistics
Matches: 61, Mismatches: 22, Indels: 16
0.62 0.22 0.16
Matches are distributed among these distances:
42 17 0.28
43 27 0.44
44 17 0.28
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
Found at i:781420 original size:86 final size:86
Alignment explanation
Indices: 781275--781530 Score: 415
Period size: 86 Copynumber: 3.0 Consensus size: 86
781265 AACAGCGAAG
**
781275 TTAACAGCGAAGCAGATAAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA
1 TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA
781340 AGCAGATCTTGCCTTCCTGCA
66 AGCAGATCTTGCCTTCCTGCA
781361 TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA
1 TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA
*
781426 AGCGGATCTTGCCTTCCTGCA
66 AGCAGATCTTGCCTTCCTGCA
* * * *
781447 TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCTTCTC-TCGGTTGTAGCGGAGCTGGTTGAAG
1 TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAG
*
781511 ACAACAGATCTTGCCTTCCT
65 A-AGCAGATCTTGCCTTCCT
781531 CAGCAGTAGT
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
86 142 0.89
87 17 0.11
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (86 bp):
TTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA
AGCAGATCTTGCCTTCCTGCA
Found at i:781623 original size:43 final size:40
Alignment explanation
Indices: 781572--781668 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
781562 ATCTTAACTT
*
781572 CCTAAGCAGTAGTGAAGTAGATTTAAGCCA-CCAGTCCTATCTC
1 CCTAAGCAGTAGTGAAGTAGA--TAA--CATCAAGTCCTATCTC
* * *
781615 CCTAAGCAGTAGTGGAGTAGATCACATCAAGTCTTATCTC
1 CCTAAGCAGTAGTGAAGTAGATAACATCAAGTCCTATCTC
781655 CCTAAGCAGTAGTG
1 CCTAAGCAGTAGTG
781669 GAGCAGACGA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.04
40 25 0.51
41 2 0.04
43 20 0.41
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (40 bp):
CCTAAGCAGTAGTGAAGTAGATAACATCAAGTCCTATCTC
Found at i:781664 original size:40 final size:40
Alignment explanation
Indices: 781563--781742 Score: 148
Period size: 43 Copynumber: 4.3 Consensus size: 40
781553 AGACGGCGAA
* * * * **
781563 TCTTAACTTCCTAAGCAGTAGTGAAGTAGATTTAAGCCACCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGA-TCAAATCA--AG
* *
781606 TCCTATCTCCCTAAGCAGTAGTGGAGTAGATCACATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAATCAAG
* **
781646 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATC-AAATCAA--G
* **
781688 ATCTTATCTCACTAAGCAGTAGTGGA-TCAGATCGTATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGT-AGATCAAATCAAG
781729 TCTTATCTCCCTAA
1 TCTTATCTCCCTAA
781743 ATAATAGTGG
Statistics
Matches: 111, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 47 0.42
41 1 0.01
42 5 0.05
43 56 0.50
44 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAATCAAG
Found at i:781696 original size:83 final size:83
Alignment explanation
Indices: 781601--781783 Score: 253
Period size: 83 Copynumber: 2.2 Consensus size: 83
781591 GATTTAAGCC
* * *
781601 ACCAGTCCTATCTCCCTAAGCAGTAGTGGAGT-AGATCACATCAAGTCTTATCTCCCTAAGCAGT
1 ACCAATCCTATCTCCCTAAGCAGTAGTGGA-TCAGATCACATCAAGTCTTATCTCCCTAAACAAT
781665 AGTGGAGCAGAC-GAAAGAA
65 AGTGGAGCAGACAG-AAGAA
* * * ** *
781684 ACCGATCTTATCTCACTAAGCAGTAGTGGATCAGATCGTATCAAGTCTTATCTCCCTAAATAATA
1 ACCAATCCTATCTCCCTAAGCAGTAGTGGATCAGATCACATCAAGTCTTATCTCCCTAAACAATA
781749 GTGGAGCAGACAGAAGAA
66 GTGGAGCAGACAGAAGAA
781767 ACCAATCCTATCTCCCT
1 ACCAATCCTATCTCCCT
781784 GAAGTTACAG
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
82 1 0.01
83 84 0.98
84 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
ACCAATCCTATCTCCCTAAGCAGTAGTGGATCAGATCACATCAAGTCTTATCTCCCTAAACAATA
GTGGAGCAGACAGAAGAA
Found at i:784226 original size:107 final size:105
Alignment explanation
Indices: 784035--784241 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 105
784025 TTTCTAAATA
* *
784035 AGGCAATATTTTGCTTTTGGAAAATCGAGAAAACGTGCGCTAACGTGCTGGGTTTCGATTTCTCG
1 AGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCG
* *
784100 TTCGACCAAGTAGCAAAATATCCTTTTTAAACTTTCAGAACG
66 TTCGACCAAATAGCAAAATAT-CTTCTT-AACTTTCAGAACG
*
784142 AGGCAATGTTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTG-TCGGGTTTCGATTTCTC
1 AGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCT-GGGTTTCGATTTCTC
*
784206 GTTCGACCAAATAGCTAAATATCTTCTTAACTTTCA
65 GTTCGACCAAATAGCAAAATATCTTCTTAACTTTCA
784242 ATCAATATTA
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
105 8 0.09
106 6 0.06
107 79 0.85
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (105 bp):
AGGCAATATTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCG
TTCGACCAAATAGCAAAATATCTTCTTAACTTTCAGAACG
Found at i:804833 original size:16 final size:16
Alignment explanation
Indices: 804812--804845 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
804802 AATATTATTT
*
804812 TTAAAAAAAATTTAAA
1 TTAAAAAAAACTTAAA
804828 TTAAAAAAAACTTAAA
1 TTAAAAAAAACTTAAA
804844 TT
1 TT
804846 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAAAAAACTTAAA
Found at i:805866 original size:21 final size:21
Alignment explanation
Indices: 805852--805904 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
805842 ACTTGATTAG
805852 TAAGTAACCAAACTTGATCCA
1 TAAGTAACCAAACTTGATCCA
* *
805873 TAAGTAACCAAAGTTGACCCA
1 TAAGTAACCAAACTTGATCCA
*
805894 CAAGTAACCAA
1 TAAGTAACCAA
805905 TCTTTAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (21 bp):
TAAGTAACCAAACTTGATCCA
Found at i:813194 original size:3 final size:3
Alignment explanation
Indices: 813186--813368 Score: 106
Period size: 3 Copynumber: 62.0 Consensus size: 3
813176 AATATTACAC
* * * * *
813186 TAT TAT TAT TAG TAG TAT TAG TAT TGT TGA- TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * * * * *
813231 TAA TAT TAT TAT TAT TCT TAC TAT TAT TAT TAG CAT TAT TAT CAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * * * * *
813280 T-T TAT TGT TAT T-T TAT TAC TAT TAA CAT CAT TAT TAG AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
813326 TAA TGT TAT TAC TAT T-T T-T TAT TAA TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
813369 GAAGGGTATA
Statistics
Matches: 132, Mismatches: 42, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
2 9 0.07
3 121 0.92
4 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:813350 original size:22 final size:22
Alignment explanation
Indices: 813322--813363 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
813312 ATTAGAATTA
* *
813322 TTATTAATGTTATTACTATTTT
1 TTATTAATATTATTAATATTTT
813344 TTATTAATATTATTAATATT
1 TTATTAATATTATTAATATT
813364 ATTATGAAGG
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:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTAATATTATTAATATTTT
Found at i:813385 original size:3 final size:3
Alignment explanation
Indices: 813379--813403 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
813369 GAAGGGTATA
813379 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
813404 TTATTATTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:813408 original size:3 final size:3
Alignment explanation
Indices: 813402--813426 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
813392 ATAATAATAA
813402 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
813427 TATACCCTTT
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):
TAT
Found at i:813760 original size:13 final size:13
Alignment explanation
Indices: 813742--813766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
813732 GTAAAACTAT
813742 GTATTTTGAGATC
1 GTATTTTGAGATC
813755 GTATTTTGAGAT
1 GTATTTTGAGAT
813767 TCGAAAAGGT
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:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
GTATTTTGAGATC
Found at i:819077 original size:17 final size:17
Alignment explanation
Indices: 819057--819184 Score: 50
Period size: 16 Copynumber: 7.5 Consensus size: 17
819047 ACATGAGAAA
819057 TTTTTTAACACGAAGA-
1 TTTTTTAACACGAAGAT
*
819073 TTTTTGAAGCA-GAA-AT
1 TTTTTTAA-CACGAAGAT
* *
819089 TTTTTTAAAAGAACGAAAGTTT
1 TTTTTT--AA-CACG-AAG-AT
*
819111 TTTTTTAACACG-AGAA
1 TTTTTTAACACGAAGAT
* * *
819127 TTTGTAAACACGAAAAT
1 TTTTTTAACACGAAGAT
** *
819144 TTTTGAAACACGAAAAT
1 TTTTTTAACACGAAGAT
** *
819161 TTTTGAAACACG-ACAT
1 TTTTTTAACACGAAGAT
819177 TTTTTTAA
1 TTTTTTAA
819185 AAACACGGGA
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
15 1 0.01
16 34 0.39
17 33 0.38
18 4 0.05
19 4 0.05
20 4 0.05
22 7 0.08
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTTTAACACGAAGAT
Found at i:819138 original size:16 final size:17
Alignment explanation
Indices: 819117--819427 Score: 148
Period size: 17 Copynumber: 17.4 Consensus size: 17
819107 GTTTTTTTTT
* *
819117 AACACGAGAATTTGT-A
1 AACACGAAAATTTTTGA
819133 AACACGAAAATTTTTGA
1 AACACGAAAATTTTTGA
819150 AACACGAAAATTTTTGA
1 AACACGAAAATTTTTGA
** *
819167 AACACGACATTTTTTTAAA
1 AACACGA-AAATTTTT-GA
** *
819186 AACACGGGAATTTTTAA
1 AACACGAAAATTTTTGA
* * *
819203 AACAGGGAAATTTTAGA
1 AACACGAAAATTTTTGA
*
819220 AACACGAAAATTTTTAA
1 AACACGAAAATTTTTGA
**
819237 AACACGACATTTTTTTTGA
1 AACACGA-A-AATTTTTGA
*
819256 AACACGATTTAAAAAATTTTGA
1 AACACG-----AAAATTTTTGA
**
819278 AATGCGAGAATATTTTTGA
1 AACACGA-AA-ATTTTTGA
* *
819297 AATACAAGAAATTTTTGAA
1 AACACGA-AAATTTTTG-A
819316 AACACGAAAA--TTTGA
1 AACACGAAAATTTTTGA
**
819331 AACACGAGATTTTTTTTTGAA
1 AACACGA-A--AATTTTTG-A
* *
819352 AACGCGAAAATTTTTAAA
1 AACACGAAAATTTTT-GA
**
819370 AACATAAAAATTTTTGAA
1 AACACGAAAATTTTTG-A
*
819388 AACACG-AAAGTTTTGA
1 AACACGAAAATTTTTGA
*
819404 AA-AC-ATAAATTTTTTTA
1 AACACGA-AAA-TTTTTGA
819421 AACACGA
1 AACACGA
819428 GTTTTTTTTA
Statistics
Matches: 224, Mismatches: 45, Indels: 49
0.70 0.14 0.15
Matches are distributed among these distances:
15 10 0.04
16 24 0.11
17 76 0.34
18 49 0.22
19 41 0.18
20 5 0.02
21 7 0.03
22 10 0.04
23 1 0.00
24 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (17 bp):
AACACGAAAATTTTTGA
Found at i:819182 original size:70 final size:70
Alignment explanation
Indices: 819117--819262 Score: 213
Period size: 70 Copynumber: 2.1 Consensus size: 70
819107 GTTTTTTTTT
* *
819117 AACACGAGAATTTGT-AAACACGAAAATTTTTGAAACACGAAAATTTTTGAAACACGACATTTTT
1 AACACGAGAATTTGTAAAACACGAAAATTTTAGAAACACGAAAATTTTTAAAACACGACATTTTT
819181 TTAAA
66 TTAAA
* * * *
819186 AACACGGGAATTTTTAAAACAGGGAAATTTTAGAAACACGAAAATTTTTAAAACACGACATTTTT
1 AACACGAGAATTTGTAAAACACGAAAATTTTAGAAACACGAAAATTTTTAAAACACGACATTTTT
**
819251 TTTGA
66 TTAAA
819256 AACACGA
1 AACACGA
819263 TTTAAAAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 13 0.19
70 54 0.81
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (70 bp):
AACACGAGAATTTGTAAAACACGAAAATTTTAGAAACACGAAAATTTTTAAAACACGACATTTTT
TTAAA
Found at i:819200 original size:87 final size:85
Alignment explanation
Indices: 819045--819262 Score: 194
Period size: 87 Copynumber: 2.5 Consensus size: 85
819035 GATCCGATTG
* * * *
819045 AAACATGAGAAATTTTTTAACACGAAGATTTTTGAAGCA-GAAATTTTTTTAAAAGAACGAAAGT
1 AAACACGA-AAATTTTTAAACACGAAAATTTTTGAAACACGAAATTTTTTTAAAAGAACGAAAG-
**
819109 TTTTTTTTAACACGAG-AATTTGT-
64 -TTTTTAAAACA-GAGAAATTT-TA
* *
819132 AAACACGAAAATTTTTGAAACACGAAAATTTTTGAAACACGACATTTTTTTAAAA-ACACGGGAA
1 AAACACGAAAATTTTT-AAACACGAAAATTTTTGAAACACGAAATTTTTTTAAAAGA-AC-GAAA
*
819196 -TTTTTAAAACAGGGAAATTTTA
63 GTTTTTAAAACAGAGAAATTTTA
**
819218 GAAACACGAAAATTTTTAAAACACGACATTTTTTTTGAAACACGA
1 -AAACACGAAAATTTTT-AAACACGA-A-AATTTTTGAAACACGA
819263 TTTAAAAAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
85 3 0.03
86 22 0.20
87 51 0.46
88 17 0.15
89 17 0.15
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (85 bp):
AAACACGAAAATTTTTAAACACGAAAATTTTTGAAACACGAAATTTTTTTAAAAGAACGAAAGTT
TTTAAAACAGAGAAATTTTA
Found at i:819296 original size:19 final size:18
Alignment explanation
Indices: 819272--819316 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
819262 ATTTAAAAAA
* *
819272 TTTTGAAATGCGAGAATAT
1 TTTTGAAATACAAGAA-AT
819291 TTTTGAAATACAAGAAAT
1 TTTTGAAATACAAGAAAT
819309 TTTTGAAA
1 TTTTGAAA
819317 ACACGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTTGAAATACAAGAAAT
Found at i:819384 original size:36 final size:35
Alignment explanation
Indices: 819344--819412 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
819334 ACGAGATTTT
* *
819344 TTTTTGAAAACGCGAAAATTTTTAAAAACATAAAAA
1 TTTTTGAAAACACG-AAAGTTTTAAAAACATAAAAA
*
819380 TTTTTGAAAACACGAAAGTTTTGAAAACATAAA
1 TTTTTGAAAACACGAAAGTTTTAAAAACATAAA
819413 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAGTTTTAAAAACATAAAAA
Found at i:819455 original size:21 final size:21
Alignment explanation
Indices: 819420--819462 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
819410 AAATTTTTTT
**
819420 AAACACGAGTTTTTTTTAAAA
1 AAACACGAGAATTTTTTAAAA
*
819441 AAACACGAGAATTTTTTGAAA
1 AAACACGAGAATTTTTTAAAA
819462 A
1 A
819463 CACGAAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (21 bp):
AAACACGAGAATTTTTTAAAA
Found at i:819509 original size:17 final size:17
Alignment explanation
Indices: 819466--819509 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
819456 TTGAAAACAC
*
819466 GAAAACATGAAAATTTT
1 GAAAACACGAAAATTTT
*
819483 GAAAATACGAAAATTTTT
1 GAAAACACGAAAA-TTTT
819501 G-AAACACGA
1 GAAAACACGA
819510 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (17 bp):
GAAAACACGAAAATTTT
Found at i:819601 original size:85 final size:86
Alignment explanation
Indices: 819498--819668 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 86
819488 TACGAAAATT
819498 TTTGAAACACGAGATTTTTTTTTTTGAAAAACATGAAAACACGAATTTTTTTTTTAAAAAAGAAA
1 TTTGAAACACGAGATTTTTTTTTTTGAAAAACATGAAAACACGAATTTTTTTTTTAAAAAAGAAA
819563 GAGACACGAATATATTTTTTG
66 GAGACACGAATATATTTTTTG
819584 TTTGAAACAC-AGATTTTTTTTTTTGAAAAACATGAAAACACGAATTTTTTTTTTAAAAAAGAAA
1 TTTGAAACACGAGATTTTTTTTTTTGAAAAACATGAAAACACGAATTTTTTTTTTAAAAAAGAAA
819648 GAGACACGAATATATTTTTTG
66 GAGACACGAATATATTTTTTG
819669 AAACACAGAA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 75 0.88
86 10 0.12
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (86 bp):
TTTGAAACACGAGATTTTTTTTTTTGAAAAACATGAAAACACGAATTTTTTTTTTAAAAAAGAAA
GAGACACGAATATATTTTTTG
Found at i:819735 original size:18 final size:17
Alignment explanation
Indices: 819694--819742 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
819684 TATTATTATT
819694 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
819711 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
819728 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
819743 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:820359 original size:17 final size:18
Alignment explanation
Indices: 820339--820374 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
820329 TTTTTTCTGC
820339 TTTGCT-TTGTTTTTTTT
1 TTTGCTCTTGTTTTTTTT
820356 TTTGCTGCTTGTTTTTTTT
1 TTTGCT-CTTGTTTTTTTT
820375 CTCTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (18 bp):
TTTGCTCTTGTTTTTTTT
Found at i:820514 original size:12 final size:11
Alignment explanation
Indices: 820492--820546 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
820482 GACCCGACTG
820492 ATTTT-TTTTT
1 ATTTTCTTTTT
820502 ATTTATCTTTTT
1 ATTT-TCTTTTT
820514 ATTTTC-TTTT
1 ATTTTCTTTTT
*
820524 CTTTTCTTTCTT
1 ATTTTCTTT-TT
* *
820536 TTTTTATTTTT
1 ATTTTCTTTTT
820547 TTCTCTCCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 13 0.34
11 7 0.18
12 18 0.47
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTCTTTTT
Found at i:820535 original size:25 final size:25
Alignment explanation
Indices: 820507--820560 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
820497 TTTTTATTTA
* *
820507 TCTTTTTATT-TTCTTTTCTTTTCTT
1 TCTTTTT-TTATTCTTTTCTCTCCTT
*
820532 TCTTTTTTTATTTTTTTCTCTCCTT
1 TCTTTTTTTATTCTTTTCTCTCCTT
820557 TCTT
1 TCTT
820561 CTTCCCTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (25 bp):
TCTTTTTTTATTCTTTTCTCTCCTT
Found at i:821258 original size:30 final size:30
Alignment explanation
Indices: 821226--821283 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
821216 TAAATTTAGA
*
821226 AAAAGTTAGGGGG-TAAAACATAATTTTTG
1 AAAAGTTAGGGGGCCAAAACATAATTTTTG
* *
821255 AAAAGTTTGGGGGCCAAAACGTAATTTTT
1 AAAAGTTAGGGGGCCAAAACATAATTTTT
821284 ATTTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (30 bp):
AAAAGTTAGGGGGCCAAAACATAATTTTTG
Done.