Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold61
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: 1997344
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.30
Warning! 204170 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:465303 original size:19 final size:20
Alignment explanation
Indices: 465276--465321 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
465266 GAAAATTATA
465276 AAAAATTGT-AAAGAAATAT
1 AAAAATTGTAAAAGAAATAT
* *
465295 AAAATTTGTAAAAGAATTAT
1 AAAAATTGTAAAAGAAATAT
465315 AAAAATT
1 AAAAATT
465322 ATCGTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAAATTGTAAAAGAAATAT
Found at i:465506 original size:9 final size:9
Alignment explanation
Indices: 465494--465587 Score: 68
Period size: 9 Copynumber: 10.6 Consensus size: 9
465484 TTTTATGCAA
465494 TTTATAATT
1 TTTATAATT
*
465503 TTTATTATT
1 TTTATAATT
**
465512 TTTATAAAA
1 TTTATAATT
*
465521 TTTACAATT
1 TTTATAATT
*
465530 TTTTTATATT
1 TTTATA-ATT
*
465540 TTTATGATT
1 TTTATAATT
* *
465549 TATAT-ATA
1 TTTATAATT
465557 TTT-TAATT
1 TTTATAATT
*
465565 TTTCATAAAT
1 TTT-ATAATT
465575 TTTA-AATT
1 TTTATAATT
465583 TTTAT
1 TTTAT
465588 TAAAATTTAA
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
7 1 0.02
8 16 0.25
9 32 0.51
10 14 0.22
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:465522 original size:27 final size:27
Alignment explanation
Indices: 465483--465589 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 27
465473 TTAAAGAGTT
**
465483 TTTTTATGCAATTTATAATTTTTATTA
1 TTTTTATAAAATTTATAATTTTTATTA
*
465510 TTTTTATAAAATTTACAATTTTT-TTA
1 TTTTTATAAAATTTATAATTTTTATTA
**
465536 TATTTT-TATGATTTATATATATTTTA--A
1 T-TTTTATAAAATTTATA-AT-TTTTATTA
*
465563 TTTTTCATAAATTTTA-AATTTTTATTA
1 TTTTT-ATAAAATTTATAATTTTTATTA
465590 AAATTTAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
25 5 0.08
26 18 0.29
27 30 0.48
28 10 0.16
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTATAAAATTTATAATTTTTATTA
Found at i:465578 original size:17 final size:17
Alignment explanation
Indices: 465509--465625 Score: 69
Period size: 17 Copynumber: 6.6 Consensus size: 17
465499 AATTTTTATT
* *
465509 ATTTTTATAAAATTTACA
1 ATTTTTATTAAATTT-TA
* *
465527 ATTTTT-TTATATTTTT
1 ATTTTTATTAAATTTTA
* *
465543 ATGATTTATATATATTTTA
1 AT-TTTTAT-TAAATTTTA
465562 ATTTTTCA-TAAATTTTAA
1 ATTTTT-ATTAAATTTT-A
*
465580 ATTTTTATTAAAATTTA
1 ATTTTTATTAAATTTTA
*
465597 ATAATTTTATTAAAATTT-
1 AT--TTTTATTAAATTTTA
465615 ATTATTTATTA
1 ATT-TTTATTA
465626 TGGTTTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
16 3 0.04
17 27 0.33
18 26 0.32
19 25 0.31
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (17 bp):
ATTTTTATTAAATTTTA
Found at i:465591 original size:18 final size:18
Alignment explanation
Indices: 465556--465615 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
465546 ATTTATATAT
*
465556 ATTTTAATTTTTCA-TAAA
1 ATTTAAATTTTT-ATTAAA
*
465574 TTTTAAATTTTTATTAAA
1 ATTTAAATTTTTATTAAA
*
465592 ATTTAATAATTTTATTAAA
1 ATTTAA-ATTTTTATTAAA
465611 ATTTA
1 ATTTA
465616 TTATTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 1 0.03
18 19 0.53
19 16 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAAATTTTTATTAAA
Found at i:465593 original size:19 final size:20
Alignment explanation
Indices: 465571--465614 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
465561 AATTTTTCAT
*
465571 AAATTTTAA-ATTTTTATTA
1 AAATTTTAATAATTTTATTA
465590 AAA-TTTAATAATTTTATTA
1 AAATTTTAATAATTTTATTA
465609 AAATTT
1 AAATTT
465615 ATTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTTTAATAATTTTATTA
Found at i:465936 original size:87 final size:87
Alignment explanation
Indices: 465755--465919 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 87
465745 GAGTGCAAAA
** ** * *
465755 AAAAAAAAGAAGGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGACGTTTTAATGCATTTTGG
1 AAAAAAAAGTGGGGACTTAATTGCTTTTTTTGAAAAAAATTGAGGGACCTTTTAATGCATTTTGA
* **
465820 CAGTTCAAGTACCCAGTTGAGT
66 AAACTCAAGTACCCAGTTGAGT
465842 AAAAAAAAGTGGGGA-TTAATTGCTTTTTTTTGAAAAAAATTGA-GGACCTTTTAGATGCATTTT
1 AAAAAAAAGTGGGGACTTAATTGC-TTTTTTTGAAAAAAATTGAGGGACCTTTTA-ATGCATTTT
465905 GAAAACTCAAGTACC
64 GAAAACTCAAGTACC
465920 TGATTGAGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 17 0.25
87 50 0.75
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (87 bp):
AAAAAAAAGTGGGGACTTAATTGCTTTTTTTGAAAAAAATTGAGGGACCTTTTAATGCATTTTGA
AAACTCAAGTACCCAGTTGAGT
Found at i:471853 original size:24 final size:24
Alignment explanation
Indices: 471820--471881 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
471810 GGCAACATAG
471820 AATACACCACAAAGACATTTACCA
1 AATACACCACAAAGACATTTACCA
** ** *
471844 AATATGCCACAAAGTTATTTATCA
1 AATACACCACAAAGACATTTACCA
471868 AATACACCACAAAG
1 AATACACCACAAAG
471882 GCATCATAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (24 bp):
AATACACCACAAAGACATTTACCA
Found at i:472733 original size:29 final size:28
Alignment explanation
Indices: 472691--472779 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
472681 GACGCTCATT
* *
472691 GAATAAGAAAAGGGATGGTGACAACCATC
1 GAATATGAAAAGGGATGGT-TCAACCATC
* *
472720 GAATATGAAAAGGGATGGCTTCGATCATC
1 GAATATGAAAAGGGATGG-TTCAACCATC
*
472749 AAATATGAAAAGGGATGGTTTCAACCATC
1 GAATATGAAAAGGGATGG-TTCAACCATC
472778 GA
1 GA
472780 TTAAAGAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 49 0.98
30 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.20
Consensus pattern (28 bp):
GAATATGAAAAGGGATGGTTCAACCATC
Found at i:484203 original size:40 final size:40
Alignment explanation
Indices: 484066--484207 Score: 153
Period size: 40 Copynumber: 3.6 Consensus size: 40
484056 GATCGTCAAA
*
484066 CCAACC-GAACACACCAGATAGAAGCTCATAAGAGCTAAT
1 CCAACCGGAACACACCAGACAGAAGCTCATAAGAGCTAAT
* * * * *
484105 CCAACCGAAACACGCCAAACAAAAGCTCATAAAAGCTAAT
1 CCAACCGGAACACACCAGACAGAAGCTCATAAGAGCTAAT
* * * *
484145 CCAACTGAAACA-AGCTAGACAGAAGCTTATAAGAGCTAAT
1 CCAACCGGAACACA-CCAGACAGAAGCTCATAAGAGCTAAT
* *
484185 CCAACCGGAATACACTAGACAGA
1 CCAACCGGAACACACCAGACAGA
484208 GAGTATAACA
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 6 0.07
40 77 0.92
41 1 0.01
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.13
Consensus pattern (40 bp):
CCAACCGGAACACACCAGACAGAAGCTCATAAGAGCTAAT
Found at i:484981 original size:28 final size:28
Alignment explanation
Indices: 484930--484983 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
484920 TAGGAACAGT
* *
484930 ACAGTGTGGGCCTTAGCCTAATACAAAA
1 ACAGTGTGGGCCTAAGCCCAATACAAAA
*
484958 ACAGTGTGGGCCTAAGCCCGATACAA
1 ACAGTGTGGGCCTAAGCCCAATACAA
484984 TATCAATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACAAAA
Found at i:484993 original size:28 final size:28
Alignment explanation
Indices: 484934--484993 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
484924 AACAGTACAG
* * *
484934 TGTGGGCCTTAGCCTAATACAAAAACAG
1 TGTGGGCCTAAGCCCAATACAAAAACAA
* * *
484962 TGTGGGCCTAAGCCCGATACAATATCAA
1 TGTGGGCCTAAGCCCAATACAAAAACAA
484990 TGTG
1 TGTG
484994 ATGCAAGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (28 bp):
TGTGGGCCTAAGCCCAATACAAAAACAA
Found at i:485151 original size:26 final size:26
Alignment explanation
Indices: 485099--485151 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
485089 CACCAATATC
* *
485099 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
485125 GCAGCAGAGCTGCCAGTAGTTAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
485151 G
1 G
485152 GTGAAGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:485159 original size:26 final size:26
Alignment explanation
Indices: 485106--485160 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
485096 ATCGCAGCAT
* *
485106 AGCTGCCAGTAGTAATAATGCAGCAG
1 AGCTGCCAGTAGTAAGAATGCAGAAG
* **
485132 AGCTGCCAGTAGTTAGAATGGTGAAG
1 AGCTGCCAGTAGTAAGAATGCAGAAG
485158 AGC
1 AGC
485161 CGTAAATAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (26 bp):
AGCTGCCAGTAGTAAGAATGCAGAAG
Found at i:485269 original size:32 final size:32
Alignment explanation
Indices: 485201--485464 Score: 204
Period size: 32 Copynumber: 8.4 Consensus size: 32
485191 GAATGGCTAC
* * *
485201 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
485232 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
485264 CAGCCATCAGTAACGGTAACATGA-CTGGTAC-
1 AAGCCATCAGTAACAGTAATATGATC-GGCACA
* *
485295 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
485327 CAA-CCATCAGTAACAGTGAA-ATAATC-G-ACA
1 -AAGCCATCAGTAACAGT-AATATGATCGGCACA
* * * **
485357 CAGCCAT-TGATAAC-GATAATATGGTCGATACA
1 AAGCCATCAG-TAACAG-TAATATGATCGGCACA
* * *
485389 AAGCCATCAGTAACGGTACTATGATCGGCAAA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
485421 AAGCCATTAGTAACGGTACTATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
485453 AAGCCATCAGTA
1 AAGCCATCAGTA
485465 GCATGGCAGC
Statistics
Matches: 184, Mismatches: 35, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
29 5 0.03
30 16 0.09
31 35 0.19
32 123 0.67
33 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:485537 original size:27 final size:26
Alignment explanation
Indices: 485502--485571 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
485492 TATCGCAGCA
* *
485502 AAGCTACCAGTAATAGT-ATATGTGGCC
1 AAGCCACCAGTAACAGTGAT-TGTGG-C
485529 AAGCCACCAGTAACAGTGATTGTGGC
1 AAGCCACCAGTAACAGTGATTGTGGC
485555 AGAGCCACCAGT-ACAGT
1 A-AGCCACCAGTAACAGT
485572 ACTTCCTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.18
27 30 0.77
28 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (26 bp):
AAGCCACCAGTAACAGTGATTGTGGC
Found at i:485668 original size:24 final size:24
Alignment explanation
Indices: 485636--485717 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
485626 CCATGCTCAG
*
485636 AATCAGTCATTCAAATCATAGACA
1 AATCAGTCATTCAAATCACAGACA
*
485660 AATCAGTCATACCAAA-CACAGACA
1 AATCAGTCAT-TCAAATCACAGACA
*
485684 AATCAGTCATT-TAATCACAGACA
1 AATCAGTCATTCAAATCACAGACA
* *
485707 AAACAATCATT
1 AATCAGTCATT
485718 TGAACTCGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.04
23 17 0.34
24 27 0.54
25 4 0.08
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.22
Consensus pattern (24 bp):
AATCAGTCATTCAAATCACAGACA
Found at i:489478 original size:26 final size:26
Alignment explanation
Indices: 489447--489545 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
489437 TATCATCCTC
489447 TATTTTAAATTTTTATATATATTATT
1 TATTTTAAATTTTTATATATATTATT
* *
489473 TATTTTAAGTTGTTT-TACATATTATT
1 TATTTTAAATT-TTTATATATATTATT
*
489499 TA-TTTAAATTTCTTTTATATATTATT
1 TATTTTAAATTT-TTATATATATTATT
* * *
489525 TATTGTAAACTATTATATATA
1 TATTTTAAATTTTTATATATA
489546 ACTTTCAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 9 0.15
26 42 0.69
27 9 0.15
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (26 bp):
TATTTTAAATTTTTATATATATTATT
Found at i:489611 original size:15 final size:15
Alignment explanation
Indices: 489591--489636 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
489581 GTTTTATATG
489591 TTATTTTTATATTAT
1 TTATTTTTATATTAT
*
489606 TTA-TTTTAAATTATT
1 TTATTTTTATATTA-T
*
489621 TTATTGTTAT-TTAT
1 TTATTTTTATATTAT
489635 TT
1 TT
489637 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 12 0.46
15 10 0.38
16 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTTTTATATTAT
Found at i:489619 original size:25 final size:25
Alignment explanation
Indices: 489591--489673 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
489581 GTTTTATATG
489591 TTATTTTTATATTATTTATTTTAAA
1 TTATTTTTATATTATTTATTTTAAA
* *
489616 TTA-TTTTATTGTTATTTATTTTAAG
1 TTATTTTTA-TATTATTTATTTTAAA
* * * *
489641 TTTTTTTTATTTTGTTTATTTGAAA
1 TTATTTTTATATTATTTATTTTAAA
489666 --ATTTTTAT
1 TTATTTTTAT
489674 TATTTGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 7 0.15
24 5 0.10
25 31 0.65
26 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (25 bp):
TTATTTTTATATTATTTATTTTAAA
Found at i:489735 original size:17 final size:17
Alignment explanation
Indices: 489702--489734 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
489692 CTTATAAATC
489702 ATTTAATTTAAACTTTT
1 ATTTAATTTAAACTTTT
*
489719 ATTTACTTTAAA-TTTT
1 ATTTAATTTAAACTTTT
489735 TTATATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTAATTTAAACTTTT
Found at i:491785 original size:40 final size:40
Alignment explanation
Indices: 491741--492030 Score: 404
Period size: 40 Copynumber: 7.3 Consensus size: 40
491731 TATAGATAAT
* *
491741 TACCCCTGAATGCACATACGTGCCCCTATTTATACTTCGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
* *
491781 TACCCCTGAATGCACATAAGTGCCCCTGTTTGTACTTTGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
*
491821 TACCCCTAAATGCACATACGTGCCCCTGTTTGTACTTCGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
*
491861 TACCCCTGAATG-AGCATATGTGCCCCTGTTTGTACTTCGG
1 TACCCCTGAATGCA-CATACGTGCCCCTGTTTGTACTTCGG
* * * * *
491901 TACCCTTAAATGCATATACGTTCCCCTGTTTGTACTTAGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
*
491941 TACCCCTGAATGCACATACGTGCCCCTATTTGTACTTCGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
* * * *
491981 TACCCCTGAATGCACATACTTGCCCC-ATTTGCACTTTGG
1 TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
*
492020 TAACCCTGAAT
1 TACCCCTGAAT
492031 CAAATAGTAT
Statistics
Matches: 223, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 22 0.10
40 200 0.90
41 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (40 bp):
TACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTCGG
Found at i:491826 original size:20 final size:20
Alignment explanation
Indices: 491803--491988 Score: 70
Period size: 20 Copynumber: 9.3 Consensus size: 20
491793 CACATAAGTG
*
491803 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTAGGTA
*** * * * *
491823 CCCCTAAATGCACATACGTG
1 CCCCTGTTTGTACTTAGGTA
*
491843 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTAGGTA
** * * *
491863 CCCCTGAATG-AGCATATGTG
1 CCCCTGTTTGTA-CTTAGGTA
*
491883 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTAGGTA
* *** * * *
491903 CCCTTAAATGCA-TATACGTT
1 CCCCTGTTTGTACT-TAGGTA
491923 CCCCTGTTTGTACTTAGGTA
1 CCCCTGTTTGTACTTAGGTA
** * * * *
491943 CCCCTGAATGCACATACGTG
1 CCCCTGTTTGTACTTAGGTA
* *
491963 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTAGGTA
491983 CCCCTG
1 CCCCTG
491989 AATGCACATA
Statistics
Matches: 104, Mismatches: 58, Indels: 8
0.61 0.34 0.05
Matches are distributed among these distances:
19 2 0.02
20 100 0.96
21 2 0.02
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTAGGTA
Found at i:492788 original size:42 final size:42
Alignment explanation
Indices: 492722--492802 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
492712 GCACATTGCC
* * *
492722 TGGCACACGGGCATGTGTGTCAACTCAAAGAGTTACACGACT
1 TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACGACT
**
492764 TGGCACACAGGCATGTGGGGCAACTCAGTGAGTTACACG
1 TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACG
492803 GGTGAGCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (42 bp):
TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACGACT
Found at i:492812 original size:42 final size:42
Alignment explanation
Indices: 492722--492817 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
492712 GCACATTGCC
* * * *
492722 TGGCACACGGGCATGTGTGTCAACTCAAAGAGTTACACGACT
1 TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACGACG
** *
492764 TGGCACACAGGCATGTGGGGCAACTCAGTGAGTTACACG-GG
1 TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACGACG
492805 TGAGCACACAGGC
1 TG-GCACACAGGC
492818 TGGGATACGG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 2 0.04
42 44 0.96
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (42 bp):
TGGCACACAGGCATGTGGGGCAACTCAAAGAGTTACACGACG
Found at i:493725 original size:68 final size:68
Alignment explanation
Indices: 493616--493768 Score: 270
Period size: 68 Copynumber: 2.2 Consensus size: 68
493606 ATGGCACCAA
* *
493616 AATGTGTAAGACCATAGCTTGGCTATGGCAACATATGAAGTCTGCCAGGATAGTAAACATAGGAT
1 AATGTGTAAGACCATAGCTGGGCTATGGCAACATATAAAGTCTGCCAGGATAGTAAACATAGGAT
493681 CAT
66 CAT
* *
493684 AATGTGTAAGATCATAGCTGGGCTATGGCAACATATAAAGTCTGCCAGGATAGTAAACATGGGAT
1 AATGTGTAAGACCATAGCTGGGCTATGGCAACATATAAAGTCTGCCAGGATAGTAAACATAGGAT
493749 CAT
66 CAT
493752 AATGTGTAAGACCATAG
1 AATGTGTAAGACCATAG
493769 TCGAGCCAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 80 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (68 bp):
AATGTGTAAGACCATAGCTGGGCTATGGCAACATATAAAGTCTGCCAGGATAGTAAACATAGGAT
CAT
Found at i:502456 original size:34 final size:34
Alignment explanation
Indices: 502418--502487 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
502408 ATATAACAAT
502418 ACTGTAAAGTTCATGAAACCATATCCAACAACTC
1 ACTGTAAAGTTCATGAAACCATATCCAACAACTC
502452 ACTGTAAAGTTCATGAAACCATATCCAACAACTC
1 ACTGTAAAGTTCATGAAACCATATCCAACAACTC
502486 AC
1 AC
502488 AAGTGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (34 bp):
ACTGTAAAGTTCATGAAACCATATCCAACAACTC
Found at i:503324 original size:24 final size:25
Alignment explanation
Indices: 503268--503333 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
503258 AGGAGCTATG
* * * *
503268 AATCGATATGCTCTCACGAGTTGTA
1 AATCGGTAAGCTCTCACGAGCTGCA
503293 AATCGGTAAGCTCTCACGAGCT-CA
1 AATCGGTAAGCTCTCACGAGCTGCA
*
503317 AATTGGTAAGCTCTCAC
1 AATCGGTAAGCTCTCAC
503334 AAGTTGAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 17 0.47
25 19 0.53
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (25 bp):
AATCGGTAAGCTCTCACGAGCTGCA
Found at i:511810 original size:18 final size:18
Alignment explanation
Indices: 511789--511824 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
511779 ACAAATTTGA
511789 CCCTTTT-TACAAATTAAT
1 CCCTTTTCTA-AAATTAAT
511807 CCCTTTTCTAAAATTAAT
1 CCCTTTTCTAAAATTAAT
511825 GACATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
CCCTTTTCTAAAATTAAT
Found at i:519731 original size:26 final size:26
Alignment explanation
Indices: 519697--519765 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
519687 TATCCCGACC
*
519697 CACACCTCATGTGAGCAG-GCACATTT
1 CACAGCTCATGTGAGCAGAGC-CATTT
* *
519723 TACAGCTCATGTGAGCAGATCCATTT
1 CACAGCTCATGTGAGCAGAGCCATTT
*
519749 CACAGCTCGTGTGAGCA
1 CACAGCTCATGTGAGCA
519766 ACGATGTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 36 0.97
27 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (26 bp):
CACAGCTCATGTGAGCAGAGCCATTT
Found at i:520247 original size:68 final size:68
Alignment explanation
Indices: 520136--520271 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
520126 AAATGGTAAG
*
520136 TTGTGTTTTATGTTATAAGAACTTACTAAGCATTTTATGCTTACATAGTCTCATTTCCCATGTTT
1 TTGTGTTTTATGTTATAAGAACTTACTAAGCATTTTATCCTTACATAGTCTCATTTCCCATGTTT
520201 TAT
66 TAT
520204 TTGTGTTTTATGTTATAAGAACTTACTAAGCATTTTATCCTTACATAGTCTCATTTCCCATGTTT
1 TTGTGTTTTATGTTATAAGAACTTACTAAGCATTTTATCCTTACATAGTCTCATTTCCCATGTTT
520269 TAT
66 TAT
520272 AGATAATCGA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (68 bp):
TTGTGTTTTATGTTATAAGAACTTACTAAGCATTTTATCCTTACATAGTCTCATTTCCCATGTTT
TAT
Found at i:524412 original size:9 final size:9
Alignment explanation
Indices: 524398--524423 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
524388 ACATGTCATG
524398 TTCCATCTT
1 TTCCATCTT
524407 TTCCATCTT
1 TTCCATCTT
524416 TTCCATCT
1 TTCCATCT
524424 ATCTTCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.54
Consensus pattern (9 bp):
TTCCATCTT
Found at i:524442 original size:12 final size:12
Alignment explanation
Indices: 524425--524464 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
524415 TTTCCATCTA
**
524425 TCTTCTTTGTTT
1 TCTTCTTTACTT
524437 TCTTCTTTACTT
1 TCTTCTTTACTT
524449 TCTTCTTTACTAT
1 TCTTCTTTACT-T
524462 TCT
1 TCT
524465 AATCTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.68
Consensus pattern (12 bp):
TCTTCTTTACTT
Found at i:543517 original size:18 final size:18
Alignment explanation
Indices: 543496--543541 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
543486 ATTTGTTGCA
*
543496 ATTTTGTTATTTA-TTTTT
1 ATTTT-TTATTAATTTTTT
*
543514 ATTTTTAATTAATTTTTT
1 ATTTTTTATTAATTTTTT
543532 ATTTTTTATT
1 ATTTTTTATT
543542 CTTTATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTTATTAATTTTTT
Found at i:543535 original size:7 final size:7
Alignment explanation
Indices: 543525--543559 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
543515 TTTTTAATTA
543525 ATTTTTT
1 ATTTTTT
543532 ATTTTTT
1 ATTTTTT
*
543539 ATTCTTT
1 ATTTTTT
*
543546 ATTCTTT
1 ATTTTTT
543553 ATTTTTT
1 ATTTTTT
543560 GTGATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (7 bp):
ATTTTTT
Found at i:560299 original size:49 final size:48
Alignment explanation
Indices: 560235--560364 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 48
560225 TTGAATTTTA
*
560235 AAAACTCTTTTAAATAATAATTTAAATTCTATTTAGTTATCT-TTTATTT
1 AAAACTCTTTTAAATAATAA-TTAAATTCTATTTAGTTAT-TATTTATCT
* * * *
560284 AAAACTCTTTCAAATAATAATTAAATTATGTTTTATTTATTATTTATCT
1 AAAACTCTTTTAAATAATAATTAAATTCT-ATTTAGTTATTATTTATCT
* *
560333 AAAACTCTTTTAAATAACAACTAAATTCTATT
1 AAAACTCTTTTAAATAATAATTAAATTCTATT
560365 CCTTATTTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 11 0.16
49 58 0.84
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (48 bp):
AAAACTCTTTTAAATAATAATTAAATTCTATTTAGTTATTATTTATCT
Found at i:560418 original size:93 final size:94
Alignment explanation
Indices: 560314--560488 Score: 298
Period size: 93 Copynumber: 1.9 Consensus size: 94
560304 TTAAATTATG
* *
560314 TTTTATTTATTATTTATCTAAAACTCTTTTAAATAACAACTAAATTCTA-TTCCTTATTTGATAA
1 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAACAACTAAATTCTATTTCCTTATCTGATAA
560378 GAAATATATCAAATCCTTTTGATTTTGAA
66 GAAATATATCAAATCCTTTTGATTTTGAA
* * *
560407 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATTTTCTTATCTGATAA
1 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAACAACTAAATTCTATTTCCTTATCTGATAA
560472 GAAATATATCAAATCCT
66 GAAATATATCAAATCCT
560489 CTTTTTATCT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 46 0.61
94 30 0.39
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.47
Consensus pattern (94 bp):
TTTTAATTATTATTTATCTAAAACTCTTTTAAATAACAACTAAATTCTATTTCCTTATCTGATAA
GAAATATATCAAATCCTTTTGATTTTGAA
Found at i:563503 original size:33 final size:33
Alignment explanation
Indices: 563466--563533 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
563456 ATTTAAAAAA
*
563466 TAAATTAGGGTTTATGGTTTTTAAAAAATAAAT
1 TAAATTAGGGTTTATGATTTTTAAAAAATAAAT
*
563499 TAAATTAGGGTTTATTATTTTTAAAAAATAAAT
1 TAAATTAGGGTTTATGATTTTTAAAAAATAAAT
563532 TA
1 TA
563534 GGGTTTAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (33 bp):
TAAATTAGGGTTTATGATTTTTAAAAAATAAAT
Found at i:563575 original size:27 final size:28
Alignment explanation
Indices: 563435--563575 Score: 142
Period size: 28 Copynumber: 4.9 Consensus size: 28
563425 AGTTTTGGAG
* *
563435 AAAATAAATTAAGGTTTAGGG-ATTTAA
1 AAAATAAATTAGGGTTTAGGGTTTTTAA
*
563462 AAAATAAATTAGGGTTTATGGTTTTTAAAAA
1 AAAATAAATTAGGGTTTAGGGTTTTT---AA
***
563493 ATAAATTAAATTAGGGTTTATTATTTTTAA
1 A-AAA-TAAATTAGGGTTTAGGGTTTTTAA
563523 AAAATAAATTAGGGTTTAGGGATTTTT-A
1 AAAATAAATTAGGGTTTAGGG-TTTTTAA
* *
563551 AAAATAAATTTGTGTTTAGGGTTTT
1 AAAATAAATTAGGGTTTAGGGTTTT
563576 AGGTTTTTGT
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
27 23 0.24
28 37 0.38
29 8 0.08
30 3 0.03
31 3 0.03
32 3 0.03
33 20 0.21
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (28 bp):
AAAATAAATTAGGGTTTAGGGTTTTTAA
Found at i:563862 original size:107 final size:110
Alignment explanation
Indices: 563725--563952 Score: 284
Period size: 112 Copynumber: 2.1 Consensus size: 110
563715 GAAAAACTAA
* * *
563725 TTTTGAGAAGATGGTTCTGATAAAATAGGGTAAAAAAGGCTTC-A-A-ATGCACTATCACCAAAA
1 TTTTGAAAAGATGGTTCTGAAAAAATAGGGTAAAAAAGGCTTCAAGAGATGCACTATCAACAAAA
* * * * *
563787 GTACTGAAAAAAGCTCCTAGCT-GAACGCTATTTTTCTACTGTAGT
66 GTACTAAAAAAAGCTCCCACCTAG-ACACTATTTTTCTACAGTAGT
* * *
563832 TTTTGAAAAGATGGTTCTGAAAAAATAGGGTAAAAAATGTTTCAAGTAGGATGCACTGTCAACAA
1 TTTTGAAAAGATGGTTCTGAAAAAATAGGGTAAAAAAGGCTTCAAG-A-GATGCACTATCAACAA
*
563897 AAGTACTAAAAAAAGCTCCCACCTAGACACTCTTTTTCTACAGTAGT
64 AAGTACTAAAAAAAGCTCCCACCTAGACACTATTTTTCTACAGTAGT
*
563944 TTCTGAAAA
1 TTTTGAAAA
563953 ATAATTTTGA
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
107 39 0.38
108 1 0.01
110 1 0.01
112 60 0.59
113 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (110 bp):
TTTTGAAAAGATGGTTCTGAAAAAATAGGGTAAAAAAGGCTTCAAGAGATGCACTATCAACAAAA
GTACTAAAAAAAGCTCCCACCTAGACACTATTTTTCTACAGTAGT
Found at i:564238 original size:126 final size:124
Alignment explanation
Indices: 563832--564314 Score: 648
Period size: 126 Copynumber: 3.9 Consensus size: 124
563822 CTACTGTAGT
* * *** * *
563832 TTTTGAAAAGATGGTTCTGAAAAAATAGGGTAAAAAATGTTTCAAGTAGGATGCACTGTCAACAA
1 TTTTGAGAAGATGGTTCTGAAAAGATAGGGTAAAAAACACTTCAAGCAGGATGCACTGTCAGCAA
*
563897 AAGTACTAAAAAAAGCTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCTGAAAAATAA
66 AAGTACTAAAAAAA-CTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCTAAAAAATAA
* * *
563957 TTTTGAGAAGATGGTTCTGAAAA-ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAA
1 TTTTGAGAAGATGGTTCTGAAAAGATAGGGTAAAAAACACTTCAAGCAGGATGCACTGTCAGCAA
* * * * * *
564021 AAGTACTAAAAAAGCTCCCACTTGGACGCTCTTATT-TATAGTAGTTTCTAAAAAATAA
66 AAGTACTAAAAAAACTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCTAAAAAATAA
* * * *
564079 TTTTGAGAAGATGATTCTAAAAAGATAGGGTCAAAAACACTTCAAACAGGATGCACTGTCAGCAA
1 TTTTGAGAAGATGGTTCTGAAAAGATAGGGTAAAAAACACTTCAAGCAGGATGCACTGTCAGCAA
*
564144 AATTACTGAAAAAAACTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCTAAAAAAATAA
66 AAGTACT-AAAAAAACTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCT-AAAAAATAA
** *
564205 TTTTGAGAAGATGGTTCTGAAAAGATACAGTCAAAAACACTTCAAGTC-GGATGCACTGTCAGCA
1 TTTTGAGAAGATGGTTCTGAAAAGATAGGGTAAAAAACACTTCAAG-CAGGATGCACTGTCAGCA
* * *
564269 AAAGTATTGAAAAAAGCTCTCACCTAGACACTCTTTTTCTACAGTA
65 AAAGTACT-AAAAAAACTCCCACCTAGACACTCTTTTTCTACAGTA
564315 CATCCTGCTT
Statistics
Matches: 316, Mismatches: 37, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
122 41 0.13
123 60 0.19
124 72 0.23
125 34 0.11
126 108 0.34
127 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (124 bp):
TTTTGAGAAGATGGTTCTGAAAAGATAGGGTAAAAAACACTTCAAGCAGGATGCACTGTCAGCAA
AAGTACTAAAAAAACTCCCACCTAGACACTCTTTTTCTACAGTAGTTTCTAAAAAATAA
Found at i:564421 original size:25 final size:25
Alignment explanation
Indices: 564393--564453 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
564383 GAAATTAGAG
*
564393 AAGTTCAGAAGAATAAAAATTGAAA
1 AAGTTAAGAAGAATAAAAATTGAAA
* * * *
564418 AAGTTAAGGAGATTATAAATTGAAG
1 AAGTTAAGAAGAATAAAAATTGAAA
*
564443 AAGTTGAGAAG
1 AAGTTAAGAAG
564454 GTAGAAGTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGTTAAGAAGAATAAAAATTGAAA
Found at i:565351 original size:3 final size:3
Alignment explanation
Indices: 565343--565371 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
565333 GGGTTCGGAT
565343 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
565372 TCCGCGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:567638 original size:61 final size:61
Alignment explanation
Indices: 567508--567636 Score: 192
Period size: 59 Copynumber: 2.1 Consensus size: 61
567498 TCTATTGCCT
* * * *
567508 TATTCAAAAGAACTTCTATTTTATTAAATTGGACAAAATATAGAAATAATTTGTACAAATA
1 TATTAAAAACAACTTCTATTTTATTAAATTGGACAAAATATAAAAACAATTTGTACAAATA
567569 TATTAAAAACAACTTCTATTTTATTAAA-T-GA-AACAATATAAAAACAATTTGTACAAATA
1 TATTAAAAACAACTTCTATTTTATTAAATTGGACAA-AATATAAAAACAATTTGTACAAATA
567628 TATTAAAAA
1 TATTAAAAA
567637 AATCAATACA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
58 2 0.03
59 34 0.54
60 1 0.02
61 26 0.41
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (61 bp):
TATTAAAAACAACTTCTATTTTATTAAATTGGACAAAATATAAAAACAATTTGTACAAATA
Found at i:568615 original size:7 final size:7
Alignment explanation
Indices: 568605--568704 Score: 200
Period size: 7 Copynumber: 14.3 Consensus size: 7
568595 TTATATACAT
568605 AATACTA
1 AATACTA
568612 AATACTA
1 AATACTA
568619 AATACTA
1 AATACTA
568626 AATACTA
1 AATACTA
568633 AATACTA
1 AATACTA
568640 AATACTA
1 AATACTA
568647 AATACTA
1 AATACTA
568654 AATACTA
1 AATACTA
568661 AATACTA
1 AATACTA
568668 AATACTA
1 AATACTA
568675 AATACTA
1 AATACTA
568682 AATACTA
1 AATACTA
568689 AATACTA
1 AATACTA
568696 AATACTA
1 AATACTA
568703 AA
1 AA
568705 CAACTATGTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 93 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:569680 original size:19 final size:20
Alignment explanation
Indices: 569656--569696 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
569646 AATATTAATT
*
569656 AAAATTACATAA-ATGAAAA
1 AAAATTAAATAATATGAAAA
*
569675 AAAATTAAATAATATTAAAA
1 AAAATTAAATAATATGAAAA
569695 AA
1 AA
569697 TTGAAATTAA
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:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATTAAATAATATGAAAA
Found at i:577019 original size:3 final size:3
Alignment explanation
Indices: 577011--577037 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
577001 TGAACAGTGG
577011 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
577038 GTTTGCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:584120 original size:19 final size:18
Alignment explanation
Indices: 584097--584147 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
584087 AATAGTATTT
*
584097 TATTAATTTAATATTAAG
1 TATTAATTTAATATTAAA
584115 TGATT-ATCTTAATATTAAA
1 T-ATTAAT-TTAATATTAAA
584134 T-TTAATTTAATATT
1 TATTAATTTAATATT
584148 TATCTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.34
18 5 0.17
19 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:584239 original size:16 final size:16
Alignment explanation
Indices: 584197--584241 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
584187 AATATTAAAT
*
584197 TTAATCTAATATTTATC
1 TTAAT-TAATATTTATA
* *
584214 TTGATAAATATTTATA
1 TTAATTAATATTTATA
584230 TTAATTAATATT
1 TTAATTAATATT
584242 AAAGTGATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAATTAATATTTATA
Found at i:586962 original size:16 final size:17
Alignment explanation
Indices: 586941--586976 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
586931 CACATCATCC
586941 CTCATCCTTCATCC-CT
1 CTCATCCTTCATCCTCT
*
586957 CTCATCTTTCATCCTCT
1 CTCATCCTTCATCCTCT
586974 CTC
1 CTC
586977 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.47, G:0.00, T:0.42
Consensus pattern (17 bp):
CTCATCCTTCATCCTCT
Found at i:591557 original size:22 final size:23
Alignment explanation
Indices: 591527--591569 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
591517 AATAATCAAA
591527 ACAATAAAAGAGGGGTTTGGACG
1 ACAATAAAAGAGGGGTTTGGACG
*
591550 ACAA-AAAAGATGGGTTTGGA
1 ACAATAAAAGAGGGGTTTGGA
591570 GAATCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.42, C:0.07, G:0.33, T:0.19
Consensus pattern (23 bp):
ACAATAAAAGAGGGGTTTGGACG
Found at i:599431 original size:27 final size:27
Alignment explanation
Indices: 599351--599431 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
599341 GATGGGAACC
* * *
599351 AGTTCACCAGAACACTGGTGAACTCCC
1 AGTTCGCCAAAACACTGGTGAACTCCT
*
599378 AGTTCGCCAAAACACTGGGGAACTCCT
1 AGTTCGCCAAAACACTGGTGAACTCCT
* *
599405 AGTTCGCTGAAAACACTAGTGAA-TCCT
1 AGTTCGC-CAAAACACTGGTGAACTCCT
599432 CACTAGCGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 34 0.74
28 12 0.26
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (27 bp):
AGTTCGCCAAAACACTGGTGAACTCCT
Found at i:601154 original size:55 final size:53
Alignment explanation
Indices: 601022--601169 Score: 138
Period size: 54 Copynumber: 2.7 Consensus size: 53
601012 AACCAGTTTG
* * *
601022 TCACACAGGTTGGCACACGGCCTACGACACGACTGTGTGACCCAACTTTGAATA
1 TCACAC-GGCTGGCACACGGCTTACGACACGACCGTGTGACCCAACTTTGAATA
* * * *
601076 TACACACGGTCTGGCACATGGCTTACGACACGACCGTGTG-GCCTATTTTGAATA
1 T-CACACGG-CTGGCACACGGCTTACGACACGACCGTGTGACCCAACTTTGAATA
* * *
601130 CTCACACGGGTGGACACACGGGCTT-GGACACGATCGTGTG
1 -TCACACGGCTGG-CACAC-GGCTTACGACACGACCGTGTG
601170 TCCTGACTTC
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
53 3 0.04
54 38 0.49
55 37 0.47
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (53 bp):
TCACACGGCTGGCACACGGCTTACGACACGACCGTGTGACCCAACTTTGAATA
Found at i:604733 original size:81 final size:81
Alignment explanation
Indices: 604603--604758 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
604593 CATTACGGCC
* * * *
604603 ATTTTACCCATCGGGGGTATTTCGATAATTTTACCTTTCAATGGTATTTCGATAATTTTACCCTT
1 ATTTTACCCATCGAGGGCATTTCGATAATTTTACCTTTCAAGGGCATTTCGATAATTTTACCCTT
604668 CGGGGGTATTTCAGTA
66 CGGGGGTATTTCAGTA
** * * *
604684 ATTTTACCTTTCGAGGGCATTTTGATAATTTTATCC-TTCAGGGGCATTTCGGTAATTTTACCCT
1 ATTTTACCCATCGAGGGCATTTCGATAATTTTA-CCTTTCAAGGGCATTTCGATAATTTTACCCT
604748 TCGGGGGTATT
65 TCGGGGGTATT
604759 ACGACCATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (81 bp):
ATTTTACCCATCGAGGGCATTTCGATAATTTTACCTTTCAAGGGCATTTCGATAATTTTACCCTT
CGGGGGTATTTCAGTA
Found at i:604769 original size:54 final size:54
Alignment explanation
Indices: 604590--604770 Score: 182
Period size: 54 Copynumber: 3.4 Consensus size: 54
604580 TACCCTCTAG
* * * * *
604590 GGGCATTACGGCCATTTTACCCATCGGGGGTATTTCGATAATTTTACCTTTCAA
1 GGGCATTACGACAATTTTACCCTTCGGGGGTATTTCGGTAATTTTACCTTTCGA
* * * * *
604644 TGGTATTTCGATAATTTTACCCTTCGGGGGTATTTCAGTAATTTTACCTTTCGA
1 GGGCATTACGACAATTTTACCCTTCGGGGGTATTTCGGTAATTTTACCTTTCGA
** * * * * * *
604698 GGGCATTTTGATAATTTTATCCTTCAGGGGCATTTCGGTAATTTTACCCTTCGG
1 GGGCATTACGACAATTTTACCCTTCGGGGGTATTTCGGTAATTTTACCTTTCGA
* *
604752 GGGTATTACGACCATTTTA
1 GGGCATTACGACAATTTTA
604771 ACAATCTTTT
Statistics
Matches: 103, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGCATTACGACAATTTTACCCTTCGGGGGTATTTCGGTAATTTTACCTTTCGA
Found at i:604769 original size:81 final size:81
Alignment explanation
Indices: 604589--604770 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 81
604579 TTACCCTCTA
* * * * * *
604589 GGGGCATTACGGCCATTTTACCCATCGGGGGTATTTCGATAATTTTACCTTTCAATGGTATTTCG
1 GGGGTATTACGACCATTTTACCCATCGAGGGCATTTCGATAATTTTACCTTTCAAGGGCATTTCG
604654 ATAATTTTACCCTTCG
66 ATAATTTTACCCTTCG
* ** * *
604670 GGGGTATTTCAGTA--ATTTTACCTTTCGAGGGCATTTTGATAATTTTATCC-TTCAGGGGCATT
1 GGGGTATTAC-G-ACCATTTTACCCATCGAGGGCATTTCGATAATTTTA-CCTTTCAAGGGCATT
*
604732 TCGGTAATTTTACCCTTCG
63 TCGATAATTTTACCCTTCG
604751 GGGGTATTACGACCATTTTA
1 GGGGTATTACGACCATTTTA
604771 ACAATCTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 78 0.94
82 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (81 bp):
GGGGTATTACGACCATTTTACCCATCGAGGGCATTTCGATAATTTTACCTTTCAAGGGCATTTCG
ATAATTTTACCCTTCG
Found at i:604770 original size:27 final size:27
Alignment explanation
Indices: 604603--604758 Score: 179
Period size: 27 Copynumber: 5.8 Consensus size: 27
604593 CATTACGGCC
*
604603 ATTTTACCCATCGGGGGTATTTCGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
* ***
604630 ATTTTACCTTTCAATGGTATTTCGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
604657 ATTTTACCCTTCGGGGGTATTTC-AGTA
1 ATTTTACCCTTCGGGGGTATTTCGA-TA
* * * *
604684 ATTTTACCTTTCGAGGGCATTTTGATA
1 ATTTTACCCTTCGGGGGTATTTCGATA
* * * *
604711 ATTTTATCCTTCAGGGGCATTTCGGTA
1 ATTTTACCCTTCGGGGGTATTTCGATA
604738 ATTTTACCCTTCGGGGGTATT
1 ATTTTACCCTTCGGGGGTATT
604759 ACGACCATTT
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.98
28 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGATA
Found at i:611064 original size:102 final size:101
Alignment explanation
Indices: 610777--611076 Score: 440
Period size: 100 Copynumber: 3.0 Consensus size: 101
610767 GTTGTGCTCG
* * * * *
610777 AATGTTTGCTATGAACTCTATGTAATTTTCTACGGTTGTGTGTAATCACGGTGAATGAGTATATT
1 AATGTTTGCTATGAATTCTGTGTAATTTTCTATGGTTGTG-GTAATCACAGTGAATGAGTATGTT
* *
610842 ATGCATGCAACAAATTGTGAAAATATATGGATGCTCA
65 ATGCATGCAACAAATTCTGAAAATATATGGATGATCA
* * * * * *
610879 AATGTCTGCTATGAATTTTGTATAATTTTCTATGGCTAT-GTAATCACAGTGAATGAGTATGCTA
1 AATGTTTGCTATGAATTCTGTGTAATTTTCTATGGTTGTGGTAATCACAGTGAATGAGTATGTTA
*
610943 TGCATGCAACAAATTCTGAATATATATGGATGATCA
66 TGCATGCAACAAATTCTGAAAATATATGGATGATCA
*
610979 AATGTTTGCTATGAATTCTGTGTAATTTTCTATGGTTGTGCGTAATCACAATGAATGAGTATGTT
1 AATGTTTGCTATGAATTCTGTGTAATTTTCTATGGTTGTG-GTAATCACAGTGAATGAGTATGTT
611044 ATGCATGCAACAAATTCTGAAAATATATGGATG
65 ATGCATGCAACAAATTCTGAAAATATATGGATG
611077 CTTGCAACAT
Statistics
Matches: 174, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
100 89 0.51
102 85 0.49
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (101 bp):
AATGTTTGCTATGAATTCTGTGTAATTTTCTATGGTTGTGGTAATCACAGTGAATGAGTATGTTA
TGCATGCAACAAATTCTGAAAATATATGGATGATCA
Found at i:618169 original size:12 final size:12
Alignment explanation
Indices: 618154--618178 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
618144 CCTAAAAATA
618154 TATAATTTGAAC
1 TATAATTTGAAC
618166 TATAATTTGAAC
1 TATAATTTGAAC
618178 T
1 T
618179 CACAAAAGCA
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:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TATAATTTGAAC
Found at i:623683 original size:234 final size:242
Alignment explanation
Indices: 623276--623717 Score: 591
Period size: 247 Copynumber: 1.8 Consensus size: 242
623266 TGATATGATA
* * ***
623276 TAGTAGGAGGGCCAACTTTCAAATGTACGAAAAGTATAGGGGCTTAGAACATATTTCAACCAGTA
1 TAGTAAGAGGGCCAACTTTCAAATGTACGAAAACTATAGAAACTTAGAACATATTTCAACCAGTA
*
623341 CAATAATAAATAATAATAGATAGTAATTAATAAATAATGCACTACTATTATATATAACTATTATT
66 CAATAATAAATAATAATA-ATAGTAATTAATAAAT-AT-CACTACTATTATATATAACTACTATT
* * *
623406 ATATTATAGATGATAATAAAATATATGGTATTACATGATATTATAATGTTTAATTATTGATGCAA
128 ATATTATAAATGATAATAAAATATATAGTATTACATGATATTATAATGTTTAATCATTGATGC--
623471 ATATATATAAACTATCAATTTATTATATATTATATGATATGATATAACATTG
191 ATATATATAAACTATCAATTTATTATATATTATATGATATGATATAACATTG
* * * *
623523 TAGTAAGAGGGCTAACTTTCAAATGTACGAAAACTGTAGAAACTTAGAGCATATTTCTACCAGTA
1 TAGTAAGAGGGCCAACTTTCAAATGTACGAAAACTATAGAAACTTAGAACATATTTCAACCAGTA
* * *
623588 TAATAATAAATAATAAT-ATA-TGA-TAAT-AAT-T-ACTA-TA-TA-ATGT-ACTACTATTATA
66 CAATAATAAATAATAATAATAGTAATTAATAAATATCACTACTATTATATATAACTACTATTATA
* *
623643 TTATAAAAT-ATAATAAAATATATAGTATTATATTATATTATAATGTTTAATCATTGATGCATAT
131 TTAT-AAATGATAATAAAATATATAGTATTACATGATATTATAATGTTTAATCATTGATGCATAT
623707 ATATAAACTAT
195 ATATAAACTAT
623718 TAATATATAA
Statistics
Matches: 176, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
232 15 0.09
234 62 0.35
235 6 0.03
236 2 0.01
237 2 0.01
238 4 0.02
240 1 0.01
242 3 0.02
243 4 0.02
244 2 0.01
245 3 0.02
247 72 0.41
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (242 bp):
TAGTAAGAGGGCCAACTTTCAAATGTACGAAAACTATAGAAACTTAGAACATATTTCAACCAGTA
CAATAATAAATAATAATAATAGTAATTAATAAATATCACTACTATTATATATAACTACTATTATA
TTATAAATGATAATAAAATATATAGTATTACATGATATTATAATGTTTAATCATTGATGCATATA
TATAAACTATCAATTTATTATATATTATATGATATGATATAACATTG
Found at i:627160 original size:24 final size:24
Alignment explanation
Indices: 627128--627197 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
627118 GTTCTCTATG
*
627128 ACACCTTTGTAGCGTATTCTATAA
1 ACACCTTTGTGGCGTATTCTATAA
* * *
627152 ACGCCTTTGTGGTGTATTCTGTAA
1 ACACCTTTGTGGCGTATTCTATAA
* *
627176 ATACCTTTGTGGCATATTCTAT
1 ACACCTTTGTGGCGTATTCTAT
627198 GTTGCCTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
ACACCTTTGTGGCGTATTCTATAA
Found at i:628092 original size:80 final size:80
Alignment explanation
Indices: 627959--628118 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
627949 ATGTTTTTGG
627959 AGTCGTTGTAGCTTAATCTAGCTAGCCCAGGGACTAATTTGCAAAACCATTAAAAGGTTAGGTTT
1 AGTCGTTGTAGCTTAATCTAGCTAGCCCAGGGACTAATTTGCAAAACCATTAAAAGGTTAGGTTT
628024 TTCCCATGAATGTAT
66 TTCCCATGAATGTAT
* * *
628039 AGTCGTTGTAGCTTAATCTAGCTAGCCTAGGGACTAATTTGCAAAATCGTTAAAAGGTTAGGTTT
1 AGTCGTTGTAGCTTAATCTAGCTAGCCCAGGGACTAATTTGCAAAACCATTAAAAGGTTAGGTTT
*
628104 TTTCCATGAATGTAT
66 TTCCCATGAATGTAT
628119 TCATGTGGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (80 bp):
AGTCGTTGTAGCTTAATCTAGCTAGCCCAGGGACTAATTTGCAAAACCATTAAAAGGTTAGGTTT
TTCCCATGAATGTAT
Found at i:635233 original size:19 final size:19
Alignment explanation
Indices: 635211--635248 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
635201 TCAATATCAC
635211 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
*
635230 CCACTGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
635249 TATTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:635601 original size:37 final size:37
Alignment explanation
Indices: 635529--635601 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
635519 ATGATAAAAC
* *
635529 AATTCAATAATATAAATTAGTATAAAATGTGAAATTT
1 AATTCAATAATATAAATTAGTATAAAATATAAAATTT
*
635566 AATTTAATAATATAAA-TAGTATATATAA-ATAAAATT
1 AATTCAATAATATAAATTAGTATA-A-AATATAAAATT
635602 ATTATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 22 0.71
38 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (37 bp):
AATTCAATAATATAAATTAGTATAAAATATAAAATTT
Found at i:635844 original size:30 final size:31
Alignment explanation
Indices: 635798--635860 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
635788 GGGGGTGGGA
*
635798 TGGGAGGGGAGCAAAAGTTATGGGGGGAAAG
1 TGGGAGGGGAGCAAAAGTTATGGGAGGAAAG
* *
635829 TGGGA-GGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAGGGGAGCAAAAGTTATGGGAGGAAAG
635859 TG
1 TG
635861 AAGAGGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.49, T:0.17
Consensus pattern (31 bp):
TGGGAGGGGAGCAAAAGTTATGGGAGGAAAG
Found at i:642847 original size:15 final size:16
Alignment explanation
Indices: 642827--642864 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
642817 AAGTTGCTTC
642827 TATTATATTC-TATAA
1 TATTATATTCATATAA
642842 TATTATA-TCATATAA
1 TATTATATTCATATAA
*
642857 TATAATAT
1 TATTATAT
642865 ATAATATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTATATTCATATAA
Found at i:642866 original size:12 final size:14
Alignment explanation
Indices: 642837--642873 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
642827 TATTATATTC
642837 TATAATATTATATCA
1 TATAATA-TATATCA
642852 TATAATATA-AT-A
1 TATAATATATATCA
642864 TATAATATAT
1 TATAATATAT
642874 CTATTCATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 2 0.10
15 7 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
TATAATATATATCA
Found at i:643009 original size:28 final size:28
Alignment explanation
Indices: 642977--643032 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
642967 TTATATTATT
642977 GTAGGTATAAGTATAATTATAGCATTAA
1 GTAGGTATAAGTATAATTATAGCATTAA
643005 GTAGGTATAAGTATAATTATAGCATTAA
1 GTAGGTATAAGTATAATTATAGCATTAA
643033 AAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.36
Consensus pattern (28 bp):
GTAGGTATAAGTATAATTATAGCATTAA
Found at i:646499 original size:20 final size:20
Alignment explanation
Indices: 646474--646513 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
646464 ACAATTTAAA
646474 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
*
646494 ATATAAATTTATTAGTATAT
1 ATATAAATTTATTAATATAT
646514 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:646521 original size:20 final size:20
Alignment explanation
Indices: 646478--646521 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
646468 TTTAAAATAT
*
646478 AAATTTATTAATATATATAT
1 AAATTTATTAATATATATAA
* *
646498 AAATTTATTAGTATATGTAA
1 AAATTTATTAATATATATAA
646518 AAAT
1 AAAT
646522 AACTTTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTATTAATATATATAA
Found at i:648895 original size:23 final size:24
Alignment explanation
Indices: 648869--648934 Score: 98
Period size: 23 Copynumber: 2.7 Consensus size: 24
648859 AACATGTACT
*
648869 ATATTAAATGTAGTCTACAT-TTA
1 ATATTAAATGTAGTCTACATATCA
648892 ATATTAAATGTAGTCTACATGAATCA
1 ATATTAAATGTAGTCTACAT--ATCA
648918 ATATTAAATGTAGTCTA
1 ATATTAAATGTAGTCTA
648935 ACTTTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 20 0.51
26 19 0.49
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (24 bp):
ATATTAAATGTAGTCTACATATCA
Found at i:649768 original size:21 final size:21
Alignment explanation
Indices: 649744--649783 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
649734 TTTTCTTAAG
*
649744 ATTATGTATTTTTTTTTCCGT
1 ATTATGTATTTTTCTTTCCGT
649765 ATTATGTATTTTTCTTTCC
1 ATTATGTATTTTTCTTTCC
649784 AGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.65
Consensus pattern (21 bp):
ATTATGTATTTTTCTTTCCGT
Found at i:654352 original size:23 final size:22
Alignment explanation
Indices: 654319--654737 Score: 220
Period size: 23 Copynumber: 18.3 Consensus size: 22
654309 ACATGTTTGT
654319 TGTAAATTGAAGTGTTAAAGTGC
1 TGTAAATTGAAGTGTTAAA-TGC
* *
654342 TGCAAATTGAAGTGTTTAAATGT
1 TGTAAATTGAAGTG-TTAAATGC
* * *
654365 TGTAAATTAAAGTGTTTTAAGTAC
1 TGTAAATTGAAGTG--TTAAATGC
** * ** *
654389 TACAAATTGAATTGTTTAGTTCC
1 TGTAAATTGAAGTG-TTAAATGC
* * * *
654412 TGGAAATTG-AGATTTTTATTGC
1 TGTAAATTGAAG-TGTTAAATGC
*
654434 TGT-AATTGAAGTGTATAAATGT
1 TGTAAATTGAAGTGT-TAAATGC
* *
654456 TGTTAATAG-AGATGTTAAAGTGC
1 TGTAAATTGAAG-TGTTAAA-TGC
** *
654479 TACAAATTGAAGTGTTTAAATGT
1 TGTAAATTGAAGTG-TTAAATGC
*
654502 TGTAAATTGAAGTGTTAAAGTGT
1 TGTAAATTGAAGTGTTAAA-TGC
*
654525 TGCAAATTGAAGTGTTTAAATGC
1 TGTAAATTGAAGTG-TTAAATGC
*
654548 TGTAAATTGAAGTGTTAAAGTGT
1 TGTAAATTGAAGTGTTAAA-TGC
* * *
654571 TGCAAATTGAAGTATTTAAATGT
1 TGTAAATTGAAGT-GTTAAATGC
* * *
654594 TGT-AATTCAGGTGTATAAATGT
1 TGTAAATTGAAGTGT-TAAATGC
* *
654616 TGTTAATTG-AGATGTTAAAGTGA
1 TGTAAATTGAAG-TGTTAAA-TGC
* *
654639 TGTAAGTTGAGGTGTTTAAATGC
1 TGTAAATTGAAGTG-TTAAATGC
* **
654662 TGTAAATTGAAGTGTTTAATTAT
1 TGTAAATTGAAGTG-TTAAATGC
* *
654685 TGTAAATT-AAGGTGCTCAAATGA
1 TGTAAATTGAA-GTG-TTAAATGC
* *
654708 TGTCAATTGAAGTGTTTAAGTGC
1 TGTAAATTGAAGTG-TTAAATGC
*
654731 TGCAAAT
1 TGTAAAT
654738 AATATATAAT
Statistics
Matches: 305, Mismatches: 69, Indels: 44
0.73 0.17 0.11
Matches are distributed among these distances:
21 8 0.03
22 57 0.19
23 194 0.64
24 46 0.15
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (22 bp):
TGTAAATTGAAGTGTTAAATGC
Found at i:654378 original size:46 final size:46
Alignment explanation
Indices: 654316--654726 Score: 333
Period size: 46 Copynumber: 9.0 Consensus size: 46
654306 CCAACATGTT
654316 TGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
1 TGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
* * * * * **
654362 TGTTGTAAATTAAAGTGTTTTAAGTACTACAAATTGAATTGTTTAGT
1 TGTTGTAAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA
** * ** * * *
654409 TCCTGGAAATTG-AGAT-TTTTATTGCTG-TAATTGAAGTGTATAAA
1 TGTTGTAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
* * *
654453 TGTTGTTAATAG-AGATGTTAAAGTGCTACAAATTGAAGTGTTTAAA
1 TGTTGTAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
*
654499 TGTTGTAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAA
1 TGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
* * *
654545 TGCTGTAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTATTTAAA
1 TGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
* * * **
654591 TGTTGT-AATTCAGGTGTATAAA-TGTTGTTAATTG-AGATG-TTAAA
1 TGTTGTAAATTGAAGTGT-TAAAGTGCTGCAAATTGAAG-TGTTTAAA
* * * * *
654635 GTGATGTAAGTTGAGGTGTTTAAA-TGCTGTAAATTGAAGTGTTTAAT
1 -TGTTGTAAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA
* * *
654682 TATTGTAAATT-AAGGTGCTCAAA-TGATGTC-AATTGAAGTGTTTAA
1 TGTTGTAAATTGAA-GTG-TTAAAGTGCTG-CAAATTGAAGTGTTTAA
654727 GTGCTGCAAA
Statistics
Matches: 294, Mismatches: 57, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
44 30 0.10
45 40 0.14
46 183 0.62
47 41 0.14
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (46 bp):
TGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
Found at i:654600 original size:160 final size:156
Alignment explanation
Indices: 654322--654737 Score: 433
Period size: 160 Copynumber: 2.6 Consensus size: 156
654312 TGTTTGTTGT
* *
654322 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTAAAGTGTTTTAAG
1 AAATTGAAGTGTTTAAA-TGCTGTAAATTGAAGTG-TTAAATGTTGTAAATT-AAGTG-TTTAAA
* ** * * * * * *
654386 TACTACAAATTGAATTGTTTAGT-TCCTGGAAATTGAGATTTTTATTGCTGTAATTGAAGTGTAT
62 TGCTGTAAATTGAAGTGTTAAGTGT--TGCAAATTGAGATTTTAAATGCTGTAATTCAAGTGTAT
*
654450 AAATGTTGTTAATAGAGATGTTAAAGTGCTAC
125 AAATGTTGTTAATAGAGATGTTAAAGTGATAC
* *
654482 AAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAA-TGTTGTAAATT-AAGTGTTTAAATG
* *
654547 CTGTAAATTGAAGTGTTAAAGTGTTGCAAATTGA-AGTATTTAAATGTTGTAATTCAGGTGTATA
64 CTGTAAATTGAAGTGTT-AAGTGTTGCAAATTGAGA-T-TTTAAATGCTGTAATTCAAGTGTATA
* **
654611 AATGTTGTTAATTGAGATGTTAAAGTGATGT
126 AATGTTGTTAATAGAGATGTTAAAGTGATAC
* * * * * *
654642 AAGTTGAGGTGTTTAAATGCTGTAAATTGAAGTGTTTAATTATTGTAAATTAAGGTGCTCAAATG
1 AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTG-TTAAATGTTGTAAATTAA-GTGTTTAAATG
* * *
654707 ATGTCAATTGAAGTGTTTAAGTGCTGCAAAT
64 CTGTAAATTGAAGTG-TTAAGTGTTGCAAAT
654738 AATATATAAT
Statistics
Matches: 216, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
158 1 0.00
159 37 0.17
160 166 0.77
161 12 0.06
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (156 bp):
AAATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAATGTTGTAAATTAAGTGTTTAAATGCT
GTAAATTGAAGTGTTAAGTGTTGCAAATTGAGATTTTAAATGCTGTAATTCAAGTGTATAAATGT
TGTTAATAGAGATGTTAAAGTGATAC
Found at i:654706 original size:114 final size:115
Alignment explanation
Indices: 654490--654715 Score: 287
Period size: 114 Copynumber: 2.0 Consensus size: 115
654480 ACAAATTGAA
* *
654490 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATGCTGTAAAT
1 GTGTATAAATGTTGTAAATTGAAGTGTTAAAGTGATGCAAATTGAAGTGTTTAAATGCTGTAAAT
* * * *
654555 TGAAGTGTTAAAGTGTTGCAAATTGAAGTATTTAAATGTTGT-AATTCAG
66 TGAAGTGTTAAAGTATTGCAAATTGAAGTACTCAAATGATGTCAATTCAG
* * * *
654604 GTGTATAAATGTTGTTAATTG-AGATGTTAAAGTGATGTAAGTTGAGGTGTTTAAATGCTGTAAA
1 GTGTATAAATGTTGTAAATTGAAG-TGTTAAAGTGATGCAAATTGAAGTGTTTAAATGCTGTAAA
* * * *
654668 TTGAAGTGTTTAATTATTGTAAATT-AAGGTGCTCAAATGATGTCAATT
65 TTGAAGTGTTAAAGTATTGCAAATTGAA-GTACTCAAATGATGTCAATT
654716 GAAGTGTTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
113 4 0.04
114 87 0.92
115 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (115 bp):
GTGTATAAATGTTGTAAATTGAAGTGTTAAAGTGATGCAAATTGAAGTGTTTAAATGCTGTAAAT
TGAAGTGTTAAAGTATTGCAAATTGAAGTACTCAAATGATGTCAATTCAG
Found at i:658303 original size:16 final size:16
Alignment explanation
Indices: 658271--658304 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
658261 AATGTCATTA
**
658271 TAATGTTGTAACTTTT
1 TAATGTTGTAAAATTT
658287 TAATGTTGTAAAATTT
1 TAATGTTGTAAAATTT
658303 TA
1 TA
658305 TAACATATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TAATGTTGTAAAATTT
Found at i:658512 original size:58 final size:57
Alignment explanation
Indices: 658399--658514 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 57
658389 AATTCTCAAG
* *
658399 TATGATTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAA
1 TATGATTAAAATATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAA
* * *
658456 TATGGTTAAAATATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAA
1 TATGATTAAAATATATATTA-TTTTATTAAATTATATTTAATAATAAT-TATATTAAAA
658514 T
1 T
658515 TTAATAGCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 17 0.33
58 34 0.65
59 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
TATGATTAAAATATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAA
Found at i:658711 original size:16 final size:16
Alignment explanation
Indices: 658682--658736 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
658672 TGAATTACTG
* *
658682 ATTACAACTTTATTCT
1 ATTACAGCTCTATTCT
*
658698 ATTACTGCTCTATT-T
1 ATTACAGCTCTATTCT
*
658713 AATTACAGCTCTATTCC
1 -ATTACAGCTCTATTCT
658730 ATTACAG
1 ATTACAG
658737 TGAACCAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:668653 original size:51 final size:50
Alignment explanation
Indices: 668577--668746 Score: 151
Period size: 51 Copynumber: 3.4 Consensus size: 50
668567 TATAAACACG
** *
668577 TGTGTAGTACTAAATGCAGGCTACTACGTGTATCGATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGA-AGATAATGATCACA
** * * * * ** *
668628 TGTGTAGTACTATGTGCAGGCTACTATATGAACCAAAAATTTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGATAATGATCACA
* * * *
668678 TGTGTAGCACTATGTGAAGGCTACTACGTGTATCGAATGATAATAATTACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAA-GATAATGATCACA
* * *
668729 CGGGTGGTACTATGTGCA
1 TGTGTAGTACTATGTGCA
668747 AACCACCGAA
Statistics
Matches: 88, Mismatches: 30, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
50 39 0.44
51 49 0.56
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGATAATGATCACA
Found at i:671340 original size:41 final size:41
Alignment explanation
Indices: 671295--671415 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
671285 AGTAGCGTTA
* * *
671295 AATTGCACATATGTGCCCCTGTTTGTACTTTGAG-ACCCTTG
1 AATTGCACATATGTGCCCCTGTTTATACTTCG-GTACCCCTG
* *
671336 AATTGCACATACGTGCCCCTGTTTATAGTTCGGTACCCCTG
1 AATTGCACATATGTGCCCCTGTTTATACTTCGGTACCCCTG
* *
671377 AATTGCACATATGTGCCCC-GTTTTTACTTCAGTACCCCT
1 AATTGCACATATGTGCCCCTGTTTATACTTCGGTACCCCT
671416 AAAAACACTT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 18 0.26
41 52 0.74
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (41 bp):
AATTGCACATATGTGCCCCTGTTTATACTTCGGTACCCCTG
Found at i:674419 original size:12 final size:11
Alignment explanation
Indices: 674405--674475 Score: 63
Period size: 11 Copynumber: 6.1 Consensus size: 11
674395 AAAATTTAAT
*
674405 TAAAAATAAACT
1 TAAAAATAAA-A
*
674417 TAAAAAGATATAA
1 T-AAAA-ATAAAA
*
674430 TAAAATTAAAA
1 TAAAAATAAAA
674441 -ATAAAATAAAA
1 TA-AAAATAAAA
674452 TAAAAATAAACA
1 TAAAAATAAA-A
674464 TAAAAATAAAA
1 TAAAAATAAAA
674475 T
1 T
674476 TTATTTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
10 1 0.02
11 22 0.45
12 17 0.35
13 5 0.10
14 4 0.08
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:674420 original size:25 final size:25
Alignment explanation
Indices: 674392--674469 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
674382 AAAACTTATC
*
674392 TAAAAA-ATTTAATTAAAAATAAACT
1 TAAAAAGATATAA-TAAAAATAAACT
*
674417 TAAAAAGATATAATAAAATTAAA--
1 TAAAAAGATATAATAAAAATAAACT
* *
674440 -AATAAA-ATAAAATAAAAATAAACA
1 TAA-AAAGATATAATAAAAATAAACT
674464 TAAAAA
1 TAAAAA
674470 TAAAATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
24 3 0.07
25 17 0.39
26 5 0.11
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (25 bp):
TAAAAAGATATAATAAAAATAAACT
Found at i:674439 original size:6 final size:5
Alignment explanation
Indices: 674428--674475 Score: 51
Period size: 5 Copynumber: 8.6 Consensus size: 5
674418 AAAAAGATAT
674428 AATAA AATTAAA AATAA AATAA AATAAA AATAA ACATAAA AATAA AAT
1 AATAA AA-T-AA AATAA AATAA AAT-AA AATAA A-AT-AA AATAA AAT
674476 TTATTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 20 0.53
6 11 0.29
7 7 0.18
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:682504 original size:17 final size:16
Alignment explanation
Indices: 682482--682515 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
682472 GGGGATGGCG
682482 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
682499 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
682515 T
1 T
682516 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:700069 original size:33 final size:33
Alignment explanation
Indices: 700032--700143 Score: 84
Period size: 33 Copynumber: 3.3 Consensus size: 33
700022 AAAGATGTAC
*
700032 AAGACCATGGTTGGACCATGGCAATGTTTACAT
1 AAGACCATGGTTGGACAATGGCAATGTTTACAT
* * * * * *
700065 AAGACCATAGCG-AGG-CTATGGTGATTTTTTAGACAC
1 AAGACCAT-G-GTTGGACAATGG-CAATGTTT--ACAT
**
700101 AAGACCATGGTTGGACAATGGCAATGTTTATGT
1 AAGACCATGGTTGGACAATGGCAATGTTTACAT
700134 AAGACCATGG
1 AAGACCATGG
700144 CGAAGCTATG
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
33 24 0.41
34 9 0.16
35 9 0.16
36 16 0.28
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (33 bp):
AAGACCATGGTTGGACAATGGCAATGTTTACAT
Found at i:700115 original size:69 final size:69
Alignment explanation
Indices: 700030--700192 Score: 238
Period size: 69 Copynumber: 2.4 Consensus size: 69
700020 ATAAAGATGT
*
700030 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGCGAGGCTATGGT-GATTTTT
1 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGCGAAGCTATGGTAG-TTTTT
*
700094 TAGAC
65 CAGAC
* ** *
700099 ACAAGACCATGGTTGGACAATGGCAATGTTTATGTAAGACCATGGCGAAGCTATGGTAGTTTTTC
1 ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGCGAAGCTATGGTAGTTTTTC
700164 AGAC
66 AGAC
**
700168 GTAAGACCATGGTTGGACCATGGCA
1 ACAAGACCATGGTTGGACCATGGCA
700193 GTGTATATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
69 83 0.99
70 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (69 bp):
ACAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGCGAAGCTATGGTAGTTTTTC
AGAC
Found at i:709908 original size:21 final size:21
Alignment explanation
Indices: 709868--709908 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
709858 TACAAAGTTG
*
709868 ATAACAATTAATATATATTAT
1 ATAACAATTAATATACATTAT
709889 ATAA-AATTAATTATACATTA
1 ATAACAATTAA-TATACATTA
709909 GTTATTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAACAATTAATATACATTAT
Found at i:712494 original size:30 final size:30
Alignment explanation
Indices: 712452--712535 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
712442 GAGCATCTAT
* *
712452 AAAAAGGGATGGTTTTGATCATCGATTAATG
1 AAAAA-GGATGGTTTTGACCATCGATTAAGG
712483 AAAAAGGATGGTTTTGACCATCGATTAAGG
1 AAAAAGGATGGTTTTGACCATCGATTAAGG
* *
712513 AAAAGGGATGGTTTCGACCATCG
1 AAAAAGGATGGTTTTGACCATCG
712536 TTTAGCACAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 44 0.90
31 5 0.10
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAAAGGATGGTTTTGACCATCGATTAAGG
Found at i:726333 original size:13 final size:13
Alignment explanation
Indices: 726315--726357 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
726305 GTTAACACTT
*
726315 TGAAATGGCCATA
1 TGAAATGGCTATA
* *
726328 TGAAATTGTTATA
1 TGAAATGGCTATA
726341 TGAAATGGCTATA
1 TGAAATGGCTATA
726354 TGAA
1 TGAA
726358 TTGGTTGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (13 bp):
TGAAATGGCTATA
Found at i:729001 original size:50 final size:50
Alignment explanation
Indices: 728892--729130 Score: 241
Period size: 50 Copynumber: 4.7 Consensus size: 50
728882 ATTTGGGTAA
* * * *
728892 AGAGATCCCATGTAAGACCATGTATGGGACATGACACTGGCATCCTTGAGATCATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* **
728948 AGAGGTCCCATGTAAGACCATGTCTATGACATGGCATTGGCACCGAGACG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
728998 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * * *
729048 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGACG
*
729097 A-AACATCCCATGTAAGACCATGTCTGGGACATGG
1 AGAGC-TCCCATGTAAGACCATGTCTGGGACATGG
729131 TTTTGGCATG
Statistics
Matches: 162, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
48 4 0.02
49 32 0.20
50 83 0.51
52 1 0.01
53 4 0.02
55 2 0.01
56 36 0.22
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:732112 original size:25 final size:25
Alignment explanation
Indices: 732046--732112 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
732036 TTGACCCACC
* * *
732046 GCTCCTGTGAGCATACCAATTTATA
1 GCTCGTGTAAGCATACTAATTTATA
* *
732071 GCTCGTATAAGCATACTAATTTTTA
1 GCTCGTGTAAGCATACTAATTTATA
732096 GCTCGTGTAAGCATACT
1 GCTCGTGTAAGCATACT
732113 GATCTAAGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (25 bp):
GCTCGTGTAAGCATACTAATTTATA
Found at i:735439 original size:13 final size:13
Alignment explanation
Indices: 735421--735446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
735411 CAAAACTAGC
735421 TTTTTTTTCACAA
1 TTTTTTTTCACAA
735434 TTTTTTTTCACAA
1 TTTTTTTTCACAA
735447 CTTGATATCC
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:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:736915 original size:32 final size:32
Alignment explanation
Indices: 736879--736942 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
736869 TCAAAAATCT
*
736879 TATACTCCCTATACCATACAATTTCTTAGTTA
1 TATACTCACTATACCATACAATTTCTTAGTTA
736911 TATACTCACTATACCATACAATTTCTTAGTTA
1 TATACTCACTATACCATACAATTTCTTAGTTA
736943 ACTCATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (32 bp):
TATACTCACTATACCATACAATTTCTTAGTTA
Found at i:740114 original size:27 final size:27
Alignment explanation
Indices: 739933--740102 Score: 236
Period size: 27 Copynumber: 6.3 Consensus size: 27
739923 GATTCATAGG
* *
739933 AAAATGATTGAAATACCCTTGAAGGAT
1 AAAATGACTGAAATACCCTTGAAGGGT
739960 AAAATGACTGAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
* *
739987 AAAATAACTGAAATACCCTCT-AAGGAT
1 AAAATGACTGAAATACCCT-TGAAGGGT
740014 AAAATGACTGAAATA-CCTTCGAAGGGT
1 AAAATGACTGAAATACCCTT-GAAGGGT
* * * *
740041 GAATTGACCGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
740068 AAAATGACTGAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTTGAAGGGT
740095 AAAATGAC
1 AAAATGAC
740103 CAATATACCC
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 3 0.02
27 117 0.94
28 4 0.03
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTTGAAGGGT
Found at i:740127 original size:54 final size:53
Alignment explanation
Indices: 739943--740131 Score: 215
Period size: 54 Copynumber: 3.5 Consensus size: 53
739933 AAAATGATTG
* * *
739943 AAATACCCT-TGAAGGATAAAATGACTGAAATACCCTTGAAGGGTAAAATAACTG
1 AAATACCCTCT-AGGGATAAAATGACTGAAATACCCTTGAAGGGTAAAATGAC-C
* * *
739997 AAATACCCTCTAAGGATAAAATGACTGAAATA-CCTTCGAAGGGTGAATTGACC
1 AAATACCCTCTAGGGATAAAATGACTGAAATACCCTT-GAAGGGTAAAATGACC
*
740050 GAAATACCCTCGAAGGG-TAAAATGACTGAAATACCCTTGAAGGGTAAAATGACC
1 -AAATACCCTC-TAGGGATAAAATGACTGAAATACCCTTGAAGGGTAAAATGACC
*
740104 AATATACCCT-TAGGAGATGAAATGACTG
1 AA-ATACCCTCTAGG-GATAAAATGACTG
740132 TTATAGCCTT
Statistics
Matches: 117, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
52 3 0.03
53 7 0.06
54 99 0.85
55 8 0.07
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (53 bp):
AAATACCCTCTAGGGATAAAATGACTGAAATACCCTTGAAGGGTAAAATGACC
Found at i:740524 original size:28 final size:28
Alignment explanation
Indices: 740467--740533 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
740457 ATTGTATTGA
* *
740467 GCTAAGGCCCACACTGCTACCGTATTGG
1 GCTAAGGCCCACACTGATACCGTATAGG
*
740495 GCTAAGGCCCACACTGATACTGCT-TAGG
1 GCTAAGGCCCACACTGATACCG-TATAGG
*
740523 GCTCAGGCCCA
1 GCTAAGGCCCA
740534 GACTATTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.19
Consensus pattern (28 bp):
GCTAAGGCCCACACTGATACCGTATAGG
Found at i:746644 original size:9 final size:10
Alignment explanation
Indices: 746619--746657 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
746609 AGTTTTGTTC
746619 GCTTTTTTCT
1 GCTTTTTTCT
746629 GCTTTTTTCT
1 GCTTTTTTCT
746639 GCTTTTTTCT
1 GCTTTTTTCT
746649 -CTCTTTTTC
1 GCT-TTTTTC
746658 CCTCTTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 2 0.07
10 26 0.93
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (10 bp):
GCTTTTTTCT
Found at i:747402 original size:27 final size:27
Alignment explanation
Indices: 747363--747568 Score: 234
Period size: 27 Copynumber: 7.6 Consensus size: 27
747353 ATTCGTGGGG
*
747363 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
* * *
747390 AAATGACCAAAATATCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
747417 AAATGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
* *
747444 AAATGATCAAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
* **
747471 AAATGACCGAAATGCCCTCGTAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
*
747498 AGATGACCGAAATACGCC-CAAAGGGTA
1 AAATGACCGAAATAC-CCTCAAAGGGTA
* ** * * *
747525 AAATAACTAAAATACCTTTATAGGGTA
1 AAATGACCGAAATACCCTCAAAGGGTA
* *
747552 AAATGACTGATATACCC
1 AAATGACCGAAATACCC
747569 CTAAGAGATG
Statistics
Matches: 150, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 147 0.98
28 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCAAAGGGTA
Found at i:761163 original size:8 final size:9
Alignment explanation
Indices: 761129--761165 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
761119 ATATTTCTCA
761129 TGAAAAAAG
1 TGAAAAAAG
761138 TGATCAAAAAG
1 TGA--AAAAAG
761149 TGAAAAAAG
1 TGAAAAAAG
761158 TGAAAAAA
1 TGAAAAAA
761166 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 17 0.65
11 9 0.35
ACGTcount: A:0.65, C:0.03, G:0.19, T:0.14
Consensus pattern (9 bp):
TGAAAAAAG
Found at i:762667 original size:11 final size:11
Alignment explanation
Indices: 762651--762685 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
762641 CTCAAAACAC
762651 CCTAAGCCATA
1 CCTAAGCCATA
762662 CCTAAGCCATA
1 CCTAAGCCATA
762673 CCTAAGCCATA
1 CCTAAGCCATA
762684 CC
1 CC
762686 ACCTTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.34, C:0.40, G:0.09, T:0.17
Consensus pattern (11 bp):
CCTAAGCCATA
Found at i:767759 original size:47 final size:47
Alignment explanation
Indices: 767685--767792 Score: 135
Period size: 47 Copynumber: 2.3 Consensus size: 47
767675 AAGGTGGAAG
* * * *
767685 ATGTGGCTGTTTATCTACAAAAATGGTGGCTTGTCAACGATATTTTT
1 ATGTGGCAGTTTATATACAAAAATGGTGGCTTGTCAACAATATTATT
* * *
767732 ATGTGGCAGTTTATATGCAAAAGTGGTGGCTTGTCCACAATATTATT
1 ATGTGGCAGTTTATATACAAAAATGGTGGCTTGTCAACAATATTATT
* *
767779 AAGTGGTAGTTTAT
1 ATGTGGCAGTTTAT
767793 CTGTATTACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (47 bp):
ATGTGGCAGTTTATATACAAAAATGGTGGCTTGTCAACAATATTATT
Found at i:767806 original size:47 final size:47
Alignment explanation
Indices: 767687--767817 Score: 127
Period size: 47 Copynumber: 2.8 Consensus size: 47
767677 GGTGGAAGAT
* * * * * * * *
767687 GTGGCTGTTTATCTACAAAAATGGTGGCTTGTCAACGATATTTTTAT
1 GTGGCAGTTTATATGCAAAACTGGTGGCTTGTCCACAATATTATTAA
*
767734 GTGGCAGTTTATATGCAAAAGTGGTGGCTTGTCCACAATATTATTAA
1 GTGGCAGTTTATATGCAAAACTGGTGGCTTGTCCACAATATTATTAA
* * * ** *
767781 GTGGTAGTTTATCTGTATTACTGGTGGCTTGACCACA
1 GTGGCAGTTTATATGCAAAACTGGTGGCTTGTCCACA
767818 TTACTGGCAG
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (47 bp):
GTGGCAGTTTATATGCAAAACTGGTGGCTTGTCCACAATATTATTAA
Found at i:786072 original size:302 final size:302
Alignment explanation
Indices: 785526--786131 Score: 1016
Period size: 302 Copynumber: 2.0 Consensus size: 302
785516 CAGCTTCCGC
* *
785526 CTGTCTAGCTCCATCTCGCCCTAAATTATCATTATTTGCATCCACAGACCTGGATGCATTTACAA
1 CTGTCTAGCTCCATCTCACCCTAAATTATCATTATTTGCATCCACAAACCTGGATGCATTTACAA
* *
785591 TGTTCTCAGCAGATTCTTTCTCAATAGCTATTGTCACAGTATTTTCTTCCTCAACCTTTTCGTTC
66 TGTTCTCAACAGATTCTTTCTCAATAGCTATTGTCACAGTATTTTCTTCCTCAACCTTCTCGTTC
*
785656 ACAATTTCAACACAGGCGTCTTCTTCTTCAACAGCGGACACCTCTTGAGCAGCAATTGCGTCATC
131 ACAATTTCAACACAGGCATCTTCTTCTTCAACAGCGGACACCTCTTGAGCAGCAATTGCGTCATC
*
785721 CTCGATTAGGCTATCAATCCTTCGCATGCACTCCTCAACATCCCTTGAGTTCTCTTTTTTCTCAA
196 CTCGATTAGGCTATCAATCCTTCGCATGCACTCCTCAACATCCCTTGAGTTCTCTTCTTTCTCAA
* *
785786 AATCAGAGACATGCACAATGGGAGGGGATTCCACCGATCTGT
261 AATCAAAGACATGCACAATGGGAAGGGATTCCACCGATCTGT
* * *
785828 CTGTCTAGCTCCATCTCACTCC-AGATTATCATTATTTGCATCCGCAAACTTGGATGCATTTACA
1 CTGTCTAGCTCCATCTCAC-CCTAAATTATCATTATTTGCATCCACAAACCTGGATGCATTTACA
* * **
785892 ATGTTCTCAACCGATTCTTTCTCAATAGCTATTGTCTCAGTATTTTCTTCCTCGGCCTTCTCGTT
65 ATGTTCTCAACAGATTCTTTCTCAATAGCTATTGTCACAGTATTTTCTTCCTCAACCTTCTCGTT
* *
785957 CACAATTTCAACACAGGCATCTTCTTCTTCAACAGCGGACGCCTCTTGAGCAGTAATTGCGTCAT
130 CACAATTTCAACACAGGCATCTTCTTCTTCAACAGCGGACACCTCTTGAGCAGCAATTGCGTCAT
*
786022 CCTCGATTAGGCTATCAATCCTTCGCATGCACTCCTCAACATCTCTTGAGTTCTCTTCTTTCTCA
195 CCTCGATTAGGCTATCAATCCTTCGCATGCACTCCTCAACATCCCTTGAGTTCTCTTCTTTCTCA
* *
786087 AAATTAAAGACATGCACAATGGGAAGGGATTCCATCGATCTGT
260 AAATCAAAGACATGCACAATGGGAAGGGATTCCACCGATCTGT
786130 CT
1 CT
786132 CGGTCCCCTA
Statistics
Matches: 283, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
302 281 0.99
303 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (302 bp):
CTGTCTAGCTCCATCTCACCCTAAATTATCATTATTTGCATCCACAAACCTGGATGCATTTACAA
TGTTCTCAACAGATTCTTTCTCAATAGCTATTGTCACAGTATTTTCTTCCTCAACCTTCTCGTTC
ACAATTTCAACACAGGCATCTTCTTCTTCAACAGCGGACACCTCTTGAGCAGCAATTGCGTCATC
CTCGATTAGGCTATCAATCCTTCGCATGCACTCCTCAACATCCCTTGAGTTCTCTTCTTTCTCAA
AATCAAAGACATGCACAATGGGAAGGGATTCCACCGATCTGT
Found at i:795449 original size:15 final size:16
Alignment explanation
Indices: 795429--795458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
795419 TGGTGCCCCG
795429 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
795444 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
795459 AGCATGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:802298 original size:23 final size:23
Alignment explanation
Indices: 802271--802337 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
802261 TTGGTTTGGG
* *
802271 TTTGGTACGAAATGGTAATGTAA
1 TTTGGTACGAAATGGAAATGGAA
*
802294 TTTGGTATGAAATGGAAATGGAA
1 TTTGGTACGAAATGGAAATGGAA
802317 TTTGGTACGAAATGGAAATGG
1 TTTGGTACGAAATGGAAATGG
802338 TTCAAAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.31
Consensus pattern (23 bp):
TTTGGTACGAAATGGAAATGGAA
Found at i:803168 original size:31 final size:32
Alignment explanation
Indices: 803123--803189 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
803113 ACATGCATGC
*
803123 ACCTTGCTAAAATGAATCTCC-AA-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCAAACATTCGGCCA
*
803155 ACCTTG-TTAAATGATCCCAAACATTCGGCCA
1 ACCTTGCTAAAATGATCCCAAACATTCGGCCA
803186 ACCT
1 ACCT
803190 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 2 0.06
30 5 0.16
31 18 0.58
32 6 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCAAACATTCGGCCA
Found at i:806541 original size:19 final size:19
Alignment explanation
Indices: 806517--806562 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
806507 CTTTTCACTC
806517 TCTTTTTTCAAGTTTTC-TT
1 TCTTTTTTC-AGTTTTCTTT
*
806536 TCTTTTTTTCATTTTTCTTT
1 TC-TTTTTTCAGTTTTCTTT
806556 TCTTTTT
1 TCTTTTT
806563 CTCTCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (19 bp):
TCTTTTTTCAGTTTTCTTT
Found at i:806544 original size:20 final size:20
Alignment explanation
Indices: 806519--806562 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
806509 TTTCACTCTC
806519 TTTTTTCAAGTTTTC-TTTCT
1 TTTTTTC-AGTTTTCTTTTCT
*
806539 TTTTTTCATTTTTCTTTTCT
1 TTTTTTCAGTTTTCTTTTCT
806559 TTTT
1 TTTT
806563 CTCTCATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTCAGTTTTCTTTTCT
Found at i:809087 original size:23 final size:23
Alignment explanation
Indices: 809060--809126 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
809050 TTGGTTTGGG
* *
809060 TTTGGTACGAAATGGTAATGTAA
1 TTTGGTACGAAATGGAAATGGAA
809083 TTTGGTACGAAATGGAAATGGAA
1 TTTGGTACGAAATGGAAATGGAA
809106 TTTGGTACGAAATGGAAATGG
1 TTTGGTACGAAATGGAAATGG
809127 TTCAAAAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (23 bp):
TTTGGTACGAAATGGAAATGGAA
Found at i:809985 original size:31 final size:31
Alignment explanation
Indices: 809918--809985 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
809908 ATGCACCTTG
* * * * *
809918 CTAAATGAATCTCCACATTCGGCTAATCTTG
1 CTAAATGAACCCCCACATTCGGCCAATCCTA
809949 CTAAATGAACCCCCACATTCGGCCAA-CCTA
1 CTAAATGAACCCCCACATTCGGCCAATCCTA
809979 CATAAAT
1 C-TAAAT
809986 AGGATGAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (31 bp):
CTAAATGAACCCCCACATTCGGCCAATCCTA
Found at i:817667 original size:17 final size:17
Alignment explanation
Indices: 817637--817671 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
817627 TGTATTTTTT
**
817637 TTCTTTTTTCTTTTTAA
1 TTCTTTTTAATTTTTAA
817654 TTCTTTTTAATTTTTAA
1 TTCTTTTTAATTTTTAA
817671 T
1 T
817672 AATCATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTCTTTTTAATTTTTAA
Found at i:819553 original size:30 final size:30
Alignment explanation
Indices: 819513--819570 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
819503 TGATCGGATA
*
819513 CTTCTCGATGAGCAACATCGTGATGGGAAT
1 CTTCTCGATGAGCAACATCATGATGGGAAT
* * *
819543 CTTCTTGATGAGCTACTTCATGATGGGA
1 CTTCTCGATGAGCAACATCATGATGGGA
819571 TACCTCCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (30 bp):
CTTCTCGATGAGCAACATCATGATGGGAAT
Found at i:824552 original size:285 final size:285
Alignment explanation
Indices: 824042--824611 Score: 1086
Period size: 285 Copynumber: 2.0 Consensus size: 285
824032 CCATACCCAA
* *
824042 CATAAAGTACGAAAACCTAAAAAATTATTATTGTTAACTCTTTTCAATTCTCATTTGTCCTTTAC
1 CATAAAGTACGAAAACCTAAAAAATTATTATCGTTAACTATTTTCAATTCTCATTTGTCCTTTAC
824107 AACCAAACCTGTCTTTCTGACTTTCTCATTTTTCAGCAGGGACGGTCGTCGAAGAAGCAGACGGC
66 AACCAAACCTGTCTTTCTGACTTTCTCATTTTTCAGCAGGGACGGTCGTCGAAGAAGCAGACGGC
*
824172 TAAAGGCGGGTGAATTGGAGGCTGAAAGCCGGAAGGTGGAGGGAGATTGGAGACTAAAGAGTGAA
131 TAAAGGCGGGTGAACTGGAGGCTGAAAGCCGGAAGGTGGAGGGAGATTGGAGACTAAAGAGTGAA
824237 GAGAGGTTGAGAGAGTCAGAGAGTCAGAGAGGCCGGATGGACGAGTGACGAGAGTGGTGGTTGCC
196 GAGAGGTTGAGAGAGTCAGAGAGTCAGAGAGGCCGGATGGACGAGTGACGAGAGTGGTGGTTGCC
824302 CGGGAGGGGGTGAGTCTCGGGTTGT
261 CGGGAGGGGGTGAGTCTCGGGTTGT
824327 CATAAAGTACGAAAACCTAAAAAATTATTATCGTTAACTATTTTCAATTCTCATTTGTCCTTTAC
1 CATAAAGTACGAAAACCTAAAAAATTATTATCGTTAACTATTTTCAATTCTCATTTGTCCTTTAC
* *
824392 CACCAAACCTGTCTTTCTGACTTTCTCATTTTTCAGCAGGGACGGTCGTCGGAGAAGCAGACGGC
66 AACCAAACCTGTCTTTCTGACTTTCTCATTTTTCAGCAGGGACGGTCGTCGAAGAAGCAGACGGC
824457 TAAAGGCGGGTGAACTGGAGGCTGAAAGCCGGAAGGTGGAGGGAGATTGGAGACTAAAGAGTGAA
131 TAAAGGCGGGTGAACTGGAGGCTGAAAGCCGGAAGGTGGAGGGAGATTGGAGACTAAAGAGTGAA
824522 GAGAGGTTGAGAGAGTCAGAGAGTCAGAGAGGCCGGATGGACGAGTGACGAGAGTGGTGGTTGCC
196 GAGAGGTTGAGAGAGTCAGAGAGTCAGAGAGGCCGGATGGACGAGTGACGAGAGTGGTGGTTGCC
*
824587 CGGGAGGGGGTGGGTCTCGGGTTGT
261 CGGGAGGGGGTGAGTCTCGGGTTGT
824612 TTGTTTTTAT
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
285 279 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (285 bp):
CATAAAGTACGAAAACCTAAAAAATTATTATCGTTAACTATTTTCAATTCTCATTTGTCCTTTAC
AACCAAACCTGTCTTTCTGACTTTCTCATTTTTCAGCAGGGACGGTCGTCGAAGAAGCAGACGGC
TAAAGGCGGGTGAACTGGAGGCTGAAAGCCGGAAGGTGGAGGGAGATTGGAGACTAAAGAGTGAA
GAGAGGTTGAGAGAGTCAGAGAGTCAGAGAGGCCGGATGGACGAGTGACGAGAGTGGTGGTTGCC
CGGGAGGGGGTGAGTCTCGGGTTGT
Found at i:824812 original size:9 final size:9
Alignment explanation
Indices: 824798--824828 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
824788 GTTAAACGAA
824798 TCGAGTTAT
1 TCGAGTTAT
*
824807 TCGAGTTAA
1 TCGAGTTAT
824816 TCGAGTTAT
1 TCGAGTTAT
824825 TCGA
1 TCGA
824829 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:824898 original size:9 final size:9
Alignment explanation
Indices: 824881--824917 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
824871 TGAGTTTTCA
824881 AATTCGAAT
1 AATTCGAAT
*
824890 AACTCGAAT
1 AATTCGAAT
824899 AATTCGAAT
1 AATTCGAAT
824908 AATTCGAAT
1 AATTCGAAT
824917 A
1 A
824918 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:825466 original size:5 final size:5
Alignment explanation
Indices: 825456--825486 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
825446 NNNNAAATAT
825456 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
825487 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:825586 original size:5 final size:5
Alignment explanation
Indices: 825576--825601 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
825566 CTCGAAAAAT
825576 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
825602 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:826178 original size:87 final size:83
Alignment explanation
Indices: 826022--826193 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 83
826012 GGTGTAGAAA
* *
826022 ATTCTCAATTTTTTTTAAAAAATAATTAAGCCCTTTTTTTTTCACTCAATTGAGAACTTAAACTT
1 ATTCTCAATTTTTTTTAAAAAATAATTAAGCCCTGTTTTTTTCACTCAATTAAGAACTTAAACTT
826087 TCAAAATACATCAAAAAG
66 TCAAAATACATCAAAAAG
* *
826105 ATTCTCAATTTTTTTTCAAAAAAAGTAATTAAGCCTCTGTTTTTTTCACTCAATTAAGTACTTGA
1 ATTCTCAATTTTTTTT--AAAAAA-TAATTAAGCC-CTGTTTTTTTCACTCAATTAAGAACTTAA
*
826170 ACTTTCAAAATGCATCAAAAAG
62 ACTTTCAAAATACATCAAAAAG
826192 AT
1 AT
826194 CTTCAAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
83 16 0.20
85 6 0.08
86 10 0.12
87 48 0.60
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (83 bp):
ATTCTCAATTTTTTTTAAAAAATAATTAAGCCCTGTTTTTTTCACTCAATTAAGAACTTAAACTT
TCAAAATACATCAAAAAG
Found at i:826206 original size:87 final size:85
Alignment explanation
Indices: 826022--826226 Score: 256
Period size: 87 Copynumber: 2.4 Consensus size: 85
826012 GGTGTAGAAA
* * * *
826022 ATTCTC-AATTTTTTTTAAAAAA-TAATTAAGCCCTTTTTTTTTCACTCAATTGAGAACTTAAAC
1 ATTCTCAAAATTTTTTCAAAAAAGTAATTAAGCCCTGTTTTTTTCACTCAATTAAGAACTTAAAC
826085 TTTCAAAATACATCAAAAAG
66 TTTCAAAATACATCAAAAAG
** * *
826105 ATTCTCAATTTTTTTTCAAAAAAAGTAATTAAGCCTCTGTTTTTTTCACTCAATTAAGTACTTGA
1 ATTCTCAAAATTTTTTC-AAAAAAGTAATTAAGCC-CTGTTTTTTTCACTCAATTAAGAACTTAA
*
826170 ACTTTCAAAATGCATCAAAAAG
64 ACTTTCAAAATACATCAAAAAG
* *
826192 A-TCTTCAAAA-TTTTTCAAAATAGCAATTAAGCCCT
1 ATTC-TCAAAATTTTTTCAAAAAAGTAATTAAGCCCT
826227 TGCTCTTATT
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
83 6 0.06
84 10 0.09
85 21 0.20
86 18 0.17
87 51 0.48
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (85 bp):
ATTCTCAAAATTTTTTCAAAAAAGTAATTAAGCCCTGTTTTTTTCACTCAATTAAGAACTTAAAC
TTTCAAAATACATCAAAAAG
Done.