Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 49
Found at i:5601748 original size:21 final size:21
Alignment explanation
Indices: 5601722--5601766 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5601712 AGAGTCGGTT
*
5601722 GACGAAATGAACATCACTAAA
1 GACGAAATAAACATCACTAAA
*
5601743 GACGAAATAAACGTCACTAAA
1 GACGAAATAAACATCACTAAA
5601764 GAC
1 GAC
5601767 AAGATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (21 bp):
GACGAAATAAACATCACTAAA
Found at i:5601825 original size:43 final size:43
Alignment explanation
Indices: 5601777--5601861 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
5601767 AAGATAATTA
*
5601777 GCGGCATTTGA-AAGAAAAATGCCACTATAGATCTTGATCTTTT
1 GCGGCATTT-ATAAGAAAAATGCCACTATAGAACTTGATCTTTT
* *
5601820 GCGGCATTTATAAGAAAAATGTCGCTATAGAACTTGATCTTT
1 GCGGCATTTATAAGAAAAATGCCACTATAGAACTTGATCTTT
5601862 GGGGGCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCATTTATAAGAAAAATGCCACTATAGAACTTGATCTTTT
Found at i:5602192 original size:15 final size:16
Alignment explanation
Indices: 5602149--5602184 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
5602139 TGATGTGTTC
5602149 AAATTTATTCATAATT
1 AAATTTATTCATAATT
5602165 -AATTTATTCATAATT
1 AAATTTATTCATAATT
5602180 AAATT
1 AAATT
5602185 AATTATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTATTCATAATT
Found at i:5604890 original size:14 final size:14
Alignment explanation
Indices: 5604871--5604913 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5604861 TAAACGTATC
*
5604871 AATTAATGAA-TACT
1 AATTAATAAATTA-T
5604885 AATTAATAAATTAT
1 AATTAATAAATTAT
*
5604899 AATTAATTAATTAT
1 AATTAATAAATTAT
5604913 A
1 A
5604914 TTTTGTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
AATTAATAAATTAT
Found at i:5611013 original size:14 final size:14
Alignment explanation
Indices: 5610994--5611020 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5610984 AAACAGTTCC
5610994 TCCGATCACAAAGT
1 TCCGATCACAAAGT
5611008 TCCGATCACAAAG
1 TCCGATCACAAAG
5611021 GGCACTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (14 bp):
TCCGATCACAAAGT
Found at i:5613052 original size:19 final size:17
Alignment explanation
Indices: 5613010--5613055 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 17
5613000 TATATATTAT
5613010 TATTTTTAATTAAATCAC
1 TATTTTT-ATTAAATCAC
5613028 TATTTTTATTAAATCAC
1 TATTTTTATTAAATCAC
5613045 TCAGTTTTTAT
1 T-A-TTTTTAT
5613056 GGTGTCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (17 bp):
TATTTTTATTAAATCAC
Found at i:5626534 original size:24 final size:21
Alignment explanation
Indices: 5626480--5626542 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 21
5626470 TTTTGGTGCA
*
5626480 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
5626500 GAGGGAACCGATTCCCCCCTTT
1 GAGGGAACCGATTCCCCCC-TT
5626522 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
5626543 ACAGGGGAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 10 0.26
21 7 0.18
22 3 0.08
23 1 0.03
24 17 0.45
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:5626550 original size:21 final size:21
Alignment explanation
Indices: 5626502--5626562 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 21
5626492 CCCCCCTTGA
5626502 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGATTCCCCCC--T-AAG
5626526 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTA-AG
* *
5626547 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
5626563 ATGGGGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
24 17 0.50
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTAAG
Found at i:5626563 original size:20 final size:21
Alignment explanation
Indices: 5626524--5626563 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5626514 CCCCCTTTGA
*
5626524 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
5626545 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
5626564 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:5628058 original size:29 final size:29
Alignment explanation
Indices: 5628025--5628088 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
5628015 TATCATTTGC
5628025 ATTATGACCAATTTTGCCATTTCACATTA
1 ATTATGACCAATTTTGCCATTTCACATTA
* *
5628054 ATTATGACCAATTTTGCTATTTCACATTG
1 ATTATGACCAATTTTGCCATTTCACATTA
5628083 ATTATG
1 ATTATG
5628089 GAACTAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (29 bp):
ATTATGACCAATTTTGCCATTTCACATTA
Found at i:5629861 original size:21 final size:22
Alignment explanation
Indices: 5629835--5629875 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5629825 CCAGGACATG
5629835 GAGTATCAGTACT-CCTTTAAT
1 GAGTATCAGTACTACCTTTAAT
*
5629856 GAGTATCGGTACTACCTTTA
1 GAGTATCAGTACTACCTTTA
5629876 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGTATCAGTACTACCTTTAAT
Found at i:5633050 original size:6 final size:6
Alignment explanation
Indices: 5633039--5633075 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
5633029 TGAAGAACAA
* *
5633039 ACGGAG ACGGAG ACGGAG ACGTAG ACGTAG ACGGAG A
1 ACGGAG ACGGAG ACGGAG ACGGAG ACGGAG ACGGAG A
5633076 GAGAATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.05
Consensus pattern (6 bp):
ACGGAG
Found at i:5633753 original size:24 final size:23
Alignment explanation
Indices: 5633709--5633754 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
5633699 GAATTTAATA
5633709 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
5633733 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
5633755 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:5633798 original size:29 final size:29
Alignment explanation
Indices: 5633765--5633825 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5633755 AAATATTTAA
* *
5633765 AATA-TATTTATTAATATTTCTAATAATAT
1 AATATTATTTATTAATA-TTATAATAAAAT
*
5633794 AATATTATTTTTTAATATTATAATAAAAT
1 AATATTATTTATTAATATTATAATAAAAT
5633823 AAT
1 AAT
5633826 CAATTCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
AATATTATTTATTAATATTATAATAAAAT
Found at i:5633801 original size:26 final size:24
Alignment explanation
Indices: 5633739--5633802 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 24
5633729 TATTTTAATC
5633739 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
5633763 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
5633786 AATAATATAATATTATT
1 AA-AATAT-ATATTATT
5633803 TTTTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 12 0.35
25 3 0.09
26 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:5634018 original size:23 final size:23
Alignment explanation
Indices: 5633998--5634042 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5633988 AATAATATTT
5633998 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
5634021 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
5634043 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:5635010 original size:47 final size:47
Alignment explanation
Indices: 5634953--5635051 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
5634943 AATAATATAG
*
5634953 TTATCTCTTATATATTTAGAGATAATCACAATGCTATTCTCCATGTA
1 TTATCCCTTATATATTTAGAGATAATCACAATGCTATTCTCCATGTA
* *
5635000 TTATCCCTTATATATTTAGAGATAATCACAATGTTATTCTTCATGTA
1 TTATCCCTTATATATTTAGAGATAATCACAATGCTATTCTCCATGTA
5635047 TTATC
1 TTATC
5635052 AAATAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.44
Consensus pattern (47 bp):
TTATCCCTTATATATTTAGAGATAATCACAATGCTATTCTCCATGTA
Found at i:5636634 original size:23 final size:23
Alignment explanation
Indices: 5636594--5636650 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
5636584 AATATGATTT
*
5636594 TAAAATATTTTCATAAT-ATTATAAA
1 TAAAAT-TTTTCAGAATAATT-T-AA
5636619 TAAAATTTTT-AGAATAATTTAA
1 TAAAATTTTTCAGAATAATTTAA
5636641 TATAAATTTT
1 TA-AAATTTT
5636651 ATAAATTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 12 0.41
24 7 0.24
25 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAATTTTTCAGAATAATTTAA
Found at i:5642291 original size:17 final size:18
Alignment explanation
Indices: 5642254--5642293 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5642244 AAAACTTTAA
*
5642254 TTTTAGTCTCGAGAGCAC
1 TTTTAGTCCCGAGAGCAC
*
5642272 TTTTAGTCCCGA-ATCAC
1 TTTTAGTCCCGAGAGCAC
5642289 TTTTA
1 TTTTA
5642294 AAAATCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTTAGTCCCGAGAGCAC
Found at i:5648793 original size:65 final size:65
Alignment explanation
Indices: 5648710--5648840 Score: 217
Period size: 65 Copynumber: 2.0 Consensus size: 65
5648700 GAGAGAACCA
* ** *
5648710 ATTGTTTATAAAAAGGGGAAATGTGCTTTTGTAAACAAAGATTCAATTCTTGGGACACATCATAG
1 ATTGTTTATAAAAAGGGGAAACGTGCTTTCATAAACAAAAATTCAATTCTTGGGACACATCATAG
*
5648775 ATTGTTTATAAAATGGGGAAACGTGCTTTCATAAACAAAAATTCAATTCTTGGGACACATCATAG
1 ATTGTTTATAAAAAGGGGAAACGTGCTTTCATAAACAAAAATTCAATTCTTGGGACACATCATAG
5648840 A
1 A
5648841 ACAAGGGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (65 bp):
ATTGTTTATAAAAAGGGGAAACGTGCTTTCATAAACAAAAATTCAATTCTTGGGACACATCATAG
Found at i:5652599 original size:33 final size:32
Alignment explanation
Indices: 5652557--5652620 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
5652547 ATTCATTTAC
5652557 AAATATTACACATTAAAAAGAAGAAAAAAAGAG
1 AAATATTACACATTAAAAAGAA-AAAAAAAGAG
*
5652590 AAATATTACACATTAAAAAGAAAAGAAAAGA
1 AAATATTACACATTAAAAAGAAAAAAAAAGA
5652621 AATATCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.16
Consensus pattern (32 bp):
AAATATTACACATTAAAAAGAAAAAAAAAGAG
Found at i:5652613 original size:30 final size:32
Alignment explanation
Indices: 5652557--5652625 Score: 99
Period size: 30 Copynumber: 2.2 Consensus size: 32
5652547 ATTCATTTAC
5652557 AAATATTACACATTAAAAAGAAGAAAA-AAAGAG
1 AAATATTACACATT-AAAAGAAGAAAAGAAA-AG
5652590 AAATATTACACATT-AAA-AAGAAAAGAAAAG
1 AAATATTACACATTAAAAGAAGAAAAGAAAAG
5652620 AAATAT
1 AAATAT
5652626 CATTAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 15 0.43
31 6 0.17
33 14 0.40
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (32 bp):
AAATATTACACATTAAAAGAAGAAAAGAAAAG
Found at i:5662854 original size:18 final size:18
Alignment explanation
Indices: 5662831--5662865 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5662821 AGCAGAAGCG
5662831 GCAGCCTGAGCTGCAGCA
1 GCAGCCTGAGCTGCAGCA
*
5662849 GCAGCCTGGGCTGCAGC
1 GCAGCCTGAGCTGCAGC
5662866 TGCTTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.34, G:0.37, T:0.11
Consensus pattern (18 bp):
GCAGCCTGAGCTGCAGCA
Found at i:5668303 original size:6 final size:6
Alignment explanation
Indices: 5668288--5668344 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
5668278 CGAATGCAAT
* * * * *
5668288 ATATAT ATATAC ATAT-- ATATAT ATGTAT ATATAC ATGTAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
5668334 ATATAC ATATA
1 ATATAC ATATA
5668345 TATGTATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
4 4 0.09
6 39 0.91
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (6 bp):
ATATAC
Found at i:5668709 original size:6 final size:6
Alignment explanation
Indices: 5668301--5668701 Score: 595
Period size: 6 Copynumber: 66.8 Consensus size: 6
5668291 TATATATACA
* * * * * * * * *
5668301 TATATA TATATG TATATA TACATG TACATA TACATA TACATA TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
5668349 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
5668397 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
5668445 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * *
5668493 TATATG TATATG TATATG TATATG TATATG TACATG TATATA TACATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * * * * * *
5668541 TATATA TACATA TATATA TATATG TATATA TATATA TATATA TGTATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* *
5668589 TATATA TATATA TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
5668637 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
5668685 TATATG TATATG TATAT
1 TATATG TATATG TATAT
5668702 ATGTATATAT
Statistics
Matches: 374, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 374 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:5679980 original size:23 final size:23
Alignment explanation
Indices: 5679954--5680014 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
5679944 CAGCTCATAT
5679954 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
5679977 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
5680000 AATTGCACCGTAGTG
1 AATTGCACCGAAGTG
5680015 TCATATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:5680207 original size:103 final size:103
Alignment explanation
Indices: 5680028--5680250 Score: 437
Period size: 103 Copynumber: 2.2 Consensus size: 103
5680018 TATAATAATG
5680028 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGAATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGAATCAAGTATGTGTCT
5680093 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
5680131 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGAATCAAGTATGTGTCT
5680196 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
5680234 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
5680251 GACCCTCGAC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGAATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:5681107 original size:64 final size:64
Alignment explanation
Indices: 5680999--5681223 Score: 246
Period size: 64 Copynumber: 3.5 Consensus size: 64
5680989 TAATGAAGGT
* * * * *
5680999 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
5681062 G
64 G
* *
5681063 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* *
5681127 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATT--AATG
*
5681190 AG
63 GG
**
5681192 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
5681224 CTTCAAACAA
Statistics
Matches: 140, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
63 2 0.01
64 128 0.91
65 7 0.05
66 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:5682594 original size:2 final size:2
Alignment explanation
Indices: 5682589--5682615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5682579 TATATATATA
5682589 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
5682616 TGATCACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5683323 original size:2 final size:2
Alignment explanation
Indices: 5683311--5683343 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5683301 TAATGAGAAT
*
5683311 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5683344 TTCAGGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5686704 original size:16 final size:15
Alignment explanation
Indices: 5686678--5686707 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5686668 GTGAAATCCC
5686678 ATGTCTGTCCCTTTA
1 ATGTCTGTCCCTTTA
5686693 ATGTCATGTCCCTTT
1 ATGTC-TGTCCCTTT
5686708 TATAAAATTA
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:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGTCTGTCCCTTTA
Found at i:5689519 original size:22 final size:21
Alignment explanation
Indices: 5689485--5689543 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
5689475 TTATATTTTA
5689485 AATATTT-AAATTATAATAAT
1 AATATTTGAAATTATAATAAT
5689505 AATATCTTGAAATTATAATAAT
1 AATAT-TTGAAATTATAATAAT
*
5689527 AACATTTTTGAAATTAT
1 -A-ATATTTGAAATTAT
5689544 CAAAAGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.15
21 2 0.06
22 13 0.38
23 11 0.32
24 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
AATATTTGAAATTATAATAAT
Found at i:5692634 original size:12 final size:12
Alignment explanation
Indices: 5692617--5692643 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5692607 TACTCATTGG
5692617 TTGACAGGTTGA
1 TTGACAGGTTGA
5692629 TTGACAGGTTGA
1 TTGACAGGTTGA
5692641 TTG
1 TTG
5692644 GATATGACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.37
Consensus pattern (12 bp):
TTGACAGGTTGA
Found at i:5694997 original size:49 final size:49
Alignment explanation
Indices: 5694940--5695090 Score: 302
Period size: 49 Copynumber: 3.1 Consensus size: 49
5694930 TGATGGGAAG
5694940 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
1 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
5694989 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
1 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
5695038 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
1 AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
5695087 AAAG
1 AAAG
5695091 TTAAGCGACT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 102 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.20
Consensus pattern (49 bp):
AAAGAATTTACAAACCATTGCAATCAAAAGACCAAATTGAGTAAAATGC
Found at i:5702603 original size:46 final size:46
Alignment explanation
Indices: 5702552--5702666 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
5702542 CGGGCCAAGC
* *
5702552 TTTAGATTTTCGGGTTAATTC-GTATTGGTTTTTG-TATGGATCAATA
1 TTTAGATTTTCGGGTCAATTCAG-ATTGG-TTTTGATATGGATCAACA
** * *
5702598 TTTAGATTTTTAGGTCAATTCAGATTGGTTTTGATTTGGATCAACC
1 TTTAGATTTTCGGGTCAATTCAGATTGGTTTTGATATGGATCAACA
*
5702644 TTTAGATTTTCGAGTCAATTCAG
1 TTTAGATTTTCGGGTCAATTCAG
5702667 GTTGTTTCGG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
45 5 0.09
46 52 0.90
47 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (46 bp):
TTTAGATTTTCGGGTCAATTCAGATTGGTTTTGATATGGATCAACA
Found at i:5703009 original size:14 final size:14
Alignment explanation
Indices: 5702992--5703018 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5702982 TACATAATAA
5702992 ATATAATTTTTTTC
1 ATATAATTTTTTTC
5703006 ATATAATTTTTTT
1 ATATAATTTTTTT
5703019 TTGGTACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATAATTTTTTTC
Found at i:5704457 original size:23 final size:23
Alignment explanation
Indices: 5704401--5704459 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
5704391 AATATTTCAA
5704401 AAGCTCGATTCAAACTCGATTTT
1 AAGCTCGATTCAAACTCGATTTT
* * *
5704424 AAACCCGATTCAAACTCTATTTT
1 AAGCTCGATTCAAACTCGATTTT
* *
5704447 GAGCTCAATTCAA
1 AAGCTCGATTCAA
5704460 GCTCACTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (23 bp):
AAGCTCGATTCAAACTCGATTTT
Found at i:5705877 original size:156 final size:157
Alignment explanation
Indices: 5705632--5705948 Score: 602
Period size: 156 Copynumber: 2.0 Consensus size: 157
5705622 CCTTGTTTAG
5705632 GATTGTTTTCTTTAATTAGTTGTGTATATTTATTTTGCATGTTGATATGTTTATGTATAAGTATG
1 GATTGTTTTCTTTAATTAGTTGTGTATATTTATTTTGCATGTTGATATGTTTATGTATAAGTATG
5705697 CAAAAGATTTATTTAGGAGTCGTATAACAACATTTTGCATAA-TTGTATGTTACC-TCATGTGTA
66 CAAAAGATTTATTTAGGAGTCGTATAACAACATTTTGCATAATTTGTATGTTACCTTCATGTGTA
5705760 TAACTTAAAACCCTAAACCCTATCTCAT
131 TAACTT-AAACCCTAAACCCTATCTCAT
5705788 GATTGTTTTCTTTAATTAGTTGTGTATATTTATTTTGCATGTTGATATGTTTATGTATAAGTATG
1 GATTGTTTTCTTTAATTAGTTGTGTATATTTATTTTGCATGTTGATATGTTTATGTATAAGTATG
*
5705853 CAAAAGATTTATTTAGGAGTCGTATAACATCATTTTGCATAATTTGTATGTTACCTTCATGTGTA
66 CAAAAGATTTATTTAGGAGTCGTATAACAACATTTTGCATAATTTGTATGTTACCTTCATGTGTA
5705918 TAACTTAAACCCTAAACCCTATCTCAT
131 TAACTTAAACCCTAAACCCTATCTCAT
5705945 GATT
1 GATT
5705949 AGAAGGAATG
Statistics
Matches: 158, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
156 106 0.67
157 37 0.23
158 15 0.09
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.44
Consensus pattern (157 bp):
GATTGTTTTCTTTAATTAGTTGTGTATATTTATTTTGCATGTTGATATGTTTATGTATAAGTATG
CAAAAGATTTATTTAGGAGTCGTATAACAACATTTTGCATAATTTGTATGTTACCTTCATGTGTA
TAACTTAAACCCTAAACCCTATCTCAT
Found at i:5706622 original size:11 final size:11
Alignment explanation
Indices: 5706608--5706670 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
5706598 CTATTATAGA
5706608 ATTTTTAATAT
1 ATTTTTAATAT
5706619 ATTTTTAA-A-
1 ATTTTTAATAT
5706628 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
5706639 ATCAATAATGT
1 ATTTTTAATAT
*
5706650 ATTTTTACTAT
1 ATTTTTAATAT
5706661 ATTTTTAATA
1 ATTTTTAATA
5706671 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:5706653 original size:22 final size:25
Alignment explanation
Indices: 5706627--5706681 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
5706617 ATATTTTTAA
5706627 AATTTTA-TA-ATTATCAATAATGT
1 AATTTTACTATATTATCAATAATGT
* * *
5706650 ATTTTTACTATATTTTTAATAATGT
1 AATTTTACTATATTATCAATAATGT
5706675 AATTTTA
1 AATTTTA
5706682 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.23
24 2 0.08
25 18 0.69
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
AATTTTACTATATTATCAATAATGT
Found at i:5706742 original size:20 final size:20
Alignment explanation
Indices: 5706719--5706756 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5706709 TTTTGAGCTA
5706719 CTCAAGAGCTTTTCGAGTCG
1 CTCAAGAGCTTTTCGAGTCG
*
5706739 CTCAAGAGTTTTTCGAGT
1 CTCAAGAGCTTTTCGAGT
5706757 AGAATATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (20 bp):
CTCAAGAGCTTTTCGAGTCG
Found at i:5707560 original size:41 final size:42
Alignment explanation
Indices: 5707478--5707588 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 42
5707468 TGTGGATCAA
* * * *
5707478 TAGCGGCGTTTGTATAAAAATGCCACTAAATTAGGAGTC-TT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGACTCTTT
*
5707519 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGACTCTTT
5707561 TA-CGGCGTTTGT-TGAAAAAACGCCACTA
1 TAGCGGCGTTTGTAT--AAAAACGCCACTA
5707589 TCGATGAACC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.02
41 44 0.71
42 17 0.27
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGACTCTTT
Found at i:5707775 original size:16 final size:16
Alignment explanation
Indices: 5707754--5707792 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5707744 GGTATTTCCC
* *
5707754 GACCTGTTTTCTACCT
1 GACCTGTTATCAACCT
*
5707770 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
5707786 GACCTGT
1 GACCTGT
5707793 AATTGACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:5707968 original size:18 final size:17
Alignment explanation
Indices: 5707943--5708000 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
5707933 TACTTTTTTA
5707943 AATTTAATTTTTATATT
1 AATTTAATTTTTATATT
*
5707960 AATTATAATTTGTATATTATA
1 AATT-TAATTT-T-TA-TATT
*
5707981 AATTTAGTTTTTATATT
1 AATTTAATTTTTATATT
5707998 AAT
1 AAT
5708001 CCCAATTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 2 0.06
20 7 0.21
21 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
AATTTAATTTTTATATT
Found at i:5707997 original size:20 final size:20
Alignment explanation
Indices: 5707941--5707998 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
5707931 ATTACTTTTT
5707941 TAAATTTAATTTTTATA-T-
1 TAAATTTAATTTTTATATTA
*
5707959 T-AATTATAATTTGTATATTA
1 TAAATT-TAATTTTTATATTA
*
5707979 TAAATTTAGTTTTTATATTA
1 TAAATTTAATTTTTATATTA
5707999 ATCCCAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.12
18 11 0.33
19 1 0.03
20 13 0.39
21 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TAAATTTAATTTTTATATTA
Found at i:5708680 original size:23 final size:23
Alignment explanation
Indices: 5708645--5708702 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
5708635 ATCACTGTAC
5708645 CAATTCAACAAGTATTATTGCAT
1 CAATTCAACAAGTATTATTGCAT
**
5708668 CAATTCAGTAAGTATTATTGCAT
1 CAATTCAACAAGTATTATTGCAT
5708691 CAATTCAACAAG
1 CAATTCAACAAG
5708703 CATCCTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (23 bp):
CAATTCAACAAGTATTATTGCAT
Found at i:5708824 original size:20 final size:20
Alignment explanation
Indices: 5708799--5708852 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5708789 AACTCTTACA
** *
5708799 AATATCAAGTAGAAGCAAGC
1 AATATCAAAAAGAAGCAAAC
5708819 AATATCAAAAAGAAGCAAAC
1 AATATCAAAAAGAAGCAAAC
5708839 AATAT-AAAATAGAA
1 AATATCAAAA-AGAA
5708853 TAAAGCAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.15
Consensus pattern (20 bp):
AATATCAAAAAGAAGCAAAC
Found at i:5710691 original size:6 final size:6
Alignment explanation
Indices: 5710682--5710739 Score: 80
Period size: 6 Copynumber: 9.5 Consensus size: 6
5710672 TTGGATTCGA
* * *
5710682 GTTTGG GTTTGG GTTCGG GTTTGA GTTTGG GTTTGG GTTTTG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
5710730 GTTTCGG GTT
1 GTTT-GG GTT
5710740 AGGGGATAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
6 40 0.89
7 5 0.11
ACGTcount: A:0.02, C:0.03, G:0.45, T:0.50
Consensus pattern (6 bp):
GTTTGG
Found at i:5710698 original size:18 final size:18
Alignment explanation
Indices: 5710672--5710739 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
5710662 TAGGTTATGG
* *
5710672 TTGGATTCGAGTTTGGGT
1 TTGGGTTCGGGTTTGGGT
*
5710690 TTGGGTTCGGGTTTGAGT
1 TTGGGTTCGGGTTTGGGT
* *
5710708 TTGGGTTTGGGTTTTGGT
1 TTGGGTTCGGGTTTGGGT
5710726 TTGGGTTTCGGGTT
1 TTGGG-TTCGGGTT
5710740 AGGGGATAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 35 0.83
19 7 0.17
ACGTcount: A:0.04, C:0.04, G:0.43, T:0.49
Consensus pattern (18 bp):
TTGGGTTCGGGTTTGGGT
Found at i:5710835 original size:45 final size:45
Alignment explanation
Indices: 5710786--5710875 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
5710776 TAAACCAATA
5710786 GTTTGGGTTTTGGTTTTCAGTGTTTGTGAGGATCAAAGAAGGTTT
1 GTTTGGGTTTTGGTTTTCAGTGTTTGTGAGGATCAAAGAAGGTTT
5710831 GTTTGGGTTTTGGTTTTCAGTGTTTGTGAGGATCAAAGAAGGTTT
1 GTTTGGGTTTTGGTTTTCAGTGTTTGTGAGGATCAAAGAAGGTTT
5710876 CGGGACGAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.04, G:0.33, T:0.44
Consensus pattern (45 bp):
GTTTGGGTTTTGGTTTTCAGTGTTTGTGAGGATCAAAGAAGGTTT
Found at i:5711181 original size:111 final size:114
Alignment explanation
Indices: 5710972--5711181 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 114
5710962 GTTTGAGGAA
* *
5710972 GAACACGGATGAACAATGGATGAACTTTTGGGTGTTTGATCGAAAAAAAAACAAGAATGAGTTTT
1 GAACACGAATGAACAATGGATGAACTTTTGGGTGTTTGATC-AAAAAAAAACAAGAATGAGTTTG
* * * *
5711037 GGTTTTGGTATTTGTGAAAATCAAATAATGGTTTGGGGAAGAACTGAGAT
65 GGTTTTAGTATTTCTGAAAATCAAAGAAGGGTTTGGGGAAGAACTGAGAT
*
5711087 GAACACGAATGAAC-ATGAGATGAA-TTTTGGGTGTTTGAT--AAAAAAAACACGAAAT-AGTTT
1 GAACACGAATGAACAATG-GATGAACTTTTGGGTGTTTGATCAAAAAAAAACAAG-AATGAGTTT
* * * *
5711147 GGGTTTTAGTGTTTCTGGAGATCAAAGGAGGGTTT
64 GGGTTTTAGTATTTCTGAAAATCAAAGAAGGGTTT
5711182 TTGGGATGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
111 42 0.51
112 3 0.04
114 18 0.22
115 19 0.23
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (114 bp):
GAACACGAATGAACAATGGATGAACTTTTGGGTGTTTGATCAAAAAAAAACAAGAATGAGTTTGG
GTTTTAGTATTTCTGAAAATCAAAGAAGGGTTTGGGGAAGAACTGAGAT
Found at i:5711462 original size:33 final size:32
Alignment explanation
Indices: 5711425--5711532 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 32
5711415 CCTAGTTTTA
*
5711425 AATTTGTTCAATTTAGTCCAAATTTAATGATGC
1 AATTTATT-AATTTAGTCCAAATTTAATGATGC
* * *
5711458 AATTTATTAATTTAAGCTTCATA-TT--TCA---
1 AATTTATTAATTT-AG-TCCAAATTTAATGATGC
* *
5711486 AATTTCTTCAATTTAGTCCAAATTTAATGCTGC
1 AATTTATT-AATTTAGTCCAAATTTAATGATGC
5711519 AATTTATTAATTTA
1 AATTTATTAATTTA
5711533 AGCTTTATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 19
0.66 0.12 0.22
Matches are distributed among these distances:
27 4 0.07
28 11 0.20
29 5 0.09
30 1 0.02
31 2 0.04
32 11 0.20
33 18 0.32
34 4 0.07
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (32 bp):
AATTTATTAATTTAGTCCAAATTTAATGATGC
Found at i:5711483 original size:21 final size:20
Alignment explanation
Indices: 5711457--5711537 Score: 55
Period size: 20 Copynumber: 4.0 Consensus size: 20
5711447 TTTAATGATG
5711457 CAATTTATTAATTTAAGCTT
1 CAATTTATTAATTTAAGCTT
5711477 CATATTTCA--AATTT---CTT
1 CA-ATTT-ATTAATTTAAGCTT
* *
5711494 CAATTTAGTCCAAATTTAATGCTG
1 CAATTTA-T--TAATTTAA-GCTT
5711518 CAATTTATTAATTTAAGCTT
1 CAATTTATTAATTTAAGCTT
5711538 TATATTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 22
0.65 0.04 0.31
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 5 0.11
20 15 0.32
21 11 0.23
22 1 0.02
23 1 0.02
24 9 0.19
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CAATTTATTAATTTAAGCTT
Found at i:5711500 original size:61 final size:61
Alignment explanation
Indices: 5711424--5711560 Score: 238
Period size: 61 Copynumber: 2.2 Consensus size: 61
5711414 TCCTAGTTTT
*
5711424 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATTTATTAATTTAAGCTTCATATTTC
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATTTATTAATTTAAGCTTCATATTTA
* * *
5711485 AAATTTCTTCAATTTAGTCCAAATTTAATGCTGCAATTTATTAATTTAAGCTTTATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATTTATTAATTTAAGCTTCATATTTA
5711546 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
5711561 GATCCTTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.47
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATTTATTAATTTAAGCTTCATATTTA
Found at i:5711649 original size:33 final size:33
Alignment explanation
Indices: 5711626--5711732 Score: 198
Period size: 33 Copynumber: 3.3 Consensus size: 33
5711616 AGATATAATG
*
5711626 TTATATATACTAATGAACTATATAA-GTATAGT
1 TTATATATACTAATGAACTATATAATATATAGT
5711658 TTATATATACTAATGAACTATATAATATATAGT
1 TTATATATACTAATGAACTATATAATATATAGT
5711691 TTATATATACTAATGAACTATATAATATATAGT
1 TTATATATACTAATGAACTATATAATATATAGT
5711724 TTATATATA
1 TTATATATA
5711733 TTATATAGTT
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 25 0.34
33 48 0.66
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TTATATATACTAATGAACTATATAATATATAGT
Found at i:5711728 original size:9 final size:9
Alignment explanation
Indices: 5711716--5711748 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5711706 AACTATATAA
5711716 TATATAGTT
1 TATATAGTT
5711725 TATATA-TAT
1 TATATAGT-T
5711734 TATATAGTT
1 TATATAGTT
5711743 TATATA
1 TATATA
5711749 TACTAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (9 bp):
TATATAGTT
Found at i:5711799 original size:33 final size:31
Alignment explanation
Indices: 5711626--5711800 Score: 124
Period size: 33 Copynumber: 5.3 Consensus size: 31
5711616 AGATATAATG
*
5711626 TTATATATACTA-ATGAACTATATA-AGTATAGT
1 TTATATATACTATAT--ACTTTATATA-TATAGT
*
5711658 TTATATATACTA-ATGAACTATATAATATATAGT
1 TTATATATACTATAT--ACTTTAT-ATATATAGT
*
5711691 TTATATATACTA-ATGAACTATATAATATATAGT
1 TTATATATACTATAT--ACTTTAT-ATATATAGT
* *
5711724 TTATATATATTATATAGTTTATATATACTAATAGT
1 TTATATATACTATATA-CTT-TATATA-T-ATAGT
* *
5711759 TTGTATATACCATATACTTTATATATATAGATT
1 TTATATATACTATATACTTTATATATATAG--T
5711792 TTATATATA
1 TTATATATA
5711801 GTTCATATGT
Statistics
Matches: 126, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
31 4 0.03
32 25 0.20
33 70 0.56
34 9 0.07
35 18 0.14
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
TTATATATACTATATACTTTATATATATAGT
Found at i:5711808 original size:35 final size:34
Alignment explanation
Indices: 5711682--5711808 Score: 90
Period size: 35 Copynumber: 3.8 Consensus size: 34
5711672 GAACTATATA
* * *
5711682 ATATATAG--TTTATATATACTAATGA-ACTATAT
1 ATATATAGATTTTATATATATTCAT-ATACTTTAT
*
5711714 AATATATAG--TTTATATATATT-ATATAGTTTAT
1 -ATATATAGATTTTATATATATTCATATACTTTAT
* *
5711746 ATATACTA-ATAGTTTGTATATA-CCATATACTTTAT
1 ATATA-TAGAT--TTTATATATATTCATATACTTTAT
5711781 ATATATAGATTTTATATATAGTTCATAT
1 ATATATAGATTTTATATATA-TTCATAT
5711809 GTAAACTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
31 6 0.08
32 9 0.12
33 28 0.37
34 2 0.03
35 31 0.41
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (34 bp):
ATATATAGATTTTATATATATTCATATACTTTAT
Found at i:5711852 original size:18 final size:17
Alignment explanation
Indices: 5711676--5711856 Score: 66
Period size: 18 Copynumber: 10.8 Consensus size: 17
5711666 ACTAATGAAC
*
5711676 TATATAA-TATATAGTT
1 TATATAACTATATAGTA
*
5711692 TATATATACTA-AT-GAA
1 TATATA-ACTATATAGTA
*
5711708 CTATATAA-TATATAGTT
1 -TATATAACTATATAGTA
* *
5711725 TATATATATTATATAGTT
1 TATATA-ACTATATAGTA
*
5711743 TATATATACTA-ATAGTT
1 TATATA-ACTATATAGTA
* * *
5711760 TGTATATACCATATACT-
1 TATATA-ACTATATAGTA
5711777 T-TAT-A-TATATAG-A
1 TATATAACTATATAGTA
*
5711790 T-T-TTA-TATATAGTTCA
1 TATATAACTATATAG-T-A
*
5711806 TATGTAAACTATATAGTA
1 TATAT-AACTATATAGTA
5711824 TATATAAACTATATATGTA
1 TATAT-AACTATATA-GTA
5711843 GTATAT-ACTATATA
1 -TATATAACTATATA
5711857 AATCGTTTAT
Statistics
Matches: 134, Mismatches: 12, Indels: 36
0.74 0.07 0.20
Matches are distributed among these distances:
12 1 0.01
13 15 0.11
14 1 0.01
15 2 0.01
16 21 0.16
17 28 0.21
18 49 0.37
19 5 0.04
20 12 0.09
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (17 bp):
TATATAACTATATAGTA
Found at i:5711935 original size:15 final size:15
Alignment explanation
Indices: 5711920--5711954 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5711910 TACTTTGAAT
5711920 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
5711934 TTATATAAGTATAAA
1 TTATATAAGTATAAA
5711949 TTATAT
1 TTATAT
5711955 TATATAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:5712039 original size:7 final size:6
Alignment explanation
Indices: 5712024--5712139 Score: 65
Period size: 7 Copynumber: 18.0 Consensus size: 6
5712014 ATATGTAAAT
* *
5712024 TATACTA TATAGTA TATAT- TTTATA TATA-A TATATA GTATATA AATATA
1 TATA-TA TATA-TA TATATA TATATA TATATA TATATA -TATATA TATATA
* * * * *
5712073 AACTATA GTATGTA GTATATA AATATA AACTATA GTTTATA TATATA TATATA
1 TA-TATA -TATATA -TATATA TATATA TA-TATA -TATATA TATATA TATATA
5712126 TAGTATA TACTATA
1 TA-TATA TA-TATA
5712140 AAAATAGTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
5 9 0.10
6 32 0.36
7 47 0.53
8 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:5712041 original size:2 final size:2
Alignment explanation
Indices: 5712024--5712139 Score: 65
Period size: 2 Copynumber: 54.0 Consensus size: 2
5712014 ATATGTAAAT
*
5712024 TA TA CTA TA TA GTA TA TA T- TT TA TA TA TA -A TA TA TA GTA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
5712065 TA AA TA TA AA CTA TA GTA TG TA GTA TA TA AA TA TA AA CTA TA GTT
1 TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA -TA
5712110 TA TA TA TA TA TA TA TA TA GTA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
5712140 AAAATAGTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
1 2 0.02
2 70 0.79
3 17 0.19
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5712042 original size:25 final size:24
Alignment explanation
Indices: 5712003--5712093 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 24
5711993 TATGGTTTTT
5712003 ATATATAGT-TCATATGTAAATTATA
1 ATATATAGTAT-ATAT-TAAATTATA
* **
5712028 CTATATAGTATATATTTTATATATA
1 ATATATAGTATATATTAAAT-TATA
*
5712053 ATATATAGTATATAAATATAAACTATA
1 ATATATAGTATAT--AT-TAAATTATA
* *
5712080 GTATGTAGTATATA
1 ATATATAGTATATA
5712094 AATATAAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
24 3 0.06
25 29 0.56
26 1 0.02
27 17 0.33
28 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (24 bp):
ATATATAGTATATATTAAATTATA
Found at i:5712079 original size:27 final size:27
Alignment explanation
Indices: 5712065--5712125 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
5712055 ATATAGTATA
*
5712065 TAAATATAAACTATAGTATGTAGTATA
1 TAAATATAAACTATAGTATATAGTATA
*
5712092 TAAATATAAACTATAGTTTATA-TATA
1 TAAATATAAACTATAGTATATAGTATA
*
5712118 TATATATA
1 TAAATATA
5712126 TAGTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (27 bp):
TAAATATAAACTATAGTATATAGTATA
Found at i:5712180 original size:24 final size:24
Alignment explanation
Indices: 5712151--5712198 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5712141 AAATAGTTTC
5712151 TATAGTTCACTA-ATAAACTATATA
1 TATAGTTCA-TATATAAACTATATA
*
5712175 TATAGTTCATATGTAAACTATATA
1 TATAGTTCATATATAAACTATATA
5712199 GTTTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (24 bp):
TATAGTTCATATATAAACTATATA
Found at i:5712206 original size:33 final size:33
Alignment explanation
Indices: 5712169--5712262 Score: 188
Period size: 33 Copynumber: 2.8 Consensus size: 33
5712159 ACTAATAAAC
5712169 TATATATATAGTTCATATGTAAACTATATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTT
5712202 TATATATATAGTTCATATGTAAACTATATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTT
5712235 TATATATATAGTTCATATGTAAACTATA
1 TATATATATAGTTCATATGTAAACTATA
5712263 GTTCATATGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (33 bp):
TATATATATAGTTCATATGTAAACTATATAGTT
Found at i:5712373 original size:20 final size:20
Alignment explanation
Indices: 5712350--5712453 Score: 56
Period size: 20 Copynumber: 5.1 Consensus size: 20
5712340 ATATGTAAAC
5712350 TATAGTTTATATATCAACTA
1 TATAGTTTATATATCAACTA
*
5712370 TATAATTTATAT-TC-A-TA
1 TATAGTTTATATATCAACTA
* * *
5712387 TGTAAATTATACTATAT-ATACTC
1 TAT-AGTT-TA-TATATCA-ACTA
*
5712410 TATAGTTTATATAT-ATAATA
1 TATAGTTTATATATCA-ACTA
*
5712430 TATAGTATATAAATATCAACTA
1 TATAGT-T-TATATATCAACTA
5712452 TA
1 TA
5712454 GTATGTAGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
17 4 0.06
18 5 0.08
19 4 0.06
20 29 0.45
21 4 0.06
22 15 0.23
23 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAGTTTATATATCAACTA
Found at i:5712405 original size:91 final size:92
Alignment explanation
Indices: 5712208--5712426 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 92
5712198 AGTTTATATA
* * *
5712208 TATAGTTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCATATGT
1 TATAGCTCATATAT-AACTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCATATAT
*
5712273 AAATATCAACTATAGTTTATACGTAAAC
65 AAATATCAACTATAGTTCATACGTAAAC
* * *
5712301 TATAGTTCGTATATAACCTATATAGTTTATATATA-A-TTCATATGTAAACTATAGTTTATATAT
1 TATAGCTCATATATAA-CTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCATATAT
* * *
5712364 CAACTATAT-AATTTATA-TTCATATGTAAAT
65 -AA--ATATCAA-CTATAGTTCATACGTAAAC
*
5712394 TATA-CT-ATATAT-ACTCTATAGTTTATATATATA
1 TATAGCTCATATATAACTATATAGTTTATATATATA
5712427 ATATATAGTA
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
89 17 0.16
90 2 0.02
91 30 0.28
92 6 0.06
93 46 0.42
94 8 0.07
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (92 bp):
TATAGCTCATATATAACTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCATATATA
AATATCAACTATAGTTCATACGTAAAC
Found at i:5712425 original size:44 final size:43
Alignment explanation
Indices: 5712321--5712425 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 43
5712311 ATATAACCTA
* *
5712321 TATAGTTTATATATAATTCATATGTAAACTATAGTTTATATATC
1 TATAGTTTATATAT-ATTCATATGTAAACTATACTATATATATC
* * * *
5712365 AACTA-TATAATTTATATTCATATGTAAATTATACTATATATACTC
1 TA-TAGT-TTATATATATTCATATGTAAACTATACTATATATA-TC
5712410 TATAGTTTATATATAT
1 TATAGTTTATATATAT
5712426 AATATATAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
44 36 0.75
45 12 0.25
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (43 bp):
TATAGTTTATATATATTCATATGTAAACTATACTATATATATC
Found at i:5712427 original size:91 final size:93
Alignment explanation
Indices: 5712225--5712428 Score: 228
Period size: 91 Copynumber: 2.2 Consensus size: 93
5712215 CATATGTAAA
* *
5712225 CTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCATATGTAAATATCAACTATAGTT
1 CTATATAGTTTATATATATAATTCATATGTAAACTATAGTTCATATATAAATATCAACTATAGTT
* *
5712290 TATACGTAAACTATAGTTCGTATATAAC
66 CATACGTAAACTATAGTACGTATATAAC
* *
5712318 CTATATAG-TT-TATATATAATTCATATGTAAACTATAGTTTATATATCAACTATAT-AATTTAT
1 CTATATAGTTTATATATATAATTCATATGTAAACTATAGTTCATATAT-AA--ATATCAA-CTAT
*
5712380 A-TTCATATGTAAA-T-TA-TAC-TATATATA-
62 AGTTCATACGTAAACTATAGTACGTATATA-AC
*
5712407 CTCTATAGTTTATATATATAAT
1 CTATATAGTTTATATATATAAT
5712429 ATATAGTATA
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
89 13 0.14
90 5 0.05
91 45 0.47
92 5 0.05
93 20 0.21
94 8 0.08
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (93 bp):
CTATATAGTTTATATATATAATTCATATGTAAACTATAGTTCATATATAAATATCAACTATAGTT
CATACGTAAACTATAGTACGTATATAAC
Found at i:5712453 original size:27 final size:27
Alignment explanation
Indices: 5712423--5712493 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
5712413 AGTTTATATA
* *
5712423 TATAATATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATAAAC
*
5712450 TATAGTATGTAGTATATAAATATAAAC
1 TATAGTATATAGTATATAAATATAAAC
*
5712477 TATAGTTTATA-TATATA
1 TATAGTATATAGTATATA
5712494 GTGTATACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATAAAC
Found at i:5712473 original size:20 final size:19
Alignment explanation
Indices: 5712410--5712509 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 19
5712400 ATATATACTC
*
5712410 TATAGTTTATATATATAATA
1 TATAGTATATATATATAA-A
* *
5712430 TATAGTATATAAATATCAAC
1 TATAGTATATATATAT-AAA
*
5712450 TATAGTATGTAGTATATAAA
1 TATAGTATATA-TATATAAA
* * *
5712470 TATA-AACTATAGTTTATATA
1 TATAGTA-TATA-TATATAAA
*
5712490 TATAGTGTATACTATATAAA
1 TATAGTATATA-TATATAAA
5712510 CAATTTATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
19 1 0.02
20 54 0.89
21 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (19 bp):
TATAGTATATATATATAAA
Found at i:5712780 original size:33 final size:32
Alignment explanation
Indices: 5712732--5712811 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
5712722 ATATATTATT
*
5712732 TATAA-TTATACATAATAT-ATAAATATAAATTG
1 TATAATTTATATATAATATCAT--ATATAAATTG
*
5712764 TATAGTTTATATATAAT-TCATATATAAATTG
1 TATAATTTATATATAATATCATATATAAATTG
5712795 TATAATTTATAT-TAATA
1 TATAATTTATATATAATA
5712812 AAGTATGTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 4 0.10
31 21 0.50
32 5 0.12
33 12 0.29
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (32 bp):
TATAATTTATATATAATATCATATATAAATTG
Found at i:5713370 original size:216 final size:217
Alignment explanation
Indices: 5713007--5713480 Score: 801
Period size: 216 Copynumber: 2.2 Consensus size: 217
5712997 ACATTTAGTC
*
5713007 TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATTTGAAATTGGCCCATACTTA
1 TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCCCATACTTA
* *
5713072 TTACTTATTTATATTTTTTTAATTGGCCCATAACTTTTTAAATGGGCATAATTTAGTACTTTTTT
66 TTACTTATTTATATTTTTTAAATTGGCCCATAACTTTTTAAATGAGCATAATTTAGTACTTTTTT
5713137 GTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTT
131 GTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTG-TT
* *
5713202 TAATTTATTTAAATTTTTAA-TTG
195 TAATTTATTTAAA-TTTAAATTTA
5713225 TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATT-GCCCATACTTA
1 TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCCCATACTTA
*
5713289 TTACTTATTTATA-TTTTTAAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTTTTT
66 TTACTTATTTATATTTTTTAAATTGGCCCATAACTTTTTAAATGAGCATAATTTAGTACTTTTTT
* * *
5713353 GTTTTAATTTCAACCTCACAATTTAAAATTATTTTGATTTGATCCCTCATCAATGTGTGTTGTTT
131 GTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTT
5713418 AATTTATTTAAATTTAAATTTA
196 AATTTATTTAAATTTAAATTTA
* * *
5713440 TAATTTCATATTTGTTCAATTTAGTTCTTAAATTTGTATTT
1 TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTT
5713481 TTCATAAAAT
Statistics
Matches: 243, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
214 5 0.02
215 55 0.23
216 107 0.44
217 24 0.10
218 52 0.21
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.50
Consensus pattern (217 bp):
TAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCCCATACTTA
TTACTTATTTATATTTTTTAAATTGGCCCATAACTTTTTAAATGAGCATAATTTAGTACTTTTTT
GTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTT
AATTTATTTAAATTTAAATTTA
Found at i:5714044 original size:37 final size:37
Alignment explanation
Indices: 5714003--5714077 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
5713993 TCCTTTAGAA
5714003 ATAATAATTATGGGTACTCTTGTCCCTTTTCTGCTAT
1 ATAATAATTATGGGTACTCTTGTCCCTTTTCTGCTAT
5714040 ATAATAATTATGGGTACTCTTGTCCCTTTTCTGCTAT
1 ATAATAATTATGGGTACTCTTGTCCCTTTTCTGCTAT
5714077 A
1 A
5714078 GATAGTGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (37 bp):
ATAATAATTATGGGTACTCTTGTCCCTTTTCTGCTAT
Found at i:5714099 original size:18 final size:18
Alignment explanation
Indices: 5714076--5714111 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5714066 TTTTCTGCTA
*
5714076 TAGATAGTGGTGTTTGAG
1 TAGATAGTGGTGCTTGAG
5714094 TAGATAGTGGTGCTTGAG
1 TAGATAGTGGTGCTTGAG
5714112 AATTTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.39, T:0.36
Consensus pattern (18 bp):
TAGATAGTGGTGCTTGAG
Found at i:5714641 original size:2 final size:2
Alignment explanation
Indices: 5714634--5714663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5714624 CTGCATCCAA
5714634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5714664 CAAAATACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5716556 original size:21 final size:20
Alignment explanation
Indices: 5716532--5716580 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
5716522 TATATATATT
5716532 TTAATTAAATCAATATTTTTA
1 TTAATTAAAT-AATATTTTTA
*
5716553 TTAAATAAAAATAATATTTTTA
1 TT-AAT-TAAATAATATTTTTA
5716575 TTAATT
1 TTAATT
5716581 CGGGTTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 5 0.21
22 15 0.62
23 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTAAATAATATTTTTA
Found at i:5717277 original size:63 final size:63
Alignment explanation
Indices: 5717175--5717315 Score: 160
Period size: 63 Copynumber: 2.3 Consensus size: 63
5717165 ATAAACATCA
* * * * *
5717175 GTTCGAGTCGGGTCAAATCGGGTCGGTTGGTTTGTGAGTCGAGTCAAAATCAGATCGGTTAAT
1 GTTCGAGTCGGGTTAAATCGGATAGGTTGGTTTGCGAGTCGAGTCAAAATCAGATCAGTTAAT
* * * *
5717238 GTTCGAGTCGGGTTAATCTCGGATAGGTTGGTTT-CGAGTCGGGTCAATATCAGATCAGTTAGT
1 GTTCGAGTCGGGTTAA-ATCGGATAGGTTGGTTTGCGAGTCGAGTCAAAATCAGATCAGTTAAT
* *
5717301 -TTCAATTCGGGTTAA
1 GTTCGAGTCGGGTTAA
5717316 GCTTTAGATT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
62 13 0.20
63 39 0.59
64 14 0.21
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (63 bp):
GTTCGAGTCGGGTTAAATCGGATAGGTTGGTTTGCGAGTCGAGTCAAAATCAGATCAGTTAAT
Found at i:5717303 original size:31 final size:31
Alignment explanation
Indices: 5717176--5717312 Score: 98
Period size: 31 Copynumber: 4.4 Consensus size: 31
5717166 TAAACATCAG
* * * *
5717176 TTCGAGTCGGGTCAA-ATCGGGTCGGTTGGT
1 TTCGAGTCGGGTCAATATCAGATCAGTTAGT
* * * * *
5717206 TTGTGAGTCGAGTCAAAATCAGATCGGTTAAT
1 TT-CGAGTCGGGTCAATATCAGATCAGTTAGT
* * * *
5717238 GTTCGAGTCGGGTTAATCTCGGAT-AGGTTGGT
1 -TTCGAGTCGGGTCAATATCAGATCA-GTTAGT
5717270 TTCGAGTCGGGTCAATATCAGATCAGTTAGT
1 TTCGAGTCGGGTCAATATCAGATCAGTTAGT
* *
5717301 TTCAATTCGGGT
1 TTCGAGTCGGGT
5717313 TAAGCTTTAG
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
30 2 0.02
31 46 0.57
32 31 0.38
33 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (31 bp):
TTCGAGTCGGGTCAATATCAGATCAGTTAGT
Found at i:5717747 original size:2 final size:2
Alignment explanation
Indices: 5717740--5717796 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
5717730 TCATTCACAT
5717740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5717782 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
5717797 GTTTGAAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5717907 original size:36 final size:37
Alignment explanation
Indices: 5717810--5718052 Score: 230
Period size: 39 Copynumber: 6.5 Consensus size: 37
5717800 TGAAAATGGT
5717810 TTTTGAAAATAC-ATATAATATATAGGTTTTTTAAAA-AC
1 TTTTGAAAAT-CTATATAATATATA-G-TTTTTAAAACAC
* * *
5717848 ATTTTGAAAATGTATATAGTATATAGTTTTTAAGACAC
1 -TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
*
5717886 TTTTGAAAA-CTATATAATATATAGTTTTTAAAATA-
1 TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
* *
5717921 TTTTAGAAAA-ATATATAATATAT-GATTTTTAAAATCATT
1 TTTT-GAAAATCTATATAATATATAG-TTTTTAAAA-CA-C
* *
5717960 TTTTGAAAACCTATATAATATATAGTTTTTGAAAACAT
1 TTTTGAAAATCTATATAATATATAGTTTTT-AAAACAC
* * *
5717998 TTTTGAAAACTTCTATATAATATATAATTTTCAAAACTC
1 TTTTGAAAA--TCTATATAATATATAGTTTTTAAAACAC
*
5718037 TTTTGGAAAT-TATATA
1 TTTTGAAAATCTATATA
5718053 GTTTAAAAAA
Statistics
Matches: 176, Mismatches: 16, Indels: 27
0.80 0.07 0.12
Matches are distributed among these distances:
35 5 0.03
36 54 0.31
37 19 0.11
38 18 0.10
39 57 0.32
40 23 0.13
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATCTATATAATATATAGTTTTTAAAACAC
Found at i:5718073 original size:32 final size:32
Alignment explanation
Indices: 5718037--5718111 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
5718027 TTCAAAACTC
*
5718037 TTTTGGAAATTATATAGTTTAAAAAAAAACAT
1 TTTTGAAAATTATATAGTTTAAAAAAAAACAT
***
5718069 TTTTGAAAATTATATAGTTTTTTAAAAAACAT
1 TTTTGAAAATTATATAGTTTAAAAAAAAACAT
5718101 TTTTGAAAATT
1 TTTTGAAAATT
5718112 TTTATATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTGAAAATTATATAGTTTAAAAAAAAACAT
Found at i:5718210 original size:10 final size:10
Alignment explanation
Indices: 5718186--5718245 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
5718176 AAAAAAATAT
5718186 TTATTTATTTA
1 TTATTTA-TTA
5718197 TTA-TTATTA
1 TTATTTATTA
*
5718206 TT-TATTACTA
1 TTAT-TTATTA
5718216 TTATTTATTA
1 TTATTTATTA
*
5718226 TTATTTCTTA
1 TTATTTATTA
5718236 TTCATTTATT
1 TT-ATTTATT
5718246 TTTCTGTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTTATTA
Found at i:5718237 original size:13 final size:13
Alignment explanation
Indices: 5718190--5718230 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
5718180 AAATATTTAT
5718190 TTATTTATTATTA
1 TTATTTATTATTA
*
5718203 TTATTTATTACTA
1 TTATTTATTATTA
5718216 TTATTTATTATTA
1 TTATTTATTATTA
5718229 TT
1 TT
5718231 TCTTATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:5719679 original size:22 final size:21
Alignment explanation
Indices: 5719630--5719697 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5719620 ACTTTTCATT
** *
5719630 TTTTTTTCATTTTTTAAAAATA
1 TTTTTTTCA-TTTTTATTATTA
5719652 TTTTTTTCATTTTTATTATTA
1 TTTTTTTCATTTTTATTATTA
* *
5719673 TTCTTTTC-TTTTTTTTATATA
1 TTTTTTTCATTTTTATTAT-TA
5719694 TTTT
1 TTTT
5719698 ATTGCCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.23
21 21 0.54
22 9 0.23
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTCATTTTTATTATTA
Found at i:5720201 original size:2 final size:2
Alignment explanation
Indices: 5720194--5720218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5720184 GGCCGTGACA
5720194 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5720219 ATTATTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5723934 original size:6 final size:6
Alignment explanation
Indices: 5723923--5723948 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5723913 GGTATTGGAA
5723923 AAGGAG AAGGAG AAGGAG AAGGAG AA
1 AAGGAG AAGGAG AAGGAG AAGGAG AA
5723949 AGTGGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:5724824 original size:15 final size:15
Alignment explanation
Indices: 5724804--5724833 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5724794 ACAAGAATTC
5724804 AAAGTATACCTGGAA
1 AAAGTATACCTGGAA
5724819 AAAGTATACCTGGAA
1 AAAGTATACCTGGAA
5724834 GAATAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AAAGTATACCTGGAA
Found at i:5727290 original size:249 final size:258
Alignment explanation
Indices: 5726914--5727437 Score: 618
Period size: 263 Copynumber: 2.0 Consensus size: 258
5726904 CTAATTACTT
* *
5726914 AAAATAGATAATAATAGTTAATAAATAAATAATATATTCTCTTAGATTCAATTACGGGTTAAAAT
1 AAAATAGATAATAATAGTTAATAAATAAATAATATATTCACTTAGATTCAATTACGAGTTAAAA-
* * *
5726979 CGGGTCAAAGTTCGGTTCGGATCGAGTATGAGAAAATTAATTTTGGATTGCTTTCGGTTCGGATT
65 --GGTC--A--TCAGTTCGGATCAAGTATGAGAAAATTAATTTTAGATTGCTTTCGGTTCGGATT
* * * *
5727044 -A-A-T-TT-C-GATTCTGATTGATTTTGGTTATACTATAATTCGGGTCGGTTTTAGGTCGATTC
124 GATAGTGTTGCTGATTCGGATTGATTTTGGTTAAACTATAATTCGGGTCGGTTTCAGGTCAATTC
* * * *
5727103 GATTTATTTCGCGATTCATATCAATTTTGAGTTATCGTATACAAGTTTATATCAAGTCTTGATTC
189 GATTTATTTCACGATTCATATCAATTTTAAGTTATCATATACAAGTCTATATCAAGTCTTGATTC
5727168 ATATA
254 ATATA
*
5727173 AAAATAGATAATAATAGTTAATAAATAAATAATTTATTCACTTAGATTCAATTATCGAGTT-AAA
1 AAAATAGATAATAATAGTTAATAAATAAATAATATATTCACTTAGATTCAATTA-CGAGTTAAAA
* *
5727237 -G-C-TCAGTTCGGATCAAGTATGAGTAAATTAATTTTAGATTGTTTTCGGTTCGGATTGATTTA
65 GGTCATCAGTTCGGATCAAGTATGAGAAAATTAATTTTAGATTGCTTTCGGTTCGGATTGA--TA
* * * *
5727299 GGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTTGGTTTCAGTTCAAT
128 -G-T--GTTGC--TGATTCGGATTGATTTTGGTTAAACTATAATTCGGGTCGGTTTCAGGTCAAT
* * * *
5727364 TCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTATATCAAGTCTTGAT
187 TCGATTTATTTCACGATTCATATCAATTTTAAGTTATCATATACAAGTCTATATCAAGTCTTGAT
5727429 TCATATA
252 TCATATA
5727436 AA
1 AA
5727438 TAAGTTCAAG
Statistics
Matches: 226, Mismatches: 24, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
249 49 0.22
250 1 0.00
253 1 0.00
254 1 0.00
255 1 0.00
256 1 0.00
259 57 0.25
260 6 0.03
263 109 0.48
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (258 bp):
AAAATAGATAATAATAGTTAATAAATAAATAATATATTCACTTAGATTCAATTACGAGTTAAAAG
GTCATCAGTTCGGATCAAGTATGAGAAAATTAATTTTAGATTGCTTTCGGTTCGGATTGATAGTG
TTGCTGATTCGGATTGATTTTGGTTAAACTATAATTCGGGTCGGTTTCAGGTCAATTCGATTTAT
TTCACGATTCATATCAATTTTAAGTTATCATATACAAGTCTATATCAAGTCTTGATTCATATA
Found at i:5727680 original size:227 final size:231
Alignment explanation
Indices: 5727285--5727743 Score: 881
Period size: 227 Copynumber: 2.0 Consensus size: 231
5727275 TTGTTTTCGG
5727285 TTCGGATTGATTTAGGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTT
1 TTCGGATTGATTTAGGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTT
5727350 GGTTTCAGTTCAATTCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTA
66 GGTTTCAGTTCAATTCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTA
5727415 TATCAAGTCTTGATTCATATAAATAAGTTCAAGTAATCGAGTAC-G-AACTTTATCCGGTCTAAT
131 TATCAAGTCTTGATTCATATAAATAAGTTCAAGTAATCGAGTACAGTAACTTTATCCGGTCTAAT
5727478 TATAATCGGTGGTTG-T-TGAAATTAGATAATGTAT
196 TATAATCGGTGGTTGTTCTGAAATTAGATAATGTAT
5727512 TTCGGATTGATTTAGGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTT
1 TTCGGATTGATTTAGGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTT
5727577 GGTTTCAGTTCAATTCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTA
66 GGTTTCAGTTCAATTCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTA
5727642 TATCAAGTCTTGATTCATATAAATAAGTTCAAGTAATCGAGTACGAGTAACTTTATCCGGTCTAA
131 TATCAAGTCTTGATTCATATAAATAAGTTCAAGTAATCGAGTAC-AGTAACTTTATCCGGTCTAA
5727707 TTATAATCGGTGGTTGTTCTGAAATTAGATAATGTAT
195 TTATAATCGGTGGTTGTTCTGAAATTAGATAATGTAT
5727744 CTTTGCATAC
Statistics
Matches: 227, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
227 174 0.77
229 1 0.00
230 33 0.15
231 1 0.00
232 18 0.08
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (231 bp):
TTCGGATTGATTTAGGTTCGGTTGCTTTGATTCGGGTTGCTTTTGGTTAAACTATAATTCGGGTT
GGTTTCAGTTCAATTCGATTTATTTCACGTTTCCTATCAATTTTAAGTTATCATATGCAGGTCTA
TATCAAGTCTTGATTCATATAAATAAGTTCAAGTAATCGAGTACAGTAACTTTATCCGGTCTAAT
TATAATCGGTGGTTGTTCTGAAATTAGATAATGTAT
Found at i:5730734 original size:17 final size:19
Alignment explanation
Indices: 5730698--5730736 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
5730688 ACAAAACTAT
5730698 TATTTCTTATGCACATCAA
1 TATTTCTTATGCACATCAA
*
5730717 TATTT-TTAT-CAGATCAA
1 TATTTCTTATGCACATCAA
5730734 TAT
1 TAT
5730737 GTCTGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
TATTTCTTATGCACATCAA
Found at i:5734543 original size:162 final size:161
Alignment explanation
Indices: 5734334--5734732 Score: 566
Period size: 162 Copynumber: 2.5 Consensus size: 161
5734324 TATATATAGA
* * * * *
5734334 GATATATATAATAACTGAATCCATGTACTTTACTAGTATTGAAACTATGATTTTTGTTAATAGCA
1 GATATATAT-ATGACTGAATCCATGTACCTTGCTAGTATTGAAACTATGGTTATTGTTAATAGCA
*
5734399 GAATCCTAGTATTAAATCCATGTACATTTATGATCCATTTTCATTCATCCAATGATACTAAAAAT
65 GAATCCTAGTATTAAATCCATGTACATTTATGATCCATTTTCATTCATCCAATGATACTAAAAAA
* ** * *
5734464 GTAGCTTTATGACCTCTTATATGTGTGTGTGT
130 GTAACACTATGACCTCATATACGTGTGTGTGT
* * *
5734496 GGATATATATATGACTTAATCCATGTACCTTGCTAGTATTCAAACTATGGTTATTGTTAATGGCA
1 -GATATATATATGACTGAATCCATGTACCTTGCTAGTATTGAAACTATGGTTATTGTTAATAGCA
*
5734561 GAATCCTAGTATTAAATCCATGTACATTTATGATTCATTTTCATTCATCCAATGATACTAAAAAA
65 GAATCCTAGTATTAAATCCATGTACATTTATGATCCATTTTCATTCATCCAATGATACTAAAAAA
* *
5734626 GTAACACTATTACTTCATATACGTGTGTGTGT
130 GTAACACTATGACCTCATATACGTGTGTGTGT
* * *
5734658 -ATGGATATATATGACTGAATCCATATACCTTGGTAATATTGAAACTATGGTTATTGTTAATAGC
1 GAT--ATATATATGACTGAATCCATGTACCTTGCTAGTATTGAAACTATGGTTATTGTTAATAGC
*
5734722 ATAATCCTAGT
64 AGAATCCTAGT
5734733 TTTTCTTGGT
Statistics
Matches: 210, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
160 2 0.01
162 199 0.95
163 9 0.04
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (161 bp):
GATATATATATGACTGAATCCATGTACCTTGCTAGTATTGAAACTATGGTTATTGTTAATAGCAG
AATCCTAGTATTAAATCCATGTACATTTATGATCCATTTTCATTCATCCAATGATACTAAAAAAG
TAACACTATGACCTCATATACGTGTGTGTGT
Found at i:5736802 original size:27 final size:27
Alignment explanation
Indices: 5736744--5736803 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5736734 CCCGAATATT
**
5736744 ATTAACCGAATTATTTTTACTTTAACT
1 ATTAACCGAATTATTTTTACTTTAAAA
* *
5736771 GTTAACCGAATTGATTTTT-TTTTAAAA
1 ATTAACCGAATT-ATTTTTACTTTAAAA
5736798 ATTAAC
1 ATTAAC
5736804 TGAACCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (27 bp):
ATTAACCGAATTATTTTTACTTTAAAA
Found at i:5737860 original size:20 final size:21
Alignment explanation
Indices: 5737824--5737879 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
5737814 GGATTAGCAC
*
5737824 AGAACCGG-TAAAGAACC-AGA
1 AGAACCGGCTGAA-AACCGAGA
* *
5737844 AGAACCGGCTGAAAACCGGGG
1 AGAACCGGCTGAAAACCGAGA
*
5737865 TGAACCGGCTGAAAA
1 AGAACCGGCTGAAAA
5737880 TCGGCAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.41, C:0.21, G:0.30, T:0.07
Consensus pattern (21 bp):
AGAACCGGCTGAAAACCGAGA
Found at i:5738152 original size:24 final size:24
Alignment explanation
Indices: 5738123--5738180 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
5738113 ATTAGAAGTT
5738123 CAATTGAAGCCTAAAATTTGAGCA
1 CAATTGAAGCCTAAAATTTGAGCA
*
5738147 CAATTGAAGCCTAAAATTTGAGCT
1 CAATTGAAGCCTAAAATTTGAGCA
5738171 CAATTGAAGC
1 CAATTGAAGC
5738181 GAAAGAATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
CAATTGAAGCCTAAAATTTGAGCA
Found at i:5739924 original size:112 final size:112
Alignment explanation
Indices: 5739779--5740003 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
5739769 TCGTAAGAGT
5739779 GACAATGAAATAAACCACATAACTGCCCTCCACCCGTACACCATATGCAGTCCCATGATTTATCC
1 GACAATGAAATAAACCACATAACTGCCCTCCACCCGTACACCATATGCAGTCCCATGATTTATCC
5739844 CATGGAGTGCTTTGGGGCCTGAGAGCCTATCCAAGAAAGTTTATTGG
66 CATGGAGTGCTTTGGGGCCTGAGAGCCTATCCAAGAAAGTTTATTGG
5739891 GACAATGAAATAAACCACATAACTGCCCTCCACCCGTACACCATATGCAGTCCCATGATTTATCC
1 GACAATGAAATAAACCACATAACTGCCCTCCACCCGTACACCATATGCAGTCCCATGATTTATCC
5739956 CATGGAGTGCTTTGGGGCCTGAGAGCCTATCCAAGAAAGTTTATTGG
66 CATGGAGTGCTTTGGGGCCTGAGAGCCTATCCAAGAAAGTTTATTGG
5740003 G
1 G
5740004 GCCTCGGAGC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (112 bp):
GACAATGAAATAAACCACATAACTGCCCTCCACCCGTACACCATATGCAGTCCCATGATTTATCC
CATGGAGTGCTTTGGGGCCTGAGAGCCTATCCAAGAAAGTTTATTGG
Found at i:5742425 original size:22 final size:22
Alignment explanation
Indices: 5742397--5742471 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
5742387 TCAGCTGTTA
5742397 TAACTCCTGAAATTACATCATG
1 TAACTCCTGAAATTACATCATG
5742419 TAACTCCTGAAATTACATCATG
1 TAACTCCTGAAATTACATCATG
* * *
5742441 TAACTCTTGAAATTAAATCATA
1 TAACTCCTGAAATTACATCATG
5742463 TAACTCCTG
1 TAACTCCTG
5742472 TAACTCCTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.33
Consensus pattern (22 bp):
TAACTCCTGAAATTACATCATG
Found at i:5748296 original size:22 final size:22
Alignment explanation
Indices: 5748266--5748317 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5748256 ATTTAGTTGT
*
5748266 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
*
5748288 TGTAACTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
5748310 TATAACTC
1 TATAACTC
5748318 GTGCAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:5753033 original size:114 final size:112
Alignment explanation
Indices: 5752833--5753053 Score: 374
Period size: 114 Copynumber: 2.0 Consensus size: 112
5752823 CTCTTATCTC
*
5752833 ATTGTGTACAAGAGGAATAAATGTTGAAGCAAGACAAAATTGAAAGTGCTCATTTGTCATGTGCC
1 ATTGTGTACAAGAGGAATAAATGTTGAAGCAAGACAAAACTGAAAGTGCTCATTTGTCATGTGCC
5752898 TCTAAAGATACAGGCAAAAAAAAGAAAAGAAAAATCAGAATGAAGTTGT
66 TCTAAAGATACAGGC-AAAAAAA-AAAAGAAAAATCAGAATGAAGTTGT
*
5752947 ATTGTGTGCAAGAGGAATAAATGTTGAAGCAAGACAAAACTGAAAGTGCTCATTTGGT-ATGTGC
1 ATTGTGTACAAGAGGAATAAATGTTGAAGCAAGACAAAACTGAAAGTGCTCATTT-GTCATGTGC
*
5753011 CTCT-AAGATACGGGCAAAAAAAAAAAGAAAAATCAGAATGAAG
65 CTCTAAAGATACAGGCAAAAAAAAAAAGAAAAATCAGAATGAAG
5753054 CTGTTAAAGA
Statistics
Matches: 103, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
111 21 0.20
112 7 0.07
113 10 0.10
114 63 0.61
115 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (112 bp):
ATTGTGTACAAGAGGAATAAATGTTGAAGCAAGACAAAACTGAAAGTGCTCATTTGTCATGTGCC
TCTAAAGATACAGGCAAAAAAAAAAAGAAAAATCAGAATGAAGTTGT
Found at i:5756704 original size:21 final size:22
Alignment explanation
Indices: 5756669--5756750 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 22
5756659 CAGAACTCAT
* *
5756669 GGGGGTATCGATTCCC-T-AAA
1 GGGGGAATCGGTTCCCATCAAA
5756689 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCCA-TCAAA
*
5756713 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTT-CCCATCAAA
* *
5756735 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
5756751 TCTGTCCTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 2 0.04
21 15 0.29
22 13 0.25
23 14 0.27
24 8 0.15
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCATCAAA
Found at i:5756739 original size:22 final size:23
Alignment explanation
Indices: 5756686--5756750 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
5756676 TCGATTCCCT
5756686 AAAGGAGGGAATCGGTTCCCATTC
1 AAAGG-GGGAATCGGTTCCCATTC
*
5756710 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
* *
5756733 -AAGGGGGTATCGATTCCC
1 AAAGGGGGAATCGGTTCCC
5756751 TCTGTCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 16 0.42
23 17 0.45
24 5 0.13
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.22
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:5758217 original size:18 final size:18
Alignment explanation
Indices: 5758194--5758229 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5758184 ACCGGTCACA
5758194 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
5758212 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
5758230 TTGACCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:5760874 original size:24 final size:24
Alignment explanation
Indices: 5760768--5760874 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
5760758 ATATTTTATC
*
5760768 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
5760792 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * *
5760816 TGATTCCTAATCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
5760840 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
5760864 TGATTTATGAT
1 TGATTTCTGAT
5760875 ATCTCCGTTT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:5763021 original size:13 final size:13
Alignment explanation
Indices: 5763003--5763055 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
5762993 ACCGGTCACA
5763003 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
5763016 ACCCGACCGACCCGTTT
1 A--C--CCGACCCGTTG
5763033 ACCCGACCCGTTG
1 ACCCGACCCGTTG
5763046 ACCCGACCCG
1 ACCCGACCCG
5763056 ACTCGTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 21 0.62
15 2 0.06
17 11 0.32
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:5763037 original size:30 final size:31
Alignment explanation
Indices: 5763003--5763068 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
5762993 ACCGGTCACA
*
5763003 ACCCGACCCGTTGACCCGA-CCGACCCGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTG
*
5763033 ACCCGACCCGTTGACCCGACCCGACTCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCGTTG
5763064 ACCCG
1 ACCCG
5763069 TTGATCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCGTTG
Found at i:5763056 original size:18 final size:18
Alignment explanation
Indices: 5763003--5763068 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
5762993 ACCGGTCACA
5763003 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
5763021 A-CCGACCCGTT-----T
1 ACCCGACCCGTTGACCCG
5763033 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
5763051 ACCCGACTCGTTGACCCG
1 ACCCGACCCGTTGACCCG
5763069 TTGATCGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
12 1 0.03
13 10 0.26
17 10 0.26
18 18 0.46
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:5765704 original size:24 final size:24
Alignment explanation
Indices: 5765603--5765711 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
5765593 GAATATTTTA
* *
5765603 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
5765627 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * *
5765651 TCTGAT-TCCTAATCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
5765675 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
5765699 TTTGATTTCTGAT
1 TCTGATATCTGAT
5765712 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
23 1 0.01
24 65 0.97
25 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:5769934 original size:117 final size:117
Alignment explanation
Indices: 5769714--5769935 Score: 288
Period size: 117 Copynumber: 1.9 Consensus size: 117
5769704 CTTTCAAATC
* *
5769714 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
5769779 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * *
5769831 GAAAATTTCTTTTTCAA-AGTTTTCATATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
5769894 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
5769936 ATCATTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:5775471 original size:2 final size:2
Alignment explanation
Indices: 5775464--5775488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5775454 CCTAATATGA
5775464 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5775489 ACTATATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5775719 original size:18 final size:18
Alignment explanation
Indices: 5775693--5775787 Score: 90
Period size: 18 Copynumber: 5.3 Consensus size: 18
5775683 AAATAGCTAG
5775693 GAAATTAAATCAAAAGTA
1 GAAATTAAATCAAAAGTA
* *
5775711 GAAAATAAATAAAAAG-A
1 GAAATTAAATCAAAAGTA
*
5775728 GAAATTAAATGC-ATAGTTA
1 GAAATTAAAT-CAAAAG-TA
5775747 GGAAATTAAATCAAAAGTA
1 -GAAATTAAATCAAAAGTA
*
5775766 GAAACTAAAT-AAAGAG-A
1 GAAATTAAATCAAA-AGTA
5775783 GAAAT
1 GAAAT
5775788 AATAAAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 21 0.33
18 25 0.40
19 4 0.06
20 13 0.21
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (18 bp):
GAAATTAAATCAAAAGTA
Found at i:5775885 original size:21 final size:22
Alignment explanation
Indices: 5775839--5775886 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
5775829 GAGAAGGAAA
* *
5775839 AAATCAATTTAAAGTAAATCAT
1 AAATAAATTTAAAATAAATCAT
*
5775861 -AATAAATTTAAAATATAT-AT
1 AAATAAATTTAAAATAAATCAT
5775881 AAATAA
1 AAATAA
5775887 TAAATTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAAATTTAAAATAAATCAT
Found at i:5781438 original size:8 final size:8
Alignment explanation
Indices: 5781425--5781465 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
5781415 CTCATTTTCA
5781425 GAGAATTT
1 GAGAATTT
5781433 GAGAATTT
1 GAGAATTT
*
5781441 -AGAGTTT
1 GAGAATTT
5781448 -AGGAATTT
1 GA-GAATTT
5781456 GAGAATTT
1 GAGAATTT
5781464 GA
1 GA
5781466 AAGCTTGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 7 0.24
8 21 0.72
9 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:5781774 original size:128 final size:128
Alignment explanation
Indices: 5781546--5782276 Score: 1345
Period size: 128 Copynumber: 5.7 Consensus size: 128
5781536 ACTATTCACA
5781546 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
5781611 TATGTCACTCATTTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
* *
5781674 GAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTGTTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
* * *
5781739 CATGTCACTCATGTCCCTCGGGGACACTATTCATATTAGTACCTATTATTTCTCAAGGGACTT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
*
5781802 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
5781867 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
*
5781930 GAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
5781995 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
*
5782058 AAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
**
5782123 TATGTCACTCATGTCCCTCATGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
* *
5782186 GAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAAAGAATATGTTATCATTGCCCTAT
1 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
5782251 TATGTCACTCATGTCCCTCGGGGACA
66 TATGTCACTCATGTCCCTCGGGGACA
5782277 TTAGATGGAT
Statistics
Matches: 580, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 580 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (128 bp):
GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTT
Found at i:5801836 original size:22 final size:22
Alignment explanation
Indices: 5801806--5801861 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
5801796 ATCATTCAAT
5801806 GTAACGAAAGCAGCCATGTTTTA
1 GTAA-GAAAGCAGCCATGTTTTA
5801829 GTAAGAAAGCAGCCATGTTTTA
1 GTAAGAAAGCAGCCATGTTTTA
5801851 GTAAGAAAGCA
1 GTAAGAAAGCA
5801862 AAGAAACAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (22 bp):
GTAAGAAAGCAGCCATGTTTTA
Found at i:5802394 original size:29 final size:29
Alignment explanation
Indices: 5802352--5802407 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
5802342 GTTATACAAA
*
5802352 AATTGATAATAAGCTGAGAAAGAGAACCG
1 AATTAATAATAAGCTGAGAAAGAGAACCG
5802381 AATTAATAATAAGCTGAGAAAGAGAAC
1 AATTAATAATAAGCTGAGAAAGAGAAC
5802408 AATAAGACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (29 bp):
AATTAATAATAAGCTGAGAAAGAGAACCG
Found at i:5804143 original size:13 final size:13
Alignment explanation
Indices: 5804125--5804151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5804115 TAAAACATTA
5804125 GACGCCGTCTACT
1 GACGCCGTCTACT
5804138 GACGCCGTCTACT
1 GACGCCGTCTACT
5804151 G
1 G
5804152 TCACCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (13 bp):
GACGCCGTCTACT
Found at i:5806924 original size:21 final size:21
Alignment explanation
Indices: 5806898--5806942 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5806888 ACGATGCAAA
* *
5806898 TTTAAAAAATTATATTAAAAT
1 TTTAAAAAATAAAATTAAAAT
*
5806919 TTTAAAATATAAAATTAAAAT
1 TTTAAAAAATAAAATTAAAAT
5806940 TTT
1 TTT
5806943 TCATTACGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAAAAATAAAATTAAAAT
Found at i:5808452 original size:22 final size:22
Alignment explanation
Indices: 5808404--5808457 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
5808394 TTCAGCTGTT
* *
5808404 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
5808426 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
5808448 ATAACTCCTG
1 ATAACTCCTG
5808458 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:5813192 original size:184 final size:183
Alignment explanation
Indices: 5812850--5813218 Score: 729
Period size: 184 Copynumber: 2.0 Consensus size: 183
5812840 GTTTTCCACC
5812850 AGATTGACTTCTGAGACCACCGCAGCAATGATCTCATCATCTTCTTCTACAACGTGCATCTGTGG
1 AGATTGACTTCTGAGACCACCGCAGCAATGATCTCATCATCTTCTTCTACAACGTGCATCTGTGG
5812915 CTTGTTGTCATTCTGCAGTCTGAGCGGTGTTGGCATTGGTAAGCTTTGTGGCCAGGTAAACCGCA
66 CTTGTTGTCATTCTGCAGTCTGAGCGGTGTTGGCATTGGTAAGCTTTGTGGCCAGGTAAACCGCA
5812980 GACATAACACTTGAGCGTCTTTCCTTCAGGTTTGGCCTTTCCTGACTTCTTGA
131 GACATAACACTTGAGCGTCTTTCCTTCAGGTTTGGCCTTTCCTGACTTCTTGA
5813033 AGATTGACTTCTGAGACCACCGCAGCAATGATCTCATCATCTTCTTCTACAACGTGCATCTGTGG
1 AGATTGACTTCTGAGACCACCGCAGCAATGATCTCATCATCTTCTTCTACAACGTGCATCTGTGG
5813098 CTTGTTGTCATTCTGGCAGTCTGAGCGGTGTTGGCATTGGTAAGCTTTGTGGCCAGGTAAACCGC
66 CTTGTTGTCATTCT-GCAGTCTGAGCGGTGTTGGCATTGGTAAGCTTTGTGGCCAGGTAAACCGC
5813163 AGACATAACACTTGAGCGTCTTTCCTTCAGGTTTGGCCTTTCCTGACTTCTTGA
130 AGACATAACACTTGAGCGTCTTTCCTTCAGGTTTGGCCTTTCCTGACTTCTTGA
5813217 AG
1 AG
5813219 TTGGTAGCCT
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 79 0.43
184 106 0.57
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (183 bp):
AGATTGACTTCTGAGACCACCGCAGCAATGATCTCATCATCTTCTTCTACAACGTGCATCTGTGG
CTTGTTGTCATTCTGCAGTCTGAGCGGTGTTGGCATTGGTAAGCTTTGTGGCCAGGTAAACCGCA
GACATAACACTTGAGCGTCTTTCCTTCAGGTTTGGCCTTTCCTGACTTCTTGA
Done.