Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005168.1 Hibiscus syriacus cultivar Beakdansim tig00011662_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: 818383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:1504 original size:39 final size:40
Alignment explanation
Indices: 1432--1512 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
1422 GATTGATGAG
1432 GTGAAAACATCGTTGAGTTTGGGTCTACAAACACATGATC
1 GTGAAAACATCGTTGAGTTTGGGTCTACAAACACATGATC
1472 GTGAAAACATCGTTGAG-TTGGGTCTACAAACACATGATC
1 GTGAAAACATCGTTGAGTTTGGGTCTACAAACACATGATC
1511 GT
1 GT
1513 CAGAGGATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 24 0.59
40 17 0.41
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (40 bp):
GTGAAAACATCGTTGAGTTTGGGTCTACAAACACATGATC
Found at i:1903 original size:23 final size:23
Alignment explanation
Indices: 1877--1924 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1867 ATAAAGTACA
*
1877 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1900 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1923 AT
1 AT
1925 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2384 original size:23 final size:22
Alignment explanation
Indices: 2327--2397 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
2317 GACACTTTAC
*
2327 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
2350 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
2371 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
2394 ATAT
1 ATAT
2398 TTTACCTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:2602 original size:28 final size:28
Alignment explanation
Indices: 2545--2602 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2535 ATTTGCACAA
* *
2545 AAATTTATTTGATTTTTTGATATTTTAT
1 AAATTTATTTGAATTTTTGATATTTAAT
2573 AAATATTATTTAGAATTTTT-A-ATTTAAT
1 AAAT-TTATTT-GAATTTTTGATATTTAAT
2601 AA
1 AA
2603 TAATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 12 0.46
29 7 0.27
30 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (28 bp):
AAATTTATTTGAATTTTTGATATTTAAT
Found at i:2755 original size:420 final size:417
Alignment explanation
Indices: 1990--3013 Score: 1822
Period size: 420 Copynumber: 2.5 Consensus size: 417
1980 TATTACATTA
*
1990 TATTATATTGAAAGTGTTCATAC-TTTTATAAAAAGGATCGATACTTC-TTT-AAGTTA-GTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
2051 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
2116 TTTGCACAAAAATTATTTGATTATTTGATA-TTTATAAAATATTATTTAGAATTTTTAATTTAAT
131 TTTGCACAAAAATTATTTGATTTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAAT
2180 AATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAA
195 AATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAA
2245 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTAGGACACTTTATAAA
260 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTAGGACACTTTATAAA
2310 AAGGATAGACACTTTACATATAACCACTACCTATTACATTATAAACGATACCTATTACATTATAT
325 AAGGATA-ACACTTTACATATAACCACTACCTATTACATTATAAACGATACCTATTACATTATAT
2375 AAGCGCTACCTATTACATCATATTTTACC
389 AAGCGCTACCTATTACATCATATTTTACC
2404 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAG-TTATGTAA
2469 TTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
65 TTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTT
2534 CATTTGCACAAAAATTTATTTGATTTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTA
129 CATTTGCACAAAAA-TTATTTGATTTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTA
2599 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTAT-ATTACTAAATTAAAATC
193 ATAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATC
*
2663 TTAAAACTCACTCAAAAGATAATCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
256 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTA-GGACACTT
*
2728 T-TATAAAGGAT-ACACTTTACA-ATAACCACTACCTATTACATTATAAACGATACCTATTACAT
319 TATAAAAAGGATAACACTTTACATATAACCACTACCTATTACATTATAAACGATACCTATTACAT
*
2790 TATATAAGCGCTACCTATTACATCATATTTTTCC
384 TATATAAGCGCTACCTATTACATCATATTTTACC
2824 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
2889 TTAT-TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
2953 TTTGCACAAAAA-TATTTGA-TTTTTGATATTTTATAAA-ATATATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAATTATTTGATTTTTTGATATTTTATAAATAT-TATTTAGAATTTTTAATTTAA
3014 CAACATTAAC
Statistics
Matches: 592, Mismatches: 5, Indels: 26
0.95 0.01 0.04
Matches are distributed among these distances:
413 2 0.00
414 61 0.10
415 31 0.05
416 3 0.01
417 69 0.12
418 9 0.02
419 29 0.05
420 196 0.33
421 58 0.10
422 69 0.12
423 56 0.09
424 9 0.02
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (417 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAATTATTTGATTTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAATA
ATAATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTAAA
ACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAGTAGGACACTTTATAAAA
AGGATAACACTTTACATATAACCACTACCTATTACATTATAAACGATACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTACC
Found at i:2781 original size:21 final size:23
Alignment explanation
Indices: 2757--2817 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2747 CAATAACCAC
2757 TACCTATTACATTATA-AA-CGA
1 TACCTATTACATTATATAAGCGA
*
2778 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGA
*
2801 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2818 TTTTCCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 16 0.44
22 2 0.06
23 18 0.50
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGA
Found at i:3282 original size:39 final size:39
Alignment explanation
Indices: 3228--3313 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
3218 TCAGTTGTAG
*
3228 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
3267 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
3306 ATTTTGAT
1 ATTTTGAT
3314 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:3591 original size:24 final size:25
Alignment explanation
Indices: 3554--3602 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3544 TAGTGGAGCC
3554 GAAATATATAATTCAAACTCAAATT
1 GAAATATATAATTCAAACTCAAATT
* *
3579 GAAATTTA-AATTCAAACTCCAATT
1 GAAATATATAATTCAAACTCAAATT
3603 ACATATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (25 bp):
GAAATATATAATTCAAACTCAAATT
Found at i:4045 original size:23 final size:23
Alignment explanation
Indices: 4013--4115 Score: 145
Period size: 23 Copynumber: 4.5 Consensus size: 23
4003 GATAGATACT
*
4013 TTACAATATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
* *
4036 TTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTA
4059 TTACATTATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
*
4082 TTACATTATATAAGC-ACTACCTA
1 TTACATTATATAAACGA-TACCTA
*
4105 TTACATCATAT
1 TTACATTATAT
4116 GTTTACCTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 1 0.01
23 71 0.99
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (23 bp):
TTACATTATATAAACGATACCTA
Found at i:4110 original size:46 final size:46
Alignment explanation
Indices: 4013--4115 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
4003 GATAGATACT
* *
4013 TTACAATATATAAACGATACCTATTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
4059 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
*
4105 TTACATCATAT
1 TTACATTATAT
4116 GTTTACCTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (46 bp):
TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
Found at i:7089 original size:181 final size:179
Alignment explanation
Indices: 6691--7139 Score: 830
Period size: 180 Copynumber: 2.5 Consensus size: 179
6681 ACACATTTTA
6691 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
*
6756 CCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCTGATGT
66 CCGGTATATTTATACCGG-T-TA-TACAAAATTATCTATTACATTATAATTATGGGTTCCGATGT
6821 GTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
128 GTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
6873 GACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA-A
6937 ACCGGTATATTTATACCGGTTATACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGT
65 ACCGGTATATTTATACCGGTTATACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGT
7002 AAATGTCGACACTTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
130 AAATGTCGACAC-TTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
7053 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
7118 CCGGTATATTTATACC-GTTATA
66 CCGGTATATTTATACCGGTTATA
7140 TTGCAAATTT
Statistics
Matches: 263, Mismatches: 1, Indels: 9
0.96 0.00 0.03
Matches are distributed among these distances:
179 60 0.23
180 82 0.31
181 77 0.29
182 44 0.17
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (179 bp):
GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
CCGGTATATTTATACCGGTTATACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTA
AATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
Found at i:8628 original size:3 final size:3
Alignment explanation
Indices: 8620--8694 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
8610 ACTTGTTTGG
* * * ** * *
8620 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
8668 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
8695 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:8637 original size:12 final size:12
Alignment explanation
Indices: 8624--8706 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
8614 GTTTGGATCA
*
8624 TCATCTTCATCA
1 TCATCTTCATCG
* * *
8636 TCATCATCGTCA
1 TCATCTTCATCG
8648 TCATCTTCATCG
1 TCATCTTCATCG
* *
8660 CCAGCTTCATCG
1 TCATCTTCATCG
*
8672 TCATCATCATCG
1 TCATCTTCATCG
8684 TCATCTTCATCG
1 TCATCTTCATCG
*
8696 TCAGCTTCATC
1 TCATCTTCATC
8707 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:8668 original size:36 final size:36
Alignment explanation
Indices: 8628--8706 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
8618 GGATCATCAT
*
8628 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
8664 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
8700 CTTCATC
1 CTTCATC
8707 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:8707 original size:18 final size:18
Alignment explanation
Indices: 8648--8709 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
8638 ATCATCGTCA
*
8648 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
8666 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
8684 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
8702 TCATCTTC
1 TCATCTTC
8710 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:8709 original size:6 final size:6
Alignment explanation
Indices: 8624--8709 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
8614 GTTTGGATCA
* * * * * * * *
8624 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
8672 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
8710 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:10821 original size:197 final size:197
Alignment explanation
Indices: 10157--11224 Score: 1907
Period size: 194 Copynumber: 5.5 Consensus size: 197
10147 TTTAAATTAG
*
10157 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGACATATTCTCACAT--AACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
10220 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATTATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
10285 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
10350 AA
196 AA
10352 TATCGACACAAACTAT-TTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
10416 ATTGTACCAGTTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACC-GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
10481 TCG-CAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTCT-GAAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
10542 TAAA
195 -AAA
*
10546 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCT-CACATAAAACCGGTAT
10611 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
10676 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
10741 AAA
195 AAA
10744 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
10809 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT-GGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
10873 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTTG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
10937 AA
196 AA
10939 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
11002 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
11066 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
11129 TAA
195 AAA
*
11132 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT-
11196 AATTGTACCGGTTAGATTG-AAAATTACAT
65 AATTGTACCGGTTAGATTGAAAAATTACAT
11225 CCTTTTGGCC
Statistics
Matches: 848, Mismatches: 11, Indels: 29
0.95 0.01 0.03
Matches are distributed among these distances:
192 23 0.03
193 112 0.13
194 198 0.23
195 165 0.19
196 111 0.13
197 169 0.20
198 65 0.08
199 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
AA
Found at i:10882 original size:392 final size:392
Alignment explanation
Indices: 10157--11224 Score: 1912
Period size: 392 Copynumber: 2.7 Consensus size: 392
10147 TTTAAATTAG
*
10157 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGACATATTCTCACAT--AACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
10220 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATTATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
10285 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
10350 AATATCGACACAAACTAT-TTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
*
10414 TAATTGTACCAGTTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 TAATTGTACC-GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
10479 GATCGCAC-TTTTATATATGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTC-TGAAA
325 GATCGCACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTTG-AA
10541 ATAAA
389 A-AAA
*
10546 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCT-CACATAAAACCGGTAT
10611 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
10676 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
10741 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
10806 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT-G
260 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
10870 GATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTTGAA
325 GATCG-CACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTTGAA
10935 AAAA
389 AAAA
10939 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
11002 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
11066 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAA
* *
11129 TAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC-GT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
11193 ATAAATTGTACCGGTTAGATTG-AAAATTACAT
260 AT-AATTGTACCGGTTAGATTGAAAAATTACAT
11225 CCTTTTGGCC
Statistics
Matches: 661, Mismatches: 8, Indels: 22
0.96 0.01 0.03
Matches are distributed among these distances:
387 14 0.02
388 102 0.15
389 94 0.14
390 65 0.10
391 16 0.02
392 257 0.39
393 95 0.14
394 16 0.02
395 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (392 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGCACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTTGAAAA
AA
Found at i:11370 original size:18 final size:18
Alignment explanation
Indices: 11347--11391 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
11337 TTATATTCAC
11347 ATACAAAATATAAATCGT
1 ATACAAAATATAAATCGT
* *
11365 ATACAAATTATAAATCTT
1 ATACAAAATATAAATCGT
11383 ATACAAAAT
1 ATACAAAAT
11392 TAACCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATATAAATCGT
Found at i:13293 original size:21 final size:21
Alignment explanation
Indices: 13253--13317 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
13243 CCCCTTATGC
* *
13253 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
13274 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
13295 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
13316 CT
1 CT
13318 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:15499 original size:17 final size:18
Alignment explanation
Indices: 15477--15519 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
15467 ATATATCCGG
15477 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
15494 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
15514 TATCAT
1 TATCAT
15520 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:15537 original size:20 final size:19
Alignment explanation
Indices: 15482--15528 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
15472 TCCGGTATCA
15482 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
15501 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
15522 TTTTACC
1 TTTTACC
15529 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:15676 original size:20 final size:20
Alignment explanation
Indices: 15650--15695 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
15640 CACTTTTAAA
15650 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
15669 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
15690 TTTACC
1 TTTACC
15696 TGGTATTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:17553 original size:2 final size:2
Alignment explanation
Indices: 17546--17573 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17536 GGGTCACGAA
17546 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
17574 GATTTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17634 original size:2 final size:2
Alignment explanation
Indices: 17627--17674 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17617 AGTACGAGAC
17627 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
17669 TA TA TA
1 TA TA TA
17675 CATAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17787 original size:2 final size:2
Alignment explanation
Indices: 17782--17811 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17772 AAAAATATGG
17782 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
17812 CCTTGTAAAT
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):
TA
Found at i:19563 original size:37 final size:39
Alignment explanation
Indices: 19513--19589 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
19503 GTAATTCCTT
* *
19513 AAGTTTTTAAAGAAC-A-AGTATAATATTGTAGAACAAC
1 AAGTTTTTAAAGAACAAGAGAATAATATTATAGAACAAC
19550 AAGTTTTTAAAGAACAATGAGAATAATATTATAGAACAAC
1 AAGTTTTTAAAGAACAA-GAGAATAATATTATAGAACAAC
19590 TCCATAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 15 0.43
38 1 0.03
40 19 0.54
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.29
Consensus pattern (39 bp):
AAGTTTTTAAAGAACAAGAGAATAATATTATAGAACAAC
Found at i:22269 original size:20 final size:20
Alignment explanation
Indices: 22246--22285 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
22236 CATTTCAGAA
*
22246 CTTTCATATTTCATTTTCAT
1 CTTTCACATTTCATTTTCAT
22266 CTTTCACATTTCATTTTCAT
1 CTTTCACATTTCATTTTCAT
22286 AAACAACACT
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:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (20 bp):
CTTTCACATTTCATTTTCAT
Found at i:23587 original size:19 final size:19
Alignment explanation
Indices: 23563--23609 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
23553 ATTATCAAAC
23563 ACCATAAATCATTCAAGCA
1 ACCATAAATCATTCAAGCA
*
23582 ACCATAAATCATTCAAGCT
1 ACCATAAATCATTCAAGCA
*
23601 AGCATAAAT
1 ACCATAAAT
23610 ATCAATAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.23
Consensus pattern (19 bp):
ACCATAAATCATTCAAGCA
Found at i:24872 original size:2 final size:2
Alignment explanation
Indices: 24858--24942 Score: 154
Period size: 2 Copynumber: 43.0 Consensus size: 2
24848 AAGTGTAATT
*
24858 TA TA TA CA T- 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
24899 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
24941 TA
1 TA
24943 CATGAAAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25011 original size:4 final size:4
Alignment explanation
Indices: 25004--25029 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
24994 AAAATATATA
25004 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
25030 GAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:25612 original size:20 final size:20
Alignment explanation
Indices: 25578--25615 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25568 ATAGTATCGG
**
25578 TAATGTATGGGCAATATCTA
1 TAATGTATGAACAATATCTA
25598 TAATGTATGAACAATATC
1 TAATGTATGAACAATATC
25616 GATACCGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
TAATGTATGAACAATATCTA
Found at i:37341 original size:6 final size:6
Alignment explanation
Indices: 37323--37385 Score: 63
Period size: 6 Copynumber: 10.0 Consensus size: 6
37313 ATTTTAGAAC
* * * *
37323 TTTCAT ATTTCAT TTTCAT CTTTTAC TTTCAT ATTCAT TTTCAT TTTCACA
1 TTTCAT -TTTCAT TTTCAT -TTTCAT TTTCAT TTTCAT TTTCAT TTTCA-T
37374 TTTCAT TTTCAT
1 TTTCAT TTTCAT
37386 AACCAACACT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
6 31 0.67
7 15 0.33
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (6 bp):
TTTCAT
Found at i:37341 original size:13 final size:12
Alignment explanation
Indices: 37323--37385 Score: 63
Period size: 13 Copynumber: 5.0 Consensus size: 12
37313 ATTTTAGAAC
37323 TTTCATATTTCAT
1 TTTCAT-TTTCAT
* *
37336 TTTCATCTTTTAC
1 TTTCAT-TTTCAT
*
37349 TTTCATATTCAT
1 TTTCATTTTCAT
*
37361 TTTCATTTTCACA
1 TTTCATTTTCA-T
37374 TTTCATTTTCAT
1 TTTCATTTTCAT
37386 AACCAACACT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 13 0.32
13 27 0.68
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCATTTTCAT
Found at i:37365 original size:25 final size:24
Alignment explanation
Indices: 37321--37385 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
37311 GCATTTTAGA
*
37321 ACTTTCATATTTCATTTTCATCTTTT
1 ACTTTCATA-TTCATTTTCAT-TTTC
37347 ACTTTCATATTCATTTTCATTTTC
1 ACTTTCATATTCATTTTCATTTTC
*
37371 ACATTTCATTTTCAT
1 AC-TTTCATATTCAT
37386 AACCAACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 5 0.14
25 22 0.61
26 9 0.25
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (24 bp):
ACTTTCATATTCATTTTCATTTTC
Found at i:37441 original size:19 final size:18
Alignment explanation
Indices: 37419--37487 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 18
37409 ATTCATATTC
*
37419 AGATTCAAAACTTATTTCT
1 AGATTCATAACTTATTT-T
*
37438 AGATTCATAATTTATTTTT
1 AGATTCATAACTTA-TTTT
*
37457 CAGATTCATAGCTTAATTTT
1 -AGATTCATAACTT-ATTTT
37477 AGATTCATAAC
1 AGATTCATAAC
37488 ATAGTTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 23 0.55
20 18 0.43
21 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (18 bp):
AGATTCATAACTTATTTT
Found at i:37463 original size:39 final size:38
Alignment explanation
Indices: 37403--37486 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 38
37393 ACTTTTACAT
37403 TTCATAATTCATATTCAGATTCAAAACTT-ATTTCTAGA
1 TTCATAATTCATATTCAGATTCAAAACTTAATTT-TAGA
* * * *
37441 TTCATAATTTATTTTTCAGATTCATAGCTTAATTTTAGA
1 TTCATAATTCA-TATTCAGATTCAAAACTTAATTTTAGA
37480 TTCATAA
1 TTCATAA
37487 CATAGTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 10 0.25
39 26 0.65
40 4 0.10
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (38 bp):
TTCATAATTCATATTCAGATTCAAAACTTAATTTTAGA
Found at i:46564 original size:22 final size:22
Alignment explanation
Indices: 46533--46577 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
46523 CACTAGTAAT
*
46533 TATATGTGATGTTTATTATGAA
1 TATATATGATGTTTATTATGAA
46555 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATTATGAA
46577 T
1 T
46578 TTTTTTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATATATGATGTTTATTATGAA
Found at i:46833 original size:61 final size:61
Alignment explanation
Indices: 46734--46852 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
46724 AGTTTAACAC
* * * *
46734 TATAGTGTATATAAAGGACACTATGTGTATATGGTGGGCACGACCTTATTTGTATTAGCAT
1 TATAGTATATATAAAGGACACTATGTGCATATGATGGGCACGACCTTATGTGTATTAGCAT
*
46795 TATAGTATATATAAAGGACACT-TAGTGCATGTGATGGGCACGACCTTATGTGTATTAG
1 TATAGTATATATAAAGGACACTAT-GTGCATATGATGGGCACGACCTTATGTGTATTAG
46853 TACTTTGGTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 1 0.02
61 51 0.98
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (61 bp):
TATAGTATATATAAAGGACACTATGTGCATATGATGGGCACGACCTTATGTGTATTAGCAT
Found at i:50573 original size:15 final size:15
Alignment explanation
Indices: 50553--50585 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
50543 TTTACAAAAG
50553 CCTCAAATGCTATAA
1 CCTCAAATGCTATAA
50568 CCTCAAATGCTATAA
1 CCTCAAATGCTATAA
50583 CCT
1 CCT
50586 GACAAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.27
Consensus pattern (15 bp):
CCTCAAATGCTATAA
Found at i:51007 original size:19 final size:19
Alignment explanation
Indices: 50983--51019 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50973 ATGACCAACA
*
50983 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
51002 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
51020 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:51087 original size:20 final size:21
Alignment explanation
Indices: 51064--51110 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
51054 GATTTTGACC
* *
51064 ATCGCATTGTGATTTTCGA-A
1 ATCGCATTATGATTTTAGATA
**
51084 ATCGTGTTATGATTTTAGATA
1 ATCGCATTATGATTTTAGATA
51105 ATCGCA
1 ATCGCA
51111 ATGCAAATAT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (21 bp):
ATCGCATTATGATTTTAGATA
Found at i:51133 original size:20 final size:20
Alignment explanation
Indices: 51104--51176 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
51094 GATTTTAGAT
*
51104 AATCGCAATGCAAATATGTA
1 AATCGCAATGCGAATATGTA
*
51124 AATCGTAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
51144 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
* *
51164 AATTGCAAAGCGA
1 AATCGCAATGCGA
51177 TTCTGACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:51191 original size:20 final size:20
Alignment explanation
Indices: 51168--51289 Score: 149
Period size: 20 Copynumber: 6.1 Consensus size: 20
51158 TATGTAAATT
*
51168 GCAAAGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
51188 GCAACGCGATTCTTACTATC
1 GCAACGCGATTCTGACTATC
51208 GCAACGCGATTC-GACTATC
1 GCAACGCGATTCTGACTATC
* **
51227 ACAACGCGATAAT-ACGTGATC
1 GCAACGCGATTCTGAC-T-ATC
*
51248 GCAACGCGATTCTAACTATC
1 GCAACGCGATTCTGACTATC
*
51268 GCAACGAGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
51288 GC
1 GC
51290 GTTGCGATAA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
19 17 0.20
20 54 0.62
21 14 0.16
22 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:51488 original size:22 final size:22
Alignment explanation
Indices: 51463--51516 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
51453 GACGACATAT
51463 GTCCCTATCTCCGACAAAATCC
1 GTCCCTATCTCCGACAAAATCC
* *
51485 GTCCCCATCTCCGGCAAAATCC
1 GTCCCTATCTCCGACAAAATCC
51507 GT--CTATCTCC
1 GTCCCTATCTCC
51517 ATCTCTCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 7 0.24
22 22 0.76
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (22 bp):
GTCCCTATCTCCGACAAAATCC
Found at i:51884 original size:20 final size:20
Alignment explanation
Indices: 51844--51911 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
51834 GCGATTATCT
*
51844 CGTTGCGATAG-CCATTTCG
1 CGTTGCGATAGTCAATTTCG
*
51863 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
* *
51883 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
51903 TGTTGCGAT
1 CGTTGCGAT
51912 TTTCATTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:51917 original size:20 final size:20
Alignment explanation
Indices: 51879--51934 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
51869 GATAGTCAAA
* **
51879 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
51899 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
* *
51919 TTCATGTTGCAATTTT
1 TTCGTGTTGCGATTTT
51935 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:51941 original size:20 final size:20
Alignment explanation
Indices: 51898--51942 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
51888 CGATAATCAT
* * * *
51898 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCAATTTTAAG
51918 TTTCATGTTGCAATTTTAAG
1 TTTCATGTTGCAATTTTAAG
51938 TTTCA
1 TTTCA
51943 GAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCAATTTTAAG
Found at i:53945 original size:20 final size:20
Alignment explanation
Indices: 53920--54114 Score: 63
Period size: 20 Copynumber: 10.3 Consensus size: 20
53910 AGAAGAATAG
*
53920 TCGCAACACGAAAATGATTA
1 TCGCAACACGAAAATGACTA
* **
53940 TCGCAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
** **
53960 TCGCAATGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
* **
53980 TCAC-A-ACG-GGAT-A--A
1 TCGCAACACGAAAATGACTA
** *
53994 TCGCAATGCGAAAACGACTA
1 TCGCAACACGAAAATGACTA
* * *
54014 TTGCAACATGGAAATGACTA
1 TCGCAACACGAAAATGACTA
* **
54034 TCGCAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
**
54054 TCGC-A-ACG-GGAT-A--A
1 TCGCAACACGAAAATGACTA
** *
54068 TCGCAATGCGAAAATGACAA
1 TCGCAACACGAAAATGACTA
**
54088 TCGCAATGCGAAAATGACTA
1 TCGCAACACGAAAATGACTA
54108 TCGCAAC
1 TCGCAAC
54115 GCAAATTTAG
Statistics
Matches: 127, Mismatches: 36, Indels: 24
0.68 0.19 0.13
Matches are distributed among these distances:
14 9 0.07
15 2 0.02
16 6 0.05
17 5 0.04
18 6 0.05
19 2 0.02
20 97 0.76
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:54002 original size:34 final size:34
Alignment explanation
Indices: 53959--54093 Score: 126
Period size: 34 Copynumber: 3.8 Consensus size: 34
53949 GAATTTGACT
*
53959 ATCGCAATGCGAATTTGACTATCACAACGGGATA
1 ATCGCAATGCGAATTTGACTATCGCAACGGGATA
*** * *
53993 ATCGCAATGCGAAAACGACTATTGCAACATGGAAATGA
1 ATCGCAATGCGAATTTGACTATCGCAAC--GG-GAT-A
*
54031 CTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 --ATCGCAATGCGAATTTGACTATCGCAACGGGATA
** *
54067 ATCGCAATGCGAAAATGACAATCGCAA
1 ATCGCAATGCGAATTTGACTATCGCAA
54094 TGCGAAAATG
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
34 46 0.58
36 3 0.04
37 4 0.05
38 3 0.04
40 23 0.29
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (34 bp):
ATCGCAATGCGAATTTGACTATCGCAACGGGATA
Found at i:54045 original size:74 final size:74
Alignment explanation
Indices: 53939--54122 Score: 255
Period size: 74 Copynumber: 2.5 Consensus size: 74
53929 GAAAATGATT
* ** *
53939 ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGACTATCACAACGGGATAATCGCAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGGGATAATCGCAATGCG
*
54004 AAAACGACT
66 AAAACGACA
* *
54013 ATTGCAACATG-G-AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATG
1 ATCGC-A-ATGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGGGATAATCGCAATG
*
54076 CGAAAATGACA
64 CGAAAACGACA
*
54087 ATCGCAATGCGAAAATGACTATCGCAACGCAAATTT
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTT
54123 AGTTTCGCGT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
72 3 0.03
73 2 0.02
74 87 0.91
75 2 0.02
76 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (74 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCACAACGGGATAATCGCAATGCG
AAAACGACA
Found at i:54146 original size:19 final size:19
Alignment explanation
Indices: 54124--54160 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54114 CGCAAATTTA
54124 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
54143 GTTTTGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
54161 CTCATTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:54185 original size:33 final size:34
Alignment explanation
Indices: 54148--54224 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
54138 TTTTGGTTTT
* *
54148 GCGTTGCGATTTTCTCATTGCGATAGTC-ATTTC
1 GCGTTGCGATTATCTCATTGCGATAGTCAAATTC
*
54181 GCGTTGCGATTATCTCGTTGCGATAGTCAAATTC
1 GCGTTGCGATTATCTCATTGCGATAGTCAAATTC
54215 GCGTTGCGAT
1 GCGTTGCGAT
54225 AGTCAAATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (34 bp):
GCGTTGCGATTATCTCATTGCGATAGTCAAATTC
Found at i:54221 original size:20 final size:20
Alignment explanation
Indices: 54196--54245 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
54186 GCGATTATCT
54196 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
54216 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
54236 CGTTGCGATA
1 CGTTGCGATA
54246 ATCATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:54274 original size:20 final size:20
Alignment explanation
Indices: 54251--54295 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
54241 CGATAATCAT
54251 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
*
54271 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
54291 TTTCA
1 TTTCA
54296 GAAACTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:54864 original size:21 final size:20
Alignment explanation
Indices: 54774--54876 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 20
54764 GACTCACCTG
*
54774 TCATCGTTCAAGAGGCCTCT
1 TCATCGTTCAAGAGGCCCCT
*
54794 CCTATCGTTCAAGAGG-CCCT
1 TC-ATCGTTCAAGAGGCCCCT
** *
54814 ATCATCCCTCAAGAGTCCCCT
1 -TCATCGTTCAAGAGGCCCCT
* *
54835 CCTACCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
* *
54856 GTCATCGTTGAAGAGGTCCCT
1 -TCATCGTTCAAGAGGCCCCT
54877 CCCAACATTC
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
20 15 0.24
21 47 0.75
22 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:56335 original size:36 final size:30
Alignment explanation
Indices: 56255--56320 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
56245 ATAAGAGTTG
*
56255 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
56285 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
56315 ATTTGT
1 ATTTGT
56321 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:56495 original size:20 final size:20
Alignment explanation
Indices: 56470--56754 Score: 261
Period size: 20 Copynumber: 14.8 Consensus size: 20
56460 GCAATTTTCT
*
56470 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
56490 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
56510 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
56530 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
56550 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
56570 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
56584 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
** *
56604 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCG
* * *
56624 CATTGTGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
56638 CATTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
56658 CGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCAAATTCG
* *
56678 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
56698 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCG
* *
56718 CGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
56738 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
56755 GAATGTGTAA
Statistics
Matches: 217, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
14 20 0.09
16 2 0.01
18 2 0.01
19 2 0.01
20 191 0.88
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:56612 original size:54 final size:56
Alignment explanation
Indices: 56470--56747 Score: 269
Period size: 54 Copynumber: 4.9 Consensus size: 56
56460 GCAATTTTCT
* * ** * *
56470 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATA-T---ATTCC
* *
56530 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT-TA-TCC
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATATATTCC
** * *
56584 CGTTGCGATAGTCAAATTTGCGTTGCGATAGTCATTTTCACATTGTGAT-TA-TCC
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATATATTCC
* * *
56638 CATTGCGATATTCAAATTCACGTTGCGATAGTCATATTT-GCATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCAT-TTTCGCATTGCG--A-T-ATATTCC
* * * *
56698 CGTTGCGATAGTCATATTCACGTTGTGATAGTCATATTCGCGTTGCGATA
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATA
56748 GTCAAATGAA
Statistics
Matches: 186, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
54 89 0.48
55 4 0.02
56 2 0.01
57 2 0.01
58 2 0.01
59 4 0.02
60 83 0.45
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (56 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATATATTCC
Found at i:60107 original size:20 final size:20
Alignment explanation
Indices: 60079--60185 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
60069 AATTCAGTGA
*
60079 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
60099 TGCGATAGT-AGAATCTCAT
1 TGCGATAGTCAGAATCGCGT
*
60118 TGAGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
60138 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
60159 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
60179 TGCGATA
1 TGCGATA
60186 ACGTGTTATC
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
19 18 0.25
20 37 0.51
21 15 0.21
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:60157 original size:21 final size:20
Alignment explanation
Indices: 60131--60205 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
60121 GATAGTCAGA
60131 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGAT-ACGTATT
**
60152 ATCGCGTTGCGATA-GTCAGA
1 ATCGCGTTGCGATACGT-ATT
*
60172 ATCGCGTTGCGATAACGTGTT
1 ATCGCGTTGCGAT-ACGTATT
60193 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
60206 TTACATATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 27 0.59
22 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATACGTATT
Found at i:60225 original size:41 final size:41
Alignment explanation
Indices: 60079--60205 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
60069 AATTCAGTGA
* ** * *
60079 TGCGTTAGTCAGAATCGCGTTGCGAT-A-GTAGAATCTCAT
1 TGCGATAGTCAGAATCGCGTTGCGATAACGTATTATCGCGT
* *
60118 TGAGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAACGTATTATCGCGT
*
60159 TGCGATAGTCAGAATCGCGTTGCGATAACGTGTTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAACGTATTATCGCGT
60200 TGCGAT
1 TGCGAT
60206 TTACATATTC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 24 0.31
40 1 0.01
41 52 0.68
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
TGCGATAGTCAGAATCGCGTTGCGATAACGTATTATCGCGT
Found at i:62145 original size:18 final size:18
Alignment explanation
Indices: 62122--62157 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62112 TTTTCGAAGA
62122 TTGTTCATATAAAAAGGG
1 TTGTTCATATAAAAAGGG
62140 TTGTTCATATAAAAAGGG
1 TTGTTCATATAAAAAGGG
62158 GTATCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGTTCATATAAAAAGGG
Found at i:66776 original size:14 final size:14
Alignment explanation
Indices: 66757--66786 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66747 TAGTGTTACA
*
66757 CATAAGGTCGTGCC
1 CATAAGGTCATGCC
66771 CATAAGGTCATGCC
1 CATAAGGTCATGCC
66785 CA
1 CA
66787 CCATAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (14 bp):
CATAAGGTCATGCC
Found at i:66813 original size:26 final size:25
Alignment explanation
Indices: 66771--66822 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
66761 AGGTCGTGCC
66771 CATAAGGTCATGCCCACCATAATACA
1 CATAAGGTCATGCCCACCAT-ATACA
* *
66797 CATAAGGTCGTGGCCACCATATACA
1 CATAAGGTCATGCCCACCATATACA
66822 C
1 C
66823 TTAGTGTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (25 bp):
CATAAGGTCATGCCCACCATATACA
Found at i:68486 original size:30 final size:30
Alignment explanation
Indices: 68445--68504 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
68435 AATTATCAAT
68445 AAACCAAGACACCT-AACCTTATCATCTTCC
1 AAACCAAGACACCTAAACCTTATCAT-TTCC
*
68475 AAACCATGACACCTAAACCTTATCATTTCC
1 AAACCAAGACACCTAAACCTTATCATTTCC
68505 CATAAGTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.25
Consensus pattern (30 bp):
AAACCAAGACACCTAAACCTTATCATTTCC
Found at i:76876 original size:20 final size:20
Alignment explanation
Indices: 76851--76890 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
76841 CGTCAGACTT
*
76851 GCAAGATAAATCT-TTCCTTA
1 GCAAGA-AAATATATTCCTTA
76871 GCAAGAAAATATATTCCTTA
1 GCAAGAAAATATATTCCTTA
76891 CTGTTGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (20 bp):
GCAAGAAAATATATTCCTTA
Found at i:80497 original size:24 final size:23
Alignment explanation
Indices: 80439--80498 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
80429 AAATCCAGCA
*
80439 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
80462 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
80486 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
80499 AAAAAAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:85637 original size:20 final size:21
Alignment explanation
Indices: 85612--85658 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
85602 ATGAGCAATA
* *
85612 GATTTTAAT-GGAAAACAAGT
1 GATTTTAATAGAAAAACAAAT
*
85632 GATTTTATTAGAAAAACAAAT
1 GATTTTAATAGAAAAACAAAT
85653 GATTTT
1 GATTTT
85659 TACGGCAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (21 bp):
GATTTTAATAGAAAAACAAAT
Found at i:105701 original size:21 final size:20
Alignment explanation
Indices: 105640--105699 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
105630 CTCAACAGCG
* *
105640 AAGGGATCCATCCTTTTTGTA
1 AAGGGATCGATCTTTTTTG-A
* * *
105661 AAGGGATCAATAATGTTTTGA
1 AAGGGATCGAT-CTTTTTTGA
105682 AAGGGATCGATCTTTTTT
1 AAGGGATCGATCTTTTTT
105700 TGCGGGGGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 5 0.16
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (20 bp):
AAGGGATCGATCTTTTTTGA
Found at i:108050 original size:39 final size:39
Alignment explanation
Indices: 107925--108046 Score: 181
Period size: 39 Copynumber: 3.1 Consensus size: 39
107915 GCATATCGAT
* *
107925 TAAGCACTTCGGTGCATATGGTGGGCACGACCTTATGTG
1 TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
* * *
107964 TAATGCACTTTAGTGTATATGGTGGGCACAAACTTATGTG
1 TAA-GCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
*
108004 TAAGTACTTTGGTGCATATGGTGGGCACAACCTTATGTG
1 TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
108043 TAAG
1 TAAG
108047 TACTACGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 39 0.53
40 34 0.47
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (39 bp):
TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
Found at i:108059 original size:39 final size:37
Alignment explanation
Indices: 107936--108061 Score: 144
Period size: 39 Copynumber: 3.2 Consensus size: 37
107926 AAGCACTTCG
* *
107936 GTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTA
1 GTGCATATGGTGGGCACAACCTTATGTGTAA-GTAC--TA
* * *
107976 GTGTATATGGTGGGCACAAACTTATGTGTAAGTACTTTG
1 GTGCATATGGTGGGCACAACCTTATGTGTAAGTAC--TA
108015 GTGCATATGGTGGGCACAACCTTATGTGTAAGTACTA
1 GTGCATATGGTGGGCACAACCTTATGTGTAAGTACTA
108052 CGATGCATAT
1 -G-TGCATAT
108062 ATTGACTCGA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 46 0.61
40 28 0.37
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (37 bp):
GTGCATATGGTGGGCACAACCTTATGTGTAAGTACTA
Found at i:114013 original size:15 final size:15
Alignment explanation
Indices: 113993--114024 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
113983 GTGTTGGTAA
113993 ATGAGCGTTAGCTAT
1 ATGAGCGTTAGCTAT
114008 ATGAGCGTTAGCTAT
1 ATGAGCGTTAGCTAT
114023 AT
1 AT
114025 AGTACTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (15 bp):
ATGAGCGTTAGCTAT
Found at i:126924 original size:65 final size:63
Alignment explanation
Indices: 126820--126981 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 63
126810 AATTAAATTG
** * *
126820 AACATCGAATATATTTCATGCATCGATGCACTTACCATGCACCCATGCA-CTGAG-TATTTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCCATGCACCTG-GCTA-TTT-TG
126883 AA
63 -A
* * *
126885 AACATCGAATGCATTTGATGCATCGATGCAC-CAGTCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCCATGCAC-CTGGCTATTTTGA
*
126949 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
126982 TTAGTGCACC
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
64 32 0.38
65 43 0.51
66 4 0.05
67 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCCATGCACCTGGCTATTTTGA
Found at i:128373 original size:90 final size:89
Alignment explanation
Indices: 128229--128393 Score: 303
Period size: 90 Copynumber: 1.8 Consensus size: 89
128219 TTTTATAGCC
128229 AAGTTACCCTAATCATATTAGGGTTTTATTATTTGAAATTAATTAAATCTATATTTAATTAATTG
1 AAGTTACCCTAATCATATTAGGGTTTTATTATTTGAAATTAATTAAATCTATATTTAATTAATTG
* *
128294 GAATTTAATAATCCTCTTATATCG
66 AAATTAAATAATCCTCTTATATCG
128318 AAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTTAATTAATT
1 AAGTTACCCTAATCATATTAGGG-TTTTATTATTTGAAATTAATTAAATCTATATTTAATTAATT
128383 GAAATTAAATA
65 GAAATTAAATA
128394 TTTGGGATTA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 23 0.32
90 50 0.68
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (89 bp):
AAGTTACCCTAATCATATTAGGGTTTTATTATTTGAAATTAATTAAATCTATATTTAATTAATTG
AAATTAAATAATCCTCTTATATCG
Found at i:129680 original size:10 final size:10
Alignment explanation
Indices: 129667--129693 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
129657 ACTATGGTTT
129667 AATTTTCAAC
1 AATTTTCAAC
129677 AATTTTCAAC
1 AATTTTCAAC
129687 AATTTTC
1 AATTTTC
129694 GCACATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTTCAAC
Found at i:129867 original size:23 final size:22
Alignment explanation
Indices: 129832--129875 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
129822 AAAATAAAAT
*
129832 ATTAAAAATATTATTATTTTAAA
1 ATTAAAAATATTA-AATTTTAAA
129855 ATTAATAAA-ATTAAATTTTAA
1 ATTAA-AAATATTAAATTTTAA
129876 TCATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAAAATATTAAATTTTAAA
Found at i:131185 original size:19 final size:19
Alignment explanation
Indices: 131161--131199 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
131151 TTTGCAATGA
*
131161 ACATTAACTAATCAATAAC
1 ACATTAACGAATCAATAAC
131180 ACATTAACGAATCAATAAC
1 ACATTAACGAATCAATAAC
131199 A
1 A
131200 ATCCAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.21, G:0.03, T:0.23
Consensus pattern (19 bp):
ACATTAACGAATCAATAAC
Found at i:132722 original size:18 final size:18
Alignment explanation
Indices: 132699--132736 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
132689 TACTTGATTT
132699 CAACATCATTAGAGCTAG
1 CAACATCATTAGAGCTAG
132717 CAACATCATTAGAGCTAG
1 CAACATCATTAGAGCTAG
132735 CA
1 CA
132737 TTATCTACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (18 bp):
CAACATCATTAGAGCTAG
Found at i:136127 original size:28 final size:24
Alignment explanation
Indices: 136068--136120 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
136058 ATTAGAATTC
*
136068 AATTCTATCAAGGGAGGGAAAGTA
1 AATTCCATCAAGGGAGGGAAAGTA
136092 AATTCCATCAAGGGAGGGAAAGTA
1 AATTCCATCAAGGGAGGGAAAGTA
136116 AATTC
1 AATTC
136121 TATCCATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (24 bp):
AATTCCATCAAGGGAGGGAAAGTA
Found at i:136386 original size:38 final size:39
Alignment explanation
Indices: 136339--136421 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
136329 ATTTTTGGGT
136339 TCAGG-TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGG
1 TCAGGTTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
136376 TCAGGTTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCAGGTTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
*
136415 TCGGGTT
1 TCAGGTT
136422 TAGGGTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 5 0.12
38 10 0.23
39 28 0.65
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.40
Consensus pattern (39 bp):
TCAGGTTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:141294 original size:21 final size:21
Alignment explanation
Indices: 141270--141314 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
141260 AAATGGAATT
**
141270 AAATAAAATGAAACAAAACAA
1 AAATAAAACAAAACAAAACAA
*
141291 AAATGAAACAAAACAAAACAA
1 AAATAAAACAAAACAAAACAA
141312 AAA
1 AAA
141315 AGGTAAAATA
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:0.78, C:0.11, G:0.04, T:0.07
Consensus pattern (21 bp):
AAATAAAACAAAACAAAACAA
Found at i:141295 original size:16 final size:16
Alignment explanation
Indices: 141274--141308 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
141264 GGAATTAAAT
141274 AAAATGAAACAAAACA
1 AAAATGAAACAAAACA
141290 AAAATGAAACAAAACA
1 AAAATGAAACAAAACA
141306 AAA
1 AAA
141309 CAAAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.77, C:0.11, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAATGAAACAAAACA
Found at i:141466 original size:50 final size:46
Alignment explanation
Indices: 141367--141466 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 46
141357 ATATTGTTTA
* * *
141367 AAAAACAAGTAAAAAAAGAATAATAAATATATATAAAATACTAAGT
1 AAAAACAAATAAAAAAAAAATAATAAATATATATAAAATACTAAAT
*
141413 AAAAACAAATAAAAAGAAAAAGTAATATATATATATATAAACTTA-TAAAT
1 AAAAACAAATAAAAA-AAAAA-TAATA-A-ATATATATAAA-ATACTAAAT
141463 AAAA
1 AAAA
141467 TATTAGAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 14 0.31
47 4 0.09
48 5 0.11
49 1 0.02
50 19 0.42
51 2 0.04
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (46 bp):
AAAAACAAATAAAAAAAAAATAATAAATATATATAAAATACTAAAT
Found at i:142602 original size:26 final size:27
Alignment explanation
Indices: 142564--142625 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
142554 AAAATAAAGA
* * *
142564 ATATATAATATATGT-TTATTATAACAT
1 ATATATAATATAT-TATAAATATAACAC
142591 ATATATAA-ATATTATAAATATAACAC
1 ATATATAATATATTATAAATATAACAC
142617 ATATATAAT
1 ATATATAAT
142626 GGGACGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATATAATATATTATAAATATAACAC
Found at i:151150 original size:12 final size:11
Alignment explanation
Indices: 151118--151156 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
151108 ACCTACCTTA
151118 TTTTTTTCTTT
1 TTTTTTTCTTT
*
151129 TCTTTCTTCTTT
1 T-TTTTTTCTTT
151141 TTTCTTTTCTTT
1 TTT-TTTTCTTT
151153 TTTT
1 TTTT
151157 AATTTAGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:161504 original size:24 final size:28
Alignment explanation
Indices: 161459--161510 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
161449 GTAAATATGC
161459 AAATAATAAACAAAACTAAAAAA-GAAA
1 AAATAATAAACAAAACTAAAAAATGAAA
*
161486 AAATAATAAA-ATAA-T-AAAAATGAAA
1 AAATAATAAACAAAACTAAAAAATGAAA
161511 GTGAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 5 0.22
26 3 0.13
27 10 0.43
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (28 bp):
AAATAATAAACAAAACTAAAAAATGAAA
Found at i:161558 original size:11 final size:10
Alignment explanation
Indices: 161535--161607 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 10
161525 ATAAAATGGT
161535 AAAATAAATA
1 AAAATAAATA
161545 AAAATAAGATA
1 AAAATAA-ATA
161556 AAACA-AAATAA
1 AAA-ATAAAT-A
161567 AAAATGAATATA
1 AAAAT-AA-ATA
*
161579 AGACA-AAATA
1 A-AAATAAATA
*
161589 AAACAAAAATA
1 AAA-ATAAATA
161600 AAAATAAA
1 AAAATAAA
161608 AAGGAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
9 1 0.02
10 19 0.37
11 22 0.43
12 5 0.10
13 4 0.08
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (10 bp):
AAAATAAATA
Found at i:161564 original size:21 final size:21
Alignment explanation
Indices: 161514--161591 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
161504 AATGAAAGTG
*
161514 AAACAAAATAAATAA-AATGGTA
1 AAACAAAATAAA-AATAA-GATA
*
161536 AAA-TAAATAAAAATAAGATA
1 AAACAAAATAAAAATAAGATA
*
161556 AAACAAAATAAAAAATGAATATA
1 AAACAAAAT-AAAAAT-AAGATA
*
161579 AGACAAAATAAAA
1 AAACAAAATAAAA
161592 CAAAAATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 8 0.17
21 13 0.28
22 13 0.28
23 13 0.28
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (21 bp):
AAACAAAATAAAAATAAGATA
Found at i:161571 original size:28 final size:27
Alignment explanation
Indices: 161535--161606 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
161525 ATAAAATGGT
* *
161535 AAAATAAATAAAAATAAGATAAAACAA
1 AAAAAAAATAAAAATAAGACAAAACAA
* * *
161562 AATAAAAAATGAATATAAGACAAAATAA
1 AA-AAAAAATAAAAATAAGACAAAACAA
*
161590 AACAAAAATAAAAATAA
1 AAAAAAAATAAAAATAA
161607 AAAGGAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (27 bp):
AAAAAAAATAAAAATAAGACAAAACAA
Found at i:161599 original size:23 final size:22
Alignment explanation
Indices: 161514--161622 Score: 66
Period size: 23 Copynumber: 5.0 Consensus size: 22
161504 AATGAAAGTG
* *
161514 AAACAAAAT-AAATAAAATGGTA
1 AAACAAAATAAAAAAAAAT-ATA
* * *
161536 AAA-TAAAT-AAAAATAAGATA
1 AAACAAAATAAAAAAAAATATA
*
161556 AAACAAAATAAAAAATGAATATA
1 AAACAAAATAAAAAA-AAATATA
*
161579 AGACAAAATAAAACAAAAATA-A
1 AAACAAAATAAAA-AAAAATATA
* **
161601 AAATAAAA-AGGAAAAAATATA
1 AAACAAAATAAAAAAAAATATA
161622 A
1 A
161623 TGGAATTAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
20 12 0.18
21 18 0.26
22 15 0.22
23 21 0.31
24 2 0.03
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (22 bp):
AAACAAAATAAAAAAAAATATA
Found at i:161600 original size:21 final size:20
Alignment explanation
Indices: 161470--161602 Score: 65
Period size: 21 Copynumber: 6.2 Consensus size: 20
161460 AATAATAAAC
*
161470 AAAACTAAAA-AAGAAAAAAT
1 AAAAC-AAAATAAAAAAAAAT
*
161490 AATAA-AATAATAAAAATGAAAGT
1 AA-AACAA-AATAAAAA--AAAAT
* **
161513 GAAACAAAATAAATAAAATGGT
1 AAAACAAAATAAA-AAAA-AAT
* *
161535 AAAA-TAAATAAAAATAAGAT
1 AAAACAAAATAAAAA-AAAAT
161555 AAAACAAAATAAAAAATGAATAT
1 AAAACAAAATAAAAAA--AA-AT
*
161578 AAGACAAAATAAAACAAAAAT
1 AAAACAAAATAAAA-AAAAAT
161599 AAAA
1 AAAA
161603 ATAAAAAGGA
Statistics
Matches: 88, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
19 2 0.02
20 13 0.15
21 31 0.35
22 16 0.18
23 24 0.27
24 2 0.02
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.16
Consensus pattern (20 bp):
AAAACAAAATAAAAAAAAAT
Found at i:161627 original size:14 final size:14
Alignment explanation
Indices: 161599--161645 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
161589 AAACAAAAAT
*
161599 AAAAATAAAAAGGA
1 AAAAATAAAATGGA
*
161613 AAAAATATAATGGA
1 AAAAATAAAATGGA
*
161627 ATTAAATAAAAT-GA
1 A-AAAATAAAATGGA
161641 AAAAA
1 AAAAA
161646 AACAAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 3 0.11
14 16 0.59
15 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (14 bp):
AAAAATAAAATGGA
Found at i:161652 original size:15 final size:15
Alignment explanation
Indices: 161634--161667 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
161624 GGAATTAAAT
161634 AAAATGAAAAAAAAC
1 AAAATGAAAAAAAAC
*
161649 AAAATGAAACAAAAC
1 AAAATGAAAAAAAAC
161664 AAAA
1 AAAA
161668 AAGGTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAATGAAAAAAAAC
Found at i:161815 original size:2 final size:2
Alignment explanation
Indices: 161808--161834 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
161798 CAATAATGTA
161808 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
161835 AATAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:167643 original size:18 final size:17
Alignment explanation
Indices: 167589--167637 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
167579 TTGGACTCCT
*
167589 AGTGCATCGATGCACTAA
1 AGTGCATCGATGCA-TGA
167607 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
167625 AGTGCATTCGATG
1 AGTGCA-TCGATG
167638 TTTGAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:167658 original size:64 final size:61
Alignment explanation
Indices: 167589--167768 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 61
167579 TTGGACTCCT
* *
167589 AGTGCATCGATGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAATAGCCT
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTCAATAAA-AG-CA
167653 G
61 G
* * *
167654 -GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAAGCAG
1 AGTGCATCGATGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTCAATAAAAGCAG
*
167717 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
167769 TAATTTATTC
Statistics
Matches: 99, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 3 0.03
64 88 0.89
65 4 0.04
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (61 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTCAATAAAAGCAG
Found at i:167739 original size:19 final size:19
Alignment explanation
Indices: 167715--167765 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
167705 CAATTAAAGC
167715 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
167734 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
167753 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
167766 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:167803 original size:21 final size:20
Alignment explanation
Indices: 167779--167817 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
167769 TAATTTATTC
167779 ATTGATGCATCGATGCATGGT
1 ATTGATGCAT-GATGCATGGT
*
167800 ATTGATGCATGGTGCATG
1 ATTGATGCATGATGCATG
167818 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (20 bp):
ATTGATGCATGATGCATGGT
Found at i:170375 original size:24 final size:23
Alignment explanation
Indices: 170304--170383 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
170294 CATGGTCTTG
* *
170304 TGCATCGGTGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
170327 TGCATCGGTGCATCATGC-A--GA
1 TGCATCGATGCA-CATTCAAGGGA
170348 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
170372 TGCATCGATGCA
1 TGCATCGATGCA
170384 TTGTTAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 1 0.02
23 13 0.27
24 18 0.38
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:170396 original size:44 final size:42
Alignment explanation
Indices: 170281--170403 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 42
170271 AAAACCCGAC
* * *
170281 GGATGCATCGATGCATGGTCTTGTGCATCGGTGCACATTCAAG
1 GGATGCATCGATGCATCGT-TAGTGCATCGATGCACATTCAAG
* * * *
170324 GCATGCATCGGTGCATCATGCAGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCATCGT-TAG-TGCATCGATGCACATTC-AAG
*
170369 GGATGCATCGATGCATTGTTAAGTGCATCGATGCA
1 GGATGCATCGATGCATCGTT-AGTGCATCGATGCA
170404 TTATGCACAA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 16 0.25
44 28 0.44
45 20 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATCGTTAGTGCATCGATGCACATTCAAG
Found at i:176331 original size:18 final size:19
Alignment explanation
Indices: 176296--176345 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
176286 TAATTAAAGC
176296 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
176315 AGAGTGCATCG-TGCATGG
1 AGAGTGCATCGATGCATGG
176333 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
176346 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 10 0.34
19 11 0.38
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:176352 original size:63 final size:64
Alignment explanation
Indices: 176187--176353 Score: 216
Period size: 64 Copynumber: 2.6 Consensus size: 64
176177 CGGTACACTA
* * *
176187 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAATAGCCTGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTTAATTAATAGCCAGGTGCATCGATGCATGG
** *
176251 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAA-AG-CAGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTTTAATTAATAGCCAG-GTGCATCGATGCATG
176314 G
64 G
176315 AGAGTGCATCG-TGCATGGAATGCATTCGATGTTTTAATT
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTTTAATT
176354 TATTCATTGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 28 0.31
64 58 0.64
65 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (64 bp):
AGAGTGCATCGATGCATGAATGCATTCGATGTTTTAATTAATAGCCAGGTGCATCGATGCATGG
Found at i:176383 original size:21 final size:21
Alignment explanation
Indices: 176359--176398 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
176349 TAATTTATTC
176359 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
176380 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
176399 CCTTTGAAAA
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:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:177763 original size:80 final size:77
Alignment explanation
Indices: 177664--177821 Score: 185
Period size: 77 Copynumber: 2.0 Consensus size: 77
177654 ATATTGTAAC
** *
177664 TAAACATTAAAAGAATGTAATTTTGATTACAA-CTCTTTTAATCGATATATTTAATTCAAAATAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAAGC-C-TTTAAT-G-GATATTTAATTCAAAATAA
177728 TTAAATAAGAGTTTAAA
62 TTAAATAAGA-TTTAAA
* * * * *
177745 TAAACGTT-AAAGATTGTAATTCAGATTATAAGCCTTTAATGGATATTTAATTTAAATTAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAAGCCTTTAATGGATATTTAATTCAAAATAATTAA
177809 ATAAGATTTAAA
66 ATAAGATTTAAA
177821 T
1 T
177822 TAATTCAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 7 0.10
77 26 0.38
78 1 0.01
79 6 0.09
80 20 0.29
81 8 0.12
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (77 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAAGCCTTTAATGGATATTTAATTCAAAATAATTAA
ATAAGATTTAAA
Found at i:182155 original size:49 final size:49
Alignment explanation
Indices: 182016--182145 Score: 181
Period size: 49 Copynumber: 2.7 Consensus size: 49
182006 GGAAACTTGT
* *
182016 GTATTTATTGATGTTAAAATATAATTATTAATATATTTTGAATCAAATA
1 GTATTTATTGATGTTAAAATATAATTACTAATATATTTTTAATCAAATA
* * ***
182065 GTA-TTACTAATAAAAAATATATAATTACTAATATATTTTTAATCAAATA
1 GTATTTATTGATGTTAAA-ATATAATTACTAATATATTTTTAATCAAATA
182114 GTATTTATTGATGTTAAAATATAATTACTAAT
1 GTATTTATTGATGTTAAAATATAATTACTAAT
182146 CTTGTTTTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 9 0.13
49 49 0.73
50 9 0.13
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (49 bp):
GTATTTATTGATGTTAAAATATAATTACTAATATATTTTTAATCAAATA
Found at i:202998 original size:182 final size:181
Alignment explanation
Indices: 202646--203019 Score: 700
Period size: 182 Copynumber: 2.1 Consensus size: 181
202636 TAATCGAGAG
202646 ATCAAGCAGATTTTAGAGAAAGTTGTGAACCCAAAGCGAAAGAATTGGTCGCCAAAGTTGGATGA
1 ATCAAGCAGATTTTAGAGAAAGTTGTGAACCCAAAGCGAAAGAATTGGTCGCCAAAGTTGGATGA
202711 AGTACTTTGGGCGTACAGAACAGATTCAAAACTCCTTTGGGGATGTCACCTTCAAGCTAGTATAT
66 AGTACTTTGGGCGTACAGAACAGATTCAAAACTCCTTTGGGGATGTCACCTTCAAGCTAGTATAT
202776 GGGAAAGCTTGTCATCTCCCGGTTGAGCTTGAACATAAAGCTTATTGGACT
131 GGGAAAGCTTGTCATCTCCCGGTTGAGCTTGAACATAAAGCTTATTGGACT
202827 ATCAAGCAGATTTTAGAGAAAGTTGTGAA-CCAAAGCGAAAGAATTGGTCGCCAAAGTTGGATGA
1 ATCAAGCAGATTTTAGAGAAAGTTGTGAACCCAAAGCGAAAGAATTGGTCGCCAAAGTTGGATGA
202891 AGTAC-TTGGGCGTACAGAAACAGCATTCAAAACTCCTTTGGGGATGTCACCCTTCAAGCTAGTA
66 AGTACTTTGGGCGTACAG-AACAG-ATTCAAAACTCCTTTGGGGATGTCA-CCTTCAAGCTAGTA
202955 TATGGGAAAGCTTGTCATCTCCCGGTTGAGCTTGAACATAAAGCTTATTGGACT
128 TATGGGAAAGCTTGTCATCTCCCGGTTGAGCTTGAACATAAAGCTTATTGGACT
203009 ATCAAGC-GATT
1 ATCAAGCAGATT
203020 GAATTTCGAT
Statistics
Matches: 190, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
179 12 0.06
180 45 0.24
181 58 0.31
182 75 0.39
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (181 bp):
ATCAAGCAGATTTTAGAGAAAGTTGTGAACCCAAAGCGAAAGAATTGGTCGCCAAAGTTGGATGA
AGTACTTTGGGCGTACAGAACAGATTCAAAACTCCTTTGGGGATGTCACCTTCAAGCTAGTATAT
GGGAAAGCTTGTCATCTCCCGGTTGAGCTTGAACATAAAGCTTATTGGACT
Found at i:203851 original size:20 final size:20
Alignment explanation
Indices: 203809--203857 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
203799 TAACTTTTTC
*
203809 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
203829 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
203848 TTTTACCTTT
1 TTTTATCTTT
203858 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:208064 original size:17 final size:16
Alignment explanation
Indices: 208040--208079 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
208030 GATGTAGGAG
208040 TCTTTTTCTTATCTTTT
1 TCTTTTTCTT-TCTTTT
* *
208057 TGTTTTTCTTTTTTTT
1 TCTTTTTCTTTCTTTT
208073 TCTTTTT
1 TCTTTTT
208080 GTTGCTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (16 bp):
TCTTTTTCTTTCTTTT
Found at i:208076 original size:22 final size:23
Alignment explanation
Indices: 208040--208082 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
208030 GATGTAGGAG
208040 TCTTTTTCTTATCTTTTTGTTTT
1 TCTTTTTCTTATCTTTTTGTTTT
*
208063 TCTTTTT-TTTTCTTTTTGTT
1 TCTTTTTCTTATCTTTTTGTT
208083 GCTTTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (23 bp):
TCTTTTTCTTATCTTTTTGTTTT
Found at i:214201 original size:55 final size:56
Alignment explanation
Indices: 214116--214227 Score: 217
Period size: 55 Copynumber: 2.0 Consensus size: 56
214106 GAATGTTCTA
214116 ATTATTCCCGAATAATAACCAGATGTGCTCTAAATTTAACTGATTTTCCATATCTG
1 ATTATTCCCGAATAATAACCAGATGTGCTCTAAATTTAACTGATTTTCCATATCTG
214172 ATTATTCCCGAAT-ATAACCAGATGTGCTCTAAATTTAACTGATTTTCCATATCTG
1 ATTATTCCCGAATAATAACCAGATGTGCTCTAAATTTAACTGATTTTCCATATCTG
214227 A
1 A
214228 AAGTGGGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 43 0.77
56 13 0.23
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (56 bp):
ATTATTCCCGAATAATAACCAGATGTGCTCTAAATTTAACTGATTTTCCATATCTG
Found at i:214300 original size:27 final size:27
Alignment explanation
Indices: 214262--214316 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
214252 TTATTACTTC
214262 ATTTTCTCACTCCTACGTCTCCAGGGG
1 ATTTTCTCACTCCTACGTCTCCAGGGG
214289 ATTTTCTCACTCCTACGTCTCCAGGGG
1 ATTTTCTCACTCCTACGTCTCCAGGGG
214316 A
1 A
214317 CCACTTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (27 bp):
ATTTTCTCACTCCTACGTCTCCAGGGG
Found at i:215948 original size:15 final size:15
Alignment explanation
Indices: 215922--215960 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
215912 TATTTTTCCT
215922 TATTTATATATATATA
1 TATTT-TATATATATA
* *
215938 TATTTTATATATTTT
1 TATTTTATATATATA
215953 TATTTTAT
1 TATTTTAT
215961 TTTATTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTATATATATA
Found at i:227230 original size:1 final size:1
Alignment explanation
Indices: 227224--227251 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
227214 GAGCATCTCC
227224 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
227252 CCCAGAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:227826 original size:208 final size:211
Alignment explanation
Indices: 227468--228100 Score: 1067
Period size: 208 Copynumber: 3.0 Consensus size: 211
227458 AGGTTTTACC
*
227468 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
227533 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGGGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
227598 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-C-CTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
227661 AAC-ATTTCTCAAATT
196 AACAATTTCTCAATTT
*
227676 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
227741 ACGAAGGGACCGCTGGTTGTCAACAATCATTTCTCAAATTCCGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
227806 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
227871 AACAACTTCTCAATTT
196 AACAATTTCTCAATTT
*
227887 CAGAGCCAATTTCAACTTCAC-ATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAAT-GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * * *
227951 GGCGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAG
65 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAA
* *
228016 CGAAGAATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
129 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* *
228081 TAAACAATTTCCCAATTT
194 CAAACAATTTCTCAATTT
228099 CA
1 CA
228101 ACTTCACAAC
Statistics
Matches: 399, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
208 174 0.44
209 1 0.00
210 18 0.05
211 96 0.24
212 110 0.28
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (211 bp):
CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACAATTTCTCAATTT
Found at i:227938 original size:106 final size:105
Alignment explanation
Indices: 227468--228155 Score: 1064
Period size: 106 Copynumber: 6.7 Consensus size: 105
227458 AGGTTTTACC
227468 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
227533 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
227573 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
227638 ACGAAGGGA-C-CTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
227676 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
227741 ACGAAGGGACCGCTGGTTGTCAACAATCATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
227781 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
227846 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* *
227887 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
227952 GCGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * * *
227993 CAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
228058 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
228091 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
228150 CGACGA
64 CGACGA
228156 GGATGTCATT
Statistics
Matches: 550, Mismatches: 28, Indels: 21
0.92 0.05 0.04
Matches are distributed among these distances:
94 55 0.10
95 1 0.00
96 2 0.00
98 7 0.01
103 100 0.18
104 2 0.00
105 191 0.35
106 192 0.35
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:228752 original size:27 final size:27
Alignment explanation
Indices: 228714--228768 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
228704 TTATTACTTC
228714 ATTTTCTCACTCCTACGTCTCCAGGGG
1 ATTTTCTCACTCCTACGTCTCCAGGGG
228741 ATTTTCTCACTCCTACGTCTCCAGGGG
1 ATTTTCTCACTCCTACGTCTCCAGGGG
228768 A
1 A
228769 CCACTTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (27 bp):
ATTTTCTCACTCCTACGTCTCCAGGGG
Found at i:230427 original size:17 final size:17
Alignment explanation
Indices: 230407--230445 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
230397 TTTTCCTTTA
230407 TTTATATATATATATAT
1 TTTATATATATATATAT
* * *
230424 TTTATGTATATTTTTAT
1 TTTATATATATATATAT
230441 TTTAT
1 TTTAT
230446 TTTATTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTATATATATATATAT
Found at i:230434 original size:38 final size:39
Alignment explanation
Indices: 230388--230463 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
230378 ATTTTCATTA
* *
230388 TTATTATATTTTTCCTTTA-TTTA-TATATATATATATT
1 TTATTATATTTTTACTTTATTTTATTATACATATATATT
*
230425 TTATGTATATTTTTATTTTATTTTATTATACATATATAT
1 TTAT-TATATTTTTACTTTATTTTATTATACATATATAT
230464 ATATACATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 4 0.12
38 13 0.39
39 4 0.12
40 12 0.36
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (39 bp):
TTATTATATTTTTACTTTATTTTATTATACATATATATT
Found at i:230442 original size:44 final size:43
Alignment explanation
Indices: 230364--230467 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 43
230354 GTCCCTACTA
230364 TTAT-TATATACTATATTTTCATTATTATTATATTTT-TCCTTTAT
1 TTATATATATA-TATATTTTCATTATTATTATATTTTAT--TTTAT
*
230408 TTATATATATATATATTTT-ATGTA-TATTTTTATTTTATTTTAT
1 TTATATATATATATATTTTCAT-TATTA-TTATATTTTATTTTAT
*
230451 TATACATATATATATAT
1 T-TATATATATATATAT
230468 ACATAATCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
43 10 0.19
44 36 0.68
45 7 0.13
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (43 bp):
TTATATATATATATATTTTCATTATTATTATATTTTATTTTAT
Done.