Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009053.1 Hibiscus syriacus cultivar Beakdansim tig00112468_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: 64265
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2854 original size:30 final size:30
Alignment explanation
Indices: 2807--2874 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
2797 AAAGAAGAAG
*
2807 AAAAAAGTTAATGAAGAAATTAAAAAAACAA
1 AAAAAAGTTAA-GAAGAAAATAAAAAAACAA
* *
2838 AAAAAAGGTTAA-AAGAAAATAAATAAATAA
1 AAAAAA-GTTAAGAAGAAAATAAAAAAACAA
2868 AATAAAA
1 AA-AAAA
2875 TAAAATGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 17 0.53
31 10 0.31
32 5 0.16
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (30 bp):
AAAAAAGTTAAGAAGAAAATAAAAAAACAA
Found at i:2943 original size:22 final size:21
Alignment explanation
Indices: 2909--2958 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2899 TAGAAGAAAA
*
2909 TAAAAAAATATTAAAAAATGT
1 TAAAAAAAAATTAAAAAATGT
2930 TAAAAAGAAAATTAAAAAA--T
1 TAAAAA-AAAATTAAAAAATGT
2950 TAAAAAAAA
1 TAAAAAAAA
2959 GATTTCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 6 0.22
22 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAAAAAATTAAAAAATGT
Found at i:14574 original size:23 final size:23
Alignment explanation
Indices: 14548--14595 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
14538 ATAAAGTACA
*
14548 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
14571 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
14594 AT
1 AT
14596 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:15016 original size:23 final size:23
Alignment explanation
Indices: 14990--15049 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
14980 TAACCACTAC
14990 CTATTACATTATATAAACGATAT
1 CTATTACATTATATAAACGATAT
** *
15013 CTATTACATTATATAAGGGCTAT
1 CTATTACATTATATAAACGATAT
*
15036 CTATTACATCATAT
1 CTATTACATTATAT
15050 GTTTACCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (23 bp):
CTATTACATTATATAAACGATAT
Found at i:15505 original size:39 final size:39
Alignment explanation
Indices: 15451--15537 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
15441 TCAAGTTGTA
*
15451 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
15490 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
15529 GATTTTGAT
1 GATTTTGAT
15538 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:15819 original size:18 final size:18
Alignment explanation
Indices: 15796--15832 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15786 CGAAATATAT
15796 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
15814 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
15832 A
1 A
15833 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:16161 original size:25 final size:25
Alignment explanation
Indices: 16127--16177 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
16117 TTTTTCCAAA
*
16127 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
16152 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
16177 T
1 T
16178 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:16472 original size:21 final size:22
Alignment explanation
Indices: 16447--16498 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
16437 ACACTTTACA
*
16447 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
16470 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
16493 ATATAA
1 ATATAA
16499 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:16483 original size:23 final size:23
Alignment explanation
Indices: 16457--16519 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
16447 ATATAACCAC
16457 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
16480 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
16503 TACCTATTACATCATAT
1 TACCTATTACATTATAT
16520 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:16858 original size:25 final size:24
Alignment explanation
Indices: 16808--16866 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
16798 AAAGATGTAT
16808 ATACCTAAATAGTAGTTAACAAAC
1 ATACCTAAATAGTAGTTAACAAAC
** *
16832 ATACCTAAATATGTAGTTATTATAC
1 ATACCTAAATA-GTAGTTAACAAAC
16857 ATACCTAAAT
1 ATACCTAAAT
16867 TTAATGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (24 bp):
ATACCTAAATAGTAGTTAACAAAC
Found at i:19635 original size:184 final size:184
Alignment explanation
Indices: 19325--19852 Score: 930
Period size: 184 Copynumber: 2.9 Consensus size: 184
19315 TTCAAATTAC
* * *
19325 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
19390 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
*
19455 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATATGTAAAATGT
*
19509 TGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
19574 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
19639 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATATGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATATGTAAAATGT
19693 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* * * *
19758 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACTGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* * * **
19823 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
19853 ATGTTGAAAG
Statistics
Matches: 329, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 329 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATATGTAAAATGT
Found at i:21314 original size:3 final size:3
Alignment explanation
Indices: 21306--21392 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
21296 ACTTGTTTGG
* * * **
21306 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
21354 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
21393 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:21329 original size:18 final size:18
Alignment explanation
Indices: 21306--21407 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
21296 ACTTGTTTGG
21306 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
21324 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
21342 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
21360 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
21378 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
21396 AGCTTCATCTTC
1 ATCATCATCTTC
21408 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:21373 original size:42 final size:42
Alignment explanation
Indices: 21314--21404 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
21304 GGATCATCAT
*
21314 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
21356 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
21398 CTTCATC
1 CTTCATC
21405 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:23980 original size:199 final size:199
Alignment explanation
Indices: 22860--24614 Score: 3288
Period size: 198 Copynumber: 8.9 Consensus size: 199
22850 TTTAAATTAG
*
22860 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22925 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22990 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG--A
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
23053 AAAA
196 AAAA
23057 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
23120 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGGT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23185 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
23250 AAAA
196 AAAA
*
23254 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGATATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
23317 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGGT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23382 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
23444 AAAA
196 AAAA
23448 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23513 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23578 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-AA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
23642 AAAA
196 AAAA
23646 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23711 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23776 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
23841 AAAA
196 AAAA
23845 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23910 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
23975 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
24040 AAAA
196 AAAA
24044 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
24108 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
24173 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
24236 AAAA
196 AAAA
24240 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
24305 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
24370 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
24434 AAAA
196 AAAA
24438 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
24502 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
24567 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
24615 GGCCATATTG
Statistics
Matches: 1533, Mismatches: 13, Indels: 22
0.98 0.01 0.01
Matches are distributed among these distances:
194 67 0.04
195 176 0.11
196 155 0.10
197 376 0.25
198 444 0.29
199 315 0.21
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
AAAA
Found at i:24779 original size:19 final size:19
Alignment explanation
Indices: 24733--24781 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
24723 TTATATTCAC
*
24733 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
24752 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
24771 ATACAAAATTA
1 ATACAAAATTA
24782 ACTCAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:26606 original size:33 final size:33
Alignment explanation
Indices: 26569--26634 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
26559 CATCTTAATA
*
26569 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
26602 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
26635 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:26708 original size:21 final size:21
Alignment explanation
Indices: 26668--26732 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
26658 CCCCTTATGC
* *
26668 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
26689 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
26710 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
26731 CT
1 CT
26733 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:28964 original size:17 final size:18
Alignment explanation
Indices: 28942--28983 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
28932 ATATATCCGG
28942 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
28959 TATCATTTGTTACCGGTTT
1 TATCA-TTGTTACCGGTTT
28978 TATCAT
1 TATCAT
28984 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:29001 original size:20 final size:19
Alignment explanation
Indices: 28947--28992 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
28937 TCCGGTATCA
28947 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
28966 TGTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCAT-T
28986 TTTTACC
1 TTTTACC
28993 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:29157 original size:19 final size:19
Alignment explanation
Indices: 29112--29158 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
29102 CACTTTTAAA
* *
29112 TTTACCGGTTTTATCATTT
1 TTTACCTGTTTTATCATAT
29131 TGTTACCTGTTTTATCATAT
1 T-TTACCTGTTTTATCATAT
29151 TTTACCTG
1 TTTACCTG
29159 GTATATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTACCTGTTTTATCATAT
Found at i:29165 original size:19 final size:20
Alignment explanation
Indices: 29123--29165 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
29113 TTACCGGTTT
* * *
29123 TATCATTTTGTTACCTGTTT
1 TATCATATTGTTACCTGGTA
29143 TATCATATT-TTACCTGGTA
1 TATCATATTGTTACCTGGTA
29162 TATC
1 TATC
29166 GTTTTGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (20 bp):
TATCATATTGTTACCTGGTA
Found at i:29638 original size:220 final size:220
Alignment explanation
Indices: 29221--29654 Score: 716
Period size: 220 Copynumber: 2.0 Consensus size: 220
29211 TTAAAACTGC
29221 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGGTTTCATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATA-GTTTCATGTTTTCCACCTACAATAT
*
29286 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATATTA
65 TAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATATTA
* *
29351 GAATTTAAATTTAACAATATTAACCAAATATAATAAATATGTTTTCAACAGTGAAATAAGTTGGA
130 GAATTTAAATTTAACAATATTAACAAAATATAATAAATATGATTTCAACAGTGAAATAAGTTGGA
*
29416 CACTTTTATAAAAATGATATATACTT
195 CACTTTTATAAAAAGGATATATACTT
*
29442 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAAT-GTTTCATGTTTTCCACCTACAATAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTTTCATGTTTTCCACCTACAATAT
*
29506 TAATTTAATAATTTCATTTACACAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATAT-TTA
65 TAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATATTA
*
29569 GATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATAT-ATTTC-ACAGTGAAATAAGTA
130 GAATTTAAATTTAACAATATTAAC-AAA-AT-ATAATAAATATGATTTCAACAGTGAAATAAGT-
29632 TGGACACTTTTATAAAAAGGATA
191 TGGACACTTTTATAAAAAGGATA
29655 GATAATTACA
Statistics
Matches: 201, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
218 26 0.13
219 48 0.24
220 79 0.39
221 15 0.07
222 33 0.16
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (220 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTTTCATGTTTTCCACCTACAATATT
AATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATATTAG
AATTTAAATTTAACAATATTAACAAAATATAATAAATATGATTTCAACAGTGAAATAAGTTGGAC
ACTTTTATAAAAAGGATATATACTT
Found at i:32302 original size:71 final size:71
Alignment explanation
Indices: 32186--32328 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
32176 GGTAGAGGCC
32186 ATTATGACATGCTTCAGGTTAGGGTTTAGTTGTACATCAGTTGTGCAACAGCAGAGACCCTCCAT
1 ATTATGACATGCTTCAGGTTAGGGTTTAGTTGTACATCAGTTGTGCAACAGCAGAGACCCTCCAT
32251 GAAAGA
66 GAAAGA
32257 ATTATGACATGCTTCAGGTTAGGGTTTAGTTGTACATCAGTTGTGCAACAGCAGAGACCCTCCAT
1 ATTATGACATGCTTCAGGTTAGGGTTTAGTTGTACATCAGTTGTGCAACAGCAGAGACCCTCCAT
32322 GAAAGA
66 GAAAGA
32328 A
1 A
32329 GCGGTTCAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (71 bp):
ATTATGACATGCTTCAGGTTAGGGTTTAGTTGTACATCAGTTGTGCAACAGCAGAGACCCTCCAT
GAAAGA
Found at i:32828 original size:22 final size:21
Alignment explanation
Indices: 32803--32846 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
32793 CTCATCTAAT
32803 AGTTCTAAATTCGTGTAAAAAG
1 AGTTCTAAATT-GTGTAAAAAG
* * *
32825 AGTTTTACATTGTGTAACAAG
1 AGTTCTAAATTGTGTAAAAAG
32846 A
1 A
32847 TTTTATCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (21 bp):
AGTTCTAAATTGTGTAAAAAG
Found at i:32887 original size:14 final size:14
Alignment explanation
Indices: 32868--32904 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32858 CTTTATTTCT
32868 CTATTTTCAGTCAA
1 CTATTTTCAGTCAA
*
32882 CTATTTTCAGTCAT
1 CTATTTTCAGTCAA
32896 CTATTTTCA
1 CTATTTTCA
32905 ATAGTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (14 bp):
CTATTTTCAGTCAA
Found at i:34865 original size:15 final size:15
Alignment explanation
Indices: 34838--34885 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
34828 TGATGTCAAG
*
34838 TGATGGTGATGATGA
1 TGATGGTGGTGATGA
*
34853 TGGTGGTGGTGATGA
1 TGATGGTGGTGATGA
* *
34868 TGATGGTAGTGATAA
1 TGATGGTGGTGATGA
34883 TGA
1 TGA
34886 AGGTATGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (15 bp):
TGATGGTGGTGATGA
Found at i:34885 original size:18 final size:18
Alignment explanation
Indices: 34846--34885 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34836 AGTGATGGTG
* * *
34846 ATGATGATGGTGGTGGTG
1 ATGATGATGGTAGTGATA
34864 ATGATGATGGTAGTGATA
1 ATGATGATGGTAGTGATA
34882 ATGA
1 ATGA
34886 AGGTATGTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (18 bp):
ATGATGATGGTAGTGATA
Found at i:39059 original size:20 final size:20
Alignment explanation
Indices: 39018--39065 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39008 AAAACAGTTT
**
39018 TACCGATATTGTTCTTGTAG
1 TACCGATATTGTTCTTACAG
39038 TACCGATATTGTTCTTACAG
1 TACCGATATTGTTCTTACAG
*
39058 TATCGATA
1 TACCGATA
39066 CTACATGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (20 bp):
TACCGATATTGTTCTTACAG
Found at i:40341 original size:30 final size:30
Alignment explanation
Indices: 40306--40388 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
40296 TTTTAATATT
**
40306 GTGTTCTTGTTTGTTTATTTATTTTTGAAC
1 GTGTTCTTGTTAATTTATTTATTTTTGAAC
** *
40336 GTGTTCACGTTAATTTATTTATTTTTGAAG
1 GTGTTCTTGTTAATTTATTTATTTTTGAAC
*
40366 GTGTTCTTGTTCATTTATTTATT
1 GTGTTCTTGTTAATTTATTTATT
40389 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.17, C:0.07, G:0.16, T:0.60
Consensus pattern (30 bp):
GTGTTCTTGTTAATTTATTTATTTTTGAAC
Found at i:40445 original size:35 final size:35
Alignment explanation
Indices: 40406--40475 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
40396 AACATGTTTG
* * * * *
40406 TTTAATGTTCGCAAACGTGTTCATTTAAATTTTCA
1 TTTAATATTCACAAACATATTCATTTAAATGTTCA
*
40441 TTTAATATTCACGAACATATTCATTTAAATGTTCA
1 TTTAATATTCACAAACATATTCATTTAAATGTTCA
40476 CGAACGTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (35 bp):
TTTAATATTCACAAACATATTCATTTAAATGTTCA
Found at i:40480 original size:24 final size:24
Alignment explanation
Indices: 40437--40491 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
40427 CATTTAAATT
40437 TTCATTT-AATATTCACGAACATA
1 TTCATTTAAATATTCACGAACATA
* * *
40460 TTCATTTAAATGTTCACGAACGTG
1 TTCATTTAAATATTCACGAACATA
40484 TTCATTTA
1 TTCATTTA
40492 GCATTCATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (24 bp):
TTCATTTAAATATTCACGAACATA
Found at i:42008 original size:73 final size:73
Alignment explanation
Indices: 41818--42106 Score: 402
Period size: 71 Copynumber: 4.0 Consensus size: 73
41808 AATAAATAAA
* * * ** * *
41818 ACAAATTTATATTCTAAACCACAAAAACAAACAATACTCAAATCACCATTTGGGGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACT-A
41883 AAAAAATAAT
65 AAAAAA-AAT
* *
41893 ACAAATTTACATGCTAAACTATGAAAACAAACAATACCCAAATCCCCATTTGGAGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
41958 AAAAAAAT
66 AAAAAAAT
* * * *
41966 ACAAATTTACGTACTAAATTATGAAAACAAACAATGCTCAAATCACCATTTGGAGTAAAAACT--
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
*
42029 AAAAAAAC
66 AAAAAAAT
*
42037 ACAAATTTACATACTAAACTATGAAAGCAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
*
42102 GAAAA
66 AAAAA
42107 TAAGGGAAAT
Statistics
Matches: 191, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
71 65 0.34
73 64 0.34
74 7 0.04
75 55 0.29
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.21
Consensus pattern (73 bp):
ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
AAAAAAAT
Found at i:42098 original size:144 final size:146
Alignment explanation
Indices: 41841--42106 Score: 437
Period size: 144 Copynumber: 1.8 Consensus size: 146
41831 CTAAACCACA
* * *
41841 AAAACAAACAATACTCAAATCACCATTTGGGGTAAAAACTAAAAAAAATAATACAAATTTACATG
1 AAAACAAACAATACTCAAATCACCATTTGGAGTAAAAACT--AAAAAATAACACAAATTTACATA
*
41906 CTAAACTATGAAAACAAACAATACCCAAATCCCCATTTGGAGTAAAAACTAAAAAAAAATACAAA
64 CTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAAAAAAAAATACAAA
41971 TTTACGTACTAAATTATG
129 TTTACGTACTAAATTATG
*
41989 AAAACAAACAATGCTCAAATCACCATTTGGAGTAAAAACT-AAAAA-AACACAAATTTACATACT
1 AAAACAAACAATACTCAAATCACCATTTGGAGTAAAAACTAAAAAATAACACAAATTTACATACT
* *
42052 AAACTATGAAAGCAAACAATACCCAAATCACCATTTGGAGTAAAAACTAAGAAAA
66 AAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAAAAAAA
42107 TAAGGGAAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
144 68 0.61
145 5 0.05
148 38 0.34
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.21
Consensus pattern (146 bp):
AAAACAAACAATACTCAAATCACCATTTGGAGTAAAAACTAAAAAATAACACAAATTTACATACT
AAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAAAAAAAAATACAAATT
TACGTACTAAATTATG
Found at i:43866 original size:20 final size:20
Alignment explanation
Indices: 43838--43885 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
43828 AAATGAATGA
*
43838 ATGGGCTCCGGTGTATAGAG
1 ATGGCCTCCGGTGTATAGAG
43858 ATGGCCTCCGGTGTATAGAG
1 ATGGCCTCCGGTGTATAGAG
43878 ATGGCCTC
1 ATGGCCTC
43886 ATCGTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.25
Consensus pattern (20 bp):
ATGGCCTCCGGTGTATAGAG
Found at i:51906 original size:20 final size:21
Alignment explanation
Indices: 51881--51922 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51871 TTCGAGACAT
*
51881 ATACAT-AGGTCTTTCAGGAC
1 ATACATGAGGTCCTTCAGGAC
*
51901 ATACATGAGGTCCTTCGGGAC
1 ATACATGAGGTCCTTCAGGAC
51922 A
1 A
51923 AATTTCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
ATACATGAGGTCCTTCAGGAC
Found at i:53468 original size:59 final size:59
Alignment explanation
Indices: 53372--53899 Score: 860
Period size: 59 Copynumber: 9.0 Consensus size: 59
53362 ATGTGTGGTG
* *
53372 ATTTCTAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
* * *
53431 ATTTCCAGATAGGGTACTTCGTGTGTTAAAACAATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
*
53490 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGCATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
* *
53549 ATTTCCAAATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGAATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
53608 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
* *
53667 ATTTTCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
* * *
53726 ATTTCCAGATATGGAACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAATGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
** ** * *
53785 ATTTTTAGATAGGGCACTAAGTGTGCTAAAAAGATAAGGAAGTCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
* *
53844 ATTTCCAGATAGGGCACTTCGTGTGCTAAAA-TATAAGGAAATCATACTAATTGTAT
1 ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTAT
53900 AAAATTCCTA
Statistics
Matches: 433, Mismatches: 36, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
58 22 0.05
59 411 0.95
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (59 bp):
ATTTCCAGATAGGGCACTTCGTGTGCTAAAACGATAAGGAAATCATACTAAGTGTATGA
Found at i:56723 original size:22 final size:23
Alignment explanation
Indices: 56695--56745 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
56685 CGTTAGGCAT
*
56695 CTAAATTGA-CAAAAAAAAACAC
1 CTAAATTAACCAAAAAAAAACAC
*
56717 CTAAATTAACCAAAAAAAAGCAC
1 CTAAATTAACCAAAAAAAAACAC
56740 CTAAAT
1 CTAAAT
56746 AGAAAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.16
Consensus pattern (23 bp):
CTAAATTAACCAAAAAAAAACAC
Found at i:58001 original size:44 final size:43
Alignment explanation
Indices: 57928--58013 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
57918 AACTGTCAGA
* *
57928 AATTGGAATCCAATTCCATATTCTGTTTGGTTGGCATGAAATGG
1 AATTAGAATCCAATTCCATATTCTGTTTGGTTCGCA-GAAATGG
* *
57972 AATTAGAATTCAATTTCATATTCTGTTTGGTTCGCAGAAATG
1 AATTAGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAATG
58014 TCAGATGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (43 bp):
AATTAGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAATGG
Found at i:58404 original size:37 final size:38
Alignment explanation
Indices: 58315--58409 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
58305 TTTTCACCCT
* *
58315 AAACCCGAACCCAACCCGACCTGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
*
58354 AAACCCGATCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
*
58392 AAA-CTGACCCGACCCGAC
1 AAACCCGACCCGACCCGAC
58410 TAAAATAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 13 0.25
38 31 0.61
39 7 0.14
ACGTcount: A:0.40, C:0.38, G:0.11, T:0.12
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:63963 original size:21 final size:21
Alignment explanation
Indices: 63937--63978 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
63927 CCAGAATGGG
**
63937 GGGAATCGGTACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
63958 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
63979 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:64107 original size:19 final size:19
Alignment explanation
Indices: 64083--64149 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
64073 TGAGCCTCGG
*
64083 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
* *
64102 TTACTGGTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* * *
64121 ATACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
64140 TTACTATTCA
1 TTACTGTTCA
64150 TAAAAACATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Done.