Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005130.1 Hibiscus syriacus cultivar Beakdansim tig00011548_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: 78675
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:10323 original size:54 final size:54
Alignment explanation
Indices: 10259--10460 Score: 260
Period size: 54 Copynumber: 3.7 Consensus size: 54
10249 TGCTTCGTTT
*
10259 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACATG
1 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACCTG
** * * * * * *
10313 TCACTCTCTTGCTGTTGGAAATCGTATATGTCTTGTAATGACGTAAGATACCTG
1 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACCTG
* * *
10367 TCACTCTCTTGCACTTGAAAATCAAGTCTGTCTTGTAATAATGTAGGATACCTA
1 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACCTG
* * * *
10421 TCCCTCTCTTGCAGTTGAAAATCATGTCTATCTTGTAATA
1 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATA
10461 GCATAGGATG
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (54 bp):
TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACCTG
Found at i:10455 original size:108 final size:108
Alignment explanation
Indices: 10259--10459 Score: 303
Period size: 108 Copynumber: 1.9 Consensus size: 108
10249 TGCTTCGTTT
* *
10259 TCACTCTCTTGCACTTGAAAATCATGTATGTCTTGTAATAATGTAGGATACATGTCACTCTCTTG
1 TCACTCTCTTGCACTTGAAAATCAAGTATGTCTTGTAATAATGTAGGATACATATCACTCTCTTG
* * * *
10324 CTGTTGGAAATCGTATATGTCTTGTAATGACGTAAGATACCTG
66 CAGTTGAAAATCATATATATCTTGTAATGACGTAAGATACCTG
* * *
10367 TCACTCTCTTGCACTTGAAAATCAAGTCTGTCTTGTAATAATGTAGGATACCTATCCCTCTCTTG
1 TCACTCTCTTGCACTTGAAAATCAAGTATGTCTTGTAATAATGTAGGATACATATCACTCTCTTG
* *
10432 CAGTTGAAAATCATGTCTATCTTGTAAT
66 CAGTTGAAAATCATATATATCTTGTAAT
10460 AGCATAGGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 82 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (108 bp):
TCACTCTCTTGCACTTGAAAATCAAGTATGTCTTGTAATAATGTAGGATACATATCACTCTCTTG
CAGTTGAAAATCATATATATCTTGTAATGACGTAAGATACCTG
Found at i:17546 original size:62 final size:62
Alignment explanation
Indices: 17449--17570 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
17439 GTAATACGTT
*
17449 GACACAATAAACGGTAAAAAACAAACGATACCCTTTTCCAGGCTGGTTGCCGGAAACACCTC
1 GACACAACAAACGGTAAAAAACAAACGATACCCTTTTCCAGGCTGGTTGCCGGAAACACCTC
* ** *
17511 GACACAACAAACGGTTAAAAATGAATGATACCCTTTTCCAGGCTGGTTGCCGGAAACACC
1 GACACAACAAACGGTAAAAAACAAACGATACCCTTTTCCAGGCTGGTTGCCGGAAACACC
17571 GTGTTTACCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (62 bp):
GACACAACAAACGGTAAAAAACAAACGATACCCTTTTCCAGGCTGGTTGCCGGAAACACCTC
Found at i:20659 original size:12 final size:13
Alignment explanation
Indices: 20644--20695 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
20634 TAAATGAGGG
20644 AAAAAATAAAATA
1 AAAAAATAAAATA
**
20657 AAAAAATGGAATA
1 AAAAAATAAAATA
20670 AAAATAATAAAATA
1 AAAA-AATAAAATA
20684 AATAATAATAAA
1 AA-AA-AATAAA
20696 TAGGGTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 15 0.45
14 9 0.27
15 9 0.27
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:20671 original size:18 final size:17
Alignment explanation
Indices: 20647--20695 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
20637 ATGAGGGAAA
20647 AAATAAAATAAAAAAAT
1 AAATAAAATAAAAAAAT
* *
20664 GGAATAAAAATAATAAAAT
1 -AAAT-AAAATAAAAAAAT
20683 AAATAATAATAAA
1 AAATAA-AATAAA
20696 TAGGGTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 12 0.48
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAAATAAAAAAAT
Found at i:20697 original size:19 final size:19
Alignment explanation
Indices: 20647--20697 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
20637 ATGAGGGAAA
20647 AAATAAAATAAA-AAAATG
1 AAATAAAATAAATAAAATG
*
20665 GAATAAAA-ATAATAAAAT-
1 AAATAAAATA-AATAAAATG
20683 AAATAATAATAAATA
1 AAATAA-AATAAATA
20698 GGGTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 14 0.52
19 11 0.41
20 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAATAAAATAAATAAAATG
Found at i:21511 original size:33 final size:33
Alignment explanation
Indices: 21474--21552 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
21464 TTATGCTCGA
* *
21474 GTATTTCGTATGTATGGGTGTAAAAAAAAACTT
1 GTATTTCATATCTATGGGTGTAAAAAAAAACTT
*
21507 GTATTTCATATCTATGGGTGTAAAAAAAATCTT
1 GTATTTCATATCTATGGGTGTAAAAAAAAACTT
21540 GTATTTCATATCT
1 GTATTTCATATCT
21553 CTTTCCCCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (33 bp):
GTATTTCATATCTATGGGTGTAAAAAAAAACTT
Found at i:22818 original size:148 final size:152
Alignment explanation
Indices: 22549--22975 Score: 547
Period size: 148 Copynumber: 2.8 Consensus size: 152
22539 ATTGATAGAT
* * * * * * **
22549 AGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGAGCCTTAGAGCTGAGTATAGTCAAACTCGA
1 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGA
* * *
22614 AGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGTGCCCTCGAAGCTGA
66 AGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGA
22679 GTGTAATCGAACTC-G-AGG-G
131 GTGTAATCGAACTCAGTAGGAG
* *
22698 -GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGA
1 AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGA
22762 AGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGA
66 AGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGA
*
22827 GTGTAATCGAACTCAAGGGTCTTTGGCAG
131 GTGTAATCGAACTC-A--G---TAGG-AG
22856 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
1 --AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
* * * *
22921 GAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGAT
64 GAAGGTC--T--TTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
22976 AAGCCTTGGA
Statistics
Matches: 241, Mismatches: 20, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
148 130 0.54
152 1 0.00
156 2 0.01
158 1 0.00
161 67 0.28
163 1 0.00
165 39 0.16
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (152 bp):
AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGA
AGGTCTTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGA
GTGTAATCGAACTCAGTAGGAG
Found at i:22959 original size:84 final size:84
Alignment explanation
Indices: 22699--23304 Score: 677
Period size: 84 Copynumber: 7.3 Consensus size: 84
22689 ACTCGAGGGG
* *
22699 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
22764 GTCTTTGG-T---AGATAA
66 GTCTTTGGTTGGCAGATAA
* * * *** * *
22779 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTC-AA
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
22843 GGGTC--T--TTGGCAGATAG
65 -GGTCTTTGGTTGGCAGATAA
* *
22860 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
22925 GTCTTTGGTTGGTAGATAA
66 GTCTTTGGTTGGCAGATAA
* ** *
22944 CCCTTCTCGACTTAAGTTATACTGCAAATGATAAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
23009 GTTTTTTGG-TGACAGATAA
66 G-TCTTTGGTTGGCAGATAA
* * * * * * * * * *
23028 CCCTTCTAGTCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC-AA
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
23092 GGGTCTTTGG-T---AGATAG
65 -GGTCTTTGGTTGGCAGATAA
* * *
23109 CCATTCTGGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
23174 GTCTTTGGTTGGCAGATAA
66 GTCTTTGGTTGGCAGATAA
* *
23193 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
23258 ATCTTTTGG-TGACAGATAA
66 GTC-TTTGGTTGGCAGATAA
* * *
23277 CCCTTCTAGCCTTGAGTTATGCTGCAAA
1 CCCTTCTCGACTTAAGTTATGCTGCAAA
23305 CAGTTTCTAA
Statistics
Matches: 439, Mismatches: 67, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.00
79 1 0.00
80 88 0.20
81 99 0.23
82 1 0.00
84 214 0.49
85 35 0.08
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAGATAA
Found at i:23104 original size:165 final size:162
Alignment explanation
Indices: 22699--23304 Score: 700
Period size: 165 Copynumber: 3.7 Consensus size: 162
22689 ACTCGAGGGG
* * * *
22699 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * ***
22764 GTC-TTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAG
66 GTCTTTTGGTAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAG
* * *
22828 TGTAATCGAACTCAAGGGTCTTT-G-GCAGATAG
130 CGTAGTCGAACTCAA-GGTCTTTGGTGCAGATAA
* * * *
22860 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * **
22925 GTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATAAGCCTTGGAGCTG
66 GTC-TT--TTGGTAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTG
*
22990 AGCGTAGTCGAACTCAAAGGTTTTTTGGTGACAGATAA
128 AGCGTAGTCGAACTC-AAGG-TCTTTGGTG-CAGATAA
* * * * * * * * *
23028 CCCTTCTAGTCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC-AA
1 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * *
23092 GGGTC-TTTGGTAGATAGCCATTCTGGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGA
65 -GGTCTTTTGGTAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGA
23156 GCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
129 GCGTAGTCGAACTC-AAGGTCTTTGG-T-GCAGATAA
23193 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * *
23258 ATCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
66 GTCTTTTGGT---AGATAACCCTTCTAGACTTAAGTTATGCTGCAAA
23305 CAGTTTCTAA
Statistics
Matches: 375, Mismatches: 52, Indels: 29
0.82 0.11 0.06
Matches are distributed among these distances:
161 66 0.18
163 1 0.00
164 54 0.14
165 161 0.43
166 2 0.01
167 2 0.01
168 64 0.17
169 25 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTTGGTAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAGGTCTTTGGTGCAGATAA
Found at i:23137 original size:249 final size:249
Alignment explanation
Indices: 22699--23304 Score: 986
Period size: 249 Copynumber: 2.4 Consensus size: 249
22689 ACTCGAGGGG
* * *
22699 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
22764 G-TCTTTGGT---AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCT
66 GTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCAAAGCT
*
22825 GAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
131 GAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATG
*
22890 ATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGTAGATAA
196 ATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAA
* * *
22944 CCCTTCTCGACTTAAGTTATACTGCAAATGATAAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * *
23009 GTTTTTTGGTGACAGATAACCCTTCTAGTCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCT
66 GTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCAAAGCT
* * * *
23074 GAGTGTAATCGAACTCAAGGGTCTTTGGTAGATAGCCATTCTGGACTTAAGTTATGTTGCAAATG
131 GAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATG
*
23139 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
196 ATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAA
*
23193 CCCTTCTCGACTTAAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
23258 ATCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
66 GTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
23305 CAGTTTCTAA
Statistics
Matches: 329, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
245 60 0.18
246 7 0.02
249 262 0.80
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (249 bp):
CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCAAAGCT
GAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATG
ATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAA
Found at i:27405 original size:13 final size:15
Alignment explanation
Indices: 27387--27418 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
27377 GTTAGATTGT
27387 AAAAATAAA-AT-AA
1 AAAAATAAATATGAA
27400 AAAAATAAATATGAA
1 AAAAATAAATATGAA
27415 AAAA
1 AAAA
27419 GGGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAATAAATATGAA
Found at i:32791 original size:20 final size:20
Alignment explanation
Indices: 32766--32815 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
32756 CAGCTGAGGA
* *
32766 AAAAGATTCACCTTTGTCAG
1 AAAAGAGTCACATTTGTCAG
32786 AAAAGAGTCACATTTGTCAG
1 AAAAGAGTCACATTTGTCAG
32806 AAAAGAGTCA
1 AAAAGAGTCA
32816 ACCAACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAAGAGTCACATTTGTCAG
Found at i:37995 original size:4 final size:4
Alignment explanation
Indices: 37988--38029 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
37978 AATGTGAAAT
*
37988 TAAA TAAA -AAA TTAAA TTAAA GAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA -TAAA -TAAA TAAA TAAA TAAA TAAA TAAA T
38030 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 23 0.68
5 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:37999 original size:12 final size:12
Alignment explanation
Indices: 37983--38029 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
37973 AAATAAATGT
37983 GAAATTAAATAAA
1 GAAA-TAAATAAA
37996 -AAATTAAATTAAA
1 GAAA-TAAA-TAAA
38009 GAAATAAATAAA
1 GAAATAAATAAA
*
38021 TAAATAAAT
1 GAAATAAAT
38030 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 20 0.65
13 8 0.26
14 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (12 bp):
GAAATAAATAAA
Found at i:38327 original size:32 final size:30
Alignment explanation
Indices: 38269--38369 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 30
38259 CTTTAATCTC
*
38269 TAAATTTTAGAT-ACATATCTAATTTGACTCT
1 TAAATTTTAGATAAAATATC-AATTTGAC-CT
* *
38300 TAAAATTTT-GTTGAAAATATCATTTTGACCCT
1 T-AAATTTTAGAT-AAAATATCAATTTGA-CCT
*
38332 TAACTTTTAGATAAAATATCAATTTGACCTT
1 TAAATTTTAGATAAAATATCAATTTGACC-T
38363 TAAATTT
1 TAAATTT
38370 GATCAAAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
30 2 0.04
31 30 0.53
32 18 0.32
33 7 0.12
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (30 bp):
TAAATTTTAGATAAAATATCAATTTGACCT
Found at i:40951 original size:20 final size:21
Alignment explanation
Indices: 40867--40944 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
40857 AATGTCATCT
*
40867 CAAACCCTAAAACATATACTA
1 CAAACCCTAAAACATAGACTA
40888 CAAACCCTAAAACATAGACTA
1 CAAACCCTAAAACATAGACTA
40909 CAAACCCTAAAACATAGACTA
1 CAAACCCTAAAACATAGACTA
*
40930 TAAACCCT-AAACATA
1 CAAACCCTAAAACATA
40945 TCCTATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
20 7 0.13
21 48 0.87
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (21 bp):
CAAACCCTAAAACATAGACTA
Found at i:41172 original size:2 final size:2
Alignment explanation
Indices: 41165--41205 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41155 ATCATAACTC
41165 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
41206 CAATGAACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41541 original size:23 final size:26
Alignment explanation
Indices: 41488--41542 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 26
41478 TTAAAAACTT
*
41488 TAATTTCATTTAATTGTTTTAGTTATAA
1 TAATTTCATATAATTGTTTTA--TATAA
41516 TAATTTCATATAATT-TTTTAATATAA
1 TAATTTCATATAATTGTTTT-ATATAA
41542 T
1 T
41543 GTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 15 0.60
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TAATTTCATATAATTGTTTTATATAA
Found at i:43469 original size:18 final size:18
Alignment explanation
Indices: 43430--43469 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43420 ATGATGTAGC
*
43430 CATGGCATGAGTCACCTG
1 CATGGCATGAGTCACCTA
*
43448 CATGGCATGAGTCAGCTA
1 CATGGCATGAGTCACCTA
43466 CATG
1 CATG
43470 AGTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (18 bp):
CATGGCATGAGTCACCTA
Found at i:44885 original size:19 final size:19
Alignment explanation
Indices: 44857--44893 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44847 ATTTCTGTAT
44857 ATCATATAATACATATAAC
1 ATCATATAATACATATAAC
* *
44876 ATCATGTAATTCATATAA
1 ATCATATAATACATATAA
44894 TACATTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCATATAATACATATAAC
Found at i:45225 original size:23 final size:21
Alignment explanation
Indices: 45199--45245 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 21
45189 GTACTCATGT
45199 CATTTCTCTTGTGATCACATAT-A
1 CATTTCT-TT-TG-TCACATATCA
45222 CATTTCTTTTGTCACATATCA
1 CATTTCTTTTGTCACATATCA
45243 CAT
1 CAT
45246 GTATGTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 2 0.09
23 7 0.30
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (21 bp):
CATTTCTTTTGTCACATATCA
Found at i:50859 original size:19 final size:19
Alignment explanation
Indices: 50831--50867 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50821 ATTTTTATAT
50831 ATCATATAATACATATAAC
1 ATCATATAATACATATAAC
* *
50850 ATCATGTAATTCATATAA
1 ATCATATAATACATATAA
50868 TACATTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCATATAATACATATAAC
Found at i:52705 original size:3 final size:3
Alignment explanation
Indices: 52697--52756 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
52687 TTCCAAGGGG
* * *
52697 AGA AGA AGA TGA AGA AG- AGA AGGG AGA AGA AGA TGA AGA AG- AGA
1 AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA
*
52741 AGGG AGA AGA AGA AGA
1 A-GA AGA AGA AGA AGA
52757 TAACTCTTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.82
4 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:52757 original size:27 final size:24
Alignment explanation
Indices: 52694--52753 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
52684 AGCTTCCAAG
52694 GGGAGAAGAAGATGAAGAAGAGAA
1 GGGAGAAGAAGATGAAGAAGAGAA
52718 GGGAGAAGAAGATGAAGAAGAGAA
1 GGGAGAAGAAGATGAAGAAGAGAA
52742 GGGAGAAGAAGA
1 GGGAGAAGAAGA
52754 AGATAACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.03
Consensus pattern (24 bp):
GGGAGAAGAAGATGAAGAAGAGAA
Found at i:54420 original size:49 final size:49
Alignment explanation
Indices: 54367--54671 Score: 337
Period size: 49 Copynumber: 6.3 Consensus size: 49
54357 ACTTCTCTAA
* * * * *
54367 AATGAAAGTTAAATGTCTAACGGTGCATTTTTGGTAGAGAGGTGCCACT
1 AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
* * * * *
54416 AATGAAAGTTAGATGACAAATGGTTCA-TTTTGGCAGAAATGTGCCACT
1 AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
*** * *
54464 AATGCAAGTTAAATG-CCTCTCGGTGCATTTTTGGTAGAAAAGTGTCACT
1 AATGCAAGTTAAATGACAAAT-GGTGCATTTTTGGTAGAAAGGTGCCACT
* *
54513 AATGCAAGTTAGATGACAAATGGTGCA-TTATGGTAGAAAGGTGCCACT
1 AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
* * * * *
54561 AATGCAAGTTAAATGCCTAATTGTGCATTTTTAGTAGAAAGGTGCTACT
1 AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
* * * * *
54610 AATGCAAGTTAGATGACAAATTGTGCATTTTAGGCAGATAGGTGCCACT
1 AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
54659 AATGCAAGTTAAA
1 AATGCAAGTTAAA
54672 AACATAACGG
Statistics
Matches: 212, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
47 2 0.01
48 77 0.36
49 131 0.62
50 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (49 bp):
AATGCAAGTTAAATGACAAATGGTGCATTTTTGGTAGAAAGGTGCCACT
Found at i:54551 original size:97 final size:96
Alignment explanation
Indices: 54367--54671 Score: 423
Period size: 97 Copynumber: 3.1 Consensus size: 96
54357 ACTTCTCTAA
* * * * *
54367 AATGAAAGTTAAATGTCTAACGGTGCATTTTTGGTAGAGAGGTGCCACTAATGAAAGTTAGATGA
1 AATGCAAGTTAAATGCCTATCGGTGCATTTTTGGTAGAAAGGTG-CACTAATGCAAGTTAGATGA
* *
54432 CAAATGGTTCATTTTGGCAGAAATGTGCCACT
65 CAAATGGTGCATTTTGGCAGAAAGGTGCCACT
* *
54464 AATGCAAGTTAAATGCCTCTCGGTGCATTTTTGGTAGAAAAGTGTCACTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTATCGGTGCATTTTTGGTAGAAAGGTG-CACTAATGCAAGTTAGATGA
* *
54529 CAAATGGTGCATTATGGTAGAAAGGTGCCACT
65 CAAATGGTGCATTTTGGCAGAAAGGTGCCACT
* *
54561 AATGCAAGTTAAATGCCTAAT-TGTGCATTTTTAGTAGAAAGGTGCTACTAATGCAAGTTAGATG
1 AATGCAAGTTAAATGCCT-ATCGGTGCATTTTTGGTAGAAAGGTGC-ACTAATGCAAGTTAGATG
* *
54625 ACAAATTGTGCATTTTAGGCAGATAGGTGCCACT
64 ACAAATGGTGCATTTT-GGCAGAAAGGTGCCACT
54659 AATGCAAGTTAAA
1 AATGCAAGTTAAA
54672 AACATAACGG
Statistics
Matches: 185, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
96 1 0.01
97 155 0.84
98 29 0.16
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (96 bp):
AATGCAAGTTAAATGCCTATCGGTGCATTTTTGGTAGAAAGGTGCACTAATGCAAGTTAGATGAC
AAATGGTGCATTTTGGCAGAAAGGTGCCACT
Found at i:54684 original size:146 final size:146
Alignment explanation
Indices: 54384--54689 Score: 339
Period size: 146 Copynumber: 2.1 Consensus size: 146
54374 GTTAAATGTC
* * * * *
54384 TAACGGTGCATTTTTGGTAGAGAGGTGCCACTAATGAAAGTTAGATGACAAATGGTTCATTTTGG
1 TAACGGTGCA-TTATGGTAGAAAGGTGCCACTAATGAAAGTTAAATGACAAATGGTGCATTTTAG
* *** * * *
54449 CAGAAATGTGCCACTAATGCAAGTTAAATGCCTCTCGGTGCATTTTTGGTAGAAAAGTGTCACTA
65 CAGAAAGGTGCCACTAATGCAAGTTAAATGCAAATCGGTGCATTTTAGGCAGAAAAGTGCCACTA
**
54514 ATGCAAGTTAGATGACA
130 ATGCAAGTTAGAAAACA
* * * * *
54531 -AATGGTGCATTATGGTAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAATTGTGCATTTTTAG
1 TAACGGTGCATTATGGTAGAAAGGTGCCACTAATGAAAGTTAAATGACAAATGGTGCA-TTTTAG
* * * * * *
54595 TAGAAAGGTGCTACTAATGCAAGTTAGATGACAAAT-TGTGCATTTTAGGCAGATAGGTGCCACT
65 CAGAAAGGTGCCACTAATGCAAGTTAAATG-CAAATCGGTGCATTTTAGGCAGAAAAGTGCCACT
54659 AATGCAAGTTA-AAAACA
129 AATGCAAGTTAGAAAACA
54676 TAACGGTGCATTAT
1 TAACGGTGCATTAT
54690 CGACATGGAA
Statistics
Matches: 130, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
145 44 0.34
146 84 0.65
147 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (146 bp):
TAACGGTGCATTATGGTAGAAAGGTGCCACTAATGAAAGTTAAATGACAAATGGTGCATTTTAGC
AGAAAGGTGCCACTAATGCAAGTTAAATGCAAATCGGTGCATTTTAGGCAGAAAAGTGCCACTAA
TGCAAGTTAGAAAACA
Found at i:59853 original size:49 final size:49
Alignment explanation
Indices: 59789--59906 Score: 164
Period size: 49 Copynumber: 2.4 Consensus size: 49
59779 CTTAGAAATA
* * * *
59789 TGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAAG
1 TGCCACTAATGCAAGTTAAATGACAAACGGTGCATTTTAGGCAGAAAAG
* * * *
59838 TGTCACTAATGCAAGTTAGATGACAAATGGTGCATTTTAGGCAGAAAGG
1 TGCCACTAATGCAAGTTAAATGACAAACGGTGCATTTTAGGCAGAAAAG
59887 TGCCACTAATGCAAGTTAAA
1 TGCCACTAATGCAAGTTAAA
59907 CGGATAATAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (49 bp):
TGCCACTAATGCAAGTTAAATGACAAACGGTGCATTTTAGGCAGAAAAG
Found at i:59920 original size:49 final size:48
Alignment explanation
Indices: 59789--59942 Score: 146
Period size: 49 Copynumber: 3.1 Consensus size: 48
59779 CTTAGAAATA
** * * * *
59789 TGCCACTAATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAAG
1 TGCCACTAATGCAAGTTAAA-GGATAATGGTGCATTTTAGGCAGAAAGG
* * * *
59838 TGTCACTAATGCAAGTTAGATGACAAATGGTGCATTTTAGGCAGAAAGG
1 TGCCACTAATGCAAGTTAAAGGA-TAATGGTGCATTTTAGGCAGAAAGG
* * *
59887 TGCCACTAATGCAAGTTAAACGGATAATAGTGCATTATCGGCATGAAAGG
1 TGCCACTAATGCAAGTTAAA-GGATAATGGTGCATTTTAGGCA-GAAAGG
59937 ATGCCA
1 -TGCCA
59943 TAAATGAAAA
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
49 71 0.85
50 8 0.10
51 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (48 bp):
TGCCACTAATGCAAGTTAAAGGATAATGGTGCATTTTAGGCAGAAAGG
Found at i:59978 original size:24 final size:24
Alignment explanation
Indices: 59951--59999 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
59941 CATAAATGAA
59951 AATACATAACGGTGCA-TAATCGAC
1 AATACATAACGGTGCATTAA-CGAC
59975 AATACATAACGGTGCATTAACGAC
1 AATACATAACGGTGCATTAACGAC
59999 A
1 A
60000 TATAAAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (24 bp):
AATACATAACGGTGCATTAACGAC
Found at i:61264 original size:17 final size:17
Alignment explanation
Indices: 61242--61275 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61232 TCTACCAACC
61242 TTCTAATGTAAAAGATA
1 TTCTAATGTAAAAGATA
61259 TTCTAATGTAAAAGATA
1 TTCTAATGTAAAAGATA
61276 AGGGTACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
TTCTAATGTAAAAGATA
Found at i:61436 original size:23 final size:23
Alignment explanation
Indices: 61401--61459 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
61391 ATCAAGCACA
* *
61401 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
61424 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
61447 ATAATAAAATAGG
1 ATAATATAATAGG
61460 CATTTAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:61534 original size:87 final size:87
Alignment explanation
Indices: 61373--61535 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
61363 TATGTTATAT
61373 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
**
61438 AGCGCTTATATAATAAAATAGG
66 AGCAATTATATAATAAAATAGG
* *
61460 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
61525 AGCAATTATAT
66 AGCAATTATAT
61536 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
AGCAATTATATAATAAAATAGG
Found at i:62258 original size:182 final size:181
Alignment explanation
Indices: 61918--62269 Score: 535
Period size: 182 Copynumber: 1.9 Consensus size: 181
61908 TGTTAACCTA
** *
61918 TTTTCTCATATTTTTAGTTGTTATATTGTTATCGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTCTCATATTTTTACCTGTTATATTGTTATCGATCGATACATTTTCATAAAGTATCGACACTT
61983 TTTAACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGAA
66 TTTAACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGAA
* * * * *
62048 ACTTTCAGCATATCAGGTATCCTTTTACCGGTTTTGTCATTTTGTGACCGG
131 ACTTGCAACATATCAGATAGCCTTTTACCAGTTTTGTCATTTTGTGACCGG
* * *
62099 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-TTAAAAGTATCGACACT
1 TTTTCTCATATTTTTACCTGTTATATTGTTATCGATCGATACATTTTCAT-AAAGTATCGACACT
*
62163 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
65 TTTTA-ACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * * *
62228 ACACTTGCAATATATCCGATAGCGTTTTACCAGTTTTGTCAT
129 AAACTTGCAACATATCAGATAGCCTTTTACCAGTTTTGTCAT
62270 ATTTTTACCT
Statistics
Matches: 153, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
180 1 0.01
181 61 0.40
182 91 0.59
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (181 bp):
TTTTCTCATATTTTTACCTGTTATATTGTTATCGATCGATACATTTTCATAAAGTATCGACACTT
TTTAACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGAA
ACTTGCAACATATCAGATAGCCTTTTACCAGTTTTGTCATTTTGTGACCGG
Found at i:62273 original size:162 final size:162
Alignment explanation
Indices: 62098--62431 Score: 571
Period size: 162 Copynumber: 2.1 Consensus size: 162
62088 TTTGTGACCG
*
62098 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT-TAAAAGTATCGACAC
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTAT-AAAGTATCGACAC
62162 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
65 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
* * *
62227 GACACTTGCAATATATCCGATAGCGTTTTACCA
130 GACACTTGCAACAAATCCGATAGCATTTTACCA
*
62260 GTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTGTCGACACT
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
*
62325 TTTTAGGCGCTATAACTTCTTCTTTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
66 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
62390 ACACTTGCAACAAATTCGATATCATTTTACCG
131 ACACTTGCAACAAATCCGATAGCATTTTACCA
62422 GTTTTGTCAT
1 GTTTTGTCAT
62432 TTTGAGACTG
Statistics
Matches: 162, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
162 161 0.99
163 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (162 bp):
GTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
ACACTTGCAACAAATCCGATAGCATTTTACCA
Found at i:65247 original size:21 final size:21
Alignment explanation
Indices: 65205--65247 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
65195 TTTATGGGTT
*
65205 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
65226 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
65247 A
1 A
65248 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:66204 original size:103 final size:103
Alignment explanation
Indices: 65773--66196 Score: 758
Period size: 103 Copynumber: 4.1 Consensus size: 103
65763 GTAGAGGGTC
*
65773 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
65838 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
65876 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
**
65941 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
65979 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
66044 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
66082 TATATGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
66147 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATTA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66185 TATGTGGTCCTT
1 TATGTGGTCCTT
66197 ATGGACATTA
Statistics
Matches: 308, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 308 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:66248 original size:23 final size:24
Alignment explanation
Indices: 66217--66275 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
66207 TTATATGGCA
66217 TTACGGTGCAATTCTACGCAGCAC
1 TTACGGTGCAATTCTACGCAGCAC
**
66241 -TACGGTGCAATTCTACGTGGCAC
1 TTACGGTGCAATTCTACGCAGCAC
66264 TTA-GGTGCAATT
1 TTACGGTGCAATT
66276 ATATGAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (24 bp):
TTACGGTGCAATTCTACGCAGCAC
Found at i:72357 original size:21 final size:21
Alignment explanation
Indices: 72315--72357 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
72305 TTTCTGGGCT
*
72315 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
72336 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
72357 A
1 A
72358 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:72410 original size:20 final size:20
Alignment explanation
Indices: 72385--72422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
72375 GAACGCTAGA
*
72385 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
72405 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
72423 TAATAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:73344 original size:103 final size:103
Alignment explanation
Indices: 72913--73336 Score: 749
Period size: 103 Copynumber: 4.1 Consensus size: 103
72903 GTAGAGGGTC
72913 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
72978 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *** *
73016 TATGTGGTCTTTTATGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
73081 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
73119 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
73184 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
73222 TATGTGGTCATTCGGGACATATATGTATTCTTGGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
73287 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATTA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
73325 TATGTGGTCCTT
1 TATGTGGTCCTT
73337 ATGGACATTA
Statistics
Matches: 303, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 303 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:73386 original size:23 final size:23
Alignment explanation
Indices: 73355--73415 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
73345 TATTATATGA
73355 CACTACGGTGCAATTCTACGCCG
1 CACTACGGTGCAATTCTACGCCG
* **
73378 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCCG
73401 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
73416 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCCG
Done.