Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004970.1 Hibiscus syriacus cultivar Beakdansim tig00011163_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: 113335
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:10265 original size:2 final size:2
Alignment explanation
Indices: 10258--10288 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10248 AGCTCTGCCC
10258 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 A
10289 AATTTAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15304 original size:136 final size:136
Alignment explanation
Indices: 15144--15419 Score: 543
Period size: 136 Copynumber: 2.0 Consensus size: 136
15134 TTGATATATA
15144 TATATATATATATATCACTTAATTGCCGAATTTAACAGGTATTAGAATCAAAATACCTAAAAGTA
1 TATATATATATATATCACTTAATTGCCGAATTTAACAGGTATTAGAATCAAAATACCTAAAAGTA
15209 TAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACATTTAAAGTTAA
66 TAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACATTTAAAGTTAA
15274 TTCGAG
131 TTCGAG
*
15280 TATATATATATATATCACTTAATTGCCGAATTTAACAGGTATTAGAATCAAAATATCTAAAAGTA
1 TATATATATATATATCACTTAATTGCCGAATTTAACAGGTATTAGAATCAAAATACCTAAAAGTA
15345 TAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACATTTAAAGTTAA
66 TAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACATTTAAAGTTAA
15410 TTCGAG
131 TTCGAG
15416 TATA
1 TATA
15420 GTTTAGATAA
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 139 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (136 bp):
TATATATATATATATCACTTAATTGCCGAATTTAACAGGTATTAGAATCAAAATACCTAAAAGTA
TAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACATTTAAAGTTAA
TTCGAG
Found at i:15623 original size:15 final size:15
Alignment explanation
Indices: 15603--15631 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15593 CTGATAATTT
15603 AAAAAAATTAAAATA
1 AAAAAAATTAAAATA
15618 AAAAAAATTAAAAT
1 AAAAAAATTAAAAT
15632 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAAATTAAAATA
Found at i:16385 original size:19 final size:19
Alignment explanation
Indices: 16357--16393 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16347 TTTTCATTCC
*
16357 ATATCAATTTGTTTAATTT
1 ATATCAATTTATTTAATTT
*
16376 ATATCCATTTATTTAATT
1 ATATCAATTTATTTAATT
16394 AGCCCAATAT
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:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATCAATTTATTTAATTT
Found at i:16569 original size:23 final size:22
Alignment explanation
Indices: 16469--16585 Score: 87
Period size: 23 Copynumber: 5.2 Consensus size: 22
16459 CACCACTGCT
*
16469 CACATAATTTG-CACTGAAGTG-C
1 CACATAATTTGTC-CCGAAG-GAC
* *
16491 CACAT-ATTTGTCCCAAAGGAT
1 CACATAATTTGTCCCGAAGGAC
* * *
16512 CATATAGATTTGTCCTGAATGAC
1 CACATA-ATTTGTCCCGAAGGAC
**
16535 CACATGGGTTTGTCCCGAAGGAC
1 CACAT-AATTTGTCCCGAAGGAC
*
16558 CACATAATTTTGTCTCGAAGGAC
1 CACATAA-TTTGTCCCGAAGGAC
16581 CACAT
1 CACAT
16586 TGAACCCTCG
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 13 0.18
22 6 0.08
23 53 0.73
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (22 bp):
CACATAATTTGTCCCGAAGGAC
Found at i:16570 original size:46 final size:46
Alignment explanation
Indices: 16497--16585 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
16487 GTGCCACATA
* * *
16497 TTTGTCCCAAAGGATCATATAGATTTGTC-CTGAATGACCACATGGG
1 TTTGTCCCAAAGGACCACATAGATTTGTCTC-GAAGGACCACATGGG
*
16543 TTTGTCCCGAAGGACCACATA-ATTTTGTCTCGAAGGACCACAT
1 TTTGTCCCAAAGGACCACATAGA-TTTGTCTCGAAGGACCACAT
16586 TGAACCCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 1 0.03
46 35 0.95
47 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
TTTGTCCCAAAGGACCACATAGATTTGTCTCGAAGGACCACATGGG
Found at i:18805 original size:21 final size:21
Alignment explanation
Indices: 18777--18828 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
18767 GTCTTTCGGG
18777 ACATATATGTAATTCAGTGGA
1 ACATATATGTAATTCAGTGGA
*
18798 ATATATATGTAATTCAGTGGA
1 ACATATATGTAATTCAGTGGA
18819 ACATATATGT
1 ACATATATGT
18829 GGTACTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
ACATATATGTAATTCAGTGGA
Found at i:18944 original size:18 final size:18
Alignment explanation
Indices: 18886--18953 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
18876 TTAAGGAGTA
*
18886 GTCCTTCGGGAGATAGTG
1 GTCCTTCGGGACATAGTG
* *
18904 GTCTTTTGGGACAAATCAGTG
1 GTCCTTCGGGAC--AT-AGTG
*
18925 GTCCTTAGGGACATAGTG
1 GTCCTTCGGGACATAGTG
18943 GTCCTTCGGGA
1 GTCCTTCGGGA
18954 AAAATATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 23 0.56
19 2 0.05
20 2 0.05
21 14 0.34
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:19267 original size:2 final size:2
Alignment explanation
Indices: 19260--19305 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
19250 TAGTGAACGC
19260 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
19302 TA TA
1 TA TA
19306 CGCACATAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24324 original size:21 final size:21
Alignment explanation
Indices: 24300--24339 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
24290 TAATTAAAGG
24300 AAAA-GATATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
24321 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAGATAAGT
24340 GGTGCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:25976 original size:6 final size:6
Alignment explanation
Indices: 25965--26030 Score: 96
Period size: 6 Copynumber: 11.0 Consensus size: 6
25955 AAGCTTCATG
* *
25965 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA GGAAGA TGAAGA GGAAGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA
* *
26013 GGAAGA TGAAGA GGAAGA
1 TGAAGA TGAAGA TGAAGA
26031 AGAGAAAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (6 bp):
TGAAGA
Found at i:26573 original size:14 final size:14
Alignment explanation
Indices: 26554--26582 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26544 AATTAGGTGC
26554 TTATTTAACTTAAT
1 TTATTTAACTTAAT
26568 TTATTTAACTTAAT
1 TTATTTAACTTAAT
26582 T
1 T
26583 AAGTTTAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTAACTTAAT
Found at i:33011 original size:27 final size:26
Alignment explanation
Indices: 32981--33045 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 26
32971 GATATTTGTG
*
32981 AATGAAGAGAGAGAAGAGGAAGCATAA
1 AATGAAGAGA-AGAAGAAGAAGCATAA
33008 AATG-A-AGAAGAAGAAGAAGCATAA
1 AATGAAGAGAAGAAGAAGAAGCATAA
33032 AATGAAGAAGAAGA
1 AATGAAG-AGAAGA
33046 GGAAATGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 19 0.56
25 4 0.12
26 1 0.03
27 10 0.29
ACGTcount: A:0.60, C:0.03, G:0.29, T:0.08
Consensus pattern (26 bp):
AATGAAGAGAAGAAGAAGAAGCATAA
Found at i:33026 original size:24 final size:24
Alignment explanation
Indices: 32992--33045 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
32982 ATGAAGAGAG
*
32992 AGAAGAGGAAGCATAAAATGAAGA
1 AGAAGAAGAAGCATAAAATGAAGA
33016 AGAAGAAGAAGCATAAAATGAAGA
1 AGAAGAAGAAGCATAAAATGAAGA
33040 AGAAGA
1 AGAAGA
33046 GGAAATGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.04, G:0.28, T:0.07
Consensus pattern (24 bp):
AGAAGAAGAAGCATAAAATGAAGA
Found at i:42816 original size:24 final size:22
Alignment explanation
Indices: 42776--42821 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
42766 CGATTCCCCT
42776 AAGGGGGAATCAGTTCCCATTCA
1 AAGGGGGAATCAGTTCCC-TTCA
*
42799 AAGGGGGAATCGGTTTCCCTTCA
1 AAGGGGGAATCAG-TTCCCTTCA
42822 TGGGGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (22 bp):
AAGGGGGAATCAGTTCCCTTCA
Found at i:43550 original size:16 final size:16
Alignment explanation
Indices: 43537--43573 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
43527 TATCTAATTT
43537 GCATCCTCCATAATCC
1 GCATCCTCCATAATCC
43553 GCATCCTCCATAATCC
1 GCATCCTCCATAATCC
43569 GCATC
1 GCATC
43574 AGAAAAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.43, G:0.08, T:0.24
Consensus pattern (16 bp):
GCATCCTCCATAATCC
Found at i:52136 original size:21 final size:21
Alignment explanation
Indices: 52107--52165 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
52097 CCTTTAAAGA
52107 AAGGGATCAATCATTTTCCTC
1 AAGGGATCAATCATTTTCCTC
* *
52128 AATGGATCAATCATTTTCCTT
1 AAGGGATCAATCATTTTCCTC
* *
52149 AAGGGATCGATCTTTTT
1 AAGGGATCAATCATTTT
52166 TGTAAAGCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (21 bp):
AAGGGATCAATCATTTTCCTC
Found at i:56271 original size:37 final size:37
Alignment explanation
Indices: 56216--56298 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
56206 TCCATATATT
56216 CTGACATCGAATCATGTTATTTTTTTTGAATAAATC-A
1 CTGA-ATCGAATCATGTTATTTTTTTTGAATAAATCTA
*
56253 CTGATATCGAATCATGTTATTTTTTTTTAATAAATCTA
1 CTGA-ATCGAATCATGTTATTTTTTTTGAATAAATCTA
56291 CTGAATCG
1 CTGAATCG
56299 TGTTATTTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 38 0.88
38 5 0.12
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (37 bp):
CTGAATCGAATCATGTTATTTTTTTTGAATAAATCTA
Found at i:58075 original size:10 final size:10
Alignment explanation
Indices: 58042--58084 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
58032 AACAAATATT
*
58042 AAATAAATCA
1 AAATAAATAA
*
58052 AAATAAAGAGA
1 AAATAAATA-A
*
58063 AAATATATAA
1 AAATAAATAA
58073 AAATAAATAA
1 AAATAAATAA
58083 AA
1 AA
58085 GGACAAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (10 bp):
AAATAAATAA
Found at i:58124 original size:14 final size:14
Alignment explanation
Indices: 58105--58131 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58095 AAATGGAAAA
58105 AAATAGAAAATAAC
1 AAATAGAAAATAAC
58119 AAATAGAAAATAA
1 AAATAGAAAATAA
58132 ATCAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AAATAGAAAATAAC
Found at i:58175 original size:19 final size:20
Alignment explanation
Indices: 58151--58195 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
58141 ATAAAGTAAG
58151 AATAAAAGATG-CTTTAAAA
1 AATAAAAGATGTCTTTAAAA
*
58170 AATAAAAGATGTTTTTAAAA
1 AATAAAAGATGTCTTTAAAA
58190 AA-AAAA
1 AATAAAA
58196 AAGAACCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (20 bp):
AATAAAAGATGTCTTTAAAA
Found at i:58196 original size:20 final size:19
Alignment explanation
Indices: 58154--58196 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
58144 AAGTAAGAAT
*
58154 AAAAGATGCTTTAAAAAAT
1 AAAAGATGCTTTAAAAAAA
*
58173 AAAAGATGTTTTTAAAAAAA
1 AAAAGATG-CTTTAAAAAAA
58193 AAAA
1 AAAA
58197 AGAACCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (19 bp):
AAAAGATGCTTTAAAAAAA
Found at i:59334 original size:26 final size:26
Alignment explanation
Indices: 59305--59359 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
59295 TTGTTTGACT
59305 TGTGCATTGGACTGGATTCTTAGACC
1 TGTGCATTGGACTGGATTCTTAGACC
59331 TGTGCATTGGACTGGATTCTTAGACC
1 TGTGCATTGGACTGGATTCTTAGACC
59357 TGT
1 TGT
59360 ACAAACACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (26 bp):
TGTGCATTGGACTGGATTCTTAGACC
Found at i:59394 original size:12 final size:12
Alignment explanation
Indices: 59370--59448 Score: 58
Period size: 12 Copynumber: 6.7 Consensus size: 12
59360 ACAAACACCG
*
59370 AAAA-AAATGAT
1 AAAATAAATAAT
59381 AAAATAAATAAT
1 AAAATAAATAAT
* *
59393 AAAACAAAAAAT
1 AAAATAAATAAT
*
59405 AAATAATAAA-ACAA
1 -AA-AATAAATA-AT
59419 AAAATAAATAAT
1 AAAATAAATAAT
*
59431 TAAA-AAA-AAT
1 AAAATAAATAAT
59441 AAAATAAA
1 AAAATAAA
59449 ATACTATATG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 6 0.11
11 10 0.19
12 26 0.48
13 6 0.11
14 6 0.11
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:59405 original size:19 final size:19
Alignment explanation
Indices: 59381--59443 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
59371 AAAAAATGAT
59381 AAAATAAATAATAAAACAA
1 AAAATAAATAATAAAACAA
59400 AAAATAAATAATAAAACAA
1 AAAATAAATAATAAAACAA
*
59419 AAAATAAATAAT-TAA-AA
1 AAAATAAATAATAAAACAA
59436 AAAATAAA
1 AAAATAAA
59444 ATAAAATACT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
17 10 0.23
18 2 0.05
19 31 0.72
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAATAAATAATAAAACAA
Found at i:59562 original size:35 final size:35
Alignment explanation
Indices: 59464--59789 Score: 210
Period size: 35 Copynumber: 9.3 Consensus size: 35
59454 ATATGATATA
* * *
59464 AAAAAATGTTTTAAAACTTTATATAATATATATTTC
1 AAAAAATGTTTTAAAACTATATATTATATA-ATTTT
* ** *
59500 AAAGATAT-TTTCCAAACCATATATTATATAATTTT
1 AAA-AAATGTTTTAAAACTATATATTATATAATTTT
* * *
59535 AAAAAATGTTTTCAAACTATAT-GT-TATAGTTTT
1 AAAAAATGTTTTAAAACTATATATTATATAATTTT
* * *
59568 CAAAAACGTTTTAAAAC--TATATTATAT-GTTTT
1 AAAAAATGTTTTAAAACTATATATTATATAATTTT
* *
59600 CAAAAATGTTTTTTTAAAACTATATATTATATAAATTT
1 AAAAAATG---TTTTAAAACTATATATTATATAATTTT
* *
59638 -CAAAATGATTTTAAAACTATATATTATATAA-ATT
1 AAAAAATG-TTTTAAAACTATATATTATATAATTTT
*
59672 ATCAAAATGGTTTTAAAACTATATATTATAT-ATTTT
1 A-AAAAAT-GTTTTAAAACTATATATTATATAATTTT
* * *
59708 CTAAAAACGTTTTAAAAACTATATA-TAT-T-GTTTT
1 -AAAAAATGTTTT-AAAACTATATATTATATAATTTT
** *
59742 CAAAGGTATTTTTTAAAAACTATATATTATATACATTTT
1 -AAA-AAATGTTTT-AAAACTATATATTATATA-ATTTT
*
59781 -CAAAATGTT
1 AAAAAATGTT
59790 ATTTTTTAAA
Statistics
Matches: 232, Mismatches: 37, Indels: 42
0.75 0.12 0.14
Matches are distributed among these distances:
31 3 0.01
32 13 0.06
33 25 0.11
34 14 0.06
35 77 0.33
36 71 0.31
37 22 0.09
38 3 0.01
39 4 0.02
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAAAATGTTTTAAAACTATATATTATATAATTTT
Found at i:59573 original size:33 final size:33
Alignment explanation
Indices: 59465--59789 Score: 164
Period size: 36 Copynumber: 9.3 Consensus size: 33
59455 TATGATATAA
*
59465 AAAAATGTTTTAAAACTTTATATAATATA-TATTTC
1 AAAAATGTTTTAAAAC-TTATAT-TTATAGT-TTTC
* * * * * *
59500 AAAGATATTTTCCAAACCATATATTATATAATTTTA
1 AAAAATGTTTT--AAAACTTATATT-TATAGTTTTC
*
59536 AAAAATGTTTTCAAAC-TATATGTTATAGTTTTC
1 AAAAATGTTTTAAAACTTATAT-TTATAGTTTTC
*
59569 AAAAACGTTTTAAAAC-TATA-TTATATGTTTTC
1 AAAAATGTTTTAAAACTTATATTTATA-GTTTTC
**
59601 AAAAATGTTTTTTTAAAACTATATATTATATAAATTTC
1 AAAAATG---TTTTAAAACT-TATATT-TATAGTTTTC
* *
59639 -AAAATGATTTTAAAACTATATATTATATAAATTATC
1 AAAAATG-TTTTAAAACT-TATATT-TAT-AGTTTTC
59675 -AAAATGGTTTTAAAACTATATATTATATA-TTTTC
1 AAAAAT-GTTTTAAAACT-TATATT-TATAGTTTTC
* * *
59709 TAAAAACGTTTTAAAAAC-TATATATATTGTTTTC
1 -AAAAATGTTTT-AAAACTTATATTTATAGTTTTC
* * *
59743 AAAGGTATTTTTTAAAAACTATATATTATATACATTTTC
1 AAA--AATGTTTT-AAAACT-TATATT-TATA-GTTTTC
59782 -AAAATGTT
1 AAAAATGTT
59790 ATTTTTTAAA
Statistics
Matches: 233, Mismatches: 32, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
31 5 0.02
32 12 0.05
33 37 0.16
34 18 0.08
35 56 0.24
36 65 0.28
37 21 0.09
38 10 0.04
39 9 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (33 bp):
AAAAATGTTTTAAAACTTATATTTATAGTTTTC
Found at i:59761 original size:71 final size:67
Alignment explanation
Indices: 59472--59785 Score: 233
Period size: 71 Copynumber: 4.5 Consensus size: 67
59462 TAAAAAAATG
* * * ** * * * *
59472 TTTTAAAACTTTATATAATATATATTTCAAAGATATTTTCCAAACCATATATTATATAATTTTAA
1 TTTTAAAACTATATATTATATAT-TTTCAAAAACGTTTT-AAAACTATATA-TATAT-GTTTTCA
* *
59537 AAAATG
62 AATATT
* * *
59543 TTTTCAAACTATATGTTATA-GTTTTCAAAAACGTTTTAAAACTATAT-TATATGTTTTCAAAAA
1 TTTTAAAACTATATATTATATATTTTCAAAAACGTTTTAAAACTATATATATATGTTTTC--AAA
*
59606 TGTTT
64 T-ATT
* * * *
59611 TTTTAAAACTATATATTATATAAATTTC-AAAATGATTTTAAAACTATATATTATATAAATTATC
1 TTTTAAAACTATATATTATAT-ATTTTCAAAAACG-TTTTAAAACTATATA-TATAT--GTTTTC
*
59675 AAA-ATGG
61 AAATAT-T
59682 TTTTAAAACTATATATTATATATTTTCTAAAAACGTTTTAAAAACTATATATAT-TGTTTTCAAA
1 TTTTAAAACTATATATTATATATTTTC-AAAAACGTTTT-AAAACTATATATATATGTTTTCAAA
59746 GGTATT
64 --TATT
59752 TTTTAAAAACTATATATTATATACATTTTCAAAA
1 TTTT-AAAACTATATATTATAT--ATTTTCAAAA
59786 TGTTATTTTT
Statistics
Matches: 194, Mismatches: 29, Indels: 39
0.74 0.11 0.15
Matches are distributed among these distances:
65 4 0.02
66 5 0.03
67 3 0.02
68 34 0.18
69 17 0.09
70 30 0.15
71 63 0.32
72 28 0.14
73 6 0.03
74 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (67 bp):
TTTTAAAACTATATATTATATATTTTCAAAAACGTTTTAAAACTATATATATATGTTTTCAAATA
TT
Found at i:62309 original size:38 final size:36
Alignment explanation
Indices: 62216--62552 Score: 142
Period size: 38 Copynumber: 9.6 Consensus size: 36
62206 TGATTTTCGA
* **
62216 AAATTTATATATTATATAGTTTTTGAAAATATTTTTT
1 AAATTTATATATTATATAG-TTTTGAAAACATTTTGG
* *
62253 AAATATATATAATATATAGTTTTGAAAACATTTTGG
1 AAATTTATATATTATATAGTTTTGAAAACATTTTGG
*
62289 AAACGTTTATATATTATATAGTTTTTAAAACA--TT--
1 AAA--TTTATATATTATATAGTTTTGAAAACATTTTGG
*
62323 --A--TATA-A-TATATAGTTTTGAAAAC--G----
1 AAATTTATATATTATATAGTTTTGAAAACATTTTGG
* * * *
62347 ---TTTATATATTATATAATTTTTAAAACACTTTGA
1 AAATTTATATATTATATAGTTTTGAAAACATTTTGG
** * *
62380 AAACATATATAGTATATAGTTTTAAAAACATTTTTTGTG
1 AAATTTATATATTATATAGTTTTGAAAACA--TTTTG-G
* * *
62419 AAA-TTATATAATATATAGTTTTAAAAACATTTTTGA
1 AAATTTATATATTATATAGTTTTGAAAACA-TTTTGG
* * **
62455 AAACTTATATAATATATAATA-TTTTTAAAACGGTTT-G
1 AAATTTATAT-AT-TAT-ATAGTTTTGAAAACATTTTGG
** * * * *
62492 AAAACTATGTAATATATAGTTTTCTAAAACGTATTTTTG
1 AAATTTATATATTATATAGTTTT-GAAAAC--ATTTTGG
*
62531 AAATATATATATTATATAGTTT
1 AAATTTATATATTATATAGTTT
62553 ATATCATATT
Statistics
Matches: 235, Mismatches: 37, Indels: 54
0.72 0.11 0.17
Matches are distributed among these distances:
25 4 0.02
26 17 0.07
27 16 0.07
28 4 0.02
32 1 0.00
34 3 0.01
35 7 0.03
36 51 0.22
37 36 0.15
38 59 0.25
39 34 0.14
40 3 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
AAATTTATATATTATATAGTTTTGAAAACATTTTGG
Found at i:62313 original size:27 final size:27
Alignment explanation
Indices: 62283--62372 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
62273 TTTGAAAACA
*
62283 TTTTGGAAACGTTTATATATTATATAG
1 TTTTGAAAACGTTTATATATTATATAG
* * *
62310 TTTTTAAAAC-ATTATATAATATATAG
1 TTTTGAAAACGTTTATATATTATATAG
*
62336 TTTTGAAAACGTTTATATATTATATAA
1 TTTTGAAAACGTTTATATATTATATAG
*
62363 TTTTTAAAAC
1 TTTTGAAAAC
62373 ACTTTGAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.43
27 30 0.57
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (27 bp):
TTTTGAAAACGTTTATATATTATATAG
Found at i:62332 original size:26 final size:26
Alignment explanation
Indices: 62295--62373 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
62285 TTGGAAACGT
62295 TTATATATTATATAGTTTTTAAAACA
1 TTATATATTATATAGTTTTTAAAACA
* * *
62321 TTATATAATATATAGTTTTGAAAACGT
1 TTATATATTATATAGTTTTTAAAAC-A
*
62348 TTATATATTATATAATTTTTAAAACA
1 TTATATATTATATAGTTTTTAAAACA
62374 CTTTGAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 23 0.51
27 22 0.49
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (26 bp):
TTATATATTATATAGTTTTTAAAACA
Found at i:62426 original size:127 final size:126
Alignment explanation
Indices: 62219--62449 Score: 313
Period size: 127 Copynumber: 1.8 Consensus size: 126
62209 TTTTCGAAAA
* * * ** * *
62219 TTTATATATTATATAGTTTTTGAAAATATTTTTTAAATATATATAATATATAGTTTTGAAAACAT
1 TTTATATATTATATAATTTTTGAAAACACTTTGAAAACATATATAATATATAGTTTTAAAAACAT
* *
62284 TTTGGAAACGTTTATATATTATATAGTTTTTAAAACATTATATAATATATAGTTTTGAAAACG
66 TTTGGAAAC--TTATATAATATATAGTTTTAAAAACATTATATAATATATAGTTTTGAAAACG
*
62347 TTTATATATTATATAATTTTT-AAAACACTTTGAAAACATATATAGTATATAGTTTTAAAAACAT
1 TTTATATATTATATAATTTTTGAAAACACTTTGAAAACATATATAATATATAGTTTTAAAAACA-
62411 TTTTTGTGAAA-TTATATAATATATAGTTTTAAAAACATT
65 -TTTTG-GAAACTTATATAATATATAGTTTTAAAAACATT
62450 TTTGAAAACT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
127 61 0.68
128 20 0.22
129 5 0.06
130 4 0.04
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (126 bp):
TTTATATATTATATAATTTTTGAAAACACTTTGAAAACATATATAATATATAGTTTTAAAAACAT
TTTGGAAACTTATATAATATATAGTTTTAAAAACATTATATAATATATAGTTTTGAAAACG
Found at i:62481 original size:113 final size:112
Alignment explanation
Indices: 62336--62552 Score: 287
Period size: 113 Copynumber: 1.9 Consensus size: 112
62326 TAATATATAG
* *
62336 TTTTGAAAACGTTTATATATTATATAATTTTTAAAACACTTTGAAAACATATATAGTATATAGTT
1 TTTTGAAAACG-TTATATAATATATAATTTTTAAAACACTTTGAAAAC-TATATAATATATAGTT
*
62401 TT-AAAAACATTTTTTGTGAAAT-TATATAATATATAGTTTTAAAAACAT
64 TTCAAAAACATATTTT-TGAAATATATATAATATATAGTTTTAAAAACAT
** *
62449 TTTTGAAAAC-TTATATAATATATAATATTTTTAAAACGGTTTGAAAACTATGTAATATATAGTT
1 TTTTGAAAACGTTATATAATATAT-A-ATTTTTAAAACACTTTGAAAACTATATAATATATAGTT
* * *
62513 TTCTAAAACGTATTTTTGAAATATATATATTATATAGTTT
64 TTCAAAAACATATTTTTGAAATATATATAATATATAGTTT
62553 ATATCATATT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
111 12 0.13
112 23 0.25
113 56 0.62
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (112 bp):
TTTTGAAAACGTTATATAATATATAATTTTTAAAACACTTTGAAAACTATATAATATATAGTTTT
CAAAAACATATTTTTGAAATATATATAATATATAGTTTTAAAAACAT
Found at i:62583 original size:19 final size:19
Alignment explanation
Indices: 62561--62609 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
62551 TTATATCATA
*
62561 TTATTTATTTTATTTTATT
1 TTATTTATTTTATTTAATT
* *
62580 TTATTAATTTAATTTAATT
1 TTATTTATTTTATTTAATT
* *
62599 TCATATATTTT
1 TTATTTATTTT
62610 TTTCCTCCAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTATTTTATTTAATT
Found at i:63973 original size:22 final size:22
Alignment explanation
Indices: 63948--63990 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
63938 ACTTTAACCC
*
63948 TTTT-TTTTATCTATTTTTATTA
1 TTTTATTTTA-CTATTGTTATTA
63970 TTTTATTTTACTATTGTTATT
1 TTTTATTTTACTATTGTTATT
63991 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTACTATTGTTATTA
Found at i:71455 original size:37 final size:37
Alignment explanation
Indices: 71400--71495 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
71390 TCCATATATT
*
71400 CTGACATCGAATCATGTTATTTTTTTTGAATAAATCA
1 CTGATATCGAATCATGTTATTTTTTTTGAATAAATCA
*
71437 CTGATATCGAATCATGTTATTTTTTTTTAATAAATCA
1 CTGATATCGAATCATGTTATTTTTTTTGAATAAATCA
*
71474 CTGATA-CTGAATCGTGTTATTT
1 CTGATATC-GAATCATGTTATTT
71496 ACTACTACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (37 bp):
CTGATATCGAATCATGTTATTTTTTTTGAATAAATCA
Found at i:76163 original size:16 final size:16
Alignment explanation
Indices: 76127--76163 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
76117 TGTGAATATC
76127 ATTATTTTTTGTGAAA
1 ATTATTTTTTGTGAAA
76143 A-TATTTTTTGT-AATA
1 ATTATTTTTTGTGAA-A
76158 ATTATT
1 ATTATT
76164 AACACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTATTTTTTGTGAAA
Found at i:76542 original size:16 final size:16
Alignment explanation
Indices: 76521--76560 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
76511 TTTGTCATTT
76521 TTACTAAAACTTTTAG
1 TTACTAAAACTTTTAG
76537 TTACTAAAACTTTTAG
1 TTACTAAAACTTTTAG
76553 TTAC-AAAA
1 TTACTAAAA
76561 GTTGTCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (16 bp):
TTACTAAAACTTTTAG
Found at i:77538 original size:35 final size:35
Alignment explanation
Indices: 77482--77605 Score: 176
Period size: 35 Copynumber: 3.5 Consensus size: 35
77472 CTCAAAAAAA
* *
77482 TCGATTAAAGTAGAACAGAAGGAAGCATCGCACTT
1 TCGATTCAAGTAGAACGGAAGGAAGCATCGCACTT
*
77517 TCGATTCAAGTCGAACGGAAGGAAGCATCGCACTT
1 TCGATTCAAGTAGAACGGAAGGAAGCATCGCACTT
* * * *
77552 TTGATTTAAATAGAACGGAAGGAAGCATCGCATTT
1 TCGATTCAAGTAGAACGGAAGGAAGCATCGCACTT
*
77587 TCGATTCAACTAGAACGGA
1 TCGATTCAAGTAGAACGGA
77606 TGGTTTACTA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (35 bp):
TCGATTCAAGTAGAACGGAAGGAAGCATCGCACTT
Found at i:78294 original size:39 final size:39
Alignment explanation
Indices: 78240--78357 Score: 133
Period size: 39 Copynumber: 3.1 Consensus size: 39
78230 ATTTTCAAAT
78240 TATTTCAC-TCTAACATTCTAAATTCCTAATTTCTTAAAA
1 TATTTCACAT-TAACATTCTAAATTCCTAATTTCTTAAAA
** *
78279 T-TTTCTATCA-TAACATTCTAAATTTTTAATTTCTTAAAT
1 TATTTC-A-CATTAACATTCTAAATTCCTAATTTCTTAAAA
78318 TATTTCACATTAACATTCTAAA-T--TAATTT-TTAAAA
1 TATTTCACATTAACATTCTAAATTCCTAATTTCTTAAAA
78353 TATTT
1 TATTT
78358 TTACTTTCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
35 10 0.14
36 6 0.09
38 7 0.10
39 42 0.60
40 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.49
Consensus pattern (39 bp):
TATTTCACATTAACATTCTAAATTCCTAATTTCTTAAAA
Found at i:78567 original size:23 final size:23
Alignment explanation
Indices: 78537--78588 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
78527 ATGAACCAAA
*
78537 TACCCGTGATCCGAAAATACAGG
1 TACCCGTGATCCGAAAATACAAG
78560 TACCCGTGATCCGAAAATACAAG
1 TACCCGTGATCCGAAAATACAAG
78583 TACCCG
1 TACCCG
78589 GATGTCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (23 bp):
TACCCGTGATCCGAAAATACAAG
Found at i:92007 original size:33 final size:33
Alignment explanation
Indices: 91959--92058 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 33
91949 GTTTGGCAAG
*
91959 ATTGGAAATTTAATCTTGGTTGGTGGCCAACTT
1 ATTGGAAAATTAATCTTGGTTGGTGGCCAACTT
* * *
91992 ATTGAAAAATTAATCTTGGTTAGTGGCCAACTC
1 ATTGGAAAATTAATCTTGGTTGGTGGCCAACTT
* *
92025 ATTGGAAAATT-CT-TTGGTAGGTGGCCAACTT
1 ATTGGAAAATTAATCTTGGTTGGTGGCCAACTT
92056 ATT
1 ATT
92059 TTTCATGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.31
32 1 0.02
33 39 0.67
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (33 bp):
ATTGGAAAATTAATCTTGGTTGGTGGCCAACTT
Found at i:101672 original size:43 final size:42
Alignment explanation
Indices: 101624--101930 Score: 346
Period size: 43 Copynumber: 7.1 Consensus size: 42
101614 AAGGAAATTA
* *
101624 GCGGCGTTTGTATAAAAAAACGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTGACCTTTT
*
101667 GCGGCGTTTGTTCCAAAAAAACGCCGCTATATATCTGACCTTTT
1 GCGGCGTTTGTT-C-AAAAAACGCCGCTATAGATCTGACCTTTT
* **
101711 GCAGCGTTTGTATCAAAAAATACCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTGACCTTTT
** * * *
101754 GCGATGTTTGTTCCAAAAAACGCCACTATATATCTGACCTATT
1 GCGGCGTTTGTT-CAAAAAACGCCGCTATAGATCTGACCTTTT
* *
101797 GCGGCGTTTGTTTC-AAAAACGCCGCTATAGATATCAACCTTTT
1 GCGGCGTTTG-TTCAAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
101840 ACGGCGTTTGTTCCAAAAACGCCACTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACCTTTT
* * * *
101883 GCGGCGTTTGTTCCAAAAATGCCGCTATAGATCTTAACCTATT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATC-TGACCTTTT
101926 GCGGC
1 GCGGC
101931 ATTTTTGGTT
Statistics
Matches: 225, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
42 22 0.10
43 161 0.72
44 41 0.18
45 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:101804 original size:86 final size:86
Alignment explanation
Indices: 101624--101930 Score: 395
Period size: 86 Copynumber: 3.6 Consensus size: 86
101614 AAGGAAATTA
* *
101624 GCGGCGTTTGTATAAAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCCAAAAAAAC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC-AAAAAAC
*
101689 GCCGCTATATATCTGACCTTTT
65 GCCACTATATATCTGACCTTTT
* ** **
101711 GCAGCGTTTGTATCAAAAAATACCGCTATAGATCTGACCTTTTGCGATGTTTGTTCCAAAAAACG
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAACG
*
101776 CCACTATATATCTGACCTATT
66 CCACTATATATCTGACCTTTT
* * * *
101797 GCGGCGTTTGTTTC-AAAAACGCCGCTATAGATATCAACCTTTTACGGCGTTTGTTCC-AAAAAC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAAAC
*
101860 GCCACTATAGATCTCGACCTTTT
65 GCCACTATATATCT-GACCTTTT
* * * *
101883 GCGGCGTTTGT-TCCAAAAATGCCGCTATAGATCTTAACCTATTGCGGC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATC-TGACCTTTTGCGGC
101931 ATTTTTGGTT
Statistics
Matches: 192, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
85 38 0.20
86 103 0.54
87 51 0.27
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (86 bp):
GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAACG
CCACTATATATCTGACCTTTT
Found at i:106288 original size:19 final size:19
Alignment explanation
Indices: 106264--106309 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
106254 TTGGTGAGCT
106264 TAATGAGCAATGAGGCGAG
1 TAATGAGCAATGAGGCGAG
106283 TAATGAGCAATGAGGCGAG
1 TAATGAGCAATGAGGCGAG
106302 TAATGAGC
1 TAATGAGC
106310 TTAAATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.35, T:0.17
Consensus pattern (19 bp):
TAATGAGCAATGAGGCGAG
Found at i:112025 original size:21 final size:20
Alignment explanation
Indices: 111999--112095 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
111989 ATCAGTTTCT
111999 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
112020 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
* ** *
112039 ACAATTCGCATTGCGATTTTCC
1 A-AAATCGCAACGCGATTTT-G
* *
112061 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
112081 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
112096 ACACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 30 0.50
21 28 0.47
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:112109 original size:61 final size:59
Alignment explanation
Indices: 111939--112110 Score: 161
Period size: 61 Copynumber: 2.9 Consensus size: 59
111929 AAATGACCAA
* * * *
111939 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATCAGTTTC
* * * * * * * *
111998 TAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTAC-AATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATA-CACAAAATCGCAAT-C-AGTTTC
112060 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAA
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAA
112111 CGCGTATCCG
Statistics
Matches: 87, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
59 17 0.20
60 3 0.03
61 45 0.52
62 22 0.25
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (59 bp):
CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATCAGTTTC
Found at i:112124 original size:20 final size:20
Alignment explanation
Indices: 112062--112291 Score: 214
Period size: 20 Copynumber: 11.5 Consensus size: 20
112052 CGATTTTCCA
* ** *
112062 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
112082 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
112102 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
112122 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* **
112142 AAATCGCAACGCATATGGGT
1 AAATCGCAACGCGTATCCGT
* *
112162 AAATCGCAATGCATATCCGT
1 AAATCGCAACGCGTATCCGT
*
112182 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
112202 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
112222 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
112242 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
112262 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
112282 AAATCACAAC
1 AAATCGCAAC
112292 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:113012 original size:24 final size:24
Alignment explanation
Indices: 112973--113019 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
112963 AAATTTGGTC
112973 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
112997 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
113020 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:113204 original size:12 final size:12
Alignment explanation
Indices: 113187--113211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113177 ATATAATCCT
113187 GAAGAAGAAAAA
1 GAAGAAGAAAAA
113199 GAAGAAGAAAAA
1 GAAGAAGAAAAA
113211 G
1 G
113212 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Done.