Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004115.1 Hibiscus syriacus cultivar Beakdansim tig00009005_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: 53222
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:107 original size:23 final size:23
Alignment explanation
Indices: 81--130 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
71 TATGGCAATA
81 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
* *
104 CGGTGTAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
127 CGGT
1 CGGT
131 ATTTATACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:1621 original size:32 final size:32
Alignment explanation
Indices: 1585--1648 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1575 ATCTTAACAA
*
1585 ACTCTCTCTCTTCTCTAACGTCCTAACGTTCT
1 ACTCTCTCTCTCCTCTAACGTCCTAACGTTCT
1617 ACTCTCTCTCTCCTCTAACGTCCTAACGTTCT
1 ACTCTCTCTCTCCTCTAACGTCCTAACGTTCT
1649 TTCCCTCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.39, G:0.06, T:0.39
Consensus pattern (32 bp):
ACTCTCTCTCTCCTCTAACGTCCTAACGTTCT
Found at i:2608 original size:2 final size:2
Alignment explanation
Indices: 2603--2627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2593 AAAAAATGTT
2603 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2628 TCATGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5828 original size:6 final size:6
Alignment explanation
Indices: 5817--5854 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
5807 AACTAGGACC
5817 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
1 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
5855 ACAGAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
AGTGAG
Found at i:9092 original size:27 final size:26
Alignment explanation
Indices: 9054--9110 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
9044 GAACTCCACC
* *
9054 TAAATTTTATAT-TTAATATATTATTGA
1 TAAATTTGATATATTAA-ATAATATT-A
9081 TAAATTTGATATATTAAATAATATTA
1 TAAATTTGATATATTAAATAATATTA
9107 TAAA
1 TAAA
9111 AAAGTACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 18 0.67
28 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
TAAATTTGATATATTAAATAATATTA
Found at i:10352 original size:7 final size:7
Alignment explanation
Indices: 10319--10350 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
10309 AAAATATGAT
10319 AATTTTA
1 AATTTTA
10326 AATTTTA
1 AATTTTA
10333 AATTTTA
1 AATTTTA
*
10340 AATTATA
1 AATTTTA
10347 AATT
1 AATT
10351 ATCCTGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTTA
Found at i:12023 original size:14 final size:14
Alignment explanation
Indices: 12004--12030 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11994 TGAGTCATCC
12004 CGTTGACTTTGACT
1 CGTTGACTTTGACT
12018 CGTTGACTTTGAC
1 CGTTGACTTTGAC
12031 CCAAAAAGTT
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:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (14 bp):
CGTTGACTTTGACT
Found at i:19182 original size:12 final size:12
Alignment explanation
Indices: 19165--19190 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19155 TGGTGATCAG
19165 ATCGGGTTTAGA
1 ATCGGGTTTAGA
19177 ATCGGGTTTAGA
1 ATCGGGTTTAGA
19189 AT
1 AT
19191 GAAAAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.35
Consensus pattern (12 bp):
ATCGGGTTTAGA
Found at i:20186 original size:2 final size:2
Alignment explanation
Indices: 20175--20229 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
20165 TAATATTTAC
20175 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20216 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
20230 TAGTATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:21667 original size:16 final size:16
Alignment explanation
Indices: 21646--21678 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21636 TCTTTTGTCT
*
21646 TTATTATTATTTTATA
1 TTATTATTATTATATA
21662 TTATTATTATTATATA
1 TTATTATTATTATATA
21678 T
1 T
21679 ATATCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTATATA
Found at i:21831 original size:2 final size:2
Alignment explanation
Indices: 21809--21873 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
21799 TTAGGTTTCT
* * *
21809 TA TA TT TA TA CA TA CA 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
21851 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
21874 GTTCTACACG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23040 original size:10 final size:10
Alignment explanation
Indices: 23025--23064 Score: 62
Period size: 11 Copynumber: 3.8 Consensus size: 10
23015 TCCTTTACCA
23025 TTTATTTTTT
1 TTTATTTTTT
23035 TTTATTTTATT
1 TTTATTTT-TT
23046 TTTATTTATTT
1 TTTATTT-TTT
23057 TTTATTTT
1 TTTATTTT
23065 ACTAACCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.32
11 18 0.64
12 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:23043 original size:22 final size:23
Alignment explanation
Indices: 23018--23066 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
23008 TGTTTTTTCC
23018 TTTACCATTTATTT-TTTTTTAT
1 TTTACCATTTATTTATTTTTTAT
**
23040 TTTA-TTTTTATTTATTTTTTAT
1 TTTACCATTTATTTATTTTTTAT
23062 TTTAC
1 TTTAC
23067 TAACCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTACCATTTATTTATTTTTTAT
Found at i:23045 original size:15 final size:15
Alignment explanation
Indices: 23025--23057 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23015 TCCTTTACCA
*
23025 TTTATTTTTTTTTAT
1 TTTATTTTTATTTAT
23040 TTTATTTTTATTTAT
1 TTTATTTTTATTTAT
23055 TTT
1 TTT
23058 TTATTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:23049 original size:11 final size:11
Alignment explanation
Indices: 23025--23065 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
23015 TCCTTTACCA
23025 TTTATTTT-TT
1 TTTATTTTATT
23035 TTTATTTTATT
1 TTTATTTTATT
23046 TTTA-TTTATTT
1 TTTATTTTA-TT
23057 TTTATTTTA
1 TTTATTTTA
23066 CTAACCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 12 0.43
11 12 0.43
12 4 0.14
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:32529 original size:60 final size:60
Alignment explanation
Indices: 32455--32572 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
32445 AATACTTCGC
* * *
32455 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGA-AAAAAAAAGAAGAAGAAA-AGAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAA-AAGAA-AAAGAGAACGT
* *
32515 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAAAAAGAGAAC
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAAAAGAAAAAGAGAAC
32573 AAAAGAAGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 3 0.06
60 41 0.80
61 7 0.14
ACGTcount: A:0.49, C:0.13, G:0.26, T:0.12
Consensus pattern (60 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAAAAAAAGAAAAAGAGAACGT
Found at i:33119 original size:12 final size:11
Alignment explanation
Indices: 33102--33130 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
33092 AGGAGCATCT
33102 AAAAAAAAAAC
1 AAAAAAAAAAC
33113 AAAAAAAAAAC
1 AAAAAAAAAAC
33124 AAAAAAA
1 AAAAAAA
33131 GAATGTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:33530 original size:105 final size:104
Alignment explanation
Indices: 33344--34277 Score: 1300
Period size: 105 Copynumber: 9.0 Consensus size: 104
33334 AGGTTTTACC
33344 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33409 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTC-CAATTT
*
33449 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
33514 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTC-CAATTT
*
33554 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33619 ACGAAGGGACCGCTGGTTGTCAA-TAA-A----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCAATTT
* *
33652 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
33717 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-A-TTTCCAATTT
* * * * *
33758 CAGAGCCAATTTCAACTTCACAACGAATGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33823 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTC-CAATTT
*
33863 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
33928 ACGAAGGGACCGCTGGTTGTCAA-TAA-A----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCAATTT
*
33961 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
34026 ACGAAGGGACCGCTGGTTGTCAA-TAA-A----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCAATTT
34059 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
34120 ACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
66 ACGAAGGGACCGCTGGTTGTC----AACAA----AC-ATTT-----CCAATTT
* * * *
34173 CAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
34238 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTT-CCAATT
34278 CCAACTTCAC
Statistics
Matches: 755, Mismatches: 41, Indels: 65
0.88 0.05 0.08
Matches are distributed among these distances:
94 79 0.10
98 196 0.26
99 3 0.00
101 1 0.00
103 2 0.00
104 7 0.01
105 278 0.37
106 96 0.13
110 6 0.01
114 11 0.01
118 76 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (104 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCAATTT
Found at i:33902 original size:309 final size:307
Alignment explanation
Indices: 33344--34271 Score: 1462
Period size: 309 Copynumber: 3.0 Consensus size: 307
33334 AGGTTTTACC
*
33344 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * * *
33409 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAATG
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTC-CAATTTCAGAGCCAATTTCAACTTCACAACG
33474 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
33539 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
195 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACAC
33604 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
260 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
33652 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
33717 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAATAAACAA-TT-CCAATTTCAGAGCCAATTTCAACTTCACAAC
* * * * * *
33782 GAATGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAAC
129 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
33847 AAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACG
194 AAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACA
33912 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
259 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
33961 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
34026 ACGAAGGGACCGCTGGTTGTCAAT--A-AA---CAATTTC----CCAATTTCAACTTCACAACGA
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTCCAATTTCAGAGCCAATTTCAACTTCACAACGA
*
34081 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAA
131 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC----A
* * * *
34146 ACAACTTCCCAATTTCAGAGCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGC
192 ACAA----AC-ATTTC----TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
34211 CCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
248 TCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
34271 C
1 C
34272 CCAATTCCAA
Statistics
Matches: 576, Mismatches: 29, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
297 74 0.13
301 12 0.02
305 1 0.00
306 7 0.01
307 1 0.00
308 90 0.16
309 290 0.50
310 101 0.18
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (307 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTCCAATTTCAGAGCCAATTTCAACTTCACAACGA
AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
ACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:34032 original size:43 final size:43
Alignment explanation
Indices: 33971--34126 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
33961 CAGAGCCAAT
*
33971 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
34014 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
34065 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
34108 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
34127 GACTGCTGGT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
43 38 0.46
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:34127 original size:94 final size:95
Alignment explanation
Indices: 33763--34162 Score: 570
Period size: 98 Copynumber: 4.1 Consensus size: 95
33753 AATTTCAGAG
* * * * * *
33763 CCAATTTCAACTTCACAACGAATGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACGATGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
33828 GGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGA
66 GGGACCGCTGGTTGTCAA-TAA-A-----CAATTTC--A
*
33867 GCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
33932 AGGGACCGCTGGTTGTCAATAAACAATTTCAGA
65 AGGGACCGCTGGTTGTCAATAAACAATTTC--A
*
33965 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGA
1 -CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
34030 AGGGACCGCTGGTTGTCAATAAACAATTTC-
65 AGGGACCGCTGGTTGTCAATAAACAATTTCA
34060 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
34125 GGGACTGCTGGTTGTCAATAAACAACTTC-
66 GGGACCGCTGGTTGTCAATAAACAATTTCA
34154 CCAATTTCA
1 CCAATTTCA
34163 GAGCCAATTT
Statistics
Matches: 282, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
94 100 0.35
98 103 0.37
103 1 0.00
104 2 0.01
105 76 0.27
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (95 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCA
Found at i:34171 original size:12 final size:12
Alignment explanation
Indices: 34154--34186 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
34144 AAACAACTTC
34154 CCAATTTCAGAG
1 CCAATTTCAGAG
34166 CCAATTTCAGAG
1 CCAATTTCAGAG
34178 CCAATTTCA
1 CCAATTTCA
34187 ACTTCACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (12 bp):
CCAATTTCAGAG
Found at i:34197 original size:94 final size:92
Alignment explanation
Indices: 33868--34162 Score: 401
Period size: 94 Copynumber: 3.1 Consensus size: 92
33858 AATTTCAGAG
* **
33868 CCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAA-GATATTCAACTCCA-ACAACGCAAGTTCAACTTCACGACGAA
*
33933 GGGACCGCTGGTTGTCAATAAACAATTTC
64 GGGACCGCTGGTTGTCAATAAACAACTTC
** *
33962 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAA-GATATTCAACTCCA-ACAACGCAAGTTCAACTTCACGA
*
34027 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
60 CGAAGGGACCGCTGGTTGTCAATAAACAACTTC
**
34060 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAA-GATATTCAACTCCA-ACAACGCAAGTTCAACTTCACGACGAA
*
34125 GGGACTGCTGGTTGTCAATAAACAACTTC
64 GGGACCGCTGGTTGTCAATAAACAACTTC
34154 CCAATTTCA
1 CCAATTTCA
34163 GAGCCAATTT
Statistics
Matches: 192, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
94 100 0.52
98 92 0.48
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (92 bp):
CCAATTTCAACTTCACAACGAAGATATTCAACTCCAACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTC
Found at i:34216 original size:118 final size:118
Alignment explanation
Indices: 34060--34277 Score: 382
Period size: 118 Copynumber: 1.8 Consensus size: 118
34050 AAACAATTTC
* * *
34060 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACGACGAA
*
34125 GGGACTGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAGAG
*
34178 CCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACGACGAA
*
34243 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
66 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATT
34278 CCAACTTCAC
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 94 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (118 bp):
CCAATTTCAACTTCACAACGAAGGAGATTGGACCCCAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAGAG
Found at i:36140 original size:16 final size:16
Alignment explanation
Indices: 36119--36151 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36109 TCTTTTGTCT
*
36119 TTATTATTATTTTATA
1 TTATTATTATTATATA
36135 TTATTATTATTATATA
1 TTATTATTATTATATA
36151 T
1 T
36152 ATATCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTATATA
Done.