Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003234.1 Hibiscus syriacus cultivar Beakdansim tig00006806_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: 77029
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1592 original size:19 final size:19
Alignment explanation
Indices: 1529--1584 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
1519 AATGTCGAGT
*
1529 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
1548 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1567 TAATTTTGTATACGATTT
1 TAATTTTGTATACGATTT
1585 TATATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:2381 original size:194 final size:199
Alignment explanation
Indices: 1673--2811 Score: 1885
Period size: 194 Copynumber: 5.8 Consensus size: 199
1663 TTAAGGGTCA
* *** *
1673 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1737 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAAT
66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1802 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1866 TAATG
195 TAATG
1871 TGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
1935 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2000 GT--TATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTAT--GAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
2060 TAATG
195 TAATG
2065 TGTCG--ACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
2126 CATAAAGTGTCGATCC-ATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCAATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2190 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
2255 TAATG
195 TAATG
*** *
2260 TGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTT-CCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
2322 AATAAAGTGTCGATCC-ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
2385 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
2450 AATG
196 AATG
2454 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
2519 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2584 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-ATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
2648 TAATG
195 TAATG
* *** *
2653 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
2717 AATAAAGTGTCGATCC-ATATATAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAG--TAATG
66 AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
2778 TAATATGTAATTTTTTAATCTAACCAGTACAATT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATT
2812 TGCTTCTCGA
Statistics
Matches: 896, Mismatches: 27, Indels: 41
0.93 0.03 0.04
Matches are distributed among these distances:
189 5 0.01
190 44 0.05
191 68 0.08
192 42 0.05
193 43 0.05
194 164 0.18
195 36 0.04
196 89 0.10
197 108 0.12
198 120 0.13
199 83 0.09
200 94 0.10
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:2659 original size:393 final size:391
Alignment explanation
Indices: 1673--2811 Score: 1946
Period size: 393 Copynumber: 2.9 Consensus size: 391
1663 TTAAGGGTCA
* *** *
1673 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
1737 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1802 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
***
1866 TAATGTGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTT-CCAGAATGAATT-TTTACAAGGT
* *
1930 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
258 GCATCAATAAAGTGTCGATCC--ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1995 ATAATGT--TATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTA
320 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTA
2058 AATAATG
385 AATAATG
2065 TGTCG--ACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
2126 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2190 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
2255 TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA
2320 TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
261 TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
2385 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
326 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTAT--GAGAATAAGTCTAAAT
2450 AATG
388 AATG
2454 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
2519 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
2584 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-ATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
2648 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCG--ATTTTTTTTCCAGAATGAATTTTTACAAGGTG
2713 CATCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAG--TA
259 CATCAATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
2775 ATGTAATATGTAATTTTTTAATCTAACCAGTACAATT
323 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATT
2812 TGCTTCTCGA
Statistics
Matches: 716, Mismatches: 15, Indels: 31
0.94 0.02 0.04
Matches are distributed among these distances:
384 44 0.06
385 4 0.01
386 37 0.05
387 31 0.04
388 99 0.14
389 133 0.19
390 20 0.03
391 3 0.00
392 6 0.01
393 153 0.21
394 95 0.13
395 61 0.09
396 30 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (391 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA
TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTAAATAAT
G
Found at i:5149 original size:23 final size:23
Alignment explanation
Indices: 5118--5180 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5108 ATAGGTAAAC
*
5118 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5141 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5164 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
5181 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5188 original size:23 final size:23
Alignment explanation
Indices: 5118--5190 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5108 ATAGGTAAAC
* * **
5118 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
5141 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
5164 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
5187 ATAT
1 ATAT
5191 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:6184 original size:2 final size:2
Alignment explanation
Indices: 6179--6221 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
6169 ACACACATAA
6179 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6219 AT A
1 AT A
6222 CTTTATAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14974 original size:15 final size:15
Alignment explanation
Indices: 14954--14985 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14944 GGAGGTCAAG
*
14954 GAAGATGAAAAGGGA
1 GAAGATGAAAAGAGA
14969 GAAGATGAAAAGAGA
1 GAAGATGAAAAGAGA
14984 GA
1 GA
14986 TACCTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (15 bp):
GAAGATGAAAAGAGA
Found at i:17582 original size:21 final size:22
Alignment explanation
Indices: 17541--17584 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17531 TTATATTGAT
*
17541 TTTAAAAGAACAAATAATTTAA
1 TTTAAAAAAACAAATAATTTAA
*
17563 TTTAAAAAAATAAA-AATTTAA
1 TTTAAAAAAACAAATAATTTAA
17584 T
1 T
17585 ATATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TTTAAAAAAACAAATAATTTAA
Found at i:18254 original size:92 final size:89
Alignment explanation
Indices: 18082--18265 Score: 305
Period size: 92 Copynumber: 2.0 Consensus size: 89
18072 CTTTACCAGG
18082 AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA
1 AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA
* *
18147 TTGAGGGTGGAGTTCAGAAGCAGC
66 TGGAGGATGGAGTTCAGAAGCAGC
* *
18171 AAAAATAAAAAAAGGGTGAAGTAAAAAAGAAAATATTAGAAAACGGGTGCAGTACCTGAGGCAGA
1 AAAAAT-AAAAAA-GGTGAAGTAAAAAAGAAAATATTAGAAAA-GGGAGCAGTACCGGAGGCAGA
18236 GGATGGAGGATGGAGTTCAGAAGCAGC
63 GGATGGAGGATGGAGTTCAGAAGCAGC
18263 AAA
1 AAA
18266 GGTTTGAGAG
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
89 6 0.07
90 6 0.07
91 29 0.33
92 47 0.53
ACGTcount: A:0.48, C:0.08, G:0.30, T:0.14
Consensus pattern (89 bp):
AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA
TGGAGGATGGAGTTCAGAAGCAGC
Found at i:25521 original size:19 final size:21
Alignment explanation
Indices: 25478--25522 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
25468 TTAACTTTTT
*
25478 TTTATAAATAAAATAATATAT
1 TTTATAAATAAAATAATATAA
*
25499 TTTA-AAATAAAA-AATCTAA
1 TTTATAAATAAAATAATATAA
25518 TTTAT
1 TTTAT
25523 TGTTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 8 0.38
21 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTATAAATAAAATAATATAA
Found at i:26592 original size:21 final size:20
Alignment explanation
Indices: 26568--26685 Score: 109
Period size: 19 Copynumber: 5.9 Consensus size: 20
26558 TTGAAGTTCG
* *
26568 CGTTGCGATTTATTACAAATT
1 CGTTGCGA-TTAGTCCAAATT
*
26589 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
* *
26608 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTAGTCCAAATT
*
26627 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTAGTCCAAATT
*
26650 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
26669 CGTTGCGA-TAGTCCAAA
1 CGTTGCGATTAGTCCAAA
26686 ATCGCAACGA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
19 51 0.61
21 24 0.29
23 8 0.10
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTAGTCCAAATT
Found at i:26611 original size:19 final size:19
Alignment explanation
Indices: 26587--26684 Score: 133
Period size: 19 Copynumber: 4.9 Consensus size: 19
26577 TTATTACAAA
26587 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
*
26606 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
* *
26625 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCCAAG
26648 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
26667 TTCGTTGCGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
26685 AATCGCAACG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
19 45 0.65
21 16 0.23
23 8 0.12
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TTCGTTGCGATAGTCCAAG
Found at i:26628 original size:61 final size:61
Alignment explanation
Indices: 26549--26681 Score: 248
Period size: 61 Copynumber: 2.2 Consensus size: 61
26539 GGAAACTGAT
*
26549 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
*
26610 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
26671 TTGCGATAGTC
1 TTGCGATAGTC
26682 CAAAATCGCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (61 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:26646 original size:42 final size:40
Alignment explanation
Indices: 26587--26677 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 40
26577 TTATTACAAA
* * *
26587 TTCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
26625 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TT--CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
26667 TTCGTTGCGAT
1 TTCGTTGCGAT
26678 AGTCCAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.04
40 17 0.37
42 27 0.59
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (40 bp):
TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:29019 original size:26 final size:26
Alignment explanation
Indices: 28990--29039 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28980 TGTCAAGGTT
* *
28990 GAATTTATAAATTTTTAAGAGAATAC
1 GAATTCATAAAGTTTTAAGAGAATAC
* *
29016 GAATTCATAACGTTTTATGAGAAT
1 GAATTCATAAAGTTTTAAGAGAAT
29040 GAAAATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (26 bp):
GAATTCATAAAGTTTTAAGAGAATAC
Found at i:37780 original size:19 final size:19
Alignment explanation
Indices: 37753--37789 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37743 TTAAAAATGT
*
37753 AATATAATATTTTTATTTC
1 AATAGAATATTTTTATTTC
37772 AATAGAATATTTTTATTT
1 AATAGAATATTTTTATTT
37790 TAGTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
AATAGAATATTTTTATTTC
Found at i:41436 original size:17 final size:18
Alignment explanation
Indices: 41389--41441 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
41379 AGTTTAATAT
*
41389 TTATATATAATAGACTTAAA
1 TTATATATTATA-A-TTAAA
*
41409 TTATTTATTATAATTAAA
1 TTATATATTATAATTAAA
41427 -TATATATTAT-ATTAA
1 TTATATATTATAATTAA
41442 GGCTAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 5 0.17
17 9 0.30
18 5 0.17
19 1 0.03
20 10 0.33
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATATATTATAATTAAA
Found at i:42461 original size:32 final size:32
Alignment explanation
Indices: 42400--42463 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
42390 ATTATCACAT
* * * *
42400 CAATACTATTAATAATATTTCTTTAAAAAAAC
1 CAATACTACTAATAACATGTCGTTAAAAAAAC
*
42432 CAATACTACTAATAACATGTCGTTGAAAAAAC
1 CAATACTACTAATAACATGTCGTTAAAAAAAC
42464 AACGAAAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (32 bp):
CAATACTACTAATAACATGTCGTTAAAAAAAC
Found at i:49049 original size:86 final size:86
Alignment explanation
Indices: 48899--49069 Score: 306
Period size: 86 Copynumber: 2.0 Consensus size: 86
48889 TAACATTATC
* *
48899 GTTGGTTATAAAATGATCCTTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA
1 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA
*
48964 TTGTATCTAATGAGTTAGATA
66 TTATATCTAATGAGTTAGATA
*
48985 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACGTGACGAAAACACAACTAGA
1 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA
49050 TTATATCTAATGAGTTAGAT
66 TTATATCTAATGAGTTAGAT
49070 CATTGACCGC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (86 bp):
GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA
TTATATCTAATGAGTTAGATA
Found at i:49823 original size:21 final size:21
Alignment explanation
Indices: 49797--49841 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49787 GATTTCTGGG
* *
49797 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
49818 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
49839 CAA
1 CAA
49842 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:50442 original size:18 final size:18
Alignment explanation
Indices: 50419--50453 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
50409 CTAGGAGATT
50419 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
50437 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
50454 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:51515 original size:143 final size:143
Alignment explanation
Indices: 51347--51651 Score: 476
Period size: 145 Copynumber: 2.1 Consensus size: 143
51337 GAGTCGAGGG
** *
51347 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTC-TG-GTGAGAC-A
1 TCTACGCGGTCCTTCGGG--ATATATATATTC--TGGAACATGTGTGAAGTCTTGAAAGACACAA
51409 -TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
62 CTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
51473 TGGCACTACGGTGCAAT
127 TGGCACTACGGTGCAAT
51490 TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACATACTT
1 TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACA-AC-T
*
51555 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATG
64 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
51620 GCACTACGGTGCAAT
129 GCACTACGGTGCAAT
51635 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
51652 TGCAATTATA
Statistics
Matches: 151, Mismatches: 4, Indels: 12
0.90 0.02 0.07
Matches are distributed among these distances:
139 18 0.12
140 2 0.01
141 16 0.11
143 19 0.13
144 1 0.01
145 95 0.63
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (143 bp):
TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACAACTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
ACTACGGTGCAAT
Found at i:51652 original size:23 final size:23
Alignment explanation
Indices: 51619--51663 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
51609 ATTATTATAT
*
51619 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
51642 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
51664 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:53370 original size:16 final size:15
Alignment explanation
Indices: 53349--53399 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
53339 AGTTATGGAG
53349 AAGAAAAGTGAAGAAA
1 AAGAAAAG-GAAGAAA
*
53365 AAGAAAGAAGAAGAAA
1 AAGAAA-AGGAAGAAA
53381 AATGAAGAA-GAAGAAA
1 AA-GAA-AAGGAAGAAA
53397 AAG
1 AAG
53400 GTGGAATTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.03
16 24 0.77
17 5 0.16
18 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (15 bp):
AAGAAAAGGAAGAAA
Found at i:53380 original size:26 final size:26
Alignment explanation
Indices: 53347--53396 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53337 GTAGTTATGG
*
53347 AGAAGAAAAGTGAAGAAAAAGAAAGA
1 AGAAGAAAAATGAAGAAAAAGAAAGA
*
53373 AGAAGAAAAATGAAGAAGAAGAAA
1 AGAAGAAAAATGAAGAAAAAGAAA
53397 AAGGTGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (26 bp):
AGAAGAAAAATGAAGAAAAAGAAAGA
Found at i:56863 original size:14 final size:14
Alignment explanation
Indices: 56822--56873 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
56812 AACAGACATA
*
56822 AGATTTTAAATAAAT
1 AGATTTT-AATATAT
56837 AGA-TTTAAT-TAT
1 AGATTTTAATATAT
56849 AGATTTTAATATAT
1 AGATTTTAATATAT
* *
56863 ATATATTAATA
1 AGATTTTAATA
56874 ACATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 5 0.16
13 9 0.28
14 15 0.47
15 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (14 bp):
AGATTTTAATATAT
Found at i:58172 original size:3 final size:3
Alignment explanation
Indices: 58164--58189 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58154 TTAAGCTCCT
58164 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
58190 TGTCGTCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:65043 original size:3 final size:3
Alignment explanation
Indices: 65037--65097 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
65027 AATAATTATT
* **
65037 TAA TAA TAA T-A TAA TAT TATA TATA TAA TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA
65083 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
65098 AAATGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:74631 original size:18 final size:18
Alignment explanation
Indices: 74604--74639 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
74594 AATACTCCAT
74604 AAATCTATTGA-AAAAGA
1 AAATCTATTGAGAAAAGA
74621 AAATACTATTGAGAAAAGA
1 AAAT-CTATTGAGAAAAGA
74640 GAAACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (18 bp):
AAATCTATTGAGAAAAGA
Found at i:76477 original size:21 final size:21
Alignment explanation
Indices: 76451--76491 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
76441 CTAGCATAGC
76451 CCTTAACAATCTCCTAAGCTT
1 CCTTAACAATCTCCTAAGCTT
76472 CCTTAACAATCTCCTAAGCT
1 CCTTAACAATCTCCTAAGCT
76492 AAAAGCGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (21 bp):
CCTTAACAATCTCCTAAGCTT
Done.