Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006351.1 Hibiscus syriacus cultivar Beakdansim tig00015190_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: 77023
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:1864 original size:15 final size:13
Alignment explanation
Indices: 1846--1910 Score: 69
Period size: 13 Copynumber: 4.8 Consensus size: 13
1836 ATGAAGAAAC
*
1846 AAAAAAGAAAGAA
1 AAAAAAGAAAAAA
*
1859 GAAAAAGAAAAAA
1 AAAAAAGAAAAAA
1872 AATAGAAAGAAAAAA
1 AA-A-AAAGAAAAAA
1887 AAAAAA-AAATAAA
1 AAAAAAGAAA-AAA
*
1900 AAAAAACAAAA
1 AAAAAAGAAAA
1911 TGGAAAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
12 3 0.07
13 25 0.56
14 5 0.11
15 12 0.27
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:1867 original size:9 final size:8
Alignment explanation
Indices: 1825--1927 Score: 59
Period size: 8 Copynumber: 12.8 Consensus size: 8
1815 CATATTATAT
1825 AAAAAATAG
1 AAAAAA-AG
**
1834 AAATGAAG
1 AAAAAAAG
*
1842 AAACAAA-
1 AAAAAAAG
*
1849 AAAGAAAG
1 AAAAAAAG
1857 AAGAAAAAG
1 AA-AAAAAG
1866 AAAAAAA-
1 AAAAAAAG
* *
1873 ATAGAAAG
1 AAAAAAAG
*
1881 AAAAAAAA
1 AAAAAAAG
*
1889 AAAAAAAT
1 AAAAAAAG
1897 AAAAAAA-
1 AAAAAAAG
*
1904 AACAAAATGG
1 AA-AAAA-AG
*
1914 AAAGAAAG
1 AAAAAAAG
1922 AAAAAA
1 AAAAAA
1928 TGAGAGAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
7 13 0.18
8 43 0.60
9 14 0.19
10 2 0.03
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1870 original size:21 final size:20
Alignment explanation
Indices: 1826--1927 Score: 82
Period size: 20 Copynumber: 4.9 Consensus size: 20
1816 ATATTATATA
*
1826 AAAAATAGAAATGAAGAAACAAA
1 AAAAAAAGAAA-GAA-AAA-AAA
*
1849 AAAGAAAG-AAGAAAAAGAAA
1 AAAAAAAGAAAGAAAAA-AAA
*
1869 AAAAATAGAAAGAAAAAAAA
1 AAAAAAAGAAAGAAAAAAAA
*
1889 AAAAAAATAAA-AAAAAACAA
1 AAAAAAAGAAAGAAAAAA-AA
**
1909 AATGGAAAGAAAGAAAAAA
1 AA-AAAAAGAAAGAAAAAA
1928 TGAGAGAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 6 0.09
20 28 0.43
21 17 0.26
22 8 0.12
23 6 0.09
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAAAGAAAAAAAA
Found at i:1873 original size:24 final size:23
Alignment explanation
Indices: 1839--1895 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
1829 AATAGAAATG
*
1839 AAGAAACAAAAAAGAAAGAAGAAA
1 AAGAAAAAAAAAAGAAAGAA-AAA
*
1863 AAGAAAAAAAATAGAAAGAAAAA
1 AAGAAAAAAAAAAGAAAGAAAAA
1886 AA-AAAAAAAA
1 AAGAAAAAAAA
1896 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 8 0.26
23 5 0.16
24 18 0.58
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAAAGAAAGAAAAA
Found at i:1901 original size:37 final size:38
Alignment explanation
Indices: 1825--1927 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 38
1815 CATATTATAT
1825 AAAAAATAGAAATGAAGAAACAAAAAAGAAAGAAGAAAAAGAA
1 AAAAAATAGAAA-G-A-AAA-AAAAAAGAAAGAAGAAAAA-AA
*
1868 AAAAAATAGAAAGAAAAAAAAAA-AAA-AATAAAAAAA
1 AAAAAATAGAAAGAAAAAAAAAAGAAAGAAGAAAAAAA
* *
1904 AACAAAATGGAAAGAAAGAAAAAA
1 AA-AAAATAGAAAGAAAAAAAAAA
1928 TGAGAGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
36 4 0.07
37 26 0.46
38 3 0.05
39 6 0.11
40 3 0.05
41 1 0.02
42 1 0.02
43 12 0.21
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.05
Consensus pattern (38 bp):
AAAAAATAGAAAGAAAAAAAAAAGAAAGAAGAAAAAAA
Found at i:1910 original size:16 final size:16
Alignment explanation
Indices: 1839--1905 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 16
1829 AATAGAAATG
*
1839 AAGAAACAAAAAAGAAAG
1 AAGAAA-AAAAAA-AAAA
1857 AAGAAAAAGAAAAAAAA
1 AAGAAAAA-AAAAAAAA
*
1874 TAGAAAGAAAAAAAAAA
1 AAGAAA-AAAAAAAAAA
1891 AA-AAATAAAAAAAAA
1 AAGAAA-AAAAAAAAA
1906 CAAAATGGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 12 0.28
17 19 0.44
18 12 0.28
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAAAAAAAA
Found at i:1911 original size:15 final size:15
Alignment explanation
Indices: 1860--1911 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1850 AAGAAAGAAG
*
1860 AAAAAGAAAAAAAATA
1 AAAAATAAAAAAAA-A
*
1876 GAAAGA-AAAAAAAAA
1 -AAAAATAAAAAAAAA
1891 AAAAATAAAAAAAAA
1 AAAAATAAAAAAAAA
*
1906 CAAAAT
1 AAAAAT
1912 GGAAAGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 8 0.26
17 4 0.13
ACGTcount: A:0.87, C:0.02, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAAATAAAAAAAAA
Found at i:15469 original size:47 final size:47
Alignment explanation
Indices: 15412--15659 Score: 433
Period size: 47 Copynumber: 5.3 Consensus size: 47
15402 GGCTATTGTC
15412 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
*
15459 TACGAACTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
15506 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* * *
15553 TACAAGCTTATGGAATTTAAATGGTAAGTATGTTGATAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
* * *
15600 TACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCT
1 TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
15647 TACGAGCTTATGG
1 TACGAGCTTATGG
15660 GATAAATGGT
Statistics
Matches: 193, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 193 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (47 bp):
TACGAGCTTATGGAATTTAAATGGCAAGTATATTGATAAAATAAGCT
Found at i:16770 original size:32 final size:32
Alignment explanation
Indices: 16734--16831 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 32
16724 TCTAAATGTG
*
16734 ATATTGGCTATAATGTGCATTATTTGAATACA
1 ATATTGGATATAATGTGCATTATTTGAATACA
* * *
16766 ATATT-GATTTTATGGTGCATTATTTGAATGCA
1 ATATTGGATATAAT-GTGCATTATTTGAATACA
* * * * *
16798 ATACTGGTTCTATTGTGCATTATCTGAATACA
1 ATATTGGATATAATGTGCATTATTTGAATACA
16830 AT
1 AT
16832 GACTCTGTTG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 5 0.09
32 44 0.83
33 4 0.08
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
ATATTGGATATAATGTGCATTATTTGAATACA
Found at i:20244 original size:21 final size:21
Alignment explanation
Indices: 20220--20263 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20210 ATTAAACATC
* * *
20220 AAATCCTAAACCTTAAATCTT
1 AAATCCCAAACCCTAAACCTT
20241 AAATCCCAAACCCTAAACCTT
1 AAATCCCAAACCCTAAACCTT
20262 AA
1 AA
20264 GGCTTAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATCCCAAACCCTAAACCTT
Found at i:20445 original size:126 final size:126
Alignment explanation
Indices: 20289--20540 Score: 486
Period size: 126 Copynumber: 2.0 Consensus size: 126
20279 GCCTAAAATA
20289 TAAACCTTAAACCCTAAAGCTTAATATCTAAACCCTAATCCTAACCCTAAAAAGGAAAAATATTA
1 TAAACCTTAAACCCTAAAGCTTAATATCTAAACCCTAATCCTAACCCTAAAAAGGAAAAATATTA
*
20354 TTTTACTATGGATTAAAGAAATATTTATTTATGGGTTGTAAATTTTAGTTAAATCTGAGAT
66 TTTTACTATGGATTAAAGAAATATTTATTTATGGGTTGTAAATTTTAGTTAAATCCGAGAT
*
20415 TAAACCTTAAACCCTAAAGCTTAATCTCTAAACCCTAATCCTAACCCTAAAAAGGAAAAATATTA
1 TAAACCTTAAACCCTAAAGCTTAATATCTAAACCCTAATCCTAACCCTAAAAAGGAAAAATATTA
20480 TTTTACTATGGATTAAAGAAATATTTATTTATGGGTTGTAAATTTTAGTTAAATCCGAGAT
66 TTTTACTATGGATTAAAGAAATATTTATTTATGGGTTGTAAATTTTAGTTAAATCCGAGAT
20541 ATTTATTTAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (126 bp):
TAAACCTTAAACCCTAAAGCTTAATATCTAAACCCTAATCCTAACCCTAAAAAGGAAAAATATTA
TTTTACTATGGATTAAAGAAATATTTATTTATGGGTTGTAAATTTTAGTTAAATCCGAGAT
Found at i:21093 original size:235 final size:233
Alignment explanation
Indices: 20637--21102 Score: 545
Period size: 237 Copynumber: 2.0 Consensus size: 233
20627 TGTGTGTTAG
*
20637 GATCCACTTACACCTAGTGTAAAAACTTTTAGTTTTACACCTTTTTAGGATCGTTGGATGAGCCA
1 GATCCACTTACACCTAGTGTAAAAACTTTTAGTTTTACACCTTTTTAGGATAGTTGGATGA-CCA
* *
20702 AAAACAAATACTGGAATTAACTCATTATTTTTTCAGTGAATATATTCTCATTTACTATTATTAAT
65 AAAACAAATAATGGAATTAACTCATTATTTTTTCAGTGAATATATTCTCATTTACTACTATTAAT
* *
20767 CTCAACCTTTGATTTTCCCTCATACAACAATCCTAAATAGTGTAAAACTTTTTAGTTTTCCACTA
130 CTCAACCTTTGATTTTCCCTCATACAACAATCATAAAAAGTGTAAAACTTTTTAGTTTT-CACTA
* *
20832 TGTAATTGGATTATAGCCATATATATATATATATATAGTCAA
194 -GCAATTGGATCATAGCCATATATATATATAT-TATAGTCAA
*
20874 GATCCACTTACACCTAGTGT-AGAACTTTTAGTTTTACACC-TTTTAGGATAGTTGGATGA-CAG
1 GATCCACTTACACCTAGTGTAAAAACTTTTAGTTTTACACCTTTTTAGGATAGTTGGATGACCA-
* * * * *
20936 AAAATCAAA-AGATGGGATTAACTCTTTATTTTTTTCCATTGAATATCTTCTCATTT-CTTACTG
65 AAAA-CAAATA-ATGGAATTAACTCATTA-TTTTTT-CAGTGAATATATTCTCATTTAC-TACTA
* * * * * * **
20999 TTAATCTTAGCCTTTGGTTTTTCCTTATCCAATGATCATAAAAAGGTGTAAAACTTTTTAGTTTT
125 TTAATCTCAACCTTTGATTTTCCCTCATACAACAATCATAAAAA-GTGTAAAACTTTTTAGTTTT
*
21064 -AC-A-CAATTTGATCAT-GTCCCTATATATATATATATTATA
189 CACTAGCAATTGGATCATAG--CC-ATATATATATATATTATA
21103 CGATTAGGAT
Statistics
Matches: 197, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
232 1 0.01
233 11 0.06
234 11 0.06
235 51 0.26
236 28 0.14
237 75 0.38
238 20 0.10
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (233 bp):
GATCCACTTACACCTAGTGTAAAAACTTTTAGTTTTACACCTTTTTAGGATAGTTGGATGACCAA
AAACAAATAATGGAATTAACTCATTATTTTTTCAGTGAATATATTCTCATTTACTACTATTAATC
TCAACCTTTGATTTTCCCTCATACAACAATCATAAAAAGTGTAAAACTTTTTAGTTTTCACTAGC
AATTGGATCATAGCCATATATATATATATTATAGTCAA
Found at i:22423 original size:2 final size:2
Alignment explanation
Indices: 22416--22451 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22406 AATCGGGATT
22416 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22452 AAAGAGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:26082 original size:17 final size:17
Alignment explanation
Indices: 26060--26093 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26050 CACTCCCCTC
26060 AAGCTGGAGAATATACA
1 AAGCTGGAGAATATACA
26077 AAGCTGGAGAATATACA
1 AAGCTGGAGAATATACA
26094 TTGTATAATC
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:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
AAGCTGGAGAATATACA
Found at i:30347 original size:30 final size:31
Alignment explanation
Indices: 30254--30344 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
30244 CAAATTTTGG
* *
30254 TTAGTGACCAAAACATAAA--TTTTCAAAGT
1 TTAGGGACCAAAACATAAATTTTTTAAAAGT
* **
30283 TTAGTGG-CC-AAAGATAAATTTTGAAAAAGT
1 TTAG-GGACCAAAACATAAATTTTTTAAAAGT
*
30313 TTAGGGACCAAAATATAAATTTTTTAAAAGT
1 TTAGGGACCAAAACATAAATTTTTTAAAAGT
30344 T
1 T
30345 AGGTATTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
28 8 0.16
29 8 0.16
30 14 0.29
31 19 0.39
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TTAGGGACCAAAACATAAATTTTTTAAAAGT
Found at i:44038 original size:29 final size:29
Alignment explanation
Indices: 43993--44051 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
43983 TAAATTTTGG
* *
43993 TTAGTGACCAAAATATAAATTTTGAAAGT
1 TTAGGGACCAAAATATAAATTTTAAAAGT
* *
44022 TTAGGGACCAAAGTATAATTTTTAAAAGT
1 TTAGGGACCAAAATATAAATTTTAAAAGT
44051 T
1 T
44052 AGGTATTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (29 bp):
TTAGGGACCAAAATATAAATTTTAAAAGT
Found at i:44955 original size:9 final size:9
Alignment explanation
Indices: 44941--44969 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
44931 TTCCAGAGAC
44941 TCATCTTCT
1 TCATCTTCT
44950 TCATCTTCT
1 TCATCTTCT
44959 TC-TCTTCT
1 TCATCTTCT
44967 TCA
1 TCA
44970 ACGTGAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.34, G:0.00, T:0.55
Consensus pattern (9 bp):
TCATCTTCT
Found at i:45967 original size:30 final size:31
Alignment explanation
Indices: 45911--45974 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
45901 GTTATATGAG
45911 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
45942 CTATGTGATAAAGGTATGG-AAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
45972 CTA
1 CTA
45975 CGCGATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (31 bp):
CTATGTGATAAAGGTATGGAAAATGATATGT
Found at i:46109 original size:21 final size:23
Alignment explanation
Indices: 46064--46111 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
46054 AAGGGTCTAC
46064 GTGGTCCTTCGGGACAAAATTATAT
1 GTGGTCCTTCGGGAC--AATTATAT
46089 GTGGTCCTTCGGGAC-A-TATAT
1 GTGGTCCTTCGGGACAATTATAT
46110 GT
1 GT
46112 ATTCTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 1 0.04
25 15 0.65
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (23 bp):
GTGGTCCTTCGGGACAATTATAT
Found at i:46294 original size:24 final size:24
Alignment explanation
Indices: 46219--46304 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 24
46209 TATTATATGT
*
46219 CACTACGGTGC-AATTCTACGTGG
1 CACTTCGGTGCAAATTCTACGTGG
* *
46242 CACTTCGGTGC-AATTCTATGCGG
1 CACTTCGGTGCAAATTCTACGTGG
**
46265 TTCTTCGG-GACAAATTCTACGTGG
1 CACTTCGGTG-CAAATTCTACGTGG
46289 CACTTCGGTGCAAATT
1 CACTTCGGTGCAAATT
46305 TATACGAGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.02
23 27 0.53
24 22 0.43
25 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
CACTTCGGTGCAAATTCTACGTGG
Found at i:48173 original size:24 final size:24
Alignment explanation
Indices: 48079--48174 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
48069 TGTTTATCGA
**
48079 TCATGT-TTAGTACATTTGTGTAC
1 TCATGTATTAGTACATTCATGTAC
* * * *
48102 TCTTGTATTAGTGCATTCTTGCAC
1 TCATGTATTAGTACATTCATGTAC
* * * * *
48126 TCCTGTATTTGTACCTTTAGGTAC
1 TCATGTATTAGTACATTCATGTAC
48150 TCATGTATTAGTACATTCATGTAC
1 TCATGTATTAGTACATTCATGTAC
48174 T
1 T
48175 TCTGGCACTA
Statistics
Matches: 54, Mismatches: 18, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
23 5 0.09
24 49 0.91
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (24 bp):
TCATGTATTAGTACATTCATGTAC
Found at i:59613 original size:70 final size:70
Alignment explanation
Indices: 59500--59639 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
59490 CAAAGTACAT
59500 TCAAGTGGTGCGATAATTTTGGGAGTTTCCTTTCCCTTGGGTCTAGTGCAAGTCGTTAAAAGGTA
1 TCAAGTGGTGCGATAATTTTGGGAGTTTCCTTTCCCTTGGGTCTAGTGCAAGTCGTTAAAAGGTA
59565 TGTGC
66 TGTGC
* *
59570 TCAAGTGGTGCGATAATTTTGGGAGTTTCCTTTCCCTTGGGTCTGGTGCAAGTCGTTGAAAGGTA
1 TCAAGTGGTGCGATAATTTTGGGAGTTTCCTTTCCCTTGGGTCTAGTGCAAGTCGTTAAAAGGTA
59635 TGTGC
66 TGTGC
59640 CTCCCAAAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.36
Consensus pattern (70 bp):
TCAAGTGGTGCGATAATTTTGGGAGTTTCCTTTCCCTTGGGTCTAGTGCAAGTCGTTAAAAGGTA
TGTGC
Found at i:61932 original size:42 final size:42
Alignment explanation
Indices: 61880--61965 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
61870 ATGAGTATAC
*
61880 TTCTGTTTGTTTGAAAGGTGTTGGCCTTTGTTATTTTTATCA
1 TTCTGTTTGTTTGAAAGGTGTTGGCCTTGGTTATTTTTATCA
*
61922 TTCTTTTTGTTTGAAAGGTGTTGGCCTTGGTTATTTTTATCA
1 TTCTGTTTGTTTGAAAGGTGTTGGCCTTGGTTATTTTTATCA
61964 TT
1 TT
61966 ATGGTGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.14, C:0.09, G:0.21, T:0.56
Consensus pattern (42 bp):
TTCTGTTTGTTTGAAAGGTGTTGGCCTTGGTTATTTTTATCA
Found at i:63727 original size:30 final size:31
Alignment explanation
Indices: 63669--63727 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
63659 AACCATTCAC
* *
63669 AACTTTTCCAAAATTACTGAATTGGTCCCTT
1 AACTTTTCAAAAATTACTGAATTAGTCCCTT
63700 AACTTTTCAAAAATTA-TAGAA-TAGTCCC
1 AACTTTTCAAAAATTACT-GAATTAGTCCC
63728 CATATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTACTGAATTAGTCCCTT
Found at i:65151 original size:32 final size:31
Alignment explanation
Indices: 65089--65150 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
65079 TAAAAGTAGA
*
65089 TCAAACATAAATCCATAAAGTACCAAAAAATT
1 TCAAACATAAAACCATAAAGTACC-AAAAATT
*
65121 TCAAACATAAAACAACATAAAGTTCCAAAA
1 TCAAACATAAAAC--CATAAAGTACCAAAA
65151 TAAATCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 4 0.15
34 10 0.38
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (31 bp):
TCAAACATAAAACCATAAAGTACCAAAAATT
Found at i:68628 original size:20 final size:20
Alignment explanation
Indices: 68603--68737 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
68593 AATTGGGAAA
*
68603 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
68623 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
68643 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
68664 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
68684 TTCGTAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
68704 TTCGCAACGCGATTCTTACT
1 ATCGCAACGCGATACTGACT
*
68724 TTCGCAACGCGATA
1 ATCGCAACGCGATA
68738 ATACATAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:68647 original size:61 final size:61
Alignment explanation
Indices: 68600--68716 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
68590 GCGAATTGGG
* * * * *
68600 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
68661 AAAATCGCAACGAGATACTGACTTTCGTAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
68717 TCTTACTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:68668 original size:41 final size:40
Alignment explanation
Indices: 68623--68757 Score: 128
Period size: 41 Copynumber: 3.3 Consensus size: 40
68613 GATACTGACT
* * *
68623 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTTACTTTCGCAACGCGATAATAC-AA
* * * ** *
68664 ATCGCAACGAGATACTGACTTTCGTAACGCGATTCTGAC-T
1 ATCGCAACGCGATACTTACTTTCGCAACGCGATAAT-ACAA
* *
68704 TTCGCAACGCGATTCTTACTTTCGCAACGCGATAATACATA
1 ATCGCAACGCGATACTTACTTTCGCAACGCGATAATACA-A
*
68745 ATCGCAATGCGAT
1 ATCGCAACGCGAT
68758 TTTCAAAGCG
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
39 2 0.03
40 29 0.40
41 39 0.54
42 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
ATCGCAACGCGATACTTACTTTCGCAACGCGATAATACAA
Found at i:69477 original size:25 final size:24
Alignment explanation
Indices: 69423--69477 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
69413 TGTTTATTAT
* *
69423 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
69447 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
69473 TGTTT
1 TGTTT
69478 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:70627 original size:18 final size:18
Alignment explanation
Indices: 70606--70650 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
70596 TCCACTTCGG
*
70606 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
70624 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
70642 GAGCCATCA
1 GAGCCATCA
70651 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:71186 original size:19 final size:20
Alignment explanation
Indices: 71134--71177 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
71124 GTTTACTTTT
*
71134 GCAACACGAAAATGACTATC
1 GCAACACGGAAATGACTATC
*
71154 GCAACACGGAAATGGCTATC
1 GCAACACGGAAATGACTATC
71174 GCAA
1 GCAA
71178 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
GCAACACGGAAATGACTATC
Found at i:71225 original size:18 final size:18
Alignment explanation
Indices: 71171--71251 Score: 107
Period size: 18 Copynumber: 4.7 Consensus size: 18
71161 GGAAATGGCT
71171 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
71190 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
71204 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
71222 ATCGCAACGCGAAATGAA
1 ATCGCAATGCGAAATGAA
71240 ATCGCAATGCGA
1 ATCGCAATGCGA
71252 TTGTGTTTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
14 9 0.17
16 4 0.07
17 4 0.07
18 30 0.56
19 7 0.13
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:71281 original size:14 final size:14
Alignment explanation
Indices: 71262--71319 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
71252 TTGTGTTTCG
71262 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
71276 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
71292 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
71308 CGTTGCGATTTT
1 CGTTGCGATTTT
71320 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:71293 original size:32 final size:33
Alignment explanation
Indices: 71257--71335 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
71247 TGCGATTGTG
*
71257 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
71289 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
71322 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
71336 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:71354 original size:20 final size:19
Alignment explanation
Indices: 71320--71375 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
71310 TTGCGATTTT
*
71320 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
71339 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
71359 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
71376 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:73254 original size:14 final size:14
Alignment explanation
Indices: 73235--73270 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
73225 ATTGTTTAAT
73235 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
73249 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
73263 TGATTTGT
1 TGATTTGT
73271 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:73433 original size:18 final size:19
Alignment explanation
Indices: 73397--73437 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
73387 GCAATGAGAG
73397 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
73416 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
73434 AATC
1 AATC
73438 ACAACGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:73552 original size:20 final size:20
Alignment explanation
Indices: 73485--73574 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
73475 GCGATTTTGT
73485 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
* *
73504 CGTTGCGATAGCTATTTTTG
1 CGTTGCGATAGCCATTTTCG
* *
73524 CGATCCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
* *
73544 TGTTGCGATAGCCATTGTCG
1 CGTTGCGATAGCCATTTTCG
73564 CGTTGCGATAG
1 CGTTGCGATAG
73575 TCAAATGAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 13 0.22
20 46 0.78
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:74578 original size:24 final size:24
Alignment explanation
Indices: 74551--74604 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
74541 GTATTCGAAA
*
74551 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
* *
74575 TTTGATATTGGTCGATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
74599 TTTGAT
1 TTTGAT
74605 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:74796 original size:12 final size:12
Alignment explanation
Indices: 74779--74803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74769 ATATAATCCT
74779 GAAGAAGAAAAA
1 GAAGAAGAAAAA
74791 GAAGAAGAAAAA
1 GAAGAAGAAAAA
74803 G
1 G
74804 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.