Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000767.1 Hibiscus syriacus cultivar Beakdansim tig00001491_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: 65329
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4546 original size:16 final size:17
Alignment explanation
Indices: 4519--4551 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4509 CGTCGCTTGC
4519 TTCCCATTTTTCTCTTT
1 TTCCCATTTTTCTCTTT
4536 TTCCC-TTTTTCTCTTT
1 TTCCCATTTTTCTCTTT
4552 GCAACCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCCCATTTTTCTCTTT
Found at i:8821 original size:85 final size:85
Alignment explanation
Indices: 8720--8897 Score: 293
Period size: 85 Copynumber: 2.1 Consensus size: 85
8710 ATACAATCAC
* * * *
8720 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
*
8785 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
8805 GACACACAAATGTGTGTCATCTTCATTTATGACGGAGGCCTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
8870 AATGCGCGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
8890 GACGCACA
1 GACACACA
8898 GTTGCGCGTC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:8909 original size:85 final size:85
Alignment explanation
Indices: 8720--8921 Score: 269
Period size: 85 Copynumber: 2.4 Consensus size: 85
8710 ATACAATCAC
* * * * * *
8720 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGCGCGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
*
8785 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* * *
8805 GACACACAAATGTGTGTCATCTTCATTTATGACGGAGGCCTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGCGCGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
8870 AATGCGCGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* ** *
8890 GACGCACAGTTGCGCGTCATCTTAAATTTATG
1 GACACACAAATGCGCGTCATCTT-CATTTATG
8922 TCGGTGACTT
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 97 0.93
86 7 0.07
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
GACACACAAATGCGCGTCATCTTCATTTATGACGGAGGCCTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:11364 original size:21 final size:17
Alignment explanation
Indices: 11324--11358 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11314 ATGATCTTTG
11324 TTTATGTAAACATGGAT
1 TTTATGTAAACATGGAT
11341 TTTATGTAAACATGGAT
1 TTTATGTAAACATGGAT
11358 T
1 T
11359 GATTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (17 bp):
TTTATGTAAACATGGAT
Found at i:15508 original size:15 final size:15
Alignment explanation
Indices: 15488--15517 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15478 GTTGATGACT
15488 TTTACCATTAATAAA
1 TTTACCATTAATAAA
15503 TTTACCATTAATAAA
1 TTTACCATTAATAAA
15518 GAAATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTACCATTAATAAA
Found at i:24977 original size:32 final size:31
Alignment explanation
Indices: 24941--25000 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
24931 GTAAAATTTT
*
24941 TGTTTATAATATTATAATATTATTTTTTATTA
1 TGTTTATAATATTA-AATATAATTTTTTATTA
*
24973 TGTTTATAATATTAATTATAATTTTTTA
1 TGTTTATAATATTAAATATAATTTTTTA
25001 ACATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (31 bp):
TGTTTATAATATTAAATATAATTTTTTATTA
Found at i:29342 original size:28 final size:28
Alignment explanation
Indices: 29299--29373 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
29289 TGCTTGCAAG
* * *
29299 CACTAACTCGATGACATAATGTTTCAAA
1 CACTAACTCAACGACATAATATTTCAAA
* * *
29327 TACTAACTTAACGACATAATATTTCAAG
1 CACTAACTCAACGACATAATATTTCAAA
29355 CACTAACTCAACGACATAA
1 CACTAACTCAACGACATAA
29374 CGTAAACGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.27
Consensus pattern (28 bp):
CACTAACTCAACGACATAATATTTCAAA
Found at i:31842 original size:23 final size:23
Alignment explanation
Indices: 31780--31858 Score: 122
Period size: 24 Copynumber: 3.3 Consensus size: 23
31770 AAAAATAATT
*
31780 CAGGTCAAGTATCATATCAGAATC
1 CAGGTC-AGTATCAGATCAGAATC
31804 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCA-GTATCAGATCAGAATC
*
31828 CATGTCAGTATCAGATCAGAATC
1 CAGGTCAGTATCAGATCAGAATC
31851 CAGGTCAG
1 CAGGTCAG
31859 ATAACAGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
23 24 0.47
24 27 0.53
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (23 bp):
CAGGTCAGTATCAGATCAGAATC
Found at i:35498 original size:17 final size:17
Alignment explanation
Indices: 35476--35511 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35466 GTCAACAGAA
35476 GTCAACGCCGGTCAACG
1 GTCAACGCCGGTCAACG
*
35493 GTCAACGCTGGTCAACG
1 GTCAACGCCGGTCAACG
35510 GT
1 GT
35512 TTGGGTCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (17 bp):
GTCAACGCCGGTCAACG
Found at i:36303 original size:12 final size:12
Alignment explanation
Indices: 36281--36311 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
36271 ATTAGTAGAG
36281 TTAAC-GACACA
1 TTAACAGACACA
36292 TTAACAGACACA
1 TTAACAGACACA
36304 TTAACAGA
1 TTAACAGA
36312 AAGATCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (12 bp):
TTAACAGACACA
Found at i:38186 original size:18 final size:19
Alignment explanation
Indices: 38165--38207 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38155 ACATTTATAA
* *
38165 TATAAGTTATATTTATT-T
1 TATAAGATATATTAATTAT
38183 TATAAAGATATATTAATTAT
1 TAT-AAGATATATTAATTAT
38203 TATAA
1 TATAA
38208 TATTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TATAAGATATATTAATTAT
Found at i:38186 original size:23 final size:22
Alignment explanation
Indices: 38157--38241 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
38147 AATTAAATAC
*
38157 ATTTATAATATAAGTTATATTT
1 ATTTATAATATAAGTTATATTA
*
38179 ATTT-T-ATA-AAGATATATTA
1 ATTTATAATATAAGTTATATTA
* *
38198 ATTATTATAATATTAATTTA-AATA
1 A-T-TTATAATA-TAAGTTATATTA
38222 CATTTATAATATAAGTTATA
1 -ATTTATAATATAAGTTATA
38242 AAACTAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
19 10 0.20
20 4 0.08
21 3 0.06
22 11 0.22
23 12 0.24
24 4 0.08
25 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTATAATATAAGTTATATTA
Found at i:38250 original size:35 final size:35
Alignment explanation
Indices: 38135--38256 Score: 105
Period size: 33 Copynumber: 3.6 Consensus size: 35
38125 AGTTTTAATC
38135 AGTTATAAAACTAA-TTAAATACATTTATAATATA
1 AGTTATAAAACTAATTTAAATACATTTATAATATA
** * * *
38169 AGTTAT--ATTTATTTTATAA-AGATATATTAAT-T-
1 AGTTATAAAACTAATTTA-AATACATTTA-TAATATA
* *
38201 A-TTATAATATTAATTTAAATACATTTATAATATA
1 AGTTATAAAACTAATTTAAATACATTTATAATATA
*
38235 AGTTATAAAACTAATTAAAATA
1 AGTTATAAAACTAATTTAAATA
38257 TAATAATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
31 4 0.06
32 10 0.15
33 22 0.33
34 13 0.20
35 17 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (35 bp):
AGTTATAAAACTAATTTAAATACATTTATAATATA
Found at i:38555 original size:17 final size:16
Alignment explanation
Indices: 38507--38555 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
38497 ATGTTACAAA
38507 TATATATTTTAATTAAT
1 TATATATTTTAA-TAAT
* *
38524 TCTATAATTTAATAAT
1 TATATATTTTAATAAT
*
38540 TGATATATTTTTATAA
1 T-ATATATTTTAATAA
38556 AATAAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TATATATTTTAATAAT
Found at i:39699 original size:2 final size:2
Alignment explanation
Indices: 39694--40044 Score: 153
Period size: 2 Copynumber: 176.5 Consensus size: 2
39684 TAAAAAATTG
* * * *
39694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG CT AT GT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
39736 GT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AA ACT AT AT AG AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
39777 AT -T AT AT A- AT AT AT AA ACT AT GT A- AT TT AT AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
39816 AT AT AT AA AT -T AT AT AT GA- AT -T AT AT AT AA ACT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT AT
* *
39857 ACT AT AT AT AG ACT AT AT AGT TT AT AT AT AT AT AT AT AT ACT AT
1 A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT
* * *
39901 AT AT AT AA AT -T AT AT A- AT TT AT AT AT -T A- ACT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
39940 AT -T AT AT AT AT -T AT TT AT AT AA ACT AC AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT
* * * * * *
39981 TT AC AT AT AA ACT AT AT AT AT AA ACT AT AT AT AA ACC AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT
* *
40024 ACT AC AT AT AT A- AA AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT A
40045 GTTTATTAAT
Statistics
Matches: 258, Mismatches: 57, Indels: 68
0.67 0.15 0.18
Matches are distributed among these distances:
1 18 0.07
2 221 0.86
3 19 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:39783 original size:37 final size:41
Alignment explanation
Indices: 39696--39791 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 41
39686 AAAAATTGAT
* * *
39696 ATATATATATATATATATATATATATAAGCTATGTAGTTTGTA
1 ATATATATATATATATATATATATATAAACTA-GTAG-TAGAA
39739 ATATATATATATATATATATAT-TATAAACTA-TA-TAGAA
1 ATATATATATATATATATATATATATAAACTAGTAGTAGAA
39777 AT-TATATA-ATATATA
1 ATATATATATATATATA
39792 AACTATGTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
36 7 0.14
37 6 0.12
38 5 0.10
40 2 0.04
42 8 0.16
43 22 0.44
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (41 bp):
ATATATATATATATATATATATATATAAACTAGTAGTAGAA
Found at i:39958 original size:9 final size:9
Alignment explanation
Indices: 39694--39959 Score: 89
Period size: 9 Copynumber: 30.9 Consensus size: 9
39684 TAAAAAATTG
39694 ATATATA-T
1 ATATATATT
39702 ATATATA-T
1 ATATATATT
39710 ATATATA-T
1 ATATATATT
*
39718 ATATA-AGCT
1 ATATATA-TT
*
39727 ATGTAGT-TT
1 ATATA-TATT
*
39736 GTA-ATA-T
1 ATATATATT
39743 ATATATATAT
1 ATATATAT-T
39753 ATATATATT
1 ATATATATT
*
39762 ATAAACTA-T
1 ATATA-TATT
* *
39771 ATAGAAATT
1 ATATATATT
39780 ATATA-A-T
1 ATATATATT
* *
39787 ATATAAACT
1 ATATATATT
*
39796 ATGTA-ATT
1 ATATATATT
39804 -TATAT-TT
1 ATATATATT
39811 ATAT-TA-T
1 ATATATATT
*
39818 ATATAAATT
1 ATATATATT
39827 ATATATGAATT
1 ATATAT--ATT
*
39838 ATATATA-A
1 ATATATATT
*
39846 ACTATATATAA
1 A-TATATAT-T
*
39857 ACTATATATAG
1 A-TATATAT-T
39868 ACTATATAGTT
1 A-TATATA-TT
39879 -TATATA-T
1 ATATATATT
39886 ATATATA-T
1 ATATATATT
39894 ATACTATA-T
1 ATA-TATATT
*
39903 ATATAAATT
1 ATATATATT
39912 ATATA-ATT
1 ATATATATT
39920 -TATATATT
1 ATATATATT
39928 A-ACTATA-T
1 ATA-TATATT
39936 ATA-A-ATT
1 ATATATATT
39943 ATATATATT
1 ATATATATT
*
39952 ATTTATAT
1 ATATATAT
39960 AAACTACATA
Statistics
Matches: 206, Mismatches: 19, Indels: 65
0.71 0.07 0.22
Matches are distributed among these distances:
6 1 0.00
7 32 0.16
8 58 0.28
9 75 0.36
10 11 0.05
11 28 0.14
12 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (9 bp):
ATATATATT
Found at i:40002 original size:31 final size:32
Alignment explanation
Indices: 39839--40011 Score: 79
Period size: 35 Copynumber: 5.2 Consensus size: 32
39829 ATATGAATTA
** *
39839 TATATAAACTATATATAAACTATATATA-GAC
1 TATATAATTTATATATAAACTATATATATAAC
*
39870 TATATAGTTTATATAT--A-TATATATAT-AC
1 TATATAATTTATATATAAACTATATATATAAC
** **
39898 TATATATATAAATTATATAATTTATATAT-TAAC
1 TATATA-ATTTA-TATATAAACTATATATATAAC
* **
39931 TATATATAAATTATATATATTATTTATATAAACTACATATAC
1 --TATAT-AATT-TATATATAAACTATAT--A-T--ATA-AC
*
39973 TATATAATTTACATATAAACTATATATATAAAC
1 TATATAATTTATATATAAACTATATATAT-AAC
40006 TATATA
1 TATATA
40012 TAAACCATAT
Statistics
Matches: 109, Mismatches: 14, Indels: 36
0.69 0.09 0.23
Matches are distributed among these distances:
28 16 0.15
29 3 0.03
30 5 0.05
31 13 0.12
32 1 0.01
33 19 0.17
34 1 0.01
35 21 0.19
36 3 0.03
37 1 0.01
38 13 0.12
39 4 0.04
40 5 0.05
41 2 0.02
42 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (32 bp):
TATATAATTTATATATAAACTATATATATAAC
Found at i:40016 original size:11 final size:11
Alignment explanation
Indices: 39815--40044 Score: 135
Period size: 11 Copynumber: 21.5 Consensus size: 11
39805 ATATTTATAT
*
39815 TATATATAAAT
1 TATATATAAAC
* *
39826 TATATATGAAT
1 TATATATAAAC
39837 TATATATAAAC
1 TATATATAAAC
39848 TATATATAAAC
1 TATATATAAAC
*
39859 TATATATAGAC
1 TATATATAAAC
39870 TATATAGT----
1 TATATA-TAAAC
*
39878 T-TATATATA-
1 TATATATAAAC
*
39887 TATATATATAC
1 TATATATAAAC
*
39898 TATATATATAAA
1 TATATATA-AAC
**
39910 T-TATATAATT
1 TATATATAAAC
*
39920 TATATATTAAC
1 TATATATAAAC
*
39931 TATATATAAAT
1 TATATATAAAC
*
39942 TATATATATTA-
1 TATATATA-AAC
*
39953 TTTATATAAAC
1 TATATATAAAC
*
39964 TACATAT--AC
1 TATATATAAAC
**
39973 --TATATAATT
1 TATATATAAAC
*
39982 TACATATAAAC
1 TATATATAAAC
39993 TATATATATAAAC
1 --TATATATAAAC
40006 TATATATAAAC
1 TATATATAAAC
* *
40017 CATATATACTAC
1 TATATATA-AAC
*
40029 -ATATATAAAA
1 TATATATAAAC
40039 TATATA
1 TATATA
40045 GTTTATTAAT
Statistics
Matches: 172, Mismatches: 29, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
6 1 0.01
7 8 0.05
8 1 0.01
9 3 0.02
10 12 0.07
11 131 0.76
12 6 0.03
13 10 0.06
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.43
Consensus pattern (11 bp):
TATATATAAAC
Found at i:40022 original size:13 final size:13
Alignment explanation
Indices: 39985--40024 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39975 TATAATTTAC
*
39985 ATATAAACTATAT
1 ATATAAACCATAT
39998 ATATAAA-C-TAT
1 ATATAAACCATAT
40009 ATATAAACCATAT
1 ATATAAACCATAT
40022 ATA
1 ATA
40025 CTACATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 10 0.42
12 1 0.04
13 13 0.54
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAACCATAT
Found at i:40083 original size:20 final size:20
Alignment explanation
Indices: 39814--40084 Score: 106
Period size: 20 Copynumber: 12.9 Consensus size: 20
39804 TATATTTATA
* *
39814 TTATATATAAATTATATATGAA
1 TTATATATAAACTATATA-G-T
39836 TTATATATAAACTATATA-T
1 TTATATATAAACTATATAGT
* *
39855 AAACTATATATAGACTATATAGT
1 ---TTATATATAAACTATATAGT
*
39878 TTATATATATATA-TATATACT
1 TTATATATA-A-ACTATATAGT
* * *
39899 ATATATATAAATTATATAAT
1 TTATATATAAACTATATAGT
*
39919 TTATATATTAACTATATA-T
1 TTATATATAAACTATATAGT
* *
39938 AAATTATATATATTA-TTTATA-T
1 ---TTATATATA-AACTATATAGT
** * * *
39960 AAACTACATATACTATATAAT
1 TTA-TATATAAACTATATAGT
*
39981 TTACATATAAACTATATA-T
1 TTATATATAAACTATATAGT
*
40000 ATAAACTATATATAAACCATATATACT
1 -T----TATATATAAA-C-TATATAGT
** *
40027 ACATATATAAAATATATAGT
1 TTATATATAAACTATATAGT
*
40047 TTAT-TAATAAACCATATAGT
1 TTATAT-ATAAACTATATAGT
*
40067 TTATATATGAACTATATA
1 TTATATATAAACTATATA
40085 TAAACTAAGG
Statistics
Matches: 190, Mismatches: 35, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
19 7 0.04
20 89 0.47
21 18 0.09
22 57 0.30
23 2 0.01
24 9 0.05
25 1 0.01
26 6 0.03
27 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATATATAAACTATATAGT
Found at i:41971 original size:2 final size:2
Alignment explanation
Indices: 41867--41951 Score: 83
Period size: 2 Copynumber: 45.0 Consensus size: 2
41857 AAAAATAAAC
* * *
41867 TA TA CA TA T- TA TA TA TA TA AA T- TA TA TA -A TT TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
41904 TGA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41947 T- TA TA
1 TA TA TA
41952 AACCATATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
1 6 0.09
2 61 0.90
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42003 original size:22 final size:22
Alignment explanation
Indices: 41956--42036 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
41946 ATTATAAACC
**
41956 ATATAAACTATATATACTTTTAT
1 ATATAAACTATATATA-AATTAT
*
41979 ATATGAACTATATATAAATTAT
1 ATATAAACTATATATAAATTAT
* * *
42001 ATATAAACCATGTAT-ACTATAT
1 ATATAAACTATATATAAAT-TAT
42023 ATATAAACTATATA
1 ATATAAACTATATA
42037 GTTTATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 2 0.04
22 31 0.65
23 15 0.31
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATAAACTATATATAAATTAT
Found at i:42617 original size:24 final size:24
Alignment explanation
Indices: 42590--42636 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42580 AAAAACTCAA
42590 GAAAAAA-AAACA-AAAACATAATAT
1 GAAAAAAGAAA-AGAAAA-ATAATAT
42614 GAAAAAAGAAAAGAAAAATAATA
1 GAAAAAAGAAAAGAAAAATAATA
42637 ATCACCGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (24 bp):
GAAAAAAGAAAAGAAAAATAATAT
Found at i:42793 original size:31 final size:31
Alignment explanation
Indices: 42757--42816 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
42747 GATAGTTATG
*
42757 CTATATTGGTTAC-TCATGAACTATATATATA
1 CTATATAGGTTACAT-ATGAACTATATATATA
*
42788 CTATATAGTTTACATATGAACTATATATA
1 CTATATAGGTTACATATGAACTATATATA
42817 AAAACTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (31 bp):
CTATATAGGTTACATATGAACTATATATATA
Found at i:42810 original size:20 final size:20
Alignment explanation
Indices: 42787--42856 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
42777 CTATATATAT
42787 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
** *
42807 ACTATATA-TAAAAACTATATAA
1 ACTATATAGT--TTAC-ATATGA
42829 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
42849 ACTATATA
1 ACTATATA
42857 TATAAACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.03
20 21 0.52
21 4 0.10
22 13 0.32
23 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (20 bp):
ACTATATAGTTTACATATGA
Found at i:42837 original size:42 final size:44
Alignment explanation
Indices: 42775--42873 Score: 166
Period size: 42 Copynumber: 2.3 Consensus size: 44
42765 GTTACTCATG
42775 AACTATATATATACTATATAGTTTACATATGAACTATATATAAA
1 AACTATATATATACTATATAGTTTACATATGAACTATATATAAA
*
42819 AACTATATA-A-ACTATATAGTTTACATATGAACTATATATATA
1 AACTATATATATACTATATAGTTTACATATGAACTATATATAAA
*
42861 AACTATATTTATA
1 AACTATATATATA
42874 AATTCAAAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 39 0.76
43 2 0.04
44 10 0.20
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.39
Consensus pattern (44 bp):
AACTATATATATACTATATAGTTTACATATGAACTATATATAAA
Found at i:42856 original size:22 final size:22
Alignment explanation
Indices: 42789--42858 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
42779 ATATATATAC
42789 TATATAGTTTACATATGAACTA
1 TATATAGTTTACATATGAACTA
*** *
42811 TATATA-AAAACTATATAAAC--
1 TATATAGTTTAC-ATATGAACTA
42831 TATATAGTTTACATATGAACTA
1 TATATAGTTTACATATGAACTA
42853 TATATA
1 TATATA
42859 TAAACTATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 13 0.36
21 4 0.11
22 19 0.53
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (22 bp):
TATATAGTTTACATATGAACTA
Found at i:42864 original size:13 final size:13
Alignment explanation
Indices: 42801--42875 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
42791 TATAGTTTAC
*
42801 ATATGAACTATAT
1 ATATAAACTATAT
*
42814 ATAAAAACTATAT
1 ATATAAACTATAT
* * * *
42827 AAACTATATAGTTTAC
1 --A-TATAAACTATAT
*
42843 ATATGAACTATAT
1 ATATAAACTATAT
42856 ATATAAACTATAT
1 ATATAAACTATAT
*
42869 TTATAAA
1 ATATAAA
42876 TTCAAAGTAT
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
13 36 0.80
14 1 0.02
15 1 0.02
16 7 0.16
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:42901 original size:42 final size:42
Alignment explanation
Indices: 42855--42935 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
42845 ATGAACTATA
*
42855 TATATAAACTATA-TTTATAAATTCAAAGTATATACTATAGTT
1 TATATAAA-TATACTATATAAATTCAAAGTATATACTATAGTT
**
42897 TATATTTATATACTATATAAATTCAAAGTATATACTATA
1 TATATAAATATACTATATAAATTCAAAGTATATACTATA
42936 TACTTTGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (42 bp):
TATATAAATATACTATATAAATTCAAAGTATATACTATAGTT
Found at i:42928 original size:22 final size:22
Alignment explanation
Indices: 42870--42937 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
42860 AAACTATATT
42870 TATAAATTCAAAGTATATACTA
1 TATAAATTCAAAGTATATACTA
**
42892 TAGT---TT-ATATTTATATACTA
1 TA-TAAATTCA-AAGTATATACTA
42912 TATAAATTCAAAGTATATACTA
1 TATAAATTCAAAGTATATACTA
42934 TATA
1 TATA
42938 CTTTGGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
22 18 0.50
23 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (22 bp):
TATAAATTCAAAGTATATACTA
Found at i:42935 original size:20 final size:20
Alignment explanation
Indices: 42870--42935 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
42860 AAACTATATT
42870 TATAAATTCAAAGTATATAC
1 TATAAATTCAAAGTATATAC
* * **
42890 TAT-AGTTTATATTTATATAC
1 TATAAATTCA-AAGTATATAC
42910 TATATAAATTCAAAGTATATAC
1 --TATAAATTCAAAGTATATAC
42932 TATA
1 TATA
42936 TACTTTGGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
22 11 0.32
23 4 0.12
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
TATAAATTCAAAGTATATAC
Found at i:43552 original size:8 final size:8
Alignment explanation
Indices: 43539--43563 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43529 ACTTGTTTTT
43539 CGCTCAAA
1 CGCTCAAA
43547 CGCTCAAA
1 CGCTCAAA
43555 CGCTCAAA
1 CGCTCAAA
43563 C
1 C
43564 CCTAAACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (8 bp):
CGCTCAAA
Found at i:43932 original size:46 final size:46
Alignment explanation
Indices: 43860--43957 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
43850 CTCTTCTTTT
* *
43860 TCTTCTGTTAATCTTCTCTAACCCTAAATCTAA-CTAAGACTATTCA
1 TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATC-AAGACTATTCA
* * * *
43906 TCTTTTGTTCATCTTCCCTAAACCTAAATCTAATCGAGACTCTTCA
1 TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATCAAGACTATTCA
43952 TCTTCT
1 TCTTCT
43958 TCTGTCTCTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.05, T:0.41
Consensus pattern (46 bp):
TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATCAAGACTATTCA
Found at i:45891 original size:22 final size:22
Alignment explanation
Indices: 45840--45882 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
45830 TTCAATTTTT
*
45840 TAATTTATTTTATTATGTTTTCA
1 TAATTT-TATTATTATGTTTTCA
45863 TAATTTTATTATTAT-TTTTC
1 TAATTTTATTATTATGTTTTC
45883 TTTATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TAATTTTATTATTATGTTTTCA
Found at i:47267 original size:58 final size:57
Alignment explanation
Indices: 47154--47303 Score: 225
Period size: 58 Copynumber: 2.7 Consensus size: 57
47144 ATATTTAAAT
* *
47154 TAATT-ATTTAATTAATCATGTTCAA-TAAATAAATTATTTTAACTTTTAATGATTA
1 TAATTAATTTAATTAATCATGTTCAATTAAATAAATTATTTTAACTTGTAATAATTA
*
47209 TAATTAATTTAATTAATCATGTTCAATTCCAATAAATTATTTTAACTTGTAATAATTA
1 TAATTAATTTAATTAATCATGTTCAATT-AAATAAATTATTTTAACTTGTAATAATTA
* *
47267 TAATTAATTTAATAAATAATGTTCAA-TAAATAAATTA
1 TAATTAATTTAATTAATCATGTTCAATTAAATAAATTA
47304 ATAAAATTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
55 5 0.06
56 29 0.34
57 2 0.02
58 50 0.58
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (57 bp):
TAATTAATTTAATTAATCATGTTCAATTAAATAAATTATTTTAACTTGTAATAATTA
Found at i:47275 original size:29 final size:29
Alignment explanation
Indices: 47185--47275 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
47175 TCAATAAATA
* *
47185 AATTATTTTAACTTTTAATGATTATAATT
1 AATTATTTTAACTTGTAATAATTATAATT
* * ** *
47214 AATT-TAATTAATCATGT--TCAATTCCAATA
1 AATTAT-TTTAA-CTTGTAAT-AATTATAATT
47243 AATTATTTTAACTTGTAATAATTATAATT
1 AATTATTTTAACTTGTAATAATTATAATT
47272 AATT
1 AATT
47276 TAATAAATAA
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
28 6 0.14
29 33 0.75
30 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (29 bp):
AATTATTTTAACTTGTAATAATTATAATT
Found at i:47318 original size:14 final size:12
Alignment explanation
Indices: 47266--47319 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 12
47256 TGTAATAATT
*
47266 ATAATTAATTTA
1 ATAAATAATTTA
47278 ATAAATAATGTTCA
1 ATAAATAAT-TT-A
*
47292 ATAAATAAATTA
1 ATAAATAATTTA
47304 ATAAAATTAATTTA
1 AT-AAA-TAATTTA
47318 AT
1 AT
47320 GATTATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 11 0.31
13 7 0.20
14 17 0.49
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (12 bp):
ATAAATAATTTA
Found at i:47531 original size:16 final size:16
Alignment explanation
Indices: 47510--47543 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47500 AGTAATTTAT
47510 AAGTTACATAAATATC
1 AAGTTACATAAATATC
**
47526 AAGTTAGGTAAATATC
1 AAGTTACATAAATATC
47542 AA
1 AA
47544 ATCAATTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (16 bp):
AAGTTACATAAATATC
Found at i:54741 original size:13 final size:13
Alignment explanation
Indices: 54725--54758 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54715 CATCTAAATC
54725 TTTCTTTCT-TTAT
1 TTTCTTT-TATTAT
54738 TTTCTTTTATTAT
1 TTTCTTTTATTAT
54751 TTTCTTTT
1 TTTCTTTT
54759 CCCAATGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTATTAT
Found at i:58523 original size:14 final size:14
Alignment explanation
Indices: 58504--58533 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58494 TATTGATCTT
58504 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
*
58518 AAGTTTTATTGAGA
1 AAGTTTTATTAAGA
58532 AA
1 AA
58534 CTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Found at i:59169 original size:33 final size:31
Alignment explanation
Indices: 59086--59189 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 31
59076 GATGGTTTGA
* *
59086 TTTCGGTTCGGATTAATTTCTA-TTTAGGTTGC
1 TTTCGG-TCGGATTAAATTC-AGTTCAGGTTGC
**
59118 TTTCAGGTCGGATTAAATTTGGTTCAGGTTGC
1 TTTC-GGTCGGATTAAATTCAGTTCAGGTTGC
* * * *
59150 TTTCGGATTGGGTTAAAATTCAGTTCTGGTTGT
1 TTTCGG-TCGGATT-AAATTCAGTTCAGGTTGC
59183 TTTCGGT
1 TTTCGGT
59190 TCAAGTTAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
31 2 0.03
32 34 0.59
33 22 0.38
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (31 bp):
TTTCGGTCGGATTAAATTCAGTTCAGGTTGC
Found at i:59236 original size:22 final size:22
Alignment explanation
Indices: 59195--59240 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
59185 TCGGTTCAAG
*
59195 TTAGTTTCGGTTCGTGTTAATT
1 TTAGTTTCGGTTCGTATTAATT
59217 TTAGTTTCGGTTC-TAATTAATT
1 TTAGTTTCGGTTCGT-ATTAATT
59239 TT
1 TT
59241 GGATCGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (22 bp):
TTAGTTTCGGTTCGTATTAATT
Found at i:61464 original size:3 final size:3
Alignment explanation
Indices: 61458--61501 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
61448 TATGTACGAG
61458 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
61502 AACATGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:63588 original size:60 final size:59
Alignment explanation
Indices: 63489--63636 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 59
63479 TTTCTTTATC
* * * *
63489 GAGTCTCTTGACTATTAAAAGTTATGAAACATCCCTTTGACTATATGGCATTATTTT-GT
1 GAGTCTATTGACTATTAAAAGTTAT-AAACATCCCTTTGACTATAAGACATTATTTTCCT
* * * * *
63548 AGAGTCTGTTGACTATTAAAAGTTATAATACGGT-CTTTTGATTATAAGATATTATTTTCCT
1 -GAGTCTATTGACTATTAAAAGTTATAA-AC-ATCCCTTTGACTATAAGACATTATTTTCCT
* *
63609 GAGTCCATTGACTAATAAAAGTTATAAA
1 GAGTCTATTGACTATTAAAAGTTATAAA
63637 ATAGTCATCA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
59 3 0.04
60 69 0.93
61 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (59 bp):
GAGTCTATTGACTATTAAAAGTTATAAACATCCCTTTGACTATAAGACATTATTTTCCT
Found at i:64406 original size:32 final size:32
Alignment explanation
Indices: 64365--64430 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
64355 GGTGAAATTA
64365 TTTAGATATTCTATTTGAGTCTTTTTTTTTAC
1 TTTAGATATTCTATTTGAGTCTTTTTTTTTAC
64397 TTTAGATATTCTATTTGAGTCTTTTTTTTTAC
1 TTTAGATATTCTATTTGAGTCTTTTTTTTTAC
64429 TT
1 TT
64431 ATAAAGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (32 bp):
TTTAGATATTCTATTTGAGTCTTTTTTTTTAC
Done.