Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004536.1 Hibiscus syriacus cultivar Beakdansim tig00010018_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: 60337
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:4138 original size:14 final size:14
Alignment explanation
Indices: 4119--4146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4109 AAGTGAAAGA
4119 ATAGTTATATAATT
1 ATAGTTATATAATT
4133 ATAGTTATATAATT
1 ATAGTTATATAATT
4147 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:5875 original size:2 final size:2
Alignment explanation
Indices: 5870--5912 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5860 ATATTGTGTG
5870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5912 T
1 T
5913 TCAATTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8856 original size:28 final size:27
Alignment explanation
Indices: 8817--8874 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
8807 ATTCTCAAAA
* * *
8817 AAAAAACTCAAAAAACTCCTAAATTCT
1 AAAAAACTCAAAAAAATCATAAACTCT
*
8844 AAAAAATTCCAAAAAAATCATAAACTCT
1 AAAAAACT-CAAAAAAATCATAAACTCT
8872 AAA
1 AAA
8875 TCATAATCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (27 bp):
AAAAAACTCAAAAAAATCATAAACTCT
Found at i:9905 original size:21 final size:21
Alignment explanation
Indices: 9881--9952 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
9871 TGTAAGGGTA
9881 GTATCAATACCCCAAAGAATG
1 GTATCAATACCCCAAAGAATG
*
9902 GTATCGATACCCCAAAGAATG
1 GTATCAATACCCCAAAGAATG
* *
9923 GTATCGATACCCCAAATAATG
1 GTATCAATACCCCAAAGAATG
9944 GTATCAATA
1 GTATCAATA
9953 ACAATTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
GTATCAATACCCCAAAGAATG
Found at i:10823 original size:21 final size:21
Alignment explanation
Indices: 10797--10890 Score: 100
Period size: 21 Copynumber: 4.4 Consensus size: 21
10787 GTCGAGGGTT
*
10797 TTATGTGGTCCTCCGGGATAA
1 TTATGTGGTCATCCGGGATAA
*
10818 TTATGTGGTCATTCGGGATAA
1 TTATGTGGTCATCCGGGATAA
* * *
10839 ATATGTGGT-ATTGCGGTGAAAA
1 TTATGTGGTCA-TCCGG-GATAA
*
10861 CCTATGTGGTCATCCGGGATAA
1 -TTATGTGGTCATCCGGGATAA
10883 TTATGTGG
1 TTATGTGG
10891 CACTTCAGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 38 0.63
22 8 0.13
23 12 0.20
24 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCATCCGGGATAA
Found at i:16093 original size:20 final size:21
Alignment explanation
Indices: 16040--16099 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
16030 TAGGAAATTA
16040 TTAAGGGTAGTATCGATAGCTG
1 TTAAGGGTAGTATCGATA-CTG
*
16062 TTGAAGAG--GTATCGATACTG
1 TT-AAGGGTAGTATCGATACTG
16082 -TAAGGGTAGTATCGATAC
1 TTAAGGGTAGTATCGATAC
16100 CCCAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 13 0.39
21 9 0.27
22 2 0.06
23 4 0.12
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (21 bp):
TTAAGGGTAGTATCGATACTG
Found at i:17009 original size:21 final size:21
Alignment explanation
Indices: 16985--17053 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
16975 TATGTGGTCC
16985 TTCGGGACAAATATGTGGCAT
1 TTCGGGACAAATATGTGGCAT
*
17006 TTCGGTG-CAAACCTATATGGTCAT
1 TTCGG-GACAAA--TATGTGG-CAT
* *
17030 TT-GGGATAATTATGTGGCAT
1 TTCGGGACAAATATGTGGCAT
17050 TTCG
1 TTCG
17054 ATGCAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 5 0.13
21 16 0.42
22 2 0.05
23 10 0.26
24 5 0.13
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCGGGACAAATATGTGGCAT
Found at i:17907 original size:30 final size:29
Alignment explanation
Indices: 17863--17950 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
17853 GATTATGATT
* *
17863 TAGAGTTTATGATTTTTTTTTGAATTTT-
1 TAGAATTTAGGATTTTTTTTTGAATTTTC
*
17891 TAGGAATTTAGGGATTTTTTTAT-AGATTTTC
1 TA-GAATTTA-GGATTTTTTTTTGA-ATTTTC
* *
17922 TAGAATTTATGATTTTTTTTGAGAATTTT
1 TAGAATTTAGGATTTTTTTT-TGAATTTT
17951 AATAATTTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.04
29 16 0.33
30 27 0.56
31 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.16, T:0.58
Consensus pattern (29 bp):
TAGAATTTAGGATTTTTTTTTGAATTTTC
Found at i:17910 original size:29 final size:29
Alignment explanation
Indices: 17876--17950 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
17866 AGTTTATGAT
17876 TTTTTTTTGA-ATTTT-TAGGAATTTAGGGA
1 TTTTTTTTGAGATTTTCTA-GAATTTA-GGA
*
17905 TTTTTTTAT-AGATTTTCTAGAATTTATGA
1 TTTTTTT-TGAGATTTTCTAGAATTTAGGA
17934 TTTTTTTTGAGAATTTT
1 TTTTTTTTGAG-ATTTT
17951 AATAATTTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 1 0.03
29 19 0.47
30 18 0.45
31 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.15, T:0.60
Consensus pattern (29 bp):
TTTTTTTTGAGATTTTCTAGAATTTAGGA
Found at i:17957 original size:29 final size:29
Alignment explanation
Indices: 17868--17958 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
17858 TGATTTAGAG
* *
17868 TTTATGATTTTTTTTTGA-ATTTTTAGGAA
1 TTTATGA-TTTTTTTTGAGAATTTTAAGAA
* *
17897 TTTAGGGATTTTTTTAT-AG-ATTTTCTAGAA
1 TTTA-TGATTTTTTT-TGAGAATTTT-AAGAA
*
17927 TTTATGATTTTTTTTGAGAATTTTAATAA
1 TTTATGATTTTTTTTGAGAATTTTAAGAA
17956 TTT
1 TTT
17959 GGGTTTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 33 0.67
30 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.59
Consensus pattern (29 bp):
TTTATGATTTTTTTTGAGAATTTTAAGAA
Found at i:18480 original size:15 final size:16
Alignment explanation
Indices: 18460--18498 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
18450 GATAAAATAA
18460 AATGATTAAATG-CTG
1 AATGATTAAATGACTG
*
18475 AATGATTCAATGACCTG
1 AATGATTAAATGA-CTG
18492 AATGATT
1 AATGATT
18499 CAAAGGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (16 bp):
AATGATTAAATGACTG
Found at i:18494 original size:17 final size:15
Alignment explanation
Indices: 18460--18501 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
18450 GATAAAATAA
*
18460 AATGATTAAATGCTG
1 AATGATTCAATGCTG
18475 AATGATTCAATGACCTG
1 AATGATTCAATG--CTG
18492 AATGATTCAA
1 AATGATTCAA
18502 AGGCTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (15 bp):
AATGATTCAATGCTG
Found at i:19203 original size:21 final size:22
Alignment explanation
Indices: 19174--19226 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
19164 ATTCTGACTA
19174 TCGCATTGCGATTTT-CTAAAT
1 TCGCATTGCGATTTTCCTAAAT
*
19195 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
19216 TCGCAATGCGA
1 TCGCATTGCGA
19227 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:19237 original size:20 final size:20
Alignment explanation
Indices: 19212--19308 Score: 185
Period size: 20 Copynumber: 4.8 Consensus size: 20
19202 GCGATTTTCC
19212 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
19232 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
19252 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
19272 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
*
19292 TAAATCGCAACGCGAAT
1 TAAATCGCAATGCGAAT
19309 CTGACTATCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:19319 original size:40 final size:40
Alignment explanation
Indices: 19235--19361 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
19225 GAATACGTAA
* *
19235 ATCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTA-A
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACT
19275 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
* * * * *
19315 ATCGCAACGCG-ATTC-TGACTATCGCAACGAGATTCTGACT
1 ATCGCAATGCGAATACGT-A-AATCGCAACGCGAATCTGACT
19355 ATCGCAA
1 ATCGCAA
19362 CGAGATTCTG
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 69 0.91
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACT
Found at i:19339 original size:60 final size:60
Alignment explanation
Indices: 19215--19406 Score: 173
Period size: 60 Copynumber: 3.2 Consensus size: 60
19205 ATTTTCCTAA
* * * * *
19215 ATCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTA-AATCGCAATGCGAATAC-GTA-A
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACTATCGCAACGCG-ATTCTG-ACT
19275 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGATTCTGACT
* * * * **
19335 ATCGCAA--CGAGATTC-TGACTATCGCAACGAGATTCTGACTATCGCAACAAGATTCTGACT
1 ATCGCAATGCGA-ATACGT-A-AATCGCAACGCGAATCTGACTATCGCAACGCGATTCTGACT
19395 ATCGCAATGCGA
1 ATCGCAATGCGA
19407 TTCTGACTAT
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
58 4 0.04
59 10 0.09
60 95 0.85
62 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (60 bp):
ATCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGATTCTGACT
Found at i:19422 original size:20 final size:20
Alignment explanation
Indices: 19295--19421 Score: 200
Period size: 20 Copynumber: 6.3 Consensus size: 20
19285 GAATACGTAA
* *
19295 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
*
19315 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
19335 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
19355 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
19375 ATCGCAACAAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
* *
19395 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
19415 ATCGCAA
1 ATCGCAA
19422 TACTGAATTT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:22758 original size:20 final size:20
Alignment explanation
Indices: 22733--22826 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
22723 GACATTCATT
22733 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
22753 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
22773 TGACTATCGCAGCGCGGAAT
1 TGACTATCGCAACGCGGAAA
22793 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
22813 TGACTATCGCAACG
1 TGACTATCGCAACG
22827 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:22837 original size:14 final size:14
Alignment explanation
Indices: 22818--22876 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
22808 GGAAATGACT
22818 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
22832 ATCGCAATGAGAAATGAAA
1 ATCGCAACGAG--A-G--A
22851 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
22865 ATCGCAATGAGA
1 ATCGCAACGAGA
22877 AAATGAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
16 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:22886 original size:34 final size:33
Alignment explanation
Indices: 22809--22893 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
22799 TCGCAACGCG
**
22809 GAAATGACTATCGCAACGAGAGAATCGCAATGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGA
22842 GAAATGAAAATCGCAACGAGAGAATCGCAATGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGA
22875 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
22894 TGAATTTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 32 0.65
34 17 0.35
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGA
Found at i:22971 original size:33 final size:33
Alignment explanation
Indices: 22908--22992 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
22898 TTTAGTTTCG
* *
22908 CGTTGCGATTTTCATTTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGAGATTCTCT
22942 CGTTGCGATTTTCATTTCGCATTGAGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGAGATTCTCT
**
22975 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
22993 CGCGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.70
34 14 0.30
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGAGATTCTCT
Found at i:23128 original size:14 final size:15
Alignment explanation
Indices: 23109--23146 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
23099 CATCAATTAA
23109 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
23123 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
23137 ACAAATCAAT
1 ACAAATCAAT
23147 TAAACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:24567 original size:21 final size:20
Alignment explanation
Indices: 24543--24634 Score: 62
Period size: 21 Copynumber: 4.4 Consensus size: 20
24533 GGACCTCTCC
24543 AACGATGACAGTGGCCTCTTG
1 AACGATGA-AGTGGCCTCTTG
* *
24564 AACGGTGGGAAG-GGACTCTTG
1 AACGAT--GAAGTGGCCTCTTG
** *
24585 AGGGATGATAGGGGCCTCTTG
1 AACGATGA-AGTGGCCTCTTG
*
24606 AACGAT-AGGTGATGCCTCTTG
1 AACGATGAAGTG--GCCTCTTG
24627 AACGATGA
1 AACGATGA
24635 CAGGTGAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.07
20 3 0.06
21 42 0.78
22 3 0.06
23 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (20 bp):
AACGATGAAGTGGCCTCTTG
Found at i:24827 original size:12 final size:12
Alignment explanation
Indices: 24812--24846 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
24802 AAATAAACAA
*
24812 ACATAATATTAG
1 ACATGATATTAG
24824 ACATGATATTAG
1 ACATGATATTAG
24836 ACATGATATTA
1 ACATGATATTA
24847 AACAGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (12 bp):
ACATGATATTAG
Found at i:25164 original size:20 final size:20
Alignment explanation
Indices: 25141--25229 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
25131 GAAACTTAAA
*
25141 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
25161 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* ** *
25181 ATCGCAATGCGAATTTGATT
1 ATCGCAACGCGAAAATGACT
* **
25201 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
25221 ATCGCAACG
1 ATCGCAACG
25230 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:25317 original size:20 final size:20
Alignment explanation
Indices: 25272--25320 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
25262 GCGATTCTTT
25272 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
25292 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
25312 CGTTGCGAT
1 CGTTGCGAT
25321 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:25332 original size:34 final size:34
Alignment explanation
Indices: 25294--25387 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
25284 CAAATTCGCA
* * * * *
25294 TTGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
25328 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
25361 TTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
25388 AGTAAACTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:27751 original size:22 final size:22
Alignment explanation
Indices: 27690--27755 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
27680 TGACCGTGAA
* **
27690 TGATTTCGCCGGAGATGAAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
27712 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
27734 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
27756 GGATGTCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:27972 original size:20 final size:20
Alignment explanation
Indices: 27949--28021 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
27939 CGATAGTCAG
*
27949 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
27969 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
27989 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
28009 ATTCGCATTGCGA
1 ATTCGCATTGCGA
28022 ATTAAGAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:28042 original size:21 final size:21
Alignment explanation
Indices: 28018--28058 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28008 TATTCGCATT
*
28018 GCGAATTAAGAAAGTCGCAAC
1 GCGAATTAAGAAAATCGCAAC
*
28039 GCGAATTTAGAAAATCGCAA
1 GCGAATTAAGAAAATCGCAA
28059 TACGATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:28594 original size:42 final size:45
Alignment explanation
Indices: 28517--28605 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 45
28507 ATATCACCAC
*
28517 TTGATTAGAGGATTTAATTTTTTTTTAATTGAATTAA-AG-ATAT
1 TTGATTAGAAGATTTAATTTTTTTTTAATTGAATTAAGAGAATAT
28560 TTGATTAGAAGATTTAA-TTTTTTTTAATTGAATTAAGAGAATAT
1 TTGATTAGAAGATTTAATTTTTTTTTAATTGAATTAAGAGAATAT
28604 TT
1 TT
28606 AAGTAATGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
42 19 0.44
43 18 0.42
44 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (45 bp):
TTGATTAGAAGATTTAATTTTTTTTTAATTGAATTAAGAGAATAT
Found at i:34775 original size:32 final size:32
Alignment explanation
Indices: 34739--34807 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
34729 TGGATGATAT
* * *
34739 ATATTTTTCGGGTCA-GATTAGGTGGAGGGTAA
1 ATATTTTTCGAGT-AGGATCAGGTGGAGAGTAA
*
34771 ATATTTTTCGAGTAGGATCAGGTGGAGAGTAT
1 ATATTTTTCGAGTAGGATCAGGTGGAGAGTAA
34803 ATATT
1 ATATT
34808 ATTTGGGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.28, C:0.06, G:0.30, T:0.36
Consensus pattern (32 bp):
ATATTTTTCGAGTAGGATCAGGTGGAGAGTAA
Found at i:36228 original size:16 final size:16
Alignment explanation
Indices: 36207--36239 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36197 TAATAAATAA
*
36207 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
36223 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
36239 A
1 A
36240 AATTTTTTTT
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:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:36320 original size:10 final size:10
Alignment explanation
Indices: 36305--36363 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
36295 CATTTAATAA
36305 ATAAACGAAC
1 ATAAACGAAC
36315 ATAAACGAAC
1 ATAAACGAAC
** *
36325 ACGAAC-ATAA
1 ATAAACGA-AC
36335 ATGAACACGAAC
1 AT-AA-ACGAAC
36347 ATAAACGAAC
1 ATAAACGAAC
36357 ATAAACG
1 ATAAACG
36364 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:36330 original size:16 final size:16
Alignment explanation
Indices: 36309--36357 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
36299 TAATAAATAA
36309 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
36325 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
36341 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
36357 A
1 A
36358 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:37127 original size:24 final size:24
Alignment explanation
Indices: 37087--37161 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
37077 GATTGTGTTA
*
37087 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
37111 AACATAATCGAACGAACATAAATG
1 AACATAATCGAACGAACATAAACG
* * *
37135 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
37159 AAC
1 AAC
37162 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:37151 original size:14 final size:14
Alignment explanation
Indices: 37106--37162 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
37096 GAATGAACAT
*
37106 AAACGAACATAATC
1 AAACGAACATAACC
*
37120 GAACGAACAT----
1 AAACGAACATAACC
*
37130 AAATGAACATAACC
1 AAACGAACATAACC
37144 AAACGAACATAACC
1 AAACGAACATAACC
*
37158 GAACG
1 AAACG
37163 TTCACGAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.24
14 26 0.76
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:42740 original size:7 final size:7
Alignment explanation
Indices: 42728--42790 Score: 126
Period size: 7 Copynumber: 9.0 Consensus size: 7
42718 GAAAAGAAAA
42728 GAAGAGG
1 GAAGAGG
42735 GAAGAGG
1 GAAGAGG
42742 GAAGAGG
1 GAAGAGG
42749 GAAGAGG
1 GAAGAGG
42756 GAAGAGG
1 GAAGAGG
42763 GAAGAGG
1 GAAGAGG
42770 GAAGAGG
1 GAAGAGG
42777 GAAGAGG
1 GAAGAGG
42784 GAAGAGG
1 GAAGAGG
42791 ACGACAAAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:42858 original size:6 final size:6
Alignment explanation
Indices: 42847--42882 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
42837 TCATTATCTA
42847 TTCCAC TTCCAC TTCCAC TTCCAC TTCCAC TTCCAC
1 TTCCAC TTCCAC TTCCAC TTCCAC TTCCAC TTCCAC
42883 ACTCTCGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TTCCAC
Found at i:57659 original size:13 final size:13
Alignment explanation
Indices: 57641--57679 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
57631 TTTAAAAATA
57641 TTATTATTATTAT
1 TTATTATTATTAT
*
57654 TTATTATTAATAT
1 TTATTATTATTAT
57667 TT-TT-TTATTAT
1 TTATTATTATTAT
57678 TT
1 TT
57680 TTGTATGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:59280 original size:14 final size:14
Alignment explanation
Indices: 59263--59296 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
59253 TACGATTCCA
59263 ATTATTTACCTTTG
1 ATTATTTACCTTTG
59277 ATTA-TTACCTTTG
1 ATTATTTACCTTTG
59290 ATTATTT
1 ATTATTT
59297 CAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (14 bp):
ATTATTTACCTTTG
Done.