Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004200.1 Hibiscus syriacus cultivar Beakdansim tig00009192_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: 31256
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:92 original size:30 final size:31
Alignment explanation
Indices: 58--124 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
48 CTTTTAATAT
*
58 TTATATTTTTTATCC-CT-AAACTTTCTAAAA
1 TTATATTTTTTAGCCACTAAAACTTTC-AAAA
*
88 TTATA--CTTTAGCCACTAAAACTTTCAAAA
1 TTATATTTTTTAGCCACTAAAACTTTCAAAA
117 -TATATTTT
1 TTATATTTT
125 GGTCACCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
28 10 0.33
29 6 0.20
30 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.01, T:0.46
Consensus pattern (31 bp):
TTATATTTTTTAGCCACTAAAACTTTCAAAA
Found at i:4188 original size:17 final size:17
Alignment explanation
Indices: 4166--4198 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4156 TTTGAGCTTA
4166 TTTTCAAAATCAAATAG
1 TTTTCAAAATCAAATAG
4183 TTTTCAAAATCAAATA
1 TTTTCAAAATCAAATA
4199 TTGAATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTTCAAAATCAAATAG
Found at i:4631 original size:17 final size:17
Alignment explanation
Indices: 4608--4649 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4598 TTATTTCTTT
4608 ATTTTTACT-TTAAATC
1 ATTTTTACTATTAAATC
* *
4624 ACTTTTTATTATTTAATC
1 A-TTTTTACTATTAAATC
4642 ATTTTTAC
1 ATTTTTAC
4650 CAAACCCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACTATTAAATC
Found at i:8196 original size:19 final size:20
Alignment explanation
Indices: 8149--8206 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
8139 TAAATCAGGT
*
8149 CAAGTAACAGATCGGAATCAGG
1 CAAGTAACAGATCAGAATC--G
8171 TCAAGTAACAGATCAGAATC-
1 -CAAGTAACAGATCAGAATCG
8191 CAAGTAA-AGTATCAGA
1 CAAGTAACAG-ATCAGA
8207 TCAGAATCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
23 18 0.55
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (20 bp):
CAAGTAACAGATCAGAATCG
Found at i:8206 original size:24 final size:24
Alignment explanation
Indices: 8147--8261 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
8137 CATAAATCAG
* * *
8147 GTCAAGTAACAGATCGGAAT-CAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
8170 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
8194 GTAAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
8218 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
8242 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
8262 TCAAATCGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
23 21 0.27
24 56 0.71
25 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:12055 original size:170 final size:172
Alignment explanation
Indices: 11760--12103 Score: 584
Period size: 170 Copynumber: 2.0 Consensus size: 172
11750 TGCTCCAGTT
* *
11760 TCGTGCACATCTTTTTATTAAACGATGCATGTTATCATTACCTTTTAGTAGGCTGAAGCACATTA
1 TCGTGCACATCTTTTTATTAAACGACGCATATTATCATTACCTTTTAGTAGGCTGAAGCACATTA
* *
11825 GCCAAACCCTTCAAAACATTTGTCACCTATTCTAAAGCATATACTTGTTGCCGTCCATTCACCTA
66 GCCAAACCCTTCAAAAAATTTGTCACCTATTCTAAAGCATATACTTGTTGCCGCCCATTCACCTA
* *
11890 TCCCTTTCTTTCTTCTTTTTCATTGATTATAGGCTTCACATA
131 TCCCTTTCTTTCTTCTTTTGCATTGATTATAGGCCTCACATA
* *
11932 TCGTGCGCATC-TTTTATTAAACGACGCATATTATCATTTCC-TTTAGTAGGCTGAAGCACATTA
1 TCGTGCACATCTTTTTATTAAACGACGCATATTATCATTACCTTTTAGTAGGCTGAAGCACATTA
11995 GCCAAACCCTTCAAAAAATTTGTCACCTATTCTAAAGCATATACTTGTTGCCGCCCATTCACCTA
66 GCCAAACCCTTCAAAAAATTTGTCACCTATTCTAAAGCATATACTTGTTGCCGCCCATTCACCTA
* *
12060 TCCCTTTCTTTTTTCTTTTGCGTTGATTATAGGCCTCACATA
131 TCCCTTTCTTTCTTCTTTTGCATTGATTATAGGCCTCACATA
12102 TC
1 TC
12104 CTATCTCCCC
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
170 125 0.77
171 27 0.17
172 10 0.06
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (172 bp):
TCGTGCACATCTTTTTATTAAACGACGCATATTATCATTACCTTTTAGTAGGCTGAAGCACATTA
GCCAAACCCTTCAAAAAATTTGTCACCTATTCTAAAGCATATACTTGTTGCCGCCCATTCACCTA
TCCCTTTCTTTCTTCTTTTGCATTGATTATAGGCCTCACATA
Found at i:14772 original size:76 final size:77
Alignment explanation
Indices: 14643--14853 Score: 259
Period size: 76 Copynumber: 2.8 Consensus size: 77
14633 CCGTTGTACA
* * * * *
14643 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTTCGAGCATACTGGAATTCTCAGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCAGAG
*
14707 -C-AAAACTGTTT
66 CCAAAAAC-ATTT
* * *
14718 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCAGAG
14783 CCAAAAACATTT
66 CCAAAAACATTT
* * *
14795 A-GGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
14854 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
75 19 0.16
76 58 0.49
77 5 0.04
78 36 0.31
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCAGAG
CCAAAAACATTT
Found at i:17544 original size:36 final size:33
Alignment explanation
Indices: 17487--17725 Score: 101
Period size: 36 Copynumber: 6.8 Consensus size: 33
17477 ATAAAATTTT
17487 AAACCATATCATACATTTTTTTTAAAAATGTTTTAA
1 AAACCATAT-AT-CATTTTTTTT-AAAATGTTTTAA
* *
17523 AAACCATATATCATTCGTTTTTT-TAAT-TTTAAAAAA
1 AAACCATATATCATT--TTTTTTAAAATGTTT---TAA
* * *
17559 AAACCATATATTATTCGTTTTTAAAATGGTTTCAA
1 AAACCATATATCATT-TTTTTTAAAAT-GTTTTAA
* * * * *
17594 AAACTATATATTATTTGTTTCAAAATTATTTTAA
1 AAACCATATATCATTTTTTTTAAAA-TGTTTTAA
* * *
17628 AAACCATATTAT-ATGTTTTTAAAATTATTATTTTAA
1 AAACCATA-TATCATTTTTTTTAAA--A-TGTTTTAA
* * *
17664 AAACTATATA-CTATATGTTTTCAAAAT-TAATTTAA
1 AAACCATATATC-AT-TTTTTTTAAAATGT--TTTAA
*
17699 AAACCATATACTACATGTTTTTTAAAA
1 AAACCATATA-T-CATTTTTTTTAAAA
17726 CCATTTTATA
Statistics
Matches: 158, Mismatches: 25, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
33 4 0.03
34 36 0.23
35 44 0.28
36 61 0.39
37 9 0.06
38 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.45
Consensus pattern (33 bp):
AAACCATATATCATTTTTTTTAAAATGTTTTAA
Found at i:17596 original size:35 final size:34
Alignment explanation
Indices: 17505--17652 Score: 117
Period size: 36 Copynumber: 4.3 Consensus size: 34
17495 TCATACATTT
*
17505 TTTTTAAAAATGTTTTAAAAACCATATATCATTCG
1 TTTTT-AAAATGTTTTAAAAACCATATATTATTCG
** *
17540 TTTTTTTAAT-TTTAAAAAAAAACCATATATTATTCG
1 TTTTTAAAATGTTT---TAAAAACCATATATTATTCG
* * *
17576 TTTTTAAAATGGTTTCAAAAACTATATATTATTTG
1 TTTTTAAAAT-GTTTTAAAAACCATATATTATTCG
* *
17611 -TTTCAAAATTATTTTAAAAACC--ATATTATAT-G
1 TTTTTAAAA-TGTTTTAAAAACCATATATTAT-TCG
17643 TTTTTAAAAT
1 TTTTTAAAAT
17653 TATTATTTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 19
0.73 0.11 0.15
Matches are distributed among these distances:
32 9 0.10
33 11 0.12
34 19 0.21
35 23 0.25
36 26 0.29
38 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (34 bp):
TTTTTAAAATGTTTTAAAAACCATATATTATTCG
Found at i:17708 original size:35 final size:35
Alignment explanation
Indices: 17557--17760 Score: 157
Period size: 35 Copynumber: 5.8 Consensus size: 35
17547 AATTTTAAAA
* **
17557 AAAAACCATATATTAT-TCGTTTTTAAAA-TGGTTT
1 AAAAACCATATATTATAT-GTTTTCAAAATTAATTT
* * *
17591 CAAAAACTATATATTATTTG-TTTCAAAATTATTTT
1 -AAAAACCATATATTATATGTTTTCAAAATTAATTT
*
17626 AAAAACC--ATATTATATGTTTTTAAAATTATTATTTT
1 AAAAACCATATATTATATGTTTTCAAAATTA--A-TTT
* *
17662 AAAAACTATATACTATATGTTTTCAAAATTAATTT
1 AAAAACCATATATTATATGTTTTCAAAATTAATTT
* * * ** *
17697 AAAAACCATATACTACATGTTTTTTAAAACCATTTT
1 AAAAACCATATATTATATG-TTTTCAAAATTAATTT
* * *
17733 ATAAACTATATATTATATGTATTCAAAA
1 AAAAACCATATATTATATGTTTTCAAAA
17761 ACTATATTTT
Statistics
Matches: 137, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
32 9 0.07
33 10 0.07
34 13 0.09
35 47 0.34
36 38 0.28
38 20 0.15
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAAACCATATATTATATGTTTTCAAAATTAATTT
Found at i:17732 original size:71 final size:70
Alignment explanation
Indices: 17592--17760 Score: 216
Period size: 71 Copynumber: 2.4 Consensus size: 70
17582 AAATGGTTTC
* * * *
17592 AAAAACTATATATTATTTG-TTTCAAAATTATTTTAAAAACCATATTATATGTTTTTAAAATTAT
1 AAAAACTATATATTATATGTTTTCAAAATTAATTTAAAAACCATATTACATGTTTTTAAAA-TAC
*
17656 TATTTT
65 CATTTT
* *
17662 AAAAACTATATACTATATGTTTTCAAAATTAATTTAAAAACCATATACTACATGTTTTTTAAA-A
1 AAAAACTATATATTATATGTTTTCAAAATTAATTTAAAAACCATAT--TACATGTTTTTAAAATA
17726 CCATTTT
64 CCATTTT
* *
17733 ATAAACTATATATTATATGTATTCAAAA
1 AAAAACTATATATTATATGTTTTCAAAA
17761 ACTATATTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
70 17 0.20
71 56 0.65
73 13 0.15
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (70 bp):
AAAAACTATATATTATATGTTTTCAAAATTAATTTAAAAACCATATTACATGTTTTTAAAATACC
ATTTT
Found at i:17762 original size:36 final size:35
Alignment explanation
Indices: 17592--17760 Score: 128
Period size: 36 Copynumber: 4.8 Consensus size: 35
17582 AAATGGTTTC
* * **
17592 AAAAACTATATATTATTTG-TTTCAAAATTATTTT
1 AAAAACTATATACTATATGTTTTCAAAACCATTTT
* * **
17626 AAAAACCATAT--TATATGTTTTTAAAATTATTATTTT
1 AAAAACTATATACTATATG-TTTTCAAA--ACCATTTT
** *
17662 AAAAACTATATACTATATGTTTTCAAAATTAATTT
1 AAAAACTATATACTATATGTTTTCAAAACCATTTT
* * *
17697 AAAAACCATATACTACATGTTTTTTAAAACCATTTT
1 AAAAACTATATACTATATG-TTTTCAAAACCATTTT
* * *
17733 ATAAACTATATATTATATGTATTCAAAA
1 AAAAACTATATACTATATGTTTTCAAAA
17761 ACTATATTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
32 5 0.05
34 16 0.15
35 31 0.28
36 45 0.41
37 7 0.06
38 6 0.05
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
AAAAACTATATACTATATGTTTTCAAAACCATTTT
Found at i:19723 original size:32 final size:32
Alignment explanation
Indices: 19687--19769 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
19677 GCTCATGTGT
* * *
19687 ATTATCTAAATGCAACATTAACTCTGATATTC
1 ATTATCTAAATGCAACACTAACACTGATATGC
19719 ATTATCTAAATGCAACACTAACACTGATATGC
1 ATTATCTAAATGCAACACTAACACTGATATGC
*
19751 ATTATCTGAATGCAACACT
1 ATTATCTAAATGCAACACT
19770 GATTGTTCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (32 bp):
ATTATCTAAATGCAACACTAACACTGATATGC
Found at i:22338 original size:18 final size:17
Alignment explanation
Indices: 22311--22357 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
22301 AATTAATGGA
22311 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
22328 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
22346 G-AATAAAAATAA
1 GTAA-AAAAATAA
22358 TGTGTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:22492 original size:16 final size:17
Alignment explanation
Indices: 22460--22515 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
22450 TATTAAGAGA
22460 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
22477 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
22493 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
22512 AAAA
1 AAAA
22516 ATAGAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:22563 original size:37 final size:36
Alignment explanation
Indices: 22495--22586 Score: 116
Period size: 37 Copynumber: 2.6 Consensus size: 36
22485 GTAAAAATAT
22495 AATATATATAAATAAATAAAAATAGAATATTAAGAA
1 AATATATATAAATAAATAAAAATAGAATATTAAGAA
* *
22531 AATATATATAAA-AACGTATAAAATATAATATTAAGAA
1 AATATATATAAATAA-ATA-AAAATAGAATATTAAGAA
* *
22568 AAAATATATACAT-AATAAA
1 AATATATATAAATAAATAAA
22587 TGGAGAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.08
36 16 0.33
37 28 0.58
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (36 bp):
AATATATATAAATAAATAAAAATAGAATATTAAGAA
Found at i:22664 original size:14 final size:14
Alignment explanation
Indices: 22645--22672 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22635 ATAAGATATT
22645 TATAATATAAATAA
1 TATAATATAAATAA
22659 TATAATATAAATAA
1 TATAATATAAATAA
22673 AAAGAAAGGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATAATATAAATAA
Found at i:22711 original size:14 final size:14
Alignment explanation
Indices: 22692--22728 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
22682 AATAAAGTAA
22692 ATAAATAAAAATAT
1 ATAAATAAAAATAT
22706 ATAAATAAAAATAT
1 ATAAATAAAAATAT
*
22720 ATATATAAA
1 ATAAATAAA
22729 TGGAGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATAAAAATAT
Found at i:24497 original size:68 final size:63
Alignment explanation
Indices: 24408--24556 Score: 165
Period size: 68 Copynumber: 2.3 Consensus size: 63
24398 AAGATATCTG
* * * * **
24408 TTGTTTCATGAAAAACGGTCTCAAGGGAAATAAAATTTTGTTTTAAGG-GAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAA--TT-TTTT-AGGAGAAATAAATTCAAAGA
24472 TTT
62 -TT
*
24475 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTAGGAGAAATAAATTCAAAGATT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTTTAGGAGAAATAAATTCAAAGATT
*
24539 TTGTTTCAAGGGAAACTG
1 TTGTTTCAAGAGAAACTG
24557 GAAACTGTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
63 16 0.22
64 6 0.08
65 18 0.25
66 2 0.03
67 1 0.01
68 29 0.40
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (63 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTTTAGGAGAAATAAATTCAAAGATT
Found at i:24914 original size:105 final size:105
Alignment explanation
Indices: 24701--24915 Score: 254
Period size: 105 Copynumber: 2.0 Consensus size: 105
24691 TGTATTGTTC
* *
24701 TGAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTTTGGAACTAAGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
* * *
24766 GCCAGCCGCCCTTCGCTGTAAAGTTAAGCTTGTGCTGTTT
66 ACCAGCCGCCCTTCGCTGTAAAGTTAAGCTTATGCTGTCT
* * * **
24806 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTGTTGACA
1 TGAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
** * ** *
24870 ACCAGTCTTCCCTTCGTTGTGGAGTTGAA-CTTATGTTGTCT
66 ACCAG-CCGCCCTTCGCTGTAAAGTT-AAGCTTATGCTGTCT
24911 TGAGT
1 TGAGT
24916 GGCACGATAT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
104 16 0.17
105 74 0.80
106 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (105 bp):
TGAGTCCAATATCCTCCGCTGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACA
ACCAGCCGCCCTTCGCTGTAAAGTTAAGCTTATGCTGTCT
Found at i:25532 original size:32 final size:32
Alignment explanation
Indices: 25491--25608 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
25481 TTTGCATCAG
* * *
25491 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CCAAAAATGCCCCAACATTT
* *
25523 GATGTTGAATCTCAAAAAATTCCCCAACATTT
1 GATGTTGAATCTCCAAAAATGCCCCAACATTT
*
25555 GATGTTAAATCT--AAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAAATGCCCCAACATTT
* *
25585 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTCCAAAAATGCCC
25609 TCATTGTTCC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
30 28 0.38
32 45 0.61
33 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAAATGCCCCAACATTT
Found at i:26725 original size:13 final size:12
Alignment explanation
Indices: 26709--26757 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 12
26699 TTTTCTTCAA
26709 TTTTCCTTTGTTT
1 TTTTCCTTT-TTT
26722 TTTT-CTTTTTT
1 TTTTCCTTTTTT
*
26733 TTTTTCTCTTTTT
1 TTTTCCT-TTTTT
26746 TTTT-CTTTTTT
1 TTTTCCTTTTTT
26757 T
1 T
26758 CTTTTTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.38
12 8 0.24
13 13 0.38
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTCCTTTTTT
Found at i:26734 original size:32 final size:32
Alignment explanation
Indices: 26693--26768 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
26683 TATGCATCTG
*
26693 TCTTTTTTTTCTTCAATTTTCCTTTGTTTTTT
1 TCTTTTTTTTCTTCAATTTTCCTTTCTTTTTT
* ** **
26725 TCTTTTTTTTTTTCTCTTTTTTTTTCTTTTTT
1 TCTTTTTTTTCTTCAATTTTCCTTTCTTTTTT
*
26757 TCTTTTTGTTCT
1 TCTTTTTTTTCT
26769 GATTGAATCT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (32 bp):
TCTTTTTTTTCTTCAATTTTCCTTTCTTTTTT
Found at i:26736 original size:24 final size:24
Alignment explanation
Indices: 26709--26757 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
26699 TTTTCTTCAA
26709 TTTTCCT-TTGTTTTTTTCTTTTTT
1 TTTTCCTCTT-TTTTTTTCTTTTTT
*
26733 TTTTTCTCTTTTTTTTTCTTTTTT
1 TTTTCCTCTTTTTTTTTCTTTTTT
26757 T
1 T
26758 CTTTTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (24 bp):
TTTTCCTCTTTTTTTTTCTTTTTT
Found at i:26742 original size:14 final size:13
Alignment explanation
Indices: 26709--26763 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
26699 TTTTCTTCAA
* *
26709 TTTTCCTTTGTTT
1 TTTTCTTTTTTTT
26722 TTTTC-TTTTTTT
1 TTTTCTTTTTTTT
*
26734 TTTTC-TCTTTTT
1 TTTTCTTTTTTTT
26746 TTTTCTTTTTTTCT
1 TTTTCTTTTTTT-T
26760 TTTT
1 TTTT
26764 GTTCTGATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 22 0.59
13 10 0.27
14 5 0.14
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:31154 original size:17 final size:16
Alignment explanation
Indices: 31128--31185 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
31118 GTGAGAATAT
31128 AAAT-AAAATAATAAA
1 AAATAAAAATAATAAA
*
31143 AAATAGAAAATAACAAA
1 AAATA-AAAATAATAAA
** *
31160 CACGTAAAAATAATAGA
1 -AAATAAAAATAATAAA
31177 AAATAAAAA
1 AAATAAAAA
31186 AAACAAAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 19 0.58
18 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AAATAAAAATAATAAA
Found at i:31203 original size:33 final size:35
Alignment explanation
Indices: 31129--31212 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 35
31119 TGAGAATATA
*
31129 AATAAAATAATAAAAAATAGAAAATAACAAACACG
1 AATAAAATAATAAAAAATAGAAAAAAACAAACACG
* * *
31164 TA-AAAATAATAGAAAATA-AAAAAAACAAA-ATG
1 AATAAAATAATAAAAAATAGAAAAAAACAAACACG
**
31196 AATAAAATGTTAAAAAA
1 AATAAAATAATAAAAAA
31213 CAAAGACACA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 3 0.08
33 21 0.52
34 15 0.38
35 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.17
Consensus pattern (35 bp):
AATAAAATAATAAAAAATAGAAAAAAACAAACACG
Done.