Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001432.1 Hibiscus syriacus cultivar Beakdansim tig00002780_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: 127402
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12875 original size:31 final size:31
Alignment explanation
Indices: 12822--12900 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
12812 ACTTGCTGAT
*
12822 ATTTAATTCTTAA-CTTTATATTTTTGGTAC
1 ATTTAATTCTTAACCTTTATATTTTAGGTAC
12852 ATTTAATTCTTTAACCTTT-TATTTTAGGTAC
1 ATTTAATTC-TTAACCTTTATATTTTAGGTAC
*
12883 ATTTGATTCCTTAACCTT
1 ATTTAATT-CTTAACCTT
12901 ATTACCTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 9 0.20
31 30 0.68
32 5 0.11
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54
Consensus pattern (31 bp):
ATTTAATTCTTAACCTTTATATTTTAGGTAC
Found at i:14057 original size:20 final size:21
Alignment explanation
Indices: 14019--14058 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
14009 TCCTAGAGGG
14019 TGGGAAGAACAAAAAGAAGAA
1 TGGGAAGAACAAAAAGAAGAA
* *
14040 TGGGAA-AACAGAATGAAGA
1 TGGGAAGAACAAAAAGAAGA
14059 TGCTGGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.05, G:0.30, T:0.07
Consensus pattern (21 bp):
TGGGAAGAACAAAAAGAAGAA
Found at i:19059 original size:2 final size:2
Alignment explanation
Indices: 19046--19097 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
19036 TCACATAAGC
19046 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19089 TA TA TA TA T
1 TA TA TA TA T
19098 GAACATAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20455 original size:13 final size:13
Alignment explanation
Indices: 20437--20484 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
20427 TGCGTCATAA
*
20437 ATTTATGACGCGC
1 ATTTATGACACGC
**
20450 ATTTATGACACAT
1 ATTTATGACACGC
20463 ATTTATGACACGC
1 ATTTATGACACGC
20476 ATTTATGAC
1 ATTTATGAC
20485 GTTCATTGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:20675 original size:2 final size:2
Alignment explanation
Indices: 20668--20696 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20658 TTATTATTAT
20668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20697 TTTAGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25402 original size:16 final size:17
Alignment explanation
Indices: 25381--25414 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25371 GTGCACAACC
25381 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
25397 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
25414 T
1 T
25415 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:26935 original size:21 final size:21
Alignment explanation
Indices: 26911--26954 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
26901 AAGGGAAATG
26911 TTAGGGATTTCTGTTGATGGA
1 TTAGGGATTTCTGTTGATGGA
26932 TTAGGGATTTCTGTTGATGGA
1 TTAGGGATTTCTGTTGATGGA
26953 TT
1 TT
26955 GGGGGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (21 bp):
TTAGGGATTTCTGTTGATGGA
Found at i:28834 original size:19 final size:18
Alignment explanation
Indices: 28815--28863 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
28805 GTTGTTTTTA
28815 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
28833 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
28852 AAATAAACAAAT
1 AAATAAA-AAAT
28864 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:29065 original size:32 final size:32
Alignment explanation
Indices: 29023--29084 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
29013 TTTAAACTAA
29023 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
29054 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
29085 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:29108 original size:44 final size:44
Alignment explanation
Indices: 29054--29186 Score: 103
Period size: 44 Copynumber: 3.3 Consensus size: 44
29044 ATATAAAAAT
29054 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
1 AATA-CCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
* *
29099 AATACCTAAAA-ATAAGATAAAATA-TAAAA---A--T-AA-T--
1 AATACCTAAAACTTAA-TTAAAATACTAAAACCTATTTAAACTAA
* * *
29133 -AT-CCTAAAACTTAATTCAAACACTATAACCTATTTAAACTAA
1 AATACCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
*
29175 AATACATAAAAC
1 AATACCTAAAAC
29187 AAATATAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 29
0.64 0.08 0.28
Matches are distributed among these distances:
32 12 0.18
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 10 0.15
44 21 0.32
45 4 0.06
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (44 bp):
AATACCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
Found at i:29119 original size:76 final size:74
Alignment explanation
Indices: 28990--29219 Score: 318
Period size: 76 Copynumber: 3.0 Consensus size: 74
28980 AAGGACAAAT
28990 CTTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAAT
1 CTTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAA-AAA-ATAAAATATAAAAAT
29054 AATATCCTAAAA
63 AATATCCTAAAA
*
29066 CTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAATAAGATAAAATATAAAAATA
1 CTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAA-AA-ATAAAATATAAAAATA
29131 ATATCCTAAAA
64 ATATCCTAAAA
* * * * * * *
29142 CTTAATTCAAACACTATAACCTATTTAAACTAAAATACATAAAACAAATATAATATTTAAAATAT
1 CTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATAAAATA-TAAAAATAA
*
29207 TATCTTAAAA
65 TATCCTAAAA
29217 CTT
1 CTT
29220 GAGTTTAATT
Statistics
Matches: 140, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
74 7 0.05
75 27 0.19
76 106 0.76
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (74 bp):
CTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATAAAATATAAAAATAAT
ATCCTAAAA
Found at i:31649 original size:20 final size:21
Alignment explanation
Indices: 31612--31653 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
31602 GTCATGCAAC
31612 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
31633 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
31653 T
1 T
31654 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:36309 original size:20 final size:21
Alignment explanation
Indices: 36272--36313 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
36262 GTCATGCAAC
36272 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
36293 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
36313 T
1 T
36314 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:47194 original size:6 final size:6
Alignment explanation
Indices: 47183--47208 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47173 AACAAGGATC
47183 AAGTTG AAGTTG AAGTTG AAGTTG AA
1 AAGTTG AAGTTG AAGTTG AAGTTG AA
47209 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (6 bp):
AAGTTG
Found at i:48265 original size:60 final size:60
Alignment explanation
Indices: 48151--48266 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
48141 GCGTAGTTAA
* * * * **
48151 AAAGCTTAATTACCGATGTAGATAATCGTTGTTACTTAGGGAAATTTAGGTAATCGCGTG
1 AAAGCCTAATTACCAATGTAGATAATAGTTGTTACTTAGGAAAATTTAAATAATCGCGTG
*
48211 AAAGCCTAATTACCAATGTATG-TAATATTTGTTACTTAGGAAAATTTAAATAATCG
1 AAAGCCTAATTACCAATGTA-GATAATAGTTGTTACTTAGGAAAATTTAAATAATCG
48267 TTGGTCGGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (60 bp):
AAAGCCTAATTACCAATGTAGATAATAGTTGTTACTTAGGAAAATTTAAATAATCGCGTG
Found at i:64683 original size:156 final size:155
Alignment explanation
Indices: 64417--64747 Score: 414
Period size: 156 Copynumber: 2.1 Consensus size: 155
64407 TGAGCATGCG
* * **
64417 GTTCAAATTTGGTGAAAATGAACTTGAAATAAATGATGAATTGAAGAAATAAGGAAATAATGAAA
1 GTTCAAATTTGGTAAAAATGAACTTGAAATAAAGGATGAATTGAAGAAATAAAAAAATAATGAAA
* * * * * *
64482 AGTTGAGGGATTAAATTGAAAATTAGAAAATTTATTATCAAAAAAGGAATTGAAAGTACATATGT
66 AATTAAGGAATTAAATTGAAAAATAGAAAATTTATTATCAAAAAAGGAATTAAAAATACATATGT
* * *
64547 ATTCTACAATGGTTTAGGAACATGT
131 ATTCTACAATAGTTTAAGAACATAT
* * *
64572 AGTTCAAATTTGGTAAAAAT-ATACTTGAAATGAAGGATGAATTGATGAAATAAAAAAAATTATG
1 -GTTCAAATTTGGTAAAAATGA-ACTTGAAATAAAGGATGAATTGAAGAAAT-AAAAAAATAATG
* *
64636 AAAAATTAAGGAATTAAATTGAAAAATAGAAAATTTGTTATC-GAAAAGGAATTAAAAATACATA
63 AAAAATTAAGGAATTAAATTGAAAAATAGAAAATTTATTATCAAAAAAGGAATTAAAAATACATA
* * *
64700 TGTATTTTACGATAGTTTAAGAGCATAT
128 TGTATTCTACAATAGTTTAAGAACATAT
*
64728 GATTCAAATTAGGTAAAAAT
1 G-TTCAAATTTGGTAAAAAT
64748 TGGACTTAAA
Statistics
Matches: 150, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
155 2 0.01
156 102 0.68
157 46 0.31
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (155 bp):
GTTCAAATTTGGTAAAAATGAACTTGAAATAAAGGATGAATTGAAGAAATAAAAAAATAATGAAA
AATTAAGGAATTAAATTGAAAAATAGAAAATTTATTATCAAAAAAGGAATTAAAAATACATATGT
ATTCTACAATAGTTTAAGAACATAT
Found at i:64855 original size:32 final size:32
Alignment explanation
Indices: 64814--64876 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
64804 AAATACTTAT
64814 TCAAATTTTTTATTTTTCTAGTAACACAAAAA
1 TCAAATTTTTTATTTTTCTAGTAACACAAAAA
* *
64846 TCAAATTTTTTATTTTTTTAGTAACTCAAAA
1 TCAAATTTTTTATTTTTCTAGTAACACAAAA
64877 TTTCAACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (32 bp):
TCAAATTTTTTATTTTTCTAGTAACACAAAAA
Found at i:65782 original size:13 final size:13
Alignment explanation
Indices: 65764--65789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65754 ACCGGCATGC
65764 CAATTATTAAGTA
1 CAATTATTAAGTA
65777 CAATTATTAAGTA
1 CAATTATTAAGTA
65790 AAAGTATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
CAATTATTAAGTA
Found at i:66338 original size:27 final size:28
Alignment explanation
Indices: 66287--66347 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
66277 GGTGCAAAAG
66287 CATTAGTTCAGGAAAAAAAAGGTTAAGT
1 CATTAGTTCAGGAAAAAAAAGGTTAAGT
66315 CATTAGTTCAGG-AAAAAAAGGTTAAGT
1 CATTAGTTCAGGAAAAAAAAGGTTAAGT
*
66342 AATTAG
1 CATTAG
66348 AACACCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (28 bp):
CATTAGTTCAGGAAAAAAAAGGTTAAGT
Found at i:77934 original size:15 final size:15
Alignment explanation
Indices: 77914--77962 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
77904 TCACATCCAA
77914 ATTTTTAAAAAATAT
1 ATTTTTAAAAAATAT
*
77929 ATTTTTAAATAATATT
1 ATTTTTAAAAAATA-T
*
77945 TTATTTTAAAAAATAT
1 AT-TTTTAAAAAATAT
77961 AT
1 AT
77963 AAACATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTTAAAAAATAT
Found at i:83897 original size:14 final size:13
Alignment explanation
Indices: 83880--83949 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 13
83870 ATTAGGTACC
83880 AAACTAGAACGAAA
1 AAACTAGAAC-AAA
*
83894 AAACGTTAG-ACAAC
1 AAAC--TAGAACAAA
83908 AAACTAGAACAAAA
1 AAACTAGAAC-AAA
*
83922 AAACGTTAG-ACAAC
1 AAAC--TAGAACAAA
83936 AAACTAGAACAAA
1 AAACTAGAACAAA
83949 A
1 A
83950 GGCATACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
12 6 0.13
13 7 0.16
14 22 0.49
15 4 0.09
16 6 0.13
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.10
Consensus pattern (13 bp):
AAACTAGAACAAA
Found at i:83902 original size:28 final size:27
Alignment explanation
Indices: 83879--83949 Score: 124
Period size: 28 Copynumber: 2.6 Consensus size: 27
83869 CATTAGGTAC
83879 CAAACTAGAACGAAAAAACGTTAGACAA
1 CAAACTAGAAC-AAAAAACGTTAGACAA
83907 CAAACTAGAACAAAAAAACGTTAGACAA
1 CAAACTAGAAC-AAAAAACGTTAGACAA
83935 CAAACTAGAACAAAA
1 CAAACTAGAACAAAA
83950 GGCATACATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 4 0.10
28 38 0.90
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.10
Consensus pattern (27 bp):
CAAACTAGAACAAAAAACGTTAGACAA
Found at i:107771 original size:17 final size:17
Alignment explanation
Indices: 107749--107787 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
107739 GTTCATCATT
107749 ATTGAACAAAGAAATAA
1 ATTGAACAAAGAAATAA
107766 ATTGAACAAAGAAATAA
1 ATTGAACAAAGAAATAA
107783 ATTGA
1 ATTGA
107788 TAATGAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (17 bp):
ATTGAACAAAGAAATAA
Found at i:108420 original size:35 final size:35
Alignment explanation
Indices: 108376--108452 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
108366 AAAACAAAAC
108376 AACCATAATAAAAGCCAAGGGTAACAGCTGACTAA
1 AACCATAATAAAAGCCAAGGGTAACAGCTGACTAA
108411 AACCATAATAAAAGCCAAGGGTAACAGCTGACTAA
1 AACCATAATAAAAGCCAAGGGTAACAGCTGACTAA
108446 AACCATA
1 AACCATA
108453 GAAGCCAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.14
Consensus pattern (35 bp):
AACCATAATAAAAGCCAAGGGTAACAGCTGACTAA
Found at i:112859 original size:37 final size:38
Alignment explanation
Indices: 112806--112887 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 38
112796 GTGGAATCTG
* *
112806 ATAATTGTACATAATTTAACAAGGACTAAGAAAT-ATA
1 ATAATTATACAGAATTTAACAAGGACTAAGAAATGATA
* * *
112843 ATAATTATACAGAATTTAATAAGGATTAATAAATGATA
1 ATAATTATACAGAATTTAACAAGGACTAAGAAATGATA
*
112881 ATTATTA
1 ATAATTA
112888 AAAGAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
37 29 0.76
38 9 0.24
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (38 bp):
ATAATTATACAGAATTTAACAAGGACTAAGAAATGATA
Found at i:115895 original size:21 final size:20
Alignment explanation
Indices: 115871--115915 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
115861 GAAATTAAGG
* *
115871 TTTTGTATAAATATAATAATA
1 TTTTGTATAAAAAAAATAA-A
*
115892 TTTTGTGTAAAAAAAATAAA
1 TTTTGTATAAAAAAAATAAA
115912 TTTT
1 TTTT
115916 AAAAGTACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTTGTATAAAAAAAATAAA
Found at i:118327 original size:14 final size:15
Alignment explanation
Indices: 118308--118340 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
118298 AGAGATCATA
118308 ATATTAT-TTTTTTC
1 ATATTATATTTTTTC
*
118322 ATATTATATTTTTTT
1 ATATTATATTTTTTC
118337 ATAT
1 ATAT
118341 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTATATTTTTTC
Done.