Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003014.1 Hibiscus syriacus cultivar Beakdansim tig00006245_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: 75992
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15038 original size:26 final size:26
Alignment explanation
Indices: 15006--15059 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
14996 TCATCTAAGA
15006 GAATCGAAGTAGATAGATCTAAGGTG
1 GAATCGAAGTAGATAGATCTAAGGTG
15032 GAATCGAAGTAGATAGATCTAAGGTG
1 GAATCGAAGTAGATAGATCTAAGGTG
15058 GA
1 GA
15060 TGTAATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.31, T:0.22
Consensus pattern (26 bp):
GAATCGAAGTAGATAGATCTAAGGTG
Found at i:28813 original size:12 final size:12
Alignment explanation
Indices: 28782--28815 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28772 TTTCTAGCCT
*
28782 CACCACCACCAC
1 CACCACCGCCAC
28794 CACCACCGCCAC
1 CACCACCGCCAC
*
28806 CGCCACCGCC
1 CACCACCGCC
28816 GAAAACAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.68, G:0.09, T:0.00
Consensus pattern (12 bp):
CACCACCGCCAC
Found at i:33279 original size:23 final size:23
Alignment explanation
Indices: 33243--33308 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
33233 CATATTTGTT
33243 TAAAA-TCGCAAACATGTTCATC
1 TAAAATTCGCAAACATGTTCATC
* * **
33265 TAACATTCGCGAACATGTTTGTC
1 TAAAATTCGCAAACATGTTCATC
33288 TAAAATT-GCAAACATGTTCAT
1 TAAAATTCGCAAACATGTTCAT
33309 TTAATGTTCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (23 bp):
TAAAATTCGCAAACATGTTCATC
Found at i:33304 original size:22 final size:22
Alignment explanation
Indices: 33231--33305 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
33221 AGTGTTTGAG
* * *
33231 AACATATTTGTTTAAAATCGCA
1 AACATGTTTGTCTAAAATTGCA
** * *
33253 AACATGTTCATCTAACATTCGCG
1 AACATGTTTGTCTAAAATT-GCA
33276 AACATGTTTGTCTAAAATTGCA
1 AACATGTTTGTCTAAAATTGCA
33298 AACATGTT
1 AACATGTT
33306 CATTTAATGT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 23 0.56
23 18 0.44
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
AACATGTTTGTCTAAAATTGCA
Found at i:34828 original size:21 final size:20
Alignment explanation
Indices: 34804--34868 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
34794 AAATAAAATC
34804 TTAAAGTTAGAAATCTAAGTA
1 TTAAA-TTAGAAATCTAAGTA
* * * *
34825 TTAAAAT-GATAGCTAAAGATG
1 TTAAATTAGAAATCT-AAG-TA
34846 TTAAAATTAGAAATCTAAGTA
1 TT-AAATTAGAAATCTAAGTA
34867 TT
1 TT
34869 TAATCCAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 11 0.34
22 7 0.22
23 5 0.16
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (20 bp):
TTAAATTAGAAATCTAAGTA
Found at i:48088 original size:15 final size:15
Alignment explanation
Indices: 48068--48100 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
48058 ACACATTTAA
48068 TTTTAATA-AATAAAT
1 TTTTAATATAA-AAAT
48083 TTTTAATATAAAAAT
1 TTTTAATATAAAAAT
48098 TTT
1 TTT
48101 ACAGACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAATATAAAAAT
Found at i:48976 original size:17 final size:17
Alignment explanation
Indices: 48954--48987 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48944 ATCATAAAAG
*
48954 AATATTTTATTTTTTTA
1 AATATTTTATATTTTTA
48971 AATATTTTATATTTTTA
1 AATATTTTATATTTTTA
48988 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATATTTTATATTTTTA
Found at i:49752 original size:18 final size:18
Alignment explanation
Indices: 49695--49752 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
49685 AGTAAAATAG
*
49695 AAAA-ATAATA-ATTATA
1 AAAATATAATATAATATA
* *
49711 ACAATAATAATAGTAATATG
1 AAAAT-ATAATA-TAATATA
49731 AAAATATAATATAATATA
1 AAAATATAATATAATATA
49749 AAAA
1 AAAA
49753 AAACCAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.09
18 16 0.48
19 6 0.18
20 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAATATAATATA
Found at i:49753 original size:19 final size:19
Alignment explanation
Indices: 49707--49752 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
49697 AAATAATAAT
*
49707 TATAACAATAATAATAGTAA
1 TATAAAAAT-ATAATAGTAA
*
49727 TATGAAAATATAATA-TAA
1 TATAAAAATATAATAGTAA
49745 TATAAAAA
1 TATAAAAA
49753 AAACCAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
19 6 0.26
20 7 0.30
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
TATAAAAATATAATAGTAA
Found at i:50421 original size:37 final size:37
Alignment explanation
Indices: 50375--50470 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
50365 GGATCATATC
* *
50375 TTTATGAGTTTAAATCATAGTAAAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAAAACTCTATCCTATT
* **
50412 TTTAGGAGTTTAAATCCTAGCAAATTTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAAAACTCTATCCTATT
*
50449 TTTAGGAGTTTGAATCCTAGTA
1 TTTAGGAGTTTAAATCCTAGTA
50471 GGACGAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAAAACTCTATCCTATT
Found at i:51519 original size:106 final size:106
Alignment explanation
Indices: 51204--52893 Score: 2468
Period size: 106 Copynumber: 16.0 Consensus size: 106
51194 TTGTTCTGAA
* * ** * * * *
51204 TCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAACT
1 TCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
* * *
51268 AGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
65 AG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * * *
51310 TCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAATCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* * *
51369 GTC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG-G
66 G-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAG
* * * * *
51410 TCCAAGATCCTTCGCCGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTAATAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* *
51475 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGTG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* *
51516 TCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
51581 GCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * * * *
51622 TCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAATCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* * *
51687 GCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTATTTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
51728 TCCAATATCCTTTGCTGTGAAGTTGAAATTGGATCTAAAATTGGGAAGTTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
51793 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
51834 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
51899 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * * *
51940 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTATTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
52005 GCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
52046 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* *
52111 ACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
52152 TCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGCGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
52217 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
** * * * *
52258 TCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
52323 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
52364 TCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATT-ACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* *
52428 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* *
52469 TCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
52534 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * *
52575 TCCAATATCATTC-CTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAACC
1 TCCAATATCCTTCGC-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACC
* *
52639 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGGAG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* *
52681 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* *
52746 GCGGTCCCATCATCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* ** *
52787 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* * * *
52852 GCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
52893 T
1 T
52894 GGCACGATAT
Statistics
Matches: 1442, Mismatches: 129, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
100 78 0.05
101 5 0.00
102 4 0.00
104 3 0.00
105 106 0.07
106 1244 0.86
107 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
Found at i:53423 original size:266 final size:266
Alignment explanation
Indices: 52949--53484 Score: 1027
Period size: 266 Copynumber: 2.0 Consensus size: 266
52939 TTCGAGCTAG
52949 ATATCCTTCGTTGTGAAGTTGAAATCTACTCTCGAGAAAATTGTGAGTTCGAGAGAAACTTTCAA
1 ATATCCTTCGTTGTGAAGTTGAAATCTACTCTCGAGAAAATTGTGAGTTCGAGAGAAACTTTCAA
*
53014 TCTATCGAGTTGGTCGAAGTGTAGCTTCTTGCTGCTGAGTTAAGCAACCAACATAAATCTTTAAA
66 TCTATCGAGTTGGTCGAAGTGTAGCTTCTTACTGCTGAGTTAAGCAACCAACATAAATCTTTAAA
53079 GGTGCTTTTAAATCGAGTATCCTTCGTCTTGAAGTCAAAACTTGACTCTAAAAGCTGCAAAAAAT
131 GGTGCTTTTAAATCGAGTATCCTTCGTCTTGAAGTCAAAACTTGACTCTAAAAGCTGCAAAAAAT
53144 TATGTATGTGGAAAATGATAAATATGATGCTCTAAAATGTATGCATAATATGCATGTAACATGAA
196 TATGTATGTGGAAAATGATAAATATGATGCTCTAAAATGTATGCATAATATGCATGTAACATGAA
53209 TTGGTT
261 TTGGTT
*
53215 ATATCCTTCGTTGTGAAGTTGAAATCTACTCTCGAGCAAATTGTGAGTTCGAGAGAAACTTTCAA
1 ATATCCTTCGTTGTGAAGTTGAAATCTACTCTCGAGAAAATTGTGAGTTCGAGAGAAACTTTCAA
* *
53280 TCTGTCGAGTTGGTCGAAGTGTAGCTTCTTACTGCTGAGTTAAGCAACCAACATGAATCTTTAAA
66 TCTATCGAGTTGGTCGAAGTGTAGCTTCTTACTGCTGAGTTAAGCAACCAACATAAATCTTTAAA
*
53345 GGTGCTTTTGAATCGAGTATCCTTCGTCTTGAAGTCAAAACTTGACTCTAAAAGCTGCAAAAAAT
131 GGTGCTTTTAAATCGAGTATCCTTCGTCTTGAAGTCAAAACTTGACTCTAAAAGCTGCAAAAAAT
53410 TATGTATGTGGAAAATGATAAATATGATGCTCTAAAATGTATGCATAATATGCATGTAACATGAA
196 TATGTATGTGGAAAATGATAAATATGATGCTCTAAAATGTATGCATAATATGCATGTAACATGAA
53475 TTGGTT
261 TTGGTT
53481 ATAT
1 ATAT
53485 TTTATCTCCT
Statistics
Matches: 265, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 265 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (266 bp):
ATATCCTTCGTTGTGAAGTTGAAATCTACTCTCGAGAAAATTGTGAGTTCGAGAGAAACTTTCAA
TCTATCGAGTTGGTCGAAGTGTAGCTTCTTACTGCTGAGTTAAGCAACCAACATAAATCTTTAAA
GGTGCTTTTAAATCGAGTATCCTTCGTCTTGAAGTCAAAACTTGACTCTAAAAGCTGCAAAAAAT
TATGTATGTGGAAAATGATAAATATGATGCTCTAAAATGTATGCATAATATGCATGTAACATGAA
TTGGTT
Found at i:54015 original size:22 final size:21
Alignment explanation
Indices: 53965--54016 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
53955 TTTTTGGTCA
53965 AAAGTTTGGCATTTGATGCTC
1 AAAGTTTGGCATTTGATGCTC
* *
53986 ATAGGTTTGGTATTTGATGCTC
1 A-AAGTTTGGCATTTGATGCTC
54008 AACAGTTTG
1 AA-AGTTTG
54017 ATGGGGTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (21 bp):
AAAGTTTGGCATTTGATGCTC
Found at i:54692 original size:164 final size:167
Alignment explanation
Indices: 54414--54752 Score: 490
Period size: 172 Copynumber: 2.0 Consensus size: 167
54404 TAAATAGGCC
* * * * *
54414 CAAACAAGTGTTTCAGGATGTTGAACCAATGATCAATTCATTCTGATGCTTTTAATCATGTCCTG
1 CAAACAAGTGTTTCAGGATGTTGAACCAAGGATCAATTCATTATGAT-CATCT-ATCATATCCTG
54479 CTCAAAATGTCTCTCTCTTGATGCTCTATGATATTCGAGTGAAGTGATTC-G-GGAATGATTGTG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATATTCGAGTGAAGTGATTCAGAGGAATGATTGTG
54542 CTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 CTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
54581 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGAT-ATCT-TCA-ATCCTGCT
1 CAAACAAGTGTTTCAGGATGTTGAACCAAGGATCAATTCATTATGATCATCTATCATATCCTGCT
*
54643 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATATTCGAGTGAAGTGATTCA--G----AGGAATG
54708 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
123 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
54753 TTTAGGGAAT
Statistics
Matches: 155, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
162 14 0.09
163 3 0.02
164 40 0.26
165 2 0.01
167 45 0.29
172 51 0.33
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (167 bp):
CAAACAAGTGTTTCAGGATGTTGAACCAAGGATCAATTCATTATGATCATCTATCATATCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATATTCGAGTGAAGTGATTCAGAGGAATGATTGTGCT
TGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:54804 original size:23 final size:23
Alignment explanation
Indices: 54775--54818 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54765 TTGCATGTGT
54775 TTTTTGTCCCTT-TTTCTTTTTGA
1 TTTTTGT-CCTTGTTTCTTTTTGA
*
54798 TTTTTGTTCTTGTTTCTTTTT
1 TTTTTGTCCTTGTTTCTTTTT
54819 TTTCTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.02, C:0.14, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTTTGTCCTTGTTTCTTTTTGA
Found at i:54832 original size:30 final size:29
Alignment explanation
Indices: 54784--54859 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
54774 TTTTTTGTCC
*
54784 CTTTTTCTTTTTGA-TTTTTG-TTCTTGTTT
1 CTTTTTTTTTTTGATTTTTTGCTT-TT-TTT
*
54813 CTTTTTTTTCTTTGCTTTTTTGCTTTTTTT
1 CTTTTTTTT-TTTGATTTTTTGCTTTTTTT
*
54843 CTTTTTTGTTATTGATT
1 CTTTTTT-TTTTTGATT
54860 GGATCTTCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 8 0.21
30 19 0.49
31 10 0.26
32 2 0.05
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (29 bp):
CTTTTTTTTTTTGATTTTTTGCTTTTTTT
Found at i:59372 original size:8 final size:8
Alignment explanation
Indices: 59359--59385 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59349 TGTGTAAGAG
59359 GAAAAAAT
1 GAAAAAAT
59367 GAAAAAAT
1 GAAAAAAT
59375 GAAAAAAT
1 GAAAAAAT
59383 GAA
1 GAA
59386 GAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:59494 original size:18 final size:18
Alignment explanation
Indices: 59445--59498 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
59435 AAAATAGAAA
*
59445 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
59466 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
59485 AATA-TAATATAAAA
1 AATAGTAATATAAAA
59499 AAACCAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:59499 original size:18 final size:19
Alignment explanation
Indices: 59449--59499 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
59439 TAGAAAAATA
*
59449 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
59469 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
59488 ATAATATAAAAA
1 ATAATATAAAAA
59500 AACCAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:59711 original size:19 final size:19
Alignment explanation
Indices: 59689--59773 Score: 62
Period size: 19 Copynumber: 4.2 Consensus size: 19
59679 GTAAAATATT
59689 TAAATATATATATAAATAA
1 TAAATATATATATAAATAA
*
59708 TAAATATAGTATTAAAAAATAA
1 TAAATATA-TA-T-ATAAATAA
* *
59730 CCAAATGAATATAAATAAATAA
1 -TAAAT--ATATATATAAATAA
* * *
59752 AAAATATATGTATAGATAA
1 TAAATATATATATAAATAA
59771 TAA
1 TAA
59774 TAGGACTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
19 21 0.41
20 2 0.04
21 5 0.10
22 14 0.27
23 4 0.08
24 2 0.04
25 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAATATATATATAAATAA
Found at i:60183 original size:37 final size:37
Alignment explanation
Indices: 60142--60237 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
60132 GGATCATATC
* *
60142 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCATAGTAAAACTCTATCCTATT
* * * *
60179 TTTAGGAGTTTGAATCCTAGCAAAATTTTATCCTATT
1 TTTAGGAGTTTGAATCATAGTAAAACTCTATCCTATT
* *
60216 TTTAAGAGTTTGAATCTTAGTA
1 TTTAGGAGTTTGAATCATAGTA
60238 TGACGAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAGTAAAACTCTATCCTATT
Found at i:69392 original size:13 final size:13
Alignment explanation
Indices: 69376--69400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69366 AAAATATTTG
69376 AATAATTATAATT
1 AATAATTATAATT
69389 AATAATTATAAT
1 AATAATTATAAT
69401 GTACAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTATAATT
Done.