Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007525.1 Hibiscus syriacus cultivar Beakdansim tig00020981_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: 67581
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:8043 original size:22 final size:22
Alignment explanation
Indices: 8010--8064 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
8000 ATACTGATGG
8010 GGTATCGATACTAAAAAAGGGA
1 GGTATCGATACTAAAAAAGGGA
*
8032 GGTATC-AGTACTAACAAAGGGA
1 GGTATCGA-TACTAAAAAAGGGA
*
8054 AGTATCGATAC
1 GGTATCGATAC
8065 CATGGATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (22 bp):
GGTATCGATACTAAAAAAGGGA
Found at i:14866 original size:45 final size:45
Alignment explanation
Indices: 14815--15024 Score: 257
Period size: 45 Copynumber: 4.6 Consensus size: 45
14805 GAAAGGATGC
* * *
14815 CATAATTGAAATGCATATGGGTGCATTACTGGCATGAAAATATAT
1 CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAAAGATAA
* **
14860 CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAATGATGC
1 CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAAAGATAA
14905 CATAATTGAAATGCATATGGGTGCATTATTGGCAT-AAAAGGA-AGA
1 CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAAA-GATA-A
* * * *
14950 CATAATTAAAATGCATATGGGTGCATTATTAGCATGAAAGGAT-G
1 CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAAAGATAA
14994 CTATAATTGAAAATGCATAAT-GGTGCATTAT
1 C-ATAATTG-AAATGCAT-ATGGGTGCATTAT
15025 AAACATGAAT
Statistics
Matches: 145, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
44 4 0.03
45 118 0.81
46 21 0.14
47 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (45 bp):
CATAATTGAAATGCATATGGGTGCATTATTGGCATGAAAAGATAA
Found at i:14890 original size:23 final size:23
Alignment explanation
Indices: 14819--14935 Score: 78
Period size: 23 Copynumber: 5.2 Consensus size: 23
14809 GGATGCCATA
14819 ATTGAAATGCATATGGGTGCATT
1 ATTGAAATGCATATGGGTGCATT
* ** * * *** *
14842 ACTGGCATGAAAATATAT-CATA
1 ATTGAAATGCATATGGGTGCATT
14864 ATTGAAATGCATATGGGTGCATT
1 ATTGAAATGCATATGGGTGCATT
** * * *
14887 ATTGGCATG-AAAT-GATGCCATA
1 ATTGAAATGCATATGGGTG-CATT
14909 ATTGAAATGCATATGGGTGCATT
1 ATTGAAATGCATATGGGTGCATT
14932 ATTG
1 ATTG
14936 GCATAAAAGG
Statistics
Matches: 62, Mismatches: 28, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
21 3 0.05
22 26 0.42
23 30 0.48
24 3 0.05
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTGAAATGCATATGGGTGCATT
Found at i:14938 original size:90 final size:90
Alignment explanation
Indices: 14805--15024 Score: 320
Period size: 90 Copynumber: 2.4 Consensus size: 90
14795 AAGGATATTG
* * * *
14805 GAAAGGATGCCATAATTGAAATGCATATGGGTGCATTACTGGCATGAAAA-TATA-TCATAATTG
1 GAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATTGGCAT-AAAAGGA-AGACATAATTA
*
14868 AAATGCATATGGGTGCATTATTGGCAT
64 AAATGCATATGGGTGCATTATTAGCAT
*
14895 GAAATGATGCCATAATTGAAATGCATATGGGTGCATTATTGGCATAAAAGGAAGACATAATTAAA
1 GAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATTGGCATAAAAGGAAGACATAATTAAA
14960 ATGCATATGGGTGCATTATTAGCAT
66 ATGCATATGGGTGCATTATTAGCAT
*
14985 GAAAGGATGCTATAATTGAAAATGCATAAT-GGTGCATTAT
1 GAAAGGATGCCATAATTG-AAATGCAT-ATGGGTGCATTAT
15025 AAACATGAAT
Statistics
Matches: 118, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
89 5 0.04
90 93 0.79
91 18 0.15
92 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (90 bp):
GAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATTGGCATAAAAGGAAGACATAATTAAA
ATGCATATGGGTGCATTATTAGCAT
Found at i:18299 original size:17 final size:17
Alignment explanation
Indices: 18279--18311 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18269 TAAAGATAAC
18279 AAAACAA-AACAATATGT
1 AAAACAAGAA-AATATGT
18296 AAAACAAGAAAATATG
1 AAAACAAGAAAATATG
18312 GAGAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (17 bp):
AAAACAAGAAAATATGT
Found at i:18978 original size:23 final size:23
Alignment explanation
Indices: 18952--19010 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
18942 ATAGCCTCCA
*
18952 ATGATTTTCATT-TTAATATAAAT
1 ATGATTTTAATTGTTAAT-TAAAT
*
18975 ATGATTTTAATTGTTGATTAAAT
1 ATGATTTTAATTGTTAATTAAAT
* *
18998 ATTAATTTAATTG
1 ATGATTTTAATTG
19011 ATATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (23 bp):
ATGATTTTAATTGTTAATTAAAT
Found at i:19252 original size:18 final size:18
Alignment explanation
Indices: 19229--19273 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
19219 TTTTAGAGAT
19229 GAAAATATATTATCAATA
1 GAAAATATATTATCAATA
19247 GAAAATATATTATCAATA
1 GAAAATATATTATCAATA
*
19265 TAAAATATA
1 GAAAATATA
19274 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (18 bp):
GAAAATATATTATCAATA
Found at i:22264 original size:37 final size:37
Alignment explanation
Indices: 22214--22289 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
22204 CCAAGCATAT
22214 CATTACAATCCATAAAATATCTGCATCTGAAGGAACC
1 CATTACAATCCATAAAATATCTGCATCTGAAGGAACC
22251 CATTACAGA-CCATAAAATATCTGCATCTGAAGGAACC
1 CATTACA-ATCCATAAAATATCTGCATCTGAAGGAACC
22288 CA
1 CA
22290 AAAACCTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (37 bp):
CATTACAATCCATAAAATATCTGCATCTGAAGGAACC
Found at i:25548 original size:23 final size:22
Alignment explanation
Indices: 25508--25551 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
25498 TTTCTCTTGT
*
25508 AATTTTAAAAAAAATTATATAA
1 AATTTAAAAAAAAATTATATAA
25530 AATTTAAAAATAAAATTATATA
1 AATTTAAAAA-AAAATTATATA
25552 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTTAAAAAAAAATTATATAA
Found at i:25578 original size:24 final size:23
Alignment explanation
Indices: 25534--25579 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25524 ATATAAAATT
** *
25534 TAAAAATAAAATTATATATTTTA
1 TAAAAATAAAAACATACATTTTA
25557 TAAAAATAAAACACATACATTTT
1 TAAAAATAAAA-ACATACATTTT
25580 GAAATAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATAAAAACATACATTTTA
Found at i:27225 original size:21 final size:21
Alignment explanation
Indices: 27185--27225 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27175 CAACAAATCA
* *
27185 CTTCATCAAATGATCTTAACT
1 CTTCATCAAAAGATCATAACT
*
27206 CTTCATCAAAAGGTCATAAC
1 CTTCATCAAAAGATCATAAC
27226 CTTTTGATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (21 bp):
CTTCATCAAAAGATCATAACT
Found at i:43159 original size:13 final size:13
Alignment explanation
Indices: 43141--43169 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43131 GACCTAAACT
43141 AAAATAAAAATAA
1 AAAATAAAAATAA
43154 AAAATAAAAATAA
1 AAAATAAAAATAA
43167 AAA
1 AAA
43170 CAAAGGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:44221 original size:80 final size:80
Alignment explanation
Indices: 44079--44227 Score: 201
Period size: 80 Copynumber: 1.9 Consensus size: 80
44069 AAGGCAATTC
* * * *
44079 CTCACTCCTACCATGCAGTTGATGCTCTCTTGATCTAAGTGGAATTGAACTCAAAAAATTTGGTC
1 CTCACTCCTACCATGCAGTCGATGCTCTCTCGAGCTAAGTGGAATCGAACTCAAAAAATTTGGTC
44144 AACAAAATAGATCTT
66 AACAAAATAGATCTT
* * * **
44159 CTCACTGCTACCATGC-GATCGATGCTCTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGT
1 CTCACTCCTACCATGCAG-TCGATGCTCTCTCGAGCTAAGTGGAATCGAACTCAAAAAATTTGGT
44223 CAACA
65 CAACA
44228 GATAACTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.02
80 58 0.98
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (80 bp):
CTCACTCCTACCATGCAGTCGATGCTCTCTCGAGCTAAGTGGAATCGAACTCAAAAAATTTGGTC
AACAAAATAGATCTT
Found at i:44608 original size:200 final size:196
Alignment explanation
Indices: 44185--44631 Score: 543
Period size: 200 Copynumber: 2.3 Consensus size: 196
44175 GATCGATGCT
* * * *
44185 CTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGTCAACAGATAACTCTTCTCGCCTTAAGT
1 CTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGTCGACAGATAACTCTTATCACCTTAAGC
* *
44250 TATGTCGAAACTTGACTGAGAAGTGGTTATTTCAACATTACAGTTAACCTAGGTCTTCTTCTTGG
66 TATGTCGAAACTTAACTGAGAAGTGGTTATTTCAACATCACAGTTAACCTAGGTCTTCTTCTTGG
* * * *** *
44315 CTTAAAGACCTCGGTTTGAATTTTGAGCGGAAGGTAGTTCCTTGTTGCTACCATGTGGTCGATAC
131 CTTAAAGACCTCGGTTTGAATTTTGAACGGAAGGTAATTCCTTGTTACTACCATGAAATCAATAC
44380 A
196 A
* * * * * *
44381 CACTAGAGCTGAGTGGAATCAAACTCGAAAGGTTTGGTCGACATATAGCTCTTATTACCTTAAGC
1 CTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGTCGACAGATAACTCTTATCACCTTAAGC
* * * * *
44446 TATGTCGAAACTTAACTGGGAAGTGGTTTTTTGTTGCCACATCGCAGTTAACCTTGGTCTTCTTC
66 TATGTCGAAACTTAACTGAGAAGTGG--TTAT-TT-CAACATCACAGTTAACCTAGGTCTTCTTC
* * * * *
44511 TTGGCTTAAAGACCTCGGTTTGAGTTTTTAATGGAAGGTAATTCTTTGTTACTACCATGAAATTA
127 TTGGCTTAAAGACCTCGGTTTGAATTTTGAACGGAAGGTAATTCCTTGTTACTACCATGAAATCA
*
44576 ATGCA
192 ATACA
* * * * *
44581 TTCTCGAGCTCAGTGAAATCGAACTCGAAAGCTTTGGTTGACAGATAACTC
1 CTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGTCGACAGATAACTC
44632 CTTTTACTTG
Statistics
Matches: 207, Mismatches: 40, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
196 79 0.38
198 3 0.01
199 2 0.01
200 123 0.59
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (196 bp):
CTCTCGAGCTGAGTGGAATCGAACTCGAAAGGTTTGGTCGACAGATAACTCTTATCACCTTAAGC
TATGTCGAAACTTAACTGAGAAGTGGTTATTTCAACATCACAGTTAACCTAGGTCTTCTTCTTGG
CTTAAAGACCTCGGTTTGAATTTTGAACGGAAGGTAATTCCTTGTTACTACCATGAAATCAATAC
A
Found at i:48442 original size:18 final size:18
Alignment explanation
Indices: 48419--48453 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48409 ACCTAGAAAA
48419 CCCATCCACGAATGAGGT
1 CCCATCCACGAATGAGGT
* *
48437 CCCATCTATGAATGAGG
1 CCCATCCACGAATGAGG
48454 AAAGGGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (18 bp):
CCCATCCACGAATGAGGT
Found at i:54754 original size:14 final size:14
Alignment explanation
Indices: 54722--54760 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
54712 TTAATATGAT
*
54722 GAAGAGAAG-AAAA
1 GAAGAAAAGAAAAA
54735 -AAGAAAAGAAAAA
1 GAAGAAAAGAAAAA
54748 GAAGAAAAGAAAA
1 GAAGAAAAGAAAA
54761 TAAACAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
GAAGAAAAGAAAAA
Found at i:55393 original size:21 final size:20
Alignment explanation
Indices: 55350--55394 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
55340 TTACTTGAAA
*
55350 AAATAAAAATAATCAAAGGT
1 AAATAAAAATAATCAAAGAT
55370 AAATAAAAATGAATCGAAA-AT
1 AAATAAAAAT-AATC-AAAGAT
55391 AAAT
1 AAAT
55395 TCAAAACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 9 0.41
22 3 0.14
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (20 bp):
AAATAAAAATAATCAAAGAT
Found at i:57093 original size:17 final size:18
Alignment explanation
Indices: 57051--57093 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
57041 AAATGAAAAT
*
57051 AAATAAAAAAACAAAGAG
1 AAATAAAAAAACAAAGAA
* *
57069 AAAGAAAAAAA-TAAGAA
1 AAATAAAAAAACAAAGAA
57086 AAATAAAA
1 AAATAAAA
57094 TTAAAAAGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (18 bp):
AAATAAAAAAACAAAGAA
Found at i:57169 original size:43 final size:42
Alignment explanation
Indices: 57121--57216 Score: 110
Period size: 41 Copynumber: 2.3 Consensus size: 42
57111 ATGTAATATA
*
57121 TATATATATATATATAT-ATTT-AAAACCTATATTTTTCAAAAAC
1 TATATATATATAT-TATGATTTCAAAA-CTAT-GTTTTCAAAAAC
* *
57164 TATATA-ATATATTATGTTTTCAAAACTATGTTTTCAAAAAT
1 TATATATATATATTATGATTTCAAAACTATGTTTTCAAAAAC
57205 TATATAT-TATAT
1 TATATATATATAT
57217 GTGTTTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
41 24 0.51
42 13 0.28
43 10 0.21
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (42 bp):
TATATATATATATTATGATTTCAAAACTATGTTTTCAAAAAC
Found at i:57195 original size:14 final size:14
Alignment explanation
Indices: 57176--57202 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57166 TATAATATAT
57176 TATGTTTTCAAAAC
1 TATGTTTTCAAAAC
57190 TATGTTTTCAAAA
1 TATGTTTTCAAAA
57203 ATTATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (14 bp):
TATGTTTTCAAAAC
Found at i:57273 original size:19 final size:18
Alignment explanation
Indices: 57212--57273 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
57202 AATTATATAT
*
57212 TATATGTGTTTTCAAAAA
1 TATATATGTTTTCAAAAA
* *
57230 T-TATATATTTTCAAAAT
1 TATATATGTTTTCAAAAA
57247 TATAATATGTTTTCAAAAA
1 TAT-ATATGTTTTCAAAAA
57266 CTATATAT
1 -TATATAT
57274 ATTATATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.39
18 2 0.06
19 17 0.47
20 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (18 bp):
TATATATGTTTTCAAAAA
Found at i:57292 original size:30 final size:29
Alignment explanation
Indices: 57245--57328 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 29
57235 TATTTTCAAA
57245 ATTATAATATGTTTTCAAAAACTATATAT
1 ATTATAATATGTTTTCAAAAACTATATAT
*
57274 ATTATATATATTTTTTCAAAAA-T-TATAT
1 ATTATA-ATATGTTTTCAAAAACTATATAT
57302 A--AT-ATA--TTTTCAAAAACTATATTAT
1 ATTATAATATGTTTTCAAAAACTATA-TAT
57327 AT
1 AT
57329 ATTTTTTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
22 10 0.20
23 1 0.02
24 5 0.10
25 4 0.08
26 2 0.04
28 6 0.12
29 7 0.14
30 14 0.29
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTATAATATGTTTTCAAAAACTATATAT
Found at i:57311 original size:22 final size:22
Alignment explanation
Indices: 57274--57357 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
57264 AACTATATAT
*
57274 ATTATAT-ATATTTTTTCAAAA
1 ATTATATAATATATTTTCAAAA
57295 ATTATATAATATATTTTCAAAA
1 ATTATATAATATATTTTCAAAA
* * **
57317 ACTATATTATATATTTT-TTAA
1 ATTATATAATATATTTTCAAAA
*
57338 A-TATATAA-ATATATTCAAAA
1 ATTATATAATATATTTTCAAAA
57358 CCACATATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
19 6 0.12
20 8 0.15
21 10 0.19
22 28 0.54
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTATATAATATATTTTCAAAA
Found at i:57313 original size:52 final size:50
Alignment explanation
Indices: 57231--57328 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 50
57221 TTTCAAAAAT
*
57231 TATATATTTTCAAAATTATAATATGTTTTCAAAAACTATA-TATATTATA
1 TATATATTTTCAAAATTATAATATATTTTCAAAAACTATATTATATTATA
*
57280 TATATTTTTTCAAAAATTATATAATATATTTTCAAAAACTATATTATAT
1 TATATATTTTC-AAAA-T-TATAATATATTTTCAAAAACTATATTATAT
57329 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 10 0.23
50 4 0.09
51 1 0.02
52 23 0.53
53 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (50 bp):
TATATATTTTCAAAATTATAATATATTTTCAAAAACTATATTATATTATA
Found at i:60135 original size:45 final size:43
Alignment explanation
Indices: 60060--60163 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 43
60050 TTGGAATTTC
* *
60060 AACTTATTTCTCTCAATATGTTGGAACTATTACCAACATTGCCA
1 AACTTATTTC-CTAAATATGTTGGAACTATTACCAACATTACCA
* * * *
60104 AACTTATTTCCTAAGACTATGTTGGAGCTATTACTAGCATTACCC
1 AACTTATTTCCTAA-A-TATGTTGGAACTATTACCAACATTACCA
60149 AACTTATTTCCTAAA
1 AACTTATTTCCTAAA
60164 CCTCTCATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.06
44 12 0.23
45 37 0.71
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (43 bp):
AACTTATTTCCTAAATATGTTGGAACTATTACCAACATTACCA
Found at i:65204 original size:102 final size:102
Alignment explanation
Indices: 65028--65232 Score: 324
Period size: 102 Copynumber: 2.0 Consensus size: 102
65018 ACTTCAAATC
* *
65028 TTTTTTTAAACATACTTTAAGGGGAGTCATCTCATCACACTTCCATCCCACACTCTAAGTGAAAG
1 TTTTTTTAAACATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAG
*
65093 GGAGCATACCTTCCATCCCC-GAGCTAGTC-GAGTAGAG
66 GAAGCATACCTTCCA-CCCCTGAGCTAGTCAG-GTAGAG
* * *
65130 TTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCGTCACACTACCATCTCACACTCTAAGTGAAAG
1 TTTTTTTAAACATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAG
65195 GAAGCATACCTTCCACCCCTGAGCTAGTCAGGTAGAG
66 GAAGCATACCTTCCACCCCTGAGCTAGTCAGGTAGAG
65232 T
1 T
65233 AATCTCGTGA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
101 4 0.04
102 90 0.95
103 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (102 bp):
TTTTTTTAAACATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAG
GAAGCATACCTTCCACCCCTGAGCTAGTCAGGTAGAG
Done.