Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006911.1 Hibiscus syriacus cultivar Beakdansim tig00017699_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: 85468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3239 original size:15 final size:15
Alignment explanation
Indices: 3221--3252 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3211 TATTTTTTAG
*
3221 TTGATTTTTTTCCAT
1 TTGATTTTTTCCCAT
3236 TTGATTTTTTCCCAT
1 TTGATTTTTTCCCAT
3251 TT
1 TT
3253 TTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.66
Consensus pattern (15 bp):
TTGATTTTTTCCCAT
Found at i:6541 original size:121 final size:121
Alignment explanation
Indices: 6327--6554 Score: 278
Period size: 121 Copynumber: 1.9 Consensus size: 121
6317 CATAAATCAG
* * * * *** **
6327 ATCAAGCTGCAGAAATTCTCGACCATGATTTGGAACCAATGAATGTGACTTTCACTTGTTAGGAC
1 ATCAAGCTGCAGAAATTCTCCAACATGATATGGAACCAACGAATCCAACTTTCACTTACTAGGAC
* *
6392 ACAATATTTGACTATCATAACAACTTAAGAACTAGTAGACATTCTCGTAAAACCAT
66 ACAATATTTGACTATCATAACAACTTAAGAACCAGAAGACATTCTCGTAAAACCAT
* * *
6448 ATCAAGCTGTAGAAATTCTCCAACATGATATGGAATCAACGAATCCAACTTT-ACTTACTAGGGC
1 ATCAAGCTGCAGAAATTCTCCAACATGATATGGAACCAACGAATCCAACTTTCACTTACTAGGAC
* * * *
6512 CCAATCTTTGTCTATCATAATAACTTTAAGAACCAGAAGACAT
66 ACAATATTTGACTATCATAACAAC-TTAAGAACCAGAAGACAT
6555 ATCCTACAGC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
120 29 0.33
121 59 0.67
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (121 bp):
ATCAAGCTGCAGAAATTCTCCAACATGATATGGAACCAACGAATCCAACTTTCACTTACTAGGAC
ACAATATTTGACTATCATAACAACTTAAGAACCAGAAGACATTCTCGTAAAACCAT
Found at i:23132 original size:23 final size:23
Alignment explanation
Indices: 23106--23154 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23096 GTTCTCTCTA
* *
23106 TTTATGGTATGCTTATCTCTACC
1 TTTATGGCACGCTTATCTCTACC
* *
23129 TTTATGGCACGTTTCTCTCTACC
1 TTTATGGCACGCTTATCTCTACC
23152 TTT
1 TTT
23155 CGGTAGCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.49
Consensus pattern (23 bp):
TTTATGGCACGCTTATCTCTACC
Found at i:28181 original size:3 final size:3
Alignment explanation
Indices: 28173--28204 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28163 TGCTCGACGT
*
28173 TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28205 GCACGCGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29889 original size:15 final size:16
Alignment explanation
Indices: 29866--29899 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29856 TTCCCTCTTT
*
29866 TCTCATTCCCTTCCAC
1 TCTCATTCCCTGCCAC
29882 TCTC-TTCCCTGCCAC
1 TCTCATTCCCTGCCAC
29897 TCT
1 TCT
29900 GCAACATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.09, C:0.50, G:0.03, T:0.38
Consensus pattern (16 bp):
TCTCATTCCCTGCCAC
Found at i:30975 original size:4 final size:4
Alignment explanation
Indices: 30949--30991 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
30939 AAATATATAG
30949 TTTA TATTA TATTA -TTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
30992 TCTTTCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 6 0.16
4 23 0.62
5 8 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:37069 original size:94 final size:94
Alignment explanation
Indices: 36900--37259 Score: 540
Period size: 94 Copynumber: 3.7 Consensus size: 94
36890 ATATCGTGCC
* *
36900 ACTCGAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
36965 AATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCACAACGAAGGATATTGG
* *
36994 ACTCCAGACAACGCAAGATCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
37059 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCACAACGAAGGATATTGG
37088 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----C
37153 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
* *
37194 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
37259 A
66 A
37260 GTTCCAGAGC
Statistics
Matches: 243, Mismatches: 11, Indels: 24
0.87 0.04 0.09
Matches are distributed among these distances:
94 142 0.58
96 1 0.00
97 2 0.01
98 6 0.02
102 7 0.03
103 2 0.01
104 1 0.00
106 82 0.34
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (94 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAACTTCACAACGAAGGATATTGG
Found at i:37123 original size:43 final size:43
Alignment explanation
Indices: 36971--37123 Score: 108
Period size: 43 Copynumber: 3.4 Consensus size: 43
36961 TCCCAATTTT
* *
36971 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGATC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTC
* *** ** * * * *
37014 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
1 AACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CACAAGTTC
*
37065 AACTTCGCAACGAAGGATATTGGACTCCAGACAACACAAGTTC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTC
*
37108 AACTTCACGACGAAGG
1 AACTTCACAACGAAGG
37124 GACCGCTGGT
Statistics
Matches: 78, Mismatches: 24, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
43 34 0.44
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 18 0.23
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (43 bp):
AACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTC
Found at i:37203 original size:200 final size:188
Alignment explanation
Indices: 36900--37259 Score: 576
Period size: 200 Copynumber: 1.9 Consensus size: 188
36890 ATATCGTGCC
* *
36900 ACTCGAGACAACACAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
36965 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGATCAACTTCACGACGAAGG
66 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGATCAACTTCACGACGAAGG
37030 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCGCAACGAAGGATATTGG
131 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCGCAACGAAGGATATTGG
37088 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
37153 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AA--T---------TTT-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGATCAACT
*
37218 TCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCA
119 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
37260 GTTCCAGAGC
Statistics
Matches: 156, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
188 65 0.42
190 1 0.01
199 3 0.02
200 87 0.56
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (188 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGATCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCGCAACGAAGGATATTGG
Found at i:37242 original size:106 final size:106
Alignment explanation
Indices: 37057--37302 Score: 438
Period size: 106 Copynumber: 2.3 Consensus size: 106
37047 AAACAATTTC
*
37057 CCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
*
37122 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTCCAGAG
*
37163 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
* *
37228 GGGACCGCTGGTTGTCAATAAATAATTTCCCAGTTCCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTCCAGAG
*
37269 CCAATTTCAACTTCACAACGGAGGATATTGGACT
1 CCAATTTCAACTTCACAACGAAGGATATTGGACT
37303 TGGAACAATA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 134 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTCCAGAG
Found at i:40905 original size:22 final size:24
Alignment explanation
Indices: 40858--40910 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 24
40848 TAAAAAATTC
*
40858 AATTCAATGGATTAAGTATAATAAT
1 AATT-AATGGATTAACTATAATAAT
40883 -ATTAATGG-TTAACTAT-ATGAAT
1 AATTAATGGATTAACTATAAT-AAT
40905 AATTAA
1 AATTAA
40911 CAATGTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 10 0.40
23 10 0.40
24 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
AATTAATGGATTAACTATAATAAT
Found at i:41382 original size:2 final size:2
Alignment explanation
Indices: 41375--41411 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
41365 CCCAATTTAT
41375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41412 AGAGTGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51974 original size:303 final size:300
Alignment explanation
Indices: 51430--52032 Score: 949
Period size: 303 Copynumber: 2.0 Consensus size: 300
51420 CGTCACCTCC
* *
51430 ACCAGAATTTTGAATACCCTAGCCGTTTATAGCCGACGGGATTGGGGCTATAAATAGATGTTTGG
1 ACCAGAATTTTGAATACCCTAGCCGTTTATAGCCGACAGGATTAGGGCTATAAATAGATGTTTGG
* *
51495 AGTTTTGGTTTATCATAATCAACTATTTCTAAAAAAAATCTAAAAAAAATCCTACTTTATGTGAA
66 AGTTTTGGTTTATCATAATCAACTATTTCAAAAAAAAATCTAAAAAAAATCCTACTTTAAGTGAA
* *
51560 AATCCCCAAAATAGTTCCCTAAGAAGAAATATTGCGCCTCGACAACATCCATATTCGTTGATCAA
131 AATCCCCAAAATAGCTCCCCAAGAAGAAATATTGCGCCTCGACAACATCCATATTCGTTGATCAA
*
51625 ACTCCAAACGGAAGAAGAACAAAGTATTCGTCAGCACGAGATGACATTGAGAAATCTTCAGCAAT
196 ACTCCAAACGGAAGAAGAACAAAGTATTCGTCAGCACGAGATGACATTAAGAAATCTTCAGCAAT
* * *
51690 CCGGTCTATTTTCAGCCATATTTGTATGTGGCTTCGAGGT
261 CCGATCTATTTTCAACCATATTTGTATGTGGCTTCAAGGT
*
51730 ACCAGAATTTTGAATACCCTAGCCGTTTATAGCCGACAGGATTAGGGCTATAAATAGGTGTTTGG
1 ACCAGAATTTTGAATACCCTAGCCGTTTATAGCCGACAGGATTAGGGCTATAAATAGATGTTTGG
* * *
51795 AGTTTTGGTTTGTCATAATCATCTATTTCGAAGAGAATAAAATCT-GAAAAAATCCTACTTTAAG
66 AGTTTTGGTTTATCATAATCAACTATTTC-AA-A-AA-AAAATCTAAAAAAAATCCTACTTTAAG
* * * * *
51859 TGAAAATCCTCAAAATAGCTCCCCAAGAATAAATGTTGCGCCTCGACAACGTTCATATTCGTTGA
127 TGAAAATCCCCAAAATAGCTCCCCAAGAAGAAATATTGCGCCTCGACAACATCCATATTCGTTGA
* * *
51924 TCGAACTCCGAACGGAAGAAGAACAGAA-TATTCGTCAGCACGGGATGACATTAAGAAATCTTCA
192 TCAAACTCCAAACGGAAGAAGAACA-AAGTATTCGTCAGCACGAGATGACATTAAGAAATCTTCA
51988 GCAATCCGATCTATTTTCAACCATATTTGTATGTGGCTTCAAGGT
256 GCAATCCGATCTATTTTCAACCATATTTGTATGTGGCTTCAAGGT
52033 GTACCCAGTG
Statistics
Matches: 276, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
300 89 0.32
301 1 0.00
302 1 0.00
303 176 0.64
304 9 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (300 bp):
ACCAGAATTTTGAATACCCTAGCCGTTTATAGCCGACAGGATTAGGGCTATAAATAGATGTTTGG
AGTTTTGGTTTATCATAATCAACTATTTCAAAAAAAAATCTAAAAAAAATCCTACTTTAAGTGAA
AATCCCCAAAATAGCTCCCCAAGAAGAAATATTGCGCCTCGACAACATCCATATTCGTTGATCAA
ACTCCAAACGGAAGAAGAACAAAGTATTCGTCAGCACGAGATGACATTAAGAAATCTTCAGCAAT
CCGATCTATTTTCAACCATATTTGTATGTGGCTTCAAGGT
Found at i:52575 original size:13 final size:13
Alignment explanation
Indices: 52557--52582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52547 CTGGAAGGTG
52557 ATTTTTTAACTTT
1 ATTTTTTAACTTT
52570 ATTTTTTAACTTT
1 ATTTTTTAACTTT
52583 TTAATTTGAT
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTAACTTT
Found at i:57180 original size:24 final size:24
Alignment explanation
Indices: 57136--57185 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
57126 ATAAAGAACC
*
57136 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
57160 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
57184 AA
1 AA
57186 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:61911 original size:15 final size:16
Alignment explanation
Indices: 61891--61934 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
61881 AGTTCTCGAA
*
61891 TTTATATG-GAATATG
1 TTTATATGCAAATATG
61906 TTTATATGCAAATATG
1 TTTATATGCAAATATG
*
61922 TTTATATGTAAAT
1 TTTATATGCAAAT
61935 GTACCTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (16 bp):
TTTATATGCAAATATG
Found at i:64495 original size:300 final size:306
Alignment explanation
Indices: 63917--64528 Score: 1085
Period size: 300 Copynumber: 2.0 Consensus size: 306
63907 TCTTTTCCTC
63917 AGAAAGTGTAGGGTAAGCAAATCCATCTTTGGACAAAACATTACTGAAAATCTCCTATAAGAAAG
1 AGAAAGTGTAGGGTAAGCAAATCCATCTTTGGACAAAACATTACTGAAAATCTCCTATAAGAAAG
*
63982 CCCATTGAACAACGAATAAAAGAATTTCAATCACGCTCTAGAGTAAGTAGCTGCTCAAAGTACTC
66 CCCATTGAACAACGAATAAAAGAATTTCAATCACGCTCTAGAGTAAGTAGCTGCTCAAAGCACTC
64047 AGCAAATTCGGAAAAACTGCTACCCAGAAGTTCAGAAAAACACAAAATGATAGCACAATTAACCA
131 AGCAAATTCGGAAAAAC-GCTACCCAGAAGTTC--AAAAACACAAAATGATAGCACAATTAACCA
*
64112 AAACCGAGATCATCCACAGAATTCAATCTGAAGCAAGGCAGAAATGGGATTAAAATAGCCATATA
193 AAACCGAGATCATCCACAGAATTCAATCTGAAGCAAGGCAGAAATGGGATTAAAATAGCCACATA
64177 TTTCCATGATTTCTAAAGCTACAAATCCATAAACTGAGTTCAGCTGCAG
258 TTTCCATGATTTCTAAAGCTACAAATCCATAAACTGAGTTCAGCTGCAG
64226 AGAAAGTGTAGGGTAAGCAAATCCATCTTTGGACAAAACATTACTGAAAATCTCCTATAAGAAAG
1 AGAAAGTGTAGGGTAAGCAAATCCATCTTTGGACAAAACATTACTGAAAATCTCCTATAAGAAAG
* * * *
64291 CCCGTTGAACAACGAATAAAATAATTTCAATCACGCTCTAGA-TCAAGTCGCTGTTCAAAGCACT
66 CCCATTGAACAACGAATAAAAGAATTTCAATCACGCTCTAGAGT-AAGTAGCTGCTCAAAGCACT
64355 C-GCAAATTCGG-AAAA-GCTACCCAGAAGTTC-AAAA-A-AAAATGATAGCACAATTAACCAAA
130 CAGCAAATTCGGAAAAACGCTACCCAGAAGTTCAAAAACACAAAATGATAGCACAATTAACCAAA
64414 ACCGAGATCATCCACAGAATTCAATCTGAAGCAAGGCAGAAATGGGATTAAAATAGCCACATATT
195 ACCGAGATCATCCACAGAATTCAATCTGAAGCAAGGCAGAAATGGGATTAAAATAGCCACATATT
64479 TCCATGATTTCTAAAGCTACAAATCCATAAACTGAGTTCAGCTGCAG
260 TCCATGATTTCTAAAGCTACAAATCCATAAACTGAGTTCAGCTGCAG
64526 AGA
1 AGA
64529 TCTCCTAGAA
Statistics
Matches: 296, Mismatches: 6, Indels: 11
0.95 0.02 0.04
Matches are distributed among these distances:
300 138 0.47
301 1 0.00
302 4 0.01
305 15 0.05
307 4 0.01
308 11 0.04
309 123 0.42
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (306 bp):
AGAAAGTGTAGGGTAAGCAAATCCATCTTTGGACAAAACATTACTGAAAATCTCCTATAAGAAAG
CCCATTGAACAACGAATAAAAGAATTTCAATCACGCTCTAGAGTAAGTAGCTGCTCAAAGCACTC
AGCAAATTCGGAAAAACGCTACCCAGAAGTTCAAAAACACAAAATGATAGCACAATTAACCAAAA
CCGAGATCATCCACAGAATTCAATCTGAAGCAAGGCAGAAATGGGATTAAAATAGCCACATATTT
CCATGATTTCTAAAGCTACAAATCCATAAACTGAGTTCAGCTGCAG
Found at i:68751 original size:21 final size:19
Alignment explanation
Indices: 68714--68752 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
68704 ATATTAATTT
*
68714 GATTTGTTTAACGAATATA
1 GATTTGTTTAACAAATATA
68733 GATTTGTATATAACAAATAT
1 GATTTGT-T-TAACAAATAT
68753 TATTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (19 bp):
GATTTGTTTAACAAATATA
Found at i:70108 original size:54 final size:54
Alignment explanation
Indices: 70033--70135 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
70023 ATTAATTTAC
*
70033 TTACTATTACAATTTACTCTAAATATATTTACTGACCAAATTATATTTTTATAA
1 TTACAATTACAATTTACTCTAAATATATTTACTGACCAAATTATATTTTTATAA
* * * ** **
70087 TTACAATTATAATTTATTCTAAATATTTTTGTTGGTCAAATTATATTTT
1 TTACAATTACAATTTACTCTAAATATATTTACTGACCAAATTATATTTT
70136 GTTATAAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (54 bp):
TTACAATTACAATTTACTCTAAATATATTTACTGACCAAATTATATTTTTATAA
Found at i:71611 original size:20 final size:21
Alignment explanation
Indices: 71561--71611 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
71551 TTAATATAAT
*
71561 TTTAATAA-AATTATTAATTA
1 TTTAATAATATTTATTAATTA
* * *
71581 TTAAATTATATTTATTGA-TA
1 TTTAATAATATTTATTAATTA
71601 TTTAATAATAT
1 TTTAATAATAT
71612 ATATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAATAATATTTATTAATTA
Found at i:71694 original size:25 final size:25
Alignment explanation
Indices: 71601--71694 Score: 61
Period size: 25 Copynumber: 3.8 Consensus size: 25
71591 TTTATTGATA
*
71601 TTTAATAATATATATATATATTTTAT
1 TTTAATAATATATA-ATAAATTTTAT
** * *
71627 TTT-ATTGT-TATAAT-TATATTAT
1 TTTAATAATATATAATAAATTTTAT
* * * *
71649 TATAAT-ATTTGTATTACAATTTTAT
1 TTTAATAATATATAATA-AATTTTAT
71674 TTTAATAATATATAATAAATT
1 TTTAATAATATATAATAAATT
71695 ATTAATAAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
22 10 0.20
23 8 0.16
24 4 0.08
25 18 0.36
26 10 0.20
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTAATAATATATAATAAATTTTAT
Found at i:71983 original size:15 final size:14
Alignment explanation
Indices: 71963--71992 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
71953 ATTTTAATAG
71963 TAATATTAACATAAA
1 TAATATTAA-ATAAA
71978 TAATATTAAATAAA
1 TAATATTAAATAAA
71992 T
1 T
71993 TATTCTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATATTAAATAAA
Found at i:77418 original size:90 final size:90
Alignment explanation
Indices: 77264--77437 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 90
77254 GTCTTAAATT
* * * *
77264 ATTATATGTAATCACTTTGAGTATTTTAATTATTTTTTGGTTAAAATAAGTTCTCAAACTATATC
1 ATTATATGTAACCACTTTGAGTATCTTAACTATTTTTTGGTCAAAATAAGTTCTCAAACTATATC
*
77329 TCTTTTCTCCTTTAAGCCCCTAAAAA
66 -CTTTTCTCCTTTAAACCCCTAAAAA
*
77355 ATTATATGTAACCACTTTGAGTATCTTAACTA-TTTTTGGTCAAAATAAGTTCTTAAACTATATC
1 ATTATATGTAACCACTTTGAGTATCTTAACTATTTTTTGGTCAAAATAAGTTCTCAAACTATATC
* *
77419 CTTTTTTGCTTTAAACCCC
66 CTTTTCTCCTTTAAACCCC
77438 AATTATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 16 0.21
90 30 0.40
91 29 0.39
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (90 bp):
ATTATATGTAACCACTTTGAGTATCTTAACTATTTTTTGGTCAAAATAAGTTCTCAAACTATATC
CTTTTCTCCTTTAAACCCCTAAAAA
Done.