Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001144.1 Hibiscus syriacus cultivar Beakdansim tig00002286_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: 55071
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11804 original size:11 final size:10
Alignment explanation
Indices: 11776--11825 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
11766 ATGCTTGAAG
*
11776 AAAAGAAAGA
1 AAAAGAAAAA
11786 AAAAGAAAAA
1 AAAAGAAAAA
11796 AAAAGGAAAAA
1 AAAA-GAAAAA
* *
11807 AGAA-AAAGA
1 AAAAGAAAAA
11816 AAAAGAAAAA
1 AAAAGAAAAA
11826 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 7 0.21
10 17 0.52
11 9 0.27
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:11805 original size:7 final size:6
Alignment explanation
Indices: 11781--11826 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
11771 TGAAGAAAAG
*
11781 AAAGAA AAAGAA AAA-AA AAGGAAA AAAGAA AAAGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AAAGAA AAAGAA AAAG
11827 GGGTCAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:13167 original size:83 final size:84
Alignment explanation
Indices: 12925--13334 Score: 740
Period size: 83 Copynumber: 4.9 Consensus size: 84
12915 GATATCCCAG
12925 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
12990 CTGATCTGGTTTGGACAGA
66 CTGATCTGGTTTGGACAGA
13009 A-CAATCATTGAATTTAGAAGATGAATTTGTC-ATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
13072 CTGATCTGGTTTGG-CAGA
66 CTGATCTGGTTTGGACAGA
13090 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
13155 CTGATCTGGTTTGG-CAGA
66 CTGATCTGGTTTGGACAGA
*
13173 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
13238 CTGATCTGG-TTGGACAGA
66 CTGATCTGGTTTGGACAGA
* * *
13256 ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
*
13321 CTGATCTAGTTTGG
66 CTGATCTGGTTTGG
13335 TAGGAACTAC
Statistics
Matches: 318, Mismatches: 4, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
81 5 0.02
82 80 0.25
83 228 0.72
84 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (84 bp):
ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGACAGA
Found at i:14483 original size:113 final size:113
Alignment explanation
Indices: 14088--14475 Score: 672
Period size: 113 Copynumber: 3.4 Consensus size: 113
14078 TGTATTGACA
*
14088 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
14153 AGAATTTGTTCAACCTTTT-GTCTGAATTCATCACTTGATGGATTA-TT
66 AGAATTTGTTCAACCTTTTACT-TGAATCCATCATTTGATGGATCAGCT
*
14200 TTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
14265 AAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCT
65 AAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCT
14314 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
14379 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCT
*
14427 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
14476 TTTGTTCAAC
Statistics
Matches: 266, Mismatches: 7, Indels: 5
0.96 0.03 0.02
Matches are distributed among these distances:
112 3 0.01
113 258 0.97
114 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCT
Found at i:14512 original size:206 final size:199
Alignment explanation
Indices: 14264--14660 Score: 571
Period size: 206 Copynumber: 2.0 Consensus size: 199
14254 TTCATAATGA
* * * * **
14264 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
* *
14329 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 CATAATGAGAAGAACTCATATGAA-AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA--
* * *
14394 TTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACT
127 TTTT--TTGAATCCATCA-TTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACT
14458 CATCTAAAGAAG
188 CATCTAAAGAAG
* * *
14470 GAAGAATTTGTTCAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
14535 CATAATGAGAAGAACTCATATGAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTT
66 CATAATGAGAAGAACTCATATGAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTT
* *
14600 TTGAATTCATCATTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATC
131 TTGAATCCATCATTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATC
14661 ATCTGAAGAA
Statistics
Matches: 174, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
198 1 0.01
199 43 0.25
200 11 0.06
202 4 0.02
204 34 0.20
205 2 0.01
206 79 0.45
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (199 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
CATAATGAGAAGAACTCATATGAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTT
TTGAATCCATCATTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTAAA
GAAG
Found at i:14550 original size:93 final size:93
Alignment explanation
Indices: 14377--14553 Score: 273
Period size: 93 Copynumber: 1.9 Consensus size: 93
14367 TTCATAATGA
* * * * **
14377 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
14442 CATAATGAGAAGAACTCATCTAAAGAAG
66 CATAATGAGAAGAACTCATCTAAAGAAG
* * *
14470 GAAGAATTTGTTCAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
14535 CATAATGAGAAGAACTCAT
66 CATAATGAGAAGAACTCAT
14554 ATGAAAAGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (93 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTAAAGAAG
Found at i:14910 original size:116 final size:115
Alignment explanation
Indices: 14470--14945 Score: 566
Period size: 116 Copynumber: 4.2 Consensus size: 115
14460 TCTAAAGAAG
* * * * * **
14470 GAAGAATTTGTTCAACCTTTTA-CATGAATCCATTACTTGATGGAGCATCATCCCCAGCGAAAGT
1 GAAGAACTTGTTCAACCTTTTATC-TGAATTCATCACTTGATGGATCAACATTGCCAG-GAAAGT
*
14534 TCATAATGAGAAGAA---CTCATATGAA-AAG-AAGAAGAAGTTCATAATGA
64 TCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
*
14581 GAAGAACTTGTTCAA--TTTT-T-TGAATTCATCA-TTGATGGATCAACATTGCCAGGTAGAGTT
1 GAAGAACTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCAACATTGCCAGG-AAAGTT
* *
14641 CATAATGAGAAGAACTCATCATCTGAAGAAGGAAA-AAGAAGTTCATAATAA
65 CATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAGAAGTTCATAATAA
* * *
14692 GAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGT
1 GAAGAACTTGTTCAACCTTTT-ATCTGAATTCATCACTTGATGGATCAACATTGCCAGGAA-AGT
* * * *
14757 TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
64 TCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
* * * *
14809 GAAGAATTTGTTCAACCTTTTATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGAGAAAG
1 GAAGAACTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCA--ACATTGCCAG-GAAAG
14872 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
63 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
*
14925 GAAGAACTTGTTCAACTTTTT
1 GAAGAACTTGTTCAACCTTTT
14946 GCATAATTCT
Statistics
Matches: 318, Mismatches: 28, Indels: 33
0.84 0.07 0.09
Matches are distributed among these distances:
105 1 0.00
106 36 0.11
107 9 0.03
109 12 0.04
110 2 0.01
111 45 0.14
112 2 0.01
113 4 0.01
115 1 0.00
116 110 0.35
117 95 0.30
118 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (115 bp):
GAAGAACTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCAACATTGCCAGGAAAGTTC
ATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
Found at i:15184 original size:3 final size:3
Alignment explanation
Indices: 15176--15215 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
15166 TCCATATTTA
15176 TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
15216 AATATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15198 original size:17 final size:17
Alignment explanation
Indices: 15173--15211 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
15163 TTATCCATAT
*
15173 TTATATTATTATTATTA
1 TTATTTTATTATTATTA
15190 TTATTTTATTATTATTA
1 TTATTTTATTATTATTA
15207 TTATT
1 TTATT
15212 ATTAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTATTATTATTA
Found at i:15201 original size:20 final size:21
Alignment explanation
Indices: 15170--15214 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
15160 TTTTTATCCA
15170 TATTTATATTATTATTATTAT
1 TATTTATATTATTATTATTAT
15191 TATTT-TATTATTATTATTAT
1 TATTTATATTATTATTATTAT
15211 TATT
1 TATT
15215 AAATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTATATTATTATTATTAT
Found at i:15678 original size:18 final size:18
Alignment explanation
Indices: 15655--15692 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
15645 ACCTGAAAAA
15655 AAAAAAAAACG-GAGACAG
1 AAAAAAAAA-GAGAGACAG
15673 AAAAAAAAAGAGAGACAG
1 AAAAAAAAAGAGAGACAG
15691 AA
1 AA
15693 CCGAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAGAGACAG
Found at i:28583 original size:24 final size:24
Alignment explanation
Indices: 28538--28598 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
28528 GAATTGGAGT
* *
28538 GAATATAAATGAACGAACATAAAC
1 GAATATAAACGAACGAAAATAAAC
*
28562 GAATATAAACGAAC-ATAAATAAAT
1 GAATATAAACGAACGA-AAATAAAC
*
28586 GAACATAAACGAA
1 GAATATAAACGAA
28599 TGAATTATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (24 bp):
GAATATAAACGAACGAAAATAAAC
Found at i:28594 original size:10 final size:10
Alignment explanation
Indices: 28549--28580 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
28539 AATATAAATG
28549 AACGAACATA
1 AACGAACATA
*
28559 AACGAATATA
1 AACGAACATA
28569 AACGAACATA
1 AACGAACATA
28579 AA
1 AA
28581 TAAATGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.12
Consensus pattern (10 bp):
AACGAACATA
Found at i:33781 original size:3 final size:3
Alignment explanation
Indices: 33773--33820 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
33763 CAGTTTACTT
*
33773 TTA TTA TTA -TA TTA TTA TACA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
33818 TTA
1 TTA
33821 AATAAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:34685 original size:4 final size:4
Alignment explanation
Indices: 34678--34723 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
34668 AGAGAGAGAG
34678 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
34724 TGAGAAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35468 original size:129 final size:129
Alignment explanation
Indices: 35322--35576 Score: 440
Period size: 129 Copynumber: 2.0 Consensus size: 129
35312 AAGAAATGGA
*
35322 CTGTCTTAAAGAACCTAGAAGTCCTTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATA
1 CTGTCTTAAAGAACCTAGAAGTCCTTTTATGATATTCTTAAATAAATAAATATCCTATTTTTATA
35387 AATTATATATTAATTTATTTTAATTATTTTTAGAGAAAT-GTTTATTAATATTTATTTATTGGG
66 AATTATATATTAATTTATTTTAATTATTTTTAGAGAAATAGTTTATTAATATTTATTTATTGGG
* *
35450 CTGTCCTTAAAGCACCTAGAAGTCCTTTTATGATATTCTTAAATAAATAAATATCTTATTTTTAT
1 CTGT-CTTAAAGAACCTAGAAGTCCTTTTATGATATTCTTAAATAAATAAATATCCTATTTTTAT
* * *
35515 AAATTATATATTAGTTTATTTTAATTATTTTTAGATAAATATTTTATTAATATTTATTTATT
65 AAATTATATATTAATTTATTTTAATTATTTTTAGAGAAATAGTTTATTAATATTTATTTATT
35577 TTTAATATTA
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
128 4 0.03
129 95 0.80
130 20 0.17
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (129 bp):
CTGTCTTAAAGAACCTAGAAGTCCTTTTATGATATTCTTAAATAAATAAATATCCTATTTTTATA
AATTATATATTAATTTATTTTAATTATTTTTAGAGAAATAGTTTATTAATATTTATTTATTGGG
Found at i:38200 original size:43 final size:44
Alignment explanation
Indices: 38139--38225 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
38129 TGGCTTTAGA
* *
38139 GAAGTTAGGAGGGAAAGTTATCCCCTATATAT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
* * *
38182 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
38226 TGATGCACGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
Found at i:38464 original size:14 final size:14
Alignment explanation
Indices: 38445--38486 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38435 TTTGTATTTA
38445 CATTTACATTTTTG
1 CATTTACATTTTTG
*
38459 CATTTACATATTTG
1 CATTTACATTTTTG
38473 CATAATTACATTTT
1 CAT--TTACATTTT
38487 ATTTCAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.67
16 8 0.33
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (14 bp):
CATTTACATTTTTG
Found at i:38483 original size:16 final size:14
Alignment explanation
Indices: 38439--38475 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38429 TTTACGTTTG
*
38439 TATTTACATTTACA
1 TATTTGCATTTACA
*
38453 TTTTTGCATTTACA
1 TATTTGCATTTACA
38467 TATTTGCAT
1 TATTTGCAT
38476 AATTACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (14 bp):
TATTTGCATTTACA
Found at i:40849 original size:11 final size:11
Alignment explanation
Indices: 40833--40873 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
40823 TAAAAAAAAC
40833 AAAAAGAAAGA
1 AAAAAGAAAGA
40844 AAAAAGAAAGA
1 AAAAAGAAAGA
*
40855 AAAAA-AAAGG
1 AAAAAGAAAGA
*
40865 AACAAGAAA
1 AAAAAGAAA
40874 AAAGGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:40853 original size:15 final size:15
Alignment explanation
Indices: 40835--40877 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
40825 AAAAAAACAA
40835 AAAGAAAGAAAAAAG
1 AAAGAAAGAAAAAAG
40850 AAAGAAA-AAAAAAG
1 AAAGAAAGAAAAAAG
* *
40864 GAA-CAAGAAAAAAG
1 AAAGAAAGAAAAAAG
40878 GAAAAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 16 0.64
15 7 0.28
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAG
Found at i:40857 original size:21 final size:21
Alignment explanation
Indices: 40824--40873 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40814 ACTCATTCAT
*
40824 AAAAA-AAACAAAAAGAAAGA
1 AAAAAGAAACAAAAAAAAAGA
* *
40844 AAAAAGAAAGAAAAAAAAAGG
1 AAAAAGAAACAAAAAAAAAGA
*
40865 AACAAGAAA
1 AAAAAGAAA
40874 AAAGGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAGAAACAAAAAAAAAGA
Found at i:40878 original size:14 final size:14
Alignment explanation
Indices: 40840--40880 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40830 AACAAAAAGA
* *
40840 AAGAAAAAAGAAAG
1 AAGAAAAAAGGAAC
*
40854 AAAAAAAAAGGAAC
1 AAGAAAAAAGGAAC
40868 AAGAAAAAAGGAA
1 AAGAAAAAAGGAA
40881 AAAATTGAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAGGAAC
Found at i:42588 original size:43 final size:43
Alignment explanation
Indices: 42535--42622 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
42525 GCCAAATCTA
*
42535 CTCATTAATTGCTCCAACCAATCACCATTCAATTCCTGCACAT
1 CTCATCAATTGCTCCAACCAATCACCATTCAATTCCTGCACAT
** * * * *
42578 CTCATCAATTGCTCCAACTGATCATCATTTAGTTCTTGCACAT
1 CTCATCAATTGCTCCAACCAATCACCATTCAATTCCTGCACAT
42621 CT
1 CT
42623 GCTTTCAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (43 bp):
CTCATCAATTGCTCCAACCAATCACCATTCAATTCCTGCACAT
Found at i:44308 original size:54 final size:54
Alignment explanation
Indices: 44242--44393 Score: 173
Period size: 54 Copynumber: 2.8 Consensus size: 54
44232 CAGAAATCTG
* * *
44242 GGCAGAAACCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACAT-CT
1 GGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAAATCCA
* * * * *
44295 GGCTAGGAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACGAAAATCCA
1 GGC-AGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAAATCCA
* * * *
44350 GGCAGAAGCCACGAGAAGA-ATGAATGTATTGTCACATGTTTTAC
1 GGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTAC
44394 AAACCAGTGA
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
53 23 0.29
54 53 0.66
55 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (54 bp):
GGCAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAAATCCA
Found at i:44780 original size:22 final size:22
Alignment explanation
Indices: 44752--44818 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
44742 TATCTACATC
44752 TACATTCTTCAAAGATGATAGA
1 TACATTCTTCAAAGATGATAGA
*
44774 TACATTCTTCAAAGAGGATAGA
1 TACATTCTTCAAAGATGATAGA
* *
44796 TTC-TCTTTTCAAAGATGATAGA
1 TACAT-TCTTCAAAGATGATAGA
44818 T
1 T
44819 TATCTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
TACATTCTTCAAAGATGATAGA
Found at i:44819 original size:22 final size:22
Alignment explanation
Indices: 44759--44835 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
44749 ATCTACATTC
* *
44759 TTCAAAGATGATAGATACAT-TC
1 TTCAAAGATGATAGATTC-TCTT
*
44781 TTCAAAGAGGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
44803 TTCAAAGATGATAGATTATCTT
1 TTCAAAGATGATAGATTCTCTT
*
44825 TTTAAAGATGA
1 TTCAAAGATGA
44836 AAGCCTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:45579 original size:45 final size:45
Alignment explanation
Indices: 45512--45879 Score: 664
Period size: 45 Copynumber: 8.2 Consensus size: 45
45502 CTTTAAGACT
*
45512 TTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
*
45557 TTCAGTGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
45602 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* *
45647 TTTAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCA
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
45692 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
45737 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* *
45782 TTCCGTGAATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
*
45827 TTCAGTGCATGATGTTTTCAAAAACTTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCC
45873 TTCAGTG
1 TTCAGTG
45880 GAAGATGATA
Statistics
Matches: 310, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
45 278 0.90
46 32 0.10
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (45 bp):
TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
Found at i:46068 original size:3 final size:3
Alignment explanation
Indices: 46060--46115 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
46050 CAGTTTGTTT
* *
46060 TTA TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TACA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
46107 TTA TTA TTA
1 TTA TTA TTA
46116 AATAAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 43 0.91
4 4 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:46092 original size:13 final size:13
Alignment explanation
Indices: 46062--46110 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
46052 GTTTGTTTTT
*
46062 ATTATTATTAT-T
1 ATTATTATTATAC
46074 ATTATTATTATAC
1 ATTATTATTATAC
46087 ATTATTATTATAC
1 ATTATTATTATAC
46100 ATTATTATTAT
1 ATTATTATTAT
46111 TATTAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTATTATAC
Found at i:47566 original size:37 final size:35
Alignment explanation
Indices: 47525--47627 Score: 84
Period size: 37 Copynumber: 2.8 Consensus size: 35
47515 TAATTACTAG
47525 TTTTATTACTTTTTATATTTTAATATTATAGTTTTAA
1 TTTTATTA-TTTTTATATTTTAATATTATA-TTTTAA
** *
47562 TTTTATTTATTTTGGTCATTGTTTAT-TTATATTTTAA
1 TTTTA-TTATTTTTAT-ATT-TTAATATTATATTTTAA
*
47599 TTTTA-TATGTTTTTTATATTTAATTATTA
1 TTTTATTAT-TTTTATAT-TTTAA-TATTA
47628 CTGTTATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
35 8 0.15
36 6 0.11
37 24 0.45
38 11 0.21
39 4 0.08
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (35 bp):
TTTTATTATTTTTATATTTTAATATTATATTTTAA
Found at i:47999 original size:2 final size:2
Alignment explanation
Indices: 47987--48023 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
47977 ATATCTTATT
*
47987 TA TA AA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48024 TTTCTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49979 original size:16 final size:17
Alignment explanation
Indices: 49958--50041 Score: 80
Period size: 18 Copynumber: 4.8 Consensus size: 17
49948 GTTTCAGATT
*
49958 CAGATTCCATTTCCT-A
1 CAGATTCCAATTCCTCA
*
49974 CAGATTCCAATTCTTTCA
1 CAGATTCCAATTC-CTCA
49992 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCC-TCA
* **
50010 CAGATTCTAATTATTTCA
1 CAGATTCCAATT-CCTCA
*
50028 CAGATTCTAATTCC
1 CAGATTCCAATTCC
50042 CTCAGAAACA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
16 12 0.21
17 1 0.02
18 43 0.77
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:49996 original size:18 final size:18
Alignment explanation
Indices: 49973--50040 Score: 100
Period size: 18 Copynumber: 3.8 Consensus size: 18
49963 TCCATTTCCT
49973 ACAGATTCCAATTCTTTC
1 ACAGATTCCAATTCTTTC
*
49991 ACAGATTCCAATTCCTTC
1 ACAGATTCCAATTCTTTC
* *
50009 ACAGATTCTAATTATTTC
1 ACAGATTCCAATTCTTTC
*
50027 ACAGATTCTAATTC
1 ACAGATTCCAATTC
50041 CCTCAGAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (18 bp):
ACAGATTCCAATTCTTTC
Found at i:50006 original size:34 final size:36
Alignment explanation
Indices: 49958--50041 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
49948 GTTTCAGATT
* *
49958 CAGATTCCATTTCC-T-ACAGATTCCAATTCTTTCA
1 CAGATTCCAATTCCTTCACAGATTCCAATTATTTCA
*
49992 CAGATTCCAATTCCTTCACAGATTCTAATTATTTCA
1 CAGATTCCAATTCCTTCACAGATTCCAATTATTTCA
*
50028 CAGATTCTAATTCC
1 CAGATTCCAATTCC
50042 CTCAGAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 13 0.30
35 1 0.02
36 30 0.68
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (36 bp):
CAGATTCCAATTCCTTCACAGATTCCAATTATTTCA
Found at i:51177 original size:2 final size:2
Alignment explanation
Indices: 51170--51269 Score: 95
Period size: 2 Copynumber: 52.5 Consensus size: 2
51160 TTTGCTCACT
51170 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
51211 AA AA CTA TA TA T- TT TA TA -A CA TA CA TA -A TA TA -A TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51250 TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
51270 TATTGTATAG
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
1 6 0.07
2 76 0.92
3 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:53598 original size:4 final size:4
Alignment explanation
Indices: 53589--53619 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
53579 ACACTCATGG
53589 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
53620 AATTTCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Done.