Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003503.1 Hibiscus syriacus cultivar Beakdansim tig00007401_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: 68098
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1728 original size:21 final size:21
Alignment explanation
Indices: 1704--1756 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1694 AGAGAGCAGC
1704 AGCAGAAGCAGCCAGATCAGT
1 AGCAGAAGCAGCCAGATCAGT
1725 AGCAGAAGCAGCCAGATCAGT
1 AGCAGAAGCAGCCAGATCAGT
*
1746 AGCGGAAGCAG
1 AGCAGAAGCAG
1757 AGAAAGAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.32, T:0.08
Consensus pattern (21 bp):
AGCAGAAGCAGCCAGATCAGT
Found at i:2250 original size:43 final size:43
Alignment explanation
Indices: 2213--2373 Score: 198
Period size: 43 Copynumber: 3.7 Consensus size: 43
2203 GAAAAATGCT
* *
2213 GCTAAACATCATA-ACCTATTACGGCGTTTGTCTGAAAAAACACC
1 GCTAAATATCA-ACACCTATTGCGGCGTTTGTCTG-AAAAACACC
* * * * *
2257 ACTAAATATCAACACCTATTGCGGCGTTTTTCTGACAATCGCC
1 GCTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAACACC
** *
2300 GCTAAATATCAACACCTATTGCGGCGTTTGTCACAAAAACACA
1 GCTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAACACC
*
2343 GCTAAATATCAATACCTATTGCGGCGTTTGT
1 GCTAAATATCAACACCTATTGCGGCGTTTGT
2374 TCATGTCATC
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 72 0.72
44 28 0.28
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
GCTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAACACC
Found at i:2277 original size:87 final size:86
Alignment explanation
Indices: 2177--2371 Score: 218
Period size: 87 Copynumber: 2.3 Consensus size: 86
2167 GCCGCAAAAC
* * *
2177 ATCAACACCTATTGCGATGTTTTAGAGAAAAAT-GCTGCTAAACATCATA-ACCTATTACGGCGT
1 ATCAACACCTATTGCGACGTTTTACAG-AAAATCGCCGCTAAACATCA-ACACCTATTACGGCGT
2240 TTGTCTGA-AAAAACACCA-CTAAAT
64 TTGTC--ACAAAAACA-CAGCTAAAT
* * * * * *
2264 ATCAACACCTATTGCGGCGTTTTTCTGACAATCGCCGCTAAATATCAACACCTATTGCGGCGTTT
1 ATCAACACCTATTGCGACGTTTTACAGAAAATCGCCGCTAAACATCAACACCTATTACGGCGTTT
2329 GTCACAAAAACACAGCTAAAT
66 GTCACAAAAACACAGCTAAAT
* *
2350 ATCAATACCTATTGCGGCGTTT
1 ATCAACACCTATTGCGACGTTT
2372 GTTCATGTCA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
85 3 0.03
86 39 0.41
87 52 0.55
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (86 bp):
ATCAACACCTATTGCGACGTTTTACAGAAAATCGCCGCTAAACATCAACACCTATTACGGCGTTT
GTCACAAAAACACAGCTAAAT
Found at i:2370 original size:86 final size:86
Alignment explanation
Indices: 2213--2371 Score: 234
Period size: 86 Copynumber: 1.8 Consensus size: 86
2203 GAAAAATGCT
2213 GCTAAACATCATAACCTATTACGGCGTTTGTCTGAAAAAACACCACTAAATATCAACACCTATTG
1 GCTAAACATCATAACCTATTACGGCGTTTGTC-GAAAAAACACCACTAAATATCAACACCTATTG
2278 CGGCGTTTTTCTGACAATCGCC
65 CGGCGTTTTTCTGACAATCGCC
* * *
2300 GCTAAATATCA-ACACCTATTGCGGCGTTTGTC-ACAAAAACA-CAGCTAAATATCAATACCTAT
1 GCTAAACATCATA-ACCTATTACGGCGTTTGTCGA-AAAAACACCA-CTAAATATCAACACCTAT
2362 TGCGGCGTTT
63 TGCGGCGTTT
2372 GTTCATGTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
85 3 0.05
86 35 0.53
87 28 0.42
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (86 bp):
GCTAAACATCATAACCTATTACGGCGTTTGTCGAAAAAACACCACTAAATATCAACACCTATTGC
GGCGTTTTTCTGACAATCGCC
Found at i:3069 original size:21 final size:20
Alignment explanation
Indices: 3045--3084 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3035 TTTGGATTCG
*
3045 AGTATCGATACTGGGATGAAC
1 AGTATCAATA-TGGGATGAAC
*
3066 AGTATCAATATTGGATGAA
1 AGTATCAATATGGGATGAA
3085 TTAGGGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (20 bp):
AGTATCAATATGGGATGAAC
Found at i:5472 original size:23 final size:23
Alignment explanation
Indices: 5402--5478 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
5392 AAAAATTAGG
* *
5402 AGCTCGATTGAAGCTCGAGACTCG
1 AGCTCGATTCAAGCTCGA-ACTCA
** * *
5426 AGCTCGATTTTGAGCTTG-ATTCA
1 AGCTCGA-TTCAAGCTCGAACTCA
5449 AGCTCGATTCAAGCTCGAACTCA
1 AGCTCGATTCAAGCTCGAACTCA
*
5472 AACTCGA
1 AGCTCGA
5479 ATTTTAACCT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
22 7 0.17
23 20 0.49
24 7 0.17
25 7 0.17
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGAACTCA
Found at i:8646 original size:7 final size:7
Alignment explanation
Indices: 8636--8683 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
8626 ATGTTTAATA
8636 TTTAGGG
1 TTTAGGG
8643 TTTAGGG
1 TTTAGGG
8650 TTTAGGG
1 TTTAGGG
8657 TTTAGGG
1 TTTAGGG
8664 TTTAGGG
1 TTTAGGG
8671 TTTAGGG
1 TTTAGGG
8678 TTTAGG
1 TTTAGG
8684 ATTCATTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:8652 original size:21 final size:21
Alignment explanation
Indices: 8613--8683 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
8603 CACATAATCG
* **
8613 GATTTAGGATTTAATGTTTAA
1 GATTTAGGGTTTAGGGTTTAA
* *
8634 TATTTAGGGTTTAGGGTTTAG
1 GATTTAGGGTTTAGGGTTTAA
* *
8655 GGTTTAGGGTTTAGGGTTTAG
1 GATTTAGGGTTTAGGGTTTAA
*
8676 GGTTTAGG
1 GATTTAGG
8684 ATTCATTACA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
GATTTAGGGTTTAGGGTTTAA
Found at i:9197 original size:11 final size:11
Alignment explanation
Indices: 9183--9240 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
9173 TATAGAATTA
9183 TTAATATATTT
1 TTAATATATTT
9194 TTAA-A-ATTT
1 TTAATATATTT
**
9203 TATAAT-TATCA
1 T-TAATATATTT
* *
9214 ATAATGTATTT
1 TTAATATATTT
9225 TTAATATATTT
1 TTAATATATTT
9236 TTAAT
1 TTAAT
9241 TATGTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
9 5 0.14
10 8 0.22
11 23 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTAATATATTT
Found at i:9227 original size:31 final size:32
Alignment explanation
Indices: 9184--9243 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
9174 ATAGAATTAT
9184 TAATATATTTTTAA-A-ATTTTATAATTATCAA
1 TAATATATTTTTAATATATTTT-TAATTATCAA
*
9215 TAATGTATTTTTAATATATTTTTAATTAT
1 TAATATATTTTTAATATATTTTTAATTAT
9244 GTAATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.50
32 8 0.31
33 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (32 bp):
TAATATATTTTTAATATATTTTTAATTATCAA
Found at i:10271 original size:200 final size:201
Alignment explanation
Indices: 9936--10300 Score: 447
Period size: 200 Copynumber: 1.8 Consensus size: 201
9926 TTTGAAAGGC
* *
9936 ATTTTCGGGTAGTTAATCTAAAAAATTTCATAATTTATAAGATAAGAGGTGTAGTGTTGGAATTT
1 ATTTTCAGGTAGTTAATCTAAAAAATTTCATAATTTATAAGATAAGAGGTGTAGTGTTGGAACTT
* *
10001 ATCTTTCAGTTGAGGTCAATATTGACACATAAGAGATATGGTAAACGGGTTAAAAATCGCTTTGA
66 ATCTTTCAATTGAGGTCAATATAGACACATAAGAGATATGGTAAACGGGTTAAAAATCGCTTTGA
* *
10066 AAATGGTTTCAAAGCTTG-TTTTGTGCATTAAGAAAAAGCTAAAATTGTTTGATAGGCATATTCA
131 AAATGGTTCCAAAGCTTGATTTTGTGCATGAAGAAAAAGCTAAAATTGTTTGATAGGCATATTCA
10130 AGAGGT
196 AGAGGT
** ** * * * *
10136 ATTTTCAGGTAGTTAATCTAAAATTTTTTGTAATTTATAAGATTATAGGTTTAGTGTTGTAACTT
1 ATTTTCAGGTAGTTAATCTAAAAAATTTCATAATTTATAAGATAAGAGGTGTAGTGTTGGAACTT
* * * *
10201 ATCTTTTAATTGAGGGT-AATATCAGA-ATATAAGAGACT-TTGTGAAGA-GGG-TAAAAGTCG-
66 ATCTTTCAATTGA-GGTCAATAT-AGACACATAAGAGA-TATGGT-AA-ACGGGTTAAAAATCGC
* *
10260 TGTTTAAAATGGTTCCAAAGTTTGATTTTGTGCATGAAGAA
126 T-TTGAAAATGGTTCCAAAGCTTGATTTTGTGCATGAAGAA
10301 CAAGATTAGA
Statistics
Matches: 138, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
199 1 0.01
200 110 0.80
201 26 0.19
202 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (201 bp):
ATTTTCAGGTAGTTAATCTAAAAAATTTCATAATTTATAAGATAAGAGGTGTAGTGTTGGAACTT
ATCTTTCAATTGAGGTCAATATAGACACATAAGAGATATGGTAAACGGGTTAAAAATCGCTTTGA
AAATGGTTCCAAAGCTTGATTTTGTGCATGAAGAAAAAGCTAAAATTGTTTGATAGGCATATTCA
AGAGGT
Found at i:13132 original size:14 final size:14
Alignment explanation
Indices: 13113--13142 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13103 GGCAATCGAG
*
13113 CATCATGTCCACAT
1 CATCATATCCACAT
13127 CATCATATCCACAT
1 CATCATATCCACAT
13141 CA
1 CA
13143 CCATCGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (14 bp):
CATCATATCCACAT
Found at i:16347 original size:2 final size:2
Alignment explanation
Indices: 16340--16387 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
16330 ATAATTATTT
16340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16382 TA -A TA T
1 TA TA TA T
16388 TAATAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25111 original size:19 final size:19
Alignment explanation
Indices: 25080--25142 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
25070 CATTTCATAT
*
25080 ATTTTATTTTAAAAAACTCA
1 ATTTTA-TTTAAAAAACTTA
*
25100 ATTTTATTT-AAAAA-TTT
1 ATTTTATTTAAAAAACTTA
25117 ATTTTA-TTAAAAGAACTTA
1 ATTTTATTTAAAA-AACTTA
25136 ATTTTAT
1 ATTTTAT
25143 ATGTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 2 0.06
17 10 0.28
18 7 0.19
19 11 0.31
20 6 0.17
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTATTTAAAAAACTTA
Found at i:26638 original size:44 final size:44
Alignment explanation
Indices: 26567--26691 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
26557 GTACCTTTCT
* * *
26567 TTTAGCTCGATTCCATCACATAGGGAGTTGGATCAGCATCAACA
1 TTTAGCTTGATTCCATCACATAAGGAGTTGAATCAGCATCAACA
* * * *
26611 TTTCGCTTGATTCCATCATATAAGGAGTTGAATCAACATCACCA
1 TTTAGCTTGATTCCATCACATAAGGAGTTGAATCAGCATCAACA
* ** *
26655 TTTTGCTTGATTCTGTCACATAATGAGTTGAATCAGC
1 TTTAGCTTGATTCCATCACATAAGGAGTTGAATCAGC
26692 GTCGTCACTG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
TTTAGCTTGATTCCATCACATAAGGAGTTGAATCAGCATCAACA
Found at i:26796 original size:36 final size:37
Alignment explanation
Indices: 26740--26882 Score: 195
Period size: 36 Copynumber: 4.0 Consensus size: 37
26730 TCATTTCACT
26740 CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAAA
1 CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAAA
*
26777 CAAG-TTTTATCTCAATTGAGATTATTTTTCTTAAAA
1 CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAAA
* *
26813 C-AGATTTTATCTGACTTGAGATTGTTTTTCTTAAAA
1 CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAAA
* * * *
26849 -TAGATTCTATCTCACTTGATATT-TTTTCCTTAAA
1 CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAA
26883 TTTTTTTTTA
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
35 12 0.12
36 80 0.83
37 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (37 bp):
CAAGATTTTATCTCACTTGAGATTATTTTTCTTAAAA
Found at i:30399 original size:33 final size:33
Alignment explanation
Indices: 30357--30424 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
30347 CCAGCTGGGA
*
30357 TCTTCTAGAAGGTTCCAGAAGAGTCTTTCATCC
1 TCTTCTAGAAGGTTCCAGAAGAGTCTCTCATCC
*
30390 TCTTCTAGAAGGTTCCAGCAGAGTCTCTCATCC
1 TCTTCTAGAAGGTTCCAGAAGAGTCTCTCATCC
30423 TC
1 TC
30425 CAACAGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (33 bp):
TCTTCTAGAAGGTTCCAGAAGAGTCTCTCATCC
Found at i:30599 original size:12 final size:12
Alignment explanation
Indices: 30582--30613 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30572 CGATTACCAG
*
30582 GCCCGATACTCA
1 GCCCGATACCCA
30594 GCCCGATACCCA
1 GCCCGATACCCA
30606 GCCCGATA
1 GCCCGATA
30614 AATATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.44, G:0.19, T:0.12
Consensus pattern (12 bp):
GCCCGATACCCA
Found at i:30717 original size:38 final size:38
Alignment explanation
Indices: 30632--30718 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
30622 AAATAATTAT
30632 TATATATATATACATAATATTAATAAATTTAATTTAAA
1 TATATATATATACATAATATTAATAAATTTAATTTAAA
* * * *
30670 T-TAAAATATATATATAATATTTATATATTTAATTTAAA
1 TAT-ATATATATACATAATATTAATAAATTTAATTTAAA
30708 TATATATATAT
1 TATATATATAT
30719 CCGACCCGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 40 0.95
39 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (38 bp):
TATATATATATACATAATATTAATAAATTTAATTTAAA
Found at i:36026 original size:37 final size:37
Alignment explanation
Indices: 35973--36048 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
35963 ACTTACACTG
*
35973 GTGTAAGTATGCGTTAATTGCTAAGATATTGAAAGAT
1 GTGTAAATATGCGTTAATTGCTAAGATATTGAAAGAT
* * *
36010 GTGTAAATATGTGTTAATTTCTAAGATATTGAGAGAT
1 GTGTAAATATGCGTTAATTGCTAAGATATTGAAAGAT
36047 GT
1 GT
36049 ATATACTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (37 bp):
GTGTAAATATGCGTTAATTGCTAAGATATTGAAAGAT
Found at i:36090 original size:53 final size:55
Alignment explanation
Indices: 36010--36136 Score: 188
Period size: 53 Copynumber: 2.4 Consensus size: 55
36000 ATTGAAAGAT
* * *
36010 GTGTAAATATGTGTTAATT-TCTAAGATATTGAGAGATGTATATACTT-ACAATG
1 GTGTAAGTATGTGTTAATTGTCTAAGATATTGAGAGATGTACATACTTAACAACG
* *
36063 GTGTAAGTATTTGTTAATTGT-TAAGATATTGAGAGATGTACATACTTAACACCG
1 GTGTAAGTATGTGTTAATTGTCTAAGATATTGAGAGATGTACATACTTAACAACG
36117 GTGTAAGTATGTGTTAATTG
1 GTGTAAGTATGTGTTAATTG
36137 CTATAATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
53 42 0.64
54 24 0.36
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (55 bp):
GTGTAAGTATGTGTTAATTGTCTAAGATATTGAGAGATGTACATACTTAACAACG
Found at i:37014 original size:26 final size:27
Alignment explanation
Indices: 36982--37045 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
36972 TTTTCGATTA
*
36982 TATCTTTCT-TTAATCTTGTATTAGAC
1 TATCTTTCTCTTAATCTTATATTAGAC
*
37008 TGTCTTT-TCTTAATCTTATATTAGAC
1 TATCTTTCTCTTAATCTTATATTAGAC
37034 TATCTTTC-CTTA
1 TATCTTTCTCTTA
37046 TATATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (27 bp):
TATCTTTCTCTTAATCTTATATTAGAC
Found at i:39535 original size:26 final size:25
Alignment explanation
Indices: 39505--39558 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
39495 TCTGTCTCCG
*
39505 AAAATTATTTTATATTTAATGAGTGA
1 AAAATTATTTTATATTTAA-GAATGA
39531 AAAATTATTTTATATTTAAGAATGA
1 AAAATTATTTTATATTTAAGAATGA
39556 AAA
1 AAA
39559 TCAATCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (25 bp):
AAAATTATTTTATATTTAAGAATGA
Found at i:39760 original size:39 final size:40
Alignment explanation
Indices: 39700--39781 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 40
39690 ATAAGATCAG
39700 TGAAATTTTTTAACTTAAATTGTGTTGGCGCAGATGTTTA
1 TGAAATTTTTTAACTTAAATTGTGTTGGCGCAGATGTTTA
*
39740 TGAAATTTTTTAAC-TAAATTGTGTTGGTGCAGATGTTTA
1 TGAAATTTTTTAACTTAAATTGTGTTGGCGCAGATGTTTA
39779 TGA
1 TGA
39782 GAGACTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 27 0.66
40 14 0.34
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (40 bp):
TGAAATTTTTTAACTTAAATTGTGTTGGCGCAGATGTTTA
Found at i:40488 original size:61 final size:61
Alignment explanation
Indices: 40415--40535 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
40405 TGTTTTCCAC
** *
40415 TTTTCCTAATGGTGTCCCACATGGAAACAGT-GTTGACATGGTGTATTACGCACCGAACATG
1 TTTTCCTAATGGTGTCCCACATGGAAACA-TCGTCAACATGATGTATTACGCACCGAACATG
*
40476 TTTTCCTAATGGTGTCCCACATGGAAACATCGTCAACATGATGTATTACGTACCGAACAT
1 TTTTCCTAATGGTGTCCCACATGGAAACATCGTCAACATGATGTATTACGCACCGAACAT
40536 TGTAGAATGA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 1 0.02
61 54 0.98
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (61 bp):
TTTTCCTAATGGTGTCCCACATGGAAACATCGTCAACATGATGTATTACGCACCGAACATG
Found at i:41081 original size:29 final size:31
Alignment explanation
Indices: 41040--41098 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
41030 ACTATTTTTT
*
41040 TAAGTGCCTAAAG-TAT-ATTTTGGTCAAAA
1 TAAGTGCCAAAAGTTATCATTTTGGTCAAAA
* *
41069 TAAGTTCCAAAAGTTATCTTTTTGGTCAAA
1 TAAGTGCCAAAAGTTATCATTTTGGTCAAA
41099 TAGGTACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 3 0.12
31 11 0.44
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (31 bp):
TAAGTGCCAAAAGTTATCATTTTGGTCAAAA
Found at i:41095 original size:31 final size:31
Alignment explanation
Indices: 41057--41141 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
41047 CTAAAGTATA
*
41057 TTTTGGTCAAAATAAGTTCC-AAAAGT-TATCT
1 TTTTGGTCAAAATAAGTACCTAAAA-TAT-TCT
* *
41088 TTTTGGTC-AAATAGGTACCTAAAATATTTT
1 TTTTGGTCAAAATAAGTACCTAAAATATTCT
*
41118 TTTTGGTCAAAATAGGTACCTAAA
1 TTTTGGTCAAAATAAGTACCTAAA
41142 GTAATCAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 20 0.42
31 28 0.58
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTTGGTCAAAATAAGTACCTAAAATATTCT
Found at i:41268 original size:29 final size:28
Alignment explanation
Indices: 41236--41327 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
41226 TTGAATACTT
* *
41236 TACCTATTTTAACCAAAAAATATTTTAGG
1 TACCTATTTTAA-AAAAAAATACTTTAGG
* * *
41265 TACCTATTTTGAATAAAAATATAAGTTTAAG
1 TACCTATTTT-AA-AAAAAAAT-ACTTTAGG
* *
41296 TACTTATTTTGATAAAAAAATACTTTAGG
1 TACCTATTTT-AAAAAAAAATACTTTAGG
41325 TAC
1 TAC
41328 TTGAAAGAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
29 19 0.37
30 15 0.29
31 17 0.33
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (28 bp):
TACCTATTTTAAAAAAAAATACTTTAGG
Found at i:56906 original size:3 final size:3
Alignment explanation
Indices: 56898--57002 Score: 210
Period size: 3 Copynumber: 35.0 Consensus size: 3
56888 TATTTTGATT
56898 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56946 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56994 TAA TAA TAA
1 TAA TAA TAA
57003 AGTGTTAAAG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57224 original size:18 final size:17
Alignment explanation
Indices: 57199--57271 Score: 92
Period size: 18 Copynumber: 4.2 Consensus size: 17
57189 TGAATTCTAA
57199 ATATTTACAGTTATCAG
1 ATATTTACAGTTATCAG
57216 ATGATTTACAGTTATCAG
1 AT-ATTTACAGTTATCAG
* **
57234 ATAATTACAAATATCAG
1 ATATTTACAGTTATCAG
*
57251 ATATTTTATAGTTATCAG
1 ATA-TTTACAGTTATCAG
57269 ATA
1 ATA
57272 CATATTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 17 0.36
18 30 0.64
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (17 bp):
ATATTTACAGTTATCAG
Found at i:57411 original size:41 final size:41
Alignment explanation
Indices: 57366--57447 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
57356 AAGTGAGTAC
* *
57366 TTATCAGTTCAACTTTGGTACATTCGTGTATTAATATTCAG
1 TTATCAGTTCAACTTTGGTACATTCATGTATCAATATTCAG
* *
57407 TTATCAGTTCATCTTTGGTACATTCATGTATCAATGTTCAG
1 TTATCAGTTCAACTTTGGTACATTCATGTATCAATATTCAG
57448 CATCGTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.44
Consensus pattern (41 bp):
TTATCAGTTCAACTTTGGTACATTCATGTATCAATATTCAG
Found at i:65581 original size:18 final size:18
Alignment explanation
Indices: 65544--65584 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
65534 AGAACAACAC
*
65544 GAGGAACAAGCATGAATA
1 GAGGAACAAGCATCAATA
65562 GAGGAACAAGCA-CAACTA
1 GAGGAACAAGCATCAA-TA
65580 GAGGA
1 GAGGA
65585 TCAAATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.49, C:0.15, G:0.29, T:0.07
Consensus pattern (18 bp):
GAGGAACAAGCATCAATA
Done.