Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004650.1 Hibiscus syriacus cultivar Beakdansim tig00010423_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: 66677
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4774 original size:40 final size:40
Alignment explanation
Indices: 4724--4804 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
4714 TTCCCCGAAA
*
4724 TCCCTTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGT
* * *
4764 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGT
4804 T
1 T
4805 TTTCAGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.46
Consensus pattern (40 bp):
TCCCGTGTTTGTTTCACGTAATTCATTTTCCAGAAAATGT
Found at i:5074 original size:19 final size:20
Alignment explanation
Indices: 5050--5087 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5040 ATTTTTAATA
5050 TTTTTAATAATAT-ATAAAT
1 TTTTTAATAATATAATAAAT
*
5069 TTTTTAATATTATAATAAA
1 TTTTTAATAATATAATAAA
5088 ATAATCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTTAATAATATAATAAAT
Found at i:5146 original size:21 final size:22
Alignment explanation
Indices: 5054--5150 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 22
5044 TTAATATTTT
*
5054 TAATA-ATATATAAATTTTTTAA
1 TAATATATA-ATAAATTATTTAA
* * * *
5076 TATTATAATAAAATAATCATTATAT
1 TAATAT-ATAATA-AATTATT-TAA
*
5101 TATATAATATAATATATTATTTTAA
1 TA-AT-ATATAATAAATTA-TTTAA
5126 TAATATATAATAAATTA-TTAA
1 TAATATATAATAAATTATTTAA
5147 TAAT
1 TAAT
5151 GAATAGTATA
Statistics
Matches: 57, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
21 8 0.14
22 4 0.07
23 14 0.25
24 10 0.18
25 11 0.19
26 8 0.14
27 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATAATAAATTATTTAA
Found at i:5298 original size:31 final size:28
Alignment explanation
Indices: 5256--5345 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 28
5246 ACCCTATTAC
*
5256 TTTATTAAATAAAATATAATTTATAATATT
1 TTTATT-AATAAAATATAATAT-TAATATT
5286 TTTATTTCAAT-AAATATACCATATTAATATT
1 TTTA-TT-AATAAAATATA--ATATTAATATT
* * *
5317 TTTATTAATAAATTATAAAAATAATATT
1 TTTATTAATAAAATATAATATTAATATT
5345 T
1 T
5346 AAAAATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.20
29 3 0.06
30 19 0.37
31 16 0.31
32 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTATTAATAAAATATAATATTAATATT
Found at i:5348 original size:13 final size:13
Alignment explanation
Indices: 5323--5355 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5313 TATTTTTATT
5323 AATAAATTATAAA
1 AATAAATTATAAA
5336 AATAATATT-TAAA
1 AATAA-ATTATAAA
5349 AATAAAT
1 AATAAAT
5356 AAATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 14 0.74
14 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAATTATAAA
Found at i:5589 original size:20 final size:20
Alignment explanation
Indices: 5550--5590 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5540 TTTCGAAAAA
**
5550 CGTTTTCCAGAAATGTAATT
1 CGTTTTCCAGAAATCAAATT
*
5570 CGTTTTCCAGAATTCAAATT
1 CGTTTTCCAGAAATCAAATT
5590 C
1 C
5591 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
CGTTTTCCAGAAATCAAATT
Found at i:5597 original size:29 final size:29
Alignment explanation
Indices: 5564--5622 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
5554 TTCCAGAAAT
*
5564 GTAATTCGTTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
5593 GTAATTCATTTTCCAGAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
5622 G
1 G
5623 AAAACTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:5600 original size:15 final size:14
Alignment explanation
Indices: 5573--5624 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
5563 TGTAATTCGT
5573 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
* *
5587 ATTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
5602 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
5616 TTTCCAGAA
1 TTTCCAGAA
5625 AACTAATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:12148 original size:3 final size:3
Alignment explanation
Indices: 12140--12178 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
12130 TTGCCCCGTT
*
12140 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12179 CAAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:18275 original size:25 final size:25
Alignment explanation
Indices: 18242--18303 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
18232 TTCTCAGCCT
18242 TTTTAAGGTTATAAAATTGTGTTGC
1 TTTTAAGGTTATAAAATTGTGTTGC
* *
18267 TTTTAAGGTTATAAATTTGTGTTTC
1 TTTTAAGGTTATAAAATTGTGTTGC
18292 TTTTAAGGTTAT
1 TTTTAAGGTTAT
18304 GAGCAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (25 bp):
TTTTAAGGTTATAAAATTGTGTTGC
Found at i:19172 original size:18 final size:17
Alignment explanation
Indices: 19151--19191 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
19141 GAAAAAGGGG
19151 GAAAAGGAAAAAAAAAGA
1 GAAAAGG-AAAAAAAAGA
*
19169 GAAAATGAAAAAAAAGA
1 GAAAAGGAAAAAAAAGA
19186 GAAAAG
1 GAAAAG
19192 AAAGCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
GAAAAGGAAAAAAAAGA
Found at i:20766 original size:33 final size:34
Alignment explanation
Indices: 20703--20766 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
20693 TACGACTTGG
* *
20703 AATGTTGGGGGAATTTTGAACGCTCGTATCAGCA
1 AATGTTGGGGGAATTTTGAACGCCCATATCAGCA
* *
20737 AATGTT-GGGGCATTTTGAAGGCCCATATCA
1 AATGTTGGGGGAATTTTGAACGCCCATATCA
20767 TACGAGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 20 0.77
34 6 0.23
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (34 bp):
AATGTTGGGGGAATTTTGAACGCCCATATCAGCA
Found at i:25075 original size:10 final size:10
Alignment explanation
Indices: 25057--25087 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25047 GACAACAAAC
25057 AATAGAGAAA
1 AATAGAGAAA
*
25067 AATACAGAAA
1 AATAGAGAAA
25077 AATAGAGAAA
1 AATAGAGAAA
25087 A
1 A
25088 GATATCGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.10
Consensus pattern (10 bp):
AATAGAGAAA
Found at i:26205 original size:13 final size:13
Alignment explanation
Indices: 26177--26220 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
26167 TTTTGTTTTA
26177 TTTTAATAAA-TT
1 TTTTAATAAATTT
26189 TTTTAATAAATTT
1 TTTTAATAAATTT
26202 TTTTAATAAATTT
1 TTTTAATAAATTT
*
26215 TATTAA
1 TTTTAA
26221 AATAACCTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTAATAAATTT
Found at i:27722 original size:58 final size:58
Alignment explanation
Indices: 27651--27929 Score: 436
Period size: 58 Copynumber: 4.8 Consensus size: 58
27641 CATATTTCCC
* * *
27651 ATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCAGACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
27709 ATACGAAAATTCATACACCTAGTATGAATTTATTAACTTTTTGCATACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
*
27767 ATA-AAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
27825 ATACGGAAATTCATACACTTAGTATGAATTTCTTAA-TGTTTTGTACACAAAGTACCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACT-TTTTGCACACAAAGTGCCCA
27883 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACA
27930 ATTAGTGTCA
Statistics
Matches: 202, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
57 2 0.01
58 199 0.99
59 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (58 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
Found at i:33395 original size:58 final size:58
Alignment explanation
Indices: 33043--33368 Score: 573
Period size: 58 Copynumber: 5.6 Consensus size: 58
33033 GAGCTCTTTG
* *
33043 ATACACTTAGTATGAATCTT-TTAACTTTCTGCACACAAAGTGGCCAATACGGAAATTC
1 ATACACTTAGTATGAAT-TTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
* * * *
33101 ATACACTTAGTATGAATCTCTAAACTTTTTGCACACAAAGTGCCCAATATGAAAATTC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
*
33159 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATAAGGAAATTC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
33217 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
33275 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
33333 ATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
1 ATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
33369 TTAGTGTCAT
Statistics
Matches: 256, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
57 1 0.00
58 255 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (58 bp):
ATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGGAAATTC
Found at i:33722 original size:20 final size:20
Alignment explanation
Indices: 33697--33749 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
33687 TAGTTCTTTA
*
33697 GTATCGATACCCTTACCATG
1 GTATCGATACCCATACCATG
* *
33717 GTATCGATACTATCATACTATG
1 GTATCGATAC--CCATACCATG
33739 GTATCGATACC
1 GTATCGATACC
33750 ATTTTTGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (20 bp):
GTATCGATACCCATACCATG
Found at i:35469 original size:66 final size:66
Alignment explanation
Indices: 35387--35517 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
35377 TAACTAATCA
35387 CTAAATTGCTCATCTCTAAGTGTGAGTGCTGCAGTCATGTGTAAAGGGGTGTCAGGAACCATTTT
1 CTAAATTGCTCATCTCTAAGTGTGAGTGCTGCAGTCATGTGTAAAGGGGTGTCAGGAACCATTTT
35452 T
66 T
* *
35453 CTAAATTGCTCATCTCTAAGTGTGAGTGCTGCAGTCGTGTGTAAAGGGGTGTCATGAACCATTTT
1 CTAAATTGCTCATCTCTAAGTGTGAGTGCTGCAGTCATGTGTAAAGGGGTGTCAGGAACCATTTT
35518 CGACAACAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (66 bp):
CTAAATTGCTCATCTCTAAGTGTGAGTGCTGCAGTCATGTGTAAAGGGGTGTCAGGAACCATTTT
T
Found at i:36176 original size:42 final size:42
Alignment explanation
Indices: 36112--36194 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
36102 GCACTTGCGG
* *
36112 CGATAGGAAAAACACTGCAAGAAGCGTCGGCCATACCAGCGA
1 CGATAGGAAAAACACCGCAAGAAGCGCCGGCCATACCAGCGA
*
36154 CGATAGGAAAAACACCGTAAGAAGCGCCGGCCATACCAGCG
1 CGATAGGAAAAACACCGCAAGAAGCGCCGGCCATACCAGCG
36195 TCGCTAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.28, G:0.27, T:0.08
Consensus pattern (42 bp):
CGATAGGAAAAACACCGCAAGAAGCGCCGGCCATACCAGCGA
Found at i:36363 original size:43 final size:43
Alignment explanation
Indices: 36256--36393 Score: 188
Period size: 43 Copynumber: 3.2 Consensus size: 43
36246 TTTATAGCAG
* * * *
36256 CAAATGCCGCAAAAGGTCAGATCTGTAGTGGCGTTTTTGGA-A
1 CAAACGCCGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATA
* **
36298 CAAATGTTGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATA
1 CAAACGCCGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATA
* *
36341 TAAACGCCGCAAAAGGTCGGATCTATAGCGGCTTTTTTGGATA
1 CAAACGCCGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATA
36384 CAAACGCCGC
1 CAAACGCCGC
36394 CAAATATGCA
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 36 0.43
43 48 0.57
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
CAAACGCCGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATA
Found at i:40439 original size:28 final size:28
Alignment explanation
Indices: 40376--40440 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
40366 ATTAAATGGC
* *
40376 AAATCTTAAACCCTAAAATCCTAACTCT
1 AAATCATAAAACCTAAAATCCTAACTCT
* * *
40404 AAACCATAAAACCTTAAATTCTATACTCT
1 AAATCATAAAACCTAAAATCCTA-ACTCT
40433 -AATCATAA
1 AAATCATAA
40441 CTCCTTGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (28 bp):
AAATCATAAAACCTAAAATCCTAACTCT
Found at i:41169 original size:32 final size:30
Alignment explanation
Indices: 41131--41226 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 30
41121 GTATGATAAA
*
41131 TTTAATGATCATTTTATAGTATTTTGAAAAAG
1 TTTAATGATCATTTTATAATATTTT--AAAAG
41163 TTTAATG-TCCATTTTATAAATATTTTAAAAG
1 TTTAATGAT-CATTTTAT-AATATTTTAAAAG
* *
41194 TTTAATGATCATTTTATAA-CTTTTAAAAA
1 TTTAATGATCATTTTATAATATTTTAAAAG
41223 TTTA
1 TTTA
41227 GCAATAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
29 12 0.21
30 2 0.03
31 21 0.36
32 16 0.28
33 7 0.12
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTAATGATCATTTTATAATATTTTAAAAG
Found at i:41196 original size:31 final size:32
Alignment explanation
Indices: 41131--41212 Score: 116
Period size: 31 Copynumber: 2.6 Consensus size: 32
41121 GTATGATAAA
*
41131 TTTAATGATCATTTTAT-AGTATTTTGAAAAAG
1 TTTAATGATCATTTTATAAATATTTT-AAAAAG
41163 TTTAATG-TCCATTTTATAAATATTTT-AAAAG
1 TTTAATGAT-CATTTTATAAATATTTTAAAAAG
41194 TTTAATGATCATTTTATAA
1 TTTAATGATCATTTTATAA
41213 CTTTTAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 23 0.50
32 16 0.35
33 7 0.15
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.49
Consensus pattern (32 bp):
TTTAATGATCATTTTATAAATATTTTAAAAAG
Found at i:44934 original size:2 final size:2
Alignment explanation
Indices: 44927--44992 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
44917 GTGATACTCT
44927 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
44969 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
44993 GAATGAAGTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45586 original size:31 final size:30
Alignment explanation
Indices: 45551--45629 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
45541 GTGTGACATG
45551 TCATCACTTTTGACACATG-ACATGTGTTATA
1 TCATCACTTTTGACACATGCACA--TGTTATA
* * **
45582 TCATCATTTTTTGGCATGTGCACATGTTATA
1 TCATCA-CTTTTGACACATGCACATGTTATA
45613 TCATCACTTTTTGACAC
1 TCATCAC-TTTTGACAC
45630 GCGGCATATG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
31 26 0.68
32 9 0.24
33 3 0.08
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (30 bp):
TCATCACTTTTGACACATGCACATGTTATA
Found at i:45770 original size:17 final size:18
Alignment explanation
Indices: 45737--45779 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
45727 TTGCATATAG
45737 TTGCATGTAAATATACAT
1 TTGCATGTAAATATACAT
*
45755 TTGCATGT-AGTATACAT
1 TTGCATGTAAATATACAT
45772 TTGCATGT
1 TTGCATGT
45780 GGTGGATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (18 bp):
TTGCATGTAAATATACAT
Found at i:48643 original size:23 final size:22
Alignment explanation
Indices: 48597--48645 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
48587 ACGACTCAAT
*
48597 TATACAAAATAGGGATTCAAAA
1 TATACAAAATAAGGATTCAAAA
* *
48619 TATACAAAATGAAGGTTTCAGAA
1 TATACAAAAT-AAGGATTCAAAA
48642 TATA
1 TATA
48646 AATGCCCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (22 bp):
TATACAAAATAAGGATTCAAAA
Found at i:49420 original size:20 final size:20
Alignment explanation
Indices: 49375--49420 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
49365 AAAAATAGGT
49375 GACTAGTATCGATACTACCA
1 GACTAGTATCGATACTACCA
49395 -ACCTAGTATCGATACT-CACA
1 GA-CTAGTATCGATACTAC-CA
49415 GACTAG
1 GACTAG
49421 GGTATTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (20 bp):
GACTAGTATCGATACTACCA
Found at i:53789 original size:76 final size:77
Alignment explanation
Indices: 53618--53821 Score: 266
Period size: 76 Copynumber: 2.7 Consensus size: 77
53608 GAACAAGAAT
* * * * * * * * * *
53618 AACAAAAGGAAGCATCGCGCTTTTGAATCAAGTTGAAAGAAATGAGGCATAACACTTTCGATTCT
1 AACAGAAGAAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCAATTAT
*
53683 CGTATAAAGTAG
66 CCTATAAAGTAG
*
53695 AACAGAAGTAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACAC-TTCAATTAT
1 AACAGAAGAAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCAATTAT
*
53759 CCTCTAAAGTAG
66 CCTATAAAGTAG
* *
53771 AACAGAAGAAAGCATCGCACTTTCAATTCAAGTAGAACGAAAGGAGACATA
1 AACAGAAGAAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATA
53822 GGACTTTTGA
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
76 65 0.58
77 47 0.42
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (77 bp):
AACAGAAGAAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCAATTAT
CCTATAAAGTAG
Found at i:58863 original size:21 final size:20
Alignment explanation
Indices: 58839--58880 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
58829 AATTCAAAGT
58839 AGAAAATGATTTGATTTTGAA
1 AGAAAAT-ATTTGATTTTGAA
* *
58860 AGAAAATTTTTTATTTTGAA
1 AGAAAATATTTGATTTTGAA
58880 A
1 A
58881 AATAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (20 bp):
AGAAAATATTTGATTTTGAA
Found at i:58877 original size:20 final size:20
Alignment explanation
Indices: 58852--58889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58842 AAATGATTTG
58852 ATTTTGAAAGAA-AATTTTTT
1 ATTTTGAAA-AATAATTTTTT
58872 ATTTTGAAAAATAATTTT
1 ATTTTGAAAAATAATTTT
58890 GAGCTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
ATTTTGAAAAATAATTTTTT
Found at i:59897 original size:38 final size:38
Alignment explanation
Indices: 59846--59929 Score: 168
Period size: 38 Copynumber: 2.2 Consensus size: 38
59836 TGAAACTTAA
59846 AGTTTGAATTATTTTTTATATAACAGGGGAGAAGTATG
1 AGTTTGAATTATTTTTTATATAACAGGGGAGAAGTATG
59884 AGTTTGAATTATTTTTTATATAACAGGGGAGAAGTATG
1 AGTTTGAATTATTTTTTATATAACAGGGGAGAAGTATG
59922 AGTTTGAA
1 AGTTTGAA
59930 AAATTCAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (38 bp):
AGTTTGAATTATTTTTTATATAACAGGGGAGAAGTATG
Found at i:63503 original size:26 final size:27
Alignment explanation
Indices: 63437--63504 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
63427 TTTTTAAAAA
63437 TATAA-AAATAAAATTTAAATGATTAT
1 TATAATAAATAAAATTTAAATGATTAT
* *
63463 TATATTGATAAAATAAAATTT-ATTGATTGT
1 TATA---AT-AAATAAAATTTAAATGATTAT
63493 TATAATAAATAA
1 TATAATAAATAA
63505 TATTATTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 10 0.29
27 2 0.06
29 1 0.03
30 11 0.31
31 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (27 bp):
TATAATAAATAAAATTTAAATGATTAT
Found at i:63912 original size:38 final size:39
Alignment explanation
Indices: 63862--63941 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
63852 CACAAATAAC
***
63862 TTAATATAATTTTCTATTATTTATAACTT-ATATATATTT
1 TTAATATAATTTTCTA-TACAAATAACTTAATATATATTT
*
63901 TTAATA-AATTTTTTATACAAATAACTTAATATATATTT
1 TTAATATAATTTTCTATACAAATAACTTAATATATATTT
63939 TTA
1 TTA
63942 TTTATTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 9 0.25
38 21 0.58
39 6 0.17
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (39 bp):
TTAATATAATTTTCTATACAAATAACTTAATATATATTT
Found at i:64141 original size:50 final size:51
Alignment explanation
Indices: 64025--64144 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
64015 AGATGTACAT
* **
64025 ACTTACGCTGGTGTAAGTATGTGTTAAATGTTACACTTTCTTATTTTATTC
1 ACTTACACTGGTGTAAGTATGTGTTAAATACTACACTTTCTTATTTTATTC
* * * * **
64076 ACTTACACCGATGTAAGTATTTGTTAATTACTATTCTTT-TTATTTTATTC
1 ACTTACACTGGTGTAAGTATGTGTTAAATACTACACTTTCTTATTTTATTC
*
64126 ACTTACATTGGTGTAAGTA
1 ACTTACACTGGTGTAAGTA
64145 CATGTTAAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
50 27 0.47
51 30 0.53
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (51 bp):
ACTTACACTGGTGTAAGTATGTGTTAAATACTACACTTTCTTATTTTATTC
Found at i:65895 original size:33 final size:34
Alignment explanation
Indices: 65809--65885 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
65799 AATGGTAATA
* *
65809 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAACAAAAAGTCC
65844 AACAAATTTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAAATAAATTAACAA-AAAGTCC
65877 AACCAAATT
1 AA-CAAATT
65886 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 21 0.55
35 10 0.26
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAACAAAAAGTCC
Found at i:66106 original size:18 final size:18
Alignment explanation
Indices: 66080--66116 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
66070 CTGTCATCAC
66080 CATCATCATCGTAGTCGT
1 CATCATCATCGTAGTCGT
* *
66098 CATCGTCATCGTCGTCGT
1 CATCATCATCGTAGTCGT
66116 C
1 C
66117 GTGAGCAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (18 bp):
CATCATCATCGTAGTCGT
Done.