Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006166.1 Hibiscus syriacus cultivar Beakdansim tig00014650_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: 50009
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:64 original size:13 final size:13
Alignment explanation
Indices: 20--72 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
10 TTGGAAGTAT
20 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
33 TTATGTGAGTT-AA
1 TTAAGT-ATTTCAA
46 -TAAGTATTTCAA
1 TTAAGTATTTCAA
*
58 TTAAGTATTTGAA
1 TTAAGTATTTCAA
71 TT
1 TT
73 TATCGAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.09
12 6 0.19
13 20 0.62
14 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:314 original size:20 final size:21
Alignment explanation
Indices: 267--322 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
257 TGGAGCGTGG
*
267 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
288 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
309 -GGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
323 AAGTAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:649 original size:15 final size:17
Alignment explanation
Indices: 623--654 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
613 TTTCTATGAG
623 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
639 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
655 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1079 original size:16 final size:16
Alignment explanation
Indices: 1040--1085 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1030 AAGTGGAAAC
* *
1040 ATTATGAATACGGATA
1 ATTATGAGTATGGATA
1056 ATTATGAGTATGGATA
1 ATTATGAGTATGGATA
1072 ATTATGAGTATGGA
1 ATTATGAGTATGGA
1086 AAATGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (16 bp):
ATTATGAGTATGGATA
Found at i:10430 original size:10 final size:10
Alignment explanation
Indices: 10415--10444 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10405 AAAAAATTAG
10415 TGAATATTTT
1 TGAATATTTT
10425 TGAATA-TTT
1 TGAATATTTT
10434 TGAATATTTT
1 TGAATATTTT
10444 T
1 T
10445 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (10 bp):
TGAATATTTT
Found at i:11611 original size:30 final size:30
Alignment explanation
Indices: 11538--11612 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
11528 AAATAAAACA
* *
11538 AATATTTTATAAAAAGTTTAAGGGTTAAATT
1 AATA-TTTATATAAAGTTTAAGAGTTAAATT
* *
11569 AACATTTAATATAAAG-TTAAGAGTTGAATT
1 AATATTT-ATATAAAGTTTAAGAGTTAAATT
11599 AATAGTTTATATAA
1 AATA-TTTATATAA
11613 GATCAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (30 bp):
AATATTTATATAAAGTTTAAGAGTTAAATT
Found at i:16263 original size:18 final size:18
Alignment explanation
Indices: 16240--16274 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16230 CCGACACGTT
16240 GACCCGAACCGTTGACCC
1 GACCCGAACCGTTGACCC
*
16258 GACCCGACCCGTTGACC
1 GACCCGAACCGTTGACC
16275 GGTGTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.46, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGAACCGTTGACCC
Found at i:16274 original size:13 final size:13
Alignment explanation
Indices: 16227--16263 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16217 GACCGGTCAC
*
16227 GACCCGACACGTT
1 GACCCGACCCGTT
*
16240 GACCCGAACCGTT
1 GACCCGACCCGTT
16253 GACCCGACCCG
1 GACCCGACCCG
16264 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.43, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:16358 original size:30 final size:29
Alignment explanation
Indices: 16305--16431 Score: 107
Period size: 29 Copynumber: 4.3 Consensus size: 29
16295 TTCGATTTTG
16305 GTGCTATTTTGGGAATTAATTCGAAATGA
1 GTGCTATTTTGGGAATTAATTCGAAATGA
* ** *
16334 GTGCTATTTTTGGTAATTTTTTCGAAA-AA
1 GTGCTA-TTTTGGGAATTAATTCGAAATGA
* * *
16363 G-GTTATATTCGGGGAATTAATTTGAAATTG-
1 GTGCTAT-TT-TGGGAATTAATTCGAAA-TGA
* * *
16393 GTGCTATTTTGGGAATTAATTCAAAAAGG
1 GTGCTATTTTGGGAATTAATTCGAAATGA
16422 GTGCTATTTT
1 GTGCTATTTT
16432 AGTGTAATTA
Statistics
Matches: 75, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
27 1 0.01
28 6 0.08
29 44 0.59
30 20 0.27
31 4 0.05
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTCGAAATGA
Found at i:16450 original size:31 final size:29
Alignment explanation
Indices: 16304--16451 Score: 82
Period size: 29 Copynumber: 5.0 Consensus size: 29
16294 ATTCGATTTT
** *
16304 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTAAAAAAG
* * ** *
16333 AGTGCTATTTTTGGTAATTTTTTCGAAAAA-
1 GGTGCTA-TTTTGGGAATTAATT-AAAAAAG
** ** ** **
16363 GGTTATATTCGGGGAATTAATTTGAAATT
1 GGTGCTATTTTGGGAATTAATTAAAAAAG
*
16392 GGTGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGGAATTAATTAAAAAAG
* *
16421 GGTGCTATTTTAGTGTAATTATTTAAAAAAG
1 GGTGCTATTTT-G-GGAATTAATTAAAAAAG
16452 TGCTATATGT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
28 3 0.04
29 48 0.56
30 17 0.20
31 17 0.20
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTAAAAAAG
Found at i:17443 original size:42 final size:41
Alignment explanation
Indices: 17384--17630 Score: 316
Period size: 42 Copynumber: 5.8 Consensus size: 41
17374 GAAGTATTAT
17384 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* *
17426 CAGGTCCCTTTGCTGTGTGCAAGGGTAAACCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
17468 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* *
17510 CAAGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* * * *
17552 CAGGTCCCTTTGCTGTGTACAAGGATAAACCTTATAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTAC
* *
17594 CTAGG-CTCCTCTGCTTTGTGCATAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
17631 TGGTGTATAG
Statistics
Matches: 181, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
41 6 0.03
42 147 0.81
43 17 0.09
44 11 0.06
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:17525 original size:84 final size:84
Alignment explanation
Indices: 17384--17591 Score: 355
Period size: 84 Copynumber: 2.5 Consensus size: 84
17374 GAAGTATTAT
*
17384 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAAGTCCCTTTGCTGTGTGCAAG
17449 GGTAAACCTTACAGTTTCC
66 GGTAAACCTTACAGTTTCC
17468 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAAGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAAGTCCCTTTGCTGTGTGCAAG
*
17533 GGTAAGCCTTACAGTTTCC
66 GGTAAACCTTACAGTTTCC
* * *
17552 CAGGTCCCTTTGCTGTGTAC-AAGGATAAACCTTATAGTTT
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTT
17592 TCCTAGGCTC
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 4 0.03
84 114 0.97
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAAGTCCCTTTGCTGTGTGCAAG
GGTAAACCTTACAGTTTCC
Found at i:19569 original size:2 final size:2
Alignment explanation
Indices: 19562--19635 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
19552 CGTTTTGCGT
19562 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
19604 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
19636 ACAAACAAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20553 original size:3 final size:3
Alignment explanation
Indices: 20545--20582 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20535 TAAAATTCAA
20545 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20583 ATAAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21003 original size:134 final size:134
Alignment explanation
Indices: 20792--21142 Score: 542
Period size: 134 Copynumber: 2.6 Consensus size: 134
20782 CGTCCAAGGG
* * * * * * *
20792 TGACACGGTTCCTACGTGATGAGGAAATTTGGTCAGCGGATGACACAGCTCATACGTGATGCAA-
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATG-AAG
* *
20856 AGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTTGTTATCT
65 AGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACTTGTTATCT
20921 ATGGT
130 ATGGT
*
20926 TGACACGACTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGA
* * *
20991 GTTCTAGCCATCTTTAGGAAGGGCGATAACATGGTTCCTACGTGATGTGGACGACTTGTTATCTA
66 GTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACTTGTTATCTA
21056 TGGT
131 TGGT
* *
21060 TGACACGGCTCCTACGTGATGAAAAGATCTGGTCGGTGGATGACACGGCTCATATGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGA
*
21125 GTTCTGGCCATCATTAGG
66 GTTCTGGCCATCTTTAGG
21143 GATACTGATT
Statistics
Matches: 198, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 2 0.01
134 196 0.99
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (134 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACTTGTTATCTA
TGGT
Found at i:21188 original size:29 final size:29
Alignment explanation
Indices: 21155--21212 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
21145 TACTGATTTC
21155 AAAAGAAACCA-ACTCAAAGATGATGTTTT
1 AAAAGAAA-CAGACTCAAAGATGATGTTTT
*
21184 AAAAGAAACAGACTCAAGGATGATGTTTT
1 AAAAGAAACAGACTCAAAGATGATGTTTT
21213 TCAAAAGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAAGAAACAGACTCAAAGATGATGTTTT
Found at i:21386 original size:32 final size:32
Alignment explanation
Indices: 21339--21477 Score: 127
Period size: 32 Copynumber: 4.0 Consensus size: 32
21329 CAAAGATCGG
*
21339 TGTTTCGAGAGAAACAAACTCAAAGATTTTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATTTTTT
* *
21371 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAGA-----TTT-TTT
* *
21409 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT--T--TTTT
21445 TGTTTCCAA-AGAAACAAACTCAAAGATTTTTT
1 TGTTT-CAAGAGAAACAAACTCAAAGATTTTTT
21477 T
1 T
21478 TCTCAAAAGA
Statistics
Matches: 87, Mismatches: 9, Indels: 22
0.74 0.08 0.19
Matches are distributed among these distances:
32 27 0.31
33 1 0.01
34 1 0.01
35 1 0.01
36 25 0.29
37 6 0.07
38 26 0.30
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTTTCAAGAGAAACAAACTCAAAGATTTTTT
Found at i:22461 original size:106 final size:104
Alignment explanation
Indices: 22245--22462 Score: 249
Period size: 106 Copynumber: 2.1 Consensus size: 104
22235 GAGATTACTT
*
22245 TTGTCTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGAAAAAAATGTCTCAAACGAGACGAA
1 TTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGAAAAAAATGTCTCAAACGAGACGAA
* * * ** **
22310 ATTTGTTTTGAAAGAAATAACAATCTCAAGTGAGATTAATT
66 ATTTATTTTGAAAGAAAT-A-AATCTCAAGCGAAAAAAAAA
* * *
22351 TTGTTTCAAGTGAATCGAATTCGAAATTTGTATCTCAAAGAAAAAAAATGTCTCAAGCGAGACGA
1 TTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAG-AAAAAAATGTCTCAAACGAGACGA
* * * *
22416 AGTTTATTTTTAAGAGGAAT-TATCTCAAGCGAAACAAAAAA
65 AATTTATTTTGAA-AGAAATAAATCTCAAGCGAAA-AAAAAA
22457 TTGTTT
1 TTGTTT
22463 TAAAACTCTC
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
105 11 0.12
106 45 0.48
107 33 0.35
108 5 0.05
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (104 bp):
TTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGAAAAAAATGTCTCAAACGAGACGAA
ATTTATTTTGAAAGAAATAAATCTCAAGCGAAAAAAAAA
Found at i:22813 original size:4 final size:4
Alignment explanation
Indices: 22804--22841 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
22794 TTTATGCATC
22804 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
22842 TTTCTCGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 30 0.94
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:28843 original size:2 final size:2
Alignment explanation
Indices: 28836--28863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28826 CGTTTTGCAT
28836 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
28864 ACAAACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29781 original size:3 final size:3
Alignment explanation
Indices: 29762--29808 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
29752 TAAAATTCAA
*
29762 AAT AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT -AT AAAT AA- AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
29807 AA
1 AA
29809 AAAAAAACCG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 29 0.76
4 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:34740 original size:33 final size:31
Alignment explanation
Indices: 34703--34774 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
34693 TCATCCAAAA
*
34703 GATGCACTTTTAACTGATCAGTTGATCAACAAG
1 GATGCACTTTTAAATGAT--GTTGATCAACAAG
** *
34736 GATGCAAATTTAAATTATGTTGATCAACAAG
1 GATGCACTTTTAAATGATGTTGATCAACAAG
34767 GAT-CACTT
1 GATGCACTT
34775 GATTCCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 16 0.48
33 14 0.42
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (31 bp):
GATGCACTTTTAAATGATGTTGATCAACAAG
Found at i:39998 original size:36 final size:37
Alignment explanation
Indices: 39933--40002 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
39923 GAAAAAATGG
*
39933 TTTTCAAAGTTTAGTAAATGTTTCTTTGAAAAATAAT
1 TTTTCAAAGTTTAGTAAATGTTTCGTTGAAAAATAAT
* *
39970 TTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 TTTTCAAAGTTTAGTAAATGTTTCGTTGAAAAAT
40003 GATAATTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (37 bp):
TTTTCAAAGTTTAGTAAATGTTTCGTTGAAAAATAAT
Found at i:40434 original size:16 final size:16
Alignment explanation
Indices: 40413--40444 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40403 CCTATTCACA
*
40413 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
40429 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
40445 ATCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:44529 original size:21 final size:21
Alignment explanation
Indices: 44505--44565 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
44495 AACTTTGAAA
44505 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
44526 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
44540 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
44561 AAATG
1 AAATG
44566 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:44596 original size:37 final size:37
Alignment explanation
Indices: 44497--44615 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
44487 TGGTAACCAA
44497 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
44534 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
44569 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
44606 -GTTGAAAAAT
1 CTTTGAAAAAT
44616 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:49861 original size:16 final size:16
Alignment explanation
Indices: 49812--49863 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
49802 AATCACTCTA
49812 ATTTATTTTATTAATA-
1 ATTT-TTTTATTAATAT
49828 ATTTTTTTGACATT-ATAT
1 ATTTTTTT---ATTAATAT
49846 ATTTTTTTATTAATAT
1 ATTTTTTTATTAATAT
49862 AT
1 AT
49864 AATTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 3 0.10
18 11 0.35
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTTTTTATTAATAT
Done.